bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2677: MSIClass–Identification and classification of microsatellite unstable using cell-free DNA from ultra-low-pass sequencing
Authors: Maruvka Yosef E. , Frazer Ruslana , Grimsby Jonna , Cibulskis Carrie , Adalsteinsson Viktor , Corcoran Ryan , Getz Gad 
Published: August 2019

Abstract
The acquisition of mismatch repair deficiency is common in many tumor types. A unique subtype of mismatch repair deficient tumors, called tumors with microsatellite instability (MSI), has been recently approved for treatment with PD-1\PD-L1 blockade immunotherapy. Therefore, developing a quick, inexpensive, and easy-to-implement technique for classifying tumors as MSI is of utmost importance. Here, we describe such a method using next-generation sequencing data, and show that it can detect MSI from cell-free DNA (cfDNA), even when there is low fraction of tumor DNA in the cfDNA.
We first analyzed the unique mutational features of MSI vs. microsatellite stable (MSS) tumors. Using our SignatureAnalyzer tool, we analyzed the signatures of the different insertions and deletions within microsatellite loci (MS-indels), and found that MSI tumors harbor elevated MS-indels of certain types, which we further validated using whole genome sequencing data from The Cancer Genome Atlas.
We next used this information to develop a method (MSIClass) that analyzes the WGS data of a given sample by capturing the features unique to MSI tumors. This method assigns each sample a score based on aggregating information from all MS loci simultaneously; since MSIClass is a sample-based tool, it can call the MSI status of tumor samples that have no patient-matched normal sample. We further demonstrate that MSIClass requires minimal genomic information; indeed, sequencing coverage as low as 0.05x (current sequencing cost of ~$2/sample) is sufficient for accurate classification by MSIClass.
Using in silico and in vitro DNA mixing we show that MSIClass can accurately identify MSI cases in very low purity cases, at 0.1% tumor DNA (using 0.5x sequencing coverage). We show that MSIClass, applied on cfDNA, could accurately classify 29 colon cases – 22 MSS and 7 MSI cases, 3 of which are early stage disease and with low tumor content.
These results demonstrate that MSIClass is an inexpensive MSI test that can be applied in various cases: bulk sequencing where a matched normal is not available, cases of very low purity tumors, and even using cfDNA from blood in cases a biopsy is not available or possible. Finally, this methodology can be the basis for monitoring minimal residual disease, and potential be used for early detection of MSI tumors.
Citation Format: Yosef E. Maruvka, Ruslana Frazer, Jonna Grimsby, Carrie Cibulskis, Viktor Adalsteinsson, Ryan Corcoran, Gad Getz. MSIClass–Identification and classification of microsatellite unstable using cell-free DNA from ultra-low-pass sequencing [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 2677.
Abstract 270: Temozolomide resistant MGMT negative/MMR proficient cancer cells rely on ATR signaling and homologous recombination for DNA repair and survival
Authors: Touny Lara El , Harris Erik , Hose Curtis , Connelly John , Vengsarkar Diana , Monks Anne , Parchment Ralph E. , Doroshow James H. , Teicher Beverly A. , Rapisarda Annamaria 
Published: August 2019

Abstract
MGMT loss is used to predict response to temozolomide (TMZ), however, some patients do not benefit, suggesting that additional criteria for selection remain to be identified. Using patient derived and well-established cancer lines cancer lines we observed a 100% association between mismatched repair (MMR) defects and TMZ resistance; however, only 16% of MGMT-/MMR+ lines were sensitive to TMZ at clinically relevant concentrations. Activation of DNA damage and repair signaling was noted in both sensitive and resistant bladder cancer cell lines in response to TMZ but protracted DNA damage, accompanied by persistent G2/M arrest, was observed only in the sensitive models. ATR inhibition sensitized MGMT-/MMR proficient resistant models to TMZ resulting in measurable DNA damage, prolonged G2/M arrest and persistent growth inhibition: an effect that was mediated by Chk1. Homologous recombination and repair has been shown to play an important role in repairing TMZ-induced DNA damage. We demonstrate that ATR inhibition abrogated homologous recombination (HR) activity in a MGMT-/MMR proficient TMZ resistant bladder model and that a TMZ sensitive bladder model had minimal HR (assessed by pDR-GFP/SceI assay). Moreover, HR -deficiency (mediated by BRCA1 defects or RAD51 inhibition) conferred sensitivity to TMZ in combination with an ATR inhibitor. Our in vitro data suggest that a MGMT-/MMR+/HR-Deficiency profile identifies models that respond to TMZ/ATR inhibitor combination. Indeed, one Patient-derived Xenograft (PDX) model (available in the Patient Derived Models Repository), selected by this criterion (MGMT-/MMR+ and LOH&gt;40%) showed delayed tumor growth and increased survival in the TMZ-VX970 combination arm, compared to single agents. Overall, our data suggest that MGMT-/MMR+ cells rely on ATR-dependent signaling for repair of TMZ-induced DSBs and that HR defects should be evaluated as criteria for selecting patients that will benefit from an ATR inhibitor/TMZ combination regimen. Funded by NCI Contract No. HHSN261200800001E. This research was supported, in part, by the Developmental Therapeutics Program in the Division of Cancer Treatment and Diagnosis of the National Cancer Institute.
Citation Format: Lara El Touny, Erik Harris, Curtis Hose, John Connelly, Diana Vengsarkar, Anne Monks, Ralph E. Parchment, James H. Doroshow, Beverly A. Teicher, Annamaria Rapisarda. Temozolomide resistant MGMT negative/MMR proficient cancer cells rely on ATR signaling and homologous recombination for DNA repair and survival [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 270.
Abstract 2712: Effect of combined PD-1 and IL-6 blockade on K-ras mutant lung cancer
Authors: Ramos-Castaneda Marco A. , Daga Neha , Peng Stephen , Deng Shanshan , Velazco Walter , Caetano Mauricio Da Silva , Moghaddam Seyed 
Published: August 2019

Abstract
Lung cancer is the leading cause of cancer death and the second most common cancer diagnosed worldwide in both males and females. K-ras gene mutations are among the most common mutations encountered in non-small cell lung cancer (NSCLC), encompassing up to 30% of them, and are unfortunately associated with chemoresistance and poor prognosis. Recently, immunotherapy treatment of several cancers including NSCLC, particularly by targeting the co-inhibitory molecules program cell death protein 1 (PD-1) and program death-ligand 1 (PD-L1), have shown promising results given either in combination with standard chemotherapy or as neoadjuvant therapy. We have previously shown an important role for IL-6 in K-ras mutant lung tumorigenesis by reprogramming myeloid contexture in the lung tumor microenvironment (TME) and promoting tumor cell proliferation and angiogenesis through the activation of STAT3 pathway. Accordingly, we hypothesized that targeting both immunosuppressive TME and IL-6 driven pro-tumor immune response, through the use of immune checkpoint blockade (ICB), and inhibition of IL-6 would give us a synergistic/additive response and increases the tumor inhibitory effect of ICB. Briefly, starting at the age of 6 weeks, 4 cohorts of K-ras mutant mice (LSL-K-rasG12D/ CCSPCre) (CC-LR) were injected intraperitoneally with vehicle alone (PBS1x), anti-PD-1 (CD279) antibody alone (Clone: 29F.1A12- Bioxcell - BE0273-CUST) (200µg), anti-IL-6 antibody alone (Clone: MP5-20F3 - Bioxcell - BE0046-CUST) (20 mg/kg), or a combination of both. After 8 weeks of treatment, tumor burden and inflammation were studied and quantified. We found a significant (2-fold) decrease in tumor burden in the anti-PD1 alone treated group which was further reduced in the combined anti-PD-1 and anti-IL-6 treated group compared to age and sex matched vehicle treated group. There was also a significant difference in the lung macrophage infiltration in combined anti-PD1/anti-IL-6 treated group similar to what we previously observed in anti-IL-6 alone treated group. Our results suggest that immunomodulatory approaches by targeting cytokine networks like IL-6 blockade could be used to increase the efficacy of immunotherapy, i.e. PD-1 blockade, as a preventive and/or therapeutic strategy for K-ras mutant lung cancer.
Citation Format: Marco A. Ramos-Castaneda, Neha Daga, Stephen Peng, Shanshan Deng, Walter Velazco, Mauricio Da Silva Caetano, Seyed Moghaddam. Effect of combined PD-1 and IL-6 blockade on K-ras mutant lung 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 2712.
Abstract 2713: Discovery and characterization of AZD8701, a high affinity antisense oligonucleotide targeting FOXP3 to relieve immunosuppression in cancer
Authors: Sinclair Charles , Revenko Alexey S. , Johnson R B. , Peter Alison , Taylor Molly A. , Hettrick Lisa A. , Klein Stephanie , Solanki Anisha , Chapman Melissa , Yates James , Angell Helen K. , Watt Andrew , Gattis Danielle , Monia Brett P. , Barry Simon T. , Lyne Paul , Edbrooke Mark , Goldberg Frederick , Macleod A R. 
Published: August 2019

Abstract
Regulatory T cells (Treg) critically maintain immuno-suppression in the tumor microenvironment, representing an attractive immuno-oncology target. The Treg lineage is defined by expression of the FOXP3 transcription factor, which controls immune-suppressive functions. We have developed the clinical candidate AZD8701, a next-generation antisense oligonucleotide inhibitor of FOXP3 (utilizing the Ionis Gen 2.5 cEt-modified ASO platform). AZD8701 treatment knocked down FOXP3 in primary human Tregs via free uptake (IC50 65nM), which was also associated with modulation of known FOXP3 target genes including 25-50% reduction in CTLA4, ICOS, CCR8 and GITR. Tregs treated with AZD8701 further exhibited reduced suppressive functions in in vitro suppression assays, which confirmed the functional effects of FOXP3 modulation. Finally, AZD8701 promoted dose-dependent knockdown of FOXP3 in humanized mice, including &gt;50% FOXP3 knockdown at doses that can be feasibly achieved with the Gen 2.5 ASO platform in the clinic. To support the importance of FOXP3 in immuno-oncological settings, we characterized murine surrogate FOXP3 ASOs in the context of syngeneic tumour bearing mice. Murine FOXP3 ASOs similarly promoted &gt;50% FOXP3 knockdown in mice and were well tolerated with no overt toxicological findings at high doses, over a maximum of 12 weeks of treatment. Murine FOXP3 ASOs significantly attenuated tumour growth in A20 and ID8-VEGF syngeneic models, which was associated with some complete tumour regressions. Moreover, we found that mouse surrogate FOXP3 ASOs promoted additive/enhanced therapeutic effects when combined with immune checkpoint blockade. Collectively, FOXP3 ASOs represent a first-in-class strategy to target Tregs in cancer in a highly selective manner. The clinical application of AZD8701 may provide therapeutic benefit to patients either as a monotherapy or in combination with immune checkpoint blocking agents.
Citation Format: Charles Sinclair, Alexey S. Revenko, R B. Johnson, Alison Peter, Molly A. Taylor, Lisa A. Hettrick, Stephanie Klein, Anisha Solanki, Melissa Chapman, James Yates, Helen K. Angell, Andrew Watt, Danielle Gattis, Brett P. Monia, Simon T. Barry, Paul Lyne, Mark Edbrooke, Frederick Goldberg, A R. Macleod. Discovery and characterization of AZD8701, a high affinity antisense oligonucleotide targeting FOXP3 to relieve immunosuppression in 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 2713.
Abstract 2719: Metabolic product of inositol-trisphosphate 3-kinase B confers chemotherapy resistance by managing redox homeostasis
Authors: Pan Chaoyun , Chun Jaemoo , Boese Austin , Kang Jihoon , Li Jie , Jin Lingtao , Kang Sumin 
Published: August 2019

Abstract
How altered metabolism contributes to chemotherapy resistance in cancer cells remains unclear. Through a metabolism-related kinome RNAi screen, we identified inositol-trisphosphate 3-kinase B (ITPKB) as a critical enzyme that contributes to cisplatin-resistant tumor growth. We demonstrate that inositol (1,3,4,5) tetrakisphosphate (IP4), the product of ITPKB, plays a critical role in redox homeostasis upon cisplatin exposure by reducing cisplatin-induced ROS through inhibition of a ROS-generating enzyme NADPH oxidase 4 (NOX4), which promotes cisplatin- resistant tumor growth. Mechanistically, IP4 competes with the NOX4 cofactor NADPH for binding and consequently inhibits NOX4. Targeting ITPKB with shRNA or its small molecule inhibitor resulted in attenuation of NOX4 activity, imbalanced redox status, and sensitized cancer cells to cisplatin treatment in patient-derived xenografts. Our findings provide insight into the crosstalk between kinase-mediated metabolic regulation and platinum-based chemotherapy resistance in human cancers. Our study also suggests a distinctive signaling function of IP4 that regulates NOX4. Furthermore, pharmaceutical inhibition of ITPKB displayed synergistic attenuation of tumor growth with cisplatin suggesting ITPKB as a promising synthetic lethal target for cancer therapeutic intervention to overcome cisplatin resistance.
Citation Format: Chaoyun Pan, Jaemoo Chun, Austin Boese, Jihoon Kang, Jie Li, Lingtao Jin, Sumin Kang. Metabolic product of inositol-trisphosphate 3-kinase B confers chemotherapy resistance by managing redox homeostasis [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 2719.
Abstract 2739: EZH2 promotes breast cancer bone metastasis
Authors: Qu Jingkun , Zhang Lin , Zhou Zhifen , Yu Dihua 
Published: August 2019

Abstract
Metastasis causes about 90% of cancer deaths and approximately 55% of breast cancer patients develop bone metastases. Although significant advances in the cure of breast cancer, effective therapies targeted bone metastases are still not available. To develop novel therapies for patients with bone metastasis, better understanding of underlying mechanisms of bone metastasis is critical. EZH2 is a classic histone methyl transferase that generally suppresses downstream target genes through tri-methylation of H3K27. EZH2 is considered as a breast cancer oncogene and is frequently over expressed in breast cancer, but the effect of EZH2 on bone metastasis is unknown. To explore the function of EZH2 in bone metastasis, we intracardially injected into nude mice control MDA.MB.231 breast cancer cells expressing readily detectable EZH2 or a MDA.MB.231 subline having EZH2 knocked out (231.EZH2.ko). We found that the mice injected with 231.EZH2.ko had prolonged bone metastasis-free survival compared to the control group of mice. To gain initial insight on the underlying mechanism of EZH2-mediated bone metastasis, we co-cultured MDA.MB.231 cells or 231.EZH2.ko with pre-osteoclasts (RAW264.7) and osteoblasts (MC3T3) under TGF-β treatment (triple co-culture) to mimic bone metastasis tumor microenvironment. We examined osteoclast maturation and breast cancer cell proliferation because osteolysis induced by mature osteoclasts is critical for breast cancer cell growth in the bone metastasis. In triple co-culture of MDA.MB.231 cells, more RAW264.7 pre-osteoclasts were differentiated to mature osteoclasts, as measured by TRAP+ staining, a marker of mature osteoclasts, and MDA.MB.231 cells grew faster than the triple co-culture of 231.EZH2.ko cells. Furthermore, we found that the mRNA level of PTHrP, a master regulator of bone metastasis and a TGF-β downstream cytokine, was expressed at significantly higher level in MDA.MB.231 cells than that in 231.EZH2.ko cells under TGF-β stimulation. PTHrP was known to promote the “vicious cycle” of bone destruction in bone metastasis. The data suggests EZH2 promotes breast cancer bone metastasis through PTHrP. Currently, we are further exploring how EZH2 regulates PTHrP in breast cancer cells to promote bone metastasis. Our studies may reveal novel biomarkers and/or therapeutic targets for bone metastasis.
Citation Format: Jingkun Qu, Lin Zhang, Zhifen Zhou, Dihua Yu. EZH2 promotes breast cancer bone metastasis [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 2739.
Abstract 2744: Blocking CXCR4 alleviates desmoplasia, increases T-lymphocyte infiltration, and improves immunotherapy in metastatic breast cancer
Authors: Chen Ivy X. , Chauhan Vikash P. , Posada Jessica , Ng Mei R. , Wu Michelle , Adstamongkonkul Pichet , Huang Peigen , Lindeman Neal , Langer Robert , Jain Rakesh K. 
Published: August 2019

Abstract
Metastatic breast cancers (mBCs) are largely resistant to immune checkpoint blockade, but the mechanisms remain unclear. Primary breast cancers are characterized by a dense fibrotic stroma, which is considered immunosuppressive in multiple malignancies, but the stromal composition of breast cancer metastases and its role in immunosuppression are largely unknown. Here we show that liver and lung metastases of human breast cancers tend to be highly fibrotic, and unlike primary breast tumors, they exclude cytotoxic T-lymphocytes (CTLs). Unbiased analysis of the TCGA database of human breast tumors revealed a set of genes that are associated with stromal T-lymphocyte exclusion. Among these we focused on CXCL12 as a relevant target based on its known roles in immunosuppression in other cancer types. We found that the CXCL12 receptor CXCR4 is highly expressed in both human primary tumors and metastases. To gain insight into the role of CXCL12/CXCR4 axis, we inhibited CXCR4 and found that CXCR4 blockade decreases fibrosis, alleviates solid stress, decompresses blood vessels, increases CTL infiltration, and decreases immunosuppression in murine mBC models. We confirmed that these immunosuppressive effects are dependent on cancer-associated fibroblast (CAF) signaling through genetic deletion of Cxcr4 in aSMA+ cells. Accordingly, CXCR4 inhibition more than doubles the response to immune checkpoint blockers in mice bearing mBCs. These findings demonstrate that CXCL12/CXCR4-mediated desmoplasia in mBC promotes immunosuppression and is a potential target for overcoming therapeutic resistance to immune checkpoint blockade in mBC patients.
Citation Format: Ivy X. Chen, Vikash P. Chauhan, Jessica Posada, Mei R. Ng, Michelle Wu, Pichet Adstamongkonkul, Peigen Huang, Neal Lindeman, Robert Langer, Rakesh K. Jain. Blocking CXCR4 alleviates desmoplasia, increases T-lymphocyte infiltration, and improves immunotherapy in metastatic breast 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 2744.
Abstract 2761: Development of synthetic guide RNA libraries for CRISPR-mediated transcriptional activation screening for gain-of-function studies
Authors: Vermeulen Annaleen , Strezoska Zaklina , Dickerson Sarah M. , Gross Maren M. , Chou Eldon T. , Maksimova Elena , Perkett Matthew R. , McClelland Shawn , Smith Anja V. 
Published: August 2019

Abstract
Functional gene analysis studies have been empowered by development of CRISPR-Cas9 gene knockout tools, however the CRISPR-Cas9 system has also been adapted for inhibition or activation of gene transcription. A nuclease-deactivated Cas9 (dCas9) can be fused to various effector domains to produce an RNA-guided transcription factor for either inhibition (CRISPRi) or activation (CRISPRa) of target genes. For overexpression studies, CRISPRa holds significant advantages over traditional vector-based gene expression, because genes are upregulated from their native promoter and endogenous genomic context. The majority of CRISPRa research performed to date has utilized single guide RNA (sgRNA) expressed from a DNA vector, primarily in the context of pooled lentiviral screening approaches. Here we describe the development of CRISPRa synthetic guide RNAs for the use in arrayed screening, so that we combine this next-generation transcriptional activation method with the ability to support more complex assays in a one-gene-per well format. Considerations for arrayed activation screens will be shown. The combination of gain-of-function from CRISPRa with loss-of-function using RNAi or canonical CRISPR-Cas9 for gene knockout allows for robust characterization of gene mechanisms and pathways.
Citation Format: Annaleen Vermeulen, Zaklina Strezoska, Sarah M. Dickerson, Maren M. Gross, Eldon T. Chou, Elena Maksimova, Matthew R. Perkett, Shawn McClelland, Anja V. Smith. Development of synthetic guide RNA libraries for CRISPR-mediated transcriptional activation screening for gain-of-function studies [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 2761.