bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 363: Role of the SAGA histone acetylation module in lung cancer
Authors: Mustachio Lisa Maria , Roszik Jason , Dent Sharon YR
Published: August 2018

Lung cancer causes the highest mortality in cancer-related deaths. Definition of novel molecular targets is needed since these cancers often become resistant to existing therapies. Epigenetic modifications may provide such targets. Recent reports suggest that the histone acetyltransferase (HAT) module within the transcriptional coactivator SAGA complex plays a role in cancer, creating a new link between epigenetic regulators and this disease. We are working to define the role of the SAGA HAT protein GCN5 in the regulation and function of oncogenes in lung cancers. Since our prior work indicates that GCN5 serves as a coactivator for MYC target genes, we hypothesize that inhibition of GCN5 will reduce lung oncogenesis by suppressing MYC functions. We also propose that inhibition of GCN5 will reduce lung cancer formation and progression in mouse models of lung cancer. Our preliminary data indicate that both GCN5 and MYC expression levels are upregulated and positively associated in mouse and human lung cancers. Both proteins are also associated with MYC target genes in lung cancer tissues. Inhibition of the GCN5 active site or bromodomain significantly (p < 0.05) reduces cell proliferation compared to normal lung epithelium cells. Studies investigating how GCN5 inhibition affects other lung cancer phenotypes are underway. Specific genes and pathways affected by GCN5 loss will be determined using RNA-Seq and RPPA assays to identify mechanisms behind observed phenotypes. In addition, we will determine whether knockout of Gcn5 reduces lung formation and progression in the KrasLA2 lung cancer mouse model. Our ongoing studies will determine whether targeting GCN5 represses multiple oncogenic pathways in cancer and whether it inhibits oncoproteins difficult to directly target, such as MYC. We expect that our findings will highlight the importance of epigenetic regulators in carcinogenesis and extend beyond our current research focus to other cancer types.

Citation Format: Lisa Maria Mustachio, Jason Roszik, Sharon YR Dent. Role of the SAGA histone acetylation module in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 363.
Abstract 3631: Passenger fusion genes are novel predictive biomarker of anti-PD-1 antibody nivolumab for ovarian cancer
Authors: Hamanishi Junzo , Murakami Ryusuke , Brown John B. , Baba Tsukasa , Abiko Kaoru , Suzuki Eiji , Mandai Masaki
Published: August 2018

Background: Immune checkpoint PD-1 signal blockade provides significant clinical efficacy and durable response for several cancer patients. However it is crucial to identify a biomarker to predict the response to PD-1 signal blockade. Herein we analyzed the somatic mutanomes and transcriptomes of tumor samples from ovarian cancer patients treated with nivolumab to identify potential biomarkers of antitumor response.

Methods: We previously reported a phase II clinical trial for resistant ovarian cancer with nivolumab (UMIN000005714) and showed disease control rate was 45% including 2 complete responders. To estimate the somatic mutation burden (TMB) of tumor samples, the number of non-synonymous single nucleotide variants (nsSNVs), insertions and deletions of genes was analyzed by whole exome sequencing of formalin fixed paraffin embedded tumor tissues. Next, to evaluate whole transcriptome of these samples, we performed an RNAseq analysis and detected several fusion genes in some patients. We evaluated the correlation between clinical anti-tumor response for nivolumab treatment with the numbers of somatic mutations or transcriptomic alignments containing gene fusions.

Results: 16 tumor samples (7 responders, 9 non-responders and 1 loss) for whole exome sequencing and 17 samples (7 responders and 10 non-responders) for RNA sequencing were available. Contrary to expectations generated by previously reported papers in melanoma or lung cancers, the levels of TMB including nsSNVs, insertions and deletions of genes were not significantly correlated to antitumor response. However, more than 2 fusion genes were detected (mean=6.3, range 0-15) in 6 of 7 responders, while 8 of 10 non-responders did not have any fusion genes and the remaining non-responders had only 1 fusion gene each (mean=0.2, range, 0-1). Therefore an antitumor response to nivolumab was strongly correlated to the number of fusion genes in ovarian cancer (p=0.0003, sensitivity: 86% [6/7] specificity: 100% [10/10]).

Conclusions: This study, to our knowledge, is the first to describe passenger fusion genes of tumors, and might provide a clinically useful and novel predictive biomarker of antitumor response to anti-PD-1/PD-L1 antibody therapy for ovarian cancer.

Citation Format: Junzo Hamanishi, Ryusuke Murakami, John B. Brown, Tsukasa Baba, Kaoru Abiko, Eiji Suzuki, Masaki Mandai. Passenger fusion genes are novel predictive biomarker of anti-PD-1 antibody nivolumab for ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3631.
Abstract 364: Differentially methylated super-enhancers regulate gene expression in human papillomavirus-related head and neck squamous cell carcinoma
Authors: Flam Emily L. , Kelley Dylan Z. , Stavrovskaya Elena , Danilova Ludmila , Guo Theresa , Considine Michael , Qian Jiang , Califano Joseph A. , Favorov Alexander V. , Fertig Elana J. , Gaykalova Daria A.
Published: August 2018

Human papillomavirus-related head and neck squamous cell carcinoma (HPV+ HNSCC) is characterized by abundant gene expression changes, which cannot be explained by limited genetic alterations alone. We hypothesized that epigenetically regulated super-enhancers (SEs) are the drivers of aberrant gene expression in HPV+ HNSCC. We used integrated analysis of DNA methylation and gene expression data for cancer and noncancer oropharyngeal tissues to discover actionable SEs that regulate expression of target genes in HPV+ HNSCC. Since no SEs are currently defined for any HNSCC samples; we investigated 6196 SE elements that were obtained from the public domain for closely related tissues, including normal and tumor lung, and cervical cancer cell lines. We analyzed the methylation of these elements and gene expression of their nearby genes for 47 HPV+ HNSCC and their 25 noncancer controls. Overall, we found 122 differentially methylated SEs that had putative target (nearby) genes whose expression was correlated with enhancer methylation in HPV+ HNSCC. Of these, 107 were hypermethylated, and 15 were hypomethylated in tumors relative to normal samples. The pathway analysis revealed that the inferred SE-regulated genes were associated with pathways known to regulate carcinogenesis. Our data demonstrate that gene expression in HPV+ HNSCC may be regulated by epigenetic alterations in SE elements of related tissues.

Citation Format: Emily L. Flam, Dylan Z. Kelley, Elena Stavrovskaya, Ludmila Danilova, Theresa Guo, Michael Considine, Jiang Qian, Joseph A. Califano, Alexander V. Favorov, Elana J. Fertig, Daria A. Gaykalova. Differentially methylated super-enhancers regulate gene expression in human papillomavirus-related head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 364.
Abstract 3643: Utility of peritoneal and pleural lavages for detection of somatic alterations: A proof-of-concept study
Authors: Ariza Núria Jordana , Ibañez Mónica Garzón , Martinez-Bueno Alejandro , Caldero Sonia Gatius , casas Clara Mayo de las , Velasco Ana , Ruiz Maria , Canal Berta Roman , Alamillo Jordi Bertran , Rodríguez Muñoz Sonia , Fuentes Raquel Campos , García Beatriz , Bel Ariadna Balada , Villatoro Sergi , Molina-Vila Miguel Ángel , Matias-Guiu Xavier
Published: August 2018

Background: Surgical resection remains the best treatment option for early-stage endometrial (CE), colorectal (CRC) and lung cancer (LC) patients. However, a proportion of patients (p) develop tumor recurrence, even after curative resection. Peritoneal or pleural lavages may be performed during surgery but little data is available about their potential as liquid biopsies with predictive value for recurrence. This proof-of concept study aimed to determine if somatic mutations can be detected in these lavages.

Methods: We analyzed mutations in paired surgical biopsies, blood and peritoneal or pleural lavages supernatants in an early-stage cohort of 25 EC, 12 CRC and 19 LC p. Molecular characterization of surgical biopsies was performed using the GeneReader NGS platform (Qiagen) and the Actionable Insight Tumor Panel, which includes 12 genes (KRAS, NRAS, KIT, BRAF, PDGFRA, ALK, EGFR, ERBB2, PIK3CA, ERBB3, ESR1, and RAF1). cfDNA was purified from blood and lavages using an automatic extractor and the hotspot mutations identified in tumor tissue were tested using a sensitive Taqman assay for codons 12, 13, and 61 in KRAS, codons 542, 545 and 1047 in PIK3CA and codon 600 in BRAF.

Results: NGS of tumor biopsies revealed hotspot KRAS, PIK3CA or BRAF mutations in a total of 11/25 (44%) early-stage EC p, 7/12 (58%) early-stage CRC p and 6/19 (32%) early-stage LC p. In peritoneal lavages, hotspot mutations were found in 6/11 (55%) EC p and 2/7 (29%) CRC p and, in pleural lavages, hotspot mutations appeared in 2/6 (33%) LC p. Furthermore, 2/11 (18%) blood samples from EC p, 1/7 (14%) blood samples from CRC p and 1/6 (17%) blood samples from LC p were positive.

Conclusions: Our study reveals that mutational analysis in peritoneal or pleural lavages from early stage tumors is feasible and that mutations are more frequently detected in lavages than in blood. Further research will determine if positivity in blood or lavages is associated with early relapse.

Citation Format: Núria Jordana Ariza, Mónica Garzón Ibañez, Alejandro Martinez-Bueno, Sonia Gatius Caldero, Clara Mayo de las casas, Ana Velasco, Maria Ruiz, Berta Roman Canal, Jordi Bertran Alamillo, Sonia Rodríguez Muñoz, Raquel Campos Fuentes, Beatriz García, Ariadna Balada Bel, Sergi Villatoro, Miguel Ángel Molina-Vila, Xavier Matias-Guiu. Utility of peritoneal and pleural lavages for detection of somatic alterations: A proof-of-concept study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3643.
Abstract 3656: Detecting MSI in plasma: Implications for early detection of lynch associated tumors
Authors: Srinivasan Preethi , Tran Christina , Reichel Jonathan , Patel Juber Ahamad , Hasan Maysun , Meng Fanli , Jing Xiaohong , Middha Sumit , Zehir Ahmet , Yaeger Rona D. , Reidy Diane , Tsui Dana , Stadler Zsofia , Berger Michael F.
Published: August 2018

Lynch Syndrome (LS) is characterized by germline mutations in mismatch repair pathway genes. The increased cancer susceptibility risk in these patients and the association of these tumors with microsatellite instability (MSI) provides a transformative opportunity for early detection of cancer in these patients. The presence of microsatellite unstable DNA fragments or zygosity changes of the MMR mutations in the plasma of LS patients is predictive of the presence of cancer. Here we describe an approach to detect MSI from plasma cell-free DNA (cfDNA) of LS associated cancer patients. First, to determine the background rate of MSI in cfDNA of microsatellite stable patients, we screened plasma samples collected from a large number of advanced cancer patients using MSK-IMPACT, a custom sequencing assay targeting 468 cancer genes encompassing ~1.5 megabases. MSK-IMPACT is approved by the NYS Department of Health and authorized by the FDA for clinical testing, including MSI assessment based on more than 1,000 microsatellite regions covered by the assay, and has been used to profile more than 20,000 patients at our institution. We were also able to confirm the ability to detect MSI in cfDNA in a small cohort of plasma samples collected from patients with MSI High tumors, and determine thresholds to delineate MSI from MSS cases from plasma. Using MSK-IMPACT, we detected MSI in the plasma of four patients with advanced MSI-H cancer, including one with confirmed LS. Three of these were patients with confirmed MSI signature from tumor tissue (one prostate cancer and two colorectal cancers. The fourth patient with prostate cancer had no tissue available for sequencing, though MSI was independently confirmed. To improve the sensitivity to detect MSI in patients with earlier stage disease where the fraction of tumor-derived cfDNA is lower, we have developed a novel targeted panel with optimized sequencing process and informatics, incorporating a set of highly informative microsatellite regions as well as SNPs to assess tumor-specific zygosity changes in mismatch repairs pathway genes. Through this work, we demonstrate the ability of our assay to detect MSI in plasma cfDNA with high sensitivity.

Citation Format: Preethi Srinivasan, Christina Tran, Jonathan Reichel, Juber Ahamad Patel, Maysun Hasan, Fanli Meng, Xiaohong Jing, Sumit Middha, Ahmet Zehir, Rona D. Yaeger, Diane Reidy, Dana Tsui, Zsofia Stadler, Michael F. Berger. Detecting MSI in plasma: Implications for early detection of lynch associated tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3656.
Abstract 366: Association of MLL2/KMT2D and MLL3/KMT2C with chronic myeloid leukemia
Authors: Ramos Doralina do Amaral Rabello , Ferreira Vivian D'Afonseca da Silva , Berzoti-Coelho Maria Gabriela , Burin Sandra Mara , Magro Cíntia Leticia , Cacemiro Maira da Costa , Simões Belinda Pinto , Saldanha-Araujo Felipe , Castro Fabíola Attié , Pittella-Silva Fábio
Published: August 2018

Chronic myeloid leukemia (CML) is a clonal myeloproliferative neoplasm linked to the Philadelphia chromosome presence that generates the BCR-ABL1 fusion oncogene. Tyrosine kinase inhibitors (TKI) such as imatinib mesylate (IM) dramatically improved the treatment efficiency and survival of CML patients by targeting BCR-ABL tyrosine kinase. Although patients in the chronic phase respond well to treatment, patients in the accelerated phase or blast crisis usually show therapy resistance and CML relapse. It is crucial, therefore, to identify biomarkers to predict CML genetic evolution and resistance to TKI therapy, considering not only the effects of genetic aberrations but also the role of epigenetic alterations during the disease. Although dysregulations in epigenetic modulators such as histone methyltrasnferases have already been described for some hematologic malignancies, to date very limited data is available for CML, especially when considering the MLL2/KMT2D and MLL3/KMT2C genes of histone methyltrasnferases. Here we investigated the expression profile of both genes in CML patients in different stages of the disease, in patients showing different responses to therapy with IM and in non-neoplastic control samples. Imatinib sensitive and resistant CML cell lines were also used to investigate whether treatment with other tyrosine kinase inhibitors interfered in their expression. Both genes were either upregulated or with basal expression level during the chronic phase compared to controls. Interestingly, MLL3/KMT2C and specially MLL2/KMT2D levels decreased during disease progression correlating with distinct clinical stages. Furthermore, MLL2/KMT2D was decreased in patients resistant to IM treatment. Our results established a new association between MLL2/KMT2D and MLL3/KMT2C genes with CML and suggest that MLL2/KMT2D is associated with disease evolution and may be a potential marker to predict the development of therapy resistance.

Citation Format: Doralina do Amaral Rabello Ramos, Vivian D'Afonseca da Silva Ferreira, Maria Gabriela Berzoti-Coelho, Sandra Mara Burin, Cíntia Leticia Magro, Maira da Costa Cacemiro, Belinda Pinto Simões, Felipe Saldanha-Araujo, Fabíola Attié Castro, Fábio Pittella-Silva. Association of MLL2/KMT2D and MLL3/KMT2C with chronic myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 366.
Abstract 3663: Non-invasive detection of fusion, splicing and mutation events from circulating cell-free RNA in cancers
Authors: Zhao Zhixin
Published: August 2018

Circulating cell-free DNA (cfDNA) and cell-free RNA (cfRNA) in cancer patients are valuable resource of biomarkers for early detection, diagnosis, treatment and monitoring of disease progression. Compared to cfDNA, cfRNA is more labile to degrade and fluctuate, and thus more challenging to be detected in blood. In the present study, we reported PrediSeq, a validated NGS-based liquid biopsy assay to detect fusions, splicing and mutation events using cfRNA. By using Predicine proprietary ultra-sensitive DeepSeaTM (Deterministic, Efficient, Precise, Sensitive Algorithm) variant detection algorithm, pre-analytical study demonstrated RNA-based detection of fusion, RNA splicing, and mutations using reference materials. In a LOD study, PrediSeq NGS assay is more sensitive than the digital PCR based assay in terms of mutation detection. In clinical validation study, tissue and plasma samples from various types of cancer patients (lung, breast, prostate etc) were used, where concordant fusion events with tissue were observed and RNA mutations confirmed variants detected at DNA level. In conclusion, a highly sensitive and accurate RNA-based liquid biopsy test has been developed to complement the use of cfDNA for detection of fusion, splicing and mutations.

Citation Format: Zhixin Zhao. Non-invasive detection of fusion, splicing and mutation events from circulating cell-free RNA in cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3663.
Abstract 3667: Technical advances in plasma genomic biomarkers for mutation detection and monitoring in cancer patients
Authors: Fitzgerald Sandra , Lasham Annette , Blenkiron Cherie , Shields Paula , Lawrence Ben , Print Cristin
Published: August 2018

A sea-change is imminent for cancer medicine, due to the use of non-invasive genomic biomarkers in blood to inform screening, diagnosis and the selection of treatment. This technology may be used routinely in oncology within five years. Although numerous studies, including work in our laboratory, have shown that genomic analysis of blood can detect the presence and even the type of cancer, researchers have only scratched the surface of what this technology can do. In our laboratory, we are generating new methods to improve the sensitivity and accuracy of such tests. Cell-free DNA from a metastatic colorectal cancer patient has been used to directly compare the sensitivity of mutation detection across three platforms - a custom QiaSeq Targeted amplicon sequencing panel, droplet digital PCR (ddPCR) and UltraSEEK lung panel. UltraSEEK and ddPCR platforms show better sensitivity for detection of the KRAS G12A mutation, compared to the QiaSeq Targeted DNA sequencing panel. This pilot study shows that when looking to specifically detect a small number of known mutations, UltraSEEK or ddPCR gives the highest sensitivity, but when mutations are not limited to a few or are completely unknown, the QiaSeq Targeted DNA panel allows identification of the entire repertoire of mutations in specific cancer-associated genes.

Citation Format: Sandra Fitzgerald, Annette Lasham, Cherie Blenkiron, Paula Shields, Ben Lawrence, Cristin Print. Technical advances in plasma genomic biomarkers for mutation detection and monitoring in cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3667.
Abstract 3669: Assessing the genetic heterogeneity of localized, multifocal prostate cancer via cell-free DNA
Authors: Chen Emmalyn , Cario Clinton L. , Leong Lancelote , Lopez Karen , Simko Jeffry P. , Carroll Peter R. , Tai Caroline , Witte John S.
Published: August 2018

At the time of diagnosis, it is common to find multiple spatially distinct foci within a single prostate gland in men with prostate cancer. Recent studies evaluating the genetic heterogeneity of localized, multifocal prostate cancers through whole-genome sequencing and whole-exome sequencing have only recently been described. These tumors were highly heterogeneous for single-nucleotide variants, copy number alterations, and genomic rearrangements. One exciting use of cfDNA is its potential ability to simultaneously capture all genetically distinct tumor subclones. Currently, the degree to which a cfDNA sample is representative of the entire genetic landscape of localized prostate cancer is unknown. The objective of this study is to determine if somatic mutations identified in tumor tissue are detectable in cfDNA. Tumor tissue and blood samples have been collected from twenty-nine patients undergoing radical prostatectomy. Samples from fourteen patients have already been subjected to whole-exome sequencing with a target sequencing depth of 200X (HiSeq 4000). Preliminary analyses indicate that tumor foci within a single prostate gland in an individual are genetically heterogeneous. Further analysis of mutational concordance between tumor tissue DNA and cfDNA along with clinical data will be performed.

Citation Format: Emmalyn Chen, Clinton L. Cario, Lancelote Leong, Karen Lopez, Jeffry P. Simko, Peter R. Carroll, Caroline Tai, John S. Witte. Assessing the genetic heterogeneity of localized, multifocal prostate cancer via cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3669.
Abstract 3670: Urine- and blood-based DNA+RNA liquid biopsy tests in prostate, bladder and kidney cancers
Authors: Wang Amy , Zhao Zhixin , Xie Cheng , Cheung Tak , Montesinos Carlos , Zhang Phoebe , Du Pan , Yu Jianjun , Jia Shidong
Published: August 2018

The estimated incidence of genitourinary (GU) cancers (prostate, bladder, and kidney) will be over 2 million worldwide and responsible for ∼800 000 deaths by 2020. Current diagnosis and monitoring methods of GU cancer patients are often invasive and/or lack sensitivity and specificity. The recent tremendous success in cell-free DNA (cfDNA) blood test has laid the groundwork for using body fluids such as blood and urine as minimally invasive “liquid biopsies” to identify RNA- and DNA-based molecular biomarkers in urologic malignancies.

Here we report the development and clinical application of PrediSeq panel, a urine- and blood-based next generation sequencing-based diagnostics assay that offers integrated genomic cfDNA and cell-free RNA (cfRNA) profiling of genitourinary cancers to detect RNA-based splicing variants (e.g. AR-V7) and rearrangement (e.g. TMPRSS2-ERG), DNA/RNA-based point mutation (e.g. p53, PIK3CA, FGFRs), DNA-based copy number change (e.g. AR) as well as tumor mutation burden (TMB) and microsatellite instability (MSI) using a single tube of blood and/or urine sample in prostate, bladder, and kidney cancers, respectively. In addition to NGS-based multiplex test, we also developed a Bio-Rad digital PCR assay measuring drug response and resistance biomarkers including AR-V7 and PD-L1.

Collectively, PrediSeq NGS and ddPCR assays offer comprehensive genomic profiling of both cfDNA and cfRNA using blood and/or urine samples in patients with genitourinary cancers. The successful development and clinical validation of these tests has potential to enable early diagnosis, cancer screening, and precision medicine in genitourinary cancers.

Citation Format: Amy Wang, Zhixin Zhao, Cheng Xie, Tak Cheung, Carlos Montesinos, Phoebe Zhang, Pan Du, Jianjun Yu, Shidong Jia. Urine- and blood-based DNA+RNA liquid biopsy tests in prostate, bladder and kidney cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3670.
Abstract 3673: Targeting the epigenome of small cell hypercalcemic carcinoma of the ovary, hypercalcemic type (SCCOHT)
Authors: Wang Yemin , Chen Shary Yu-ting , Colborne Shane , Orlando Krystal , Lang Jessica , Karnezis Anthony , Hendricks William , Morin Gregg , Weissman Bernard , Trent Jeffrey , Huntsman David
Published: August 2018

Small cell carcinoma of the ovary hypercalcemic type (SCCOHT) is a rare and poorly differentiated cancer that impacts young women with an average 2-year survival of less than 35%. We and others have discovered the inactivating mutations of SMARCA4 as the only consistent genetic alternation in SCCOHT genomes. SMARCA4 is the ATPase of the SWI/SNF chromatin-remodeling complex, which modulates chromatin accessibility to regulate transcription and plays critical roles in many biologic processes such as cell cycle control, apoptosis, and differentiation. SCCOHT also lacks the expression of SMARCA2, the alternative ATPase in the complex, contrasting the requirement of SMARCA2 for survival of most SMARCA4-deficient cancer cells. This suggest that the complete loss of chromatin-remodeling activity may rewire the epigenome and create opportunities for synthetic lethal targeting. A rational epigenetic drug screen identified EZH2 inhibitors and HDAC inhibitors as promising therapeutic agents in SCCOHT cells. We confirm that catalytic inhibition of EZH2 selectively suppressed the growth of SCCOHT cells in vitro and in xenograft models through activation of apoptosis and differentiation. Pan-HDAC inhibitors also displayed a more robust anticancer effect in SCCOHT cells than other in other ovarian cancer cell lines. Furthermore, combined treatment of EZH2 inhibitors and pan-HDAC inhibitors increased the global acetylation level at histone H3K27 site and synergistically suppressed the growth of SCCOHT cell lines and xenografts through robust induction of apoptosis. Although EZH2 or HDAC inhibitor treatment led to re-expression of SMARCA2, depletion of SMARCA2 had only minimal effect on drug response. Proteomic analysis identified key signaling pathways underlying the efficacy of epigenetic therapy that are under investigation. Therefore, inactivation of SWI/SNF chromatin remodeling complex may drive SCCOHT development through PRC2-dependent rewiring of the epigenome. Targeting these oncogenic events can be the feasible strategies for treatment of SCCOHT that warrant clinical investigation.

Citation Format: Yemin Wang, Shary Yu-ting Chen, Shane Colborne, Krystal Orlando, Jessica Lang, Anthony Karnezis, William Hendricks, Gregg Morin, Bernard Weissman, Jeffrey Trent, David Huntsman. Targeting the epigenome of small cell hypercalcemic carcinoma of the ovary, hypercalcemic type (SCCOHT) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3673.
Abstract 3675: Loss of alveolar type II epithelial and endothelial cell lineages in invasive mucinous adenocarcinoma of the lung (IMA)
Authors: Tomoshige Koichi , Guo Minzhe , Tsuchiya Tomoshi , Fink-Baldauf Iris , Nagayasu Takeshi , McKillip Kelsey Dillehay , Maeda Yutaka
Published: August 2018

Background: Invasive mucinous adenocarcinoma of the lung (IMA) is pathologically characterized as lung tumor cells with goblet cell morphology containing abundant intracytoplasmic mucin. IMA has been reported to account for 2-10% of lung adenocarcinomas. Genetically, the majority of IMA harbor KRAS mutations. Recently, by analyzing RNA-seq data using human IMA cases, we reported mucus-related genes specifically expressed in IMA, which includes MUC5AC, MUC5B, MUC3, SPDEF, FOXA3 and HNF4 (Guo, Tomoshige et al., 2017). Notably, immunohistochemical analyses have determined that NKX2-1 (also known as TTF-1) is reduced in IMA (Travis et al., 2011); however, other than NKX2-1, genes reduced in IMA compared to normal lungs have not been determined.

Methods: In order to further understand the demographic occurrence of IMA, we surveyed the clinical records at the University of Cincinnati College of Medicine in the U.S. and Nagasaki University of School of Medicine in Japan. Genes reduced in IMA compared to normal lungs were identified using the RNA-seq datasets as we have previously reported (Guo, Tomoshige et al., 2017). Using single-cell and sorted RNA-seq datasets (LGEA; Du et al., 2017), genes were further categorized into groups that define different cell types that exist in normal lungs.

Results: IMA occurred in 4.6% (3/65 cases in 2017) and 1.9% (2/105 cases in 2017) of lung adenocarcinomas at the University of Cincinnati College of Medicine and Nagasaki University of School of Medicine, respectively. Importantly, analysis using normal lung cell type specification markers obtained from the single-cell and sorted RNA-seq datasets identified that genes that define alveolar type II epithelial cells (e.g., SFTPC and ABCA3) and endothelial cells (e.g., FOXF1 and SOX17) were significantly reduced in IMA compared to normal lungs.

Conclusion: IMA comprises mucus-producing goblet cell lineage populations devoid of alveolar type II epithelial and endothelial cell-lineage populations, suggesting a unique tumor microenvironment distinct from other lung adenocarcinomas.

Citation Format: Koichi Tomoshige, Minzhe Guo, Tomoshi Tsuchiya, Iris Fink-Baldauf, Takeshi Nagayasu, Kelsey Dillehay McKillip, Yutaka Maeda. Loss of alveolar type II epithelial and endothelial cell lineages in invasive mucinous adenocarcinoma of the lung (IMA) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3675.
Abstract 3676: CMS classification of colorectal adenomas
Authors: Komor Malgorzata A. , Bosch Linda J. , Bounova Gergana , Bolijn Anne S. , Diemen Pien Delis-van , Rausch Christian , Hoogstrate Youri , Stubbs Andrew , Jong Mark de , Jenster Guido , Grieken Nicole C. an , Carvalho Beatriz , Wessels Lodewyk , Jimenez Connie R. , Fijneman Remond J. , Meijer Gerrit A. , Consortium NGS-ProToCol
Published: August 2018

Background Consensus molecular subtyping (CMS) is an RNA-expression-based classification of colorectal cancers (CRC). Genomic alterations, resulting in specific RNA-expression patterns, accumulate during CRC pathogenesis, including the premalignant adenoma stage.

Aim This study aimed to investigate whether differentiation of colorectal neoplasia into CMS classes can already be recognized at the adenoma stage, and whether specific CMS classes could be associated with DNA copy number aberrations that mark adenomas at high-risk of progressing to CRC.

Materials and Methods RNA-sequencing was performed on 62 advanced adenomas and 59 CRCs. DNA copy number analysis in adenomas was performed by low-coverage DNA-sequencing (n=30) or array-Comparative Genomic Hybridization (n=32). Microsatellite instability (MSI) status was determined by PCR methods. Adenomas and CRCs were classified into CMS subtypes together with CRCs (n=556) from The Cancer Genome Atlas, using the Random Forest CMS classifier.

Results The majority of the adenomas were classified as CMS3 (n=45; 72%), the 'metabolic subtype', recognized as least common among CRCs. No adenomas were classified as the 'mesenchymal' CMS4 subtype. One adenoma was classified as the 'MSI immune' CMS1 (2%), and 8 adenomas as the 'canonical' CMS2 (13%) type. The remaining 8 (13%) could not be classified. The CMS3 class was enriched with adenomas at low-risk of progression.

Conclusion Most adenomas were successfully classified. The lack of CMS4 adenomas is consistent with the fact that adenomas lack invasion-associated stroma. Adenomas showing cancer-associated chromosomal instability (CIN) or MSI (24%) were mostly classified as CMS2 and CMS1, respectively. The CMS3 subtype appeared to be the predominant adenoma signature.

Citation Format: Malgorzata A. Komor, Linda J. Bosch, Gergana Bounova, Anne S. Bolijn, Pien Delis-van Diemen, Christian Rausch, Youri Hoogstrate, Andrew Stubbs, Mark de Jong, Guido Jenster, Nicole C. an Grieken, Beatriz Carvalho, Lodewyk Wessels, Connie R. Jimenez, Remond J. Fijneman, Gerrit A. Meijer, NGS-ProToCol Consortium. CMS classification of colorectal adenomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3676.
Abstract 3679: PD-L1 driven excluded phenotype in melanoma
Authors: Morrison Carl , Conroy Jeffrey , Nesline Mary , Glenn Sean , Burgher Blake , Qin Maochun , Andreas Jonathan , Giamo Vincent , Lenzo Felicia L. , Omilian Angela , Bshara Wiam , Papanicolau-Sengos Antonios , Wang Yirong , Ernstoff Marc , Gardner Mark , Pabla Sarabjot
Published: August 2018

Background: The excluded phenotype has been previously described by the presence of abundant immune cells that do not penetrate the parenchyma of these tumors but instead are retained in the stroma that surrounds nests of tumor cells. These features support a pre-existing anti-tumor immune-related response, but the details of this mechanism are not well elucidated.

Methods: 300 formalin-fixed, paraffin-embedded (FFPE) metastatic cutaneous melanoma samples were evaluated by the RNA-seq component of a comprehensive immune profile panel to measure transcript levels of immune-related genes. Resultant data was QC filtered, normalized and ranked based on an assorted reference population of various tumor types. The expression of PD-L1 on the surface of tumor cells was assessed in tumor samples by means of an automated IHC assay (28-8, Dako). A tumor was considered PD-L1 positive if ≥1% of viable tumor cells exhibited complete circumferential or partial linear plasma membrane staining at any intensity. Excluded pattern of T-cell infiltration was defined by CD8 immunohistochemistry by the following definition: Restriction of more than 95% of all CD8+ T-cells present in a tumor to the periphery or interstitial stromal areas and not actively invading nest or groups of neoplastic cells.

Results: The excluded phenotype was identified in 34 of 300 (11%). PD-L1 by IHC was positive (≥1%) in the neoplastic cases in 16 of 34 (47%) cases. Membranous staining in immune cells was identified in only 3 of 34 (9%) cases, but was present in >90% of all cases in a non-membranous pattern. In more than one-half of all cases the non-membranous pattern of PD-L1 IHC staining was restricted to the excluded TILs. Higher expression of PD-L1 by RNA-seq was associated with this excluded PD-L1 pattern of staining.

Conclusion: In 300 metastatic cutaneous melanoma cases we demonstrated that the excluded phenotype is frequent and represents ~10% of all cases. Moreover, in a significant number of excluded cases expression of PD-L1 by IHC was distinctly limited to the excluded TILs. This finding would support a unique mechanism of PD-L1 anti-tumor immune-related response that needs further investigation.

Citation Format: Carl Morrison, Jeffrey Conroy, Mary Nesline, Sean Glenn, Blake Burgher, Maochun Qin, Jonathan Andreas, Vincent Giamo, Felicia L. Lenzo, Angela Omilian, Wiam Bshara, Antonios Papanicolau-Sengos, Yirong Wang, Marc Ernstoff, Mark Gardner, Sarabjot Pabla. PD-L1 driven excluded phenotype in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3679.
Abstract 3702: A novel nanoparticle-based theranostic agent targeting low-density lipoprotein receptor-related protein-1 enhances the efficacy of neoadjuvant radiotherapy in colorectal cancer
Authors: Lee Kyoung Jin , Park Serk In , Jeong Seong-Yun , Choi Eun Kyung
Published: August 2018

Neoadjuvant radiotherapy is becoming an important therapeutic option for colorectal cancer (CRC) patients, although complete tumor response is observed only in 20 to 30% patients. However, precise biologic mechanisms underlying resistance to radiotherapy remain to be elucidated. In this study, we established a radiotherapy-resistant CRC patient-derived xenograft (PDX) mouse model, and we discovered that low-density lipoprotein receptor-related protein-1 (LRP-1) is increased in radiotherapy-resistant tumors compared with radiotherapy-sensitive tumors. Immunohistochemistry, mRNA and protein expression analyses of radiotherapy-sensitive vs. -refractory CRC patient samples confirmed a statistically significant association between LRP-1 levels and radiotherapy resistance of CRC. We also found that LRP-1 expression is significantly associated with the prognosis of CRC patients by analyzing gene expression data of CRC patients in Gene Expression Omnibus public database. Subsequently, aiming to develop radio-sensitizing nanoparticles targeting LRP-1 for chemotherapeutic drug delivery and in vivo imaging, we screened and identified an LRP-1-binding peptide in a radiotherapy-resistant CRC PDX mouse model using M13 phage display. We next engineered human serum albumin nanoparticles (HSA NPs) containing the LRP-1-binding peptide (for tumor localization), 5-FU (for cytotoxic chemotherapy) and Cy7 fluorophore (for in vivo imaging). When administered in CRC PDX-bearing mice, the LRP-1-targeting HSA NPs accumulated specifically in the CRC tumor tissue and dramatically increased the efficacy of radiotherapy. In addition, whole-body fluorescence imaging of PDX CRC-bearing mice showed that the HSA-NP accumulated only in radiation-treated tumors with high ROI values. In summary, we identified that LRP-1 is a novel signature protein of radiotherapy-resistant CRC, and validated that LRP-1 is closely associated with the progression of CRC. We developed a novel HSA nanoparticle-based theranostic agent loaded with LRP-1-binding peptide, 5-FU and a fluorophore that is applicable to both diagnostic imaging and radio-sensitizing neoadjuvant therapy of CRC. This approach is clinically applicable to improve the effectiveness of neoadjuvant radiotherapy and increase the ratio of complete tumor response in radio-resistant CRC.

Citation Format: Kyoung Jin Lee, Serk In Park, Seong-Yun Jeong, Eun Kyung Choi. A novel nanoparticle-based theranostic agent targeting low-density lipoprotein receptor-related protein-1 enhances the efficacy of neoadjuvant radiotherapy in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3702.
Abstract 3709: Characterization, in vitro and in vivo efficacy studies of docetaxel trastuzumab stealth immunoliposome in human breast cancer models
Authors: Rodallec Anne , Brunel Jean Michel , Robert Stephane , Giacometti Sarah , Savina Ariel , Bouquet Fanny , Lacarelle Bruno , Ciccolini Joseph , Fanciullino Raphaelle
Published: August 2018

In HER2-positive breast cancer, the Trastuzumab + Docetaxel doublet has a significant efficacy but is hampered by frequent toxicities that could be addressed with nanoparticles. We have developed an Antibody-Nano Conjugate (ANC), combining docetaxel encapsulated in a stealth liposome engrafted with trastuzumab. This entity is expected to improve the efficacy/toxicity balance of this doublet, by improving trafficking and delivery to the tumors. ANCs were synthesized using thin-film method and trastuzumab was grafted via sulfydryl groups on maleimide polyethylene glycol. Two compositions (ANC-1 and ANC-2) were tested and compared (i.e., size, morphology, encapsulation rate, engrafting rate, and stability). Antiproliferative activity was tested on a panel of human breast cancer models ranging fromHER2-negative (MDA-MB-231) to HER2-positive (MDA-MB-453) or -overexpressing (SKBR3), both on 2D and spheroid models. Biodistribution, efficacy and survival were tested in MDAMB-231 and MDA-MB-453 bearing nude mice. ANC-1 presented a greater size (140 ± 3 nm), docetaxel encapsulation rate (73 ± 6 %) and stability as compared with ANC-2. In vitro, both ANCs were found to be more efficient than standard docetaxel + trastuzumab, with a better performance for ANC-1. In vivo, ANC-1 accumulated better in tumors, resulting in a higher reduction in tumor growth (i.e. >+36%) and prolonged survival (i.e. >+33%) as compared with standard treatment. Both in vitro and in vivo results suggest that higher antiproliferative efficacy and efficient drug delivery can be achieved in breast cancer models. Of note, although modest, even Her2- model (i.e., MDA231) was found to benefit from the nanoparticle.

Citation Format: Anne Rodallec, Jean Michel Brunel, Stephane Robert, Sarah Giacometti, Ariel Savina, Fanny Bouquet, Bruno Lacarelle, Joseph Ciccolini, Raphaelle Fanciullino. Characterization, in vitro and in vivo efficacy studies of docetaxel trastuzumab stealth immunoliposome in human breast cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3709.
Abstract 3738: Three-dimensional treatment-resistant breast cancer spheroids as a predictive model of in vivo response to endocrine therapy
Authors: Rosales Carlo I. , Zhao Jiong , Gutgesell Lauren M. , Xiong Rui , Tonetti Debra A. , Thatcher Gregory R.
Published: August 2018

1 out of every 8 U.S. women will develop invasive breast cancer during her lifetime, making it the second most common form of cancer affecting women. Breast cancer is also a leading cause of cancer related deaths for women in the U.S., second only to lung cancer. Activation of estrogen receptor alpha (ERα) is the primary proliferative mechanism of breast cancer cells, making it a logical target for therapy. ER ligands with antiestrogenic activity, such as the selective estrogen receptor modulator (SERM), tamoxifen, and selective estrogen receptor degrader (SERD), fulvestrant, have proven clinically successful as treatments for breast cancer; however, resistance in up to 50% of patients provides a therapeutic challenge. Once resistant, breast cancer cells become endocrine-independent, because of this, there is an urgent need for both novel therapy and improved models of resistant breast cancer. Our lab has created a panel of various endocrine-independent cell lines to mimic SERM and SERD resistance. Along with traditional 2D cell culturing, 3D spheroids have also been utilized to gain a better understanding of resistance. Importantly, the response to therapeutic agents, of cell lines in 2D versus 3D cultures is not identical. We observe that 3D cultures better replicate observations in mouse xenograft models, demonstrating that elements of the spheroid microenvironment, such as cell-cell interactions and the presence of extracellular matrix (EM), mimic aspects of the tumor microenvironment in vivo. Cells cultured as spheroids are therefore a suitable in vitro model for drug discovery, predictive of response in preclinical animal models, in contrast to 2D monolayer cell cultures.

Citation Format: Carlo I. Rosales, Jiong Zhao, Lauren M. Gutgesell, Rui Xiong, Debra A. Tonetti, Gregory R. Thatcher. Three-dimensional treatment-resistant breast cancer spheroids as a predictive model of in vivo response to endocrine therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3738.
Abstract 3744: Multiple endocrine-resistant breast cancer cell lines retain ER and sensitivity to endocrine therapy
Authors: Gutgesell Lauren M. , Xiong Rui , Zhao Jiong , Zhao Huiping , Tonetti Debra A. , Thatcher Gregory R.
Published: August 2018

Endocrine therapy is the standard of care for breast cancer expressing estrogen receptor (ER),

which occurs in 70% of patients. Unfortunately, acquired or de novo resistance to endocrine

therapy is observed in up to 50% of patients, leaving a significant portion of patients with

insufficient treatment options. Endocrine-resistance, usually defined as resistance to tamoxifen

and aromatase inhibitor (AI) therapy, can also include resistance to selective estrogen receptor

degraders (SERDs), since these also target ER. Since multiple mechanisms contribute to

resistance, development of multiple resistant cell lines is needed for drug discovery and to identify

characteristics that may suggest susceptibility to alternative and combination therapies. We have

developed 5 stable, endocrine-resistant cell lines from a parent MCF-7 cell line, which all retain

ER: one of these cell lines, MCF-7:CFR is resistant to the SERD fulvestrant. Clinical metastatic

breast cancers that have gained endocrine resistance are overwhelmingly ER+. In addition to ER,

progesterone receptor (PR) and glucocorticoid receptor (GR) status of these lines was assessed,

and correlated with the response of these cells in culture to four classes of endocrine therapeutics:

SERDs, selective ER modulators (SERMs), and selective human ER partial agonists (ShERPAs).

Growth of all 5 cell lines was endocrine independent, indicating resistance to AI therapy. Two of

the ER+, PR- cell lines were most resistant to the spectrum of endocrine therapies, but these cell

lines both showed sensitivity to ShERPAs, especially in combination with non-endocrine targeted

therapies, such as the PI3K inhibitor, alpelisib. Paradoxically, all endocrine-resistant cell lines

responded to at least one of the endocrine therapies tested, demonstrating that if ER is not lost

in the metastatic state, it remains a vulnerability suitable for therapeutic targeting.

Citation Format: Lauren M. Gutgesell, Rui Xiong, Jiong Zhao, Huiping Zhao, Debra A. Tonetti, Gregory R. Thatcher. Multiple endocrine-resistant breast cancer cell lines retain ER and sensitivity to endocrine therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3744.