bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1313: Genomic and transcriptomic profiles of primary prostate cancer identify unique targets for therapeutic intervention
Authors: Chakravarty Dimple , Wang Zichen , Rossi Michael , Ratnani Parita , Reva Boris , Rykunov Dmitry , Bhatt Kamala , Wagaskar Vinayak , Weil Rachel , Beaumont Kristin , Beaumont Michael , Maayan Avi , Sebra Robert , Bhardwaj Nina , Nair Sujit S. , Tewari Ashutosh K. 
Published: September 2020

Abstract
The tumor microenvironment and genomic landscape of intermediate and high-risk primary localized prostate cancers are clinically heterogeneous and result in variable treatment response in individuals. Cancer-specific alterations at DNA and RNA level is a critical driver of intra-tumoral heterogeneity that significantly impacts the molecular processes which influence the path of disease progression and outcome. In this study, we have performed genomic and transcriptomic analysis of 267 primary prostate cancer. Our analysis revealed actionable alterations and gene signatures for risk stratification and decision support. Clinically significant variants were detected in DNA repair (HR and Mismatch pathway), PI3/AKT, and TP53 signaling pathways with a strong association with disease progression. Further, single-cell analysis (scRNA-seq) of prostate cancer that progressed to metastasis post-therapy identified the unique tumor and immune cell-clusters. Functional annotation of these clusters and drug repurposing studies revealed novel targets for therapeutic intervention that was validated using organoid cultures. Our studies show that an Integrated analysis using genomic, clinical, and pathological features has the potential to define prostate cancer subtypes or phenotypes associated with poor prognosis. Our approach can advance prostate cancer treatment in patients with adverse clinical features by providing treatment options beyond the standard of care (surgery or radiation) and with better therapeutic benefit.
Citation Format: Dimple Chakravarty, Zichen Wang, Michael Rossi, Parita Ratnani, Boris Reva, Dmitry Rykunov, Kamala Bhatt, Vinayak Wagaskar, Rachel Weil, Kristin Beaumont, Michael Beaumont, Avi Maayan, Robert Sebra, Nina Bhardwaj, Sujit S. Nair, Ashutosh K. Tewari. Genomic and transcriptomic profiles of primary prostate cancer identify unique targets for therapeutic intervention [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1313.
Abstract 1320: The landscape of somatic substitutions in the repetitive genome across cancer types
Authors: Tarabichi Maxime , Demeulemeester Jonas , Verfaillie Annelien , Van Loo Peter , Konopka Tomasz 
Published: September 2020

Abstract
Somatic mutation calling from bulk DNA sequencing is a complex problem susceptible to elevated false positive rates. High mapping quality is considered an important feature of reliable variant calls. At the resolution of short reads, ~10% of the genome displays high sequence similarity with at least one other genomic region and is assigned low mapping quality by alignment algorithms. These low-mapping-quality regions represent recurrent blind spots for mutation callers, which discard many of the variants they harbor, overlooking true biological variation.
Here, we developed a pipeline to call substitutions in the low-mapping-quality genome. We used a published thesaurus approach to annotate the variant positions with their high-similarity links. We trained a classifier to emulate high-quality consensus calls made in unique regions using 20 features unrelated to mapping quality, reaching ~95% accuracy in those regions. In an independent sample more than 90% of the thesaurus calls were validated through linked-read sequencing. We then applied the classifier to all candidate substitutions of 2,658 cancer whole genomes from the PCAWG/ICGC consortium including variants falling in low-mapability regions.
We retrieve hidden thesaurus variants genome-wide in ~6% of the genome, including genic, coding, and promoter regions. Thesaurus calls are directly proportional in numbers to somatic calls falling in the low-mapping-quality genome and share a similar trinucleotide context spectrum. Rescuing these mutations reveal hidden signal in known cancer genes, including PIK3CA, and excess of mutations genome-wide in promoter, untranslated, and coding regions of many other genes. We also find potential excess of non-synonymous mutations, including in genes from the TRIM and POTE families, having been previously implicated in multiple cancer types.
Altogether, we developed a pipeline to call somatic substitutions in the low-mapping-quality genome and uncovered hidden somatic changes along the genomes of human cancers. In the future, this pipeline could be extended to indels and structural variants, and applied to the study of de novo germline variants.
Citation Format: Maxime Tarabichi, Jonas Demeulemeester, Annelien Verfaillie, Peter Van Loo, Tomasz Konopka. The landscape of somatic substitutions in the repetitive genome across cancer types [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1320.
Abstract 1330: Scalable single-day workflows for variant calling with the Genexus Integrated Sequencer
Authors: Gioia Jason , Casuga Iris R. , Chan Frances , Commins James , Conners David , Kratzer Marla , Seeger Collyn , Yaccarino David 
Published: September 2020

Abstract
The purpose of this study is to test the speed, scalability, and flexibility of variant detection with the Genexus Integrated Sequencer. This research use only instrument uses nucleic acid input and executes the steps of library preparation, sequencing, analysis, and variant calling. Taking advantage of the instrument's flexibility in sample plexy, the authors used the Oncomine™ Comprehensive Assay v3 and commercially available control samples to detect SNPs, InDels, and fusions reliably at up to 6-plex paired DNA and RNA samples. The instrument can accommodate 1, 2, 4, or 6 paired DNA and RNA samples when using 1, 2, 3, or 4 lanes of the GX5 chip. Regardless of the number of samples analyzed, the system achieved at least 98% sensitivity, 98% positive predictive value, 95% agreement to known truth for de novo variants, and 98% agreement to known truth for hotspot variants in the Acrometrix™ Oncomine Hotspot Control. Also regardless of sample plexy, the system achieved at least 97% agreement to known truth for Fusions within the SeraSeq® Fusion RNA Mix v3. The flexible workflows allow for fast turn-around times of as little as 18 hours for a single sample pair and less than 30 hours for 6 paired DNA and RNA samples. Stability of system initialization is an important feature for flexible use of an NGS system, and read length is a limiting performance metric for evaluating stability. In order to test the Genexus system's read length and stability features the Oncomine™ TCR Beta-LR Assay GX was used. Instruments were initialized with sequencing consumables and tested for performance on day 1 and day 15. There was no statistically significant difference in total reads (3.5 ± 1.0 M at day 1 vs. 3.1 ± 1.0 M at day 15), the fraction of reads that are low quality reads (13% ± 2% vs. 14% ± 2%), or mean read length (301 ± 6 bases vs. 296 ± 6 bases) between the two time points. In conclusion, the Genexus integrated sequencer is a robust NGS system that facilitates rapid turn-around time, flexibility in sample plexy, and stability in system consumables use.
Citation Format: Jason Gioia, Iris R. Casuga, Frances Chan, James Commins, David Conners, Marla Kratzer, Collyn Seeger, David Yaccarino. Scalable single-day workflows for variant calling with the Genexus Integrated Sequencer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1330.
Abstract 1335: Analytical evaluation of a targeted solid tumor next-generation sequencing assay
Authors: Tsai Jeff H. , Montel Valerie , Mouttham Nathalie 
Published: September 2020

Abstract
With the growing interest in personalized medicine for cancer patients, next generation sequencing (NGS) variant screening assays are becoming a powerful clinical tool for tumor classification. The AmpliSeqTM for Illumina Focus Panel is a targeted sequencing approach that interrogate 52 of the most common solid tumor genes for single nucleotide variants (SNVs), insertion/deletions (indels), and copy number variants (CNVs) in DNA and gene fusions in RNA concurrently. To evaluate the performance of the Focus assay, an analytical performance study was conducted. Using an automated workflow with high quality DNA reference samples, both intra-assay and inter-assay experiments resulted in high reproducibility (R2 &gt;0.95) for detecting expected variants at various frequencies. Similarly, using high quality RNA reference samples, 100% of all expected fusions were detected in all experiments, demonstrating accuracy and precision of the Focus panel assay with high quality samples. To evaluate assay sensitivity, limit of detection (LOD) studies were carried out by titrating the nucleic acid input into the assay. Using a 5% variant allele frequency threshold (empirically established in the analysis pipeline), the assay detected all expected SNVs and indels across sample across sample input amounts. Using extracted DNA from a human cell line model (HL-60) with a confirmed MYC gene gain, results showed reliable MYC gain detection down to 4 copies in a diploid background. Similarly, extracted RNA from a confirmed EML4-ALK fusion positive cell line (H2228) diluted into background RNA showed 100% positive fusion calling down to 250pg or 133 copies. Finally, to understand the assay performance on clinically-relevant FFPE samples, somatic variant detection in 8 human cell lines and 68 total FFPE samples was evaluated. For FFPE DNA samples, the libraries averaged &gt;90% on-target alignment and coverage uniformity with &gt;3000x mean coverage across all samples. While FFPE RNA showed lower alignment for poor quality samples, the assay showed overall high positive and negative predictive value for variant and fusion calling. In summary, the AmpliSeqTM for Illumina Focus panel is an automation-compatible small panel NGS assay with robust performance to assess somatic variants in solid tumors.
Citation Format: Jeff H. Tsai, Valerie Montel, Nathalie Mouttham. Analytical evaluation of a targeted solid tumor next-generation sequencing assay [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1335.
Abstract 1344: Simultaneous mRNA, protein, and immune repertoire profiling of antigen-specific T cells by single cell sequencing
Authors: Siddique Imteaz , Shi Xiaoshan , Nakamoto Margaret , Mortimer Stefanie 
Published: September 2020

Abstract
High-throughput single cell RNA-seq (scRNA-seq) has transformed our understanding of complex and heterogenous immune populations. New advances in scRNA-seq are expanding the molecules that can be profiled at the single cell level, such as oligo-conjugated antibody technologies that enable protein expression profiling alongside mRNA. Although the ability to sequence the immune repertoire can provide crucial insights into understanding the complexities of the adaptive immune system and advancing discoveries in immuno-oncology, the ability to extract this information from single cells requires new technology to profile regions of the mRNA that are missed by conventional 3' scRNA-seq. In this study we utilized an ex vivo antigen stimulation system to measure antigen-specific T-cell activation and clonal amplification. Stimulated T cells from two donors were loaded onto the BD Rhapsody™ Single-Cell Analysis System to extract immune repertoire information in addition to gene and protein expression information from the same cells. In a single workflow, we profiled a panel of 400 mRNA targets, 20 BD® AbSeq protein markers associated with different status of T-cell activation, and the hypervariable region of T-cell receptors at the single cell resolution. The study is a proof of concept of combining mRNA, protein and immune repertoire analysis at the single cell level to deconvolute the heterogeneity and different activation of stimulated T cells.
For Research Use Only. Not for use in diagnostic or therapeutic procedures.
BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.
Citation Format: Imteaz Siddique, Xiaoshan Shi, Margaret Nakamoto, Stefanie Mortimer. Simultaneous mRNA, protein, and immune repertoire profiling of antigen-specific T cells by single cell sequencing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1344.
Abstract 1368: 4NQO shows formation of yH2AX foci, oxidative base damage and activates DNA repair pathway preferentially in HPV positive HNSCC cells
Authors: Shishodia Gauri , Toledo Rhodee Ric G. , Rong Xiahuao , Xiao Adam Y. , Harrison Lynn , Nathan Cherie Ann 
Published: September 2020

Abstract
Background: There is an epidemic of HPV associated head and neck squamous cell carcinoma (HNSCC) There is controversy as to whether HPV positive SCC patients who have a &gt;10 pack year smoking history have a worse prognosis than HPV associated non-smokers. Tobacco exposure is associated with alteration of DNA damage repair (DDR) pathway which is often activated in several cancers including HNSCC. A mutational profile of HPV associated smokers determined there was no significant difference in the mutational profile between HPV associated non-smokers and smokers. Hence we wanted to test this observation by analyzing the effects of 4NQO, a mutagen and carcinogen which serves as a surrogate for tobacco exposure, in HPV positive and HPV negative HNSCC cells.
Methods: Protein and mRNA expression were analyzed by western blotting and real time PCR respectively. yH2AX staining and oxidative DNA damage analysis were performed using immunofluorescence and FPG-modified alkaline comet assay respectively.
Results: Our preliminary data shows that 4NQO activates DDR pathway preferably in NOK E6/E7 and HPV positive UMSCC47 and SCC104 HNSCC cells as seen by increased phosphorylation of BRCA1, Rad50 and RAD51, chk1 and increased p21 levels in a time- and concentration-dependent fashion. Real time PCR data showed higher mRNA transcript levels of RAD51 and BRCA1 in NOK E6/E7 and HPV positive UMSCC47 and SCC104 HNSCC cells as compared to NOK and HPV negative SCC40 HNSCC cells upon 4NQO treatment. 4NQO causes yH2AX foci formation suggesting double strand breaks (DSBs) formation and an increase in DNA damage in HNSCC cells. 4NQO increased oxidative base damage in NOK E6/E7, UMSCC47 and SCC104 HPV positive HNSCC cells, and to a lesser degree in NOK and SCC40 HPV negative HNSCC cells.
Conclusion: Our preliminary study shows for the first time that HPV E6/E7 oncogenes promote DNA repair in NOK and HPV positive HNSCC cells in response to 4NQO treatment. This could explain why HPV associated HNSCC have a better prognosis irrespective of smoking history.
Citation Format: Gauri Shishodia, Rhodee Ric G. Toledo, Xiahuao Rong, Adam Y. Xiao, Lynn Harrison, Cherie Ann Nathan. 4NQO shows formation of yH2AX foci, oxidative base damage and activates DNA repair pathway preferentially in HPV positive HNSCC cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1368.
Abstract 1377: Identification and validation of WRN as a novel synthetic lethality target in context of microsatellite instability
Authors: Ding Zhihu (Jeff) , Zhang Jing , Pedamallu Chandra Sekhar , Rowley Steve , Cheng Jane , Dai Shujia , Zhou Bridget , Koundinya Malvika , Guo Zhuyan , Poirier Stephane , Hopke Joern , Lennon Amanda , Buell Jennifer , Cindhuchao May , Wong Karen , Wang Emma , Protopopov Alexei , Zhang Bailin , Hoffmann Dietmar , Sun Fangxian , Pollard Jack , Debussche Laurent , Bouaboula Monsif 
Published: September 2020

Abstract
Despite the significant clinical success of the Immuno-Oncology treatment of microsatellite instability (MSI) patients, there remains huge unmet medical need because of mechanisms of resistance. Through an effort to analyze publicly available large-scale shRNA screening and CRISPR screening, we surprisingly found that WRN is a potent synthetic lethality target in the context of MSI. WRN is an enzyme known as the “Werner syndrome ATP-dependent helicase”. WRN is involved in multiple cellular functions, including DNA repair and telomere maintenance. Silencing of WRN by RNAi and CRISPRi in a panel of MSI-H cells lead to tumor cell growth inhibition in vitro and in vivo, thus demonstrated WRN is a novel synthetic lethality target in context of MSI. Our discovery has recently been cross-validated by multiple independent studies1-4. Furthermore, we also report here the first time that silencing of WRN by RNAi and CRISPRi in DLD1, a MSI-H cell, does not lead to tumor cell inhibition. Taken together, our data using independent genetic approach CRISPRi in vitro and in vivo, further highlight fundamental importance of WRN as a synthetic lethality target in some, but not all, MSI context.
References: 1 Chan E.M. et al. (2019). Nature. 568(7753):551-556. 2 Behan F.M. et al (2019). Nature. 2019 568(7753):511-516. 3 Kategaya L. et al. (2019). iScience. 13:488-497. 4 Lieb S. et al. (2019). Elife. 8. pii: e43333.
Citation Format: Zhihu (Jeff) Ding, Jing Zhang, Chandra Sekhar Pedamallu, Steve Rowley, Jane Cheng, Shujia Dai, Bridget Zhou, Malvika Koundinya, Zhuyan Guo, Stephane Poirier, Joern Hopke, Amanda Lennon, Jennifer Buell, May Cindhuchao, Karen Wong, Emma Wang, Alexei Protopopov, Bailin Zhang, Dietmar Hoffmann, Fangxian Sun, Jack Pollard, Laurent Debussche, Monsif Bouaboula. Identification and validation of WRN as a novel synthetic lethality target in context of microsatellite instability [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1377.
Abstract 1402: Preclinical evaluation of a novel senescence-associated miRNA miR-3140-3p for malignant pleural mesothelioma
Authors: Yamamoto Yuki , Nishiura Ayaka , Yano Kimiyoshi , Matsuda Noriaki , Takahashi Ryou-u , Tsutani Yasuhiro , Okada Morihito , Tahara Hidetoshi 
Published: September 2020

Abstract
Cellular senescence acts as a natural barrier against tumor progression Our previous study showed that selective induction of senescence using miR-22, one of senescence-associated microRNAs (SA-miRNAs), suppressed tumor progression (JCB 2011) In this study, we developed functional screening system using miRNA library to identify a potent SA-miRNA that suppress malignant tumor such as anti-cancer drug resistant and cancer stem cells.
We focused on microRNA inducing the senescent phenotype in normal human fibroblast cell After transfection of 2028 miRNA mimics library in normal human fibroblast TIG-3, we evaluate the senescence phenotypes such as cell growth arrest and size enlargement using high content analyzer, and found that 349 miRNAs induced cellular senescence More importantly, we identified miR-3140-3p as potent SA-miRNA that significantly suppressed tumor cell proliferation in several types of cancer cells including cancer stem cells and anti-cancer drug resistant cells.
We focused on malignant pleural mesothelioma (MPM) which is an aggressive tumor developed from the mesothelial lining cells of the pleura MPM is caused by direct asbestos exposure and is an incurable tumor type for the lack of effective treatment In addition, as Japan is one of the world's highest importers and users of asbestos, the cases of mesothelioma are expected to increase in the near future Therefore, we investigated the possibility of whether SA-miRNAs showed tumor suppressive effects against MPM cell lines Moreover, we tried to develop a new treatment or medicine for the MPM patients using SA-miRNA In vitro and in vivo analysis revealed that several SA-miRNAs drastically suppressed the tumor cell proliferation
Based on these findings, the modulation of SA-miRNA is a promising approach to improve the treatment of MPM patients In addition, we performed and completed pre-clinical trials and design first-in-human study in Japan.
Citation Format: Yuki Yamamoto, Ayaka Nishiura, Kimiyoshi Yano, Noriaki Matsuda, Ryou-u Takahashi, Yasuhiro Tsutani, Morihito Okada, Hidetoshi Tahara. Preclinical evaluation of a novel senescence-associated miRNA miR-3140-3p for malignant pleural mesothelioma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1402.