bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4288: Predicting DNA methylation in cervical cancer using somatic mutations in a classified mixed model prediction
Authors: Ramos Jairo D. , Rao J. Sunil 
Published: April 2023

Abstract
In cervical cancer, the promoter CpG islands of several tumor suppressor genes have been found with abnormal DNA methylation (DNAm) levels, which results in transcriptional silencing. Genetic databases from tumor samples are available without the corresponding DNAm profile. To fulfill this gap and contribute to deciphering the link between genetic variants and DNAm, we performed this study to find a good statistical model for predicting DNAm using genetic data. To address this, we downloaded from the TCGA dataset the genes with significant somatic mutations, as reported by the BROAD Institute, and the DNAm beta values, in known CpG sites, from 307 Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) samples. Clinical data were also downloaded from patients, including race, age, gender, and cancer stage. We tested five mixed models containing both fixed and random effects to include the unmeasured source of variations in DNAm, for which we used the clustering of samples based on DNAm patterns. Models tested were: Classified mixed model prediction (CMMP), Linear regression model (LM), High dimensional shrinkage estimator based on the elastic net (ENET), a combination of CMMP - ENET, and Random Forest prediction (RF). Besides the significantly mutated genes, the clinical variables were also included as covariates to predict DNAm. We used shared random effects to borrow strength across racial groups, which improves predictive accuracy. Models were enhanced by combining other types of cancers to increase data heterogeneity and the number of samples. Lung Adenocarcinoma (LUAD) and Liver Hepatocellular Carcinoma (LIHC) were selected using Gini and Gap statistics for optimal clustering. Model fitting was evaluated using the average mean squared prediction error (MSPE). Results revealed that the CMMP model with CESC LIHC and LUAD data combined showed the best prediction results (lowest MSPE). The plot of the averaged estimated ENET coefficients indicated that the most important-significantly mutated genes to predict DNAm were CTNNB1, DMD, XIRP2, and PIK3CA. SNPs in these genes linked to cervical cancer include rs121913396, rs121913403 (CTNNB1), rs867262025, and rs121913279 (PIK3CA).In summary, we developed a mixed-effects model for accurately predicting DNAm levels in cervical cancer, using genes with significant somatic mutations (SNVs and INDELs). These results also align with growing evidence suggesting that genetic variation plays a role in DNAm.
Citation Format: Jairo D. Ramos, J. Sunil Rao. Predicting DNA methylation in cervical cancer using somatic mutations in a classified mixed model prediction. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4288.
Abstract 4292: Gene model correction for PVRIG and TIGIT in single cell sequencing data enables accurate detection and study of its functional relevance
Authors: Nemzer Sergey , Sabath Niv , Wool Assaf , Altber Zoya , Ando Hirofumi , Pardoll Drew M. , Ganguly Sudipto , Turpaz Yaron , Levine Zurit , Granit Roy Z. 
Published: April 2023

Abstract
Single cell RNA sequencing (scRNA-seq) has gained increased popularity in recent years and has revolutionized the study of cell populations; however, this technology presents several caveats regarding specific gene expression measurement. Here we examine the expression levels of several immune checkpoint genes, which are currently assessed in clinical studies. We find that unlike in most bulk sequencing studies, PVRIG and murine TIGIT suffers from poor detection in 10x Chromium scRNA-seq and other types of assays that utilize the GENCODE gene model. We show that the default GENCODE gene model, typically used in the analysis of such data, is incorrect in the PVRIG genomic region and contains also a predicted read-through transcript to which PVRIG reads co-align, causing these to be discarded and hence hindering its proper detection. Moreover, we find that the murine TIGIT 3’ UTR is mis-annotated, leading to the loss of legitimate reads. We thus generated a corrected reference genome, by removing the faulty read-through in the case of PVRIG and by extending the TIGIT 3’ UTR and demonstrate that by employing these changes we can correctly capture genuine expression levels of these checkpoints, and which align with our findings at the protein level using FACS and CITEseq. Furthermore, we show that specialized read multimap algorithms such as RSEM and STARsolo can also partially improve the detection of PVRIG. Our study provides means to better interrogate the expression of PVRIG and murine TIGIT in scRNA-seq and emphasize the importance of optimizing gene models and alignment algorithms to enable accurate gene expression measurement in scRNA-seq and bulk sequencing. Moreover, our results support detailed study of the expression of immune checkpoints in clinical and pre-clinical studies towards the development of cancer immunotherapy treatments.
Citation Format: Sergey Nemzer, Niv Sabath, Assaf Wool, Zoya Altber, Hirofumi Ando, Drew M. Pardoll, Sudipto Ganguly, Yaron Turpaz, Zurit Levine, Roy Z. Granit. Gene model correction for PVRIG and TIGIT in single cell sequencing data enables accurate detection and study of its functional relevance. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4292.
Abstract 4293: Strategies and resources for applying a quantitative multiplex IHC imaging workflow to characterize immune contexture in solid tumors
Authors: Sivagnanam Shamilene , Betts Courtney M. , Kirchberger Nell , Betre Konjit , Coussens Lisa M. 
Published: April 2023

Abstract
Conventional immunohistochemistry (IHC) is a standardized diagnostic technique used in tissue pathology. However, the capacity to label only one marker per tissue section is a critical limitation. Multiplex immunohistochemistry (mIHC) is a powerful imaging technique used in basic, translational research and clinical settings to simultaneously detect the expression of multiple epitopes in a single formalin-fixed paraffin-embedded (FFPE) tissue section, allowing for characterization and quantification of cells while maintaining their spatial location. This technique allows for a comprehensive view of the immune milieu, expression patterns, and interactions between cell types that can help elucidate the complexity of the tumor-immune microenvironment (TiME). Multiplex imaging has emerged as a powerful tool to better understand tumor progression, response or resistance to therapy, and potentially identify predictive biomarkers. However, this technique requires careful tissue considerations and generates enormous amounts of hierarchical data, including single cell marker expressions, locations, and shape features, resulting in complex and challenging analyses. We previously published a validated platform using nine matched primary and recurrent head and neck squamous cell carcinoma (HNSCC) sections stained sequentially with a panel of 29 antibodies identifying malignant tumor cells, and 17 distinct leukocyte lineages and their functional states1. Here, we have optimized and consolidated important considerations, including tissue quality and QC steps necessary for generating high quality data from multiplex imaging studies. We demonstrate strategies for a streamline analytic pipeline using our quantitative workflow developed to characterize immune cells and infiltration patterns within spatial compartments of solid tumors in FFPE tissues, and herein, provide strategies and resources to practically adapt and utilize our analytic mIHC pipeline.
1. Banik, G., et al., Methods Enzymol., 2020
Citation Format: Shamilene Sivagnanam, Courtney M. Betts, Nell Kirchberger, Konjit Betre, Lisa M. Coussens. Strategies and resources for applying a quantitative multiplex IHC imaging workflow to characterize immune contexture in solid tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4293.
Abstract 4347: A pivotal clinical trial of cResponse, a functional assay for cancer precision medicine
Authors: Salpeter Seth , Bar Vered , Neev Guy , Zundelevich Adi , Rosen Gil , Hanks Sandra , Costelloe Naoise , Krell Jonathan , Straussman Ravid 
Published: April 2023

Abstract
Precision cancer therapy has the potential to revolutionize treatment outcome. While genomic analysis has become central to cancer personalized medicine, recent studies have not shown that it drastically improves the patient’s survival as compared to standard drug selection. Additionally, genomic mutations may suggest several treatment protocols without elucidating which approach will yield the best clinical response. To advance cancer precision guidance, we have developed cResponse, a combined genomic-functional drug sensitivity platform to determine individualized patient treatment regimens. Fresh patient cancer samples are taken by biopsy or resection and sectioned into 250uM slices which when cultured in cResponse platform demonstrate similar architecture and tissue proliferation to those found in vivo. An initial clinical study showed that cResponse can preserve human cancer tissue in 3D culture together with its microenvironment, including endothelial and immune cells, at a high viability (&gt;90%) with continued cell division for more than 7 days. On a cohort of 34 patients treated with neoadjuvant therapy or systemic therapy for metastatic disease, the assay was able to predict patient response to drug treatment with a sensitivity of 96% and a specificity of 77.7%. To further validate the capacity of the cResponse platform to predict patient response to cancer therapy, a follow up pivotal clinical study was established at 7 major cancer centers located in the UK with the goal of recruiting a total of 170 patients to provide a large statistical validation of the previous results. Here we report on the outcome of the first 50 patients recruited to the pivotal trial and describe the predictive results correlated to patient response.
Citation Format: Seth Salpeter, Vered Bar, Guy Neev, Adi Zundelevich, Gil Rosen, Sandra Hanks, Naoise Costelloe, Jonathan Krell, Ravid Straussman. A pivotal clinical trial of cResponse, a functional assay for cancer precision medicine. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4347.
Abstract 4386: Comparison of cytotoxicity of anthracycline based antineoplastic drugs in breast cancer
Authors: Singhal Mitali , Gomez Jacobo Elies , Nayak Sanjit , Suman Kirsten Riches , Estrada Amalia Ruiz 
Published: April 2023

Abstract
Mitoxantrone (MTX) is used for the chemotherapeutic treatment of breast cancer, but it has a dose-limiting cardiotoxicity. One of the mechanisms of MTX cytotoxicity is by inhibiting the topoisomerase II enzyme, which is crucial for maintaining cellular processes like replication. The aim of the study is to investigate if an alternative analog of MTX, named KP71 would be a suitable antineoplastic drug with reduced cardiovascular side effects. Cytotoxicity of both drugs in breast cancer cell lines MDA-MB-468, MDA-MB-231, MCF7, the non-neoplastic breast cell line MCF10, cardiac human fibroblasts (HFB), and human umbilical vein endothelial cells (HUVEC) was assessed by MTT at 96h. The IC50 values (nM) for MTX/KP71 were as shown in table below. DNA decatenation assay demonstrated topoisomerase II inhibition with values of IC50 = 2.9/12.3 µM for topoisomerase IIα, and 2.1/7.0 µM for topoisomerase IIβ for MTX/KP71 respectively. Western blotting showed DNA damage by the gradation in γH2AX expression at different concentrations of MTX and KP71 at 6 h and 24 h treatment. KP71 was found to retain the ability to inhibit the proliferation of neoplastic cell lines in vitro with a slower profile of cytotoxicity on non-neoplastic cell lines as compared to MTX. KP71 partly exerted cytotoxicity by damaging DNA and inhibiting topoisomerase II enzyme activity. Organotypic HFB-HUVEC co-cultures were used to investigate the effects of anthracycline drugs in angiogenesis. Although both drugs reduced the number of tubules (and branches) compared to control (absence of drug), there were not significant differences between MTX and KP71.
MTT IC50 (nM) MTX KP71 MDA-MB-468 27 50 MDA-MB231 38 169 MCF7 63 150 MCF10 35 90 HFB 160 1177 HUVEC 56 93
Citation Format: Mitali Singhal, Jacobo Elies Gomez, Sanjit Nayak, Kirsten Riches Suman, Amalia Ruiz Estrada. Comparison of cytotoxicity of anthracycline based antineoplastic drugs in breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4386.
Abstract 45: Elephant p53 protects mice from carcinogen induced death
Authors: Abegglen Lisa M. , Fowles Jared S. , Preston Aidan J. , Rogers Aaron , Bhachech Niraja , Barney Brayden B. , Kennington Ryan , Lum David H. , Mitchell Gareth , Schiffman Joshua D. 
Published: April 2023

Abstract
Elephants naturally have low rates of cancer, potentially due to evolved genetic changes in tumor suppressor elephant TP53 (EP53) and amplification of 19 TP53 retrogenes. A better understanding of the mechanisms of cancer suppression in elephants by EP53 and its retrogenes could lead to more effective human cancer therapeutics. EP53 induces a strong apoptotic response compared to human TP53, especially when combined with EP53-RETROGENE 9 (EP53-R9). EP53-R9 encodes a truncated p53 protein that induces apoptosis of human cancer cells independent of EP53 through a transcription-independent mechanism. To characterize EP53 and EP53-R9’s role in cancer suppression, transgenic mice were generated to replace mouse TRP53 with EP53. Additionally, a tetracycline inducible EP53-R9 gene was inserted into a safe harbor locus in mice. Carcinogenesis studies with 3-Methylcholanthene injection revealed that EP53 mice survived significantly longer compared to heterozygous or homozygousTRP53 mice (p &lt;0.0001, 0.0102). Experiments to assess the protective role of EP53-R9 alone and combined with EP53 are ongoing. Several mouse embryonic fibroblast (MEF) cell lines were generated from these transgenic mice with 14 distinct genotypes with different combinations of TRP53, EP53, and EP53-R9. p53 target gene expression studies showed that MEFs with EP53 induce higher expression of MDM2 and p21 compared to TRP53-containing MEFs, suggesting that the cancer-protective effect observed in EP53 mice is due, in part, to greater activation of p53 signaling. These results support the need for future work to assess the potential of EP53-based therapeutics for human cancer.
Citation Format: Lisa M. Abegglen, Jared S. Fowles, Aidan J. Preston, Aaron Rogers, Niraja Bhachech, Brayden B. Barney, Ryan Kennington, David H. Lum, Gareth Mitchell, Joshua D. Schiffman. Elephant p53 protects mice from carcinogen induced death [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 45.
Abstract 4517: Novel prognostic and predictive biomarker for neuroblastoma
Authors: Somasundaram Dinesh Babu , Yu Zhongxin , Baker Ashley , Aravindan Natarajan 
Published: April 2023

Abstract
Recently we showed that Retinal degeneration protein 3 (RD3) is constitutively expressed in healthy adult and fetal tissues beyond retina and, its gradient expression from high to low in ganglioneuroma, ganglioneuroblastoma and neuroblastoma (NB). Crucially, our sequential in vitro and in vivo studies identified that RD3 regulates NB progression and metastasis, and its loss prompts the evolution of therapy defying progressive disease (PD). Here we investigated the prognostic significance of RD3 in NB, its predictive benefit and, its association to clinical outcomes. RNA-Seq data mining (4 independent study cohorts, total n = 1013) indicated that high RD3 can predict good NB prognosis. RD3 expression (immunohistochemistry) gauged in our NB patient cohort (n = 100) showed a positive correlation with longer overall survival (OS, P = 1.0E-04) and relapse-free survival (RFS, P = 2.1E-02). Similarly, high RD3 correlated with longer OS (P = 1.2E-03) and RFS (P = 2.1-02) in children presented with high-risk NB (HR-NB), irrespective of MYCN amplification status (MYCN amplified, P = 1.4E-02; non-amplified, P = 5.5E-03) and patient age (&lt;2Y age, P = 2.8E-02; &gt;2Y age, P = 1.0E-04) groups. Significantly, we observed a gradient loss of RD3 with NB progression, from stage 1 through stage 4 disease. Consistently, RD3 loss was substantial in metastatic disease when compared to the primary neuroblastomas, and this loss associated with poor OS in patients presented with metastatic disease (P = 4.0E-02). More importantly, RD3 is significantly lost in therapy resistant progressive NB and corroborated significantly (P = 9.5E-03) with the poor progression free survival. Multivariate analysis identified RD3 as an independent (P = 4.4E-02) prognostic factor for NB. These results demonstrate that RD3-loss can forecast poor prognosis in NB, and further imply that assessing RD3 loss could serve as the good predictor for therapy response and/or PD evolution. Together, these data identify a novel prognostic and predictive factor for neuroblastoma. Funding: This work was partially or in full, funded by Oklahoma Center for the Advancement of Science and Technology, OCAST-HR19-045; National Institutes of Health, NIH-P20GM103639 and Department of Defense DoD-CA210339
Citation Format: Dinesh Babu Somasundaram, Zhongxin Yu, Ashley Baker, Natarajan Aravindan. Novel prognostic and predictive biomarker for neuroblastoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4517.
Abstract 4554: Head and neck cancer HuBiogel-embedded microtumor assay system for therapeutic efficacy testing of patient tumor specimens
Authors: Willey Christopher D. , Ying Yedeh P. , Morlandt Anthony B. , Amm Hope M. , Hicks Patricia H. , Anderson Joshua C. , Beierle Andee M. , Thomas Carissa M. , Warram Jason M. , Chen Jingsong , Thomas Jeffrey A. , Banko Katie , Singh Raj K. 
Published: April 2023

Abstract
Head and neck (HN) cancer recurrence is common, and selecting effective salvage systemic therapy remains difficult, particularly for oral cavity cancers. Developing a rapid, robust and predictive therapeutic testing system could support clinical decision-making and improve patient outcomes. We developed a Patient Therapy Evaluation System (PTES) that employs a three-dimensional (3D) fully human microtumor drug testing assay using tissue specimens collected during surgery of HN cancers. Remnant fresh tumor tissue from patients is dissociated into single-cell suspension that is embedded using a novel HuBiogel-cell encapsulation technology (3D microtumors). This high-throughput assay platform allows morphologic, functional, and molecular evaluations in parallel by real-time imaging, cell proliferation, and biomarker protocols. Microtumor viability, growth profiles, and drug screening data are captured at multiple time points up to 14 days. Our initial cohort included 57 patient specimens (53 squamous cell carcinomas, 1 verrucous carcinoma, 1 osteosarcoma, 1 ameloblastoma, and 1 non-cancerous lichenoid mucositis). HuBiogel-embedded tumor cells formed numerous multicellular colonies exhibiting distinct organization and growth patterns in 14-day microtumor cultures. Interestingly, epithelial, stromal and stem-cell like populations were preserved in HN microtumor models based on marker expression. Treatment with single (cisplatin, 5FU, docetaxel) drugs and their combinations resulted in tumor inhibitory responses (IC50) evaluated by CellTiter-Glo assay, and residual surviving cells were also recorded by Calcein-AM staining of 3D Microtumors. While patient-derived HN microtumors were produced with high success rates, factors associated with lower microtumor yield included smaller tumor specimens and low viability after dissociation. In conclusion, our new all human microtumor assay models replicating phenotypic, functional, and molecular properties ex vivo provide a potential theranostic tool for rapidly predicting drug sensitivity and improving treatment strategy for HN cancer patients.
Citation Format: Christopher D. Willey, Yedeh P. Ying, Anthony B. Morlandt, Hope M. Amm, Patricia H. Hicks, Joshua C. Anderson, Andee M. Beierle, Carissa M. Thomas, Jason M. Warram, Jingsong Chen, Jeffrey A. Thomas, Katie Banko, Raj K. Singh. Head and neck cancer HuBiogel-embedded microtumor assay system for therapeutic efficacy testing of patient tumor specimens. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4554.
Abstract 4718: Analyses of epigenetic marks and mechanisms in disease: Your guide to a successful CUT&RUN assay
Authors: Guo Angela H. , Comeau Christopher R. , Chen Fang , Fry Christopher J. 
Published: April 2023

Abstract
Like the chromatin immunoprecipitation (ChIP) assay, Cleavage Under Targets & Release Using Nuclease (CUT&RUN) is a powerful and versatile technique used for probing protein-DNA interactions within the natural chromatin context of the cell. The CUT&RUN assay can be combined with downstream qPCR or NG-seq to analyze histone modifications and binding of transcription factors, DNA replication factors, or DNA repair proteins at specific target genes or across the entire genome. CUT&RUN provides a rapid, robust, and true low cell number assay for detection of protein-DNA interactions in the cell. Unlike the ChIP assay, CUT&RUN is free from formaldehyde cross-linking, chromatin fragmentation, and immunoprecipitation. Previously, we have shown that, compared to ChIP, CUT&RUN requires fewer starting cells (100K), has a much faster protocol (one day from cells to DNA), generates lower background signal (requires less sequencing depth), and offers spike-in control DNA for effective normalization of signal between samples and between experiments. We recently updated the CST CUT&RUN Assay Kit for use with 5,000-20,000 cells and added protocols for fixed cells and tissue. I will discuss the basics of the CUT&RUN assay and important factors to consider when setting up your experiment. In addition, I will provide data showing the versatility of this assay for mapping various histone modifications, transcription factor, and transcription cofactor binding across multiple sample types. Finally, I will discuss how the general protocol is optimized for greater signal to noise ratio, reduced number of starting cells, and provide an alternative digestion method to prepare the input DNA as a critical control of the CUT&RUN experiment.
Citation Format: Angela H. Guo, Christopher R. Comeau, Fang Chen, Christopher J. Fry. Analyses of epigenetic marks and mechanisms in disease: Your guide to a successful CUT&RUN assay. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4718.