bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 6251: High expression level of GSK3β in basal triple negative breast cancer: Effects of the HDAC inhibitor, vorinostat
Authors: Lyn-Cook Beverly D. , Emamzaden Fatemeh Nouri , Word Beverly , Hammons George
Published: April 2023

High expression levels of glycogen synthases kinase 3 beta (GSK3β) have been correlated with poor prognosis in triple negative breast cancer (TNBC) patients. GSK3β is a multifaceted kinase and is a key regulator of a number of cellular processes. It is known to function as a positive regulator of epithelial-mesenchymal transition (EMT). Usually, cells that undergo EMT are known to acquire stem cell properties and these cells have properties that are known to be resistant to chemotherapies. Inhibition of GSK3β has been shown to decrease markers of EMT and reduce cancer stem cells. High levels of GSK3β were found in the basal-2 subtype of triple negative breast cancer cells, HCC1806. Histone deacetylases (HDACs) are expressed at high levels in some cancers, including TNBC. In this study, vorinostat, a histone deacetylase inhibitor, was shown to down regulate GSK3 expression in HCC1806 cells at both the gene and protein level using qPCR and western blots. Furthermore, cancer stem cells (CSC) cell markers CD44/CD24 using flow cytometry and immunostaining were significantly decreased. Previous studies published from our laboratory have shown vorinostat’s ability to decrease TNBC cells invasion compacity, as well as cell growth. This study suggests that targeting GSK3β may be a potential therapeutic target for certain subtypes of TNBC. Triple negative breast cancer remains one of the most aggressive breast cancers, often having a high mortality rate in younger women.

Citation Format: Beverly D. Lyn-Cook, Fatemeh Nouri Emamzaden, Beverly Word, George Hammons. High expression level of GSK3β in basal triple negative breast cancer: Effects of the HDAC inhibitor, vorinostat [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 6251.
Abstract 6258: The discovery and preclinical characterization of the potent covalent KRASG12C inhibitor UCT-001024
Authors: Rose Tristin E. , O'Boyle Brendan M. , Hilf Justin A. , Baker-Tripp Emma L. , Feng Zhengao , Yang Kevin , Bartberger Michael D. , Losón Oliver C. , O'Brien Neil A. , McDermott Martina S. , Kamranpour Naeimeh , Jia Weiping , Luo Tong , Ayala Raul , Glasby John , Stoltz Brian M. , Slamon Dennis J.
Published: April 2023

Small molecule inhibitors of KRASG12C have garnered substantial interest as a targeted therapy for lung, colon and pancreatic cancers bearing this mutation. Data from multiple clinical programs have shown strong efficacy in lung tumors but diminished and differential efficacy for other tumor sites including lung-derived brain metastases. We undertook a series of in vitro and in vivo studies to evaluate clinically staged KRASG12C inhibitors in an effort to elucidate pharmacological factors underlying these clinical differences and identified potency, permeability/efflux, and clearance as impediments to efficacy, particularly in the context of brain metastases. Adagrasib is reportedly efficacious in patients with brain metastases. Our preclinical experimentation suggests that distinguished potency and pharmacokinetics are critical to therapeutic benefit, particularly in the context of brain metastases. Using both structure- and ligand-based design approaches, we identified a development candidate UCT-001024, which is a covalent KRASG12C inhibitor that demonstrates superior target-engagement kinetics and cellular potency in vitro. UCT-001024 also demonstrates improved plasma and whole brain unbound clearance, and in vivo potency in ectopic xenograft models and a brain-tropic NSCLC metastasis model relative to adagrasib. Additionally, UCT-001024 shows a favorable DDI profile and ion channel safety in an in vitro iPSC-derived cardiomyocyte cardiac proarrhythmia assay.

Citation Format: Tristin E. Rose, Brendan M. O'Boyle, Justin A. Hilf, Emma L. Baker-Tripp, Zhengao Feng, Kevin Yang, Michael D. Bartberger, Oliver C. Losón, Neil A. O'Brien, Martina S. McDermott, Naeimeh Kamranpour, Weiping Jia, Tong Luo, Raul Ayala, John Glasby, Brian M. Stoltz, Dennis J. Slamon. The discovery and preclinical characterization of the potent covalent KRASG12C inhibitor UCT-001024 [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 6258.
Abstract 6401: HMGB1 release predicts chemotherapy combinatorial efficacy with TIM-3 blockade
Authors: Onimus Alexis , Mandula Jessica , Rodriguez Paulo , Ruffell Brian
Published: April 2023

We have recently shown that TIM-3 blockade promotes response to paclitaxel chemotherapy in preclinical breast cancer models through its ability to suppress uptake of HMGB1-DNA complexes by dendritic cells. However, it remains unclear why paclitaxel is necessary for response to TIM-3 blockade. Here we demonstrate that the taxanes paclitaxel and docetaxel induce the loss of HMGB1 from breast cancer cells in vitro and in vivo. Interestingly, this does not occur through loss of cellular integrity, but rather through an active secretion process involving ADP-ribosylation of HMGB1 by PARP1. PARP1 was activated by docetaxel treatment, as measured by detection of its cleaved form in the cytoplasm, and HMGB1 release was prevented by the use of the PARP inhibitor niraparib. Both PARP1 activation and ADP-ribosylation of HMGB1 were dependent upon the activity of TLR4, a known receptor for paclitaxel, as demonstrated with CRISPR/Cas9-generated knockout cells and TLR4 inhibitors. However, TLR4 stimulation alone was insufficient to induce HMGB1 release. By understanding how taxanes promote the release of HMGB1 we may be able to develop biomarkers for the selection of patients most likely to respond to the combination of chemotherapy and immunotherapy with TIM-3 blocking antibodies.

Citation Format: Alexis Onimus, Jessica Mandula, Paulo Rodriguez, Brian Ruffell. HMGB1 release predicts chemotherapy combinatorial efficacy with TIM-3 blockade. [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 6401.
Abstract 6414: Concomitant anti-tumor immunity and checkpoint blockade responses are restored by depletion of CD62L expressing cells
Authors: Burke Brianna , Plaza-Rojas Lourdes , Perez Cynthia , Kostenko Elena , Austin Anna , Boucher Justin , Prajapati Kushal , Reyes Michael Delos , Chung Christine , Guevara-Patino Jose-Alejandro
Published: April 2023

Studies have shown the importance of CD62L in leukocyte trafficking. However, the significance of CD62L-expressing cells in concomitant anti-tumor immunity has not been investigated. Using a model of post-surgical tumor immunity, we show that in vivo depletion of CD62L-expressing cells before or immediately after surgical tumor resection enabled the development of anti-tumor concomitant responses against poorly immunogenic B16 (melanoma) or MTE-Ras (head & neck cancer) tumor cells. Anti-CD62L mAb administration depleted the cellular immune components that express CD62L, including NK, NKT, Mo, Ma, B, and T cells. Within the T cell compartment, naïve T cells (CD44lo CD62Lhi), effector (CD44hi CD62Llo), memory (CD44hi CD62Lhi) and regulatory T cells (Treg, CD4 CD25 Foxp3) were also depleted, while effector CD62L-negative T cells were spared in the TDLN. Tumor immunity did not occur in the absence of a primary tumor (sham surgery group) or after CD8 depletion. Whereas anti-CTLA-4 or anti-PD-1 mAbs failed as monotherapies, their administration during CD62L depletion restored their anti-tumor properties. The unified global gene expression analysis of the TDLN shows the significant enrichment of biological processes involved in the CD8 T cell effector phase, IL-2/IL-15, TNF-α, IFN-γ, IFN-α, IL-6, responses, mitotic cell division, glycolysis, and acetylation. Also, genes related to Treg responses were downregulated. These data point to a process in which depletion of CD62L cells in tumor-bearing hosts transforms the TDLN into a highly active immunological site in which tumor-reactive effector CD8 T cells (CD62L-negative) actively divide in the absence of Treg, accompanied by a cytokine response, glucose consumption, and acetylation of transcriptional factors and histones. These results identify an unrecognized role of CD62L-expressing cells in regulating concomitant anti-tumor immunity and restoring anti-tumor responses by checkpoint blockade inhibitors. Our study provides a new framework that could help understand how anti-tumor responses are limited.

Citation Format: Brianna Burke, Lourdes Plaza-Rojas, Cynthia Perez, Elena Kostenko, Anna Austin, Justin Boucher, Kushal Prajapati, Michael Delos Reyes, Christine Chung, Jose-Alejandro Guevara-Patino. Concomitant anti-tumor immunity and checkpoint blockade responses are restored by depletion of CD62L expressing cells [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 6414.
Abstract 6493: Ethnic disparities in breast cancer survival in Guam
Authors: Badowski Grazyna , Teria Rodney , Dulana Louis , Aguon Cabrini , Wilkens Lynne , Shvetsov Yurii , Novotny Rachel , Guerrero Rachael T. Leon
Published: April 2023

Background: Breast cancer is the second leading cause of cancer-related death among women in Guam. The breast cancer mortality rate is higher in Guam than in the U.S. (27.3 vs 20.3 per 100,000 women, age-adjusted, 2013-2017 data); even though the incidence rate remains lower (86.6 vs 126.8 respectively). Guam has major ethnic disparities in breast cancer survival with CHamoru (indigenous people) and Micronesian (immigrants from other Micronesian Islands) faring much worse than other ethnic groups. The purpose of this study was to determine the survival rates of breast cancer patients in Guam and examine the effects of demographic and other mortality risk factors on breast cancer survival.

Methods: This study included 1105 women diagnosed with primary invasive breast cancer and reported to the Guam Cancer Registry from 1998-2020. Five-year and 10-year survival rates were calculated using the Kaplan-Meier method and were compared using the log-rank test across different ethnic groups: CHamoru (N = 528), Filipino (N = 336), Asian (N = 66), Micronesian (N = 51), and Caucasian (N = 71). The Cox proportional hazards regression was used to investigate the effects of age, year of diagnosis, ethnicity, breast cancer staging, and cancer treatment status on the risk of all-cause mortality.

Results: Mean age at diagnosis was 58.2 years. Significant differences in the 5-year and 10-year survival rates were found across ethnic groups. Micronesians had the lowest 5-year and 10-year survival rates (55.9% and 48.5%) followed by CHamorus (81.1% and 68.1%, respectively). All-cause mortality was higher among CHamoru (HR = 2.28, 95% CI: 1.65, 3.16) and Micronesian women (HR=5.33, 95% CI: 3.30, 8.61) compared with Filipino women after adjusting for age, year of diagnosis, staging, and cancer treatment status. All-cause mortality among White and Asian women was not statistically significantly different from that among Filipino women. Cancer staging also indicated significantly higher hazard rate for late-stage patients when compared to early-stage patients (HR = 3.62, 95% CI: 2.70, 4.85).

Conclusion: The analysis suggests significant differences in breast cancer 5-year and 10-year survival rates across different ethnic groups, with Micronesian women exhibiting the highest hazard rate among women in Guam.

Acknowledgement: This study was supported by the PIPCHE/U54 Grant (U54CA143728), a partnership between the University of Hawai'i Cancer Center and the University of Guam.

Citation Format: Grazyna Badowski, Rodney Teria, Louis Dulana, Cabrini Aguon, Lynne Wilkens, Yurii Shvetsov, Rachel Novotny, Rachael T. Leon Guerrero. Ethnic disparities in breast cancer survival in Guam. [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 6493.
Abstract 6508: Eclipse, an automated CRISPR platform for the large-scale generation of cell models
Authors: Deng Peter , Rowe Matthew , King Anna , Sailor Dana , Chair Antinea , Morell Montse , Sommer Andreia G. , Holden Kevin
Published: April 2023

Major advances in gene editing using CRISPR have improved accessibility for the creation of disease relevant in vitro models, allowing researchers to readily interrogate oncogenic driver mutations and elucidate novel targets to overcome challenges within cancer research such as drug resistance. Despite this, the rapid generation of disease relevant cell lines at the scale needed for successful and efficient therapeutic development remains challenging in part due to the sheer number of potential oncogenic driver mutations and cancer targets along with using traditional manual approaches. Specific challenges include: the efficient generation of gene knockouts and corresponding loss of protein; efficient knock-in of gene tags and single nucleotide variants; and controlling the zygosity of these genetic outcomes. To address these limitations, we describe the use of our automated, high throughput CRISPR editing platform, ECLIPSE, for the rapid generation of cell models such as immortalized cells and induced pluripotent stem cells. We leveraged our chemically modified synthetic sgRNAs, optimized nucleofection methods, and automated pipelines for the generation of CRISPR-edited cells at various scales to address the needs of researchers. This scale ranges from individual edited cell clones for drug target validation to the generation of hundreds of knockout cell pools in a ready-to-assay arrayed format for gene target identification in drug screening. The utilization of automated systems such as the ECLIPSE platform are critical catalysts for the rapid generation of engineered cell lines at relevant scales to address the challenges of cancer research.

Citation Format: Peter Deng, Matthew Rowe, Anna King, Dana Sailor, Antinea Chair, Montse Morell, Andreia G. Sommer, Kevin Holden. Eclipse, an automated CRISPR platform for the large-scale generation of cell models [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 6508.
Abstract 6514: Liquid biopsy for lung cancer based on extracellular vesicles
Authors: Hinestrosa Juan P. , Dhani Harmeet , Lewis Jean M. , Schroeder Gregor K. , Balcer Heath I. , Kurzrock Razelle , Billings Paul
Published: April 2023

Background Liquid biopsy approaches for lung cancer are becoming increasingly common for diagnosis, prognosis, and management of the disease. Of the Approximately 236K new lung cancer cases that will be diagnosed in 2023, over 70% of those will be regional or distant with diminished chances of curative resection. Therefore, highly sensitive and specific approaches for early detection are key for mortality reduction. Extracellular vesicles (EVs), a new class of blood-based cell-free biomarker, can be informative for the diagnosis of lung cancer at its earliest stages.

Methods A case-control cohort of blood plasma samples from 146 pathologically confirmed lung cancer cases (stage I = 90, II = 42, III = 14; median age = 63 yrs.) and 491 controls (median age = 58 yrs) was used in this study. EVs were isolated using a proprietary technology and the EV protein cargo was analyzed via immunoassay. A machine learning engine was employed to determine the most informative biomarkers and algorithm for differentiation between cases and controls in a detection setting.

Results Using a stratified cross-validation approach, we found a biomarker signature that yielded an AUC of 0.966 (95% CI: 0.949 - 0.979) with an overall sensitivity of 91.1% (CI: 85.4% - 94.7%) at a specificity of 91.0% (CI: 88.2% - 93.3%). By stage, the following sensitivities were obtained: stage I: 92.2%, stage II: 88.1%, stage III: 92.8%. The algorithm developed includes 13 EV-protein biomarkers using the adaptive boosted tree methodology.

Conclusions Our pilot study demonstrates utility of a blood-based approach that can detect lung cancer at early stages, when treatment can be more effective. By combining multiple EV protein signatures, it is possible to achieve high sensitivity and specificity. Independently collected cohorts including confounding conditions, such as benign lung nodules and COPD, are being evaluated for validation purposes to improve performance in clinical settings.

Citation Format: Juan P. Hinestrosa, Harmeet Dhani, Jean M. Lewis, Gregor K. Schroeder, Heath I. Balcer, Razelle Kurzrock, Paul Billings. Liquid biopsy for lung cancer based on extracellular vesicles. [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 6514.
Abstract 6526: Investigation levels of trace elements in breast cancer types using laser spectroscopic techniques
Authors: Ahmed Ola Sayed , imam hisham
Published: April 2023

Breast cancer (BC) is the 2nd leading cause of death from cancer in women. Women have a lifetime risk of breast cancer of around 31%, which makes it the first most common malignancy in women. Diagnosing cancer and classifying its types is a complex process that relies heavily on sample analysis. Early detection of cancer diseases is one of the important and main factors in determining treatment and saving many patients before the disease worsens and reaches dangerous stages. Alterations in the levels of trace elements have been observed in breast cancer (BC) patients. However, the relationships between these alterations and the metabolic and clinical consequences of BC are unknown. The aim of the present work is to study in vitro possibilities and the effectiveness of introducing an efficient optical spectroscopic technique such as LIBS for the identification types of breast cancer, as well as determining the disease grade and severity. The ultimate goal of this work is to investigate the concentrations of several trace elements in BC patients, and their relationships with the molecular subtypes of tumors. The atomic transition of the neutral element lines of Fe, Al, Na, Ca, K, V, Co and Pb was chosen to determine the trace element levels of four breast cancer types. We found that the measured average level of trace elements can differentiate between different types of breast cancer.

Citation Format: Ola Sayed Ahmed, hisham imam. Investigation levels of trace elements in breast cancer types using laser spectroscopic techniques [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 6526.
Abstract 6527: Fusion genes as novel putative biomarkers for head and neck squamous cell carcinomas
Authors: Valerio Yabdiel A. Ramos , Van Wyk Hannah C. , Peguero Esther Peterson , Santiago Josué Pérez
Published: April 2023

Head and neck squamous cell carcinomas (HNSCC) are highly aggressive types of cancers with a complex molecular etiology of disease and consequently result in delayed clinical detection, poor prognosis, and limited treatment strategies. Fusion genes, a hallmark of cancer, may be targeted for early identification and treatment of HNSCC; however, studies characterizing fusion genes in HNSCC remain limited. Oral Human Papillomavirus (HPV) infection is a major cause of HNSCC and can also promote the acquisition of fusion genes due to the genomic instability induced by its integration. Here, we retrieved RNA-sequencing data from 36 HNSCC tumors (18 HPV+ and 18 HPV-, GEO Accession: GSE74956) to identify fusion genes using the STAR fusion algorithm in each sample. Statistical analyses were performed in R statistical software. A total of 10 fusion genes were identified in at least 4 of the samples regardless of HPV status. We identified 3 fusion genes that were present in at least 4 of the HPV+ tumors: PMS2P9-CCDC146, MACC1-AC005062.1, AC096711.2-RPL7AP28, and one solely present in HPV- tumors: CTSC-RAB38. The remaining 6 fusion genes were present in both HPV+ and HPV- tumors: TVP23C-CDRT4, AC009271.1-LINC01905, MIR205HG-AOPEP, SEPTIN7P2-PSPH, KRT5-KRT84, KANSL1-ARL17A. While 4 of the identified fusion genes had been previously associated with cancer, there were 6 novel identified fusion genes, in which one or both partner genes have been associated with different cancers. Additionally, the identified fusion genes may be a product of transcription read-through of neighbor genes. The fusion genes associated with HPV infection might explain biological disparities in HPV+ versus HPV- HNSCC and may be targets for the prevention and diagnosis of HNSCC. Future studies need to determine the functional impact of the identified fusion genes in HPV+ tumors.

Citation Format: Yabdiel A. Ramos Valerio, Hannah C. Van Wyk, Esther Peterson Peguero, Josué Pérez Santiago. Fusion genes as novel putative biomarkers for head and neck squamous cell carcinomas [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 6527.
Abstract 6553: The development of homologous recombination repair deficiency (HRD) score methodology using WES data and its application in patient-derived xenograft models
Authors: Wang Jixin , Kinneer Krista , Zhong Wenyan , Lai Zhongwu
Published: April 2023

Homologous recombination repair deficiency (HRD) and mutations in genes involved with homologous recombination repair (HRR) are associated with sensitivity to platinum-based chemotherapy, topoisomerase 1 inhibitors and inhibitors targeting DNA repair pathway. Use of the Myriad HRD test for HRD determination in preclinical models is not feasible globally. To address this challenge, we developed an approach to generate HRD scores from whole exome sequencing (WES) data and applied it to assess HRD status in patient-derived xenograft (PDX) models.

We used python package CNVkit for segmentation and gene-level/allele-specific copy number calling with customized settings according to CNVkit documentation. The reference was constructed using the WES BED file and hg38 reference genome when there are no paired control samples available. Next R package scarHRD was used to determine the HRD score that is the sum of loss of heterozygosity (LOH), telomere allele imbalances (TAI), and large fragment migrations (LST). The method was applied to the WES of 25 Xentech triple negative breast cancer (TNBC) PDX models to derive HRD scores. The samples were also separately profiled using Myriad’s MyChoice CDx assay. The two scores showed moderate correlation with Pearson r = 0.56. However, when n = 6 PDX models with low coverages (average depth <100x) were excluded, the Pearson r improved to r = 0.76. We also found that the absolute value of HRD score calculated by CNVkit/scarHRD is lower than that of Myriad HRD score.

Furthermore, we evaluated the genomic landscape in this cohort of TNBC PDX models for the selected genes of HRR pathway (BRCA1, BRCA2, ATM, BRIP1, PALB2, RAD51C, BARD1, CDK12, CHEK1/2, FANCL, RAD51B, RAD51D, RAD54L). Sixteen models found to carry HRR mutations, with ATM and BRCA1 mutations being the most common ones, being found in 9 and 5 of 25 models, respectively. Although HRRm positive (HRRm+) models have higher HRD score for both Myriad HRD score and HRD score generated with CNVkit/scarHRD approach, the association between HRR (HRRm+/HRRm-) and Myriad HRD (HRD+/HRD- defined by HRD threshold of 42) is not statistically significant (Fisher’s exact test p value = 0.1998, odds ratio=3.5), likely due to small cohort sizes.

These results suggest that combination of CNVkit and scarHRD for HRD score calculation may be an alternative approach for HRD identification in preclinical PDX models.

Citation Format: Jixin Wang, Krista Kinneer, Wenyan Zhong, Zhongwu Lai. The development of homologous recombination repair deficiency (HRD) score methodology using WES data and its application in patient-derived xenograft models [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 6553.
Abstract 6560: Identification of distinct patterns in diffuse large B-cell lymphoma through alternative splicing analysis
Authors: An Sanyeowool , Koh Youngil , Yoon Sung-Soo
Published: April 2023

Background Aberrant splicing in cancer cells contributes to cellular proliferation, escape from cell death, growth inhibition, invasion and metastasis, and immune escape. Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma, but the effect of AS on its pathogenesis has not been fully elucidated, so it is essential to find out DLBCL-specific splicing patterns and their potential as treatment targets.

Material and Method RNA-Seq dataset from DLBCL patients was retrieved from The Cancer Genome Atlas (TCGA) DLBCL (N=48) and Pan-cancer Analysis of Whole Genomes (PCAWG) DLBC (N=7) were used as the cancer group. In order to identify spliced genes that are significantly different from normal tissue, RNA-Seq data of normal lymphoid tissue produced in two studies of E-MTAB-513 (N=1) and E-MTAB-1733 (N=13) from the BioStudies were downloaded. Sequence reads were aligned to the GRCh38 reference genome using STAR aligner.

Results 5,470 genes identified as differentially spliced compared to normal in both rMATS and MAJIQ tools were studied. After sorting the AS events of these genes in order of highest average PSI value, events with an average PSI value of 0.7 or more in the top 2/3 samples and events with an average PSI value of 0.3 or less in the bottom 2/3 samples are selected. 8 exons of 7 genes were involved in Exon skipping (ES) events, 6 exons of 5 genes were involved in mutually exclusive exon (MXE) events, and an exon of a gene was involved in alternative 5' splice site (A5SS) Among these genes, exons 6 and 7 in CD53 showed high PSI values between exons 4 and 9. The average PSI values for exons 6 and 7 of CD53 in DLBCL were 0.923855 and 0.89096, respectively, which were significantly higher than the Normal group (p<0.05). CD53 mediates IL-7R signaling and plays a role in the regulation of normal B-cell development. As a gene coding for cell surface protein, it is involved in various immune systems in T-cell and B-cell surfaces. In healthy tissue, transcripts that skip exon 5 and have a junction between exon 4 and exon 6 or 7 are not yet known and should be further studied. In addition, SLAMF8, which has an exon with a PSI value specific to DLBCL, is also involved lymphocyte activation and regulates B-cell receptor signaling.

Conclusion These DLBCL-specific patterns of selective exon usage are expected to be potential targets for cancer immunotherapy.

Citation Format: Sanyeowool An, Youngil Koh, Sung-Soo Yoon. Identification of distinct patterns in diffuse large B-cell lymphoma through alternative splicing analysis [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 6560.
Abstract 6561: Specific binding mode of RNA binding protetin FAM120A to lncRNA
Authors: Kawai Kenichiro
Published: April 2023

Long noncoding RNAs (lncRNAs) are defined as transcripts >200 nucleotides in length with no protein-coding potential. LncRNAs play diverse roles in regulating gene transcription, post-transcription, translation, and epigenetic modification through interaction with RNA binding proteins (RBPs). Here, we analyzed binding motif of a RBP, family with sequence similarity 120A (FAM120A), which is highly expressed in multiple cancer types and associated with poor prognosis. To investigate FAM120A interacting RNAs genome-wide, we conducted cross-linking immunoprecipitation combined with deep sequencing (CLIP-seq) using an anti-FAM120A antibody in osteosarcoma cell line, U2OS. We identified 37,151 FAM120A-binding clusters by a peak detection algorithm. Up to 92% of these clusters were found within about 5,700 mRNAs, with the highest enrichment at 3'-UTRs. Interestingly, other clusters located within 959 lncRNAs, with peaks at 5’ and 3’ end. Fold enrichment analysis of CLIP reads in comparison with input reads revealed that FAM120A binds more preferentially to lncRNA than mRNA (median fold enrichments, 4.81 (lncRNA) versus 4.41 (mRNA), P<0.001, Mann-Whitney U test). Motif analysis using the HOMER algorithm showed that FAM120A enriched sequence motifs in 3’ of mRNAs, 5’ and 3’ of lncRNAs were completely distinct. These results suggest that FAM120A may exhibit a motif-dependent selective binding to lncRNA in cancer cells. Given that RBPs bind to RNA molecules immediately after their transcription on chromatin, FAM120A may also selectively recognize RNA species and classify lncRNA and mRNA at the transcriptional stage. Since lncRNAs play pivotal roles in cancers FAM120A may exert oncogenic effects by the post-transcriptional regulation of a certain set of lncRNAs.

Citation Format: Kenichiro Kawai. Specific binding mode of RNA binding protetin FAM120A to lncRNA [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 6561.
Abstract 6564: Biomarker discovery in triple negative breast cancer using RNA-sequencing analysis
Authors: Poulsen Jenna B. , Dobbs Mauri E. , Rapier-Sharman Naomi , Pickett Brett E.
Published: April 2023

Breast cancer is the most common form of cancer, and afflicted over 2.2 million people in 2020. The sheer volume of patients who suffer from breast cancer warrants continued research and discovery efforts to improve treatment options. Triple negative breast cancer (TNBC) affects 10-15% of breast cancer patients. Unlike other forms of breast cancer, TNBC does not have estrogen or progesterone receptors and makes little to none of the HER2 protein. Due to the lack of these biomarkers that are typical treatment targets for other kinds of breast cancers, the hormone therapies and drugs that target other breast cancers are often ineffective against TNBC. This leaves chemotherapy and radiation therapy as the main treatment options. Although chemotherapy and radiation have treatment benefits, the recurrence rate after treatment is around 40%. Furthermore, these treatment options are very detrimental to the body, resulting in a weaker patient and a necessary recovery time between treatments. In this study, we analyzed publicly available RNA-sequencing (RNA-seq) data to identify the upregulated and downregulated transcriptional mechanism(s) that play a role in TNBC compared to healthy breast tissue. The analysis of the RNA-seq data was completed with the Automated Reproducible Modular Workflow for Preprocessing and Differential Analysis of RNA-seq Data (ARMOR), which trims, maps, and quantifies the mRNA sequencing reads to the human transcriptome for each read. The ARMOR program identified more than 12,000 differentially expressed genes between TNBC and healthy breast tissue samples. We then applied an artificial intelligence-based classification method, a random forest algorithm, to identify new biomarkers that best differentiate TNBC cells from healthy cells. These specific transcriptional biomarkers for TNBC could potentially be used as diagnostic biomarkers or as therapeutic targets. We anticipate that this data may expand the treatment options for TNBC.

Citation Format: Jenna B. Poulsen, Mauri E. Dobbs, Naomi Rapier-Sharman, Brett E. Pickett. Biomarker discovery in triple negative breast cancer using RNA-sequencing analysis [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 6564.
Abstract 6572: A lung cancer cell line explorer
Authors: Cai Ling , Girard Luc , DeBerardinis Ralph , Xiao Guanghua , Minna John , Xie Yang
Published: April 2023

Over 300 lung cancer cell lines have been established in the past few decades with clinical annotations. Efforts from multiple institutions comprehensively profiled these cell lines for their genetic and epigenetic variations, gene and protein expression, metabolism, and functional liabilities. These data provide an unprecedented opportunity to accelerate lung cancer research. We developed a lung cancer cell line explorer at https://lccl.shinyapps.io/LCCL/ integrating over 35 datasets. We also incorporated engineered features such as pathway enrichment scores from copy number-denoised transcriptomic data and neuroendocrine scores. Our web application allows users to 1) query and download the processed datasets, 2) assess data reproducibility across studies, 3) review genomic abnormalities, 4) perform ad hoc bivariate analyses with the option to add filtering or coloring by a third feature, 5) generate heatmaps and correlation maps, 6) perform global association test to screen for significant association between a feature of interest and all features from a dataset of interest, and 7) upload their own datasets to be analyzed in conjunction with our in-house datasets. In summary, this online tool will greatly facilitate the utilization of high-dimensional datasets that characterize lung cancer cell lines.

Citation Format: Ling Cai, Luc Girard, Ralph DeBerardinis, Guanghua Xiao, John Minna, Yang Xie. A lung cancer cell line explorer [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 6572.
Abstract 6591: A universal atlas of cellular and oncogenic phenotypes
Authors: Weistuch Corey , Murgas Kevin , Dill Ken , Norton Larry , Deasy Joseph , Tannenbaum Allen
Published: April 2023

Tumors and healthy tissues exhibit gene expression variability in many of the same pathways. We propose that these commonalities result from a performance trade-off between universal cellular phenotypes; each phenotype is defined by an orthogonal gene expression profile identified using unsupervised dimensionality reduction. Using two publicly available RNA-seq datasets (n=54 normal tissues; n=1504 cancer cell lines), we show that both healthy and cancerous cells occupy a trade-off between five canonical phenotypes: OxPhos, Warburg, Fibroblastic, Immune, and Growth. Each cell is assigned a phenotype score that, as we demonstrate, predicts differential drug sensitivities and mutational signatures, even among cancers of the same tissue type. Since these phenotype scores are defined using only healthy tissues, they can be generally applied to other diseases as well.

Citation Format: Corey Weistuch, Kevin Murgas, Ken Dill, Larry Norton, Joseph Deasy, Allen Tannenbaum. A universal atlas of cellular and oncogenic phenotypes [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 6591.
Abstract 6690: Monitoring response and resistance to EGFR inhibition with circulating tumor DNA in a non-small cell lung cancer patient-derived xenograft
Authors: Do Long H. , Pippa Raffaella , Andrews Warren , Chien Yuan , Sperry Jantzen , Nakashima Jonathan
Published: April 2023

Circulating tumor DNA (ctDNA) has been shown as a clinically relevant biomarker for non-invasive monitoring of therapy response, disease burden and disease progression in cancer patients. Patient-derived xenografts (PDX) are essential translational models used for evaluating therapeutic response and identifying novel biomarkers, but analysis of ctDNA in these models remains understudied. Here, we report the use of ctDNA for the monitoring of therapeutic response and secondary resistance of a Non-Small Cell Lung Cancer PDX treated with EGFR inhibitors. We demonstrate measurable ctDNA changes correlate with disease burden and therapeutic response. Altogether, the isolation of ctDNA from PDX models is a robust methodology for interrogating therapeutic efficacy, response, and resistance in a preclinical setting that can be translated as a viable biomarker for non-invasive monitoring in patients.

Citation Format: Long H. Do, Raffaella Pippa, Warren Andrews, Yuan Chien, Jantzen Sperry, Jonathan Nakashima. Monitoring response and resistance to EGFR inhibition with circulating tumor DNA in a non-small cell lung cancer patient-derived xenograft. [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 6690.
Abstract 76: Reprogramming of the preinvasive breast microenvironment identified by spatial nucleus barcoding
Authors: Wang Kaile , Xiao Zhenna , Lin Yiyun , Wei Runmin , Ye Jie , Ye Rui , Hu Min , Bai Shanshan , Sei Emi , Thennavan Aatish , Lim Bora , Futreal Andrew , Thompson Alastair , Krishnamurthy Savitri , Navin Nicholas
Published: April 2023

Ductal-carcinoma-in-situ (DCIS) is the most common early-stage breast cancer and a non-obligate precursor to invasive breast cancer. However our understanding of the spatial microenvironment and the reprogramming of cell types in DCIS remains limited. To address this question, we developed a Spatial Nucleus Barcoding (SNuBar) method that utilizes a single oligonucleotide adaptor to preserve spatial information followed by performing single nucleus RNA sequencing. We validated the accuracy and scalability of SNuBar in cell lines and applied this method to investigate the spatial microenvironment of 4 normal breast tissues, 7 normal adjacent DCIS tissues, and 8 DCIS cancers. The analysis of single cells isolated from 596 macrodissected spatial regions identified 13 major cell types and 43 cell states, that co-localized in different combinations across four main topographic areas. Spatial analysis revealed that vascular and myoepithelial cells were reprogrammed in localized zones near the premalignant cells, while fibroblasts, T-cells and myeloid cells were reprogrammed across broader fields. Our data shows that many diverse cell types are reprogrammed in spatially-defined areas in the DCIS microenvironment, relative to the normal breast tissue regions.

Citation Format: Kaile Wang, Zhenna Xiao, Yiyun Lin, Runmin Wei, Jie Ye, Rui Ye, Min Hu, Shanshan Bai, Emi Sei, Aatish Thennavan, Bora Lim, Andrew Futreal, Alastair Thompson, Savitri Krishnamurthy, Nicholas Navin. Reprogramming of the preinvasive breast microenvironment identified by spatial nucleus barcoding [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 76.
Abstract 82: Role of MSC-derived CXCL1 in bone-metastatic prostate cancer
Authors: Johnson Catherine S. , Costanzo-Garvey Diane , Alsamraae Massar , Frieling Jeremy S. , Cook Leah M.
Published: April 2023

In 2022, the American Cancer Society estimates that over 34,000 men will die of PCa, largely due to metastatic PCa. Up to 90% of advanced prostate cancers metastasize to bone, and there are currently no curative therapies for bone metastatic prostate cancer (BM-PCa). BM-PCa cells interact with bone-forming osteoblasts and bone-resorbing osteoclasts to induce aberrant bone remodeling, which leads to skeletal related adverse events such as increased risk of fractures, bone pain, and poor quality of life. Mesenchymal stem cells (MSCs) are multipotent stem cells that can differentiate into osteoblasts. Cook lab data show BM-PCa cells interact with MSCs and promote MSC differentiation into osteoblasts. Microarray analysis of MSC gene expression changes in response to BM-PCa show significant upregulation of CXCL8. To determine the importance of MSC-derived CXCL8 to BM-PCa, CXCL1 (the murine homolog of CXCL8) was genetically deleted in murine MSCs. While CXCL1 knock out (KO) had no significant impact on MSC proliferation, loss of CXCL1 decreased MSC migration, which suggests upregulation of MSC CXCL1 by BM-PCa cells functions to increase MSC migration into the tumor microenvironment. Additionally, CXCL1 KO MSCs have altered osteoblastic differentiation, whereas adipogenic differentiation was unchanged. RNA sequencing of MSCs stably expressing CXCL1-targeted shRNAs compared to scrambled controls show extensive gene expression changes, including altered expression of multiple osteogenic genes. In vivo data show intratibial co-injection of CXCL1 KO MSCs with murine RM1 BM-PCa cells in an immunocompetent mouse model increases tumor burden compared with co-injection of wildtype MSCs and BM-PCa cells, indicating a role for MSC-derived CXCL1 in suppressing BM-PCa tumor growth in bone. This project shows for the first time the importance of CXCL1 in MSC migration, osteogenesis, gene expression, suppression of BM-PCa progression in bone and tumor-induced bone remodeling.

Citation Format: Catherine S. Johnson, Diane Costanzo-Garvey, Massar Alsamraae, Jeremy S. Frieling, Leah M. Cook. Role of MSC-derived CXCL1 in bone-metastatic prostate 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 82.
Abstract 826: Illuminating cancer cells with a novel nano fluorescent NIR probe for bioimaging
Authors: Chauhan Neeraj , Cabrera Marco , Chowdhury Pallabita , Nagesh Prashanth K. , Dhasmana Anupam , Jaggi Meena , Chauhan Subhash C. , Yallapu Murali M.
Published: April 2023

Background: Adequate bioimaging is crucial in cancer management in many ways including screening, detection, characterization, staging and grading, therapy response, surgical guidance, and margins assessment. Indocyanine green (ICG) is one of the FDA-approved near infra-red fluorescent (NIRF) probe for cancer imaging and image-guided surgery in clinical setting. However, limitations of ICG includes poor photostability, high concentration toxicity, short circulation time, and poor cancer cell specificity. To overcome these hurdles, we engineered a nanoconstruct composed of poly(vinyl pyrrolidone) (PVP)-indocyanine green that is cloaked self-assembled with tannic acid (termed as ICG-Glow NPs) for the cancer cells/tissues specific targeting.

Methods: Pursuing the novel nanotherapy approach, our lab has developed PVP-TA based ICG (PVT-ICG) fluorescent nanoparticles via self-assembly process. Our optimized PVT-ICG nanoformulation was further characterized for its physicochemical properties. An IVIS imaging system was further used to measure NIR fluorescence of novel PVT-ICG. Moreover, Human cancer (Breast, Pancreatic, Liver and Prostate) tissue microarrays (TMAs) were histochemically stained to assess cancer cell targeting/specificity of PVT-ICG.

Results: PVT-ICG indicated particle size and surface charge ideal for cancer cell/tissue delivery. PVT-ICG, further, demonstrated improved photostability and fluorescent intensity. Additionally, TMA studies exhibited enhanced internalization and cancer targeting/specificity of PVT-ICG nanoparticles compared to free ICG dye in all cancers.

Conclusion: Collectively, our findings suggest that this NIR fluorescent probe PVT-ICG has great potential for becoming a novel and safe imaging modality for various types of cancer cells and tumors which can result in early cancer diagnosis leading to improved disease management.

Citation Format: Neeraj Chauhan, Marco Cabrera, Pallabita Chowdhury, Prashanth K. Nagesh, Anupam Dhasmana, Meena Jaggi, Subhash C. Chauhan, Murali M. Yallapu. Illuminating cancer cells with a novel nano fluorescent NIR probe for bioimaging [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 826.
Abstract 85: Senescent cells promote breast cancer tumorigenesis
Authors: Ye Jiayu (Jennifer) , Delgado Ana Paula , Ren Qihao , Powers Robert S. , Stewart Sheila A.
Published: April 2023

Age is the largest risk factor for breast cancer development. While numerous changes arise with age, we posit that the accumulation of p16INKA4 (p16)+ senescent stromal cells—which express cytokines, chemokines, and enzymes together recognized as senescence-associated secretory phenotype (SASP)—promote cancer progression. Indeed, high p16 positivity in stroma strongly correlates with breast cancer recurrence. To investigate how senescent stroma impact tumorigenesis, we crossed MMTV-PyMT (PyMT) mice that spontaneously develop mammary tumors to INK-ATTAC (INK) mice, which allows selective elimination of p16+ cells. Depletion of p16+ stroma in PyMT/INK mice led to a significantly delayed tumor onset and changes in tumor-infiltrating immune cells, both of which could be recapitulated by treating PyMT mice with a senolytic drug. scRNA-seq analyses of murine and human tumor samples revealed that senescence is restricted to a specific cancer associated fibroblasts (CAF) subpopulation that expresses numerous immune and extracellular matrix SASP factors that could impact T cells and Natural Killer (NK) cells. We refer to these cells as senescent CAFs (senCAFs). To assess the impact of senCAFs on T and NK cells’ anti-tumor effect, we depleted each population and found that the elimination of senCAFs no longer restricted tumor development in the absence of NK cells. We thus focused on addressing how senCAFs modulate NK cell function. Together our data highlight how senescent CAFs contribute to mammary gland tumorigenesis by modifying tumor microenvironment.

Citation Format: Jiayu (Jennifer) Ye, Ana Paula Delgado, Qihao Ren, Robert S. Powers, Sheila A. Stewart. Senescent cells promote breast cancer tumorigenesis [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 85.