tbuckley/cabot-search huggingface dataset:
Abstract 4307: Quantifying the cell-intrinsic and cell-extrinsic growth effects of cancer-causing mutations <i>in vivo</i>
Authors: Christopher Dennis McFarland, Jeff Maltas
Journal: Cancer Research (2024)

Abstract Adaptive driver phenotypes in cancer must confer either a cell-intrinsic (birth minus death) or cell-extrinsic (field) effect on growth. These effects can be summarized by an r/K logistic growth curve, whereby cell-intrinsic effects manifest as a change in the early, exponential growth constant (r) of a tumor population while cell-extrinsic effects alter the long-term ‘carrying capacity’ (K). Previously, we developed a novel genetically-engineered mouse model that tracks tumor growth dynamics with unprecedented precision via Tumor Barcoding, termed TuBa-seq1. Here, we quantify the growth trajectories of thousands of Kras-driven lung tumors over eight months. Median tumor size is best-described by a Gomp-Ex growth law (i.e. Nν/K where ν → +0), which also characterizes advanced-stage human tumors2. Carrying capacities of individual isogenic tumors varied by over four orders of magnitude, suggesting that microenvironmental heterogeneity profoundly impacts growth dynamics. Our approach further allowed us to track the growth effects of eleven canonical tumor suppressor gene knockouts introduced via multiplexed CRISPR/Cas genome-engineering. All but one of these secondary mutations augmented either the exponential growth rate or the carrying capacity of the tumor. However, only three tumor suppressor losses increased both growth parameters (Rb1, Setd2, and Stk11). Hence, the growth benefits of most cancer-causing mutations are missed when growth is measured only at a single time point. Clinically, we find that r-promoting and K-promoting mutations interact synergistically to create the most aggressive tumors in human patients (HR = 1.71, P-value &amp;lt; 10-10). Collectively, these results support a universal r/K framework for tumor growth and progression. References1.Rogers, Z. N. et al. A quantitative and multiplexed approach to uncover the fitness landscape of tumor suppression in vivo. Nat. Methods 14, 737-742 (2017).2.Benzekry, S. et al. Classical mathematical models for description and prediction of experimental tumor growth. PLoS Comput. Biol. 10, e1003800 (2014). Citation Format: Christopher Dennis McFarland, Jeff Maltas. Quantifying the cell-intrinsic and cell-extrinsic growth effects of cancer-causing mutations in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4307.
Abstract 2627: PanCancer epigenetic regulators of lymphocyte activation states
Authors: Alla Karpova, Nadezhda V. Terekhanova, Siqi Chen, Reyka G. Jayasinghe, Andrew Houston, Wagma Caravan, Ryan C. Fields, Li Ding
Journal: Cancer Research (2024)

Abstract Several immune cell types have been successfully targeted for immunomodulatory therapy; however, the efficacies of such therapies are hindered by incompatible immune cell activation states. CD8+ T-cell exhaustion is one of the most studied T-cell states in the context of cancer and was shown to limit checkpoint blockade efficacy. Although CD8+ T-cell exhaustion studies in mice showed this state is tightly regulated by chromatin accessibility of cis-regulatory elements (CREs) and transcription factor activation, the exploration of these mechanisms, their prevalence, and their specificity in human cancers remains limited. In addition, chromatin accessibility signatures of other lymphocyte (CD4+ and NK) states frequently found in solid tumors have not been carefully characterized in a pan-cancer setting. Here we introduce the first single-nuclei atlas of pan-cancer and disease-specific cis- and trans-regulatory elements in tumor infiltrating lymphocytes. We profiled ~140K T-cell and NK cell nuclei with snATAC-seq and snRNA-seq from 227 tumor and normal samples from eleven cancer types. We distinguished two major subpopulations among exhausted CD8+ T-cells: GZMK expressing (CD8+ GZMK+ Tex) and ITGAE+ tissue-resident (CD8+ Trm ex). CD8+ GZMK+ Tex was enriched in clear cell renal cell carcinoma, while CD8+ Trm ex was found in all other cancers. Both exhausted groups featured high motif accessibility and expression of NR4A1, NFATC2, and NFKB2 transcription factors (previously reported to regulate exhaustion), but differed in EOMES motif accessibility and gene expression. We have identified other lymphocyte subpopulations showing exhaustion signatures, including CD4+ follicular helpers (CD4+ Tfh), CD4+ regulatory cells (CD4+ Tregs), and weakly cytotoxic tissue-resident NK cells (trNK weak). All these subpopulations showed increased expression and motif accessibility of the NR4A1 transcription factor, highlighting its role in regulating dysfunctional states not only in CD8+ T-cells, but also in CD4+ and NK cells. Additionally, CD4+ Tfh and Tregs showed enhanced activity of NFKB1, NFKB2, and POU2F2, and trNK weak cells had increased activity of NR4A2 and NR2F2. To put our results into clinical perspective, we have collected cohorts of renal cancer, melanoma and triple-negative breast tumors treated with immunotherapy in clinical trial settings, and showed elevated GZMK expression in exhausted T-cells in responders compared to non-responders. Citation Format: Alla Karpova, Nadezhda V. Terekhanova, Siqi Chen, Reyka G. Jayasinghe, Andrew Houston, Wagma Caravan, Ryan C. Fields, Li Ding. PanCancer epigenetic regulators of lymphocyte activation states [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2627.
Abstract 4327: Development of bioluminescent biosensors to monitor the interaction betweenGSDMD and caspase-1 in living cells
Authors: Tynan Kelly
Journal: Cancer Research (2024)

Abstract Gasdermin D (GSDMD) is the key executioner of pyroptosis, an inflammatory form of programmed cell death implicated in various inflammation-driven diseases, including cancer, heart failure and strokes. The interaction between GSDMD and caspase-1 (CASP1) orchestrates the critical pathway of GSDMD-mediated pyroptosis. During pyroptosis, pyroptosis stimuli activate CASP1, which subsequently binds to and cleave GSDMD between GSDMD’s N- and C-terminal domains. The free N-terminal domains oligomerize and translocate to the cell membrane, forming pores and releasing proinflammatory cytokines and causing cellular lysis. Key interaction sites have been identified for GSDMD recognition and engagement by CASP1; therefore, blocking functionally significant residues presents a new therapeutic strategy for inhibiting CASP1-induced GSDMD cleavage and pyroptosis. Currently, there is no small molecule capable of specifically disrupting the GSDMD and CASP1 interaction. In response, the ongoing pursuit of identifying potential inhibitors is a driving force for developing a biosensor capable of monitoring this interaction and their roles in downstream pyroptotic effects. In this study, we utilized the NanoLuc Binary Technology (NanoBiT) to construct several bioluminescent biosensors comprising two NanoLuc luciferase enzyme fragments (LgBiT and SmBiT) fused to GSDMD and CASP1, respectively, in various combinations. Further validation of these biosensors by luciferase assays in living cells identified a GSDMD-CASP1 biosensor with highest luciferase activity. This newly developed biosensor paves the way for high-throughput screens to identify novel small molecule inhibitors disrupting the GSDMD-CASP1 interplay. These small molecule inhibitors will effectively impede GSDMD-mediated pyroptosis, holding promise for novel therapies of various human diseases. Citation Format: Tynan Kelly. Development of bioluminescent biosensors to monitor the interaction betweenGSDMD and caspase-1 in living cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4327.
Abstract 783: Early impact assessment of in-house EGFR testing for NSCLC in Kenya
Authors: Allan Njau, Samuel Nguku, Joseph Abuodha
Journal: Cancer Research (2024)

Abstract Introduction: Quality of life and survival among non-small cell lung cancer (NSCLC) patients have improved in the last two decades owing mainly to use of tyrosine kinase inhibitors (TKIs) and other targeted therapies. Low and middle-income countries (LMICs) especially in Africa, are lagging in realizing these benefits largely due to hurdles in molecular testing. In addition, quality histology and molecular data from LMICs is deficient. The aim of this study is to assess the immediate impact of improved access to epidermal growth factor receptor (EGFR) testing in Kenya, and to establish a long term-lung cancer data base. Methods: Staring mid-June 2023, an in-house PCR-based method was adopted for EGFR testing of NSCLC in order to side step the challenges of out-of-country send outs which was until then, the only option for EGFR testing. Further, a sponsored access program was created. From prospectively accrued samples, we performed a before-and-after assessment of the number of NSCLC cases intercepted, cost and turnaround times (TAT) as measures of impact. Demographic, histopathology, and EGFR mutation profiles were analyzed in comparison to Asia, USA and European data. Whole slide histology scanned images are made to compliment the database. Results: Over the four-month period, 62 NSCLC cases were accrued, median age at diagnosis was 63 with a range of 24 - 93. The male to female ratio was 1: 1.5. Adenocarcinomas comprised 89%, squamous cell carcinoma 5% and 3% were not classifiable. Metastatic disease was reported in 14 (22%) with the brain being the commonest site. EGFR mutations were identified in 16 (25%) with exon 19 deletions and L858R mutations constituting 94% of them. Monthly requisitions for EGFR have increased 3-fold, and the average TAT has been halved to 7 days. Conclusion: Similarities between our data and global patterns are noted; median age is in the seventh decade, NSCLC is more common in women, and so are the rates of EGFR mutations, adenocarcinomas are the predominant type, and there are high rates of brain metastasis at diagnosis. EGFR mutation rates appear to be higher than USA and European data but lower than Asian data. In-house and sponsored testing has had an immediate impact in reduction of costs and TAT and increased requisitions. Assessment of access to targeted therapy, clinical outcome, survival, expansion of molecular profiling beyond EGFR, and build-up of the database including virtual histology images for exploring artificial intelligence algorithms are our next steps. Citation Format: Allan Njau, Samuel Nguku, Joseph Abuodha. Early impact assessment of in-house EGFR testing for NSCLC in Kenya [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 783.
Abstract 789: GrafGen: Distance-Based Inference of Population Ancestry for <i>Helicobacter pylori</i> Genomes
Authors: William Wheeler, Difei Wang, Isaac Zhao, Yumi Jin, Charles S. Rabkin
Journal: Cancer Research (2024)

Abstract BACKGROUND: The 1.67 megabase H. pylori genome contains ~143,000 biallelic single-nucleotide polymorphisms (SNP) with minor allele frequency &amp;gt; 1%. Confounding by population stratification is a major source of bias requiring adjustment in genome-wide association studies (GWAS). Previous model- and distance-based methods for bacterial genomes yield varying results depending upon which strains are included for comparison in analyses. We therefore developed a robust classification of H. pylori ancestry to facilitate generalizable inferences about disease associations. METHODS: GrafGen is an R software package adapted from the GrafPop tool for human ancestry (Jin et al., 2017; Jin et al., 2019). The underlying classification algorithm compares SNPs of an individual genome with frequencies in reference populations to estimate subject ancestry and ancestral proportions based on calculated genetic distances. Outputs incorporate visualization tools that provide natural geometric interpretation of population structure. RESULTS: Training data were obtained from the H. pylori Genome Project (HpGP), a global survey of 1011 H. pylori genomes collected across 51 countries (Thorell et al., 2023). Based on genetic distances, HpGP sequences clustered into nine mutually exclusive populations designated by their predominant geographic source. Previously published population assignments for a test set of 255 sequences obtained from GenBank mapped to specific GrafGen classifications (Table). GrafGen assignments based on randomly selected sets of 14,300 and 1430 SNPs were &amp;gt;97% and &amp;gt;90% identical, respectively, to those based on all 143,000 SNPs. CONCLUSIONS: GrafGen's universal categorization of H. pylori ancestry has utility for bacterial GWAS. The software code is publicly available for research on this important pathogen. Theoretically, the same algorithm can be implemented to infer ancestry of any single chromosome haploid species that has sufficient sequence data for references. Citation Format: William Wheeler, Difei Wang, Isaac Zhao, Yumi Jin, Charles S. Rabkin. GrafGen: Distance-Based Inference of Population Ancestry for Helicobacter pylori Genomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 789.
Abstract 6505: Targeting <i>PINK1</i> reduces medulloblastoma progression in animal models
Authors: Reema N. Alsubaiee, Amani Alghamdi, Bahauddeen M. Alrfaei
Journal: Cancer Research (2024)

Abstract Medulloblastoma is a brain cancer that mainly arises during infancy and childhood. Medulloblastoma is the most common pediatric malignant brain tumor worldwide. It comprises of approximately 20% of all childhood brain tumors and 63% of intracranial embryonic tumors. One of the major effects of proliferating cancer cells is altered mitochondrial metabolism, as well as aberrant metabolism. Medulloblastoma patients suffer severe complications due to intensive and long-term treatments. Thus, we aim to improve applications against medulloblastoma by targeting the PINK1 gene. We hypothesize that PINK1 inactivation slows down medulloblastoma progression. PINK1 is a mitochondrial serine/threonine protein kinase that protects cells by controlling mitochondria quality in response to cellular stress. PINK1 recruits parkin to target damaged mitochondria for degradation through autophagy. In this study, PINK1 has been knocked-out using gene editing technology (CRISPR/Cas9) in two commercial medulloblastoma cell lines (DAOY, and D283 cell lines). We validated PINK1 editing using RT-PCR and Western blot. Then, cell viability was studied in comparison to the control sample. The control sample contained scramble fragments with empty CRISPR/Cas9. We studied apoptosis and performed cell cycle analysis using flow cytometry. Next, orthotopic medulloblastoma mouse model was generated which showed differential survivals comparing the PINK1 knockout group and control. The results showed a low expression of PINK1 within the PINK1 knockout group. In addition, the Western blot showed reductions in PINK1 expression in the knockout group. The knockout group showed more apoptosis (cell death) 40% more than the control. The mouse model showed increased survival of the PINK1 knockout group compared to the control with a p-value of 0.0288 (log-rank). Our analysis shows that survival differences approximately extend human life by one year. We conclude that inhibiting the PINK1 gene in medulloblastoma decreases cell metabolic activities. PINK1 Knockout in medulloblastoma enhances the apoptosis pathways. Engrafted medulloblastoma mouse model treated with PINK1 inhibitor showed superior survival than the control. These results qualify PINK1 to be used as potential therapeutic target for medulloblastoma. The Future work needs additional preclinical studies to investigate the proper dose of PINK1 inhibitor and measurement of toxicity index. Citation Format: Reema N. Alsubaiee, Amani Alghamdi, Bahauddeen M. Alrfaei. Targeting PINK1 reduces medulloblastoma progression in animal models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6505.
Abstract 277: Cancer-associated fibroblasts, educated by tumor cells, differentially facilitate cancer cell invasion in cell-line based human gastric tumoroids
Authors: Hyun Ju Hwang, Saet-Byeol Lee, Hyo-Jeong Kuh
Journal: Cancer Research (2024)

Abstract Purposes: Gastric cancer can be categorized into two subtypes: intestinal and diffuse. The latter is notorious for frequent peritoneal metastasis, resulting in a poorer prognosis. Cancer-associated fibroblasts (CAFs) in the tumor microenvironment play crucial roles in tumor invasion and metastasis. However, little is known about whether CAFs are associated with the differential progression between the two subtypes of gastric tumors. This study investigated whether differential cancer invasion may be attributed to tumor-specific CAF activation, using a cell-line-based human gastric tumoroid model. Methods: Heterotypic tumor spheroids (TS) were prepared with human gastric cancer lines of intestinal (MKN28, MKN74) and diffuse type (MKN45, KATO III) mixed with human gastric fibroblasts (HGFs) using a minipillar-array chip previously developed. Invasion phenotype and expression of epithelial-mesenchymal transition (EMT)-related proteins were evaluated in heterotypic TSs. mRNA expression in HGFs isolated from heterotypic TSs was analyzed and compared between the two subtypes. Results: While both heterotypic TSs displayed increased invasion by HGFs, the diffuse type TS showed a higher level of invasion with individual or amoeboid migration and loose binding of cancer cells with HGF. In contrast, the intestinal type TS showed collective migration and tight binding between cancer cells and HGFs. HGFs in each heterotypic TS exhibited differential morphology, matrix remodeling patterns, and gene expression in a tumor subtype-specific manner. Compared to normal HGFs, HGFs isolated from diffuse heterotypic TS showed enriched expression of cytoskeleton-associated genes and several integrins, whereas those of intestinal heterotypic TS exhibited increased expression levels of inflammatory cytokines. Conclusions: This study established tumoroid models for human gastric cancer subtypes, intestinal and diffuse, using heterotypic TS culture. Our results suggest that the subtype-specific invasion ability of tumor cells is driven by CAFs that are differentially educated by tumor cells in the tumor microenvironment. Our model not only advances our understanding of CAFs' role in tumor progression but also offers an in vitro model for assessing potential therapeutic targets and drug candidates for human gastric cancers. Citation Format: Hyun Ju Hwang, Saet-Byeol Lee, Hyo-Jeong Kuh. Cancer-associated fibroblasts, educated by tumor cells, differentially facilitate cancer cell invasion in cell-line based human gastric tumoroids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 277.
Abstract 2616: BCG033, a novel bispecific antibody-drug conjugate targeting PTK7 and TROP2, demonstrates preclinical efficacy against triple-negative breast cancer and other solid tumor xenografts
Authors: Sufei Yao, Chengzhang Shang, Gao An, Chaoshe Guo, W. Frk an, Yi Yang
Journal: Cancer Research (2024)

Abstract Metastatic triple-negative breast cancer (TNBC) patients have poor overall survival, highlighting the need for novel treatments. Although the TROP2-targeting ADC sacituzumab govitecan recently received accelerated approval from the FDA for the treatment of patients with metastatic TNBC, the on-target toxicity of this single-target agent has limited clinical efficacy. We sought to improve the specificity and efficacy of future TNBC-targeted therapies by generating a bispecific antibody-drug conjugate (bsADC) targeting TROP2 and PTK7, another tumor-associated antigen (TAA) that is highly expressed in TNBC and correlates with poor prognosis and metastatic disease. We previously generated fully human antibodies targeting PTK7 and TROP2 from Biocytogen’s fully human, common light chain antibody transgenic RenLite® mice, which were selected such that their monovalent antibodies exhibited reduced internalization profiles for improved tumor selectivity. These antibodies were then constructed into a bispecific antibody targeting PTK7 × TROP2, which demonstrated reactivity to human and cynomolgus monkey antigens and binding to multiple cancer cell lines, including TNBC, with high affinity. PTK7 × TROP2 bsAb also showed enhanced internalization in vitro compared with parental monovalent antibodies. Next, the PTK7 x TROP2 bsAb was conjugated to vcMMAE with a drug-to-antibody ratio (DAR) of 4 to generate a bsADC (BCG033). BCG033-vcMMAE demonstrated superior activity to benchmark and parental ADCs in a cell line-derived xenograft (CDX) TNBC model with low PTK7 expression. Here, we demonstrate that BCG033-vcMMAE ADCs also exhibited superior efficacy to benchmark ADCs in PDX models, including TNBC xenografts and NSCLC xenografts. We next tested the efficacy of the PTK7 x TROP2 bsAb conjugated to BLD1102, Biocytogen’s novel, proprietary linker/payload composed of a DNA Topo I inhibitor payload and a highly hydrophilic protease-cleavable linker, with a DAR of 8. BCG033-BLD1102 showed potent activity in a colorectal cancer PDX model in which benchmark ADCs were inactive, even at high doses. In summary, BCG033 conjugates demonstrate promising preclinical efficacy in vivo, which ultimately could provide a new treatment option for TNBC and other solid tumors expressing PTK7 and TROP2. Citation Format: Sufei Yao, Chengzhang Shang, Gao An, Chaoshe Guo, W. Frk an, Yi Yang. BCG033, a novel bispecific antibody-drug conjugate targeting PTK7 and TROP2, demonstrates preclinical efficacy against triple-negative breast cancer and other solid tumor xenografts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2616.