bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 401: Developing KRAS G12C inhibitor-resistant tumor models for efficacy evaluation of next-generation anticancer therapies
Authors: Zhou Jun , Ye Zi , Bo Ning , Zhang Dan , Hua Li , Nie Chenpan , Wang Jingjing , Kumari Rajendra , Price Leo , Xu Xiaoxi
Published: April 2023

Background: AMG510, a novel KRAS G12C mutation-specific inhibitor approved in 2021 by FDA, was the first therapy to directly target the KRAS oncoprotein in KRAS-mutant cancers with other direct KRAS G12C inhibitors currently being investigated in multiple clinical trials. However, the emergence of resistance in patients who initially were responsive is a challenge. Uncovering the underlying mechanism of resistance would support the identification and development of novel therapies to overcome drug resistance. In this study, we generated a panel of KRAS G12C inhibitor-resistant tumor models by introducing a secondary KRAS mutation on top of G12C for use as in vitro and in vivo tools to develop possible strategies to overcome such resistance.

Methods: First, by using CRISPR/Cas9, we introduced a secondary KRAS mutation, including Y96C, Y96D and Y96S in MIA PaCa, which harbours a homozygous KRAS G12C mutation. Point mutation knock-in was validated by sanger sequencing and cell identity was confirmed by SNP. Then cell viability was measured by CellTiter-Glo after 5 days incubation with AMG510 and MRTX849. RAS-MAPK pathway activity was assessed in the parental and mutant cell lines Y96D by Western blot. Xenograft of MIA PaCa KRAS G12C/Y96D cells l was also established.

Results: Successful homozygous point mutation knock-in was achieved as confirmed by sanger sequencing. The double mutant cells displayed the similar growth rate as well as the morphology. In cell viability assays, relative to KRAS G12C parental cells, cells expressing the double-mutant alleles showed marked resistance to AMG510 and MRTX849. Consistent with the effects on cell viability, persistent phosphorylated ERK (pERK) and pRSK levels was also observed in KRAS G12C/Y96D expressing cells even at high concentrations of MRTX849, indicating sustained RAS-MAPK activity. In addition, MIA PaCa-KRAS G12C/Y96D was able to grow in vivo and will be used for pharmacological evaluation of KRAS inhibitors.

Conclusion: These double-mutant cells can be used to assess preclinical in vitro/in vivo efficacy of KRAS-targeted therapeutics. Crown Bioscience is in the process of developing a series of KRAS G12C inhibitor-resistant cell lines to better facilitate efficacy testing of KRAS-targeted therapeutics.

Citation Format: Jun Zhou, Zi Ye, Ning Bo, Dan Zhang, Li Hua, Chenpan Nie, Jingjing Wang, Rajendra Kumari, Leo Price, Xiaoxi Xu. Developing KRAS G12C inhibitor-resistant tumor models for efficacy evaluation of next-generation anticancer therapies [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 401.
Abstract 4070: Engineering TRAIL-expressing immune cells to target GI malignancies
Authors: Srinivasan Praveen R. , Zhang Shengliang , El-Deiry Wafik S.
Published: April 2023

While adoptive cell therapies, such as chimeric antigen receptor (CAR) T cells, have had promising results in hematologic malignancies, their translation to solid tumors has been mostly unsuccessful. A significant limitation to use of adoptive cell therapy in solid tumors has been life-threatening off-target toxicities, including acute respiratory toxicity and cytokine release syndrome. The native T cell program releases a diverse range of toxic proteins upon activation, including interferons, interleukins, perforins, and granzymes. Rather than activate the native T-cell program, selective expression of tumor-targeting agents may be advantageous. TNF-related apoptosis-inducing ligand (TRAIL) is known to selectively target tumor cells with minimal toxicity to normal tissues. We therefore engineered Jurkat (a human CD4+ T cell leukemia cell line) and THP-1 (a human monocytic leukemia cell line) cells to constitutively express wild-type TRAIL using a third-generation lentivirus system. These cells killed multiple cell lines across colorectal and pancreatic cancer, thus representing a possible therapeutic strategy to target GI malignancies. Furthermore, the addition of the ferroptosis induced erastin enhanced cytotoxicity of TRAIL-engineered cells, suggesting that targeting ferroptosis in addition to apoptosis is a promising strategy for enhancing immune killing. Future work will focus on overcoming TRAIL resistance, tumor trafficking, and alteration of the tumor microenvironment.

Citation Format: Praveen R. Srinivasan, Shengliang Zhang, Wafik S. El-Deiry. Engineering TRAIL-expressing immune cells to target GI malignancies. [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 4070.
Abstract 4092: Development of nucleotide metabolic reprogrammed CAR T cell therapy suitable for solid tumors
Authors: Hu Yue , Sarkar Abhijit , Song Kevin , Hook Magnus , Heczey Andras , Song Xiaotong
Published: April 2023

CAR T cell therapy has represented an exciting breakthrough in the treatment of patients with hematologic malignancies. In contrast, the antitumor activity of CAR T cell therapy in solid tumors has been modest so far in clinical studies. The suboptimal clinical efficacy is a result of multiple factors including limited T cell trafficking, persistence, and the immunosuppressive tumor microenvironment (TME). While current strategies utilize costimulatory molecules and cytokines to activate CAR T cells, a key but largely overlooked problem of CAR T cell therapy is nutrient competition between tumor cells and T cells in the nutrient-poor TME. In our previous studies, a metabolic screen identified inosine as an alternative fuel for T cells which can support T cell growth and function in the absence of glucose. T cells could metabolize inosine into hypoxanthine and phosphorylated ribose by purine nucleoside phosphorylase. Moreover, we demonstrated that T cells have advantage over cancer cells in utilizing inosine, and supplementation with inosine enhances the antitumor efficacy of PD-1 mAb and adoptive T cell transfer in mouse models. In this study, we therefore engineered CAR T cells to express CD26 on the cell surface and a secreted adenosine deaminase (ADA) fused with an anchor. These metabolic reprogrammed CAR (designated as MRCAR) T cells exerts their activities through different mechanisms. ADA irreversibly converts adenosine to inosine, overcoming adenosine-mediated immunosuppression and providing inosine for CAR T cell growth, while CD26 induces a rich chemokine receptor profile enabling CAR T cells to traffic to solid tumors. We demonstrated that CD26-overexpressed CAR T cells displayed superior migration capacity and resisted TGF-beta suppression, while the CD26 expression on unmodified CAR T cells was significantly down-regulated by TGF-beta. We further proved that ADA is conditionally secreted in stress condition (i.e., low pH, lack of nutrient and oxygen) based on ADA’s biological characteristics, suggesting that ADA activates CAR T cells as a trans-signaling to the CAR construct in a tumor specific manner. Remarkably, we observed that the MRCAR T cells inhibit tumor growth more effectively than unmodified CAR T cells in both Huh7 human hepatocellular carcinoma (GPC3-MRCAR) and A549 human non-small cell lung cancer (HER2-MRCAR) mouse models. Thus, MR-CAR T cell therapy represents a promising approach to improve CAR T cell therapy against solid tumors.

Citation Format: Yue Hu, Abhijit Sarkar, Kevin Song, Magnus Hook, Andras Heczey, Xiaotong Song. Development of nucleotide metabolic reprogrammed CAR T cell therapy suitable for 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 4092.
Abstract 4143: Enhancing adaptive immune responses with telomerase-mediated telomere targeting therapeutics in hepatocellular carcinoma
Authors: Flusche Ann Marie , Shay Jerry , Ogunrinde Ilgen Mender
Published: April 2023

Hepatocellular carcinoma (HCC) is the most common primary malignant tumor of the liver and is the third leading cause of cancer-related deaths. In recent years, immune checkpoint inhibitors (ICIs) have improved treatment of solid tumors including HCC. However, due to low response rates with current standard of care immunotherapy and angiogenic inhibitors, there is an urgent need to develop new therapeutic strategies to improve the efficacy of immunotherapy against HCC. Our lab has shown that 6-thio-2’ deoxyguanosine (6-thio-dG), a telomerase-mediated telomere targeting agent, is incorporated into newly synthesized telomeres by telomerase and causes rapid telomere uncapping, thereby inducing telomere-associated DNA damage in cancer cells. These damaged DNA fragments can then lead to enhanced adaptive immune responses. In this study, we evaluated the therapeutic effects of 6-thio-dG in vitro and in vivo together with ICIs in liver tumors to determine whether combining immunotherapy with a telomere-targeting agent could serve as an effective strategy for HCC. To explore whether 6-thio-dG is effective in killing liver cancer cells, we ran cell viability and telomere dysfunction induced foci (TIF) assays to assess DNA damage on telomeres in vitro and compared tumor volumes of mice following 6-thio-dG monotherapy, immunotherapy, and sequential treatment of 6-thio-dG and immunotherapy in syngeneic mouse models. We observed that 6-thio-dG reduced cell viability and induced telomere dysfunction in a panel of human and mouse liver cancer cells. In addition, 6-thio-dG enhanced the therapeutic effect of immunotherapies in liver syngeneic mouse models. Overall, our findings show that the telomere-targeting anticancer agent 6-thio-dG inhibits HCC as a single monotherapy and/or sequential therapy together with immunotherapies. These results provide an experimental rationale for a potentially new immunochemotherapy strategy based on the administration of a telomere-targeting agent.

Citation Format: Ann Marie Flusche, Jerry Shay, Ilgen Mender Ogunrinde. Enhancing adaptive immune responses with telomerase-mediated telomere targeting therapeutics in hepatocellular carcinoma. [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 4143.
Abstract 4204: Incidence of early-onset and average-onset colon cancer among Medicaid beneficiaries with and without HIV: a cohort study
Authors: Joshu Corinne , Calkins Keri , Rudolph Jacqueline E. , Xu Xiaoqiang , Wentz Eryka , Kaur Maneet , Pirsl Filip , Coburn Sally B. , Moore Richard D. , Lau Bryan
Published: April 2023

Background: Colorectal cancer has increased among people living with HIV (PLWH). Studies have reported either no difference or lower risk of colorectal cancer incidence among PLWH as compared to the general population. We evaluated the incidence of colon cancer, both average-onset (diagnosed at 50 or older) and early-onset (diagnosed at less than 50), among a diverse population of people with and without HIV who have comparable sociodemographic factors and access to care.

Methods: We obtained Medicaid Analytic eXtract (MAX) data from 2001-2015 for 14 states. We included 42,244,679 unique individuals with at least 7 months of continuous eligibility. HIV and colon cancer diagnoses were identified from inpatient and other non-drug claims. We used Cox proportional hazards regression models to assess the incidence of colon cancer, controlling for age, sex, race/ethnicity, calendar year of enrollment, state of enrollment, and number of comorbidities. Analyses were also adjusted for or stratified by age, sex, and race/ethnicity.

Findings: We identified 191 colon cancer cases among 523,969 person-years among PLWH and 15,098 colon cancer cases among 63,579,078 person-years among beneficiaries without HIV. Colon cancer incidence increased with age among beneficiaries with and without HIV. Overall, HIV was modestly, inversely associated with colon cancer incidence (HR:0.84, 95%CI: 0.73, 0.98). PLWH 18-39 years old had increased hazard of colon cancer as compared to those without HIV (HR:1.67, 95%CI: 1.06, 2.65); this association was attenuated after adjustment for co-morbidities. HRs were null when early-onset colon cancer was assessed among all beneficiaries less than 50 years. PLWH had lower hazard of average-onset colon cancer compared to those without HIV (HR:0.81, 95%CI: 0.68, 0.96); this association was statistically significant among male, but not female, beneficiaries.

Interpretation: Compared to beneficiaries without HIV, PLWH had a lower risk of average-onset colon cancer. PLWH had higher incidence of early-onset colon cancer, but this difference was attenuated after adjustment for comorbid conditions.

Citation Format: Corinne Joshu, Keri Calkins, Jacqueline E. Rudolph, Xiaoqiang Xu, Eryka Wentz, Maneet Kaur, Filip Pirsl, Sally B. Coburn, Richard D. Moore, Bryan Lau. Incidence of early-onset and average-onset colon cancer among Medicaid beneficiaries with and without HIV: a cohort study. [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 4204.
Abstract 4214: Exposure to air pollution during pregnancy and risk of premenopausal breast cancer: A Swedish nation-wide cohort study including more than 1 million women
Authors: Edlund Jessica Lena , Gustafsson Malin , Linden Jenny , Wu Wendy Yi-Ying , Oudin Anna , Harlid Sophia
Published: April 2023

Background: Air pollution has been linked to an increased risk of breast cancer, but most previous studies have not considered if the exposure occurred during windows of susceptibility, such as pregnancy. Pregnancy is a period of rapid changes to both the breast tissue and the surrounding microenvironment. Exposures during this sensitive time-period could therefore result in erosion of the protective effect of pregnancy and make women more susceptible to external breast cancer risk factors. Aim: The aim of this study was to identify associations between air pollution exposure, occurring specifically during pregnancy, and risk of premenopausal breast cancer.

Method: Using nation-wide data from Swedish registers we constructed a cohort consisting of all women in Sweden who gave birth to their first child between January 1st 1991 and December 31st 2015. Women with a cancer diagnosis prior to pregnancy were excluded. Data on air pollution (yearly averages of PM10, PM2.5 and NO2), was collected from the residence of women during, and to some extent between, pregnancies. Associations between air pollution and premenopausal breast cancer is evaluated using Cox proportional hazards regression to estimate hazard ratios (HR), using age as the time scale and including appropriate confounders such as socioeconomic variables, comorbidities and family history of breast or ovarian cancer.

Results: The full cohort included 1 074 925 unique women and 2 302 256 pregnancies (the mean number of pregnancies for each woman was 1.75). During the study period, 13 292 (1.2 %) were diagnosed with breast cancer before they turned 50 years.

Conclusion: Our working hypothesis is that women exposed to higher levels of air pollution during pregnancy will have a higher risk of breast cancer. This large-scale study will have enough statistical power to detect the effect of air pollution on breast cancer risk, taking into account exposure both during and between pregnancies.

Citation Format: Jessica Lena Edlund, Malin Gustafsson, Jenny Linden, Wendy Yi-Ying Wu, Anna Oudin, Sophia Harlid. Exposure to air pollution during pregnancy and risk of premenopausal breast cancer: A Swedish nation-wide cohort study including more than 1 million women. [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 4214.
Abstract 4215: Air pollution exposure during pregnancy and risk of premenopausal breast cancer among women with a family history of cancer
Authors: Hettinger Anna , Edlund Jessica , Gustafsson Malin , Lindén Jenny , Wu Wendy Yi-Ying , Oudin Anna , Harlid Sophia
Published: April 2023

Background: Having a family history of breast or ovarian cancer is an important risk factor for premenopausal breast cancer. One reason for this could be that women with an underlying genetic susceptibility are more sensitive to environmental exposures due to gene-environment interactions. This might be especially important if the exposure occur during windows of susceptibility, such as pregnancy. Aim: The aim of this project is to determine if exposure to air pollution during pregnancy is associated with premenopausal breast cancer in a population with a known family history of breast or ovarian cancer.

Methods: The project is based on nation-wide data from Sweden’s national registers and utilizes a cohort study design. The original cohort consists of women who gave birth to their first child between 1992 and 2015 (n=1 074 925), from this cohort we will select women with at least one first degree relative with breast or ovarian cancer (confirmed through register linkage). The primary outcome is primary breast cancer diagnosed before 50 years of age, and the exposure is levels of air pollution (PM10, PM2.5 and NO2) at the participant’s home address during each pregnancy. Cox proportional hazards regression will be used to determine hazard ratios using age as the time-scale.

Results: The registry based linkage makes it possible to distinguish between both relational context (mother or sister), number of afflicted first degree relatives and type of cancer (breast or ovarian). All included women also have at least one recorded pregnancy (prior to any cancer diagnosis).

Conclusion: This large scale study will be able to provide important information about the impact of air pollution exposure during pregnancy on breast cancer risk in a population with a documented family history of breast or ovarian cancer.

Citation Format: Anna Hettinger, Jessica Edlund, Malin Gustafsson, Jenny Lindén, Wendy Yi-Ying Wu, Anna Oudin, Sophia Harlid. Air pollution exposure during pregnancy and risk of premenopausal breast cancer among women with a family history of 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 4215.
Abstract 4262: Genomic profiling of uveal melanoma patients using the GENIE database
Authors: Tashtoush Shaden , Al-Akhras Ashaar , Ghazou Alina , Syaj Sebawe
Published: April 2023

Uveal melanoma (UM) is the most common primary adult intraocular tumor. Frequently mutated genes in UM include BAP1, EIF1AX, GNA11, GNAQ CHEK2, and SF3B1. This study aims to investigate the genomic characteristics of UM patients using a large cohort of clinicogenomic data. We assessed the frequency of genetic mutations in UM patients obtained from the AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) cohort v12.1. We excluded patients with samples from a local recurrence, not otherwise specified tumor samples, and data not collected for sampling localization from our cohort. A total of 296 UM patients were included in this study, 164 (55.4%) of which were male and 131 (44.6%) were female. The sample mean age was 59.5 (SD: 14.1), and most patients were of white ethnicity (83.8%). Of 243 patients with known vital status, 32.1% (n = 78) of them were alive, while 67.9% (n = 165) of them were deceased. Sequencing samples were collected from the primary tumor in 141 patients, and from a metastatic nodule in 146 patients. We found that GNAQ and GNA11 were mutated in 43.9% and 43.6% of patients, respectively. BAP1 was mutated in 35.1%, SF3B1 in 22.3%, and EIF1AX in 13.2% of patients. No patients had GNAQ and GNA11 mutations concurrently. All patients had a median mutation count of 3, with no differences between the two genders. No significant differences were found in the frequency of mutations in regard to gender. GNAQ and GNA11 mutations were identified to be the most frequent mutations among UM patients, with a mutual exclusivity relationship between the two genes. New therapeutic modalities should consider the comprehensive genomic profiling of UM patients to improve their overall survival rate and quality of life.

Citation Format: Shaden Tashtoush, Ashaar Al-Akhras, Alina Ghazou, Sebawe Syaj. Genomic profiling of uveal melanoma patients using the GENIE database. [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 4262.
Abstract 4278: Transcriptome-driven combination design: A computational approach
Authors: Gavazzi Christina , Grushko Mikhail G. , Goldstein Jeremy M. , Samizadeh Mahta , ElSeht Zakary Y. , Arline Katherine
Published: April 2023

While rational drug combination design seeks to improve patient outcomes by leveraging biological synergy, outcomes from combination trials often fail. Only 12.4% of phase 1 trials eventually achieve regulatory approval. In vitro evidence has provided the rationale for the drug combinations in 36.6% of phase 1 combination trials, but none of those trials progressed past phase 3 (from a study by Paller CJ et al., 2019). A review of DrugCombDB, a publicly available database of experimental synergy results, supports the idea that such outcomes are mirrored in preclinical data. Analysis of the similarity of synergy scores within indication-specific subsets of cell lines from data in a 2022 paper by Douglass, et al. show that in both breast and lung cancer, combinations predicted to be synergistic in at least one cell line from that indication failed to be synergistic in the majority of indication cell lines more than half of the time.

SHEPHERD’s Gene Cluster Voting Algorithm (GCVA) was adapted to improve upon current drug combination design and anticipate transcriptome changes as the result of drug treatment. GCVA relates drug sensitivity to the transcriptome by calculating a list of biomarkers that contribute to sensitivity and resistance for specific drugs, enabling the prediction of drug sensitivity on patient transcriptomic data captured via bulk RNAseq.

Via this method, 15,137 publically available synergy data points in the Douglass paper were compared to predictions by our computational approach. For all synergy metrics contained within the dataset (ZIP, Bliss, Loewe, and HSA), the synergistic predictions made by application of GCVA have significantly higher synergy scores compared to the antagonistic predictions made by GCVA (p < .001). These test results support the potential for the application of GCVA to intelligent combination design with the ultimate goal of deployment on a patient-by-patient basis.In addition, analysis of GCVA’s drug efficacy predictions for the cell line DU145 showed that treatment with 9 kinase inhibitors consistently potentiated the predicted efficacy of between 5 and 11 additional drugs. Dasatinib, temsirolimus, and cabozantinib were newly predicted effective after treatment with each and every kinase inhibitor. This data suggests an avenue for the design of intelligent drug combinations based on anticipated transcriptomic changes that may improve on existing synergy prediction methods.

Citation Format: Christina Gavazzi, Mikhail G. Grushko, Jeremy M. Goldstein, Mahta Samizadeh, Zakary Y. ElSeht, Katherine Arline. Transcriptome-driven combination design: A computational approach. [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 4278.
Abstract 4280: Automatic identification of cancer cell-cell interfaces at the pixel level
Authors: Zhou Jie , Martinek Jan , Liu Zichao , Foroughi Pour Ali , Wu Te-Chia , Sivajothi Santhosh , Robson Paul , Palucka Karolina , Chuang Jeffrey Hsu-Min
Published: April 2023

Deciphering cell-cell interactions is critical for understanding the role of the tumor immune microenvironment. Although multiplex imaging methods are increasingly used for spatial characterization of cell communities and tissue morphologies, quantification of the interface between contacting cells has been mostly unexplored. Here we design an unsupervised pixel-level clustering method that accurately detects the contacting interface between cells. First, we observed pixel-level clusters with cell type specific phenotypes including tumor, immune infiltrates and extracellular structures in two independent melanoma datasets using cytometry time-of-flight (CyTOF) imaging mass cytometry (IMC) images. More importantly, our pixel-level approach identified clusters with mixed phenotypes, which are demonstrated to be direct contacts between T cells and myeloid cells. Specifically, pixels in the interface clusters simultaneously express T cell (CD3+, CD4+ or CD8+) and myeloid cell (CD68+) phenotypic markers at comparable levels. Spatial mapping of the pixels in interface clusters shows that interface pixels are in the physical contact regions between T cells and myeloid cells. In addition, the abundance of T cell and myeloid cell interface clusters is correlated with positive response to immune checkpoint inhibitors (ICIs) (p<0.05). We also identified other clusters indicating interfaces between the stroma, tumor cells, and immune infiltrates. Our work enables reliable delineation of cell interactions at high resolution, and therefore can unravel new information about how cancer cells interact with their environment.

Citation Format: Jie Zhou, Jan Martinek, Zichao Liu, Ali Foroughi Pour, Te-Chia Wu, Santhosh Sivajothi, Paul Robson, Karolina Palucka, Jeffrey Hsu-Min Chuang. Automatic identification of cancer cell-cell interfaces at the pixel level. [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 4280.
Abstract 4384: Does progressive disease justify pembrolizumab discontinuation: a simulation analysis
Authors: Thiagarajan Kannan , Channavazzala Madhav , Topp Brian Gregory
Published: April 2023

Background: With checkpoint inhibition becoming first line therapy in several cancer indications, there is a growing number of patients that are refractory to PD1 therapy. It is unclear if these patients should remain on PD1 inhibitors while new therapies are added on top or if PD1 should be discontinued when new therapies are initiated. Here we simulate a randomized controlled study comparing pembrolizumab + a checkpoint inhibitor (P+C) to a checkpoint inhibitor (C) in virtual patients that are refractory to PD1 therapy.

Methods: An IO QSP model was developed that includes intra-patient heterogeneity in tumor dynamics (target, non-target, and new metastatic lesions). The model was calibrated to individual lesion data from a large multicentre, open-label phase III study (Keynote-001) in patients with metastatic melanoma. A two year phase III study comparing P+C to C was simulated with 310 virtual patients in each group. Virtual patients were removed from the trial at the time of RECISTv1.1 progression or dropout due to AE or loss to follow-up.

Results: Virtual patients in the P+C arm displayed deeper (-11.5% vs 24.5%) and longer response (186.4 days vs 96.5 days) than virtual patients in the CPI arm. The percent of virtual patients displaying low prevalence progression (< 50% of the target lesions with PD) was 86% vs 52% for P+C vs. C. Median progression free survival was also longer in the P+C arm (3.8 vs 2.1 months). Difference in progression free survival were driven mainly by virtual patients that displayed oligoprogression during the pembrolizumab monotherapy run-in period.

Conclusions: Simulations presented here show that virtual patients that continued pembrolizumab treatment beyond RECISTv1.1 progression (as part of a combination) did better than virtual patients that discontinue pembrolizumab (and switch to a new therapy).

Citation Format: Kannan Thiagarajan, Madhav Channavazzala, Brian Gregory Topp. Does progressive disease justify pembrolizumab discontinuation: a simulation 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 4384.
Abstract 455: Development of an antibody-drug conjugate panel targeting high grade serous ovarian cancer
Authors: Fu Ruisi , Lou Hantao , Wang Ning , Yan Dongnan , Tresserras-Segura Clara , Lu Haonan , Aboagye Eric
Published: April 2023

Antibody drug conjugate (ADC) is a novel class of therapeutic agent which recently showed great success in both solid tumour and blood cancer. ADCs deliver potent cytotoxic payloads to tumour via cancer specific monoclonal antibodies. A few ADCs are currently evaluated in clinical trials for high grade serous ovarian cancer (HGSOC). However, most of them target FOLR1-alpha, a conventional HGSOC target which also expresses in vital organs including lungs. Thus, it is desirable to discover more specific antigen targets, and these new targets will be the foundation for the next-generation ADC for HGSOC.We propose that ovarian tumour specificity of an ADC target could contributed by three factors: 1. Lineage (e.g. fallopian tube marker FOLR1); 2. DNA amplification (e.g. ERBB2); 3. Other carcinogenesis process including epigenetic reprogramming. Then, by combining the GTEX, TCGA dataset with our own WES, long-reads RNA-sequencing and Mass spectrometry-based proteomics cohort, an array of differentially expressed genes in HGSOC tumours are identified. Out of over 50 candidates, two most promising targets are chosen for monoclonal antibodies (mAbs) production and subsequent ADC development. First, the affinity and specificity of the mAbs were confirmed by ELISA, flow cytometry and immunofluorescence. The cellular internalisation characteristics of these antibodies are confirmed by a fluorescence-based assay. Then, ADCs for these two targets are produced by conjugating monomethyl auristatin E payload to the mAbs via a cleavable linker. Finally, both ADCs show highly target-specific and sub-nanomolar cytotoxicity in model ovarian cancer cell lines. In conclusion, we identify a panel of HGSOC-specific ADC targets and develop two ADCs candidates for further pre-clinical and clinical investigations.

Citation Format: Ruisi Fu, Hantao Lou, Ning Wang, Dongnan Yan, Clara Tresserras-Segura, Haonan Lu, Eric Aboagye. Development of an antibody-drug conjugate panel targeting high grade serous ovarian 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 455.
Abstract 4551: Reconstructing the metastatic tumor microenvironment of high grade serous ovarian cancer: understanding the contribution of malignant cells
Authors: Malacrida Beatrice , Elorbany Samar , Maniati Eleni , Laforets Florian , Manchanda Ranjit , Balkwill Frances R.
Published: April 2023

Following a ‘deconstruction’ of the metastatic tumor microenvironment (TME) of high grade serous ovarian cancer (HGSOC), we developed 3-dimensional (3D) human multicellular in vitro models using patient-derived primary cells and HGSOC malignant cell lines. In this study, we used these 3D in vitro human models to study how malignant cells influence the surrounding TME. Using patient-derived primary adipocytes, fibroblasts and mesothelial cells isolated from macroscopically normal omentum (the primary site of metastasis in HGSOC) from women undergoing gynaeco-oncology surgery, we built multicellular models combining those cells with different high grade serous malignant cell lines and monocytes isolated from healthy individuals. We found that peripheral blood monocytes were able to differentiate and polarize to macrophages in our pentacultures (i.e., five different cell types) with phenotypes also found in HGSOC omental metastases. In addition, the cells in our pentaculture models self-rearranged in ways that were dependent on the HGSOC malignant cell lines used in the culture. Macrophage phenotype and cytokine secretion from the multicellular cultures was also influenced by the different malignant HGSOC cell lines used in the model. RNAseq analysis of the pentacultures showed that the cultures clustered according to the malignant cell line used. In addition, we were able to identify some gene expression clusters in the macrophages and fibroblasts of the pentacultures that matched those found by single cell RNAseq analysis of human HGSOC biopsies. These human 3D in vitro multicellular models allow us to define the contribution of each cell type to tumor growth and spread, and also provide us a semi-high throughput platform to investigate antibody or drug targets.

Citation Format: Beatrice Malacrida, Samar Elorbany, Eleni Maniati, Florian Laforets, Ranjit Manchanda, Frances R. Balkwill. Reconstructing the metastatic tumor microenvironment of high grade serous ovarian cancer: understanding the contribution of malignant 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 4551.
Abstract 4556: Matrix properties regulate 3D tumor spheroid growth and cancer drug response
Authors: Libby Jaxson R. , Li Linqing , Walker Sarah R.
Published: April 2023

3D cancer spheroids are vital in vitro models for cancer drug discovery. The current cancer spheroid generation utilizes low-adhesion plates or forced aggregation of single cells. However, certain cancers do not form stable spheroids in these protocols, nor do pre-formed tumor spheroids recapitulate in vivo development and progression. This project aims to overcome this limitation with the use of a biomimetic hydrogel system to mimic in vivo cancer cell growth and tumor development and use it as an in vitro platform for 3D cancer drug screening. The biocompatible and tunable hydrogel permits independent control of key biochemical and biophysical cues such as matrix degradation, cell adhesion, and stiffness; leading to systematic investigation of matrix parameter contribution to regulating in vitro tumor growth and treatment response. We modified a homo-polysaccharide dextran with methacrylate groups and generated dextran macromers (Dex-MA) containing ample reactive methacrylates per polymer. Cell adhesion is mediated by thiol-terminated RGD peptide added to the methacrylates, followed by crosslinking with di-thiolated MMP-labile peptides through Michael-type addition reaction. Varying the sequence of the crosslinker furthermore gives access to a range of degradability, independent of matrix stiffness. Our experiments showed that Dex-MA supported robust growth of SK-BR-3 breast cancer cells from single cell to 3D tumor spheroids, whereas the cell line failed to form tumor aggregates in low-adhesion plates. Alteration of hydrogel stiffness further revealed stiffness dependence of tumor growth, invasion, and response to treatment, suggesting the importance of matrix properties on regulating cell behavior. This dextran-based tunable hydrogel system provides key insights into how engineered matrix properties control tumor growth, critical for screening novel therapy compounds, and may reveal mechanisms for 3D tumor development, invasion, metastasis, and drug resistance.

Citation Format: Jaxson R. Libby, Linqing Li, Sarah R. Walker. Matrix properties regulate 3D tumor spheroid growth and cancer drug response. [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 4556.
Abstract 4566: 3D cancer cell-fibroblast heterospheroids forming tumor-like microenvironments are valuable tools to study immune cell infiltration and as pre-clinical drug testing models
Authors: Nielsen Boye Schnack , Madsen Natasha H. , Larsen Jesper , Larsen Hjalte M. , Gad Monika , Holmstrom Kim
Published: April 2023

3D cancer cell cultures have enabled new opportunities for replacing compound testing in experimental animals and provide a basis for high content work-flows for drug testing. Here we present data obtained from 3D multicellular tumor spheroids (MCTS) composed of cancer cell lines, fibroblasts and macrophages. We cultured HT29 and SW480 CRC cell lines (as well as others) with fibroblasts and obtained heterospheroids that could be evaluated in cell viability and apoptosis assays, by flow cytometry and high content imaging (HCI). In addition, mature MCTS were embedded in paraffin and used for traditional biomarker characterization using immunohistochemistry and in situ hybridization. The cancer cell x fibroblast interactions promoted a tumor-like microenvironment that recruited monocytes isolated from primary donors. FACS analysis indicated that the infiltrating monocytes polarized into CD163-positive M2 macrophages in HT29 MCTS, and in pancreatic MIA PaCa-2 MCTS, using Pexidartinib and anti-CSF1R mAb, we found that monocyte infiltration was strongly CSF1R dependent. Preliminary data suggest that also infiltration of T cells into the heterospheroids is possible, thus making the models useful for the study of immune cell infiltration. Whole transcriptomic analysis of mono-cultures of SW480 cancer cells and fibroblast spheroids and co-cultures (MCTS) identified traditional cell-type-related transcripts as well as a group of de novo expressed genes induced by co-culturing, such as serpin peptidase inhibitor clade A1 (serpinA1) and inhibin-β A (INHBA). The NGS analysis as well as immunohistochemical staining also showed that SW480 expressed high levels of P-glycoprotein (P-Gp, MDR1) in contrast to the fibroblasts. On the other hand, the HT29 MCTS were negative for P-Gp. Histological analysis and the apoptosis assay showed that the fibroblasts were more sensitive to 5FU and cisplatin treatment than the cancer cells. We are currently testing if the P-Gp inhibitor, PSC-833, can re-sensitize the cancer cells to 5FU and cisplatin. In conclusion, we have developed 3D multicellular heterospheroids mimicking tumor-like microspheres that can be used for drug testing of traditional drug compounds, biologics and even immunotherapeutic agents.

Citation Format: Boye Schnack Nielsen, Natasha H. Madsen, Jesper Larsen, Hjalte M. Larsen, Monika Gad, Kim Holmstrom. 3D cancer cell-fibroblast heterospheroids forming tumor-like microenvironments are valuable tools to study immune cell infiltration and as pre-clinical drug testing 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 4566.
Abstract 4657: Topological data analysis reveals pan-cancer immune phenotypes with immune-related survival differences
Authors: Murgas Kevin A. , Oh Jung H. , Deasy Joseph O. , Tannenbaum Allen R.
Published: April 2023

Cancer immune phenotypes present a wide range of heterogeneity across cases, with individual tumors displaying unique patterns of infiltrating immune cell types. Deconvolutional methods allow for scoring of various immune cell types in bulk tumor RNA as a quantification of immune phenotype. Understanding how immune phenotype relates to clinical outcome remains limited. Here, we demonstrate an approach applying topological data analysis to investigate differences of immune phenotype in a pan-cancer cohort (TCGA; n=11,373 tumors). We first define an Immune Activation Score based on relative abundance of activator and suppressor immune cell types and find this score depends on cancer type and distinguishes overall survival outcomes. We then implement a robust Mapper-based algorithm to delineate clusters of immune phenotypes of tumor samples across pan-cancer and within cancer types. Our method identifies immune-activated and immune-suppressed phenotypes with distinct survival outcomes and molecular features.

Citation Format: Kevin A. Murgas, Jung H. Oh, Joseph O. Deasy, Allen R. Tannenbaum. Topological data analysis reveals pan-cancer immune phenotypes with immune-related survival differences. [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 4657.
Abstract 4793: A role for fibroblast derived SASP factors in the activation of non-apoptotic cell death in normal mammary epithelial cells
Authors: Hom Lisa M. , Sun Seunghoon , Campbell Jamie , Murphy Ireland , Culbert Shannon
Published: April 2023

In normal tissue homeostasis, bidirectional communication between different cell types can shape numerous, biological outcomes. Fibroblasts are one cell type in constant communication with neighboring epithelial cells, and as a result, can alter various cellular parameters. Additionally, fibroblasts are prone to undergo senescence, exemplified by an irreversible cell cycle arrest, in response to a variety of stimuli. Senescent cells exhibit alterations in gene expression and are characterized by substantial changes in their secretome; termed the senescence associated secretory phenotype (SASP). The role of fibroblast derived SASP factors on normal epithelial cells is an area that remains poorly understood. Our studies have found that treatment of normal mammary epithelial cells with conditioned media from senescent fibroblasts (SASP CM) results in a robust programmed cell death. The capacity of SASP CM to cause cell death is maintained across multiple senescence-inducing stimuli. Interestingly, our data suggest that the cell death caused by SASP CM is dependent on caspase activation, but independent of canonical extrinsic or intrinsic apoptotic pathways. shRNA-mediated reduction of caspase 1 or GSDMD in normal mammary epithelial cells ameliorates the ability of the SASP CM to induce cell death, suggesting that these cells are dying by pyroptosis. Interestingly, breast cancer cells and normal mammary epithelial cells engineered to express oncogenic signals are not susceptible to this SASP CM induced cell death, suggesting that cancer cells have evolved a mechanism to evade SASP CM-mediated pyroptosis.. Taken together, our data reveal a novel relationship between the activation of senescence in stromal cells and the induction of non-apoptotic cell death in normal mammary epithelial cells.

Citation Format: Lisa M. Hom, Seunghoon Sun, Jamie Campbell, Ireland Murphy, Shannon Culbert. A role for fibroblast derived SASP factors in the activation of non-apoptotic cell death in normal mammary epithelial 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 4793.
Abstract 4794: Deciphering tumor recurrence post-therapy: Interactions between the tumor microenvironment and therapy-induced senescent glioblastoma
Authors: DeLuca Valerie , Digumarti Priya , Berens Michael E.
Published: April 2023

Glioblastoma (GBM) remains one of the most lethal forms of cancer due, in part, to the capacity of tumor cells to persist during therapy and then recover. Understanding how these residual tumor cells survive is therefore imperative to developing more effective treatment strategies. We have demonstrated that GBM cells, including those from patient-derived xenografts, undergo a state of therapy-induced senescence (TIS) rather than cell death following temozolomide (TMZ) and radiation (IR). Both TMZ and IR treatment at physiologically relevant doses result in elevated senescence-associated-β-galactosidase, altered morphology, p21 induction, and increased expression of the senescence-associated-heterochromatic-foci marker H3K9Me3. Further, despite TIS-induction in a majority of the residual cells post-treatment, GBM viable cell number increases after a prolonged stasis, indicating that populations are capable of reentering a proliferative state. However, our current understanding of how the tumor microenvironment influences this growth arrest and subsequent proliferative recovery is underdeveloped. We aim to bridge that gap by investigating the paracrine communications between astrocytes and GBM cells undergoing IR-induced senescence in order to identify how these interactions foster disease progression. Current studies are focused on evaluating the effect of astrocytes on the induction and durability of TIS in GBM cells. Proteomic studies will be pursued to characterize the secretome of astrocyte-GBM co-cultures and identify factors that drive GBM senescent response to IR. Finally, based on preliminary data demonstrating that normal astrocytes are also damaged by IR, we will undertake mechanistic studies to understand how cell-intrinsic events within the astrocyte population drive extrinsic-influence on GBM cells. We anticipate that these identified signaling events may serve as potential therapeutic targets.

Citation Format: Valerie DeLuca, Priya Digumarti, Michael E. Berens. Deciphering tumor recurrence post-therapy: Interactions between the tumor microenvironment and therapy-induced senescent glioblastoma. [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 4794.