bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4077: T cell targeting with PD-1-selective immune cell engagers based on GlycoConnect™ (GC™-ICEs) show excellent efficacy and tolerability
Authors: van Geel Remon , Verhagen Mick , Post Elias , Vugs Willem , Popal Sorraya , van Berkel Sander , van Delft Floris
Published: March 2024

Engagement of T cell cells to harness a patient’s immune system is a promising approach in immuno-oncology. An immunocytokine, i.e. a tumor-targeting antibody (fragment) genetically fused to an immunostimulatory cytokine, is specifically designed for this purpose. Fusion antibody-immunocytokines, based on molecular architectures generated by a variant of DNA recombinant technologies, have recently entered the clinic. Earlier we have demonstrated how GlycoConnect™, a site-specific conjugation technology anchoring on the native antibody glycan1, can be applied for attachment of various cytokines, including RLI or IL-15, without prior antibody engineering. The immunostimulatory activity of these GlycoConnect™ immune cell engagers (GC™-ICEs) can be modulated by tailoring linker design and payload stoichiometry. In this presentation, we demonstrate the GC™-ICE with either IL-15 or RLI can be applied to selective targeting of T cells, based on PD-1-selective binding and activation, using either protease-sensitive or non-cleavable linkers. We will show how such T cell targeting can be achieved leading to significant tumor volume reductions in syngeneic mouse models. Moreover, we have found that the GC-ICE™ can be applied without inducing systemic immune activation, thereby displaying a promising therapeutic index. In vitro and in vivo studies will be presented to showcase the biological activity of these GC™-ICEs in comparison to conventional immunocytokines obtained via genetic engineering.1Wijdeven et al., Enzymatic glycan remodeling-metal free click (GlycoConnect™) provides homogenous antibody-drug conjugates with improved stability and therapeutic index without sequence engineering. mAbs 2022, 14, DOI: 10.1080/19420862.2022.2078466.

Citation Format: Remon van Geel, Mick Verhagen, Elias Post, Willem Vugs, Sorraya Popal, Sander van Berkel, Floris van Delft. T cell targeting with PD-1-selective immune cell engagers based on GlycoConnect™ (GC™-ICEs) show excellent efficacy and tolerability [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 4077.
Abstract 4083: Pre-clinical development of IAMA-005, a long-acting cytokine fusion of modified IL-2 and IFN-α
Authors: Liu Liming , Han Zhen , Fan Yang , Pan Qi
Published: March 2024

In 1990s, both IL-2 and IFN-α were approved as the first two immunotherapies for metastatic melanoma and renal cell carcinoma; IFN-α was also approved for hairy cell leukemia. Although the response rates are relatively low, along ~25%, those who responded have long term survival benefits. However, the severe toxicity especially in high dose prohibited their broad use in oncology. Recently, there have been tremendous interests in modifying these two cytokines in the efforts to reduce the toxicity and enhance the activity. One such effort is to enhance the binding of IL-2 to the intermediate affinity β/γ receptors, which are expressed and function on CD8 T cells and NK cells. Another effort is to reduce the binding of IL-2 to high affinity α/β/γ receptors which mostly expressed on Treg and stimulate the growth of Treg cells, which suppress immune responses. Recently, whether it’s better to target intermediate affinity or high affinity for cancer therapy has become controversial with some studies showing that high affinity receptor engagements are required for robust anti-tumor activity while others favoring intermediate affinity receptor engagement for better efficacy; However, the clinical comparison is still lacking to be sure which approach is better. Here we have developed a long-acting novel IL-2-Fc-IFN-α fusion molecule termed IAMA-005 that has mutations to reduce the toxicity effects of IL-2 and IFN-α. We have characterized this molecule preclinically both in vitro and in vivo. IAMA-005 has demonstrated a potent tumor cell killing activities in numerous cancer cell lines including BT-474, SK-OV-3, NCI-N87, OE19, HCC-1954, MDA-MB-231, MDA-MB-468. When combined with IAMA-004 (a Her2-CD47-CD16 tri-specific antibody) in vitro, the tumor cell killing activities were dramatically increased. In addition, IAMA-005 was also tested in patient-derived Ex-Vivo fluids (one malignant pleural effusion and one malignant asities) and demonstrated excellent tumor cell killing efficacies. In addition, the killing activities of IAMA-005 could be attributed to the specific part of the fusion molecule because of the TME immune cell compositions. The in vivo assays to demonstrate efficacy and safety are ongoing and will be presented in the poster. These results suggest that this fusion cytokine molecule may be used in monotherapy in certain indications and an excellent complementary therapeutic to antibody targeted therapies or immunotherapies when used in combination.

Citation Format: Liming Liu, Zhen Han, Yang Fan, Qi Pan. Pre-clinical development of IAMA-005, a long-acting cytokine fusion of modified IL-2 and IFN-α [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 4083.
Abstract 4090: Gut microbiota mimics as a source of cross-reactive tumor rejection antigens
Authors: Panneton Vincent , Gigoux Mathieu , Zebboudj Abderezak , Sadek Norah , Choi Hyejin , Mangarin Levi M. , George Mariam M. , Kulakowski Guillaume , Magalhaes Joao G. , Carpier Jean-Marie , Dugat Thibaud , Gaal Camille , Strozzi Francesco , Tibaldi Lorenzo , Chene Laurent , Wolchok Jedd D. , Balachandran Vinod P. , Merghoub Taha
Published: March 2024

The crosstalk between gut microbiome and anti-tumor immunity has recently gained attention in clinical settings. The administration of antibiotics during immune checkpoint blockade (ICB) therapies has been correlated with poorer outcomes in cancer patients, suggesting that microbiome alterations affect overall responses to ICB. The establishment of microbiota-specific T cell clones with tumor cross-reactivity potential was proposed as one of the mechanisms linking the microbiome to anti-tumor responses. Vaccine-based strategies aimed at reactivating these dormant pools of T cells to help eliminate tumors have been proposed as an alternate approach, but the parameters required for successful responses remain poorly understood. Here, we performed in silico selection of bacterial peptides derived from healthy mice based on their mimicry of either tumor-associated antigens (TAAs) or neoantigens expressed by murine melanoma cells and not healthy tissue. We show that in silico predicted peptide binding affinity to MHC I correlates with experimental MHC I binding, a key factor associated with strong immune responses. Moreover, we confirmed that a significant proportion of selected peptide candidates can provoke an immune reaction in a vaccination setting. From this group of peptides, we selected candidates which triggered cross-reactive immune responses against TAAs or neoantigens. Data from preliminary tumor challenge experiments with prophylactic peptide vaccination and ICB allowed us to define key parameters such as target gene expression levels which can predict the cross-reactive potential of bacterial peptides that mimic tumor antigens. These findings provide novel insights into the design of gut microbiome peptide-based tumor vaccines and pave the way for establishing combinatorial therapies with immunomodulatory drugs.

Citation Format: Vincent Panneton, Mathieu Gigoux, Abderezak Zebboudj, Norah Sadek, Hyejin Choi, Levi M. Mangarin, Mariam M. George, Guillaume Kulakowski, Joao G. Magalhaes, Jean-Marie Carpier, Thibaud Dugat, Camille Gaal, Francesco Strozzi, Lorenzo Tibaldi, Laurent Chene, Jedd D. Wolchok, Vinod P. Balachandran, Taha Merghoub. Gut microbiota mimics as a source of cross-reactive tumor rejection antigens [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 4090.
Abstract 4132: Low-dose carbon monoxide therapies suppress cancer metastasis
Authors: Zhang Tiantian , Zhang Cheryl , Chen Xiang , Yang Xiaoxiao , Mao Qiyue , Zhang George , Chen Zhengming , Tan Adrian , Xiang Jenny Zhaoying , Hissong Erika , Chen Yao-Tseng , Wang Binghe , Du Nancy
Published: March 2024

Metastasis is the primary cause of cancer-related deaths. Novel systemic therapies for metastatic cancer are urgently needed. Carbon monoxide (CO) is an endogenously produced signaling molecule in the human body with demonstrated pharmacological activities, including organ protection and anti-inflammation. We determined the therapeutic effect of low-dose CO and CO prodrugs on cancer progression in this study. We found that low-dose CO inhibits the migration of cancer cell lines including breast, pancreatic, colon, prostate, liver, and lung cancer. We showed that low-dose CO inhibits lung metastasis of breast cancer and liver metastasis of pancreatic cancer in preclinical mouse models. Further, to provide safer and more reliable CO delivery, we developed metal-free, organic CO prodrugs and showed that CO prodrugs inhibit tumor growth and metastasis. We demonstrated that low-dose CO blocks the transcription of heme importers, leading to diminished intracellular heme levels. Altogether, our work lays a strong foundation for the development of CO-based systemic cancer therapies.

Citation Format: Tiantian Zhang, Cheryl Zhang, Xiang Chen, Xiaoxiao Yang, Qiyue Mao, George Zhang, Zhengming Chen, Adrian Tan, Jenny Zhaoying Xiang, Erika Hissong, Yao-Tseng Chen, Binghe Wang, Nancy Du. Low-dose carbon monoxide therapies suppress cancer metastasis [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 4132.
Abstract 4190: Patient-derived xenograft (PDX) models with differential HER2 expression for preclinical evaluation of HER2-targeted therapies
Authors: Yang Xiaoliu , Guo Shiying , Wang Huiyi , Su Xu , Zhao Jing , Gao Xiang , Ju Cunxiang
Published: March 2024

Human epidermal growth factor receptor 2 (HER2) is a critical therapeutic target in gastric cancer. However, the varying expression levels of HER2 in patients present a significant challenge in selecting the appropriate HER2-targeted therapies. Patient-derived xenograft (PDX) models offer a valuable tool to address this clinical concern.

We established a panel of PDX models derived from gastric cancer patients, each representing a distinct range of HER2 expression levels. These models were subsequently treated with HER2-targeted drugs, including Trastuzumab (Herceptin), Margetuximab, and Enhertu.

Our results demonstrated differential drug responses corresponding to the varying HER2 expression levels in the PDX samples. Trastuzumab, Margetuximab, and Enhertu exhibited distinct efficacies across the HER2 expression spectrum. This underscores the significance of selecting the right therapeutic approach based on the HER2 status of individual patient.

Our collection of PDX models with differential HER2 expression levels provides a robust platform for preclinical evaluation of HER2-targeted therapies. This approach not only addresses the clinical challenge of HER2 heterogeneity but also facilitates a more personalized and effective treatment strategy for gastric cancer patients.

Citation Format: Xiaoliu Yang, Shiying Guo, Huiyi Wang, Xu Su, Jing Zhao, Xiang Gao, Cunxiang Ju. Patient-derived xenograft (PDX) models with differential HER2 expression for preclinical evaluation of HER2-targeted therapies [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 4190.
Abstract 4191: Delayed onset of GvHD in PBMC humanized NCG-B2m KO mice provides an enhanced model for oncology studies
Authors: Bronson Steven , Harris David , Avrutskaya Anya , Eberle Christoph , Rowe Jenny
Published: March 2024

Humanized mice are specialized animal models incorporating components of the human immune system. These models are valuable tools for assessing the efficacy of human immunotherapies on tumors. Humanized mice are created by injecting human CD34+ hematopoietic stem cells (HSCs) or human peripheral blood mononuclear cells (PBMCs) into an immunodeficient mouse. PBMC humanized (HuPBMC) mice engraft within a few weeks and can recapitulate a robust human T cell population. One challenge when using HuPBMC mice is the onset of graft versus host disease (GvHD), limiting their lifespan compared to hCD34+ HSC humanized mice. The onset of GvHD varies in the HuPBMC model depending on the donor cells. The development of xenogeneic GvHD is dependent on the expression of major histocompatibility complex (MHC) on host cells and lowering MHC expression can delay the onset of GvHD.NCG-B2m KO mice lack beta-2 microglobulin, a component of MHC I, and have lower cell surface expression of MHC I molecules. This leads to a decrease in recognition of host cells by human immune cells. Here we compared the onset of GvHD between HuPBMC NCG-B2m KO mice and HuPBMC NCG mice. PBMC donor variability was also compared between the two PBMC humanized models by evaluating multiple donors and assessing additional collections from the same donor. After the PBMC engraftment was characterized, HuPBMC NCG mice and HuPBMC NCG-B2m KO mice were enrolled in tumor studies comparing outcomes and tumor growth kinetics in mice treated with human immune checkpoint blockade therapy.NCG and NCG-B2m KO mice were injected with 1x107 PBMCs from individual donors. Animals were weighed three times a week to monitor for changes in body weight and general health status. Peripheral blood was collected at day 10, 20, 30, 40, 60 and 90 post injection for flow cytometry screening of human immune cell engraftment (hCD45+, hCD3+, hCD4+ and hCD8+). Human PBMCs isolated from additional collections from the same donors were also injected into both NCG-B2m KO mice and NCG mice and flow cytometry was performed. HuPBMC NCG-B2m KO mice survived longer than HuPBMC NCG mice allowing for the potential use in longer term tumor studies before the results are confounded by GvHD. PBMC humanized mice are an important model for translational research using immunotherapies and the PBMC humanized NCG-B2m KO model provides an expanded study window ideal for oncology studies.

Citation Format: Steven Bronson, David Harris, Anya Avrutskaya, Christoph Eberle, Jenny Rowe. Delayed onset of GvHD in PBMC humanized NCG-B2m KO mice provides an enhanced model for oncology studies [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 4191.
Abstract 42: Tunneling CARs: Gene modifications to enhance CAR-T infiltration into solid tumors
Authors: Van Pelt Stacey N. , Omer Bilal , Talbot Lindsay , Rooney Cliona , Fernandes Rohan , Tat Candise , White Mark
Published: March 2024

Background: CAR-T therapy has been largely ineffective in solid tumors because the dense, rigid, extracellular matrices (ECMs) and basement membranes (BMs) that encapsulate these tumors exclude T cells. Tumor-specific ECMs and BMs, made of type I and type IV collagen respectively, are heavily cross-linked and characterized by small pores. T cell infiltration into tumors relies upon the enzymatic degradation of these matrix fibers, and adhesion molecule-mediated movement. Gene expression analysis of tumor infiltrating leukocytes from patient samples showed that MMP-7, an enzyme that degrades type IV collagen, and osteopontin (OPN), a molecule that interacts with adhesion molecules to mediate movement, were highly upregulated in infiltrating cells compared to those that were tumor adjacent, suggesting they may be important in navigating tumor-specific environments. We hypothesized that overexpressing MMP-7 and/or OPN in CAR-T cells will enhance their infiltration into solid tumors.

Methods: We overexpressed MMP-7 and OPN in second-generation CAR-Ts (GD2-28Z and HER2-28Z) and evaluated their infiltration in vitro using Halo invasion assays. T cell movement out of type IV collagen and into tumor droplets, composed of tumor targets polymerized in type I collagen, was visualized over time to characterize T cell movement through the tumor-specific BM and ECM, respectively. The expansion, phenotype, and cytotoxicity of OPN and MMP-7-modified GD2-28Z CAR-Ts was compared to unmodified GD2 CAR-Ts by counting, flow cytometry and chromium release, respectively. We then used a xenograft model of neuroblastoma to determine if increases in GD2 CAR-T infiltration led to reduced tumor burden.

Results: In vitro, MMP-7 overexpression increased GD2-28Z (2.05-fold, p<0.0001) and HER2-28Z (3.16-fold, p<0.0001) CAR-T infiltration, and OPN overexpression increased GD2-28Z (1.20-fold, p=0.0496) and HER2-28Z (1.49-fold, p=0.002) CAR-T infiltration. In vivo, 52 days after CAR-T infusions, mice treated with OPN-modified GD2-28Z CAR-Ts had reduced tumor burden (0.206 cm, ±0.21) compared to GD2-28Z CAR-Ts (0.903 cm, ±0.33, p=0.0449).

Conclusions: The overexpression of MMP-7 or OPN in second-generation CAR-Ts enhances CAR-T infiltration in vitro, and the expression of these genes does not impair CAR-T expansion, phenotype or cytotoxicity. The overexpression of OPN in GD2-28Z CAR-T enhances tumor clearance in a xenograft model of neuroblastoma, and may increase overall survival.

Citation Format: Stacey N. Van Pelt, Bilal Omer, Lindsay Talbot, Cliona Rooney, Rohan Fernandes, Candise Tat, Mark White. Tunneling CARs: Gene modifications to enhance CAR-T infiltration into solid tumors [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 42.
Abstract 423: Cell state-specific genomics to define plasticity along the epithelial-mesenchymal transitioncontinuum
Authors: Williams Destinee K. , Hou Nicholas
Published: March 2024

The epithelial-to-mesenchymal transition (EMT) is a biological process that allows epithelial cells to convert into a mesenchymal phenotype, acquiring increased mobility and the capacity to migrate. EMT has historically been represented as binary states; however, a growing consensus supports an EMT continuum involving multiple intermediate stable states. While we lack a comprehensive understanding of the EMT continuum, several reports indicate that the late stable states lead to optimal stem cell traits for cancer. In addition, it has been suggested that EMT heterogeneity within tumor cell populations is associated with poor patient prognosis. Hence, there is a clear need to define the genetic drivers of EM plasticity in heterogeneous cell populations along the EMT continuum. To fulfill this need, we will collect and analyze single cell RNA sequencing (scRNA-seq) data from EMT-cell-state specific genetic CRISPR screens on EMT-heterogeneous cell populations. Here, we apply a series of cloning techniques including polymerase chain reaction and Gibson ligation to engineer an adeno-associated virus (AAV) plasmid containing the avian TVA receptor gene under control of the N-cadherin promoter. Since N-cadherin is predominantly expressed in mesenchymal cells, this AAV enables us to generate cell lines that will exclusively express the TVA receptor when in a mesenchymal state. Consequently, we will be able to deliver mesenchymal-specific CRISPR gene edits via an avian retrovirus-derived RCAS system.

Citation Format: Destinee K. Williams, Nicholas Hou. Cell state-specific genomics to define plasticity along the epithelial-mesenchymal transitioncontinuum [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 423.
Abstract 4242: Preserving lung cancer patient mutations in 3D organoid models: Advancing cancer research through innovative culture systems
Authors: Park Ji-yeon , Gu Seo Rin , Lee Jiyeon , Lee Na-Gyeong , Choi Dojin , Park Sang Eun , Kim Ji Min , Rheey Jinguen
Published: March 2024

Lung cancer is one of the most prevalent cancers worldwide. There are currently many anticancer drugs available, but they have numerous issues in terms of treatment, such as drug resistance and recurrence. Culturing systems that can replace a patient's cancer tissue are crucial, and the existing 2D culturing systems have many limitations. Patient-derived cancer organoid culture is the most advanced culture system for understanding mechanism of cancers. Using a 3D organoid culture system, we have successfully established a culture system for lung cancer using biopsy/surgical specimens and malignant effusions, including a long-term culture system. There are two critical indicators to determine the success of 3D organoid culture. One is whether the organoids retain their cancer-specific mutations from patient’s lung cancer tissue, and the second is whether the organoids grow well and can be maintained in long-term culture for more than 20-30 passages. We typically assess gene mutations in EGFR, ALK, ROS, and P53 when evaluating lung cancer organoids. We confirm these mutations when we establish organoids. and currently we have established a total of 127 patient-derived lung cancer organoids. Among the 127 organoids, we completed NGS analysis on 108 of them and validated that 86.5% exhibit similarity when compared to lung cancer tissues. Additionally, we achieved a 100% retention of mutations in the long-term culturing of these organoids. Our studies indicate that patient-derived lung cancer organoids represent a meaningful organoid system for cancer tissue replacement and treatment response in the context of precision cancer medicine.

Citation Format: Ji-yeon Park, Seo Rin Gu, Jiyeon Lee, Na-Gyeong Lee, Dojin Choi, Sang Eun Park, Ji Min Kim, Jinguen Rheey. Preserving lung cancer patient mutations in 3D organoid models: Advancing cancer research through innovative culture systems [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 4242.
Abstract 4280: Regulatory T cells contribute to tumor cell dissemination by extracellular matrix remodeling
Authors: Garcia-Santillan Ailen , Lichtenberg Jessanne Y. , Shen He , Dozmorov Mikhail G. , Olex Amy L. , Hwang Priscilla Y. , Bos Paula D.
Published: March 2024

Regulatory T (Treg) cells function to enforce peripheral tolerance and are potent suppressors of tumor immunity. In breast cancer, we have shown that Treg cells promote tumor growth by favoring alternative activation of macrophages via suppression of IFN-γ. The tumor-associated extracellular matrix (ECM) is a key regulator of metastatic dissemination and is emerging as a critical regulator of tumor immunity. However, the reciprocal effects of the immune system on the ECM remain elusive. Using murine in vivo, ex vivo and bioengineering models we describe Treg cell-dependent changes in the tumor ECM that facilitate tumor cell movement and metastatic dissemination. Further, Treg cell-dependent matrisome signatures correlate with survival in human breast cancer samples. This work underscores a previously unrecognized role of Treg cells on the ECM that facilitates metastasis and is consistent with tissue Treg cell emergent function as critical regulators of tissue repair and cancer.

Citation Format: Ailen Garcia-Santillan, Jessanne Y. Lichtenberg, He Shen, Mikhail G. Dozmorov, Amy L. Olex, Priscilla Y. Hwang, Paula D. Bos. Regulatory T cells contribute to tumor cell dissemination by extracellular matrix remodeling [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 4280.
Abstract 4307: Quantifying the cell-intrinsic and cell-extrinsic growth effects of cancer-causing mutations in vivo
Authors: McFarland Christopher Dennis , Maltas Jeff
Published: March 2024

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 < 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 4311: The interplay of SYNCRIP deficiency, APOBEC activity, and extrachromosomal DNA in castration-resistant prostate cancer drug resistance
Authors: Li Xiaoling , Deng Su , Wang Choushi , Wang Yunguan , Mu Ping
Published: March 2024

Background: Prostate cancer, particularly in its castration-resistant form (CRPC), frequently develops resistance to androgen receptor (AR)-targeted therapies. This resistance involves complex factors, including tumor mutational burden and heterogeneity. APOBEC proteins, associated with mutagenesis and DNA damage, are implicated in this process. Our study centers on SYNCRIP, a key regulator of APOBEC activity, and investigates its influence on extrachromosomal DNA (ecDNA) in CRPC. Objective: This research aims to explore how SYNCRIP deficiency leads to increased APOBEC activity, and to examine its possible implications for ecDNA formation and its contribution to drug resistance and tumor heterogeneity in CRPC.

Methods: Genomic and transcriptomic analyses, such as whole exome sequencing and single-cell RNA-seq, were performed on CRPC cell lines and patient-derived samples, with an emphasis on SYNCRIP-deficient models. The study focused on understanding the relationship between elevated APOBEC activity due to SYNCRIP deficiency and potential ecDNA changes, evaluating their effect on AR-targeted drug sensitivity and overall tumor behavior.

Results: SYNCRIP was identified as a critical factor in resistance to AR therapy in both in vitro and in vivo models. Its deficiency resulted in increased therapy resistance and amplified APOBEC-mediated mutagenesis. Functional CRISPR screening identified eight key drivers of resistance in SYNCRIP-deficient tumors. Single-cell RNA sequencing revealed APOBEC-driven mutagenesis as a key factor in promoting intratumoral heterogeneity and resistance. Notably, in SYNCRIP-deficient CRPC samples, increased APOBEC activity and significant DNA damage were observed, prompting an investigation into a possible correlation between resistance and ecDNA presence.

Conclusion: The study uncovers a significant link between SYNCRIP deficiency and increased APOBEC activity in CRPC. While it also hints at a potential connection with ecDNA alterations, further research is necessary to establish this relationship firmly. This interplay contributes to the complexity of drug resistance in CRPC, highlighting the need for novel therapeutic targets. The dynamics among SYNCRIP, APOBEC activity, and ecDNA offer valuable insights into the molecular underpinnings of therapy resistance in prostate cancer, suggesting new directions for treatment strategies.

Citation Format: Xiaoling Li, Su Deng, Choushi Wang, Yunguan Wang, Ping Mu. The interplay of SYNCRIP deficiency, APOBEC activity, and extrachromosomal DNA in castration-resistant prostate cancer drug resistance [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 4311.
Abstract 437: Hydrogen sulfide switches the glucose metabolism through sulfhydration on pyruvate kinase M2
Authors: Chien Po-Chen , Wang Rong-Hsuan , Chen Pin-Ru , Chen Yue-Ting , Chen Yi-Chang , Chu Yu-Hsin , Chien Chia-Chen , Lo Shao-Yun , Wang Zhong-Liang , Tsou Min-Chen , Chen Ssu-Yu , Chiu Guang-Shen , Chen Wen-Ling , Wu Yi-Hsuan , Wang Hui-Ching , Lin Shu-Yi , Wang Wen-Ching , Kung Hsing-Jien , Wang Lu-Hai , Cheng Hui-Chun , Lin Kai-Ti
Published: March 2024

Cancer cells reprogram their glucose metabolism from oxidative phosphorylation to aerobic glycolysis. This metabolic transformation is partly based on the activity alterations of a rate limiting enzyme known as the pyruvate kinase M2 (PKM2), which is responsible for the conversion of phosphoenolpyruvate (PEP) into pyruvate. Attributed to its critical regulatory role. PKM2 is recognized as the pivotal enzyme in cancer glucose metabolism By reducing the enzyme activity of PKM2, cancer cells attain a greater fraction of glycolytic metabolites for macromolecule synthesis needed for rapid proliferation. Hydrogen sulfide (H2S), an endogenously produced gasotransmitter that acts as a critical mediator in multiple physiological processes, modifies proteins mainly through the persulfide (-SSH) bond formation, which is called sulfhydration. Our preliminary study demonstrates that H2S stimulates PKM2 sulfhydration at multiple cysteine residues, including cysteine 326, leading to the destabilization of active tetrameric PKM2 form into dimers or monomers. The PKM2 dimer/monomer further translocates into the nucleus to simulate the activation of glycolytic related genes. Blocking PKM2 sulfhydration at cysteine 326 through amino acid mutation stabilizes PKM2 tetramer and crystal structure further indicates that the tetramer organization of PKM2C326S is different from the currently known T or R states, revealing PKM2C326S as a newly identified intermediate form. Blocking PKM2 sulfhydration at cysteine 326 inhibited cell proliferation and tumor growth in xenograft mouse model. In summary, our current study illustrates that H2S-mediated sulfhydration induces the dissociation of the PKM2 tetramer, resulting in the reduced PKM2 activity and subsequently inhibits breast cancer cell proliferation and tumor growth. Targeting the sulfhydration site of PKM2 emerges as a promising therapeutic target specific for cancer metabolism.

Citation Format: Po-Chen Chien, Rong-Hsuan Wang, Pin-Ru Chen, Yue-Ting Chen, Yi-Chang Chen, Yu-Hsin Chu, Chia-Chen Chien, Shao-Yun Lo, Zhong-Liang Wang, Min-Chen Tsou, Ssu-Yu Chen, Guang-Shen Chiu, Wen-Ling Chen, Yi-Hsuan Wu, Hui-Ching Wang, Shu-Yi Lin, Wen-Ching Wang, Hsing-Jien Kung, Lu-Hai Wang, Hui-Chun Cheng, Kai-Ti Lin. Hydrogen sulfide switches the glucose metabolism through sulfhydration on pyruvate kinase M2 [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 437.
Abstract 4382: PKC-ι/ζ signaling is crucial for apoptosis/pyroptosis inhibition and invasiveness of glioblastoma cells through upregulation of β-catenin, PDK1/Akt1 and Smad cascades via 14-3-3
Authors: Lajmi Luke , Ratnayake Wishrawana S. , Khalid Khandker M. , Breedy Sloan , Todman Aaron , Smalley Tracess , Apostolatos Christopher A. , Hill Robert , Acevedo-Duncan Mildred
Published: March 2024

Glioblastoma (GB) is an aggressive form of brain cancer derived from astrocytes. Poor predictability of patient outcomes has limited the development of current therapeutic treatments of GB mainly due to the development of drug resistance. Comparative over-expression of atypical protein kinase C-iota and zeta (aPKC-ι/ζ) in GB cells and tissue samples were previously reported. This study establishes the downstream effects of PKC-ι/ζ attenuation on key cellular signaling which governs apoptosis, pyroptosis, survival, proliferation and epithelial-mesenchymal transition (EMT). Our data suggested that aPKC knockdown of expression induces apoptosis and works as an antecedent of pyroptosis. Data also suggested that involvement of Akt1 and PDK1 in aPKC maturation process weakened due to aPKC attenuation. aPKC attenuation downregulated Ras/Erk1 and canonical β-catenin pathways which resulted in reduced transcriptional activities of Stat3, c-Myc, c-Jun and β-catenin. In addition SNAIL1, SLUG, and PRRX1 were diminished that have been known to stimulate EMT. Proteins 14-3-3 and Smad2/3 acted as molecular adaptors between these pathways. A PKC-ι specific inhibitor 5-amino-1-(2,3-dihydroxy-4-(hydroxymethyl)cyclopentyl)-1H-imidazole-4-carboxamide (ICA-1S) and a PKC-ζ specific inhibitor 8-hydroxy-1,3,6-naphthalenetrisulfonic acid (ζ-Stat) were used to conduct in-vivo experiments using mouse models. Intravenous and oral administration of ICA-1S resulted in the reduction of tumor growth by approximately 30% in athymic nude mice for U-87 xenografts. Taken together, these results suggest that not only do aPKCs play a central role in GB progression, invasiveness, and cell survival, but that effective therapeutics can be developed to specifically target oncogenic aPKCs.

Citation Format: Luke Lajmi, Wishrawana S. Ratnayake, Khandker M. Khalid, Sloan Breedy, Aaron Todman, Tracess Smalley, Christopher A. Apostolatos, Robert Hill, Mildred Acevedo-Duncan. PKC-ι/ζ signaling is crucial for apoptosis/pyroptosis inhibition and invasiveness of glioblastoma cells through upregulation of β-catenin, PDK1/Akt1 and Smad cascades via 14-3-3 [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 4382.
Abstract 4411: Enhancing scalability and consistency in clinical multiomics via an optimized fixed cell ATAC-seq method​
Authors: Winders Dafne Alves , Graham Riley , Mao Xiangying , De Vito Ilaria , O'Hara Andrea , Turner Laure , Latif Haythem
Published: March 2024

ATAC-seq has an emerging role in decoding mechanisms of gene regulation, offering valuable insights into pathology and treatment response in disease models. However, clinical adoption of ATAC-seq methods has been limited by logistical hurdles, including time-sensitive processing of fresh samples and compromised viability of cryopreserved cells. These constraints, compounded by changes in open chromatin regions (OCRs) following cryopreservation, introduce unintended bias and pose significant obstacles for the translational impact of ATAC-seq experiments. ​

Here, we introduce an optimized fixed-cell ATAC-seq approach to overcome these limitations and unlock new sample types for ATAC-seq analyses. Our solution improves and simplifies the workflow from sample collection to clinical deliverable. This method enables ATAC-seq investigation of a diverse range of samples and facilitates the execution of complex experimental designs, including time course studies and high throughput screening.​To demonstrate the effectiveness of this method, we compared our optimized fixed-cell method with traditional ATAC-seq preparations in both fresh and cryopreserved GM12878 cells in parallel. Human GM12878 cell line was obtained from Coriell Institute for Medical Research5. Remarkably, we observed consistent genome-wide patterns of OCR enrichment at key regulatory elements across the three sample preparation methods. We observed consistent OCR enrichment across the promoter region of known highly-expressed B-cell genes including CD48 and LCP1, underscoring this assay’s ability to detect chromatin changes at key genes in human disease models. ​

To investigate the potential for multiomic analysis using this method, we prepared RNA-seq libraries from fixed-cell samples in parallel to ATAC-seq. We observed significantly elevated gene expression related to B-cell function and B-cell diseases, demonstrating our method’s compatibility with RNA-seq data collection and integration. This optimized fixed-cell ATAC-seq approach offers enhanced scalability and consistency over conventional methods and presents new opportunities for the multiomic analysis of chromatin and transcriptional activity genome-wide from a single sample in both clinical and research settings.

Citation Format: Dafne Alves Winders, Riley Graham, Xiangying Mao, Ilaria De Vito, Andrea O'Hara, Laure Turner, Haythem Latif. Enhancing scalability and consistency in clinical multiomics via an optimized fixed cell ATAC-seq method​ [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 4411.
Abstract 4415: Utilization of MBD-seq to elucidate differentially methylated regions in cfDNA across healthy and cancer patients
Authors: Michelon Camille , Egan Brian , Delatte Benjamin
Published: March 2024

5-Methylcytosine (5-mC) is the most abundant epigenetic DNA modification in eukaryotes. The presence of 5-mC alters gene expression and genome metabolism, and its deregulation is associated with many human diseases. Cell-free DNA (cfDNA) released from apoptotic cells has recently gained attention, as mutations or epimutations (e.g. 5-mC variations) detected in cfDNA were shown to have high diagnostic potential to assess the presence, stage and outcome of several cancers. However, 5-mC detection in cfDNA remains a challenge as input material is often very scarce. MBD-Seq is a method that leverages the ability of Methyl-CpG-binding domain protein 2 (MBD2) to capture and detect highly methylated regions of DNA genome-wide. We evaluated MBD-Seq for the detection of aberrant methylation patterns in cfDNA from healthy and diseased patients. We found MBD-seq on cfDNA to be specific (over 100-fold mC:C detection ratio) and sensitive (5 ng of input cfDNA). Applying MBD-seq to samples from healthy vs colorectal and breast cancer patients showed striking differences in methylation of key tumor-associated genes. Hence, MBD-Seq can elucidate aberrant methylation patterns from cfDNA, highlighting its potential as a diagnostics tool for the detection of cancer.

Citation Format: Camille Michelon, Brian Egan, Benjamin Delatte. Utilization of MBD-seq to elucidate differentially methylated regions in cfDNA across healthy and cancer patients [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 4415.
Abstract 4435: Taurine metabolism as a marker for pancreatic cancer
Authors: Nam Hoonsik , Lee Woohyung , Nguyen Ha T. , Mai Linh X. , Kim Song Cheol , Park Sunghyouk
Published: March 2024

Pancreatic ductal adenocarcinoma (PDAC), known for its aggressive nature and poor prognosis, presents a significantly altered metabolic landscape compared to normal pancreatic tissue, a feature that has been the focus of recent research but remains underexplored in actual pancreatic tissues. In this study, we undertook an untargeted metabolomics analysis to compare the metabolic profiles of PDAC with matched normal tissues, revealing a notable elevation in taurine levels in PDAC. This increase was further validated through immunohistochemistry in separate PDAC and normal tissue samples. To delve deeper, we conducted a comprehensive bioinformatics analysis, integrating transcriptomic and proteomic data, which identified the taurine metabolism pathway as significantly altered, with ADO emerging as a pivotal gene in this process. Further investigations, including gene modulation and xenograft models, demonstrated that ADO knockdown curtails cancer cell proliferation and tumor growth, potentially impacting the Raf-MEK-ERK signaling pathway. Clinically, the ADO-Taurine axis was found to have substantial prognostic significance, correlating with recurrence rates and survival in PDAC patients. These insights collectively suggest that the ADO-Taurine axis, through its modulation of taurine metabolism, presents as a promising biomarker for PDAC prognosis and a potential avenue for therapeutic development.

Citation Format: Hoonsik Nam, Woohyung Lee, Ha T. Nguyen, Linh X. Mai, Song Cheol Kim, Sunghyouk Park. Taurine metabolism as a marker for pancreatic cancer [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 4435.
Abstract 4463: Metabolic reprogramming through Notch1 signaling promotes a survival advantage in pancreatic neuroendocrine tumor cells
Authors: Guenter Rachael , Chen Weisheng , Herring Brendon , Golivi Yuvasri , Sammy Melissa , Whitt Jason , Jaskula-Sztul Renata , Chen Herbert , Rose J. Bart
Published: March 2024

Background: Cancer cells utilize both oxidative phosphorylation (OXPHOS) and glycolysis to generate energy. Switching between OXPHOS and glycolysis can promote tumor progression. The mechanisms governing oncogenic metabolic reprogramming are largely unknown, but recent data has suggested that Notch1 dysregulation in cancer cells can contribute to altered metabolic phenotypes. We hypothesized that Notch1 signaling supports metabolic reprogramming in pancreatic neuroendocrine tumor (pNET) cells.

Methods: We established a Notch1-knockout pNET cell line (BON-N1-KO) by deleting Notch1 at exon 3 in a pNET cell line (BON) using CRISPR/Cas9. Proliferation over time was measured using a trypan blue exclusion test. Seahorse Glycolytic Rate Assay and Mitochondria Stress Test were used to measure the glycolytic and mitochondrial activities of cells. A glycolysis deprivation assay was employed to determine cell viability at varying glucose concentrations. Single end RNAseq was performed using the Illumina NGS platform, to a read depth of 50M.

Results: Over time, pNET cells lacking Notch1 (BON-N1-KO) proliferated slower than wildtype (WT) cells (p=0.034). Compared to WT BON, the BON-N1-KO cells had reduced basal oxygen consumption rate (28.2 ± 1.3 vs. 40.7 ± 1.4; p=0.02, ATP production (21.9 ± 1.0 vs. 29.6 ± 0.98; p=0.04), and maximal respiration (39.4 ± 1.7 vs. 63.7 ± 2.1; p=0.004). BON-N1-KO cells also had a reduction in basal glycolysis, as measured by proton efflux rate, compared to WT (48.7 ± 2.6 vs. 57.7 ± 6.2; p=0.2). To further test metabolic reprogramming, WT and BON-N1-KO cells were starved of glucose (0mM), compared to normal glucose (17.5mM) and viability was measured over time. By day 5, the BON-N1-KO group had a viability of 0%, whereas 12.8% of WT cells were alive (p=0.038). To determine if Notch1 loss was associated with altered expression of established metabolic genes, we performed RNAseq. Differential gene expression analysis found that OXPHOS-related genes (UQCC2, COX15, COX20) and glycolysis-related genes (Slc1a1, Slc2a4, Hk1, Hk2) were significantly down-regulated in BON-N1-KO cells.

Conclusions: Our study shows that Notch1 signaling facilitates metabolic reprogramming as a survival advantage in pNET cells. Targeting Notch1 signaling to mediate cellular metabolism may be a novel therapeutic strategy in pNETs.

Citation Format: Rachael Guenter, Weisheng Chen, Brendon Herring, Yuvasri Golivi, Melissa Sammy, Jason Whitt, Renata Jaskula-Sztul, Herbert Chen, J. Bart Rose. Metabolic reprogramming through Notch1 signaling promotes a survival advantage in pancreatic neuroendocrine tumor 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 4463.