bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB279: The combination therapy with B7-H3 antibody drug conjugates for effective radiation treatment
Authors: Son Gawon , Ju Eunjin , Park Jin , Shin Seolhwa , Ko Eunjeong , Kwon Miri , Lee Hyewon , Seo Beomseok , Lee Sangkwang , Park Seoksoon , Jeong Seongyun , Song Siyeol , Choi Eunkyung
Published: April 2024

Purpose: Antibody-drug conjugate (ADC) is a promising treatment modality because it enables effective tumor-specific delivery of anticancer drugs by targeting cancer antigens with antibodies. By using ADC, each treatment can be used at an optimal dose, thereby minimizing side effects, and maximizing treatment effects. The ADC used in this experiment targets B7-H3, and the B7-H3 protein is highly expressed in various cancer types. Recent studies have shown that B7-H3 is increased by radiation in various cancer cells. This study aims to demonstrate the efficacy of the B7-H3 ADC and confirm its combined effect with radiotherapy.

Method: In vitro, colony forming assay, CCK-8 assay, FACs and western blotting were performed in JIMT-1 and HCT116 cell lines. In vivo, JIMT-1, HCT116 and Colon PDX models were developed to monitor tumor growth and survival rate. Biodistribution was performed through the IVIS (In Vivo Imaging System) spectrum.

Result: The B7-H3 ADC used in the experiment was developed by combining DUBA as a toxin with anti-B7-H3 antibody In in vitro experiments, the combined treatment of radiation and B7-H3 ADC reduced cell viability via apoptosis more effectively than treatment alone. In the in vivo mouse models, we observed that the combined treatment of radiation and B7-H3 ADC was more effective in inhibiting tumor growth than the single treatment groups. The survival rate of the mice was also improved when the radiation was combined with B7-H3 ADC treatment compared to the other treatment groups alone. In the biodistribution results, the accumulation of B7-H3 ADC-Cy7 was further enhanced when irradiated.

Conclusion: The results show that B7-H3 ADC can be used as a promising therapeutic agent and the combined treatment with radiation can obtain an improved anticancer effect than the single treatment, suggesting another cancer treatment method.

Citation Format: Gawon Son, Eunjin Ju, Jin Park, Seolhwa Shin, Eunjeong Ko, Miri Kwon, Hyewon Lee, Beomseok Seo, Sangkwang Lee, Seoksoon Park, Seongyun Jeong, Siyeol Song, Eunkyung Choi. The combination therapy with B7-H3 antibody drug conjugates for effective radiation treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB279.
Abstract LB289: Single-cell CRISPR screens at scale to understand T cell biology
Authors: Untermoser Nicole , Irnstorfer Johanna , Vasilyev Anatoly , Vinko Nikola , Pawar Sumit , Loregger Anke , Krejci Adam , Schmidt Henrik , Bürckstümmer Tilmann
Published: April 2024

CRISPR screens have become the primary discovery engine in modern biology and are widely used to uncover novel targets in immuno-oncology. However, these genetic screens are usually coupled to rather simplistic read-outs such as cell fitness. In contrast, CROP-Seq (or “CRISPR Droplet” Sequencing) screens combine CRISPR perturbation with single-cell transcriptomics, enabling high-content phenotyping at single-cell resolution. Briefly, cells are perturbed with a pooled sgRNA library and transcriptomic profiles of each cell are recorded using conventional single-cell RNA sequencing platforms. Currently, the scale of these screens is limited to the perturbation of a couple of hundred genes, possibly up to 1.000 genes, because of increased costs for single-cell library preparation and next generation sequencing (NGS). At Myllia, we have built a platform allowing high-content CROP-Seq screens in both CRISPR-ready cancer cell lines as well as primary immune cells, e.g., human T cells. Using CRISPR KO, CRISPR interference or CRISPR activation workflows, we can help accelerate the identification of target genes and regulatory networks involved in immuno-oncology. Primary T cells are of great interest in the immunotherapy community as they are key players in autoimmune and inflammatory disease. Engineered T-lymphocytes such as CAR-T cells are currently developed as novel cellular medicines, yet many T cell-intrinsic features involved in CAR-T potency remain elusive. To enable the discovery of novel targets, we have performed multiple customized CROP-Seq CRISPR KO screens in primary human T cells investigating T cell stemness and effector phenotypes as well as CD4+ T helper cell differentiation towards Th1, Th2, or Th17 subsets. Here, we present screens for regulators of functional T cell plasticity and Th2 commitment in which we aimed to identify genes determining critical T cell fate decisions, potentially linking gene (dys)function to either autoimmune/inflammatory disease or functional persistence of cytotoxic T cells for cancer immunotherapy. Overall, the advanced CROP-Seq platform combining large-scale perturbations and targeted sequencing (TA) read-outs will catalyse a paradigm shift for CROP-Seq enabling high-throughput functional genomic screens that support the validation of drug targets in autoimmunity, inflammation and immuno-oncology.

Citation Format: Nicole Untermoser, Johanna Irnstorfer, Anatoly Vasilyev, Nikola Vinko, Sumit Pawar, Anke Loregger, Adam Krejci, Henrik Schmidt, Tilmann Bürckstümmer. Single-cell CRISPR screens at scale to understand T cell biology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB289.
Abstract LB295: Unsaturated fatty acid synthesis is associated with poor prognosis and is differentially regulated by MYCN and tumor suppressor microRNAs in neuroblastoma
Authors: Sheeter Dennis A. , Garza Secilia , Park Hui Gyu , Benhamou Lorraine-Rana , Badi Nikki R. , Espinosa Erika C. , Kothapalli Kumar , Brenna J. Thomas , Powers John T.
Published: April 2024

Dysregulated metabolism is a hallmark of cancer. While the role of glucose metabolism in cancer has been extensively studied, relatively little has been done to understand the role of poly-unsaturated fatty acids in cancer biology. To gain insight into their contribution to cancer progression we determined the expression patterns and outcome associations of both saturated and unsaturated fatty acid synthesis (UFAS) genes in pediatric neuroblastoma (NB), and fatty acid levels in NB cell lines derived from high-risk tumors. MYCN amplification and disruption of tumor suppressor miRNAs (TSmiR) function are central drivers of poor outcomes in NB. MYC, MYCN, and TSmiRs regulate glucose metabolism; however, their role in UFAS remains poorly understood. Using complementary analysis of publicly available genomic datasets and cultured NB cell measurements we examined the potential regulation of UFAS genes through MYCN and MYC activity and posttranscriptional regulation by TSmiRs. Here we show that de novo and UFAS pathway genes FASN, ELOVL6, SCD, FADS2, and FADS1 are upregulated in high-risk NB and are associated with poor prognosis. RNA-Seq analysis of eight human NB cell lines revealed parallel UFAS gene expression patterns. Consistent with this, we found that NB-related TSmiRs were predicted to extensively target these genes. Additionally, we observed that both MYC and MYCN upregulated UFAS pathway genes while suppressing TSmiR host gene expression, thereby creating a possible UFAS regulatory network between MYCN and TSmiRs in NB. Furthermore, using mass spectrometry analysis we found NB cells to be high in de novo synthesized omega 9 (ω9) unsaturated fatty acids and low in both ω6 and ω3. This finding provides a plausible means for NB to limit cell-autonomous immune stimulation and reactive oxygen species (ROS)-driven apoptosis from ω6 and ω3 unsaturated fatty acid derivatives, respectively. We propose a model in which the UFAS pathway, through novel regulation by MYCN and TSmiRs, plays a key role in neuroblastoma pathology with implications for other MYC-driven cancers.

Citation Format: Dennis A. Sheeter, Secilia Garza, Hui Gyu Park, Lorraine-Rana Benhamou, Nikki R. Badi, Erika C. Espinosa, Kumar Kothapalli, J. Thomas Brenna, John T. Powers. Unsaturated fatty acid synthesis is associated with poor prognosis and is differentially regulated by MYCN and tumor suppressor microRNAs in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB295.
Abstract LB297: Toll-like receptor 8 in tumor associated macrophages regulates miR-192-5p expression and drug resistance in neuroblastoma
Authors: Toldo Nicolo , Rodriguez Verena Martinez , Fabbri Muller
Published: April 2024

MicroRNAs (miRs) are small non-coding RNAs (ncRNAs) with gene expression regulatory functions. MiRs are frequently dys-regulated in human cancers and orchestrate the biology of the disease, and its resistance to chemotherapy. Increasing evidence supports a role of the tumor microenvironment (TME) in promoting cancer growth and resistance to treatments. Tumor Associated Macrophages (TAMs) are a predominant cellular component of the TME of several types of cancers, including neuroblastoma (NB), the most frequent pediatric extra-cranial solid tumor. NB cells secrete miRs within small extracellular vesicles called exosomes, and these miR are shuttled to surrounding TAMs. Our lab was the first to show that cancer-derived exosomal miRs bind to Toll-like receptor 8 (TLR8) in TAMs, triggering an NF-κB-dependent production of TAM-derived miRs, that are then shuttled back to NB cells. Following up on that discovery, we identified a signature of miRs that are up/down-regulated in NB cells when co-cultured with TAMs expressing TLR8 or in which the TLR8 had been deleted with CRISPR/Cas9 engineering. We identified miR-192-5p as significantly down-regulated in NB cells when co-cultured with wild-type TAMs, however miR-192-5p expression was significantly increased in NB cells when co-cultured with TLR8-knock out TAMs, supporting a TLR8-mediated modulation of miR-192-5p in the NB TME. Additionally, we found that over-expression of miR-192-5p in NB cells increased sensitivity of NB cells to temozolomide and cisplatin, two commonly used drugs in the treatment of this malignancy. Overall, these findings support the use of TLR8 inhibitors to up-regulate miR-192-5p and increase sensitivity of NB cells to chemotherapy.

Citation Format: Nicolo Toldo, Verena Martinez Rodriguez, Muller Fabbri. Toll-like receptor 8 in tumor associated macrophages regulates miR-192-5p expression and drug resistance in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB297.
Abstract LB303: Suppression of stress granule formation is a novel vulnerability imposed by mutant p53
Authors: Thoenen Elizabeth , Ranjan Atul , Parrales Alejandro , Nishikawa Shigeto , Dixon Dan , Oka Sugako , Iwakuma Tomoo
Published: April 2024

Mutation of the tumor suppressor p53 is the most common cancer specific event. Most of these mutations are missense mutations in the DNA-binding domain of p53, causing loss of wild-type p53 (wtp53) transcriptional activity. Missense mutant p53 (mutp53) also enhances cancer malignancy in a manner independent of wtp53. Hence, mutp53 is an ideal therapeutic target due to its uniqueness and high expression levels in cancers; however, directly targeting mutp53 protein itself has been challenging. To better understand the mechanism of oncogenic function of mutp53, we performed in silico TCGA database analysis and found that patients with missense mutp53-carrying hepatocellular carcinoma (HCC), but not other types of cancer, had unexpectedly better overall survival than patients with p53-null HCC. Since sorafenib (SOR) has historically been used as a single agent chemotherapy for HCC, unlike other cancer types, we hypothesized that SOR treatment may have yet unappreciated advantages for treating mutp53-expressing tumors. Indeed, knockdown of mutp53 rendered HCC cells and xenografts more resistant to SOR. Consistent with a report showing that SOR induces ER stress-mediated pro-survival stress granule (SG) formation, mutp53-expressing HCC cells, treated with SOR or other ER stress inducers, formed significantly fewer SGs with increased apoptosis, as compared with mutp53-knockdown cells. This result was partly due to mutp53’s ability to interact with an eIF2α kinase PERK and a key SG core protein, G3BP1. Moreover, the oligomerization domain of mutp53 was required for the interaction of mutp53 with G3BP1 and subsequent suppression of ER-stress-mediated SG formation and survival. These results suggest that inhibition of SG formation is a novel vulnerability imposed by mutp53, leading to sensitization of cancer cells to ER stress. Our results also emphasize the use of ER stress inducers to treat mutp53-expressing tumors and mutp53 as a biomarker of SOR sensitivity.

Citation Format: Elizabeth Thoenen, Atul Ranjan, Alejandro Parrales, Shigeto Nishikawa, Dan Dixon, Sugako Oka, Tomoo Iwakuma. Suppression of stress granule formation is a novel vulnerability imposed by mutant p53 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB303.
Abstract LB308: Transcriptional profiling uncovers a unified program underlying the human metastatic and adjacent microenvironments
Authors: Aber Etan R. , Contreras Cristina F. , Sikder Mohd Omar , Li Kathy P. , Forbes Greta E. , Gopalan Vishaka , Hannenhalli Sridhar , Kaplan Rosandra N.
Published: April 2024

Metastasis is the primary cause of death in patients with solid tumors, yet the treatment-refractory metastatic microenvironment is poorly characterized. To gain a comprehensive understanding of microenvironmental regulation of human metastasis, we performed single-cell RNA sequencing covering endothelial, stromal, myeloid, lymphoid, and malignant cells from 28 lung and liver samples of the metastatic microenvironment and metastasis-free adjacent microenvironment from patients with metastatic adrenocortical carcinoma compared to healthy donors for a total of 275,903 cells. We discovered that the adjacent microenvironment in patients with metastatic cancer is significantly different from healthy tissue without cancer: The adjacent microenvironment has many immunosuppressive and pro-tumorigenic features similar to primary tumor and metastatic tissue. As adjacent tissues are potential sites for subsequent metastasis, the shared changes between the adjacent and metastatic microenvironments suggest that these elements of the treatment-refractory metastatic microenvironment may dictate metastasis. Importantly, these pathologic features of the adjacent and metastatic microenvironments associate with poor outcomes for patients and may be targetable. Lastly, we identify a mechanism by which tumor cells may be remotely driving and coordinating these changes in both the metastatic and adjacent microenvironments. Taken together, our study identifies shared and microenvironment-specific changes underlying a global program of metastasis.

Citation Format: Etan R. Aber, Cristina F. Contreras, Mohd Omar Sikder, Kathy P. Li, Greta E. Forbes, Vishaka Gopalan, Sridhar Hannenhalli, Rosandra N. Kaplan. Transcriptional profiling uncovers a unified program underlying the human metastatic and adjacent microenvironments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB308.
Abstract LB314: Organ-specific roles of CD83+ macrophages in breast cancer
Authors: Singh Swarnima , Bado Igor
Published: April 2024

The purpose of this study is to understand how heterogeneity in organ-specific immune infiltrates can lead to Triple Negative Breast Cancer (TNBC) progression and immunotherapies resistance in metastasis. Both innate and adaptive immune responses are essential for breast cancer progression. Using single-cell multiplexing technology on human and murine models of primary and metastatic breast cancers, we investigated the pattern of immune cell infiltration in bone and lung metastases in a temporal manner. The parallel profiling of metastasis sites revealed a strong involvement of the innate immunity in restraining tumor progression with an acute increase in Mrc1+ Cd83+ tumor-associated macrophages at the early stage of lung colonization. Interestingly, the increase was modest in bone metastasis and remained consistent overtime despite bone metastasis progression. In contrast, we saw an increase in the number of Ly6G+ Lrg1+ granulocytes. Profiling of paired TNBC patient samples from the primary and metastatic sites have shown an immunologically quiescent tumor microenvironment in metastasis as compared to the primary tumors. Hence, to further explore the role of Mrc1+ Cd83+ macrophages on therapeutic resistance, we profiled the orthotopic claudin-low TNBC models, T11 and T12, following their exposure to chemotherapy. While responsive tumors displayed a decreased infiltration of Mrc1+ Cd83+ macrophages, the opposite phenotype was observed in non-responders, suggesting their involvement in tumor progression. Overall, our results suggest differential responses in untreated lung/bone metastases and primary tumors indicating divergent roles for Cd83+ TAMs in restraining or promoting tumor progression, while also indicating some crosstalk between neutrophils and stromal cells that aid in bone metastatic progression. These site-specific differences in immune cell phenotype indicate that there is a great need to thoroughly characterize the tumor immune compartment in both the primary and the metastatic setting to improve treatment responses. Considering the inhibitory effect of macrophages on T cells in these models, this study highlights a tissue-specific reprogramming of immune cells in breast cancer metastasis.

Citation Format: Swarnima Singh, Igor Bado. Organ-specific roles of CD83+ macrophages in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB314.
Abstract LB321: Identification of a novel mode of action and scaffold for modulation of cancer-associated fibroblast through Chip-seq analysis
Authors: Yeo So-Young , Farh Mohamed , Sohn InSuk , Kim Seok-Hyung , Lee Keun-Woo
Published: April 2024

Cancer microenvironment (CME) possess a crucial function in tumor mass, in which it control tumor growth, progression, metastasis, and even chemotherapy resistance. The CME is a complex and dynamic system that is an integral part of the entire tumor. Among the components of CME, in particular, CAFs promote cancer progression and directly stimulate cancer cell proliferation. Thus, targeting CAF would be a promising approach for the treatment of cancer. Looking at models of the evolution of CAFs during tumor progression, CAFs have heterogeneous and dynamic properties. Tumor progression may be associated with a decrease in the tumor inhibitory CAF/tumor supporting CAF ratio, with tumor inhibitory CAF occurring at the highest levels in early tumor stages in response to tumor emergence and gradually switching to tumor support CAFs towards tumor progression/metastatic process. In other words, in order to suppress solid tumors accompanied by desmoplastic stroma, it is necessary to regulate CAFs, a key component. We performed ChiP-seq using an antibody against H3k27ac with CAFs that have a strong ability to promote cancer and NFs that do not. As result, we identified a novel mode of action and scaffold (ARC2-002 and ARC2-003) for modulating CAF via suppressing CAF proliferation, contraction, and collagen deposition. Finally, through 3D co-culture, we confirmed that the two novel scaffolds had excellent anticancer effects when administered alone as well as in combination with an existing anticancer drug. The compounds identified in this study may represent a new therapeutic agent targeting fibroblasts with abnormal activation, and their efficacy may be increased when combined with existing anticancer drugs.

Citation Format: So-Young Yeo, Mohamed Farh, InSuk Sohn, Seok-Hyung Kim, Keun-Woo Lee. Identification of a novel mode of action and scaffold for modulation of cancer-associated fibroblast through Chip-seq analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB321.
Abstract LB332: Spatial transcriptomic and proteomic analysis of the treatment resistant slow cycling micro environment in GBM
Authors: Chakraborty Avirup , Feier Diana , Silver Aryeh , Yang Changlin , Anica Miruna , Pittu Avinash , Sobanjo Olusegun , Hodge Ethan , Engelbart Mia , Von Roemeling Christina , Rahman Maryam , Sarkisian Matthew , Huang Jianping , Harrison Jeffrey , Mitchell Duane , Deleyrolle Loic
Published: April 2024

Within the Glioblastoma (GBM) microenvironment, there are micro-niches originating from independent lineages of cancer stem cells with distinct metabolic requirements that are characterized by Fast cycling cells (FCCs) and Slow cycling cells (SCC). The FCCs employ aerobic glycolysis for energy, while the treatment-resistant SCCs primarily rely on lipid metabolism. Our study allows for the molecular and spatial decoding of the heterogeneity within the GBM microenvironment, with a specific focus on decoding the dichotomy of the immune infiltrates and studying the interactions between the SCCs and the immune compartment in human GBM patients. Our research reveals a new paradigm of interaction within the tumor microenvironment (TME) of glioblastoma (GBM) patients, in which SCCs are instrumental in altering the tumor milieu to favor immune suppression. These SCCs actively recruit and harness sub-population of immune cells of myeloid origin that promote tumor growth and simultaneously provide metabolic aid to these treatment-resistant cells. Our research maps out the intricate metabolic dialogues within GBM and evaluates the potential therapeutic effect of disrupting this interaction to open up new treatment avenues. The findings based on our spatial transcriptomic and proteomic study on brain biopsies from human patients provide a deeper understanding of the critical links among the tumor's local environment, cellular metabolism, anti-tumor immunity, and potential treatment vulnerabilities. In summary, our investigation offers novel insights into how metabolic exchanges contribute to the evolution of GBM leading to the development of drug and immune resistant GBM. Our data is suggestive that therapies aimed at these metabolic interactions, especially those between SCCs and metabolically supporting immunosuppressive myeloid originating immune cells, hold potential as effective therapeutic strategy for GBM.

Citation Format: Avirup Chakraborty, Diana Feier, Aryeh Silver, Changlin Yang, Miruna Anica, Avinash Pittu, Olusegun Sobanjo, Ethan Hodge, Mia Engelbart, Christina Von Roemeling, Maryam Rahman, Matthew Sarkisian, Jianping Huang, Jeffrey Harrison, Duane Mitchell, Loic Deleyrolle. Spatial transcriptomic and proteomic analysis of the treatment resistant slow cycling micro environment in GBM [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB332.
Abstract LB365: Generation of a novel severely immunodeficient Sprague Dawley rat model for xenograft studies
Authors: Nie Yanhui , Zhang Meiqi , Zhong Wanling , Feng Jia , Huwatibieke Bahetiyaer , Yu Zhaoxue
Published: April 2024

The recombinant-activating gene 2 (Rag2) plays a critical role in the recombination of the immunoglobulin and T cell receptor genes during the maturation of T and B cells. Loss of Rag2 protein leads to a lack of functional T and B cells, which eliminates the adaptive immune response. However, Rag2 deficiency alone may not guarantee the success of xenograft implantation, due to NK cells and other innate cells remaining. Il2rg is a key component of several cytokine receptors involved in differentiation and/or function of numerous adaptive and innate immune cells, including NK cells, mast cells, basophils, and dendritic cells. To generate a more severely immunodeficient rat model, both the Rag2 and Il2rg genes were knocked out in Sprague Dawley (SD) rats; this model was termed B-SDG rats. The immune profile and organ weights of thymus and spleen were investigated in B-SDG rats in comparison with Rag2-/- and wild-type SD rats. The spleen weights of both Rag2-/- and B-SDG rats were similar, but significantly reduced compared to wild-type SD rats. Notably, the thymus weights of B-SDG male rats were significantly smaller than those of Rag2-/- males. The immune cell profiles in thymus, spleen and blood were next evaluated by flow cytometry. A complete lack of B and T cells was observed in both Rag2-/- and B-SDG rats. B-SDG rats lacked CD161+ NK cells in the spleen and blood, which were maintained in Rag2-/- rats. Dendritic cells, monocytes, macrophages, and neutrophils were detected in all strains. In vivo xenograft implantation with human lung, bladder, breast, pancreas, acute monocytic and myelomonocytic leukemia tumor cell lines was next evaluated in B-SDG rats, which demonstrated successful engraftment. Furthermore, several efficacy studies were performed in B-SDG rats, including cisplatin chemotherapy on human breast invasive ductal carcinoma cell (HCC1954) and human large cell lung cancer cell (NCI-H460) xenografts, and a HER2-targeting ADC therapy was tested in B-SDG rats harboring human non-small cell lung cancer tumors (NCI-H1975). Taken together, these data confirm that B-SDG rats provide a powerful immunodeficient model for preclinical in vivo evaluation of novel drug candidates.

Citation Format: Yanhui Nie, Meiqi Zhang, Wanling Zhong, Jia Feng, Bahetiyaer Huwatibieke, Zhaoxue Yu. Generation of a novel severely immunodeficient Sprague Dawley rat model for xenograft studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB365.
Abstract LB376: Tirzepatide inhibits tumor growth in mice with diet-induced obesity
Authors: Pollak Michael N. , Zeng Jibin , Huang Linxuan , Wang Ye , Rahbani Janane , Kazak Lawrence
Published: April 2024

Tirzepatide, a drug used in management of type II diabetes, is an activator of both glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide 1 (GLP-1) receptors. Tirzepatide treatment leads to weight loss in murine models of obesity, and clinical trials have shown the drug can achieve ∼ 20% weight loss in obese patients. Obesity has been shown to increase risk and/or to worsen prognosis of certain common cancers, including colon cancer, but the effect of tirzepatide on neoplasia has not been examined in detail. We studied the effects of this drug on mouse weight and energy balance and on the murine MC38 colon cancer model, which was previously shown to exhibit accelerated growth in hosts with diet-induced obesity. Tirzepatide led to substantial reductions in food intake, to reduced adipose tissue mass, and to significant decreases in circulating levels of insulin and leptin. Tirzepatide did not cause tumor regression, but reduced tumor growth rates by ∼ 50%. Tirzepatide had no effect on MC38 cancer cell proliferation in vitro, and the effect of tirzepatide on tumor growth in vivo could be phenocopied in placebo treated mice simply by restricting food intake to the amount consumed mice receiving the drug. This provides evidence that the drug acts indirectly to inhibit tumor growth. Our findings raise the possibility that use of tirzepatide or similar agents may benefit patients with obesity-related cancers.

Citation Format: Michael N. Pollak, Jibin Zeng, Linxuan Huang, Ye Wang, Janane Rahbani, Lawrence Kazak. Tirzepatide inhibits tumor growth in mice with diet-induced obesity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB376.
Abstract LB379: HLA-DQB1*05:02: An independent genetic marker for oral cavity squamous cell carcinoma susceptibility
Authors: Huang Shiang-Fu , Chien Huei-Tzu , Young Chi-Kuan , Lee Yun-Shien , Liao Chun-Ta , Cho Kai-Lun , Chen Ching-Han
Published: April 2024

Environmental exposure to carcinogens causes mucosal damage in the upper aerodigestive tract, which can lead to cancers. The genetic basis of head and neck cancer is controversial. To identify susceptibility genes in head and neck cancers, we enrolled patients with early-onset disease in Taiwan. This case-control study included 54 young male patients with oral squamous cell carcinoma (OSCC) who were treated between March 1996 and December 2016, as well as 2,400 healthy controls. A single-nucleotide polymorphism (SNP) array was used to determine genetic loci that increase susceptibility to OSCC. Sequencing-based typing (TBG Biotechnology Corp., Taipei, Taiwan) was used to determine the HLA-DQB1 genotype in another cohort of 147 OSCC patients. We analyzed the allele frequencies of 664,994 autosomal SNPs in the 54 OSCC cases. In a genome-wide association analysis, four SNPs within loci on chromosomes 6, 7, 9, and 12 were significantly different between OSCC patients and controls (corrected P < 1.0 × 10−6). HLA-DQB1 was closest to rs28451423 on chromosome 6. HLA-DQB1*05:02 in OSCC (18.5%) was significantly different from normal population (7.0%) (P = 0.009). The influence of disease onset was independently significant after adjusting cigarette smoking, alcohol drinking and areca-quid chewing (P = 0.015, OR: 3.922, 95% confidence interval: 1.311 - 11.734). Furthermore, HLA-DQB1*05:02 was associated with early-onset OSCC (P = 0.004). HLA-DQB1*05:02 is associated with OSCC independent of environmental exposures. HLA-DQB1*05:02 is also related with early onset of OSCC. It provides evidence of a genetic basis for OSCC.

Citation Format: Shiang-Fu Huang, Huei-Tzu Chien, Chi-Kuan Young, Yun-Shien Lee, Chun-Ta Liao, Kai-Lun Cho, Ching-Han Chen. HLA-DQB1*05:02: An independent genetic marker for oral cavity squamous cell carcinoma susceptibility [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB379.
Abstract LB396: The power of NetraAI: Precision medicine in oncology through sub-insight learning from small data sets
Authors: Qorri Bessi , Tsay Mike J. , Leonchyk Paul , Alphs Larry , Pani Luca , Geraci Joseph
Published: April 2024

The capabilities of artificial intelligence (AI) and machine learning (ML) are pivotal for refining patient stratification and subtype discrimination in clinical trials. Conventional ML methods often rely on large data sets for meaningful discoveries. NetraAI is a novel ML approach designed and trained to work with smaller data sets. The challenge with smaller data sets is that they do not reflect the totality of the disease that they represent. NetraAI employs a novel approach termed “Sub-Insight Learning”, utilizing validated mathematical methods to analyze even small patient data sets. This allows the system to decompose the data sets into high and low confidence patient subpopulations, enhancing predictive model accuracy and reducing overfitting. Further, the system explains what variables are driving the etiology defining the subpopulations of patients. Using two non-small cell lung cancer (NSCLC) data sets (GSE18842 and GSE10245) consisting of only 104 samples from adenocarcinoma (ADC) and squamous cell carcinoma (SCC), NetraAI distinguished the two subtypes through unique genetic signatures. Notably, nine of the ten variables identified correlate with known NSCLC markers, with PIGX emerging as a novel target. Leveraging protein-protein interaction networks (PPI) revealed connections between PIGX and BACE1. BACE1 has been implicated as a driver of NSCLC brain metastasis. These findings shed light on the biology of membrane proteins and their post-translational modifications, a factor implicated in various diseases, prompting further exploration. NetraAI demonstrates a significant breakthrough in precision medicine for oncology, capable of generating meaningful insights from small data sets. The discovery of novel biomarkers and their implications in cancer and other diseases underline the potential of this AI-driven approach in advancing current research paradigms and patient-specific treatments.

Citation Format: Bessi Qorri, Mike J. Tsay, Paul Leonchyk, Larry Alphs, Luca Pani, Joseph Geraci. The power of NetraAI: Precision medicine in oncology through sub-insight learning from small data sets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB396.
Abstract LB404: ATR inhibitors synergize with DHFR inhibitors in rhabdomyosarcoma cells by disrupting DNA damage checkpoint
Authors: Jo Ukhyun , Annor George K , Shern Jack F.
Published: April 2024

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and adolescents. RMS tumors are classified into four subtypes: embryonal, alveolar, spindle cell/sclerosing, and pleomorphic. Treatment options for RMS include a combination of surgery, chemotherapy, and radiation therapy and regimens for patients with relapsed and metastatic RMS remain limited. However, a recent study has reported that pharmacological inhibitors targeting ataxia telangiectasia and Rad3-related protein (ATR) are currently undergoing phase I/II trials and may be utilized for the treatment of alveolar RMS. Interestingly, we identified that the gene signature of replication stress positively correlated with dihydrofolate reductase (DHFR) expression in the cancer cell line database (CellMinerCDB, discover.nci.nih.gov/cellminercdb; Pearson correlation (r)=0.66). DHFR is an important therapeutic target for cancer and autoimmune diseases, and its inhibitors are routinely used and clinically approved. DHFR inhibitors are known to exhibit their anticancer effects by inhibiting nucleotide synthesis and DNA replication. In this study, we aimed to explore a potential synergistic interaction using a combination treatment of ATR inhibitors (elimusertib and ceralasertib) and DHFR inhibitors (pralatrexate, methotrexate, and raltitrexated) in multiple RMS cell lines. We used a drug matrix reduction format and found that combined treatment of ATR inhibitors and DHFR inhibitors induced a synergistically decreased RMS cell viability, showing higher synergy in fusion-positive RMS cells than in fusion-negative RMS cells. Mechanistically, ATR inhibitors abrogated DNA damage response checkpoint CHK1 activation caused by DHFR inhibitor, leading to increased γH2AX and decreased DNA replication activity. Accordingly, the accumulation of DNA damage in combination with ATR inhibitor and DHFR inhibitor triggered higher cell cycle arrest and apoptotic cell death than single agent treatment of DHFR inhibitor. Our findings warrant further research into identifying genomic regions where the DNA damage is enriched in combination treatment by using END-sequencing and synthesis-associated with repair sequencing (SAR-seq). In conclusion, this study provides promising rationale for the combination treatment of ATR and DHFR inhibitors to treat RMS patients, including those with advanced, relapsed, and metastatic states.

Citation Format: Ukhyun Jo, George K Annor, Jack F. Shern. ATR inhibitors synergize with DHFR inhibitors in rhabdomyosarcoma cells by disrupting DNA damage checkpoint [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB404.
Abstract LB430: Identification of therapeutic target in breast cancer using G-quadruplex binding ligands
Authors: Razzaq Maria , Ravichandran Subramaniyam , Parveen Nazia , Kim Kyeong Kyu
Published: April 2024

G-quadruplex (G4) motifs are noncanonical nucleic acid structures formed from staked guanine rich tetrads. G4 motifs have been shown to play significant effects on gene expression in all domains of life and are predominantly enriched in the regulatory regions such as promoters and enhancers of the human genome. G4-ligand mediated stabilization or destabilization of G4 structures has been discussed as a potential therapeutic strategy against tumor cells. However, the structure-specificity of G4-binding ligands remains a considerable challenge in determining the target-specificity. Therefore, it is necessary to understand the global effects of such G4-binding ligands at the transcriptome level to identify novel target(s) based on molecular structures and binding modes of both G4 motifs and ligands. In this study, we reported a top-down approach to extrapolate transcriptome-wide effects of two eminent G4-binding ligands Quarfloxin and Pyridostatin in human breast adenocarcinoma (MCF7) cell lines by RNA-seq analysis. Quadparser analysis was performed to analyze putative G4 forming sequences in protein coding breast cancer genes promoters. RNA-seq data was combined with Quadparser analysis to reveal that over 85% of the differentially expressed genes in both Pyridostatin and Quarfloxin contained G4 forming sequences in promoter region. Gene ontology analysis showed that both ligands affected key genes involved in extracellular matrix (ECM), architecture and cellular functions. A notable tumor suppressor deubiquitinase (DUBs) Cylindromatosis (CYLD) gene expression was particularly increased with Pyridostatin compared to Quarfloxin. In vitro assays also confirmed an increase in CYLD expression by qRT-PCR and Western blot. The detailed molecular mechanism of G4-mediated increase in CYLD expression is under study. Collectively, the current results present a new approach to identify G4-ligands binding target in breast cancer cells and provide insights into designing G4-ligands as an anti-cancer therapeutics.

Citation Format: Maria Razzaq, Subramaniyam Ravichandran, Nazia Parveen, Kyeong Kyu Kim. Identification of therapeutic target in breast cancer using G-quadruplex binding ligands [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB430.
Abstract LE21: Mechanisms of gene regulation by chromatin adaptors in development and disease
Authors: Soto-Feliciano Yadira Marie
Published: April 2024

Complex biological processes, such as organismal development, are directly influenced by the interplay between genes and the cellular structures and environmental factors that regulate them. Key players in this regulation are chromatin adaptor proteins, which can impact the genetic and epigenetic programs of cells. However, our understanding of how these proteins interact with chromatin - the physiological form of our genomes - and regulate gene activity is limited, especially in the context of diseases like cancer.

To test our central hypothesis and to understand how chromatin adaptors contribute to cell function, we are developing innovative high-throughput and biochemical approaches. These will help us systematically identify specific histone modifications that affect the binding of Menin and other adaptors to chromatin. Our experimental approach includes profiling, validation, and functional characterization using advanced genomic and epigenomic technologies, transcriptional profiling, and CRISPR gene editing. The application of these techniques will reveal, for the first time, the molecular mechanisms by which these proteins bind to specific parts of the genome and regulate gene activity.

Our findings will enhance our understanding of how chromatin adaptors, like Menin, interact with chromatin and regulate gene activity in different tissues, and how these functions are disrupted by cancer-associated mutations. This will also contribute to the development of potential new therapies that target these altered mechanisms. Furthermore, our findings can be extended to other proteins involved in chromatin and epigenetic regulation, enabling a broader application in understanding and treating cancer and other human diseases.

Citation Format: Yadira Marie Soto-Feliciano. Mechanisms of gene regulation by chromatin adaptors in development and disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LE21.
Abstract SY31-02: Nociceptor neurons control anti-tumor immunity
Authors: Eichwald Tuany , Balood Mohammad , Ahmadi Maryam , Roversi Karine , Wong Dylan , Mandl Judith , Rafei Moutih , Ghasemlou Nader , Vermeer Paola , Amit Moran , Talbot Sébastien
Published: April 2024

Cancer is the top cause of death in the USA, responsible for 30% of deaths. A cure remains undiscovered. Therapy effectiveness varies by patient and tumor type and can have negative side effects. The immune system, designed to eliminate abnormal cells, including cancer cells, is often impaired. For example, in skin cancer, extended activation of certain receptors can exhaust immune cells, reducing their cancer-fighting ability. Our lab found that cancer cells trigger nociceptor neurons in tumors, leading to neuropeptide release that exhausts CD8+ T cells. To explore their interactions, we conducted single-cell RNA sequencing on tumor-related sensory neurons, leukocytes, and cancer cells. We found a distinct group of tumor-related neurons expressingATF3, Sox10, Sprr1a, and galanin. In our study, mice with injury-resistant nociceptor neurons (NaV1.8ΔATF3) developed smaller melanoma tumors and had reduced galanin levels compared to controls. These mice also showed stronger anti-tumor immune responses, especially in cytotoxic CD8+ T-cells. Restoring galanin in mice with ATF3-deficient nociceptor neurons resulted in tumor growth similar to normal mice. We observed that galanin increases exhaustion, reduces the cytotoxic capacity of CD8+ T-cells, and leads the cells to a state of immunoparalysis. Higher galanin levels in melanoma patients were linked to worse outcomes. Using single-cell RNA sequencing from melanoma patients, we also found that cytotoxic CD8+ T cells with the galanin receptor 1(GALR1) were more exhausted than those without it. In summary, ATF3-modifiedtumor-related sensory neurons that release galanin can weaken anti-tumor immunity, suggesting cancer cells may use this aspect of neuro-immunity to promote tumor growth.

Citation Format: Tuany Eichwald, Mohammad Balood, Maryam Ahmadi, Karine Roversi, Dylan Wong, Judith Mandl, Moutih Rafei, Nader Ghasemlou, Paola Vermeer, Moran Amit, Sébastien Talbot. Nociceptor neurons control anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr SY31-02.
Abstract SY34-02: Age-related and organ-specific host mosaicism as a driver of dormant cancer cell awakening
Authors: Aguirre-Ghiso Julio A. , Papanicolaou Michael , Vela Pablo Sánchez , Yang Julie , Safonov Anton , Tao Jacqueline , Exposito Sebastia Franch , Tiedje Vera , Dalla Erica , Salazar Luis E. Valencia , Barth Nicole , Sahin Merve , Chen Kevin , Park Jinae , Wereski Matthew , Krishnan Aishwarya , Benitez Anthony Martinez , Ptashkin Ryan , Robson Mark E. , de Stanchina Elisa , Braunstein Lior Z. , Zehir Ahmet , Comen Elizabeth , Norton Larry , Berger Michael , Koche Richard , Razavi Pedram , Levine Ross
Published: April 2024

Most BC patients succumb to metastatic relapse years to decades following primary tumor resection due to reactivation of dormant disseminated cancer cells (DCCs). Improved BC patient survival has led to metastatic relapse manifesting in an older patient population. This population carries somatic mosaicism in many organs including bone marrow. Age-specific somatic mutations (e.g., DNMT3A, ASXL1, TET2) in hematopoietic stem and progenitor cells (HSPCs) results in CH, which is associated with increased inflammatory myeloid cells and risk of leukemia and intriguingly with BC-specific mortality. In this presentation I will discuss new data from a team effort to test the hypothesis that CH myeloid cells could shape target organs niches that harbor dormant DCCs to be pro-metastatic. This hypothesis has been explored in clinical trials data where the presence of CH in ER+ and HER2+ metastatic BC patient cohorts (MSK-IMPACT) was associated with the response to first line CDK4/6i/endocrine therapy or taxol/herceptin/pertuzumab, respectively. We also tested whether CH can accelerate dormant DCC awakening in a murine model of CH carrying mutations in DNMT3A (KO or point mutation) and HER2+ mammary cancer. We propose our work may provide unprecedented insights into how a traceable age-related-mosaicism in the bone marrow (CH) may shape distant organs to be drive metastatic relapse.

Citation Format: Julio A. Aguirre-Ghiso, Michael Papanicolaou, Pablo Sánchez Vela, Julie Yang, Anton Safonov, Jacqueline Tao, Sebastia Franch Exposito, Vera Tiedje, Erica Dalla, Luis E. Valencia Salazar, Nicole Barth, Merve Sahin, Kevin Chen, Jinae Park, Matthew Wereski, Aishwarya Krishnan, Anthony Martinez Benitez, Ryan Ptashkin, Mark E. Robson, Elisa de Stanchina, Lior Z. Braunstein, Ahmet Zehir, Elizabeth Comen, Larry Norton, Michael Berger, Richard Koche, Pedram Razavi, Ross Levine. Age-related and organ-specific host mosaicism as a driver of dormant cancer cell awakening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr SY34-02.