bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 454: microRNAs role in innate immunosenescence during anti-PD1 immunotherapy
Authors: Zhu Zhouting , Rana Tariq M.
Published: March 2024

Checkpoint inhibitors have achieved durable responses and long-lasting immunologic memory in cancer patients. However, the initial and acquired resistance remains an unsolved problem. It’s urgent to learn the molecular mechanisms causing resistance. microRNAs (miRNAs) are short transcripts that regulate many pathophysiological processes. Here, we investigated the miRNAs expression changes after GVAX combined with monoclonal PD-1 antibody treatment in the murine melanoma B16F10 tumors and identified microRNAs down-regulated in responsive tumors. Deletion of this family member in three different syngeneic mouse tumors did not affect their in vitro nor in vivo proliferation but sensitized anti-PD1 immunotherapy. The miRNA deletion with anti-PD1 therapy increased total CD45+ leukocyte infiltration with all types of hematopoietic cells except macrophages. Both tumor bulk RNA sequencing and single-cell RNA sequencing revealed activated innate sensing genes especially for pathogen recognition and phagosome formation. Importantly, we found specific miRNA-deletion effects rely on tumor resident macrophage, IFN-γ release in the tumor microenvironment (TME) and the miRNA regulating machinery protein Argonaut2 (Ago2). Notably, the miRNA expression status of melanoma patients correlates with the survival and innate immune sensing gene expression. Our results suggest that this family of miRNAs participate in initial resistance by escaping innate immunosurveillance. Deletion of the miRNA may turn immune “cold” tumors to “hot” tumors, providing potential therapeutic targets to overcome resistance in melanoma, colorectal, triple-negative breast cancer and possibly other cancers.

Citation Format: Zhouting Zhu, Tariq M. Rana. microRNAs role in innate immunosenescence during anti-PD1 immunotherapy [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 454.
Abstract 4616: TBK1 and GSK3 mediated TRAF2 phosphorylation confers resistance to PI3K-AKT inhibition in breast cancer cells
Authors: Habelhah Hasem , Zhang Laiqun
Published: March 2024

Breast cancer (BC) is the most frequently diagnosed malignancy and the second leading cause of cancer mortality in Western women. As is the case for most other solid tumors, metastasis and drug resistance are the main causes of death. In ~80% of BC cases, the PI3K-AKT pathway is aberrantly activated, due to the alterations in genes encoding the pathway components, such as Ras, Her2, PTEN, PIK3C and AKT. Consequently, over 100 clinical trials are currently underway worldwide to evaluate the therapeutic efficacy of PI3K and AKT inhibitors in BC; however, initial data revealed that inhibition of this pathway is either not effective or often results in development of resistance and relapse of the disease. Thus, identification of additional targets and therapeutic combinations are urgently needed. We previously reported that TBK1-mediated TRAF2 Ser-11 phosphorylation enhances NF-κB activation to promote cancer cell survival under conditions of cellular stresses. Recently, we discovered that GSK3β directly phosphorylates TRAF2 at Thr-7 upon Ser-11 phosphorylation by TBK1, and that phosphorylation of both Thr-7 and Ser-11 is essential for sustained NF-κB activation and BC cell resistance to PI3K-AKT inhibition. TBK1 and its close homologue IKKε are overexpressed in ~70% of BC and play critical roles in BC cell survival. GSK3β is a constitutively active kinase activity in unstimulated normal cells, but its activity is suppressed in most cancer cell types by AKT-mediated phosphorylation. These published reports and our new findings suggest that inhibition of AKT in BC cells leads to increased phosphorylation of TRAF2 by TBK1 and GSK3β, which confers resistance to PI3K-ATK inhibition. Bioinformatic analyses revealed that TRAF2 and GSK3β are also overexpressed in invasive BC, and significantly correlate with poor prognosis. As expected, inhibition of both AKT and TBK1 or GSK3b synergistically induced apoptosis in BC cell lines in vitro and significantly suppressed xenograft BC tumor growth in vivo. Thus, our data suggest that further investigation of the efficacies of combined PI3K/AKT and TBK1/GSK3β inhibition in PDX models of BC has the potential to develop new strategies for BC treatment.

Citation Format: Hasem Habelhah, Laiqun Zhang. TBK1 and GSK3 mediated TRAF2 phosphorylation confers resistance to PI3K-AKT inhibition in breast cancer 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 4616.
Abstract 465: Effect of Epstein-Barr virus lnc-BARTs on EBV genome maintenance in EBV-associated tumors
Authors: Liu Jiayan , Mok Bobo Wing-Yee , Chen Honglin
Published: March 2024

Most humans infected with Epstein-Barr virus (EBV) remain asymptomatic throughout the whole life. However, EBV is linked to several human cancers, including Burkitt's lymphoma, Hodgkin's disease, post-transplant lymphoproliferative disorder (PTLD), nasopharyngeal carcinoma (NPC), and gastric carcinoma. Among these EBV-associated tumors, EBV genome is present in 100% of NPC tumor cells. In NPC cells, EBV establishes a latent infection, expressing limited number of viral proteins but elevated levels of non-coding RNAs transcribed from the BamHI-A region of the EBV genome, also known as BamHI-A rightward transcripts (BARTs). The family of EBV BART RNAs includes BART-microRNAs (miRNAs) and long non-coding RNAs (lnc-BARTs). Although various functions of BART miRNAs have been identified, the role of EBV lnc-BARTs remains largely unknown. In this study, we provide evidence demonstrating that lnc-BARTs functions as a regulatory long non-coding RNA, referred to as lnc-BARTs. These lnc-BARTs play keys role in modulating the core networks that maintains EBV latency and promotes NPC oncogenesis through epigenetic mechanisms. Our study found that the apoptosis rate of NPC cells is significantly increased following the knockdown of EBV lnc-BARTs, indicating their anti-apoptotic role in EBV-associated tumors. Mass spectrometry analysis identified several host factors, including transcriptional regulators BRD4 and SC35’ interact with EBV lnc-BARTs in NPC cells. RNA-FISH assays showed lnc-BARTs co-localized with BRD4 and SC35 complexes in nuclear s peckles and such interaction were disrupted by JQ1, a BRD4 competitive inhibitor. Binding of lnc-BARTs to BRD4 RNA was confirmed using immunoprecipitation and pulldown assays. ATAC sequencing and transcriptome analyses showed that BART knockdown in EBV-harboring NPC cell line C666-1 led to reduced chromatin accessibility, downregulation of oncogenes, and decreased EBV episome replication and maintenance. Quantitative qPCR and DNA FISH analyses of cell samples treated with shRNA targeting lnc-BARTs or BRD4 reduced EBV copy numbers and EBNA1 RNA expression levels in EBV-infected NPC cells. Finally, ChIP sequencing analysis revealed that lnc-BARTs is critical for BRD4 binding to the oriP region of the EBV genome. These findings support a mechanism by which EBV lnc-BARTs epigenetically regulate host gene expression through functional interactions with elongation regulatory machinery and contribute to the maintenance of EBV latent genome by interaction with BRD4 complex.

Citation Format: Jiayan Liu, Bobo Wing-Yee Mok, Honglin Chen. Effect of Epstein-Barr virus lnc-BARTs on EBV genome maintenance in EBV-associated 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 465.
Abstract 4661: A dual degrader of HER2 and EGFR obliterates oncogenic signaling, overcomes therapy resistance, and inhibits metastatic lesions in HER2-positive breast cancer models
Authors: Yang Lu , Bhattacharya Arup , Peterson Darrell , Li Yun , Liu Xiaozhuo , Marangoni Elisabetta , Robila Valentina , Zhang Yuesheng
Published: March 2024

Background: HER2 is an oncogenic receptor tyrosine kinase (RTK) implicated in several types of human cancer. It is strongly expressed in about 20% of breast cancer (BC), known as HER2-positive BC (HER2+ BC), due to gene amplification. HER2 amplification or overexpression is a strong predictor of poor disease prognosis. HER2-targeted therapies are the linchpin of treating HER2+ BC. However, drug resistance is common. The main resistance mechanism is unknown. We exploited cell lines and mouse models (orthotopic patient-derived xenografts, and metastatic lesions in the brain and lung of therapy-resistant HER2+ BC) for experiments of genetic and pharmacologic depletion of HER2 and its family member EGFR, analysis of RTKs and no-RTKs, and evaluation of cell and tumor growth, to delineate the mechanism of HER2+ BC resistance to HER2 inhibitors and assess the therapeutic activity of PEPDG278D. PEPDG278D, a recombinant human protein, is the first-in-class dual degrader of HER2 and EGFR.

Results: Trastuzumab-resistant HER2+ BC cells and tumors are highly vulnerable to targeted degradation of HER2 and EGFR. Trastuzumab is the most commonly used HER2 inhibitor in the clinic. Targeted degradation of HER2 and EGFR by PEPDG278D, which binds to their extracellular domains, causes extensive inhibition of oncogenic signaling proteins in HER2+ BC cells resistant to trastuzumab. This is accompanied by strong growth inhibition of cultured cells, orthotopic patient-derived xenografts, and metastatic lesions in the brain and lung of trastuzumab-resistant HER2+ BC. siRNA knockdown shows that eliminating both HER2 and EGFR is important to maximize therapeutic outcome. Collectively, our results reveal the key vulnerability of trastuzumab-resistant HER2+ BC and shows a promising strategy that overcomes trastuzumab resistance by targeting this vulnerability.

Conclusions & Therapeutic Relevance: This study identifies a key therapeutic vulnerability of drug-resistant HER2+ BC and shows that an agent that targets this vulnerability is highly effective in overcoming drug resistance in this disease. The findings provide new insights and innovations to advance treatment of drug-resistant HER2+ BC that remains an unmet problem.

Citation Format: Lu Yang, Arup Bhattacharya, Darrell Peterson, Yun Li, Xiaozhuo Liu, Elisabetta Marangoni, Valentina Robila, Yuesheng Zhang. A dual degrader of HER2 and EGFR obliterates oncogenic signaling, overcomes therapy resistance, and inhibits metastatic lesions in HER2-positive breast cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4661.
Abstract 467: Genetic ablation of microRNA-10b improves treatment outcomes in mouse models of pancreatic cancer
Authors: Kempinska Katarzyna , Samuel Sudhakar , Rajesh Saiprashanth , Mallett Christiane , Sempere Lorenzo
Published: March 2024

Pancreatic ductal adenocarcinoma (PDAC) is a recalcitrant and lethal disease with an overall 5-year survival rate of less than 12%. PDAC is a heterogeneous disease characterized by highly aggressive cancer cells, extensive desmoplastic reaction, and hypovascularity. These unique features endow PDAC tumors with an array of innate resistance mechanisms against standard-of-care (SOC) chemotherapy: gemcitabine/nab-paclitaxel or FOLFIRINOX. Thus, there is clinical need to develop novel targets that enhance treatment efficacy of SOC chemotherapy. microRNA-10b (miR-10b) expression is frequently upregulated in PDAC and correlates with poor outcome. High levels of miR-10b expression within cancer cells correlates with poor treatment response to gemcitabine-containing neoadjuvant chemotherapy and poor overall clinical outcome. We and others reported that miR-10b exerts cancer cell-intrinsic pro-survival, anti-apoptotic, and pro-metastatic functions via downregulation of key target genes (i.e., BIM, PTEN, TIAM1). We hypothesize that upregulation of miR-10b expression is a chemoresistance mechanism to increase cell survival and inhibit apoptosis in PDAC. To test this hypothesis, we generated a KPC model (KrasG12D-driven, p53-deleted by Pdx1-Cre) with global Mir-10b gene knockout (Mir-10bKO). Animals were recruited when their tumor volume reached 200 mm3 by multi-mouse MR imaging and were randomly assigned to control or treatment groups (100 mg/kg of gemcitabine q4d). Tumor growth was monitored by weekly MR imaging sessions throughout the duration of the treatment. Untreated KPC;Mir-10bKO animals survived several weeks longer than untreated KPC animals (21.7 vs. 18 weeks, p = 0.056), suggesting a weak but detectable tumor promoting role of miR-10b. Remarkably, loss of miR-10b activity enhances treatment response to gemcitabine and significantly prolongs survival in this KPC model. Treated KPC animals lived only 5 weeks longer than untreated KPC (23 vs 18 weeks, p = 0.015), whereas KPC;Mir-10bKO lived 9 weeks longer (27 vs 18 weeks, p = 0.002). Notably, we observed a more durable response in treated female KPC;Mir-10bKO animals (n = 4) compared to any other experimental group (n > 5). We are currently performing tissue and molecular analyses to identify direct target genes involved in chemoresistance and sex-specific modulation of treatment response.

Citation Format: Katarzyna Kempinska, Sudhakar Samuel, Saiprashanth Rajesh, Christiane Mallett, Lorenzo Sempere. Genetic ablation of microRNA-10b improves treatment outcomes in mouse models of 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 467.
Abstract 4774: Inhibition of pancreatic acinar ductal metaplasia by novel YAP/TAZ inhibitor, CV-4-26
Authors: Perkins Corey M. , Zhou Chen , Campbell-Thompson Martha , Mao Yating , Atanasova Kalina R. , Jiang Jinmai , Ratnayake Ranjala , Luesch Hendrik , Ali Jamel , Li Chenglong , Schmittgen Thomas D.
Published: March 2024

Current challenges for pancreatic ductal adenocarcinoma (PDAC) treatment include overcoming the disease’s fibrous tumor microenvironment with limited cytotoxicity- in which tissue stiffening is believed to occur even pre-disease onset. Acinar to ductal metaplasia (ADM), the transdifferentiation of acinar cells into duct-like cells, is a predisposing event to PDAC development that is also linked to Hippo signaling, a major pathway involved in fibrosis and inflammation. Hippo activation is initiated by the yes-associated protein (YAP) in conjunction with the PDAZ binding motif (TAZ) and TEA domain (TEAD) transcription factor. Thus, the synthesis of the novel covalent TEAD autopalmitoylation inhibitor, CV-4-26, presented an opportunity to therapeutically target ADM. CV-4-26 binds to the TEAD lipid binding pocket, which, in turns, hinders TEAD palmitoylation, thereby leading to the inhibition of the Hippo pathway. Utilizing our 3D organoid p48Cre/+LSL-KRASG12D/+ (KC) mouse model, we demonstrated pronounced phenotypic and molecular inhibition of ADM by CV-4-26, resulting in a conserved acinar phenotype, as well as downregulation of downstream markers of the YAP/TAZ complex. The compound did not reverse ADM to the acinar state once ducts were visibly formed. Yet, CV-4-26 demonstrated a lack of cytotoxicity (up to 25 µM) as determined by Calcein AM staining. Biomechanical measurements of extracellular matrix stiffness acquired through calculations of fluorescent nanoparticle displacement further displayed decreased moduli as a response to inhibition treatment. Moreover, a 56-fold downregulation of collagen (COL1A1, COL1A2) mRNA, markers for PDAC development, was observed. However, less reduction in the collagens and extracellular matrix stiffness was observed in the ADM reversal treatments, corroborating our morphology and gene expression results. Our data suggest that combining CV-4-26 by ADM inhibition with standard of care therapies for PDAC may enhance the penetration of small molecules through the tumor’s extracellular matrix.

Citation Format: Corey M. Perkins, Chen Zhou, Martha Campbell-Thompson, Yating Mao, Kalina R. Atanasova, Jinmai Jiang, Ranjala Ratnayake, Hendrik Luesch, Jamel Ali, Chenglong Li, Thomas D. Schmittgen. Inhibition of pancreatic acinar ductal metaplasia by novel YAP/TAZ inhibitor, CV-4-26 [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 4774.
Abstract 4776: The role of angiogenesis in gastric tumorigenesis
Authors: Akkanapally Venu , BASU SUJIT
Published: March 2024

Introduction: Gastric or stomach cancer remains one of the most lethal malignancies, with an estimated 1,089,103 new cases and 768,793 deaths worldwide in 2020. In the United States, it is estimated that there were 26,500 new cases and 11,130 deaths from stomach cancer in 2023. Unfortunately, despite improved treatment in recent years, ~65% of gastric cancer patients present with aggressive metastatic disease, and they die within one year of diagnosis. Therefore, the identification of newer and effective therapies to target the precancerous stages of the disease promises possibilities for the prevention of gastric cancer in patients harboring these lesions. Gastric metaplasia and dysplasia are precancerous lesions that often progress to gastric cancer. Since anti-VEGF-A anti-angiogenic agents have shown efficacy in advanced gastric cancer patients, we hypothesized that VEGF-A-mediated angiogenesis has a functional role in the pathogenesis of gastric metaplasia and dysplasia.

Experimental Procedures: The Initial experiments were undertaken in human gastric metaplasia and dysplasia tissues and murine gastric metaplasia and dysplasia tissues collected from a well-established Helicobacter felis (H. felis) induced murine model of gastric tumorigenesis simulating human patients to detect angiogenesis (CD31/MVD) and identify angiogenic pathways using GeoMx DSP Spatial Proteomics and NanoString nCounter assay. Thereafter, further experiments were undertaken in the H. felis-induced murine model of gastric metaplasia and dysplasia, simulating human patients using VEGF-A hypo mice to determine the role of VEGF-A-induced angiogenesis in the progression of these lesions.

Results and Conclusion: Although our results indicated angiogenesis and VEGF-A expression in both human and mouse gastric metaplasia and dysplasia, inhibition in the progression of the precancerous gastric lesions was observed in only 40% of the VEGF-A hypo mice, thereby suggesting that VEGF-A induced angiogenesis might not be the major angiogenic pathway in these precancerous lesions in every patient. A similar phenomenon is also seen in some gastric cancer patients.

Citation Format: Venu Akkanapally, SUJIT BASU. The role of angiogenesis in gastric tumorigenesis [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 4776.
Abstract 4853: Impact of different therapeutic strategies on survival in laryngeal squamous cell carcinoma (LSCC)
Authors: Alshwayyat Sakhr , Erjan Ayah , Rawashdeh Miassar , Abdulsalam Tala , Alshwayyat Mustafa
Published: March 2024

Background: LSCC has seen a rise in cases and deaths over the past 30 years. Considering advancements in the treatment landscape, therapeutic options for patients with LSCC were evaluated to assess their efficacy in improving survival rates.

Methods: Data were retrieved from the Surveillance, Epidemiology, and End Results (SEER) (2000-2020) for localized/regional-stage cancer only, including the glottis (GC), supraglottic (SuGC), and subglottic (SC). Patients with a histologically confirmed diagnosis, no other malignancies, and complete data were included. Eight therapeutic groups were identified: surgery (Sx), chemotherapy (CTX), radiotherapy (RT), Sx + adjuvant radiotherapy (ART), Sx + CTX, Sx + RT, Sx + CTX + RT, and CTX + RT. T-tests and chi-square tests were used to compare variables, while Kaplan-Meier, log-rank tests, and Cox regression were used to identify prognostic factors for overall survival (OS) and cancer-specific survival (CSS).

Results: 68,282 patients were included (43,434 GC, 24,010 SuGC, and 838 SGC). 12.8% underwent Sx, 0.8% CTX, 0.3% Sx + CTX, 17.1% Sx + ART, 35.3% RT, 1.5% Sx + RT, 5.1% Sx + CTX + RT and 21.5% CTX + RT. 80.8% were males and 63.5% were over 60 years old and white (n=56,171). The median age was 64 years, and median tumor size was 3.2 cm. 36.5% underwent surgery with local tumor excision in 23.9 % and total laryngectomy in 5.7%. White race, regional stage, large tumor size, and CTX were poor prognostic factors for GC. Asian, white race, and total laryngectomy were good prognostic factors for SuGC, whereas male sex and older age were poor prognostic factors. In terms of SCG, Sx + ART was associated with a better prognosis, while regional and white race were associated with a poor prognosis.

Conclusion: This study shows survival differences among treatment groups and identifies factors for personalized treatment. It is the first study on all types of laryngeal tumors with a large sample size. Further research is necessary to validate and expand these results.

The 5-year survival rates (as a percentage of OS/CSS) for each therapeutic group Cancer Type Sx CTX Sx + CTX RT Sx + RT CTX + RT Sx + CTX + RT Sx + ART GC 91.9/75.5 79.8/77.3 89.2/81.8 89.8/78.1 89.5/85.3 87.8/83 79.1/90.1 90/78.1 SuGC 54.7/56.5 12.9/46.7 25.6/56.2 43.1/51.9 33.5/56.4 45.7/49.7 50.5/59.4 49.3/59.3 SGC 42.2/42.2 75/75 17.7/17.7 53/53 44.4/44.4 47.2/47.2 44.1/41.1 58.7/58.7

Citation Format: Sakhr Alshwayyat, Ayah Erjan, Miassar Rawashdeh, Tala Abdulsalam, Mustafa Alshwayyat. Impact of different therapeutic strategies on survival in laryngeal squamous cell carcinoma (LSCC) [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 4853.
Abstract 4856: Sex differences in childhood leukemia genomics
Authors: Williams Lindsay A. , Mills Lauren J. , Barragan Sofia , Gordon Peter M. , Poynter Jenny N.
Published: March 2024

Males have higher ALL and AML incidence and worse ALL survival using population-based data. Somatic genetics may play a role in ALL survival disparities and highlight potential sex specific treatment strategies for future study. Therefore, we evaluated sex differences in gene expression (RNA seq), copy number variation (CNV), and somatic mutation in ALL and AML. We stratified by cytogenomic subtypes in publicly available data from clinical cohorts using St. Jude PeCan (subtypes in Table 1). Then, we explored survival differences by sex within cytogenetic subtypes in publicly available data collected from Children’s Oncology Group patients in the NCI TARGET dataset (ALL n=387, 63% male; AML n=151, 51% male). Differentially expressed genes by sex were identified for ALL adjusting for subtype (n=214) and within subtypes (Table 1). There were no sex differentially expressed genes shared across subtypes and pathways identified from sex differentially expressed genes were few. In ETV6-RUNX1, there was as suggestion of worse 10-year survival for males (n=44, 61% male; Log-Rank p=0.068). Differentially expressed genes by sex were identified for AML adjusting for subtype (n=537) and within subtypes (Table 1). There were no differentially expressed genes by sex shared across AML subtypes. KMT2A had the highest number of pathways identified from sex differentially expressed genes (Table 1). There were no sex differences in AML survival. In ALL and AML subtypes there were no sex differences in CNVs (all t-test p>0.05) or somatic mutations (all Fisher’s Exact p>0.05). There were no sex differences in AML survival in TARGET, in agreement with population-based studies, and few differentially expressed genes identified in PeCan by subtypes. Sex differences in ALL survival were subtype specific and not heavily dependent on differentially expressed genes, CNVs, or somatic mutation. Sex differences in ALL survival may depend on treatment received, response to therapy, or other characteristics.

Table 1. Select characteristics from leukemia cases PeCan ALL SubtypeTotal n=247, 58% male N (% male) Number of differentially expressed autosomal genes by sex (male-female expression) in PeCan Number of biologic pathways identified from differentially expressed genes (Reactome) BCR-ABL1 76 (68) 48 8 DUX4-IGH 54 (57) 218 0 ETV6-RUNX1 50 (52) 86 1 hyperdiploid 14 (64) 3,199 2 iAMP21 12 (50) 120 0 KMT2A 41 (51) 216 0 AML SubtypeTotal n=149, 51% male CBFB-MYH11 34 (55) 7 0 KMT2A 44 (50) 422 19 RUNX1-RUNX1T1 61 (46) 30 1

Citation Format: Lindsay A. Williams, Lauren J. Mills, Sofia Barragan, Peter M. Gordon, Jenny N. Poynter. Sex differences in childhood leukemia genomics [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 4856.
Abstract 4905: Multimodal transformer model improves survival prediction in lung cancer compared to unimodal approaches
Authors: Tripathi Aakash , Waqas Asim , Yilmaz Yasin , Rasool Ghulam
Published: March 2024

Integrating multimodal lung data including clinical notes, medical images, and molecular data is critical for predictive modeling tasks like survival prediction, yet effectively aligning these disparate data types remains challenging. We present a novel method to integrate heterogeneous lung modalities by first thoroughly analyzing various domain-specific models and selecting the optimal model for embedding feature extraction per data type based on performance on representative pretrained tasks. For clinical notes, the GatorTron models showed the lowest regression loss on an initial evaluation set, with the large GatorTron-medium model achieving 12.9 loss. After selecting the top performers, we extracted robust embeddings on the full lung dataset built using the Multimodal Integration of Oncology Data System (MINDS) framework. MINDS provides an end-to-end platform for aggregating and normalizing multimodal patient data. We aligned the multimodal embeddings to a central pre-trained language model using contrastive representation learning based on a cosine similarity loss function. To adapt the language model to the new modalities, we employed a parameter-efficient tuning method called adapter tuning, which introduces small trainable adapter layers that leave the base model weights frozen. This avoids catastrophic forgetting of the pretrained weights. We evaluated our multimodal model on prognostic prediction tasks including survival regression and subtype classification using both public and internal lung cancer datasets spanning multiple histologic subtypes and stages. Our aligned multimodal model demonstrated improved performance over models utilizing only single modalities, highlighting the benefits of integrating complementary information across diverse lung data types. This work illustrates the potential of flexible multimodal modeling for critical lung cancer prediction problems using heterogeneous real-world patient data. Our model provides a strong foundation for incorporating emerging data types, modalities, and predictive tasks in the future.

Citation Format: Aakash Tripathi, Asim Waqas, Yasin Yilmaz, Ghulam Rasool. Multimodal transformer model improves survival prediction in lung cancer compared to unimodal approaches [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 4905.
Abstract 4906: Biopsy free virtual histology to discriminate benign from malignant squamous neoplasms
Authors: Kokikian Nelly , Wahhab Rachel , Li Jingxi , Martin Stephanie , Beynet David P. , Ozcan Aydogan , Scumpia Phillip
Published: March 2024

Reflectance confocal microscopy (RCM) is a noninvasive optical imaging modality that allows for cellular-level resolution, in vivo images of skin without performing a traditional skin biopsy. RCM image interpretation currently requires specialized training to interpret the grayscale output images that are difficult to correlate with tissue pathology. Here, we use a deep learning-based framework that uses a convolutional neural network to transform grayscale output images into virtually-stained hematoxylin and eosin (H&E)-like images allowing for the visualization of various skin layers, including the epidermis, dermal-epidermal junction, and superficial dermis layers. To train the deep-learning framework, a stack of a minimum of 7 time-lapsed, successive RCM images of excised tissue were obtained from epidermis to dermis 1.52 microns apart to a depth of 60.96 microns using the Vivascope 3000. The tissue was embedded in agarose tissue and a curette was used to create a tunnel through which drops of 50% acetic acid was used to stain cell nuclei. These acetic acid-stained images were used as “ground truth” to train a deep convolutional neural network using a conditional generative adversarial network (GAN)-based machine learning algorithm to digitally convert the images into GAN-based H&E-stained digital images. We used the already trained machine learning algorithm and retrained the algorithm with new samples to include squamous neoplasms. Through further training and refinement of the algorithm, high-resolution, histological quality images can be obtained to aid in earlier diagnosis and treatment of cutaneous neoplasms. The overall goal of obtaining biopsy-free virtual histology images with this technology can be used to provide real-time outputs of virtually-stained H&E skin lesions, thus decreasing the need for invasive diagnostic procedures and enabling greater uptake of the technology by the medical community.

Citation Format: Nelly Kokikian, Rachel Wahhab, Jingxi Li, Stephanie Martin, David P. Beynet, Aydogan Ozcan, Phillip Scumpia. Biopsy free virtual histology to discriminate benign from malignant squamous neoplasms [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 4906.
Abstract 4918: Cancer mutations converge on a constellation of molecular assemblies to predict resistance to replication stress agents
Authors: Zhao Xiaoyu , Singhal Akshat , Park SungJoon , Kong JungHo , Bachelder Robin , Ideker Trey
Published: March 2024

Rapid proliferation is a hallmark of tumor cells, associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways that are incompletely understood. Here, we develop an ensemble of predictive models that elucidate how cancer mutations impact the response to common RS-inducing (RSi) agents. The models implement recent advances in deep learning to facilitate multi-drug prediction and mechanistic interpretation. Instead of associating individual genetic alterations with RSi drug responses directly, the strategy is to project these alterations on a map of protein complexes and larger molecular assemblies associated with cancer. Initial studies in tumor cells identify 41 molecular assemblies that integrate alterations in hundreds of genes for accurate drug response prediction. These cover roles in transcription, repair, cell-cycle checkpoints, and growth signaling, of which 30 are shown by loss-of-function genetic screens to regulate drug sensitivity or replication restart. The model translates to cisplatin-treated cervical cancer patients, highlighting an RTK-JAK-STAT assembly governing resistance. This study defines a compendium of mechanisms by which mutations affect therapeutic responses, with implications for drug selection and combination.

Citation Format: Xiaoyu Zhao, Akshat Singhal, SungJoon Park, JungHo Kong, Robin Bachelder, Trey Ideker. Cancer mutations converge on a constellation of molecular assemblies to predict resistance to replication stress agents [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 4918.
Abstract 4995: Impact of radiotherapy on extracellular vesicle mediated anti-tumor immunity in oligometastatic prostate cancer
Authors: Uzendu Chisom J. , Kim Yohan , Lavoie Roxane R. , Dong Haidong , Park Sean , Lucien-Matteoni Fabrice
Published: March 2024

Metastasis-ablative radiotherapy is a new therapeutic approach that prolongs survival in patients with advanced cancers. Tumour irradiation can elicit an immunogenic cell death resulting in the expansion of tumour-reactive T cells and eradication of both irradiated and distant non-irradiated metastases, referred to as the “abscopal effect”. This abscopal response, nevertheless, is observed in a minority of patients suggesting uncharacterized mechanisms that prevent robust systemic anti-tumor immune response. Tumour-derived extracellular vesicles (TdEVs) have recently emerged as mediators of antitumor immunity but their immunomodulatory role in response to radiotherapy remains largely unknown. Recent clinical studies by our lab have demonstrated that circulating levels of tumour-derived extracellular vesicles (tdEVs) are elevated in response to radiotherapy and high tdEV concentrations are associated with reduced levels of peripheral cytotoxic CD8+ T cells and higher risk of disease recurrence in advanced prostate cancer. Based on our findings, we hypothesize that radiotherapy induces the release of tumor-derived EVs that suppress anti-tumor immunity. Prostate cancer cells (PC3 and DU145) were irradiated with clinically used doses of ionizing radiation (20Gy x 1 or 10Gy x 3 fractions) and tdEVs were co-cultured with human CD8+ T cells to measure their proliferation and cytotoxic activity. Increased levels of tdEVs were released by tumour cells treated with radiotherapy. A higher frequency of impaired T cell cytotoxic activity and a reduction in CD8 T cell proliferation was found in the 10Gy x 3 radiation regimen. Proteomic analysis and western blot showed an increased expression of the immune checkpoint molecule B7-H3 on the tumour cell surface and tdEVs in response to radiotherapy. While coculture of CD8 T cells with B7-H3 depleted tdEVs led to recovery of T-cell cytotoxic ability, overexpression of the B7-H3 in tdEVs inhibited cytotoxic activity. This study provides a rationale for future studies in which we will test the immune-mediated effects of radiotherapy-induced tdEVs in immunocompetent mouse models and investigate B7-H3 blockade as a therapeutic approach to boost abscopal response in the treatment of advanced prostate cancer.

Citation Format: Chisom J. Uzendu, Yohan Kim, Roxane R. Lavoie, Haidong Dong, Sean Park, Fabrice Lucien-Matteoni. Impact of radiotherapy on extracellular vesicle mediated anti-tumor immunity in oligometastatic prostate 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 4995.
Abstract 5004: Oncolytic Jurona-driven systemic and intratumoral immunotherapy combined with immune checkpoint blockade boost immune response and survival in hepatocellular carcinoma models
Authors: Tesfay Mulu Z. , Ferdous Khandoker U. , Cios Aleksandra , Shelton Randal S. , Simoes Camila C. , Post Steven R. , Kelly Thomas J. , Cannon Martin J. , Basnakian Alexei , Nagalo Bolni M.
Published: March 2024

The members of the vesiculovirus genus have recently become attractive immunotherapeutic agents due to their natural selectivity for tumors and lack of toxicity in humans. Here, the research shows Intratumoral (IT) or Intraperitoneal (IP) injection of JURV was found to induce dynamic tumor regression in human hepatocellular carcinoma (HCC) xenografts and syngeneic models. Furthermore, IT injections of JURV were also shown to recruit and activate cytotoxic T lymphocytes and decrease tumor-associated macrophage infiltration, resulting in the delay of tumor growth in both local and distant murine HCC tumors established in a syngeneic model. Additionally, the concurrent use of JURV and anti-PD-1 antibodies was found to synergistically modulate the tumor microenvironment (TME) via increased tumor-infiltrating CD4+ T cells and depleted CD8+ PD-1+ and NK cells. Furthermore, using RIL-175, an aggressive metastatic HCC tumor mouse model, we show that intraperitoneal (IP) (systemic) administration of JURV and anti-PD1 significantly improved long-term survival (90%) compared to the (20%) JURV or anti-PD1 alone. Through proteogenomic analysis, the activation of different effectors of the immune system was observed to cooperate to alter the TME to a favorable anti-tumor immune state. These findings further support the development of JURV as an immunovirotherapy platform for HCC, with the potential to induce abscopal effects via the activation of several tumor suppressor genes and the mechanism regulating the T helper cell responses.

Citation Format: Mulu Z. Tesfay, Khandoker U. Ferdous, Aleksandra Cios, Randal S. Shelton, Camila C. Simoes, Steven R. Post, Thomas J. Kelly, Martin J. Cannon, Alexei Basnakian, Bolni M. Nagalo. Oncolytic Jurona-driven systemic and intratumoral immunotherapy combined with immune checkpoint blockade boost immune response and survival in hepatocellular carcinoma models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5004.
Abstract 5075: Transcriptomic landscape of tumor microenvironment in gastric cancer in treatment with different types of cancer drugs
Authors: Yamashita Hiroki , Zhang Jason Guoqiang , Mashima Chiaki , Kamata Ryo , Yamamori Tomoko , Nakayama Izuma , Kawazoe Akihito , Shitara Kohei , Yano Tomonori , Xu Qunli , Ohashi Akihiro , Saito Takeshi
Published: March 2024

Gastric cancer (GC) in the fifth-leading types of cancer and the third-leading cause of death from cancer. Characterization of tumor microenvironment (TME) in GC is important not only to comprehensively understand tumor biology in GC but also to develop a novel cancer therapeutics targeting TME. In this study, we conducted multi-omics analyses of single-cell RNA sequencing (scRNA-seq), bulk RNA sequencing (bulk RNA-seq), and whole exome sequencing (WES) using biopsied tumor samples through endoscopy from 23 GC patients: 3 treatment-naïve patients, 7 patients in treatment with chemotherapy (Chemo), 5 patients in combination treatment with chemotherapy and immune checkpoint blockade (Chemo+CPI), 3 patients in combination treatment with chemotherapy and Her2-antibody targeted therapy (Chemo+Her2i), and 5 patients in third-line or later treatment. We initially classified the GC samples into 4 molecular subtypes (CIN, GS, MSI, and EBV) using datasets of WES, bulk RNA-seq and scRNA-seq, showing that our samples were mainly composed of CIN (n=7) and GS (n=16) types. In scRNA-seq, we revealed that drug treatments profoundly modulated not only proportions of TME components but also their molecular characteristics. For instance, Chemo+CPI treated patients showed higher proportion of CD8+ cytotoxic T cells with activation and/or exhaustion markers. Combination treatments with Chemo+Her2i, in addition, resulted in higher Trail and Estrogen signaling pathways in epithelial cells of TME components. These findings suggest that interventions with certain cancer therapeutic drugs could substantially convert transcriptome landscape and reconstitute GC TME components. High-resolution of GC TME analyses should provide a clue for developing a next generation of cancer therapeutic drugs.

Citation Format: Hiroki Yamashita, Jason Guoqiang Zhang, Chiaki Mashima, Ryo Kamata, Tomoko Yamamori, Izuma Nakayama, Akihito Kawazoe, Kohei Shitara, Tomonori Yano, Qunli Xu, Akihiro Ohashi, Takeshi Saito. Transcriptomic landscape of tumor microenvironment in gastric cancer in treatment with different types of cancer drugs [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 5075.
Abstract 5115: Designing targeted approaches for recurrent medulloblastoma
Authors: Blanco Jezabel Rodriguez
Published: March 2024

Designing targeted therapies for recurrent medulloblastomaPediatric brain tumors are the leading cause of cancer-related death in children, with medulloblastoma (MB) being the most common type. Despite significant progress in the field, approximately 30% of children with MB will relapse. Recurrent MB is commonly metastatic and virtually none of these patients will live beyond the one-year hallmark. These sobering statistics highlight the significant unmet need for effective therapies for recurrent MB. The likely underlying cause of the constant failure of our current clinical approaches, which are based on data obtained from disease models recapitulating primary tumors, is the disparity in genomic and transcriptomic data between primary and relapsed disease. Because of these disparities, we hypothesize that by conducting mechanistic studies and drug screens in relapse disease models, we can improve the outcomes for children with recurrent MB. Our data, obtained through a bioinformatics mining approach to predict tumor response, enabled us to identify a clinically relevant candidate drug for the treatment of recurrent MB: Minnelide. This compound acted on MYC to reduce tumor growth and the metastatic dissemination of tumors with the genetic background often found in relapsed MB patients. Additionally, to further support the translational relevance of our data, Minnelide increased the efficacy of adjuvant therapeutics used in the clinical management of MB. Our findings not only highlight the potential for repurposing Minnelide to treat children with recurrent MB, but also the potential of our research approaches aimed at identifying novel therapeutics for relapsed cancers.

Citation Format: Jezabel Rodriguez Blanco. Designing targeted approaches for recurrent medulloblastoma [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 5115.
Abstract 5117: CK2 inhibiton exhibits synergistic effect in acute lymphoblastic leukemia
Authors: Bogush Daniel Gary , Schramm Joseph , Dovat Katarina , Ding Yali , Singh Chingakham , Dovat Sinisa
Published: March 2024

Survival for pre-B cell Acute lymphoblastic leukemia (B ALL) has improved greatly, however. High risk (HR) subgroups continue to result in significant mortality and morbidity of pediatric oncology patients. Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is a lethal disease, often associated with high-risk clinical features. T-ALL therapy has made less improvement than B ALL and continues to represent a significant number of high-risk outcomes. Novel treatment strategies are required to overcome chemotherapy resistance and improve morbidity for HR B ALL. The development of treatments that can overcome chemotherapy resistance is essential for improving survival in T-ALL. Deletions of IKZF1, resulting in decreased IKAROS function, are present in High-risk ALL patients. Casein kinase 2 (CK2), a protein kinase upregulated in ALL, phosphorylates IKAROS preventing DNA binding reducing transcriptional regulation in ALL patients. Past studies have shown that pharmacologic inhibition of CK2 with CX-4945 rescues IKAROS function as a transcriptional regulator. Receptor tyrosine kinase c-KIT is transcriptionally regulated by IKAROS and is often upregulated in cancer. The purpose of this study was to determine whether restoration of IKAROS via CX-4945 would act in a synergistic manner with c-KIT inhibitor imatinib in ALL.Methods/results B-ALL Nalm6 cells were treated with imatinib over 72-hours to establish the half-maximal inhibitory concentration (IC50). The IC50 was used to determine the concentration range of imatinib to be used in combination with CX-4945 in a 72-hour synergy analysis of cytotoxicity.. Cell viability was measured using WST-1 cell proliferation assay. The data were analyzed using Calcusyn and synergy was defined as a combination index below 0.85. The study was repeated to determine a more precise range of synergy. The cytotoxicity of single drug c-KIT inhibitor, Imatinib, in Nalm6 B-ALL yielded an IC50 of 25uM while CK2 inhibitor CX-4945 resulted in 4uM. When a combination was administered with a constant dose of CX-4945 at 4uM and varying concentrations of imatinib, synergy was observed at multiple dose combinations. Conclusion: The data shows that CK2 inhibitor, CX-4945, and c-KIT inhibitor, imatinib, exhibit a synergistic therapeutic effect. Imatinib is indicated for use in Philadelphia positive (Ph+) acute lymphoblastic leukemia so future studies will include testing CX-4945/imatinib synergy in Ph+ BALL where we expect to see more potent synergistic effect.

Citation Format: Daniel Gary Bogush, Joseph Schramm, Katarina Dovat, Yali Ding, Chingakham Singh, Sinisa Dovat. CK2 inhibiton exhibits synergistic effect in acute lymphoblastic leukemia [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 5117.