bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3486: Triple hormone receptor signatures as novel prognostic markers in breast cancer
Authors: Omar Mohamed , Harrell J. Chuck , Tamimi Rulla M. , Marchionni Luigi , Ince Tan
Published: March 2024

Background: Tumor phenotype across various cancers, including breast cancer, is predominantly shaped by a synergy between genomic alterations and the cell-of-origin from which the tumor originates. These elements collectively influence crucial aspects like tumor aggressiveness, treatment response, and patient prognosis. While existing research highlights that the role of cell-of-origin in shaping the molecular architecture of breast cancer, leveraging this information for actionable clinical insights has proven challenging. Here, we introduce two robust models leveraging cellular ancestry signatures of breast luminal cells to improve patient stratification and outcome prediction.

Methods: In this study, we developed a unique gene signature anchored in the expression levels of triple hormone receptors (THR)—namely androgen (AR), estrogen (ER), and vitamin D (VDR)—in breast cancer cells. Building on this, we formulated two distinct mRNA markers, THR-50 and THR-70, aimed at categorizing breast tumors based on their THR expression profiles. These markers were rigorously validated across 65 independent breast cancer studies, involving a total of 6,679 patients, utilizing Kaplan-Meier survival curves, Cox proportional hazards models, and unsupervised clustering analyses.

Results: Our findings indicate that both THR-50 and THR-70 are robustly associated with overall survival and recurrence-free survival in breast cancer patients across all datasets evaluated. Importantly, these THR signatures demonstrate broad applicability across various breast cancer subtypes, grades, and treatment phases—unlike existing prognostic markers that tend to be subtype-specific. Additionally, the THR signatures have revealed four unique patient clusters with divergent survival outcomes, three of which are ER-positive and one is ER-negative. Additionally, we developed an immune-based signature (i20) which can further categorize patients within the ER-negative cluster into two subgroups: one with a highly favorable prognosis, comparable to the ER-positive subtypes, and another that is characterized by exceedingly poor survival outcomes.

Conclusion: The THR-based cellular ancestry signatures open a new avenue in understanding the intricacies of breast cancer biology. These signatures offer a robust and stable framework for developing other prognostic markers, thus providing an enhanced stratification of existing breast cancer categories as well as creating new classifications with more distinct survival estimates.

Citation Format: Mohamed Omar, J. Chuck Harrell, Rulla M. Tamimi, Luigi Marchionni, Tan Ince. Triple hormone receptor signatures as novel prognostic markers in breast 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 3486.
Abstract 3496: EpigenPlot: A tool for the gene-level methylation analysis of colorectal tumors
Authors: Müller Dalma , Gyorffy Balazs
Published: March 2024

Introduction. Aberrant DNA methylation patterns are frequent in colorectal adenocarcinoma (CRC) tissues. The investigation of this layer of epigenetic regulation holds the promise of a better understanding of tumour progression and the identification of novel biomarker candidates.

Purpose. Our goal was to collect and analyse publicly available DNA methylation data of colorectal samples and create a user-friendly tool for exploring and visualizing the CRC methylome.

Methods. We used Illumina Infinium Methylation Arrays, which is a popular platform for genome-wide methylation analysis of large cohorts. Gene Expression Omnibus database (GEO) and TCGA-COAD (The Cancer Genome Atlas Colon Adenocarcinoma) datasets including normal colorectal mucosa, adenoma, and adenocarcinoma samples were systematically collected and filtered. Differentially methylated regions were identified using the Kruskal-Wallis test. Genes with significant methylation changes were further analysed using ROC (Receiver Operator Characteristic) analysis. Finally, we established a web application using the shiny R package.

Results. We assembled a database including methylation data of 2,586 samples. Adenoma and adenocarcinoma samples were globally hypomethylated. Hypermethylation (p < 0.05, Δβ >= 0.2) in adenocarcinoma samples was predominantly present in regions near proximal promoters. Out of the 74 previously proposed biomarkers examined, 50 had a cross-validated AUC of over 0.8. FDA-approved biomarkers BMP3, NDRG4, and SEPT9 have shown the highest performance in the TSS200 region (cvAUC = 0.8, 0.83, and 0.76, respectively). Genes with the highest performance were ITGA4 (5’UTR, first exon: cvAUC = 0.9), MDFI (5’UTR: cvAUC = 0.9), CNRIP1 (5’UTR, first exon: cvAUC = 0.89). The established web application can visualize methylation at CpG sites and gene regions, and KEGG pathway genes. The platform is available at https://epigenplot.com.

Conclusion. We collected and analysed a sizeable database of colorectal tissue data. Gene regions with the best performance include previously proposed and novel diagnostic biomarker candidates. The web platform provides an tool for the efficient exploration of the assembled data.

Citation Format: Dalma Müller, Balazs Gyorffy. EpigenPlot: A tool for the gene-level methylation analysis of colorectal 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 3496.
Abstract 3580: Understanding and overcoming innate and acquired resistance to type I and II RAF inhibitors in anaplastic thyroid cancer using translational functional genomics
Authors: Zeng Peter , Meens Jalna , Barrett John , Cecchini Matthew J. , Ryan Sarah B. , Pan Nachuan , Karimi Amir , Jarycki Laura , Dawson Alice E. , Shaikh Mushfiq , Palma David , Winquist Eric , Boutros Paul C. , Ailles Laurie , Nichols Anthony C.
Published: March 2024

Anaplastic thyroid cancer (ATC) is one of the most lethal human cancers, with some patients succumbing to the disease within weeks of diagnosis. Despite a subset of BRAFV600E mutant ATC patients responding to monomeric type I RAF inhibitor (RAFi) dabrafenib in combination with MEK inhibitor (MEKi) trametinib, almost all patients rapidly develop adaptive or acquired resistance. These patients, along with those who do not harbor the BRAFV600E alteration, have limited treatment options. To understand the mechanism of resistance to dabrafenib and trametinib, we utilized multi-region whole genome sequencing and single nuclei profiling of ATC patient tumors to unravel genomic, transcriptomic, and microenvironmental evolution during type I RAFi and MEKi therapy. Single-cell nuclei sequencing of matched primary and resistant ATC patient tumors identified transcriptomic reactivation of MAPK-pathway, along with immunosuppressive macrophage proliferation, underlie the development of acquired resistance. Our translation genomics led us to hypothesize that deeper inhibition of the MAPK-pathway can be efficacious in overcoming treatment resistance. Screening of a panel of type II RAFis revealed that ATC cell lines are exquisitely sensitive to the type II RAFi naporafenib. We further demonstrate that naporafenib in combination with MEKi trametinib can durably and robustly overcome both innate and acquired treatment resistance to dabrafenib and trametinib using ATC cell lines and patient-derived xenograft models, including in a PDX model from an ATC patient who developed acquired resistance to dabrafenib and trametinib. Finally, we describe a novel mechanism of acquired resistance to type II RAF inhibitor and MEK inhibitor through compensatory mutations in MAST1. Taken together, our work using translational and functional genomics have unraveled the differential mechanisms of treatment resistance to type I and type II RAFi in combination with trametinib, and rationalizes the clinical investigation of type II RAFi in the setting of thyroid cancer.

Citation Format: Peter Zeng, Jalna Meens, John Barrett, Matthew J. Cecchini, Sarah B. Ryan, Nachuan Pan, Amir Karimi, Laura Jarycki, Alice E. Dawson, Mushfiq Shaikh, David Palma, Eric Winquist, Paul C. Boutros, Laurie Ailles, Anthony C. Nichols. Understanding and overcoming innate and acquired resistance to type I and II RAF inhibitors in anaplastic thyroid cancer using translational functional 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 3580.
Abstract 3590: Tumor intrinsic production of glucocorticoids in ovarian carcinoma
Authors: Hanjra Pahul , Stur Elaine , Cole Steven , Lutgendorf Susan , Sood Anil
Published: March 2024

Background: Cortisol is a glucocorticoid (GC) known to be produced by the hypothalamic-pituitary-adrenal (HPA) axis. Dysregulation of the HPA axis is prevalent in patients with ovarian cancer. These patients have elevated nighttime levels of cortisol and increased tumoral expression of the glucocorticoid receptor (GR); both of which correlate with shortened overall survival (OS). We hypothesize that outside the HPA axis, ovarian cancer may have tumor-intrinsic production of GC. In this study, we examined whether 11 beta-hydroxysteroid dehydrogenase 1 (11β-HSD1; enzyme which activates cortisone to cortisol) has steroidogenic activity in the ovarian cancer tumor microenvironment (TME).

Methods: We used the Genotype-Tissue Expression (GTex) Portal and the Cancer Cell Line Encyclopedia (CCLE) to determine expression of steroidogenic enzymes in the ovary and ovarian cancer cell lines. We further performed UMAP analysis of a single-cell RNA-seq dataset of tumor samples from patients with ovarian carcinoma to cluster for cell type. ELISAs were performed to quantify cortisol production and secretion by cells stimulated with metabolite, cortisone. Subcellular fractionation and Western blotting were performed to measure protein expression of 11β-HSD1, GR, and phospho-Ser 211 GR.

Results: HSD11B1 mRNA (which encodes 11β-HSD1) is detectable in bulk ovarian tissue at a median expression of 78.19 transcripts per million (TPM) as measured in the GTex data. In vitro, primary human ovarian fibroblasts express functional 11β-HSD1 and produce and secrete cortisol upon cortisone stimulation in a time-dependent manner, with a mean total secretion of 17.91 ± 0.21 ng/ml at 12 hours. Analysis of scRNA-seq data identifies that cancer-associated fibroblasts (CAFs) may be a source of HSD11B1 in the ovarian TME, with roughly 9% of CAFs expressing HSD11B1. In HeyA8 ovarian cancer cells (positive for 11β-HSD1), cortisone stimulation in vitro results in cortisol production with a mean total secretion of 22.04 ± 5.46 ng/ml at 12 hours. Moreover, this cortisol results in GR activation in an 11β-HSD1-dependent manner.

Discussion: We identify 11β-HSD1 as a potential mechanism of GC production within ovarian cancer, with CAFs being a putative source. We further show that 11β-HSD1 activity can lead to activation of the GR within cancer cells.

Citation Format: Pahul Hanjra, Elaine Stur, Steven Cole, Susan Lutgendorf, Anil Sood. Tumor intrinsic production of glucocorticoids in ovarian carcinoma [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 3590.
Abstract 3612: Preclinical & clinical activity of autologous mRNA engineered chimeric antigen receptor monocytes for targeted cancer immunotherapy
Authors: Wang Yuxiao , Gerber Michele , Gorgievski Michael , D'Alessandro Josephine , Diwanji Neha , Vale Ronald , Mukherjee Siddhartha , Getts Daniel
Published: March 2024

Introduction: The tumor microenvironment (TME) is a dynamic and multifaceted system that comprises largely myeloid lineage immune cells including neutrophils, macrophages, dendritic cells and monocytes. When activated, these cells are can effectively infiltrate TME and orchestrate anti-tumor immune response. Reprogramming myeloid cells by arming them with a tumor specific chimeric antigen receptor (CAR) presents an attractive strategy to overcome current limitations in solid tumor treatment. In this study, we present the isolation and mRNA-based engineering of monocytes with chimeric antigen receptors (CARs), followed by their in vivo application for cancer treatment in rodent models and in human T cell lymphoma patients.

Results: Engineered monocytes demonstrated the abilities to infiltrate the TME, undergo activation, and differentiate into macrophages and dendritic cells. Upon CAR activation, these reprogrammed myeloid cells utilized both direct and indirect mechanisms to eliminate tumor cells. This included direct tumor cell killing through phagocytosis and TNF-associated mechanisms. Furthermore, engineered monocytes exhibited the capacity to recruit natural killer (NK) cells and T cells to the TME. In the case of T cells, these engineered myeloid cells facilitated the presentation of neoantigens to T cells and stimulate an adaptive immune response. In patients with T cell lymphoma, treatment with engineered monocytes expressing a CAR targeting CD5 exhibited a favorable safety profile and was associated with TME remodeling, expansion of novel T cell clones, and promising survival outcomes.

Conclusions: These findings underscore the potential of reprogrammed myeloid cells as a novel avenue for cancer immunotherapy, offering hope for improved treatments and outcomes in the fight against cancer.

Citation Format: Yuxiao Wang, Michele Gerber, Michael Gorgievski, Josephine D'Alessandro, Neha Diwanji, Ronald Vale, Siddhartha Mukherjee, Daniel Getts. Preclinical & clinical activity of autologous mRNA engineered chimeric antigen receptor monocytes for targeted cancer 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 3612.
Abstract 3635: Insulin-like growth factor receptor predicts poor prognosis in early-stage non-small cell lung cancer
Authors: nagamine Hiroaki , Yashiro Masakazu , Mizutani Megumi , Sugimoto Akira , Matsumoto Yoshiya , Tani Yoko , Sawa Kenji , Yamada Kazuhiro , Kaneda Hiroyasu , Watanabe Tetsuya , Asai Kazuhisa , Suzuki Satoshi , Kawaguchi Tomoya
Published: March 2024

Introduction: Insulin like growth factor receptor (IGF1R) is involved in the proliferation and metastasis of various cancers. However, the clinical significance of IGF1R in non-small cell lung cancer (NSCLC) remains to be unclear. In this study, we retrospectively evaluated the correlation between IGF1R expression and clinicopathological features of NSCLC.

Method: A total of 782 specimens of NSCLC patients who underwent surgical resection of primary lung cancer between 2010 and 2019 at Osaka Metropolitan University Hospital was enrolled in this study. Immunohistochemical staining of IGF1R were performed, and the correlation between IGF1R expression and clinicopathological features of NSCLC, especially in recurrence free survival (RFS) and overall survival (OS), was evaluated. We also evaluated an association between IGF1R and programmed death ligand 1 (PD-L1) expression.

Results: IGF1R expression was positive in 279 (35.8%) patients. IGF1R-positive group had significantly longer smoking histories (median smoking index, 1,000 vs 600, p <0.01) and a higher proportion of squamous cell carcinomas (35.1% vs 14.1 %, p <0.01). IGF1R-positive group also significantly expressed PD-L1 (24.4% vs 6.4%, p<0.01). IGF1R-positive group had significantly worse RFS (10-year recurrence-free rate; 42.7% vs 53.7%, p <0.01) and OS (10-year survival rate; 54.4% vs 67.3%, p <0.01). RFS and OS were significantly worse in the IGF1R-positive NSCLC patients at stage 0 and stage I (10-year recurrence-free rate; 49.0% vs 62.9%, p <0.01, 10-year survival rate; 57.4% vs 74.2%, p<0.01), but not in stage II (10-year recurrence-free rate; 52.0% vs 43.8%, p=0.68, 10-year survival rate; 63.4% vs 47.5%, p=0.95) and III (10-year recurrence-free rate; 20.7% vs 20.8%, p=0.77, 10-year survival rate; 38.3% vs 54.6%, p=0.18). IGF1R expression was associated with poorer RFS and OS in early-stage NSCLC.

Conclusion: IGF1R is a predictor of poor prognosis in resected early-stage NSCLC.

Citation Format: Hiroaki nagamine, Masakazu Yashiro, Megumi Mizutani, Akira Sugimoto, Yoshiya Matsumoto, Yoko Tani, Kenji Sawa, Kazuhiro Yamada, Hiroyasu Kaneda, Tetsuya Watanabe, Kazuhisa Asai, Satoshi Suzuki, Tomoya Kawaguchi. Insulin-like growth factor receptor predicts poor prognosis in early-stage non-small cell lung 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 3635.
Abstract 3638: Pathologic endpoints as surrogates for survival endpoints in neoadjuvant immunotherapy clinical trials for non-small cell lung cancer
Authors: Cameron Robert B. , Hines Jacobi B. , Esposito Alessandra , Bestvina Christine , Garassino Marina C. , Torri Valter , Thawani Rajat
Published: March 2024

Background: The use of neoadjuvant immunotherapy alone or in combination has rapidly evolved in the last 5 years. There is significant debate as to whether pathologic complete response (pCR) or major pathologic response (MPR) can be considered a surrogate endpoint for survival. We therefore performed a systematic review and meta-analysis to evaluate the surrogacy of pCR and MPR for event free survival (EFS) in neoadjuvant clinical trials for early-stage NSCLC.

Methods: We performed a systematic literature search on PubMed and reviewed abstracts of the most relevant international conferences until June 2023. Relevant information relative to response rates, Odds Ratios (ORs) of response, 2-years EFS rates and Hazard ratios (HRs) were retrieved from all eligible clinical trials and the association were analyzed. To evaluate patients level surrogacy the association between response rate and 2-year EFS was evaluated. In trials presenting EFS rates by achievement of pCR and MPR a forest plot with random effect model was also produced. For trial level surrogacy, ORs for pCR and MPR and HRs for EFS were retrieved and analyzed using a linear regression model weighted by sample size. R2 and linear regression slope were used respectively to estimate the proportion of variation in EFS effect explained by pCR effect and the magnitude of change in EFS effect as a function of the magnitude of change in pCR effect. The R2 with 95% CI were calculated by bootstrapping approach.

Results: Seven RCTs were identified for a total of 2940 patients. At patient level, the R2 of pCR and MPR with 2-years EFS were 0.82 (0.66-0.94) and 0.81 (0.63-0.93), respectively, with slopes of 0.96 (0.68-1.19) and 0.64 (0.45-0.85), respectively. At trial level, R2 for association of OR for response and HR for EFS was 0.58 (0.00-0.97) and 0.61 (0.00-0.97) for pCR and MPR, respectively.

Conclusions: While we were able to show a strong correlation between pCR and EFS, trial level surrogacy was not proven. The lack of surrogacy can be related to the high heterogeneity among clinical trials and the still scarce number of data available. More research to reduce the heterogeneity (e.g., pathological evaluation, surgery, and staging harmonization) must be done to introduce pCR as a primary measure to predict EFS.

Citation Format: Robert B. Cameron, Jacobi B. Hines, Alessandra Esposito, Christine Bestvina, Marina C. Garassino, Valter Torri, Rajat Thawani. Pathologic endpoints as surrogates for survival endpoints in neoadjuvant immunotherapy clinical trials for non-small cell lung 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 3638.
Abstract 3674: Blood-based differentiation of malignant and benign pancreatic lesions using analysis of fragmentation patterns in cell-free DNA
Authors: Marcinak Clayton T. , Stephens Michelle D. , McDonald Bradon R. , Merali Nabeel , McGregor Stephanie M. , Weber Sharon M. , Frampton Adam E. , Sivakumar Shivan , Minter Rebecca M. , Murtaza Muhammed
Published: March 2024

Pancreatic ductal adenocarcinoma (PDAC) remains lethal, with a five-year survival rate of less than 10%. For patients with pancreatic cystic lesions (PCL), analysis of DNA from cyst fluid has shown promise in determining the risk of malignant transformation. However, obtaining cyst fluid requires an invasive procedure. We recently developed an approach for blood-based cancer detection by analyzing fragmentation characteristics in plasma cell-free DNA (cfDNA). In this study, we evaluate the performance of this method in differentiating between patients with malignant and benign pancreatic lesions. We collected plasma samples from 81 patients at the time of endoscopic evaluation or surgical resection of a PCL. We simultaneously obtained plasma samples from 209 PDAC patients and 56 healthy individuals. Using plasma cfDNA whole genome sequencing data from patients with PDAC and healthy individuals, we trained and cross-validated an ensemble machine learning model based on 10 genomic features capturing plasma cfDNA fragmentation patterns. This model was applied to sequencing data from patients with PCL for independent evaluation of diagnostic performance. In training and cross-validation, the model demonstrated an area under the receiver operating characteristic curve (AUROC) of 0.90 for differentiating PDAC samples from healthy individuals. Of the 81 PCL patients, ten patients (12.3%) were found to have a malignant PCL, with either high-grade dysplasia or invasive carcinoma. The trained model showed an AUROC of 0.78 for differentiating malignant from benign lesions, achieving 50% sensitivity and 62.5% positive predictive value at 95% specificity. Our results are a novel demonstration that a peripheral blood test based on plasma cfDNA analysis can enable differentiation between malignant and benign pancreatic lesions. This approach may improve risk-stratification and clinical decision-making regarding the necessity for surgical resection. Larger studies and clinical trials to validate these results and evaluate their impact on outcomes are warranted.

Citation Format: Clayton T. Marcinak, Michelle D. Stephens, Bradon R. McDonald, Nabeel Merali, Stephanie M. McGregor, Sharon M. Weber, Adam E. Frampton, Shivan Sivakumar, Rebecca M. Minter, Muhammed Murtaza. Blood-based differentiation of malignant and benign pancreatic lesions using analysis of fragmentation patterns in cell-free DNA [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 3674.
Abstract 3724: Targeting the LIFR-LCN2 pathway to sensitize liver cancer to immunotherapy
Authors: Deng Yalan , Ma Li
Published: March 2024

Liver cancer, primarily hepatocellular carcinoma (HCC), is highly lethal with limited treatment options and no biomarker to predict therapy response. The current frontline therapies for liver cancer, including sorafenib and the combination of atezolizumab (anti-PD-L1) and bevacizumab (anti-VEGF), have limited therapeutic benefits, which could be attributed, at least in part, to the highly immunosuppressive tumor microenvironment in liver cancer. Leukemia inhibitory factor receptor (LIFR) is frequently downregulated in HCC. My recent studies revealed that in oncogene-induced liver tumors, overexpression of LIFR increased, while knockout of Lifr decreased CD8+ T cell infiltration, which may be mediated by LCN2-dependent inhibition of T cell viability, proliferation, and effector function. In ongoing and future work, I will investigate whether LIFR or therapeutic LCN2 neutralization can sensitize HCC to immunotherapy. If successful, this project will illuminate how to improve liver cancer immunotherapy by targeting the LIFR-LCN2 pathway. Low LIFR expression and high LCN2 expression may be used to select HCC patients who will likely benefit from the combination therapy with the LCN2-neutralizing antibody plus immune checkpoint inhibitors.

Citation Format: Yalan Deng, Li Ma. Targeting the LIFR-LCN2 pathway to sensitize liver cancer to 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 3724.
Abstract 3725: Exosomal Galactin-3 promotes pre-metastatic niche formation that accelerates peritoneal metastases of gastric adenocarcinoma
Authors: Fan Yibo , Song Shumei , Pizzi Melissa Pool , Yoshimura Katsuhiro , Vykoukal Jody V. , Hanash Samir , Ajani Jaffer
Published: March 2024

Peritoneal carcinomatosis (PC) in gastric adenocarcinoma (GAC) lead to a short median survival (≤6 months). Pre-metastatic niche (PMN) formation, in a distant organ to prepare for tumor seeding and colonization, has long been recognized. However, the precise molecular and mechanistic contributions of exosomes in PMN formation of PC remain unclear. We identify that exosomes promote PMN formation in the peritoneal cavity by patient-derived orthotopic mouse model. Using an in-depth proteomic profiling of paired ascites cells and ascites-derived exosomes from PC patients, we discover that Galectin-3 as the exosomal payload is responsible for PC by promoting PMN formation in both patient-derived orthotopic model and syngeneic mouse model. Inhibition of exosomal Galectin-3 reverses PC. Furthermore, exosomal Galectin-3 activates cancer-associated fibroblasts (CAFs), which further activate the CXCL12/CXCR4 axis to orchestrate the immunosuppressive PMN. Simultaneous inhibition of exosomal Galectin-3, CXCR4, and PD-1 leads to tumor regression and durable anti-tumor responses. Thus, this study provides a rationale for the novel clinical strategy for GAC patients with PC.

Citation Format: Yibo Fan, Shumei Song, Melissa Pool Pizzi, Katsuhiro Yoshimura, Jody V. Vykoukal, Samir Hanash, Jaffer Ajani. Exosomal Galactin-3 promotes pre-metastatic niche formation that accelerates peritoneal metastases of gastric adenocarcinoma [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 3725.
Abstract 374: Hypoxia-induced mitochondrial glutathione transporter expression causes drug resistance in colorectal cancer
Authors: Lin Chin-Chun
Published: March 2024

Colorectal cancer (CRC) is the third most common type of cancer worldwide, with higher incidence and mortality rates. In order to adapt stress conditions during cancer progression, the cancer cells will be subject to metabolism reprogramming to increase energy production and remove hazardous substances. One of the important organelles, mitochondria is responsible for cellular ATP production, ion homeostasis, and several metabolic pathways. Therefore, mitochondria require a series of transporters called solute carrier family 25 (SLC25) to transport metabolites crossing the mitochondrial inner membrane, and dysregulation of those transporters causes abnormal cell morphology and diseases. In this study, members of the SLC25 family were analyzed in CRC via bioinformatics analysis, and a mitochondrial glutathione transporter was identified to overexpress in several public datasets of CRC and our own clinical specimens. In addition, its role has not been reported in any disease, including cancer. To systemically analyze the underlying mechanism causing overexpression of glutathione transporter during CRC progression, several stress conditions had been applied to colon cancer cells. However, only hypoxia was identified to induce its protein expression but not mRNA expression. Since a previous study reported that glutathione deprivation induced its protein expression, hypoxia didn’t alter the abundance of glutathione level suggesting that another glutathione-independent regulatory mechanism might be involve it. Interestingly, our findings revealed that hypoxia-induced glutathione transporter protein expression was mediated through the activation of internal ribosome binding site-mediated translation under hypoxia. To identify the potential role of glutathione transporter during colon cancer progression, its mitochondrial metabolite profiles from knockout cells of previous studies were further analyzed and identified that the changes of metabolites were associated with the urea cycle which had been reported to be associated with the sensitivity of oxaliplatin and 5-fluorouracil (5-FU) in cancer treatment. Importantly, our results showed that hypoxia-attenuated those chemotherapeutic effects were abolished by loss of glutathione transporter in colon cancer cells, indicating its crucial role in hypoxia-induced drug resistance. In conclusion, our study shows that glutathione transporter increased by hypoxia might lead to drug resistance of cancer therapy in colon cancer.

Citation Format: Chin-Chun Lin. Hypoxia-induced mitochondrial glutathione transporter expression causes drug resistance in colorectal 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 374.
Abstract 3764: Spatially resolved immune landscape revealed sex-biased T-cell infiltration in glioblastoma
Authors: Hao Yue , Reid George , Baker Angela , Fink Karen L. , Snipes George J. , Mickey Bruce E. , Sloan Andrew E. , Barnholtz-Sloan Jill S. , Berens Michael
Published: March 2024

Glioblastoma (GBM) multiforme is the most aggressive type of brain cancer. These lethal brain tumors are characterized by the inter- and intra-tumor molecular heterogeneity and demonstrated cell plasticity. A male:female distribution of 1.6:1; survival outcome from treatment (debulking, radiation, and temozolomide) benefits females nearly twice that for males. Through spatial transcriptomics, we interrogated the immune landscape of GBM, seeking to tease out whether distinct biological and therapeutic niches in GBM were evident, and to understand how the tumor microenvironments contributed to the heterogeneity of GBM. We designed a set of RNA hybridization probes specifically for portraying the cell identities and cell functional states within GBM tumor. The probe set was used to profile six human GBM samples from male and female cohorts on the Vizgen MERSCOPE platform. An integrated analysis of 505,614 cells from the six samples yielded a rich and varied spatial cell atlas of glioblastoma. Our preliminary findings depict distinct spatial niches of different tumor cell subpopulations that are associated with local environmental factors such as hypoxia. We identified a small cluster of cells that are in neuronal-like state, which could potentially drive invasion. We found spatial proximity of CD4+ cells and cells that express HIF1A, suggesting the dynamic interactions between tumor cells, regulatory T cells and tumor microenvironment. We also observed significant difference in the degree of CD8+ T-cell infiltration in female samples versus male samples. The average CD4+/CD8+ T-cell ratio in males is twice as high as that of females, suggesting intrinsic sex-based differences in immune response to tumor. Expansion of these studies in additional specimens will further illuminate microenvironmental influences on glioma progression and may instruct specific interventions leading to more effective and predictable immune-oncology of this disease.

Citation Format: Yue Hao, George Reid, Angela Baker, Karen L. Fink, George J. Snipes, Bruce E. Mickey, Andrew E. Sloan, Jill S. Barnholtz-Sloan, Michael Berens. Spatially resolved immune landscape revealed sex-biased T-cell infiltration in glioblastoma [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 3764.
Abstract 3770: Comparative analysis of single cell expression and digital spatial profiling in FFPE tumor tissues
Authors: Moore Anthony , O'Hara Andrea , Vishwanath Pranay , Turner Laure , Latif Haythem , Mozdzierz Chris , Zhou Ginger
Published: March 2024

Formalin Fixed Paraffin Embedded (FFPE) tissues are a staple in clinical diagnostics associated with solid tumor. Next Generation Sequencing (NGS) approaches characterize genomes, epigenomes, transcriptomes, and proteomes from a single sample source. FFPE blocks from several different tumor tissue types were serially sliced into FFPE slides. Individual slides were then utilized to explore the genome, epigenome, single cell RNA-Seq (scRNA-Seq), and Digital Spatial Profiling (DSP). Here we present a comparative analysis of two transcriptomic modalities within one FFPE tissue sample: fixed-cell scRNA-Seq of the transcriptome and digital spatial profiling of the whole transcriptome. Independent analysis of scRNA-Seq and DSP identified common trends as well as distinct differences within the same sample. Comparative analysis within sample between modalities identified statistically significant differences, driven by local tumor microenvironment, but also highlighted commonalities between methods. Cross sample comparisons showed striking differences, as indicated by tumor type. These studies highlight the strengths of each assay individually, as well as the power of a dual-assay approach for comprehensive analysis of the tumor and its microenvironment. Conclusions from this standalone analysis were further aggregated into downstream multiomics analyses, including proteomics analysis, illustrating the expanding landscape of information that can be extracted from FFPE derived tissue and the potential for novel discovery and diagnostic power integrating these complex data types holds.

Citation Format: Anthony Moore, Andrea O'Hara, Pranay Vishwanath, Laure Turner, Haythem Latif, Chris Mozdzierz, Ginger Zhou. Comparative analysis of single cell expression and digital spatial profiling in FFPE tumor tissues [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 3770.
Abstract 378: PHD3 dependent stabilization of β3-adrenoceptor induces HIF-1αactivation in Ewing sarcoma
Authors: Pasha Amada , Zocca Laura , Carrozzo Francesco , Banella Cristina , Amato Rachele , Tondo Annalisa , Favre Claudio , Calvani Maura
Published: March 2024

Hypoxia is a condition of oxygen deficiency which occurs in most growing solid tumors and stimulates a cascade of cell signals through a family of transcription factors named as hypoxia inducible factors (HIFs) that transactivate several regulatory genes involved in tumor proliferation. β3-adrenoceptors (β3-ARs) are involved in several hypoxic scenarios and in pathological conditions where hypoxia leads to important steps for cancer progression. Studies showed that β-AR blockade of mice suppressed hypoxia induction of renal HIF-1α accumulation, erythropoietin production, and erythropoiesis in vivo. In this work we assumed that through PHD3 activity, β3-AR mediates hypoxia sensing needed for HIF-1α stabilization, thus we investigated a putative correlation between β3-AR/HIF-1α and PHD3. Data showed a similar outcome of β3-ARs and HIF-1α at short time of hypoxia, and that β3-AR antagonist, SR59230A reduced HIF-1α protein expression under hypoxia. β3-AR silencing under hypoxia revealed an evident reduction of HIF-1α protein expression that confirmed the β3-AR modulation of HIF-1α expression. SR59230A treatment strongly reduced the HIF-1α target genes as GLUT1, HK-2 and HIF-1α expression at long time treatment confirming the β3-AR modulation of HIF-1α transcriptional activity. Conversely, the HIF-1α-transcriptional inhibitor Topotecan did not affect β3-AR expression confirming that β3-AR mediates HIF-1α activation. Immunofluorescence and nuclear-cytoplasmic fragmentation showed that β3-AR co-localized with the nucleus under hypoxia, more than normoxia, and presence of both β3-AR and HIF-1α in the nucleus. Co-immunoprecipitation of β3-AR/HIF-1α revealed that under hypoxia, HIF-1α dissociates from β3-AR binding, but this process was abrogated by SR59230A. HIF-1α, released under hypoxia from the link with β3-AR, can play its transcriptional activity in the nucleus, while the binding with β3-AR blocks its transcriptional activity. Moreover, the β3-AR upregulation under hypoxia occurs trough an early inhibition of PHD3 activity that did not influence HIF-1α expression. Hypoxic PHD2 inhibition results after PHD3 leading to HIF-1α upregulation. Moreover, the blockade β3-AR by SR59230A, inhibited HIF-1α upregulation by increasing PHD2 activity.

Citation Format: Amada Pasha, Laura Zocca, Francesco Carrozzo, Cristina Banella, Rachele Amato, Annalisa Tondo, Claudio Favre, Maura Calvani. PHD3 dependent stabilization of β3-adrenoceptor induces HIF-1αactivation in Ewing sarcoma [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 378.
Abstract 3783: Oral squamous carcinoma, LN metastasis
Authors: Kawai Hotaka , Eain Htoo Shwe , Ohara Toshiaki , Oo May Wathone , So Yamin , Nagatsuka Hitoshi
Published: March 2024

Due to genetically unstable nature of cancer cells, they give rise to genetically different variant subclones inside a single tumor. To enable the development of more efficacious therapies, it is crucial to understand cancer heterogeneity and subclone characteristics. Oral squamous cell carcinoma (OSCC) has high heterogeneity and plasticity. C-X3-C motif ligand 1 (CX3CL1) is the chemokine with anti- and pro-tumor functions. Our study reported CX3CL1 functions on cancer subclones with different phenotypes, both in vivo and in vitro. We found that Mouse OSCC (MOC) 1 and MOC2 cells responded in similar manners to CX3CL1 in vitro. However, in vivo, CX3CL1 increases cellular differentiation in indolent cancer (MOC1) while increasing metastasis in aggressive cancer (MOC2). These phenomena are influenced by different phenotypic tumor microenvironments created by indolent and aggressive cancer. From there, we established that when aggressive cancer cells gain CX3CL1 expression, they stimulate protumor immune system, promoting cancer metastasis via lymphatic vessels. A similar phenomenon was observed in metastatic OSCC patient samples, where CX3CL1 expression became intense in metastasis regions, consistent with aggressive subclone (MOC2) character; we correctly predicted patient outcomes by using CX3CL1 as prognostic indicator for long-term follow-up in metastatic OSCC patients. In conclusion, CX3CL1 is the key factor for stimulating aggressive cancer subclones to create new lymphatic networks for lymph node metastasis.

Citation Format: Hotaka Kawai, Htoo Shwe Eain, Toshiaki Ohara, May Wathone Oo, Yamin So, Hitoshi Nagatsuka. Oral squamous carcinoma, LN metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3783.
Abstract 3820: Impact of primary site in early-stage follicular lymphoma on patient outcomes: Analysis of a large national database
Authors: Davis Olivia , Kasht Rana , Cohoon Andrew , Day Silas , Ibrahimi Sami , Asch Adam , Al-Juhaishi Taha
Published: March 2024

Introduction: Follicular lymphoma (FL) is the most common indolent Non-Hodgkin lymphoma and is associated with better outcomes compared to other types of lymphoma. Despite this, cure is usually elusive and most patients experience multiple relapses within their lifetime. Previous studies have identified risk factors associated with worse outcomes, but little is known about the role of primary disease site in FL. We sought to investigate the outcomes of patients with extranodal early-stage FL compared to nodal disease using a large national cancer database.

Methods: The Surveillance, Epidemiology, and End Results (SEER) public database was used to identify and extract data for patients with FL. Early-stage disease was defined as stage I or II by the Ann Arbor staging system. Most patients in the database were diagnosed after 2000 so this was used as the diagnosis year cutoff and also to reflect the impact of recent management strategies on outcomes. Patients were divided into two groups based on their primary disease site. These two groups were nodal (includes spleen) and extranodal. Treatment effect (surgery, radiation, or chemotherapy) was analyzed when available. Survival was estimated using the Kaplan-Meier method and compared using log-rank tests. Cox proportional hazards models were used for adjusted survival analyses.

Results: A total of 13,400 patients with FL of all histologic grades diagnosed between 2000 and 2015 were identified in the SEER database. The median age at diagnosis was 65 years (2-100). A majority of patients were Caucasian (81%), had stage I disease (62%), and belonged to the nodal FL group (79%). Median overall survival (OS) for patients with nodal FL was 181 months [95% CI (175-187)]. Median OS for extranodal FL was 189 months [95% CI (179-195)]. Extranodal FL was associated with better OS compared to the nodal group [HR=0.89, 95% CI (0.84-0.96); p-value =0.00012] even after adjusting for age and race [HR=0.84, 95% CI (0.79-0.90); p-value <0.0001].

Conclusions: In this analysis of a large national cancer database, early-stage FL presenting as extranodal disease can be seen in about 20% of patients and is associated with slightly better outcomes.

Citation Format: Olivia Davis, Rana Kasht, Andrew Cohoon, Silas Day, Sami Ibrahimi, Adam Asch, Taha Al-Juhaishi. Impact of primary site in early-stage follicular lymphoma on patient outcomes: Analysis of a large national database [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 3820.
Abstract 3840: Can serum exosomal content predict response to immunotherapy in hepatocellular carcinoma
Authors: Savaraj Niramol , Puente Pablo , Li Ying-Ying , Wu Chunjing , Nguyen Jonathan D. , Wangpaichitr Medhi , Hosein Peter J. , Feun Lynn G.
Published: March 2024

While atezolizumab and bevacizumab combination has received FDA approval for the treatment of unresectable hepatocellular carcinoma (HCC), and recently durvalumab + tremelimumab also showed activity over sorafenib, there is no biomarker which can guild which patients can benefit from these regimens. The traditional PD-L1 positivity in the tumor by immunohistochemical staining which can predict possible response to immune checkpoint inhibitor in other solid tumors, such as melanoma and NSCLC, does not appear to apply to HCC. Thus, we attempt to explore whether exosomal content can be useful to predict response. HCC tumors exist in a complex microenvironment and serum exosomes can be generated from either tumor cells, macrophages, or other immune cells. Exosome act as new mediators for cell-cell communication transporting molecules such as lipids, proteins, and RNAs in vivo. Exosomal PD1 and PD-L1 have been implicated for possible biomarkers for immune checkpoint sensitivity. We isolated exosome from serum of unresectable HCC patients who underwent treatment with atezolizumab and bevacizumab. Blood sample was obtained prior to treatment, and then on cycle 3 and at the time of disease progression. Exosomes were isolated using the kit from System BioScience. Twenty patients were entered into the study. Five patients were not treated (received SBRT or other regional treatment), one was lost to follow up and one had atezolizumab only. In terms of antitumor response, eight patients had stable disease, three patients had partial response and two patients had progressive disease. Serum exosomal content data was available in 16 patients. Both PD1 and PDL1 are lowest in the three patients who had response followed by the group who had stable disease. In the two patients who had progressive disease, both exosomal PD-L1 and PD1 appeared to be the highest and did not change during treatment. Unlike in melanoma patients we have studied, other proteins in the antiapoptotic family such as Bcl-2 do not show any differences. While the number of patients are small and accrual is still ongoing, it appears that exosomal PD-L1/PD1 may have clinical value in predicting response to atezolizumab + bevacizumab therapy. Supported by Sylvester Comprehensive Cancer Center grant.

Citation Format: Niramol Savaraj, Pablo Puente, Ying-Ying Li, Chunjing Wu, Jonathan D. Nguyen, Medhi Wangpaichitr, Peter J. Hosein, Lynn G. Feun. Can serum exosomal content predict response to immunotherapy in hepatocellular carcinoma [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 3840.