Prognosis Of Cancer Research Articles

Downregulation of huntingtin-associated protein 1 predicts poor prognosis in gastric cancer

BACKGROUND Highly expressed in the gastrointestinal mucosa, huntingtin-associated protein 1 (HAP1) is closely associated with tumor development and prognosis. AIM To investigate the clinical utility of HAP1 expression in gastric cancer (GC). METHODS We randomly selected 124 GC patients had not undergone preoperative radiotherapy or chemotherapy, they were diagnosed at the Central Hospital of Wuhan between May 2013 and October 2018. Immunohistochemistry was used to detect HAP1 expression in paraffin-embedded GC tissues, as well as metastatic lymph nodes. Their clinical data were collected and all participants were follow up for 5 years. Western blotting and quantitative polymerase chain reaction were used to detect HAP1 levels in 20 matched pairs of fresh GC tissues. RESULTS HAP1 protein and mRNA levels were lower in fresh GC tissues than in normal mucosal tissues (P < 0.001, respectively). Immunohistochemistry also revealed lower HAP1 expression in GC tissues and metastatic lymph nodes than in normal mucosal tissues (P < 0.05). HAP1 expression in GC was closely associated with differentiation, lymph node metastasis, lymph node ratio, remote metastasis, clinical stage, tumor location, and survival time (P < 0.05). Furthermore, HAP1 expression independently predicted GC (P < 0.05) and was more accurate in advanced GC than in early GC (P < 0.05). CONCLUSION HAP1 is an important prognostic biomarker for GC, with low HAP1 expression positively correlating with poor overall survival, especially in advanced clinical stages.

Abstract 4741: HER2 status correlated with interleukin-2 (IL-2) levels after systemic therapy in hormone receptor (HR)-positive metastatic breast cancer

Abstract Introduction: The immune response plays a crucial role in prognosis in metastatic breast cancer (MBC). Detecting plasma immune components, including cytokines and circulating tumor cells (CTCs), can help predict prognosis. We previously identified Interleukin-2 (IL-2) as a biomarker associated with disease progression in MBC. Similarly, HER2 is a critical tumor marker linked to therapeutic outcomes and poor prognosis in advanced breast cancer (2018-ASCO #1090, 2022-ASCO #1057). Here, we report a novel finding: HER2 status is correlated with plasma IL-2 levels following systemic therapy in MBC patients. Methods: Whole blood samples (7.5 mL each) were collected from 42 patients with MBC, including 25 ER+, 17 ER-, 12 HER2+, and 30 HER2- patients, both before systemic therapy (baseline, BL) and 3 months after therapy (follow-up) at Northwestern Memorial Hospital (IRB-NU16B06). CTC enumeration was performed using the FDA-approved CELLTRACKS System (Menarini). Plasma Interleukin-2 (IL-2) levels were analyzed using ELISA (Fisher). Estrogen receptor (ER), progesterone receptor (PR), HER2, and Ki67 status were assessed in biopsy tissue (prior to surgery) by NU PathCore. Statistical analyses were conducted using Causal Inference with Ensemble Learning. Results: Based on pathological diagnoses, patients were categorized into 4 groups: 17 HR+/HER2- (Group 1), 8 HR+/HER2+ (Group 2), 4 HR-/HER2+ (Group 3), and 13 HR-/HER2- (Group 4). Ki67 expression was found in 9 patients in Group 1, 6 in Group 2, 1 in Group 3, and 6 in Group 4. There was no significant difference in baseline mean IL-2 levels among the groups, with values of 82.1 pg/mL, 78.6 pg/mL, 80.5 pg/mL, and 81.2 pg/mL for Groups 1, 2, 3, and 4, respectively (P > 0.05). After therapy, the mean IL-2 levels changed to 80.8 pg/mL, 69.3 pg/mL, 70.2 pg/mL, and 77.6 pg/mL at follow-up. A significant difference was observed between Groups 1 and 2 (P = 0.037), showing that IL-2 levels were notably higher in HR+/HER2- patients compared to HR+/HER2+ patients. There was no significant correlation between IL-2 and Ki67. Additionally, 20 patients (46%) had CTCs ≥5 at baseline, with 15 having HER2-negative CTCs (Group 5) and 5 having HER2-positive CTCs (Group 6). The mean IL-2 level was significantly higher in Group 5 (88.17 pg/mL) than Group 6 (66.81 pg/mL), indicating that patients with HER2-positive CTCs had significantly lower IL-2 levels (P = 0.02). Conclusion: The finding that HER2 status in CTCs correlates with lower plasma IL-2 levels, and that HER2 status in biopsy tumor tissue is associated with IL-2 levels after systemic treatment in HR-positive MBC patients, suggests that HER2 may contribute to immune suppression and weaken the immune response through its interaction with IL-2 during therapy. Exploring the HER2-IL-2 relationship could provide valuable insights into assessing therapeutic efficacy in hormone receptor-positive MBC. Citation Format: Justin W. Zhang, Qiang Zhang, Andrew A. Davis, Lorenzo Gerratana, Jianhua Jiao, Weijun Qin, Youbin Zhang, Paolo D’Amico, zheng Cai, Akhil Chawla, Lisa Flaum, Janice Lu, Leonidas C. Platanias, William J. Gradishar. HER2 status correlated with interleukin-2 (IL-2) levels after systemic therapy in hormone receptor (HR)-positive metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4741.

Abstract 4650: The impact of GLI3 mutations and expression on prognosis in gastric cancer

Abstract Background: GLI3, a member of the GLI zinc finger family, has been extensively investigated in various cancers, including gastric cancer. It has been observed that GLI3 is significantly upregulated in solid cancer types. These findings suggest the involvement of GLI3 in the malignant progression of different cancers. However, the precise impact of GLI3 mutations and expression on the prognosis of gastric cancer patients remains unclear. Further investigation is warranted to elucidate the prognostic significance of GLI3 alterations in gastric cancer. Methods: This study included 269 gastric cancer patients from TCGA and 2903 patients from China. The mutation rate of GLI3 was analyzed using Excel. Additionally, the survival rates of gastric cancer patients with GLI3 mutations were compared to those with wild-type using KM survival curves in the TCGA cohort. In addition, the impact of high and low expression of GLI3 on survival was analyzed using a 50% threshold. The expression of GLI3 in tumor tissues were evaluated using Mann-Whitney analysis to compare with those in normal tissues. Results: The mutation rate of GLI3 was 13.55% in the TCGA cohort, whereas it was significantly lower at 7.79% in the Chinese cohort. KM curve analysis demonstrated that patients with GLI3 mutations in the TCGA cohort had a significantly higher survival rate than those with the wild group (p < 0.05). Additionally, GLI3 expression was significantly higher in tumor tissues compared to normal tissues (p < 0.01). Furthermore, based on GLI3 expression analysis, patients with a 30% higher expression of GLI3 had a significantly worse prognosis compared to the remaining 70% of patients (p < 0.05). The analysis of GLI3 mutations and expression revealed that patients with GLI3 mutations had significantly lower RNA expression compared to those with the wild-type. Conclusion: The mutation rate of GLI3 was found to be higher in the TCGA cohort compared to the Chinese cohort. Both GLI3 mutations and expression were closely associated with the prognosis of gastric cancer patients. These findings highlight the significance of GLI3 as a potential prognostic indicator in gastric cancer. Further research is needed to elucidate the underlying mechanisms and validate these observations in larger and more diverse patient populations. Citation Format: Wanfu Zhang, Wendi Jin, Hongwei Wan, Chao Niu, Chu Yan, Chunxiao Wang, Juanjuan Liu, Xiaogang Li, Qinglan Zong, Ning Gao, Ding Zhang. The impact of GLI3 mutations and expression on prognosis in gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4650.

Abstract 5943: The impact of radiotherapy on prognosis in microsatellite stable rectal cancer: A national analysis

Background: Approximately 80-85% of rectal cancer cases are microsatellite stable (MSS), indicating a functional mismatch repair (MMR) system. Rectal cancer patients with microsatellite instability (MSI) exhibit better survival rates, mainly due to enhanced treatment responses linked to high tumor mutational burden (TMB). Radiotherapy (RT) induces DNA damage, increasing TMB and immune recognition. We hypothesize that RT improves prognosis in MSS rectal cancer patients. Methods: A retrospective study was conducted using the National Cancer Database (NCDB), including patients aged ≥20 years diagnosed with MSS rectal cancer between 2004 and 2020 with documented tumor stages. All patients underwent surgical resection, chemotherapy, and immunotherapy. Collected data encompassed demographics, tumor grade, TNM stage, KRAS mutation status, lymphovascular invasion, and perineural invasion. RT was categorized into short-course RT (SC-RT; 25 Gy) and long-course RT (LC-RT; 45-54 Gy). The impact of RT on overall survival was assessed using multivariable Cox proportional hazards regression, adjusting for variables significant in univariate analysis. Results: Of the 460 patients included, 70.9% received RT, while 29.1% did not. RT recipients demonstrated a 40% reduction in mortality risk compared to non-recipients (P = 0.001). Specifically, SC-RT and LC-RT were associated with 39% (P = 0.042) and 40% (P = 0.002) lower mortality risks, respectively. In stage II-III patients, LC-RT significantly reduced mortality risk (HR: 0.26, P < 0.001), whereas SC-RT showed no significant impact. In stage IV patients, neither SC-RT nor LC-RT significantly affected prognosis. Conclusion: Radiotherapy is associated with improved prognosis in MSS rectal cancer patients, particularly with long-course RT in stages II-III. These findings advocate for clinical trials to further evaluate the role of RT in MSS rectal cancers. Citation Format: Mohyeddine El Sayed, Sassine Youssef, Raymond N. DuBois. The impact of radiotherapy on prognosis in microsatellite stable rectal cancer: A national analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5943.

Abstract 2330: The Jekyll and Hyde of DARC: Balancing prognosis and metastasis in breast cancer

Abstract Background: DARC, a decoy receptor for chemokines, is implicated in breast cancer progression. Understanding its interplay with key molecular markers and its impact on tumor behaviour is crucial for developing targeted therapies. Methodology: This study employed a multi-faceted approach, including immunohistochemistry, quantitative PCR, and bioinformatical analysis of publicly available datasets (TCGA and METABRIC). The DARC, CCL8, c-MYC, ALDH1, and CHEK2 expression patterns were analyzed in breast cancer tissues. Correlation analyses and survival analyses were performed to assess the prognostic significance of these markers. Results: Our findings revealed a positive correlation between DARC and CCL8 expression, suggesting a potential role of DARC in promoting tumor cell migration and invasion through CCL8 signalling. Additionally, elevated DARC expression was associated with increased c-MYC, ALDH1, and CHEK2 levels, indicating its potential involvement in tumor cell proliferation, stemness, and chemoresistance. Bioinformatical analysis further corroborated these findings and identified DARC as a potential prognostic biomarker. Conclusion: These results highlight the complex interplay between DARC and key molecular markers in breast cancer. Targeting DARC may offer a novel therapeutic strategy to inhibit tumor progression and improve patient outcomes. Further validation studies are warranted to elucidate the precise mechanisms underlying DARC-mediated tumorigenesis. Citation Format: Joyeeta Talukdar, Trayambak Srivastava, Ruby Dhar, Subhradip Karmakar. The Jekyll and Hyde of DARC: Balancing prognosis and metastasis in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2330.

Abstract 2456: Artificial intelligence-powered spatial analysis of tumor-infiltrating lymphocytes predicts prognosis in gallbladder cancer after resection

Abstract Background: Tumor-infiltrating lymphocytes (TIL) play an essential role in various cancer types. However, their prognostic significance in resected gallbladder cancer remains largely unknown. Methods: This study included 225 patients who underwent curative resection for gallbladder cancer. H&E-stained whole slide images were analyzed using the Lunit SCOPE IO, an artificial intelligence (AI)-powered spatial TIL analyzer. Based on the density of intratumoral TILs in the cancer epithelium and stromal TILs in the cancer stroma, three immune phenotypes (IP) were defined: immune-inflamed phenotype (IIP), immune-excluded phenotype (IEP), and immune-desert phenotype (IDP). Survival outcomes were analyzed, with subgroup analysis conducted for early-stage (stage 0-II) and advanced-stage (stage III-IV) disease. Results: Of the 225 patients, 58 (25.8%) had IIP, 151 (67.1%) had IEP, and 16 (7.1%) had IDP. During a median follow-up of 71 months, 82 deaths (36.4%) were recorded. IIP and IEP were significantly associated with more prolonged disease-free survival (DFS) and overall survival (OS) compared to IDP. Conclusions: Immune phenotypes identified through AI-powered spatial TIL analysis were associated with DFS and OS in resected gallbladder cancer, particularly in late-stage disease. These findings highlight the prognostic potential of immune phenotyping, especially in advanced disease. Univariate and Multivariate Cox Regression Analyses for DFS and OS Citation Format: Hyemin Kim, Young Hoon Choi, So Jeong Yoon Yoon, Cheolyong Joe, Se-Hoon Lee, Sang Hyun Shin, In Woong Han, Jin Seok Heo, Yo Han Jeon, Kee-Taek Jang, Kwang Hyuck Lee, Jong Kyun Lee, Kyu Taek Lee, Hongbeom Kim, Jookyung Sophie Park. Artificial intelligence-powered spatial analysis of tumor-infiltrating lymphocytes predicts prognosis in gallbladder cancer after resection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2456.

Abstract 6501: The SRG RAT supports in vivo human cell xenotransplantation through enhanced tumor microenvironment interactions

Abstract The use of immunodeficient mice for human tumor engraftment has proven to be an essential model of human cancer, with uses ranging from basic science to translational research. However, low engraftment rates, slow growth, and smaller tumor volumes can be limitations. Previously, we reported a highly immunodeficient rat strain developed by Hera BioLabs, with the functional deletion of both the Rag2 and Il2rg genes on the Sprague-Dawley background (SRG RAT®), which lacks B, T, and NK cells. We have shown that the SRG rat supports the growth of multiple PDX and CDX models, however, the mechanisms underlying the supportive growth are not fully understood. Additionally, direct comparison of tumor growth and the rates of engraftment between the SRG rat and NSG mice has remained limited. Here, we subcutaneously engrafted two CDX and five PDX models into SRG or NSG animals and tracked tumor growth. These models included prostate, lung, ovarian, and uterine cancer models. In all cases, the engraftment and tumor growth rates were better supported in the SRG rat compared to the NSG mouse. Interestingly, the SRG rat is not more immunocompromised than the NSG mouse, suggesting alternative mechanisms leading to the supportive growth in the SRG rat. To understand this, we explored potential differences in the tumor microenvironment (TME) between models grown in the two host animals. We analyzed tumors from the H660 CDX model of castrate-resistant prostate cancer grown in either SRG rats or NSG mice using markers of the TME via immunohistochemistry. This analysis showed differences in the vasculature and macrophages between the two host species. We complemented this analysis using Xenium in situ by 10X genomics to allow for single-cell spatial imaging of engrafted tumors. This analysis showed upregulation of the human CXCL2, LAMP3, and other genes in H660 tumors grown in the SRG rat vs the NSG mouse. Interestingly, high expression of these two genes has been linked to poor prognosis in cancer. Combined, our data demonstrate that the SRG rat supports the growth of multiple human cancer types and displays enhanced tumor microenvironment interactions compared to NSG mice. Citation Format: Caitlin M. O'Connnor, Diane Begemann, Kaitlin P. Zawacki, Kelsey Barrie, Fallon K. Noto, Grace Walton, Gabrielle H. Onishi, Jessica Durant, Taylor Branyan, Mike Schlosser, Goutham Narla. The SRG RAT supports in vivo human cell xenotransplantation through enhanced tumor microenvironment interactions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6501.

Abstract 7122: Accelerating immuno-oncology research with flexible workflows using modular flex-fit CyTOF panels

Abstract Deep functional profiling of immuno-oncology markers and cytokines in whole blood (WB) reveals immune signatures that inform disease prognoses, immunotherapy selection, and outcomes in cancer patients. WB is best analyzed within 24 hours of collection to capture clinically relevant immune signatures; however, WB collection and cytometric analysis are often performed at different sites, which can lead to significant delays. WB stabilizers can overcome this challenge, yet not all antibody panels are compatible with these reagents. To enable flexible experimental workflows for deep profiling of immuno-oncology markers and cytokines in WB, we developed modular Flex-Fit CyTOF™ panels compatible with stabilizers. High-parameter flow cytometry mediated by CyTOF technology enables single-tube staining to identify 50-plus markers at the single-cell level. CyTOF technology provides exceptional resolution without spectral unmixing or compensation, while Flex-Fit CyTOF panels allow simple and quick panel design by combining a customizable selection of pre-validated subpanels. We built two high-parameter antibody panels for analysis of fresh and stabilized WB. The first panel has 21 markers and identifies 12 immuno-oncology markers in 10 major cell subsets. The second panel has 31 markers and identifies 10 cytokines in 32 cell subsets. Stimulated WB samples from two healthy donors were either freshly stained or stabilized with PROT1, RBC lysed and stained. Liquid antibodies in the panel were pooled together and frozen (-80 °C) as single-use aliquots for surface and intracellular staining to reduce technical variability from staining. Optimal panel design ensured that all markers in both panels could be used to accurately identify target cell populations in PROT1-stabilized WB. Following stabilization, nonspecific staining was not observed when compared with freshly stained samples. Cell populations maintained the anticipated co-expression of markers in PROT1-stabilized WB. Prominent cytokines such as IL-17A, TNF-α, IL-10, etc., could be detected in stabilized WB. Overall, we show that PROT1-compatible high-parameter antibody panels enable functional profiling of immune cells by identifying immuno-oncology markers and cytokines. Compatibility with WB stabilization reagents provides workflow flexibility for carrying out functional profiling in longitudinal and multi-center studies in clinical research and healthcare settings. Furthermore, freezing antibody cocktails is a unique feature of CyTOF flow cytometry, ensuring staining consistency. Together, flexible CyTOF workflows enable fast and convenient panel design for high-parameter cytometric analysis of WB and can facilitate biomarker discovery, immunotherapy selection and tracking disease prognoses in cancer. Citation Format: Shakir Hasan, Ling Wang, Stephen Li, Christina Loh. Accelerating immuno-oncology research with flexible workflows using modular flex-fit CyTOF panels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7122.

Abstract 6300: Global fit normalization for circulating microRNA measured by quantitative PCR

Abstract MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression at the post-transcriptional level and play a key role in cancer biology affecting cancer cells’ proliferation, metastasis, and drug resistance. Cancer cells can release miRNAs into the bloodstream and can potentially be non-invasive markers for cancer diagnosis and prognosis. However, variations in quantitative PCR (qPCR) preparation have limited their clinical utility, and normalization of circulating miRNA qPCR data remains challenging due to low amount of circulating RNA and the lack of universal housekeeping miRNAs. To address these limitations, we have developed Global Fit (GF) normalization, a novel approach that accounts for technical variations from RNA input by fitting a sigmoidal curve to the reverse cumulative distribution of miRNA cycle threshold (Ct) values and subsequently adjusting sample bias through distribution unification. Additionally, we introduce an extended normalization method that employs linear regression (LR) to further correct residual sample bias. The performance of the GF was compared against the commonly used normalization method, Global Mean (GM) using simulated data based on a murine plasma dataset and three public human cancer plasma datasets. In the murine dataset, we demonstrated that sample input bias is reflected by the horizontal shift of the cumulative distribution of Ct values, and GF normalization yielded more aligned distributions compared to GM. Simulation showed that GF outperformed GM by reducing post-normalization variability across scenarios considering different dropout rates and panel sizes. Across multiple simulations of differentially expressed miRNAs, GF showed higher statistical power compared to GM (median 51.9% vs 20.4%), while maintaining similar type I error rates. LR further improved the detection power beyond GF alone. Across three human cancer miRNA datasets, GF consistently demonstrated better correction of circulating miRNA distribution compared to GM. In ANOVA analyses, GF normalization consistently accounted for higher data variability than GM normalization. GF also outperformed other normalizers in stability score (ranked No. 1) as measured by NormFinder. Consequently, GF allowed better detection of biologically meaningful circulating miRNAs in colon and liver cancers, such as miR-210, miR-532-3p and miR-195. These findings support the use of GF normalization in circulating miRNA data analysis to enable more robust biomarker identification for cancer diagnosis and prognosis in clinical settings. Citation Format: Kai Song, Chen Wang, Jordan Wellerstein Kardos, Nandita Sarkar, Yihua Liu, Oh Kyu Yoon. Global fit normalization for circulating microRNA measured by quantitative PCR [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6300.

Abstract 2017: Eukaryotic translation initiator factor 4E in breast cancer progression and prognosis

Abstract The network of the eukaryotic translation initiator factor 4E (eIF4E), a mRNA cap-binding protein that is critical in the translation initiation of protein synthesis and the downstream effector of PI3K/AKT/mTOR and RTK/RAS/ERK signaling pathways, is implicated in tumorigenesis and tumor progression through regulation of cell proliferation, angiogenesis and metastasis. Targeting eIF4E with e.g. eIF4E/cap interaction antagonists, siRNA and antisense oligonucleotides is in preclinical and early clinical development and may evolve as one of the effective cancer treatments. However, there has been a dearth of data of eIF4E translational research for tumor progression clinically and prognosis. In this study, we investigated the expression of eIF4E by immunohistochemistry, and its association with clinicopathological factors and prognosis in a cohort of 710 cases of nonmetastatic breast cancer. eIF4E was expressed in 50% formalin-fixed and paraffin-embedded primary invasive breast cancer. The cap-binding protein in high-grade tumors was more prominent in the eIF4E-positive tumors than eIF4E-negative tumors (p=0.0005). Its expression was associated with larger tumor size (p=0.0001) and node-positive disease (p=0.006). In addition, there was more estrogen receptor/progesterone receptor negativity in eIF4E-positive than eIF4E-negative tumors. Notably, eIF4E demonstrated a significance towards association with both overall survival and recurrence-free survival (p=0.04 and p=0.03 by Gehan-Breslow-Wilcoxon test). The significance in the survival and recurrence outcomes was evident within 10 years of follow-up and the difference gradually diminished with long-term follow-up after 10 years. Taken together, eIF4E is linked to clinical tumor progression through its association with larger tumor size and nodal involvement as well as with high tumor grade. It has a role for prognosis in patients who were diagnosed with nonmetastatic breast cancer particularly within 10 years of clinical follow-up. Citation Format: Dat Nguyen, Angelo Laranjeira, John Yu, Stephen M. Hewitt, Sherry X. Yang. Eukaryotic translation initiator factor 4E in breast cancer progression and prognosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2017.

Abstract 2218: Prognostic relevance of immune phenotyping of the tumor immune microenvironment and its interactions with the mammary microbiota in Ethiopian breast cancer patients

Background: Breast cancer (BC) is a highly heterogeneous disease, and refining additional clinical parameters is crucial for its effective management. The tumor immune microenvironment, influenced by factors such as infiltrating intratumoral microbiota, has been shown to play a key role in cancer prognosis and treatment response. Methods: RNA was isolated from formalin-fixed paraffin-embedded (FFPE) tissue from 82 women with BC. Expression of 54 immune genes was analysed using Nanostring and differentially expressed genes (DEGs) were determined using ROSALIND®. Immune cell populations were profiled using Nanostring's cell type profiling module, while tumour infiltrating lymphocytes (TILs) were assessed via haematoxylin and eosin (H&E) staining. For microbiome profiling, DNA was isolated from 29 biopsy samples using MoBio PowerMag Soil DNA Isolation kit and sequenced with an Illumina MiSeq. In addition, the PIK3CA gene was genotyped for three hotspot mutations using qPCR. Log-rank test was performed to evaluate the prognostic significance of immune phenotypes. Results: Hierarchical clustering of the gene expression profiles revealed four discrete immune phenotypes (IP1-4) characterized by differential expression of immune-activating and immune-regulatory genes. An immunologically inert phenotype (IP2) was identified, marked by consistent downregulation of both immune suppressive and immune activating genes, alongside the lowest levels of immune cell infiltration. In contrast, IP4 exhibited an immunologically active TME, characterized by upregulation of key cytotoxic genes and the highest abundance of immune cells. IP1 and IP3 had intermediate characteristics. A significant association was found between IPs and BC subtypes: luminal A tumors predominated in IP2, while basal BC tumors were most common in IP3. No significant differences in PIK3CA mutations were observed across the IPs. Importantly, IPs with an active TME were associated with improved overall survival compared to those with an inert immune environment. Microbiota diversity and abundance did not show significant differences across the IPs. However, microbiota composition differed significantly between TIL groups. Notably, the Firmicutes and Verrucomicrobia phyla, as well as the Lactobacillaceae, Akkermansiaceae and Caulobacteraceae families, were more abundant in intermediate TIL groups. At the genus level, Delftia was significantly enriched in the high TIL group (P < 0.0001), while Akkermansia and Cutibacterium were more abundant in the intermediate TIL groups. Conclusion: Immune phenotyping of the TME identified distinct immune subgroups that are associated with prognosis and could guide treatment selection. Additionally, potential immune-microbiome interactions were observed, suggesting a role in modulating anti-tumor immunity. Citation Format: Meron Yohannes Nigussie, Zelalem Desalegn, Marcus Bauer, Kathrin Stückrath, Endale Anberbir1, Yonas Bekuretsion, Mathewos Assefa, Tariku Wakuma, Yasin Worku, Pablo S. Santos, Lesley Taylor, Adamu Adissie, Claudia Wickenhauser, Chiara Massa, Martina Vetter, Eva J. Kantelhardt, Barbara Seliger, Tamrat Abebe. Prognostic relevance of immune phenotyping of the tumor immune microenvironment and its interactions with the mammary microbiota in Ethiopian breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2218.

Abstract 2349: Implementation of a novel immune monitoring strategy for multicenter clinical trials to enable equity in cancer prognosis for individuals from remote settings of Australia

Abstract Improved cancer prognosis begins with the collection of high-quality data from clinical trials. However, the execution of longitudinal immune phenotyping studies by flow cytometry is complex, primarily due to logistical challenges that could affect data quality. The challenges of immune monitoring are exacerbated when considering remote and rural communities in Australia, which are burdened by both an increased prevalence and worse prognosis of cancer. Paradoxically, these communities are often underrepresented in clinical trials. Our group has developed a novel blood-based “immune signature” that robustly predicts failure to make a clinical response to checkpoint therapies targeting the PD-1/PD-L1 pathway in melanoma and lung cancer. These groundbreaking findings were achieved through applying a comprehensive 38-parameter immunophenotyping CyTOF™ panel to biobanked peripheral immune cells from cancer patients. We now aim to increase our clinical implementation in remote settings, with an expanded CyTOF panel of 50-plus-parameter analysis. Recent developments in CyTOF technology facilitate a highly simplified workflow of asynchronous sample collection and staining, compatible with current hospital laboratories that typically run on unpredictable schedules, to remote settings. This is uniquely enabled by using a dried-down cocktail of CyTOF antibodies that are stable, simple to use and yield reproducible staining while minimizing sample required. Furthermore, this workflow, unique to mass cytometry, provides flexibility and minimizes technical variation via sample barcoding and freezing of stained samples for shipment to a central site for batch acquisition. As such, this study is designed to ultimately demonstrate both clinical impact of the large panel and utility of CyTOF technology for a highly simplified and robust workflow for multi-site clinical trials. Here we present findings from the implementation of this novel workflow through a 100-sample pilot study. Remote asynchronous sample collection and surface staining was performed at five sites across Australia. Stained samples were then shipped to a central lab for multiplex barcoding and intracellular staining of several key functional markers. A combination of manual gating and automated high-dimensional clustering was performed in CellEngine, with principal component analysis of all samples demonstrating harmony across the sites. Overall, this workflow enables access to underserved communities, facilitating for the first time equity and scalability of immune phenotyping studies to harness truly geographically dispersed clinical centers. Citation Format: Natalie Smith, Michael Cohen, Julie Alipaz, Christina Loh, David King, Steven Kao, Sandra Taylor, Rajat Rai, Barbara Fazekas de St Groth, Helen McGuire. Implementation of a novel immune monitoring strategy for multicenter clinical trials to enable equity in cancer prognosis for individuals from remote settings of Australia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2349.

Abstract 4913: PREDICT Breast v4: Advancing equity in breast cancer prognosis for diverse populations

Abstract Breast cancer, the most common cancer among women globally, remains a significant public health challenge. Prognosis, influenced by factors such as tumor characteristics, patient demographics, and treatment choices, is a major concern for patients. Tools like the PREDICT Breast v3 model (https://breast.v3.predict.cam/) help weigh treatment benefits against short- and long-term risks, enabling more personalised prognostic predictions. However, its performance disparities among non-Hispanic Black and non-Hispanic Asian patients in the US highlight the need for more equitable and inclusive tools. Therefore, this study aims to develop a breast cancer prognostic model that improves predictive accuracy across diverse populations and reduces disparities in prognostic outcomes. Here, we analysed data from 273, 918 breast cancer patients in the Surveillance, Epidemiology, and End Results (SEER) database, each with clinical records and socioeconomic status (SES) information. The data were split 7:3 for model training and validation, with 10-fold cross-validation applied for parameter tuning. We first evaluated both conventional methods (PREDICT v3) and advanced machine learning models, including survival XGBoost, survival random forest, DeepHit, and DeepSurv, using calibration and discrimination as evaluation metrics. After comparing the models, we selected the DeepHit neural network as the best-performing approach due to its lowest calibration error and highest discrimination. We then examined whether incorporating SES improved performance by comparing SES-adjusted and unadjusted DeepHit models. Our results showed that the SES-adjusted DeepHit model achieved strong calibration (within 1.3% of observed deaths) and reduced racial disparities compared to PREDICT v3, which exhibited calibration errors of 30% for non-Hispanic Asians and 20% for non-Hispanic Blacks. These findings emphasise the importance of incorporating SES factors to enhance model accuracy and equity, underscoring the critical need for fairness in prognostic prediction. This work advances the application of machine learning in cancer prognosis and provides a foundation for addressing health disparities in clinical prediction tools. Citation Format: Yi-Wen Hsiao, Gordon C. Wishart, Paul D.P. Pharoah, Pei-Chen Peng. PREDICT Breast v4: Advancing equity in breast cancer prognosis for diverse populations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4913.

Abstract 4927: Tumor tissue microbiome in the high-grade serous ovarian cancer: a pilot investigation within the African American Cancer Epidemiology Study

Abstract Background: High-grade serous ovarian cancer (HGSOC) is the most common histological subtype of ovarian cancer. Notably, Black and African American (AA) women face a ∼40% higher mortality risk from this disease compared to White women. Recent studies have suggested that intratumor microbes may play a key role in shaping the tumor microenvironment and influencing the prognosis of ovarian cancer. However, to date, no studies have investigated the tumor microbiome in Black/AA women diagnosed with HGSOC using formalin-fixed paraffin-embedded (FFPE) samples and a whole metagenome sequencing approach. Methods: We analyzed tumor FFPE samples from 20 HGSOC cases who self-identified as Black/AA and participated in the African American Cancer Epidemiology Study (AACES). Tumor DNA was extracted using a standardized protocol, and microbial profiling was performed using 2bRAD sequencing for microbiome (2bRAD-M), a high-precision, reduced-metagenome sequencing technique that enables species-level resolution. To assess tumor microbial differences by cancer stage and age at diagnosis, we compared tumor tissue microbial diversity, taxonomic composition, and functional pathways. Conventional statistical analyses (two-sample t-test and analysis of variance) were employed to evaluate significant differences across groups. Results: 2bRAD-M sequencing successfully detected tumor microbial DNA in all 20 participants of this pilot study. A total of 285 microbial species were identified, including 160 genera and 11 phyla, from results that passed quality control assessments. The mean alpha diversity, as measured by the Shannon index, was 2.41, and the Chao1 index was 15. Compared to women with localized (stage 1 and 2, n=8) HGSOC, those with stage 3 HGSOC (n=12) exhibited higher Shannon (mean 2.45 vs. 1.57, p=0.12) and Chao1 indices (mean 21 vs. 13, p < 0.001). Stage 3 tumors also showed a higher relative abundance of microbial species from the phyla Pseudomonadota, Bacteroidetes, and Bacillota, compared to localized stage tumors (p < 0.001). Pathway analysis identified secondary bile acid biosynthesis as the most significantly enriched pathway in stage 3 tumors, with over 1.5-fold higher abundance of this pathway (p < 0.0001) than stage 1 and 2 tumors. Age at diagnosis was also associated with microbiome composition; women diagnosed at a younger age (<50) had higher Shannon and Chao1 indices compared to older women. Additionally, women with younger age at diagnosis vs. ≥50) were more likely to have a lower relative abundance of Bacteroidetes and a higher abundance of the prolactin signaling pathway. Conclusion: Our pilot findings suggest that HGSOC tumor microbiome features measured among Black/AA women differ by stage and age at diagnosis, and thereby may influence the progression of HGSOC. Further studies with larger sample size are warranted as the next step. Citation Format: Tengteng Wang, Lauren C. Peres, Jeffrey R. Marks, Courtney E. Johnson, Elisa V. Bandera, Joellen M. Schildkrau. Tumor tissue microbiome in the high-grade serous ovarian cancer: a pilot investigation within the African American Cancer Epidemiology Study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4927.

Abstract 2398: Pregnancy-specific glycoproteins in tumors are strong predictors of outcome in female lung adenocarcinoma patients

Abstract Pregnancy-specific glycoproteins (PSGs) are normally critical regulators of maternal immune tolerance during pregnancy, preventing fetal rejection by modulating innate and adaptive immune responses. Recent studies have identified that mRNA expression of PSG genes in tumors is associated with poor prognosis in lung, mesothelioma, breast, and ovarian cancers. Given their pregnancy-related function, we hypothesized that PSGs could exert sex-specific effects in some cancers. An analysis of sex-differential effects of PSGs as prognostic markers was conducted using two datasets from The Cancer Genome Atlas (TCGA) including 235 male and 271 female patients and Clinical Proteomic Tumor Analysis Consortium (CPTAC) including 70 male and 36 female patients. To assess the predictive power of PSGs, we evaluated whether incorporating PSG expression levels improved machine learning models for survival prediction. Lung adenocarcinoma (LUAD) was identified as showing a significant sex-specific prognostic difference. Female LUAD patients expressing PSG genes had notably worse survival outcomes compared to those without PSG expression. Male patients did not show similar effects. Combinatorial analysis showed that a combination of PSG3, PSG7, and PSG8 expression resulted in particularly poor prognosis in the female group (30% of the female patients) with p = 8.67E-06. This finding was independently validated in the smaller CPTAC dataset with p = 0.0382. Further analysis of correlated pathway changes revealed that female LUAD patients with PSG expression exhibited enrichment of the "KRAS Signaling Down" pathway, suggesting a potential mechanism underlying the observed sex-specific effects. Including the KRAS pathway activity into the PSG model demonstrated robust performance in predicting survival outcomes for female patients (validated C-index = 0.78 using the CPTAC dataset) but did not improve prediction for male patients. These findings highlight a unique role for PSGs in influencing LUAD progression and survival in a sex-dependent manner. Targeting PSG-related pathways may offer a tailored treatment strategy for female LUAD patients, potentially improving outcomes. Further research is needed to unravel the relationship between PSG expression and KRAS pathway activation. We also plan to examine the sex-specific prognostic difference, looking into pregnancy history and the influence of hormone-related genes. Since PSGs are not typically expressed in the absence of pregnancy, they could be a promising drug target. Citation Format: Jung Hun Oh, 1 Gabrielle Rizzuto, 1 Rena Elkin, 1 Corey Weistuch, 1 Larry Norton, 1 Gabriela Dveksler, 2 Joseph O. Deasy1. Pregnancy-specific glycoproteins in tumors are strong predictors of outcome in female lung adenocarcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2398.

Abstract 1580: HuB14-VA-PL2202, a novel antibody-drug conjugate targeting ASCT2, a novel ADC target over-expressed in both solid and hematological cancers

Abstract SLC1A5 (Solute Carrier family 1 member 5), also known as ASCT2 (Alanine, Serine, Cysteine Transporter 2), is a Na+ dependent antiporter with its preferred substrate being glutamine. ASCT2 expression is reported in normal tissues, however it has been shown to be dramatically increased in several solid tumors (lung, colorectal) and hematological malignancies (acute myeloid leukemia (AML), multiple myeloma). Moreover, high ASCT2 expression was associated with a worse prognosis in liver and lung cancers. Because of this profile of expression, ASCT2 is an appealing membrane protein for pharmacological targeting. We have developed a new antibody-drug conjugate (ADC) targeting ASCT2 (HuB14-VA-PL2202), composed of a humanized IgG1 directed against human ASCT2, to which PL2202, consisting of a proprietary cleavable linker and exatecan, a topoisomerase I inhibitor, has been site-specifically conjugated with a drug to antibody ratio ∼6. FcγR-mediated effector function was abrogated via mutation in the Fc portion of the antibody. The aim of this study was to characterize the in vitro cytotoxicity of HuB14-VA-PL2202 in human cancer cell lines, and determine its in vivo efficacy. The safety and tolerability of HuB14-VA-PL2202 was also evaluated in cynomolgus monkeys. Membrane expression of ASCT2 was confirmed by IHC in sections from xenograft biopsies and human tissues.In vitro, HuB14-VA-PL2202 was readily internalized by ASCT2+ve cancer cells, showed specific binding to CHO cells expressing recombinant human or cynomolgus monkey ASCT2, and displayed potent cytotoxic activity in a range of target positive cancer cell lines, both from solid and hematological tumors. In vivo, HuB14-VA-PL2202 dosed once at 6 mg/kg was able to significantly delay tumor growth in the subcutaneous (sc) G-402 human renal leiomyoblastoma cancer xenograft model. Likewise, in the sc MOLM-13 AML xenograft model, HuB14-VA-PL2202 dosed once at 10 mg/kg achieved 5/10 tumor free survivors at the end of the study. In a PK study in human FcRn Tg32 SCID mice, HuB14-VA exhibited a 7.4 day half-life; whilst in a DRF study in cynomolgus monkeys, HuB14-VA-PL2202 was tolerated at 40 mg/kg, indicating there is a favorable therapeutic index. Membrane expression of ASCT2 was confirmed by IHC, in sections of xenograft models and tissue microarray (TMA) of human cancer indications. ASCT2 expression in NSCLC and HNSCC was found to be significantly higher than in the correspondent normal tissue. In conclusion, ASCT2 represents an interesting novel tumor target for an ADC approach. HuB14-VA-PL2202 demonstrated potent and specific in vitro cytotoxicity and in vivo anti-tumor activity in both hematological and solid tumor models, and was well tolerated in cynomolgus monkeys. Together, the data generated with HuB14-VA-PL2202 warrants its further development into the clinic in cancers over-expressing ASCT2. Citation Format: Danilo Cucchi, Elizabeth Horsley, Alina Chrzastek, Ben Leatherdale, Simone Sims, Nicole Bledowski, Banusha Rajeenthira, Narinder Janghra, Lara Montolio, Abigail Kimpalu, Christopher Gallagher, Charlie Britten, Lolke de Haan, Paul W. Hogg, Chris Pickford, Patrick H. van Berkel. HuB14-VA-PL2202, a novel antibody-drug conjugate targeting ASCT2, a novel ADC target over-expressed in both solid and hematological cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1580.

Abstract 7170: Differential prognostic impacts of the germline APOBEC3B deletion polymorphism in hepato-pancreato-biliary and genitourinary cancers

Abstract The mutational signatures related to apolipoprotein B mRNA-editing enzyme catalytic polypeptides (APOBECs) are found in many cancers. We aimed to assess the impact of APOBEC3B deletion variant on the risk and prognosis of various cancers in the Golestan Cohort Study, Iran, comprising 1, 393 cancer cases and 1, 806 controls (median age: 69.2 years). The population predominantly consisted of the Turkmen ethnicity (77.5%), with 49.6% of individuals deceased during the study period. The TaqMan genotyping assay was used as a proxy to identify the rs12628403-A/C (linked to intact/deleted APOBEC3B) alleles. The APOBEC3B deletion was identified in 29.8% of individuals. Cancer cases exhibited a higher frequency of APOBEC3B deletion compared to controls, particularly among Turkmen individuals (32.9% vs. 28.5%, OR = 1.23, P = 0.019). Increased frequencies were observed for gastric cancer (OR = 1.61, P = 0.001) and collective gastrointestinal (esophageal, gastric, small intestinal, and colorectal) cancers (OR = 1.31, P = 0.012) among APOBEC3B-deleted individuals. In head and neck cancer, APOBEC3B deletion was more prevalent among cases of all origins (OR = 1.83, P = 0.036). Survival analyses revealed contrasting effects of the APOBEC3B deletion. APOBEC3B deletion was significantly associated with longer survival in pancreatic (4.0 vs. 2.7 months; P = 0.025) and biliary (29.3 vs. 3.1 months; P = 0.047) cancers, as well as the collective hepato-pancreato-biliary (hepatocellular, pancreatic, gallbladder, and biliary) cancers (4.2 vs. 2.5 months; P = 0.002). By contrast, it was predictive of shorter survival in bladder (2.1 vs. 32.8 months; P = 1.1e-4) and cervical (5.7 vs. 53.7 months; P = 0.017) cancers, and the collective genitourinary (bladder, cervical, uterus, and prostate) cancers (5.7 vs. 32.8 months; P = 1.9e-5). Multivariate Cox regression analyses confirmed a favorable prognostic impact of the APOBEC3B deletion in the collective hepato-pancreato-biliary cancers (HR = 0.634; P = 0.039), while an adverse prognostic impact in the genitourinary cancers (HR = 2.45; P = 1.9e-4) and meningioma (HR = 6.750; P = 0.025). These findings suggest the APOBEC3B deletion as a susceptibility and prognostic biomarker in specific cancers, with differential effects based on tumor type. Further studies are warranted to elucidate underlying mechanisms and potential therapeutic implications. Citation Format: Ahmadreza Niavarani, Peyvand Parhizkar Roudsari, Roya Noorbakhsh, Melineh Markarian, Reza Malekzadeh. Differential prognostic impacts of the germline APOBEC3B deletion polymorphism in hepato-pancreato-biliary and genitourinary cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7170.

Abstract 3309: Characterization of long non-coding RNAs in ependymomas: Uncovering potential biomarkers and therapeutic targets

Abstract Introduction: Ependymomas (EPNs), accounting for 5-6% of glial tumors, arise from radial glial cells and exhibit significant heterogeneity, leading to variable prognosis. Despite their clinical significance, the oncogenic drivers and potential therapeutic targets for EPNs remain poorly understood. Long non-coding RNAs (lncRNAs) are emerging as crucial regulators in many cancers, influencing tumorigenesis and therapeutic resistance. However, their role in EPN pathobiology has not been explored. This study aims to unravel the lncRNA landscape in EPNs to identify novel diagnostic biomarkers and therapeutic targets, improving patient stratification and treatment outcomes. Methods: 38 EPN tumor samples were classified into 21 supratentorial (ST), 13 posterior fossa (PF), and 4 spinal (SP) subtypes based on WHO 2021 criteria and subjected to RNA sequencing to map their RNA landscape, using 6 normal brain tissue samples as control. Raw data was normalized to identify significantly deregulated genes (padj < 0.05, -1 ≤ log2 fold change ≥ 1). qPCR validated the top deregulated lncRNAs (n = 60 extended cohort, p < 0.05). Pan-cancer analysis, functional annotation, target prediction, co-expression network construction, and prognostic relevance were assessed using ECORI, LncExplore, LncHub2, RNAInter, and Prognoscan respectively. Results: RNA sequencing identified 2, 271 upregulated and 1, 728 downregulated lncRNAs in EPN sub-groups, with 108 commonly upregulated and 187 downregulated across subtypes. qPCR confirmed LINC01971 overexpression in ST-EPNs (p < 0.001), FAM74A7 upregulation in PF and SP subtypes (p < 0.0001, p < 0.001), and LINC00320 downregulation in all subgroups (p < 0.001). Pan-cancer analysis revealed high LINC01971 in uterine endometrial and lung carcinoma, slightly increased FAM74A7 in kidney clear cell carcinoma, and low LINC00320 across all cancers. LINC01971, co-expressed with RELA, is involved in NF-kB-driven tumorigenesis and immune modulation. Pathway analysis associated with transcription factors (ESR1, SOX2, TP53, FOXA1) and chromatin modifiers (H3K27me3, H3K4me3), indicating a role in epigenetic reprogramming. FAM74A7, correlated with transcription factors (EOMES, SOX2, NANOG, FOXA1), is linked to tumor progression and epigenetic regulation, with disease associations (papillary, cellular, and myxopapillary EPNs) supporting its potential as a diagnostic and therapeutic target. LINC00320, reduced in malignant gliomas, regulates FOXA1 and H3K4me3, affecting metabolism and protein lipidation. Co-expression patterns in EPNs and gliomas highlight their role in tumor progression and neurodegenerative diseases Prognoscan links RELA, FOXA1, and SOX2 overexpression to poor prognosis in various cancers. This comprehensive transcriptomic analysis of EPNs unveils novel lncRNAs, as potential prognostic biomarkers and therapeutic targets. Citation Format: Rafat Malik, Dr. Amandeep Kumar, Dr. Vaishali Suri, Dr. Mehar Chand Sharma. Characterization of long non-coding RNAs in ependymomas: Uncovering potential biomarkers and therapeutic targets. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3309.

Utility of circulating human papillomavirus DNA as a biomarker for detection and prognosis of cervical cancer in Japanese patients.

Cervical cancer (CC), the fourth most common cancer in women, is caused predominantly by human papillomavirus (HPV). Although measuring serum squamous cell carcinoma antigen (SCC Ag) can be useful for detecting recurrence of SCC, a major type of CC, its prognostic value remains unclear. This study focuses on the utility of circulating cell-free HPV (ccfHPV) DNA in plasma as a biomarker, with particular emphasis on its relevance to high-risk HPV subtypes prevalent in Japan. A prospective study of 26 CC patients and 23 females diagnosed with pre-cancerous lesions was conducted. Patients were selected carefully to include only those with single high-risk HPV subtypes (i.e., HPV16, 18, 52, or 58), reflecting regional HPV epidemiology. ccfHPV DNA was isolated from plasma and analyzed by droplet digital PCR targeting the HPV E7 genes. The detection rate of ccfHPV DNA in CC patients before clinical treatment was 57.7%. The detection rate correlated significantly with tumor size (r = 0.624, P < 0.01) and clinicalstage (r = 0.844, P < 0.01). No ccfHPV DNA was detected in the females with pre-cancerous lesions. By contrast, of the 13 concurrent chemoradiotherapy cases, two relapsed within 6 months post-treatment. In those cases, ccfHPV DNA levels rose earlier than SCC Ag levels. The 11 CC cases in which no ccfHPV DNA was detected within 1 month post-treatment did not relapse. ccfHPV DNA is a useful biomarker for advanced-stage CC and for predicting prognosis, particularly in the Japanese clinical setting.

Abstract 1371: ChemoNETosis is associated with chemotherapy resistance in pancreatic cancer

Abstract Background: Chemotherapy resistance is a major contributor of the poor prognosis of pancreatic cancer, yet its underlying mechanisms remain poorly understood. Neutrophil Extracellular Traps (NETs), a form of neutrophil-specific cell death, have been reported to be associated with poor prognosis in various cancers because they act to suppress tumor immunity and promote metastasis. Recently, chemotherapy-stimulated NETs, termed “ChemoNETosis”, were reported to contribute to chemotherapy resistance in breast cancer (Mousset A, Cancer cell. 2023). Therefore, we investigated the role of NETs in resistance to cytotoxic chemotherapy in pancreatic cancer. Methods: The abundance of NETs in the tumor microenvironment was analyzed in relation to chemotherapy efficacy using immunohistochemical staining of resected specimens from pancreatic cancer patients treated with neoadjuvant chemotherapy. The ability of pancreatic cancer cells to induce NETs was assessed with and without gemcitabine stimulation by extracellular DNA staining in vitro and by immunohistochemical analysis in vivo. Finally, the efficacy of the combined anti-NETs treatment and gemcitabine was examined in a mouse subcutaneous tumor model. Results: NETs were more abundant in unresponsive tumors compared to responsive tumors in clinical sample. Gemcitabine-treated pancreatic cancer cells induced significantly higher levels of NETs than untreated cells in vitro as well as in vivo tumor models. This “ChemoNETosis” was effectively inhibited by Navarixin, a CXCR2 inhibitor. Combination therapy with Navarixin and gemcitabine achieved greater tumor reduction compared to gemcitabine alone with, a complete response (CR) rate of 28.6% (2/7) vs 0% (0/7). Conclusion: NETs may play a key role in chemotherapy resistance in pancreatic cancer. Targeting NETs could provide a novel approach to enhancing the efficacy of chemotherapy in preclinical models and warrants further investigation. Citation Format: Shohei Nogi, Shunsuke Kagawa, Atsuki Taniguchi, Nobuhiko Kanaya, Yoshihiko Kakiuchi, Kazuya Yasui, Satoru Kikuchi, Shinji Kuroda, Hiroshi Tazawa, Toshiyoshi Fujiwara. ChemoNETosis is associated with chemotherapy resistance in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1371.