bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3639: ARID1 mutations may serve as a predictor of MSI and TMB levels in gastric cancer
Authors: Xu Chunsheng , Lian Bo , Dai Yujie , Duan Weiming , Zhao Feilong , Li Mengbin
Published: March 2024

Background: ARID1A is a gene that produces a protein called BAF250a, which is a component of the chromatin remodeling complex. This complex plays a critical role in regulating gene expression by altering the structure of chromatin. ARID1A mutations and MSI-H are mutually exclusive in endometrial cancer, but not in ovarian cancer. ARID1A mutations are associated with high TMB in certain types of cancer, such as endometrial and gastric cancer. The relationship between ARID1B mutations and MSI-H/TMB is complex, and this study aims to clarify it in gastric cancer.

Methods: The formalin-fixed paraffin-embedded (FFPE) tissues 337 patients with gastric cancer who have underwent next-generation sequencing (NGS) include 733 genes from Nov, 2019 to Mar, 2023 in 3DMed Clinical Laboratory Inc. were investigated in this study. These patients are still being followed up.

Result: In this study, 337 patients with gastric cancer were analyzed for ARID1A and ARID1B mutations, MSI-H status, and TMB levels. The

results showed that 17.8% of the patients had ARID1A mutations, 8.9% had ARID1B mutations, and 3.6% had both mutations. Additionally, 7.7% of the all patients had MSI-H. The study found that patients with ARID1 mutations had significantly higher rates of MSI-H compared to unselected patients. Specifically, 35% of patients with ARID1A mutations, 30% with ARID1B mutations, and 75% with both mutations had MSI-H, compared to 7.7% in unselected patients. Furthermore, TMB levels were higher in patients with ARID1A or ARID1B mutations compared to wild-type and unselected patients (p<0.0001). There was no significant difference observed between patients with ARID1A and ARID1B mutation subgroups in terms of TMB levels (p = 0.3515). However, TMB levels were lower in patients with ARID1A or ARID1B mutations compared to patients with both mutations (p = 0.0036, p = 0.0104). These findings suggest that ARID1 mutations may cause genomic and chromosomal instability in gastric cancer, leading to higher rates of MSI-H and TMB.

Conclusion: The study highlights the potential clinical significance of ARID1 mutations as a biomarker for predicting MSI-H and TMB levels in gastric cancer, which could help guide personalized treatment strategies for patients with this disease. However, further research

is needed to confirm these findings and to determine the clinical implications of ARID1 mutations in gastric cancer.

Citation Format: Chunsheng Xu, Bo Lian, Yujie Dai, Weiming Duan, Feilong Zhao, Mengbin Li. ARID1 mutations may serve as a predictor of MSI and TMB levels in gastric 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 3639.
Abstract 3643: Molecular pathogenesis of lung cancer associated with interstitial pneumonia
Authors: Mizuno Daisuke , Shien Kazuhiko , Matsuoka Atsushi , Ohki Masayoshi , Tomida Shuta , Yoshichika Ryo , Higashihara Tomoaki , Mukohara Fumiaki , Hayashi Naohiro , Habu Tomohiro , Yoshikawa Mao , Suzawa Ken , Yamamoto Hiromasa , Ennishi Daisuke , Toyooka Shinichi
Published: March 2024

Background: Interstitial pneumonia (IP) is known to be associated with a high risk of developing lung cancer. While common mechanisms have been reported to be involved in the pathogenesis of IP and lung cancer, including genetic and epigenomic alterations or specific signaling pathway activations, many of the molecular mechanisms of lung cancer development in IP lesions remain unknown.

Methods: To clarify the detailed mechanisms of the pathogenesis of lung cancer associated with IP, we performed spatially resolved transcriptomics on lung cancer specimens obtained from usual interstitial pneumonia (UIP) associated lung cancer patients. In a total of 10 patients, including five lung cancers that developed inside the UIP and five lung cancers that originated outside the UIP, regions of interest (ROIs) were selected in the tumoral tissues and their adjacent non-tumor tissues. Then, gene expression profiles were comprehensively analyzed by using GeoMx digital spatial profiler in each ROI.

Results: In the UIP lesions adjacent to lung cancer, increased gene expressions associated with pulmonary fibrosis, such as COL1A1, COL3A1, and APOE, were observed, and gene set enrichment analysis (GSEA) revealed that they were associated with autoimmunity-related pathways. When we compared the tumor lesions developed inside the UIP with outside the UIP, increased gene expressions related to IP mortality were observed in the tumor cells developed inside the UIP. Interestingly, GSEA revealed that the gene set for neutrophil extracellular trap (NETs) formation was found to be upregulated in the tumor cells developed inside the UIP, suggesting that NETs plays an important role in the pathogenesis of lung cancer developed in IP lesion.

Conclusions: In our study, spatially resolved transcriptomics revealed a novel pathway related to the pathogenesis of lung cancer associated with IP.

Citation Format: Daisuke Mizuno, Kazuhiko Shien, Atsushi Matsuoka, Masayoshi Ohki, Shuta Tomida, Ryo Yoshichika, Tomoaki Higashihara, Fumiaki Mukohara, Naohiro Hayashi, Tomohiro Habu, Mao Yoshikawa, Ken Suzawa, Hiromasa Yamamoto, Daisuke Ennishi, Shinichi Toyooka. Molecular pathogenesis of lung cancer associated with interstitial pneumonia [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 3643.
Abstract 3727: Synergistic effect of CD47 blockade and EPHA3 treatment on recurrent head and neck cancers
Authors: Kim Song Hee , Han Myung Woul , Kim Ji Won , Kim Seong Who
Published: March 2024

CD47 acts as a “don’t eat me “signal and suppresses it through its interaction with signal regulatory protein (SIRP-a) on the macrophage. CD47 is expressed in many human cancer cells, including head and neck cancer. Additionally, we reported in a previous study that EphA3 is overexpressed in radioresistant head and neck cancer and may play an important role in the development of radioresistance in head and neck cancer. In our present study, we demonstrated that the blockade of EPHA3 and CD47 attenuates the function of M2-like macrophages and may contribute to macrophage polarization toward the M1 phenotype. Here, we combined a therapeutic strategy of an anti-EPHA3 and an anti-CD47 antibody. Using mRNA sequencing and fluorescence imaging, we showed that the combination treatment could significantly enhance the effectiveness of anti-EPHA3 and anti-CD47 antibodies, in reactivating macrophages and reversing macrophage polarization. In addition to using flow cytometry in vivo, combination treatments can alter the proportion of tumor-associated macrophages (TAMs). Collectively, our findings suggested that the combination treatment of anti-EphA3 and the anti-CD47 antibodies could significantly improve tumor suppression, increase the proportion of M1 macrophages, and decrease the proportion of M2 macrophages.

Citation Format: Song Hee Kim, Myung Woul Han, Ji Won Kim, Seong Who Kim. Synergistic effect of CD47 blockade and EPHA3 treatment on recurrent head and neck cancers [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 3727.
Abstract 3760: The importance of optimizing DNA extraction conditions for formalin fixed paraffin embedded tissues
Authors: Butler Matthew G. , Forson Benedicta , Cowen Maria , Ramprakash Jayanthi , Lowe Dana Ruminski , Konigshofer Yves
Published: March 2024

The pre-analytic extraction of Formalin Fixed Paraffin Embedded Tissues (FFPETs) appears to have a profound effect on the ability to obtain meaningful data from the DNA therein. FFPETs represent important materials in Pathology that are used to diagnose and analyze cancer. As part of preparing FFPETs, the formalin fixation step preserves the structure of tissues through covalent modifications but can also damage nucleic acids through that same process. Over the last decade, the emergence of Molecular Pathology, which benefits from gentler fixation compared to Histopathology and especially Immunohistopathology, has led to changes in how FFPETs are prepared. However, the remnant FFPETs from over a decade ago may be far from representative of what is now prepared for Molecular Pathology by many laboratories. Here we discuss our optimization of FFPET extraction for gently fixed samples. When we prepared our Seraseq FFPE Homologous Recombination Deficiency (HRD) reference standards using fixation conditions that are recommended for Molecular Pathology and extracted the resulting FFPETs using generic conditions, our initial coverage data from Whole Genome Shotgun (WGS) sequencing was difficult to analyze for changes in copy number across the genome. A major contributor to nonuniform coverage was identified as the formalin reversal step, where deparaffinized proteinase K-digested tissue is heated in water to near boiling to attempt to detach formaldehyde from nucleic acids through hydrolysis. Given the gentler fixation conditions, this step was found to be mostly unnecessary, and omitting it improved the resulting data substantially. A reason for this appears to be that the gentler fixation conditions that are now in use may not protect the DNA from the effects of near-boiling water, where the lack of salt lowers the melting temperature of double stranded DNA fragments and causes them to denature unless they have a higher GC content. Different kits used for the extraction of nucleic acids from FFPETs may benefit from different optimizations to obtain improved sequencing data from today’s Molecular pathology samples, and reference standards that represent such samples provide a useful tool for such optimizations.

Citation Format: Matthew G. Butler, Benedicta Forson, Maria Cowen, Jayanthi Ramprakash, Dana Ruminski Lowe, Yves Konigshofer. The importance of optimizing DNA extraction conditions for formalin fixed paraffin embedded 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 3760.
Abstract 3762: 11,000-plex aptamer based proteomics of bladder cancer urine for the discovery of novel disease biomarkers
Authors: Mohan Chandra , Vanarsa Kamala , Castillo Jessica , Wang Long , Lotan Yair
Published: March 2024

In search of more accurate, non-invasive biomarkers of bladder cancer (BC), a comprehensive aptamer-based screen of urine proteins was conducted using urine samples from a BC cohort, followed by systems biology analyses. Following an initial 1317-plex screen, an extended 11,000 plex aptamer-based proteomic screen is in progress. Based on the initial screen, 30 urine proteins were next ELISA validated in an independent cohort of 68 subjects, and the results are shown in Table 1. Of 21 urine proteins that discriminated BC from urology clinic controls (UC), urine D-dimer displayed the highest ROC AUC value (0.96) and sensitivity (95%) (Table 1). Furthermore, 9 urine proteins significantly discriminated more advanced BC (T1-T4) from earlier stages (Ta-Tis), with IL-8 and MMP-12 being the best performers. Urine MMP12 exhibited the highest specificity of 80% at fixed sensitivity for identifying advanced BC. Systems biology analysis implicated molecular functions related to extracellular matrix, collagen, integrin, heparin and transmembrane tyrosine kinase signaling in BC susceptibility, with HNF4A and NFKB1 emerging as key molecular regulators. STEM analysis of the dysregulated pathways implicated a functional role for the immune system, complement and interleukins in BC disease progression. Urine C2, D-dimer, and Elastase were additionally ELISA validated in a second BC cohort of Chinese ethnicity. Thus, comprehensive proteomics and independent ELISA validation have uncovered novel urine biomarkers for initial BC diagnosis and subsequent disease progression, that warrant further head to head comparison with current diagnostic tests.

Citation Format: Chandra Mohan, Kamala Vanarsa, Jessica Castillo, Long Wang, Yair Lotan. 11,000-plex aptamer based proteomics of bladder cancer urine for the discovery of novel disease biomarkers [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 3762.
Abstract 3774: Evaluation of FibraChek™ for non-invasive detection of hepatic fibrosis and hepatocellular carcinoma
Authors: Tanaka Sunao , Xie Guoxiang , Furuya Hideki , Jia Wei , Rosser Charles J.
Published: March 2024

Introduction and Objectives: The incidence of hepatocellular carcinoma (HCC) has almost tripled since the early 1980s in the United States where it is the fastest rising cause of cancer-related deaths. Advanced liver fibrosis and cirrhosis are ones of major risk factors for HCC. The recent evidence demonstrates that successfully treating the cause of early to moderate hepatic fibrosis may reverse most. For this reason, detecting hepatic fibrosis in an early stage is crucial. Liver biopsy is currently the gold standard for the assessment of hepatic fibrosis in clinical practice. Thus, there is an urgent clinical need for the development of non-invasive blood-based tests because of its ease of obtaining biological material. Previously, we developed FibraChek™, non-invasive blood-based tests. In this study, we tested the performance of FibraChek™ on detecting hepatic fibrosis and HCC in the US.

Methods: The performance of FibraChek™ was evaluated in a single-institutional cohort of 14 prospectively collected subjects presenting for chronic liver disease (NAFLD/NASH) patients with hepatic fibrosis, 19 prospectively collected subjects diagnosed with HCC, and 12 prospectively collected controls from the US. The algorithm uses weighted value of the 5 biomarkers: AST, ALT, Platelet, Taurocholic Acid (TCA) & Tyrosine plus age to derive a risk score. The ability of the test to identify patients harboring hepatic fibrosis or HCC was assessed. Hepatic fibrosis status was confirmed by tissue biopsy or definitive surgery. Diagnostic performance was assessed using AUC.

Results: FibraChek™ provided an AUC of 0.923 with an overall sensitivity of 93.9%, specificity of 81.8%, NPV 91.2% and PPV 81.8%. Interestingly, risk scores in HCC cohort indicated higher than those in patients with hepatic fibrosis. Thus, FibraChek™ may be also able to use for HCC detection.

Conclusions: Serum levels of a biomarker panel enabled the accurate discrimination of hepatic fibrosis and controls. The FibraChek™ test can achieve the easy, efficient, and accurate detection of hepatic fibrosis and HCC in a non-invasive patient setting.

Citation Format: Sunao Tanaka, Guoxiang Xie, Hideki Furuya, Wei Jia, Charles J. Rosser. Evaluation of FibraChek™ for non-invasive detection of hepatic fibrosis and 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 3774.
Abstract 3790: HtrA3 promotes malignant progression of colorectal cancer via PI3K-AKT-FOXO1 signaling pathway
Authors: Zheng Jing , Huang Xianhua , Peng Xian-e , Wu Yunli
Published: March 2024

High-temperature requirement protease A3 (HtrA3) is known to contribute to the progression of various carcinomas through tissue-specific actions, yet its precise role in colorectal cancer (CRC) remains unclear. Our study revealed that HtrA3 is significantly upregulated in CRC at both mRNA and protein levels. TCGA database analysis showed that higher HtrA3 expression in colon adenocarcinoma is linked to poorer patient survival. Moreover, increased HtrA3 expression in HCT116 cells boosted their proliferation, migration, and invasion, while decreasing HtrA3 in SW480 cells had the reverse effect. In HCT116 cells with high HtrA3 levels, there was an increase in p-PI3K, p-AKT, and p-FOXO1, which reduced upon treatment with the PI3K inhibitor LY294002. Conversely, in SW480 cells with lowered HtrA3, these molecular levels decreased and rose again after treatment with the PI3K activator 740Y-P. HtrA3 also promoted cell proliferation, migration, and invasion in the presence of LY294002 and 740Y-P. In vivo experiments demonstrated that HtrA3 overexpression accelerated xenograft tumor growth. This study confirms that HtrA3’s overexpression in CRC cells promotes their proliferation, migration, and invasion by activating the PI3K-AKT-FOXO1 signaling pathway. Therefore, HtrA3 could be a significant factor in the advancement of CRC and may serve as a potential prognostic marker for guiding targeted CRC therapies.

Citation Format: Jing Zheng, Xianhua Huang, Xian-e Peng, Yunli Wu. HtrA3 promotes malignant progression of colorectal cancer via PI3K-AKT-FOXO1 signaling pathway [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 3790.
Abstract 3795: Possible role of miR-375-3p in cervical lymph node metastasis of oral squamous cell carcinoma
Authors: Saika Masato , Nakashiro Koh-ichi , Tokuzen Norihiko , Shirai Hiroyuki , Uchida Daisuke
Published: March 2024

Latent cervical lymph node metastasis (LNM) is the most important prognostic factor in early oral squamous cell carcinoma (OSCC). However, no clinically useful predictors of LNM in early OSCC are available. In this study, we focused on the microRNAs (miRNAs) involved in the expression of numerous genes and explored those associated with latent cervical LNM in OSCC. Microarray analysis of miRNA expression showed that the expression levels of miR-375-3p were significantly reduced in primary OSCC tissues with latent cervical LNM. Subsequently, we quantified the expression of miR-375-3p by RT-qPCR and digital PCR. Similar to the results of miRNA microarray analysis, miR-375-3p was significantly downregulated in primary OSCC tissues with latent cervical LNM. The results of digital PCR showed a more significant difference than those of RT-qPCR. When the reference value for predicting latent cervical LNM was set to less than 57.85 copies based on the receiver operating characteristic curve, the sensitivity, specificity, accuracy, and area under the curve were 80%, 100%, 90%, and 0.942, respectively. Next, we examined the effects of miR-375-3p mimics on the growth and migration of four human OSCC cell lines (SAS-L1, HSC2, HSC3, and Ca9-22) that do not express miR-375-3p. When an miR-375-3p mimic was introduced into these cells, cell proliferation and migration were significantly suppressed. Total RNA was extracted from these cells reverse-transfected with miR-375-3p mimic for 48 hours. Microarray analysis and Ingenuity Pathway Analysis (IPA) miRNA target filter showed that miR-375-3p overexpression reduced the expression of 266 genes, of which 37 genes had the target sequences of miR-375-3p in their 3’-untranslated region. Among these target genes, CEPT1 and TIMM8A knockdown significantly inhibited the migration of all human OSCC cells, similar to miR-375-3p mimics. Furthermore, IPA core analysis revealed a decrease in expression of genes involved in the activation of PI3K-AKT pathways by miR-375-3p overexpression. These results indicated that downregulating miR-375-3p expression could promote cervical LNM by enhancing cell proliferation and migration in OSCC. We also found that CEPT1 and TIMM8A as novel target genes of miR-375-3p regulated the migration of human OSCC cells. The expression levels of miR-375-3p in primary OSCC tissues appear to be a useful biomarker for predicting latent cervical LNM.

Citation Format: Masato Saika, Koh-ichi Nakashiro, Norihiko Tokuzen, Hiroyuki Shirai, Daisuke Uchida. Possible role of miR-375-3p in cervical lymph node metastasis of oral squamous cell 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 3795.
Abstract 3834: Plasmablastic lymphoma provisional prognostic score
Authors: Haddad Philip A. , Lerner Jaren
Published: March 2024

Background Plasmablastic Lymphoma (PBL) is a rare and aggressive subtype of non-Hodgkin's lymphoma. It tends to be associated with immunosuppressive clinical contexts, such as HIV infection and immunosuppressive therapies for autoimmune disorders and organ transplants. However, due to the rarity of the disease, which needs to be better understood, varied treatment approaches have been implemented, and no optimal data or guidelines for managing PBL are available. Therefore, we conducted this study to develop a provisional PBL prognostic score (PBLPS) for this rare disease.

Methods We used our constructed PBL database, which contains retrospective data on 300 cases. Such data included demographics such as sex, age, and race. It also included disease presentation symptoms, duration of symptoms before diagnosis, site(s) of the disease, blood counts, coexisting comorbidities, disease immunohistochemical and molecular phenotype, types of treatment, and survival outcomes. Of the 300 cases, 291 had complete survival and outcomes data, the sample chosen for this study. Cox proportional-hazards model and Log-rank tests were used to assess the influence of clinicopathologic factors on overall survival (OS). We included factors that statistically impacted OS and scored them by the impact of their hazard ratios.

Results The median OS of the cohort was 25 months. The following dichotomous variables were identified as impactful prognostic factors in this cohort: LDH>500 (p=0.04), CD4<100 (p=0.006), bone marrow (BM) involvement (p<0.0001), EBER-negative (p=0.01), HHV8+ (p=0.02), and involvement of liver (p=0.003), lungs/pleura (p<0.0001), and upper GI tract (p=0.001). A prognostic model was devised using these variables to identify different levels of risk. Involvement of BM and involvement of any of the worse prognosis organs (liver, lung/pleura, and/or upper GI tract) were each assigned a score of 2 when present. CD4<100, EBER-negative, and LDH>500 were assigned 1 point each as they had the lowest hazard ratios of all the other variables. In this exploratory cohort, we assigned low risk a score of 0, intermediate risk a score of 1-2, and high risk a score of 3-7. This prognostic score system led to our cohort's most optimal risk discriminatory model, where low, intermediate, and high risk had a median OS of NR, 15, and 4 months, respectively (p<0.0001).

Conclusion This PBLPS is a promising new tool for risk-stratifying patients with PBL. However, it still requires prospective validation.

Citation Format: Philip A. Haddad, Jaren Lerner. Plasmablastic lymphoma provisional prognostic score [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 3834.
Abstract 3836: Mast cell leukemia provisional prognostic score
Authors: Haddad Philip A. , Chennapragada Sumasri
Published: March 2024

Background Mast cell leukemia (MstCL) is a rare but aggressive variant of systemic mastocytosis (SM), defined by the presence of >20% atypical mast cells in the bone marrow. It is further classified into leukemic and aleukemic variants based on the presence or absence of >10% atypical mast cells in the peripheral blood, respectively. There is a wide variation in treatment regimens used to treat MstCL. Despite this, prognosis remains poor. While MstCL often follows an aggressive course, its outcomes vary considerably. We conducted this study to develop a provisional MstCL prognostic score (MCLPS) for this rare disease.

Methods We used our constructed MstCL database, which contains retrospective data on 144 cases. Such data included demographics such as sex, age, and race. It also included disease presentation symptoms, duration of symptoms before diagnosis, site(s) of the disease, blood counts, coexisting comorbidities, disease immunohistochemical and molecular phenotype, types of treatment, and survival outcomes. Of the 144 cases, only 104 had complete survival and outcomes data, the sample chosen for this study. Cox proportional-hazards model and Log-rank tests were used to assess the influence of clinicopathologic factors on overall survival (OS). We included factors that statistically impacted OS and scored them by the impact of their hazard ratios.

Results The median OS of the cohort was 9 months. The following dichotomous variables were identified as impactful prognostic factors in this cohort: Age<55 (6 vs. 15 months), Hgb<10g/dl (3 vs. 29 months), Plt<100K (3 vs. 23 months), leukemic phase (7 vs. 18 months), and complex cytogenetics (2.3 vs. 23 months). A prognostic model was devised using these variables to identify different levels of risk. Each variable was assigned a score of 1 when present for a maximum possible score of 5. In this exploratory cohort, low risk was assigned a score of 0, intermediate risk a score of 1-2, and high risk a score of 3-5. This prognostic score system led to our cohort's most optimal risk discriminatory model, where low, intermediate, and high risk had a median OS of 29, 8, and 2.4 months, respectively (p=0.0006).

Conclusion This MCLPS is a promising new tool for risk-stratifying patients with MstCL. However, it still requires prospective validation.

Citation Format: Philip A. Haddad, Sumasri Chennapragada. Mast cell leukemia provisional prognostic score [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 3836.
Abstract 3857: Tumor-extrinsic BIRC3 promote sensitivity to checkpoint inhibition immunotherapy in breast cancer
Authors: Yang Dejuan , Sun Jiazheng , Ren Guosheng , Li Hongzhong
Published: March 2024

Baculoviral IAP repeat containing 3 (BIRC3) protein play a critical role in breast cancer. Blocking BIRC3 cause apoptosis in tumor cells, but its correlation with tumor immunity remains elusive. TCGA databases were employed to examine the expression of BIRC3 in breast cancer. The correlation between BIRC3 expression and T cell infiltration and function was employed in breast cancer tissues (n=92) by immunohistochemistry. Birinapant, a selective BIRC3 inhibitor, was then used to investigate the effect of BIRC3 blockade on tumor immune microenvironment (TIME) landscape of breast cancer syngeneic mouse models by flow cytometry. Survival analysis suggested that the low expression of BIRC3 was associated with poor overall survival (OS). Additionally, we uncovered the close association between BIRC3 expression and the profiles of immune cells in breast cancer microenvironment based on the TCGA dataset. Interestingly, we found that BIRC3 expression was positively correlated with cytotoxic T lymphocyte infiltration and T-cell effector function by immunohistochemistry. The in vivo experiments suggested that blocking BIRC3 might convert ‘hot’ tumor into ‘cold’ tumor, which was characterized by a decreased of CD8+ T cell infiltration and inhibition of CD8+T cell function. Furthermore, we observed that BIRC3 blocking combined with immune checkpoint blockade therapy (ICT) greatly restrains immunotherapy efficacy of breast cancer model. Our study revealed a positively association between BIRC3 and anti-tumor immune landscape in breast cancer. Notably, we established a validated prognosis model based on BIRC3 and BIRC3 associated immunomodulators in breast cancer.

Citation Format: Dejuan Yang, Jiazheng Sun, Guosheng Ren, Hongzhong Li. Tumor-extrinsic BIRC3 promote sensitivity to checkpoint inhibition immunotherapy 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 3857.
Abstract 3877: Multi-modal analysis of paracrine signaling in group 3/4 medulloblastoma
Authors: Yu Bohyeon , Jung Jangham , Diaz Aaron
Published: March 2024

Medulloblastoma (MB) is the most common primary brain malignancy in kids, with the group 3 and 4 subtypes (G3/4) being the most aggressive. Recent single-cell genomics studies have identified the G3/4 MB cell of origin and point to disrupted stem-cell differentiation as a key factor in MB pathogenesis. However, surprisingly little is known about the contribution of tumor-supportive paracrine signaling to the ontogeny of this disease. The spatial organization of MB cellular hierarchies is not completely understood. We profiled N=24 G3/4 MBs from UCSF patients via single-nucleus RNA sequencing (snRNA-seq). Of these cases, N=10 were profiled via single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq). To capture the spatial context, we profiled an additional 20 samples via spatial transcriptomics using the Visium and Xenium platforms. We found that the standard Xenium brain capture set was inadequate, and we developed a highly specific capture set for G3/4 MBs. In particular, our panel resolves cell-type differences in the stage of MB lineage commitment, from rhombic-lip progenitors to more differentiated unipolar brush-like cells. Altogether, over 110,000 nuclear-sequencing libraries and over 1,898,000 spatially-resolved single-cell libraries were generated. We inferred cell-cell communication signals from our snRNA-seq data by identifying co-expressed receptors and their cognate ligands. We then performed an integrated analysis of our snRNA-seq and scATAC-seq data to infer the cis-regulatory enhancers of those signaling genes, as well as the transcription factors that bind them. We employed our spatial transcriptomics data to confirm paracrine signaling networks inferred from nuclear-sequencing data. We found that distinct MB cell types corresponding to different stages of differentiation occupied specific spatial domains. The results of our ongoing analysis of this spatially-resolved single-cell atlas will be presented. This study paves the way for innovative therapeutic strategies targeting paracrine signaling in G3/4 MB.

Citation Format: Bohyeon Yu, Jangham Jung, Aaron Diaz. Multi-modal analysis of paracrine signaling in group 3/4 medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3877.
Abstract 392: MYB regulates a specific subset of hypoxia-induced genes and exhibits altered genomic occupancy under hypoxia
Authors: Anand Shashi , Khan Mohammad Aslam , Vikramdeo Kunwar Somesh , Singh Seema , Singh Ajay Pratap
Published: March 2024

Hypoxia, an unavoidable microenvironmental stress, greatly influences the tumor cell behavior and therapeutic outcomes. Under low oxygen condition, tumor cells undergo transcriptional reprogramming, largely mediated through hypoxia-inducible factors (HIFs), triggering adaptive response pathways. We recently demonstrated a significant role of MYB in hypoxic survival of pancreatic cancer cells by facilitating adaptive changes in cellular metabolism in collaboration with HIF1α. Here, we employed genome-wide deep sequencing approaches to study the impact of hypoxia on transcriptional reprogramming of pancreatic cancer cells and investigate the role of MYB in the hypoxia-dependent processes. A large number of differentially expressed genes (DEGs) were identified in pancreatic cancer cells subjected to hypoxia (1% O2) and associated with multiple adaptive response pathways. Specifically, we found that pathways related to autophagy, cell migration, epithelial-to-mesenchymal transition, endocytosis, cytoskeleton reorganization were induced, while those associated with RNA processing, ribosome biogenesis, DNA replication and cell cycle were suppressed. To analyze the role of MYB in these adaptive responses, we compared the relative abundance of transcripts in MYB-overexpressing control and MYB knockout (KO) pancreatic cancer cells when cultured under normoxic or hypoxic conditions. We observed that the transcriptional output of MYB was drastically changed under hypoxia with a vast majority of genes being distinctly altered in response to the loss of MYB expression under normoxia and hypoxia. To examine if it resulted from altered genomic occupancy of MYB under normoxia and hypoxia, we compared MYB ChIP-seq peaks under these conditions. We observed a decrease in overall MYB-bound genomic regions under hypoxia despite the fact that we did not observe a decrease in nuclear MYB expression. More interestingly, the genomic occupancy of MYB shifted substantially from regions proximal to transcription start site to distal intergenic or intronic regions under hypoxia. Studies are currently underway to examine the mechanisms underlying the altered MYB genomic occupancy and its impact on adaptive physiological response of pancreatic cancer cells under hypoxia. Together, our findings bring unprecedented insight into the mechanistic role of MYB in hypoxia adaptation and pancreatic cancer pathobiology.

Citation Format: Shashi Anand, Mohammad Aslam Khan, Kunwar Somesh Vikramdeo, Seema Singh, Ajay Pratap Singh. MYB regulates a specific subset of hypoxia-induced genes and exhibits altered genomic occupancy under hypoxia [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 392.
Abstract 3922: Quaking modulates anti-tumor immunity by regulating antigen processing and presentation in dendritic cells
Authors: Li Yating , Hu Jian , Yee Cassian
Published: March 2024

Dendritic cells are essential players in anti-tumor immunity. One of their critical roles is to process and present tumor associated antigens to T cells, thereby inducing antigen-specific T cell response. However, cellular factors and molecular pathways regulating antigen processing and presentation by DCs are not fully understood.Here, we revealed a potential regulatory role of a transcriptional co-activator, Quaking (QKI), and its binding partner, PPARδ in antigen processing and presentation by DCs. Consistent with our previous studies in neural stem cells and microglia, we found QKI and PPARδ enhance phagocytosis in DCs by upregulating genes involved in the formation of phagosome and endosomes. QKI- or PPARδ-deficient DCs showed reduced CD8+ T cell priming capacity in vitro. In vivo tumor models suggested DC-specific knocking out of QKI or PPARδ promoted the tumor growth. Furthermore, ablation of QKI or PPARδ in DCs limited the effectiveness of immune checkpoint blockade in multiple tumor models.Together, these revealed a transcriptional regulation of antigen processing and presentation by DCs through QKI and PPARδ. Our data also suggested that perturbing this important function of DC would subvert their anti-tumor activity, highlighting the pivotal role of DCs in an effective anti-tumor immune response.

Citation Format: Yating Li, Jian Hu, Cassian Yee. Quaking modulates anti-tumor immunity by regulating antigen processing and presentation in dendritic cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3922.
Abstract 3947: Non-BRCA variants in hereditary breast and ovarian cancer patients in the Northern Mexico population
Authors: Burciaga-Flores Carlos H. , Perez-Ibave Diana C. , Garza-Rodriguez Maria L. , Vidal-Gutierrez Oscar , Villarreal-Garza Cynthia M. , Mendez Dione Aguilar y
Published: March 2024

Background: Hereditary cancer syndromes explain 5-10% of all cancer cases. Germline pathogenic variants in BRCA1 and BRCA2 genes (BRCA) are present in 2-3% of all breast cancer (BC), and 15% of all ovarian cancer (OC) cases. BRCA1 and BRCA2 pathogenic variants (PV) represent 25-28% of BC and 40% of OC patients with a positive familial history. BRCAs are the most studied genes for the prevalence, family history, preventive surgeries, and target treatment options in both BC and OC. There are other genes, important in the diagnosis, pathogenesis, and treatment options of the patients: TP53, PALB2, CHEK2, among others. This study aims to identify the prevalence of non- BRCA genes related to the development of hereditary breast and ovarian cancer syndrome in patients of Northeast Mexico.

Methods: This is a multicenter study that recruited patients from two reference oncology centers in Nuevo Leon, Mexico: the CECIL (The CUCC Early Cancer Detection Clinic) Hereditary Cancer Registry and Hereditary Cancer Program from Tec Salud. From March of 2016 to March of 2023, a total of 872 patients meeting NCCN criteria were evaluated by Medical Geneticists from both centers and were tested with NGS multigene cancer panels.

Results: A total of 665 (76.26%) patients with a clinical diagnosis of HBOC (Hereditary Breast Hereditary Cancer Syndrome) were included. We found 310 (46.6%) patients had at least one variant, 180 (58%) with at least one pathogenic variant, and 130 (41%) with a VUS (a variant of uncertain significance). BRCA1 was found in 79 (43.8%) and BRCA2 in 32 (17.7%) of all PV. Non-BRCA PV were found in 69 (38.3%) patients: 4 ATM, 2 BLM, 3 BRIP1, 22 CHEK2, 4 CDKN2A, 5 MUTYH, 10 PALB2, 4 RAD51C, 2 SDHA, 2 TP53, 2 WRN, CDH1, CDK4, DICER, MSH3, NBN, PTEN, RAD50, USH2A one of each. Is remarkable that 19 of the 22 patients with CHEK2 and 5 of the 10 patients with PALB2 had the recurrent PV c.707T>C and c.2167_2168del, respectively.

Conclusions: Non-BRCA PV in Northern Mexico corresponds to one-third of the BC and OC cases, including HRD (homologous recombination deficiency) genes. HDR patient carriers are potential targets of iPARP therapies. This project reinforces the fact that multigene panels should be employed to ensure a complete diagnosis in hereditary cancer patients.

Citation Format: Carlos H. Burciaga-Flores, Diana C. Perez-Ibave, Maria L. Garza-Rodriguez, Oscar Vidal-Gutierrez, Cynthia M. Villarreal-Garza, Dione Aguilar y Mendez. Non-BRCA variants in hereditary breast and ovarian cancer patients in the Northern Mexico population [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 3947.
Abstract 3964: A cancer survival program against activated T cell attack
Authors: Wang Michael X. , Mauch Brandon E. , Williams August F. , Barazande-Pour Tania , Hoffmann Filipe Araujo , Harris Sophie H. , Lathrop Cooper P. , Turkal Claire E. , Paw Michelle H. , Gervasio David A. , Tran Tiffany , Guo Theresa , Daniels Gregory A. , Park Soo J. , Hangauer Matthew J.
Published: March 2024

The immune-cancer interactions downstream of immune checkpoint inhibition present the next targetable interface of cancer immunity. Despite evidence for cytotoxic T lymphocyte (CTL) infiltration and cytolytic activity within immunotherapy-responsive tumors, partial responses and acquired resistance are common, indicating additional barriers for complete tumor elimination. We report a survival program engaged within residual cancer cells exposed to weeks of activated CTLs. Contrary to immune-evasion mechanisms, we observe a residual antigenic cancer cell subpopulation which activates CTLs, survives within IFNγ-high environments, and withstands CTL-induced apoptosis. This cancer survival program, termed immune-induced persistence, is reversibly-driven (non-genetic) and prevents the complete CTL-mediated elimination of cancer cell populations by supporting the survival of quiescent cancer ‘persister’ cells against activated CTL attack. Persister cells display sublethal caspase activity and caspase-dependent DNA damage, consistent with CTL-induced genomic instability, and depend on the inhibitors of apoptosis proteins for survival. Notably, immune-induced persistence presents a markedly distinct survival program than drug-induced persistence, including distinctive apoptotic profiles, stress response pathways, and vulnerabilities. Thus, cancer cell populations can transiently adopt non-redundant survival programs in response to various cytotoxic environments. Features of immune-induced persistence are observed within CTL-treated human cancer cell lines, immune-treated human tumor slice cultures, and intratumor transcriptional heterogeneity programs. Under continued CTL exposure, persistent cancer populations give rise to genetically distinct cancer clones, including stably resistant immune escape variants, modeling acquired resistance to cancer immunotherapies. We propose sublethal interactions between effector immune cells and cancer persister cells as a critical and targetable variable at the interface between activated immunity and cancer.

Citation Format: Michael X. Wang, Brandon E. Mauch, August F. Williams, Tania Barazande-Pour, Filipe Araujo Hoffmann, Sophie H. Harris, Cooper P. Lathrop, Claire E. Turkal, Michelle H. Paw, David A. Gervasio, Tiffany Tran, Theresa Guo, Gregory A. Daniels, Soo J. Park, Matthew J. Hangauer. A cancer survival program against activated T cell attack [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 3964.
Abstract 3975: A therapeutic screening platform for assessing antigen-specific T cell-mediated tumor killing in vitro
Authors: Klaver Elsenoor , Leonard Henry , Lieverse Elizabeth , Brand Oliver , Reelfs Olivier , Kirkham Christopher , Schewitz-Bowers Lauren , Brackenbury Louise
Published: March 2024

Many cancers remain resistant to conventional therapies, consequently there has been an exponential rise in the number of therapeutics harnessing the power of the immune system in an oncology setting, with several remarkable examples of success. High frequencies of infiltrating tumor-specific T cells have been linked to improved patient outcomes, which highlights the importance of uncovering how therapeutics can enhance their function. To explore this functionality in a preclinical setting it is critical to have physiologically relevant models. Here, we demonstrate that common issues, such as low precursor frequencies and restricted HLA-types can be overcome via access to HLA-typed samples and use of expansion platforms which attain high numbers of antigen-specific T cells. Furthermore, we show how these systems enable vaccine immunogenicity screening and assessment of therapeutic efficacy. Healthy blood donations were screened for HLA type and antigen-specific T cells were expanded by either co-culture with peptide-pulsed dendritic cells or polyclonal stimulation following multimer enrichment and FACS sorting. Following expansion, the large number of antigen-specific T cells generated enabled the T cells to be assessed via phenotyping, cytokine secretion, or functional killing assays in a 2D or 3D tumor setting. Tumor targets with either 1) endogenous antigen expression, 2) antigen introduced via lentiviral overexpression or 3) peptide loading of MHC class I were utilized. Validated readouts for measuring antigen-specific killing included flow cytometry and time-lapse imaging (IncuCyte), alongside quantification of antigen-specific IFNɣ responses by ELISpot. These pre-clinical platforms represent a suite of physiologically relevant T cell assays which can be used to perform candidate selection in tumor associated antigen/neoantigen vaccine drug development programs, pharmacological inhibition of checkpoint pathways, or co-stimulatory agonist discovery. In combinatorial approaches with radio- or chemotherapy, the development of novel immunotherapies offers hope to many patients with treatment-resistant cancers.

Citation Format: Elsenoor Klaver, Henry Leonard, Elizabeth Lieverse, Oliver Brand, Olivier Reelfs, Christopher Kirkham, Lauren Schewitz-Bowers, Louise Brackenbury. A therapeutic screening platform for assessing antigen-specific T cell-mediated tumor killing in vitro [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 3975.
Abstract 3980: Investigating the role of host obesity in promoting immunotherapy resistance
Authors: Ogbonna Henry Nnaemeka , Roberts Zachary , Kvarnberg Haley , Dempsey Francesca , Song Patrick N. , Sorace Anna G. , Norian Lyse
Published: March 2024

Obesity is linked to an increased risk of various cancers, including renal cell carcinoma (RCC). Many RCC patients have obesity at diagnosis and treatment initiation, and our lab has found that this significantly impairs immunotherapy outcomes. Both preclinical and clinical reports, from our lab and others, have demonstrated that obesity reduces the efficacy of CD8+ T cell-dependent immunotherapy by increasing pro-tumorigenic IL-1β. Combining anti-PD-1 based therapy with anti-IL-1β triggers the recruitment of CD8+ T cells and improves the efficacy of anti-PD-1 based immunotherapy. However, the mechanistic links between obesity and increased IL-1β production remains unknown. Our objective is to identify mechanisms promoting IL-1 β-driven immunosuppression within renal tumors of obese mice. In our in vivo studies, we utilized a BALB/c mouse model of diet-induced obesity (DIO) and lean controls in combination with the Renca-Luc RCC cell line. Using flow cytometry and western blot, we respectively assessed leukocyte populations producing IL-1β and tumor energetics. Flow cytometry revealed that intra-tumoral IL-1β is produced primarily by tumor associated macrophages (TAMS). Immunoblotting demonstrated that increased IL-1β production is linked to altered mitochondrial function and ATP production. These early findings support the hypothesis that obesity driven IL-1β expression is mediated by tumor-associated macrophages and that mitochondrial dysfunction drives immune suppression. Understanding these molecular and immune-related mechanisms may pave the way for novel strategies to reduce immunosuppression in obese RCC patients, thus improving immunotherapeutic efficacy and overall clinical outcomes.

Citation Format: Henry Nnaemeka Ogbonna, Zachary Roberts, Haley Kvarnberg, Francesca Dempsey, Patrick N. Song, Anna G. Sorace, Lyse Norian. Investigating the role of host obesity in promoting immunotherapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3980.