bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5028: Integration of molecular data into cancer patient database
Authors: Chaballout Basil H. , Funkhouser Avery T. , Blair Bailey B. , Goodwin Jane L. , Strigenz Alexander M. , Arthur Connie M. , Martin Julie C. , Edenfield W. Jeffery , Blenda Anna V.
Published: June 2022

Background: Precision medicine holds promise of being a more effective method for treating complex diseases such as cancer. Nuanced care is needed, as the development and clinical course of cancer is multifactorial with influences from the general health status of the patient, germline and neoplastic mutations, co-morbidities, and environment including "lifestyle". To tailor an individualized treatment to the patient, such multifactorial data must be presented in an easy-to-use, easy-to-analyze fashion for providers to use effectively.

Purpose: To address the need, we have built a searchable database integrating cancer-critical gene mutation status, serum galectin protein markers, serum and tumor glycomic profiles, with clinical, demographic, and lifestyle data points of individual patients.

Methods: The initial data was acquired from breast, colon, and lung cancer patients’ serum and biopsy samples from the Prisma Health Cancer Institute Biorepository. The acquired data contains the status of 2,800 COSMIC cancer-critical gene mutations, individual patient profiles of five serum galectins, and serum and biopsy glycan structures from each patient’s glycomic profile. DNA from tumor cells was used to screen the regions frequently mutated in human cancer genes. Multiplex PCR using Ion AmpliSeq࣪ Cancer Hotspot panel v2 was performed by Precision Genetics. Enzyme-linked immunosorbent assay was employed to perform galectin profiling of cancer patient serum samples. Glycomic profiling of serum and biopsy samples was performed by the Emory Comprehensive Glycomic Core. In addition, healthy control values for galectin and glycomic profiles were obtained and added to the patient database for reference. The data is being stored using Microsoft SQL servers and is fed into an interactive web application using RStudio.

Results: Our interactive database allows care providers to amalgamate cohorts from these groups to find correlations between different data types with the possibility of finding a "stage signature" based upon a combination of genetic mutations, galectin serum levels, glycan signatures, and patient clinical data and lifestyle choices.

Conclusion: Our project provides a framework for an integrated interactive database to analyze molecular and clinical patterns across cancer stages and provides opportunities for increased diagnostic and prognostic power.

Citation Format: Basil H. Chaballout, Avery T. Funkhouser, Bailey B. Blair, Jane L. Goodwin, Alexander M. Strigenz, Connie M. Arthur, Julie C. Martin, W. Jeffery Edenfield, Anna V. Blenda. Integration of molecular data into cancer patient database [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5028.
Abstract 5035: Q-omics: smart software for assisting oncology and cancer research
Authors: Yoon Sukjoon , Jeong Euna , Jeong Sumin , Lee Jieun , Kim Youngju
Published: June 2022

Increased multi-level omics data has enabled data-driven studies on cancer drugs, targets and biomarkers. Thus, it is necessary to develop comprehensive tools for oncologists and cancer scientists to carry out extensive data mining without computational expertise. For this purpose, we have developed innovative software that enables user-driven analyses on cancer omics data, assisted by knowledge-based smart systems.

Publicly available multi-level omics data of mutations, gene/protein expression, patient survival, immune score (tumor infiltrating cells), drug screening and RNAi (shRNA and CRISPR) screenings on patient samples and cell lines, were integrated from the TCGA, GDSC, CCLE, NCI and DepMap databases. Q-omics provides user-friendly interface for calculation and visualization of cross-associated data pairs retrieved from integrated datasets. The optimal selection of samples, datasets and/or other filtering options is guided by knowledge-bases of the software for the quick and easy finding of significant associations between data pairs. Furthermore, implemented smart algorithms prioritize significant hits based on consensus scoring methods. Consensus scoring using multiple statistical tests with varied sample (or lineage) selection, enriches noise-free, robust cross-associated pairs in the hit list.

We believe that Q-omics provide simple but powerful tools for all areas of oncology and cancer research. The latest version of Q-omics software is available at http://qomics.sookmyung.ac.kr.

Citation Format: Sukjoon Yoon, Euna Jeong, Sumin Jeong, Jieun Lee, Youngju Kim. Q-omics: smart software for assisting oncology and cancer research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5035.
Abstract 5068: Functionalized superparamagnetic nanoparticles for theranostics of membrane-bound Hsp70 positive malignant brain tumors
Authors: Tagaeva Ruslana , Fedorov Vyacheslav , Yudintceva Natalia , Yakovleva Luidmila , Nikolaev Boris , Osnach Veronica , Shevtsov Maxim
Published: June 2022

Biomedical nanotechnologies based on superparamagnetic iron oxide nanoparticles (SPIONs) represent a promising instrument for malignant brain tumor theranostics. Due to their unique physico-chemical properties, they can be used for multimodal cancer therapy (including hyperthermia), diagnostics, and targeted delivery of therapeutic molecules. To enhance the tumor-homing properties of nanoparticles the latter were conjugated with bioligands (i.e., monoclonal antibodies, Fab-fragments, peptides, and proteins such serine protease granzyme B) that recognize 72 kDa membrane-bound heat shock protein (mHsp70) that is expressed on the plasma membrane of tumor cells, including multiforme glioblastoma (GBM), but not on normal corresponding cells. Therapeutic potential of magnetic conjugates can be attenuated by binding to the particles surface of granzyme B (GrB-SPIONs) that exerts pro-apoptotic activity. Functionalized particles significantly contrast-enhanced the orthotopic glioblastoma (U87 glioma in NMRI nu/nu mice, GL261 glioma in C57/Bl6 mice) in preclinical animal models when high-field (11 ) magnetic resonance tomography (Bruker) was employed. Furthermore, when GrB-SPIONs were applied, we detected a statistically significant delay of tumor progression and increase of overall animal survival. Anti-tumor activity of GrB-SPIONs was further synergistically potentiated by stereotactic radiotherapy combined with immune check-point inhibitors (i.e., CTLA-4). In conclusion, synthesized superparamagnetic nanoparticles targeting mHsp70-positive could be employed for theranostics of malignant brain tumors and translated into further clinical trials.This research was funded by the Ministry of Science and Higher Education of the Russian Federation (Agreement № 075-15-2020-901).

Citation Format: Ruslana Tagaeva, Vyacheslav Fedorov, Natalia Yudintceva, Luidmila Yakovleva, Boris Nikolaev, Veronica Osnach, Maxim Shevtsov. Functionalized superparamagnetic nanoparticles for theranostics of membrane-bound Hsp70 positive malignant brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5068.
Abstract 5088: Identification of NOTCH mutation as novel predictor to efficacious immunotherapy in colorectal cancer
Authors: Xia Xiaoyang , You DongShan , Cao Jing , Huang JingHui , Zhang Junling , Huang Mengli , Chen Yanan , Xia Xihua , Bai Yuezong
Published: June 2022

Background: NOTCH, as an oncogene, has been shown to be closely associated with radiation and chemotherapy, hormone therapy, and other molecular targeted therapies (such as anti-EGFR and anti-PI3K molecular targeted therapies) in a variety of tumors, and even in drug resistance mechanisms. However, the correlation between NOTCH mutations and immunotherapy in colorectal cancer (CRC) has not been reported.

Methods: We retrospectively identified NOTCH mutation and treatment outcomes. The relationship between clinical pathologic features and NOTCH were analyzed with using the two-sided chi-squared test or the Fisher exact test. Clinicopathologic characteristics associated with overall survival using Cox regression and the Kaplan-Meier method.

Results: We retrospectively analyzed 108 CRC patients who received immunotherapy, including 31 patients with NOTCH mutation (MUT) and 78 patients with NOTCH wide-type (WT). NOTCH mutation was discovered to be enriched in MSI instable and associated with significant better overall survival (HR, 0.4; 95% CI, 018-0.9; P=0.0272). Although compared with NOTCH WT, no association was observed between NOTCH1/2/4 MUT and overall survival, Kaplan-Meier survival analysis showed that patients with NOTCH3 MUT obtained better OS (not reach vs. 14 months, HR, 0.17; 95% CI 0.04-0.74; P=0.0176). In addition, in an in-house Chinese CRC cohort (n=1968), we found 322 (16.4%) patients with NOTCH mutations, including NOTCH1/2/3/4 mutation frequency were 43.5%, 32.9%, 46.9% and 12.1%, respectively. 206 (60.4%) patients had one NOTCH mutation, and only 20 (6.2%) patients had more than four mutations. NOTCH mutations were significantly associated with higher TMB levels (P<0.0001) and PD-L1 positive (P=0.0011) in the in-house Chinese CRC cohorts.

Conclusions: Our results suggest that NOTCH1/2/3/4 mutation may be a potential predictor to favorable ICI response in CRC patients. The exact mechanisms underlying NOTCH mutations are needed to be further evaluated.

Citation Format: Xiaoyang Xia, DongShan You, Jing Cao, JingHui Huang, Junling Zhang, Mengli Huang, Yanan Chen, Xihua Xia, Yuezong Bai. Identification of NOTCH mutation as novel predictor to efficacious immunotherapy in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5088.
Abstract 5090: Prognosis of renal cell carcinoma patients with VHL mutations to immune checkpoint inhibitors
Authors: Shen Dong , Huang Yufeng , Wu Zhiwei , Zhang Junling , Huang Mengli , Chen Yanan , Xia Xihua , Bai Yuezong
Published: June 2022

Background: The von Hippel-Lindau (VHL) gene is a tumor suppressor gene. Although VHL gene alterations play a key role in the pathogenesis of renal cell carcinoma (RCC), and several therapies targeting this molecular pathway have been studied, such as sunitinib, pazopanib and axitinib. However, it is not clear whether VHL mutation is a prognostic factor for immunotherapy in renal cell carcinoma.

Methods: The impact of VHL mutations on survival outcomes in RCC patients received immunotherapy or non-immunotherapy were verified in the Memorial Sloan Kettering Cancer Center (MSKCC) trials and The Cancer Genome Atlas (TCGA) RCC cohort, respectively. An in-house Chinese RCC cohort (n=950) was used for the analysis of immune-related markers. The relationship between clinical pathologic features and VHL were analyzed with using the two-sided chi-squared test or the Fisher exact test. Clinicopathologic characteristics associated with overall survival using Cox regression and the Kaplan-Meier method.

Results: In the MSKCC cohort, a total of 143 RCC patients receiving immunotherapy were enrolled, of which 117 (81.8%) were clear cell RCC and 143 (100%) microsatellite-stable RCC. VHL mutation was significantly associated with high TMB score (P =0.017). Kaplan-Meier survival analysis showed that patients with VHL mutation obtained better OS compared to VHL wild-type (50 months vs. 23 months, HR, 0.36; 95% CI 0.21-0.64; P<0.001). In the TCGA cohort, all RCC patients received non- immunotherapy. No association was observed between VHL and OS (HR, 1.00; 95% CI 0.73-1.38; P=0.981). VHL mutations were significantly associated with higher TMB levels (P=0.006) and MSI-H (P=0.004) in the in-house Chinese RCC cohorts.

Conclusions: Our results suggest that VHL mutation may be associated with better OS in RCC patients receiving immunotherapy. The exact mechanisms underlying VHL are needed to be further evaluated.

Citation Format: Dong Shen, Yufeng Huang, Zhiwei Wu, Junling Zhang, Mengli Huang, Yanan Chen, Xihua Xia, Yuezong Bai. Prognosis of renal cell carcinoma patients with VHL mutations to immune checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5090.
Abstract 5097: Influencing factors of postoperative prognosis and screening of adjuvant chemotherapy in patients with early NSCLC
Authors: Li Xiaoning , Tang Haibo , Cai Jianhong , Wu Xiaomin , Hu Xue , Zheng Yating , Huang Mengli
Published: June 2022

Introduction: The standard treatment for patients with stage I non-small cell lung cancer (NSCLC) is resection of the primary tumor. However, more than 28% of patients had recurrence or metastasis after surgery. Different studies have shown that the prognosis of stage I NSCLC is significantly different, due to the paucity of evidence for these adjuvant treatments after surgery, whether or not to apply adjuvant chemotherapy is controversial. In conclusion, postoperative adjuvant chemotherapy may be necessary for high-risk groups. Nevertheless, for patients with stage I NSCLC, the factors influencing the postoperative prognosis remains unclear.

Methods: Data from LUAD and LUSC cohorts of The Cancer Genome Atlas (TCGA) was used to analyze the disease-free survival (DFS), overall survival (OS), progression-free survival (PFS) and cancer-specific survival (CSS) of different signaling pathways. DFS and OS Kaplan-Meier curves for subgroups of patients were compared using the log-rank test. Cox proportional hazards regression analysis was utilized to identify the independent predictors of DFS.

Results: 270 LUAD and 234 LUSC of stage I patients were used in the analysis, through 16 variables, including age, sex, and 14 different signaling pathways associated with tumor development. For the LUAD patients, HR of DFS of notch signaling group is 1.89 (95%CI: 1.03-3.48, P=0.04) in univariate analysis, 2.73 (95%CI: 1.18-6.32, P=0.02) in multivariate analysis; HR of DFS of angiogenesis group is 2.30 (95%CI: 1.26-4.18, P=0.006) in univariate analysis, 2.65 (95%CI: 1.31-5.34, P=0.007) in multivariate analysis. HR of PFS of p53 group is 1.72 (95%CI: 1.08-2.73, P=0.023) in univariate analysis. Others are negatively correlated or have no significant differences. For the LUSC, all the factors are negatively correlated or have no significant differences.

Conclusions: These results suggest that harboring notch signaling pathway and angiogenesis pathway mutation may be the biomarker for adjuvant chemotherapy for the stage I LUAD patients, but further validation is needed in large clinical studies.

Citation Format: Xiaoning Li, Haibo Tang, Jianhong Cai, Xiaomin Wu, Xue Hu, Yating Zheng, Mengli Huang. Influencing factors of postoperative prognosis and screening of adjuvant chemotherapy in patients with early NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5097.
Abstract 510: Molecular subtypes related to prostate cancer disparities and disease outcome in African American and European American patients
Authors: Mori Joakin Opeli , White Jason , Karanam Balasubramanyam , Yates Clayton , Wang Honghe
Published: June 2022

Prostate cancer disproportionately affects African American (AAM) men, yet present biomarkers do not factor in prostate cancer racial disparity. The objective of this study was to identify biomarkers with potential benefits to AAM prostate cancer patients. Differentially expressed genes (DEG) analysis coupled with gene set enrichment analysis (GSEA) and leading-edge genes analysis showed that the keratin family of genes, including KRT8, KRT15, KRT19, KRT34, and KRT80, constituted the single most prominent family of genes enriched in AAM compared to European American (EAM) prostate cancer cell lines. In prostate cancer patients (TCGA and MSKCC patient cohorts), only KRT8, KRT15, and KRT19 expression were relatively higher in AAM than in EAM. The differences in the expression of KRT15 and KRT19, but not KRT8, were enhanced by Gleason score and ERG fusion status; in low Gleason (Gleason ≤ 6 [TCGA cohort] and Gleason ≤ 7 [MSKCC cohort]), the expression of KRT15 and KRT19 was significantly (p ≤ 0.05) higher in AAM than in EAM patients. Survival analysis revealed that high expression of KRT15 and KRT19 was associated with increased risk of biochemical recurrence in low Gleason category patients in the TCGA patient cohort. Interestingly, KRT15 and KRT19 expression was associated with an increased risk of death in the metastatic prostate adenocarcinoma (SU2C/PCF Dream Team, PNAS 2019) cohort, suggesting the potential to predict the risks of disease recurrence and death in the low Gleason category and advanced disease conditions respectively. Gene set enrichment analysis revealed known oncogenic gene signatures, including KRAS and ERBB2, to be enriched in patients expressing high KRT15 and KRT19. Furthermore, high KRT15 and KRT19 were linked to the basal and LumA prostate cancer subtypes associated with poor postoperative androgen deprivation therapy (ADT) response compared to the LumB subtype. Taken together, the present study identifies genes with high expression in AAM than in EAM prostate cancer. The identified genes are linked to oncogenic gene signatures, including

KRAS and ERBB2, and to basal and LumA prostate cancer subtypes that are associated with poor postoperative ADT response. The study, therefore, reveals biomarkers with the potential to address biomarker bias in prostate cancer diagnosis and/or prognosis. Future studies would explore the diagnostic and/or prognostic potential of identified markers in prostate cancer tissue samples.

Citation Format: Joakin Opeli Mori, Jason White, Balasubramanyam Karanam, Clayton Yates, Honghe Wang. Molecular subtypes related to prostate cancer disparities and disease outcome in African American and European American patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 510.
Abstract 5102: Correlation analysis of CREBBP mutation with tumor mutation burden and effect of immune checkpoint therapy in bladder cancer
Authors: Xu Abai , Chen Tingting
Published: June 2022

Background: CREB-binding protein (CREBBP, hereafter CBP) encoded the protein having intrinsic histone acetyltransferase activity, which stabilized the additional protein interactions with the transcription complex. The mutation of CREBBP has been reported that caused Rubinstein-Taybi syndrome (RTS) and associated with acute myeloid leukemia, but not been studied in bladder cancer (BLCA). Immune checkpoint therapy (ICI) has significantly became one of the primary treatment of BLCA, and Tumor mutation burden (TMB) has been regarded as the most prevalent biomarker to predict immunotherapy. The CREBBP mutation status correlation with TMB and immune response remain unknown.

Methods: Whole exome sequencing (WES) data and clinical data of 406 BLCA patients was obtained from the Cancer Genome Altas (TCGA). The mutation data of 206 FFPE tumor samples from Chinese BLCA patients were sequenced by targeted next-generation sequencing (NGS, 3DMed panel). NGS data and clinical data of 192 advanced BLCA patients treated with ICI were obtained from the MSK-IMPACT Clinical Sequencing cohort (MSKCC). The association between CREBBP mutation and TMB level in BLCA were explored. Survival analysis was determined by Kaplan-Meier (KM) analysis.

Results: In total, The CREBBP mutation frequency was 16.25% (66/406) of BLCA patients in TCGA, 14.56% (30/206) in Chinese cohort and 13.54 (26/192). In Chinese cohort, the alteration frequency of NOTCH signal pathways affected was 48.54% (100/206), in which the highest frequency genes was CREBBP. The TMB level in CREBBP mutant group was higher than wild-type group both in Chinese group (Wilcoxon test, p = 0.001) and MSKCC cohort (Wilcoxon test, p < 0.001). The survival analysis were performed on patients from TCGA cohorts without treatment information and MSKCC BLCA patients treated with ICIs, separately. In TCGA cohort, there are not significantly difference between CREBBP mutation group (n=65) and wild-type group (n=340). While in MSKCC ICIs treatment cohort, the overall survival (OS) of CREBBP mutation group (n=26) were significantly longer than wild-type group (n=166) (median OS, mutation vs wild-type = NE vs 15 months; HR 0.468 [95% CI 0.26-0.84]; P = 0.0431). Conclusion: The CREBBP gene mutation was associated with higher TMB level. Clinical cohort analysis results suggested that CREBBP might be a predictive biomarker of immune checkpoint therapy but not a prognostic factor in BLCA.

Citation Format: Abai Xu, Tingting Chen. Correlation analysis of CREBBP mutation with tumor mutation burden and effect of immune checkpoint therapy in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5102.
Abstract 5128: Identification and characterization of nasopharyngeal carcinoma prognostic subtypes based on a circRNA classifier: Implications of stratified treatment
Authors: Liang Yelin , Zhao Yuheng , Li Qian , Jiang Wei , Ma Jun , Liu Na , Li Yingqin
Published: June 2022

Accurate risk stratification for patients with locoregionally advanced nasopharyngeal carcinoma (LA-NPC) is crucial for treatment decisions and prognosis. Here, we introduce a circRNA-based classifier that could improve the prognostic stratification of LA-NPC patients. The circRNAs are identified by microarray profiling, followed by qRT-PCR validation and selection using a machine learning method in the training cohort (n = 170). Based on the proposed classifier, two prognostic-distinctive NPC subtypes are identified, namely the high-risk subtype (subtype H) and low-risk subtype (subtype L), which have significantly different disease-free survival (HR 2.99, 95% CI 1.58-5.67, P < 0.001). Validation in the internal cohort (n = 170) and external cohort (n = 150) yield similar results and the circRNA-based classifier is an independent risk factor of posttreatment relapse. Meanwhile, multiple interdependent features of different subtypes are observed, including relatively higher immune cell infiltration and immune-related pathways activation in subtype L; and predominant stromal, immunosuppressive and tumor-promoting components with moderate immune activation in subtype H. With a less aggressive and more immune-active tumor microenvironment, patients of subtype L could benefit from the addition of induction chemotherapy. In contrast, patients of subtype H, who are vulnerable to chemoresistance, display a strong tendency to benefit from additional immunotherapy. Overall, we define two NPC prognostic subtypes based on a circRNA classifier across multiple cohorts, which exhibit distinct biological ecosystems and suggest opportunities for the personalization of therapeutic regimens.

Citation Format: Yelin Liang, Yuheng Zhao, Qian Li, Wei Jiang, Jun Ma, Na Liu, Yingqin Li. Identification and characterization of nasopharyngeal carcinoma prognostic subtypes based on a circRNA classifier: Implications of stratified treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5128.
Abstract 5173: Digital spatial profiling of metastatic clear cell carcinoma reveals intra-tumor heterogeneity in epithelial-mesenchymal gradient
Authors: Wang Duncan Y.T. , Tan Tuan Zea , Tai Ya-Ting , Ye Jieru , Lin Wei-Chou , Wei Lin-Hung , Huang Ruby Y. J.
Published: June 2022

Intrinsic intra-tumor heterogeneity (ITH) has been linked to worse patient outcomes. The development of spatial profiling technology has enabled the deciphering of ITH with multiple analysis readouts. Advanced ovarian clear cell carcinoma (OCCC), known to harbor ITH, is chemoresistant, poor prognostic, and possesses distinct molecular and histological characteristics. However, detailed spatial information of the nature of ITH within OCCC remains unclear. Here, we utilized the NanoString Digital spatial profiling (DSP) GeoMx platform to perform multiplex protein expression analysis on tumor samples of primary and colonic metastatic sites from one advanced OCCC patient. The spatial resolution revealed the existence of an epithelial-mesenchymal (EM) gradient within the metastatic tumor but not the primary tumor, and similar EM gradient was not observed within the primary tumor. The EM gradient exhibited a distinct pattern from the periphery to the core of the metastatic tumor. Compared to tumor cells at the primary site, there was an intermediate zone in between the tumor periphery and the tumor core in the colonic metastasis with differential expression patterns of pan-cytokeratin (PanCK), fibronectin (FN), smooth muscle actin (SMA), neural cell adhesion molecule (NCAM), integrin alpha X (ITGAX), and Ki-67. Our study provides the first spatially resolved in situ evidence of intermediate or hybrid EM states within the tumor samples of similar morphology. This not only demonstrates the promising applications of spatial profiling in precision medicine but also provides an unprecedented view of the EM gradient during the progression of cancer such as OCCC.

Citation Format: Duncan Y.T. Wang, Tuan Zea Tan, Ya-Ting Tai, Jieru Ye, Wei-Chou Lin, Lin-Hung Wei, Ruby Y. J. Huang. Digital spatial profiling of metastatic clear cell carcinoma reveals intra-tumor heterogeneity in epithelial-mesenchymal gradient [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5173.
Abstract 5176: Tumor dynamic model-based decision support for phase Ib immunotherapy combination studies
Authors: Bruno René , Marchand Mathilde , Yoshida Kenta , Chan Phyllis , Li Haocheng , Zou Wei , Mercier Francois , Chanu Pascal , Wu Benjamin , Lee Anthony , Li Chunze , Jin Jin Y.
Published: June 2022

Background: Tumor growth inhibition (TGI)-overall survival (OS) models predict OS distributions and study outcomes (OS hazard ratio (HR)) in a number of cancers and settings (Bruno, Clin Cancer Res 2020;26:1787-95). Model-derived TGI metrics such as tumor growth rate (KG) have been considered as a promising early endpoint compared to classical response criteria (Gong J Clin Oncol 2020; doi: 10.1200/JCO.2020.38.15_suppl.9541). This work is assessing the validity of tumor growth rate estimates to inform GO/noGO decisions for Phase Ib studies.

Methods: We resampled baseline characteristics and longitudinal sum of longest diameters (SLD, RECIST 1.1) from a positive Phase III study (IMpower150, Socinski, N Engl J Med 2018;378:2288-301) to mimic a Phase Ib study of 15, 30, or 40 patients per arm (atezolizumab +bevacizumab+carboplatin+paclitaxel (A+BCP) vs. BCP) with 10 months recruitment and 6 or 3 months follow-up (FU) after the last patient recruited. Effect sizes across A+BCP vs. BCP or BCP vs. BCP were calculated as geometric mean ratio (GMR) for KG, difference (d) in objective response rate (ORR), and HR for progression-free survival (PFS) and simulated OS. For this, individual KG were estimated using a bi-exponential model (Claret, Clin Cancer Res 2018;24:3292-8); ORR and PFS were estimated per RECIST 1.1, OS was simulated using a previously published TGI-OS model (Chan CPT:PSP 2021; doi.org/10.1002/psp4.12686) with 400 patients per arm bootstrapped from the 15, 30 or 40 patients of the resampled subsamples. Correct and incorrect Go decisions were based on the probability (prob) to achieve target effect sizes in A+BCP vs. BCP and BCP vs. BCP, respectively, across 500 replicated subsamples.

Results: To not exceed an incorrect Go decision of 20% and for 40 patients/6 months FU, correct Go based on prob(KG GMR<0.90), prob(dORR>0.10), prob(OS HR<0.85) and prob(PFS HR<0.70) were 83%, 69%, 67% and 58%, respectively. For 40 patients/3 months FU, 30 patients/6 or 3 months FU, the ranking did not change and prob(KG GMR<0.90) correct Go decision rate remained around 80%.

Conclusions: This evaluation suggests that model-based estimates of on-treatment tumor growth rate could be used as an exploratory endpoint to inform early clinical decisions. Expansion of this work is planned in other settings e.g. single-arm studies commonly used in early oncology clinical development.

Citation Format: René Bruno, Mathilde Marchand, Kenta Yoshida, Phyllis Chan, Haocheng Li, Wei Zou, Francois Mercier, Pascal Chanu, Benjamin Wu, Anthony Lee, Chunze Li, Jin Y. Jin. Tumor dynamic model-based decision support for phase Ib immunotherapy combination studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5176.
Abstract 5194: BALB/c mice with humanized VISTA: A novel GEMM for preclinical evaluation of therapeutic antibodies against VISTA
Authors: Yu Weiwei , Bao Honghong , Li Shuai , Ju Chao , Sun Hongyan , Qi Hao , Ju Cunxiang , Zhao Jing , Gao Xiang
Published: June 2022

VISTA, also known as PD1H, is an immune-checkpoint receptor mainly expressed in immune cells, including macrophages, conventional dendritic cells, monocytes and circulating neutrophils. As a negative regulator of T cell activation, VISTA inhibits T cell proliferation and attenuates the production of cytokines. Studies have shown that VISTA expression is increased in infiltrating immune cells found in the tumor microenvironment and that blocking pathways that lead to VISTA activation can enhance antitumor immune responses in mice. Based on this, antibodies targeting VISTA are promising leads for cancer therapy. Preclinical efficacy evaluation of antibodies again human VISTA requires the expression of human VISTA in animal models, since difference in extracellular domains may affect antibody recognition while the overall homology between the two proteins is only 77%.

To meet this need, we established a humanized mouse model in which the extracellular domain of mVISTA is replaced with that of hVISTA while the trans-membrane and cytoplasmic domains remain intact. In order to confirm the activity of the chimeric protein in our mice, we evaluated the anti-tumor effect of proven VISTA antibodies in homozygous hVISTA mice engrafted with CT26 tumor subcutaneously. Consistent with previous studies, the growth of CT26 tumor was inhibited after VISTA antibody treatment, indicating the humanized VISTA mice are suitable for efficacy evaluation of human VISTA antibodies.

Moreover, we evaluated the anti-tumor effect of a combination of PD-L1 antibody and VISTA antibody in these mice. Interestingly, the combined use of PD-L1 antibody and VISTA antibody led to significantly enhanced tumor regression than either antibody. Taken together, BALB/c-hVISTA mouse is a novel non-human animal model appropriate for preclinical efficacy study of human VISTA antibodies.

Citation Format: Weiwei Yu, Honghong Bao, Shuai Li, Chao Ju, Hongyan Sun, Hao Qi, Cunxiang Ju, Jing Zhao, Xiang Gao. BALB/c mice with humanized VISTA: A novel GEMM for preclinical evaluation of therapeutic antibodies against VISTA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5194.
Abstract 5241: p38 MAPK/EGR1/PD-L1 axis promotes radiation resistance of nasopharyngeal carcinoma by enhancing immune evasion
Authors: Meng Dong-Fang
Published: June 2022

Radiation resistance is the main reason for treatment failure. Till present, the underlying molecular mechanism of NPC radiation resistance remains poorly understood. Recent clinical trials have demonstrated that PD-1/PD-L1 inhibitors have achieved better efficacy in the treatment of recurrent or metastatic NPC. Further studies are needed to better understand the molecular mechanisms underlying PD-1/PD-L1 inhibitors enhance response to radiation in NPC. We performed RNA-seq analysis in NPC radioresistant and wild-type cells. We identified EGR1 promotes NPC radiation resistance and is significantly correlated with NPC recurrence. We further found that EGR1 upregulated PD-L1 expression at transcriptional level in a p38 MAPK dependent manner. Moreover, EGR1 participated in CD8+T cell mediated immune evasion in NPC radioresistant cells. We therefore propose a hypothesis that p38 MAPK/EGR1 axis induced PD-L1 expression promotes radiation resistance of NPC by enhancing immune evasion. This study aims to identify the key regulatory factors in p38 MAPK/EGR1/PD-L1 axis, especially PD-L1, as a new target to improve radiosensitivity of NPC, provide theoretical basis for PD-1/PD-L1 inhibitors plus radiotherapy in the treatment of NPC. Meanwhile, this study also provides the possibility for predicting the radiosensitivity of NPC.

Citation Format: Dong-Fang Meng. p38 MAPK/EGR1/PD-L1 axis promotes radiation resistance of nasopharyngeal carcinoma by enhancing immune evasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5241.
Abstract 5252: In colorectal cancer (CRC), neuroendocrine carcinoma (NEC) is contaminated in the cancer given a confirmed diagnosis of poorly differentiated adenocarcinoma (P-ad-ca)
Authors: Rong Yuhan , Takeda Yuma , Okubo Naoki , Suzuki Akihiro , Tokuhisa Motohiko , Kobayashi Noritoshi , Ishibe Atsushi , Kato Ikuma , Yamanaka Shoji , Fujii Satoshi , Endo Itaru , Ichikawa Yasushi
Published: June 2022

Background: Most of CRC were well or moderately differentiated adenocarcinoma and P-ad-ca is very rare. In Japan, P-ad-ca was reported to be only 4-6% of all CRC. NEC is also rare. The incidence of that were reported to be less than 1%. One of their points of common is morphological poorly differentiated appearance. In this study, we evaluated the incidence of NEC contaminated in the CRC given a confirmed diagnosis as P-ad-ca.

Material and Method: From 2009 to 2019, 816 CRCs were resected in department of Yokohama City University Hospital and 74 cases showing P-ad-ca or having a small region of P-ad-ca with well or moderately differentiated ad-ca (W-ad-ca, M-ad-ca). Among the 74 cases, there were 8 of P-ad-ca, 4 of W-ad-ca with P-ad-ca, 44 of M-ad-ca with P-ad-ca, and 18 W-ad-ca and M-ad-ca with P-ad-ca. Immunohistochemistry (IHC) using neuroendocrine markers (NM) including chromogranin A, synaptophysin and insulinoma-associated protein 1 (INSM1) was performed to identified NEC. Recently, a high incidence of Rb protein loss was reported in NEC of several organs, then IHC using Rb monoclonal antibody was also performed. The cancers showing immunohistochemically positive of at least one of the three NM and negative of Rb were identified as true NEC in this study.

Results: At least one of the three NM was positive in the 39 cases. In these 39 cases, 3 cases were also Rb negative. Two of the three cases were region of P-ad-ca. These 2 P-ad-ca regions showed positive of NM. Interestingly, in the other one case, region of W-ad-ca showed positive of NM and negative of Rb. Region of P-ad-ca of the case showed positive of all three NM and Rb. From morphological appearance, this case was quite unlikely to true NEC.

Conclusion: In 74 P-ad-ca, 2 cases might be true NEC in our small evaluation. NEC might be contaminated in the P-ad-ca of CRC which is difficult to be distinguished by only pathological findings of HE staining.

Citation Format: Yuhan Rong, Yuma Takeda, Naoki Okubo, Akihiro Suzuki, Motohiko Tokuhisa, Noritoshi Kobayashi, Atsushi Ishibe, Ikuma Kato, Shoji Yamanaka, Satoshi Fujii, Itaru Endo, Yasushi Ichikawa. In colorectal cancer (CRC), neuroendocrine carcinoma (NEC) is contaminated in the cancer given a confirmed diagnosis of poorly differentiated adenocarcinoma (P-ad-ca) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5252.
Abstract 5332: Prostate cancer targeting therapy using PSA promoter-driven perforin expression vector encapsulated in liposomes conjugated with anti-PSMA antibody
Authors: Mizutani Kosuke , Kawakami Kyojiro , Fujita Yasunori , Kato Taku , Takai Manabu , Kato Daiki , Iinuma Koji , Koie Takuya , Ito Masafumi
Published: June 2022

Perforin secreted from cytotoxic T cells and natural killer cells play important roles in anti-tumor immunoreaction leading to cancer cell apoptosis. The aim of this study is to investigate whether perforin-rich tumor microenvironment could inhibit tumor growth. Advanced prostate cancer (PC) expresses high amount of prostate-specific antigen (PSA) that is a possible therapeutic target, therefore, we constructed a PSA promoter-driven perforin expression vector for its predominant expression in tumor microenvironment of PC. Prostate membrane-specific antigen (PSMA) expressed on PC cell surface is also an attractive therapeutic target. To deliver perforin expression vector to PC, it was encapsulated in liposomes conjugated with anti-PSMA antibody (PSMA-pLipo), then the anti-tumor effect of PSMA-pLipo was evaluated using docetaxel-resistant PC cell line, 22Rv1DR, expressing both PSA and PSMA. The conjugated anti-PSMA antibody on PSMA-pLipo recognized recombinant PSMA protein, and incubation with PSMA-pLipo induced perforin expression in 22Rv1DR cells but not in PC-3 cells not expressing both PSA and PSMA. Growth of 22Rv1DR and PC-3 cells was barely inhibited by PSMA-pLipo alone. Perforin functions in concert with cytotoxic lymphocytes, therefore anti-tumor effect of PSMA-pLipo was analyzed in the presence of human peripheral blood mononuclear cells (PBMCs). Low concentration of PSMA-pLipo with human PBMCs significantly inhibited growth of 22Rv1DR cells but not PC-3 cells. High concentration of PSMA-pLipo with human PBMCs showed nearly complete inhibition of 22Rv1DR cell growth. In a mouse xenograft model implanted with 22Rv1DR cells, PSMA-pLipo was intravenously administrated via tale vein and tumor volume was monitored. PSMA-pLipo inhibited growth of 22Rv1DR cells compared to injection of anti-PSMA antibody alone. The data presented here suggest that gene therapy expressing perforin specifically in PC cells could be a novel therapy for advanced PC.

Citation Format: Kosuke Mizutani, Kyojiro Kawakami, Yasunori Fujita, Taku Kato, Manabu Takai, Daiki Kato, Koji Iinuma, Takuya Koie, Masafumi Ito. Prostate cancer targeting therapy using PSA promoter-driven perforin expression vector encapsulated in liposomes conjugated with anti-PSMA antibody [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5332.
Abstract 5367: DNA-PKcs inhibitors impair OCT4-mediated MYC transcriptional activation in small cell lung cancer
Authors: Yang Inhyoung , Mohiuddin Ismail , Wei Sung-Jen , Gloria Martinez , Kang Min H.
Published: June 2022

Small cell lung cancer (SCLC) is a disease found almost exclusively in smokers and is a highly aggressive cancer with incredibly poor outcomes. Initially, most patients diagnosed with SCLC respond to platinum + etoposide (PE)-based therapy, but relapse occurs in nearly all patients and is fatal. SCLC is a cancer with a heavy mutational burden, and loss-of-function mutations of the tumor suppressor genes RB1 and TP53 are nearly ubiquitous in SCLC tumors. Amplification and overexpression of the MYC of oncogene occurs in a subset of SCLC tumors that are associated with tumor progression, treatment resistance, and poor outcomes, therefore we pursued the inhibition of the MYC activation. The purpose of this study is to inhibit a novel pathway of MYC transcriptional activation via DNA-PKcs-mediated phosphorylation of OCT4 at its Ser93 residue in SCLC, a MYC transcriptional activation pathway that we discovered. We identified OCT4 being a transcription factor that primarily induce MYC activation. Subsequently, Serine 93 residue of OCT4, a new OCT-4 binding site, was phosphorylated by DNA-PKcs that was a critical step for OCT4-induced MYC activation. In a panel of 19 small cell lung cancer, DNA-PKcs, phosphorylation of OCT4 at Ser93, and c-MYC were positively correlated. We confirmed the binding of DNA-PKcs to OCT4 and identified novel OCT4-binding sites in the MYC promoter/enhancer region that regulated MYC expression via phosphorylation by DNA-PKcs, and DNA-PKcs or OCT4 knockdown decreased c-MYC expression. DNA-PKcs inhibitors also reduced phosphorylation of OCT4 at Ser93 leading to decreases in c-MYC and showed cytotoxic effects via inducing apoptosis by DNA-PKcs inhibitors. DNA-PKcs inhibitors augments antitumor activity of Bcl-2 inhibitors cell lines and xenograft models of small cell lung cancer. In conclusion, report here that DNA-PKcs-mediated phosphorylation of OCT4 at Ser93 is a novel mechanism for activating the MYC oncogene in SCLC, and that DNA-PKcs is a viable target to decrease c-MYC expression in these highly aggressive tumors.

Citation Format: Inhyoung Yang, Ismail Mohiuddin, Sung-Jen Wei, Martinez Gloria, Min H. Kang. DNA-PKcs inhibitors impair OCT4-mediated MYC transcriptional activation in small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5367.
Abstract 5392: Magnolol induces apoptosis and inhibits invasion ability via suppression of STAT3 signaling in glioblastoma multiforme cells
Authors: Lee Sin-Rong , Chang Yuan , Chiang I-Tsang , Hsu Fei-Ting
Published: June 2022

Magnolol is a phenolic compound extracted from magnolia officinalis, exhibited anti-tumor potential against many types of cancers. Magnolol has also recognized as an anti-inflammation agent which can downregulate several inflammation signals transduction. Glioblastoma multiforme (GBM) is the most common central nervous system (CNS) tumor and associated with poor prognosis among adults due to rapid growth and aggressive invasion. However, the treatment efficacy of current standard therapy for GBM is remaining unsatisfied. Nevertheless, whether magnolol may suppress GBM progression and its underlying mechanism has not been elucidated. Thus, the purpose of this study was to investigate the mechanism and therapeutic efficacy of magnolol on GBM.First of all, we validated the potential treatment targets of GBM with the GEPIA (Gene Expression Profiling Interactive Analysis) analysis and Western blotting assay. GEPIA data indicated the PKCδ/STAT3 signaling pathway as a potential target of GBM that may affect patient survival. In our results, magnolol can effectively suppress the phosphorylation and the nuclear translocation of STAT3 in GBM cells. Then, we used the MTT assay to investigate the cytotoxicity of GBM cells after various dose of magnolol treatment. We also detected the extrinsic/intrinsic apoptosis induction ability of magnolol on GBM cells. This study also demonstrated that magnolol may significantly trigger the loss of mitochondrial membrane potential, and the activation of cleaved caspase-3, -8 and -9. Transwell invasion and wound healing assays was used to identify the suppression of migration and invasion effects of magnolol on glioblastoma cells. Meanwhile, tumor invasion and migration ability and the associated genes, including MMP9 and uPA, were all diminished by magnolol treatment. In sum, our results demonstrated that magnolol suppressed GBM progression may be associated with the inactivation of PKCδ/STAT3 signaling transduction.

Citation Format: Sin-Rong Lee, Yuan Chang, I-Tsang Chiang, Fei-Ting Hsu. Magnolol induces apoptosis and inhibits invasion ability via suppression of STAT3 signaling in glioblastoma multiforme cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5392.
Abstract 5402: Urothelial carcinomas in different anatomical positions exhibit distinct genomic and immunological characteristics
Authors: Li Ruiqian , Zhang Hushan , Wang Qilin , Yang Hong , Bai Yu , Hu Chen , Wu Hongyi , Zhang Chongjian , Wang Ziyong , Wang Qiwei , Xu Pengjie , Li Jun
Published: June 2022

Background Human bladder cancers were recently suggested to be grouped into different molecular subtypes. However, little is known about the difference in gene landscape between upper tract urothelial carcinoma (UTUC) and lower tract urothelial carcinoma (LTUC) of Chinese patients. Herein, we analyzed the genomic characteristics of primary UTUC and LTUC in China.

Methods The formalin-fixed paraffin-embedded specimens of 250 LTUC and 121 UTUC patients have been consecutively collected and have underwent next-generation sequencing (NGS) from 2018 to 2021 in 3DMed Clinical Laboratory Inc. Gene mutation and TMB level were analyzed by NGS, detected PD-L1 expression by using Dako PD-L1 IHC 22C3 pharmDx, Tumor Proportion Score (TPS) was used to determine expression of PD-L1.

Results NGS analysis showed that, in the samples of UTUC, the top ten gene mutations were CDKN2A/2B 6.6% (8/121), TP53 5.8% (7/121), FGF19 5.8% (7/121), TERT 3.3% (4/121), PREX2 3.3% (4/121), FRS2 3.3% (4/121), KDM6A 2.5% (3/121), PIK3CA 2.5% (3/121), EGFR 2.5% (3/121), MYCL 2.5% (3/121); while in the LTUC, the top gene mutations were TP53 44.4% (111/250), TERT 31.6% (79/250), CDKN2A/2B 25.7% (64/250), FGF3 18% (45/250), KDM6A 17.6% (44/250), PIK3CA 16.4% (41/250), RB1 14.0%(35/250), DGFR3 13.6% (34/250), ARID1A 12.4% (31/250). Furthermore, TMB level and PD-L1 expression in the UTUC and LTUC were also analyzed, and results showed that although the gene mutation was totally different, but no significant difference was found on TMB level (p>0.05). However, among these patients, higher PD-L1 expression level were found in UTUC than LTUC (p<0.05).

Conclusion UTUC and LTUC in Chinese patients hold different gene landscape and PD-L1 expression, this suggested these patients may have different prognosis and response differently to targetable therapy and immunotherapy.

Citation Format: Ruiqian Li, Hushan Zhang, Qilin Wang, Hong Yang, Yu Bai, Chen Hu, Hongyi Wu, Chongjian Zhang, Ziyong Wang, Qiwei Wang, Pengjie Xu, Jun Li. Urothelial carcinomas in different anatomical positions exhibit distinct genomic and immunological characteristics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5402.