bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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&lt;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

Abstract
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&lt;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

Abstract
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

Abstract
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

Abstract
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 &lt; 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

Abstract
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 &lt; 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

Abstract
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

Abstract
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&lt;0.90), prob(dORR&gt;0.10), prob(OS HR&lt;0.85) and prob(PFS HR&lt;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&lt;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.