bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2149: Subgroups of early-stage microsatellite stability endometrial, colorectal and stomach tumors based on transcriptomics have distinct disease-free survival
Authors: Zhang Shi , Liu Xinyi , Zhang Lan , Huang Mengli
Published: July 2021

Background: Microsatellite stability (MSS) is a biomarker for worse prognosis than microsatellite instability (MSI) in non-metastatic tumors. Tumors with MSS status are more probable to occur postoperative recurrence and metastasis. Some studies had revealed that endometrial and gastrointestinal tumors have distinct MSI-related features compared with other types of cancers, indicating there are potential similarities in these cancer types. The proportion of MSS population in non-metastatic endometrial and gastrointestinal tumors were about 90% and 75%. There are high heterogeneity in such wide range of patient population. The status of immune microenvironment based on immunohistochemistry or RNA-Seq profiling had been proved effective prognostic biomarker in some previous investigation. Therefore, we assume a subtype model of immune microenvironment based on transcriptomics features in endometrial and gastrointestinal tumors.

Method: 128 patients with I-III stage MSS endometrial and gastrointestinal tumors from TCGA project were included as training cohort and a meta cohort of 603 patients of colorectal and stomach cancers from GEO datasets (GSE39582,GSE62254) were included as validation cohort in our study. The RNA-Seq profiling data and disease-free survival (DFS) of patients were collected. CIBERSORT tool was conducted to evaluate the immune-related cells' enrichment. A lasso-cox model of DFS was developed based on the CIBERSORT features. Patients in training cohort were scored the recurrence risk by the model. We further investigate the differentially expressed genes between high-risk and low-risk patients. Log-rank test was used to evaluate the difference of DFS.

Result: 76 immune-related genes were identified to be differentially expressed significantly. The patients in training cohort were divided into two groups (group1 n=81, group2 n=41) based on non-negative matrix factorization (NMF) method. The DFS of group1 and group2 were significantly different (log-rank p=0.005). In validation cohort, patients were divided into group1 and group2 (group1 n=401, group2 n=202) using clustering method above. A significant difference between subgroups was also tested (log-rank p<0.0001).

Conclusion: We identified 76 immune-related genes using CIBERSORT tool. Based on this gene set, early stage MSS endometrial and gastrointestinal tumors could be divided into two subgroups with distinct disease-free survival.

Citation Format: Shi Zhang, Xinyi Liu, Lan Zhang, Mengli Huang. Subgroups of early-stage microsatellite stability endometrial, colorectal and stomach tumors based on transcriptomics have distinct disease-free survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2149.
Abstract 2150: High RRM1 expression as a potential poor prognosis factorin bladder cancer patients
Authors: Xu Ziqiao , Bei Ting , Xie Wenzhuan , Huang Mengli
Published: July 2021

Background: RRM1 encodes the M1 subunit of Ribonucleotide Reductase (RNR), a complex participating in DNA replication and repairment. RRM1 expression level has been reported to be associated with prognosis in various cancers, such as non-small-cell lung cancer, pancreatic cancer, breast cancer, and biliary tract cancer. However, the prognosis value of RRM1 expression in bladder cancer (BLCA) has not been revealed.

Method: Three bladder cancer cohorts with RNA-seq data including 2 cohorts from the GEO database and 1 from the TCGA database were used for investigating the overall survival (OS) of BLCA patients with differentiated RRM1 RNA expression. GSEA and CIBERSORT analyses were performed to study the potential mechanisms. The value of RRM1 RNA expression in predicting the clinical benefits of immune checkpoint inhibitors (ICIs) treated BLCA patients was also investigated using data from an ICI cohort (IMvigor210 cohort, n=348).

Result: We found significant differences in OS between BLCA patients with high (top 25% RRM1 RNA expression patients) and low (lowest 25% RRM1 RNA expression patients) RRM1 RNA expression in all the three bladder cancer cohorts from the TCGA and the GEO database. The multiple-variables Cox regression analysis revealed that higher RRM1 expression was associated with worse survival outcomes (HR=1.65, 95% CI = 1.05 - 2.6, P = 0.03).GSEA analysis revealed that 20 out of 50 Hallmark gene sets were enriched in the RRM1 high expression group. Among these enriched gene sets, the interferon-gamma is a well-established immune-related pathway. Furthermore, CIBERSORT analysis showed that the RRM1 high expression group had higher scores in IFN-gamma response, intra-tumor heterogeneity, and leukocyte fraction than the RRM1 low expression group. Combining results from both CIBERSORT and GSEA analysis, we hypothesized that RRM1 expression may be an efficacious predictor for ICI treatment in BLCA patients. Overall survival analysis of another external ICI cohort revealed that ICI treated BLCA patients with high RRM1 expression tended to have better OS than those with low RRM1 expression (HR = 0.77, CI95 0.54 - 1.1), but this difference was not statistically significant (P = 0.152).

Conclusion: Our study demonstrated that high RRM1 expression may serve as a poor prognostic biomarker in BLCA patients. Moreover, our study suggested that BLCA patients with high RRM1 expression may benefit more from ICIs therapies than those with low RRM1 expression.

Citation Format: Ziqiao Xu, Ting Bei, Wenzhuan Xie, Mengli Huang. High RRM1 expression as a potential poor prognosis factorin bladder cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2150.
Abstract 2158: Arsenic hexoxide has differential effects on cell proliferation and genome-wide gene expression in human primary mammary epithelial and mcf7 cells
Authors: Bunch Heeyoun , Kim Donguk , Park Na Yeon , Jeong Jaehyeon , Kang Keunsoo , Calderwood Stuart K. , Cho Dong-Hyung , Bae Ill Ju
Published: July 2021

Arsenic is reportedly a biphasic inorganic compound for its toxicity and anticancer effects in humans. Recent studies have shown that certain arsenic compounds including arsenic hexoxide (AS4O6; hereafter, AS6) induce programmed cell death and cell cycle arrest in human cancer cells and murine cancer models. However, the mechanisms by which AS6 suppresses cancer cells are incompletely understood. In this study, we report the mechanisms of AS6 through transcriptome analyses. In particular, the cytotoxicity and global gene expression regulation by AS6 were compared in human normal and cancer breast epithelial cells. Using RNA-sequencing and bioinformatics analyses, differentially expressed genes in significantly affected biological pathways in these cell types were validated by real-time quantitative polymerase chain reaction and immunoblotting assays. Our data show markedly differential effects of AS6 on cytotoxicity and gene expression in human mammary epithelial normal cells (HUMEC) and Michigan Cancer Foundation 7 (MCF7), a human mammary epithelial cancer cell line. AS6 selectively arrests cell growth and induces cell death in MCF7 cells without affecting the growth of HUMEC in a dose-dependent manner. AS6 alters the transcription of a large number of genes in MCF7 cells, but much fewer genes in HUMEC. Importantly, we found that the cell proliferation, cell cycle, and DNA repair pathways are significantly suppressed whereas cellular stress response and apoptotic pathways increase in AS6-treated MCF7 cells. Together, we provide the first evidence of differential effects of AS6 on normal and cancerous breast epithelial cells, suggesting that AS6 at moderate concentrations induces cell cycle arrest and apoptosis through modulating genome-wide gene expression, leading to compromised DNA repair and increased genome instability selectively in human breast cancer cells.

Citation Format: Heeyoun Bunch, Donguk Kim, Na Yeon Park, Jaehyeon Jeong, Keunsoo Kang, Stuart K. Calderwood, Dong-Hyung Cho, Ill Ju Bae. Arsenic hexoxide has differential effects on cell proliferation and genome-wide gene expression in human primary mammary epithelial and mcf7 cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2158.
Abstract 2171: Brain cancer map: A neural network-based clustering of brain cancer samples based on genome-wide CNV and LOH patterns
Authors: Roytman Megan , Shams Soheil
Published: July 2021

Genomic based classification of cancers has been performed using gene expression and methylation patterns (e.g. well-established gene expression profiles used to sub-classify breast cancer). However, there has been very limited progress on classifying cancers based on their global CNV and/or LOH patterns. In this study, we present a novel neural network algorithm based on Self-Organizing Maps (SOMs) that creates a 2-dimensional map of cancer based on global CNV and LOH patterns. We applied this algorithm to 636 brain tumor samples from the TCGA project as part of the Glioblastoma (GBM) and Low-Grade Glioma (LGG) TCGA data sets. The CNV and LOH profiles for the samples was generated and manually curated to adjust for sample ploidy and call fragmentation due to normal cell contamination. Our algorithm generated a 25-node map of brain tumors, where different nodes represent a unique genome-wide profile and neighboring nodes are more similar to each other than more distant nodes. The generated map included nodes representing already known and prognostically important profiles such as 1p/19q co-deletion and combination of trisomy 7, monosomy 10, and homozygous deletion of p16. This is a significant validation of the approach since these profiles were generated completely automatically. In addition to these, new profiles were generated that were further investigated for prognostic value. We then projected all 636 samples back onto the learned map and were able to detect clusters of samples that generally fell within one cancer type, but also discovered some nodes shared by GBM and LGG samples indicating similarity in the CNV profile between these cancer types. We generated Kaplan-Meier survival plot for samples mapped to each node and were able to show statistically significant differences in survival based on the clustering. This approach has the possibility to create a unique CNV based classification of brain tumors for both prognostic and therapeutic applications.

Citation Format: Megan Roytman, Soheil Shams. Brain cancer map: A neural network-based clustering of brain cancer samples based on genome-wide CNV and LOH patterns [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2171.
Abstract 2188: Urothelial cancer-GENOmic analysis to improve patient outcomes and research (UC-GENOME): a bladder cancer advocacy network (BCAN) led collaborative research study
Authors: Damrauer Jeffrey S. , Klomp Jeff , Beck Wolfgang , Zhou Mi , Plimack Elizabeth , Galsky Matthew , Grivas Petros , Hahn Noah , O'Donnell Peter , Iyer Gopa , Quinn David I. , Hoadley Katherine A. , Kim William Y. , Milowsky Matthew I.
Published: July 2021

The UC-GENOME study was designed to capitalize on The Cancer Genome Atlas (TCGA) findings in real world patients with metastatic urothelial carcinoma (UC) with co-equal aims: 1) to provide targeted DNA sequencing for potential clinical decision making at no cost to patients; and 2) to create a clinically annotated biorepository (including tissue, plasma, and PBMCs) for collaborative research. Patients with metastatic UC (n=209, median age 68 y, 74% male) were accrued at 8 academic medical centers between 2016-2019. We report on the first analysis of the targeted DNAseq (n=191) and total RNAseq (n=176) from FFPE specimens (n=169 overlap). Recurrently mutated genes were observed in a similar frequency to TCGA, including TP53 (54%), KMT2D (30%), ARID1A (26%) and FGFR3 (18%). Somatic variant patterns were correlated with previously annotated mutational signatures (COSMICv3), revealing a subset of tumors enriched for APOBEC signatures. Molecular subtypes were defined using the Bladder Cancer Molecular Taxonomy Group's consensus subtyping schema (Ba_Sq=54 [31%], Stroma-rich=64 [36%], LumP=26 [15%], LumU=24 [14%], LumNS=4 [2%], NE=4 [2%]). To further understand the tumor immune features and whether they correlate with durable clinical response, tumor microenvironment deconvolution was performed by applying MiXCR and immune gene signatures. An inflamed phenotype and enhanced T cell receptor richness but not clonality was observed within Ba_Sq and Stroma-rich subtypes, which also had the highest disease control rate (CR/PR + SD ~75%) to immunotherapy. The Stroma-rich subtype had the highest disease control rate (~88%) to chemotherapy. Future efforts will leverage the clinical, DNA and RNAseq data along with other biobanked specimens for collaborative research initiatives.

Citation Format: Jeffrey S. Damrauer, Jeff Klomp, Wolfgang Beck, Mi Zhou, Elizabeth Plimack, Matthew Galsky, Petros Grivas, Noah Hahn, Peter O'Donnell, Gopa Iyer, David I. Quinn, Katherine A. Hoadley, William Y. Kim, Matthew I. Milowsky. Urothelial cancer-GENOmic analysis to improve patient outcomes and research (UC-GENOME): a bladder cancer advocacy network (BCAN) led collaborative research study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2188.
Abstract 2223: Distinct genomic features of cutaneous, acral and mucosal melanomas in a Chinese retrospective cohort
Authors: Liu Qiuyu , Kong Lingfei , Wang Weiran , Wang Danhua , Ma Tonghui
Published: July 2021

Background: The incidence of each subtype of melanoma in different races and ethnicities is significant differences. Cutaneous melanomas dominate in the Caucasian population. In contrast, melanomas that occur in the Chinese population are mainly arising from non-cutaneous tissue (extremities and mucous). Here, we reported an analysis of genomic features in 97 acral, 52 cutaneous and 18 mucosal melanomas. Methods: Patients (pts) with melanoma were enrolled, and surgical tumor tissues were collected. Mutation profiling was performed by next-generation sequencing (NGS). Results: Comparing to cutaneous melanoma patients (Age 53±11.6), acral (Age 65±11.1, P<0.001) and mucosal (Age 64±9.7, P=0.01) melanomas occurred in older Chinese patients. Mutations were identified in 148 of melanoma patients (88.62%), including 85 acral (87.63%), 47 cutaneous (90.38%) and 16 mucosal (88.89%) melanomas. Mutations of BRAF (25/52) in cutaneous melanoma, NRAS in acral melanoma (22/97) and mucosal melanomas (5/18) were observed as the most commonly genetic variations in different subtype of melanoma, which always occurred mutual exclusivity. Furthermore, focal amplification of 11q13 (CCND1 and FGF3/4/19) was all abundant in acral melanoma (11.34%, 11/97), which was reported to affect the efficacy of immunotherapy. In total, occurrence of BRAF, NRAS, CDKN2A mutations and 11q13 amplification were significantly different in cutaneous and non-cutaneous melanomas, which suggested different pathogenesis. Conclusions: In summary, genomic characterization of melanomas may offer insights into tumorigenesis and identify potential therapeutic targets in this disease.

Citation Format: Qiuyu Liu, Lingfei Kong, Weiran Wang, Danhua Wang, Tonghui Ma. Distinct genomic features of cutaneous, acral and mucosal melanomas in a Chinese retrospective cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2223.
Abstract 2228: Usage of ctDNA analysis to identify alterations with strong evidence for response or resistance to targeted therapy in patients with NENs
Authors: Du Kunli , She Xueke , Huang Depei , Shen Xudong , Zhang Hushan , Zheng Jianyong
Published: July 2021

Background: Neuroendocrine neoplasias (NENs) are a heterogeneous group of rare tumors scattered throughout the body. For nonresectable advanced NENs, the main treatment approaches including somatostatin analog, multiple TKIs, mTOR inhibitors and peptide receptor radionuclide therapy, whereas platinum-based chemotherapy is the main treatment for advanced high-grade and poorly differentiated NECs. Currently, there is no standard second-line treatment for NECs when disease progression. ctDNA as a non-invasive diagnostic avenue, which might potentially provide treatment guidance in NENs.

Methods: We queried consecutive data from 40 NENs patients who underwent a targeted next-generation sequencing (NGS) assay performed by 3DMed Clinical Laboratory Inc., a College of American Pathologists (CAP) certified and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory of 3D Medicines Inc. between January, 2017 and June, 2020 in China, to identify the alterations detected in ctDNA. The alterations were classified based on the ranking in the OncoKB database as of January 2020.

Results: In total, 40 of NENs patients detected with at least one alteration in ctDNA. The median age was 54 years, including 28 males and 12 females. Overall, 40.0% of patients had a Level 1 alteration, 22.5% of patients had a Level 2 alteration, and 22.5% of patients had a R1 alteration (selected alterations were outlined in Table).

Conclusion: ctDNA analysis could provide information of alterations with strong evidence for targeted therapy or drug resistance based on the OncoKB database classification for NENs. Though the alterations are associated with other specific cancer types, the alterations still illustrate a part of NENs patients might have chance to be benefited from targeted therapy.

AlterationsNumber of patients (%)Total Level 1 Alterations16 (40.0%)PIK3CA7 (17.5%)BRAF V600E2 (5.0%)BRCA22 (5.0%)MSI-H1 (2.5%)Total Level 2 Alterations9 (22.5%)ERBB2 activating4 (10.0%)MET amplication1 (2.5%)Total Level R1 alterations9 (22.5%)KRAS mut9 (22.5%)

Citation Format: Kunli Du, Xueke She, Depei Huang, Xudong Shen, Hushan Zhang, Jianyong Zheng. Usage of ctDNA analysis to identify alterations with strong evidence for response or resistance to targeted therapy in patients with NENs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2228.
Abstract 2229: Landscape of RB1 alterations in 22,432 Chinese solid tumor patients
Authors: Wang Nan , She Xueke , Huang Depei , Shen Xudong , Zhang Hushan , Ji Gang
Published: July 2021

Background: The retinoblastoma susceptibility gene (RB1) is one of tumor suppressor genes. This gene is mutated at variable frequencies in a variety of other human cancers. Cancer genome sequencing revealed that most types of cancer with RB1 mutation were retinoblastomas, osteosarcomas, and small-cell lung cancers, and its mutation was also found in other cancer types with a lower frequency, for instance, prostate cancer, breast cancer and etc. RB1 protein plays a prominent role in a variety of molecular processes related to DNA including gene transcription, DNA replication, DNA repair, and mitosis. However, no comprehensive status of RB1 alterations in Chinese populations with solid tumor has been reported yet.

Methods: The Formalin-Fixed Paraffin-Embedded (FFPE) tissues from solid tumor patients who have underwent next-generation sequencing (NGS) from January 01, 2017 to April 15, 2020 in 3DMed Clinical Laboratory Inc. (a College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory) were analyzed. The diagnosis of the tissues was confirmed by hematoxylin and eosin (H&E) staining. The single nucleotide variants (SNVs), copy number variants (CNVs) and gene rearrangements data of these patients were analyzed.

Results: Of 22,432 Chinese solid tumor patients with more than 20 tumor types (58% males and 42% females, with median age was 60 years), genomic alterations in RB1 were observed in 1712 (7.6%) patients. RB1 mutations occurred most frequently in small cell lung cancer (138/165, 83.6%), followed by neuroendocrine neoplasms (42/170, 24.7%), sarcoma (127/554, 22.9%), biliary tract cancer (40/209, 19.1%), head and neck cancer (4/22, 18.2%), and liver cancer (232/1649, 14.1%). And (185/1712, 10.8%) patients were detected with germline RB1 mutation. When stratified by the mutational types, 1,443 (6.4%) patients were with SNVs, 59 (0.3%) with fusions, and 210 (0.9%) with loss in RB1 gene.

Conclusion: Our results suggested RB1 alteration was widely occurred in solid tumor patients in China, and specific alteration rates differed largely between tumor types. Our study also suggested usage of NGS in the need for individualized characterization of cancers and further investigations are warranted for the cancer treatment upon molecular profiling in the clinical therapeutic setting.

Citation Format: Nan Wang, Xueke She, Depei Huang, Xudong Shen, Hushan Zhang, Gang Ji. Landscape of RB1 alterations in 22,432 Chinese solid tumor patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2229.
Abstract 2235: A comprehensive map of genetic interactions in childhood cancer reveals multiple underlying biological mechanisms
Authors: Daub Josephine , Amini Saman , Ma Xiaotu , Jager Natalie , Zhang Jinghui , Pfister Stefan , Holstege Frank , Kemmeren Patrick
Published: July 2021

Despite increasing survival rates, childhood cancer is still the major cause of disease-related child death in developed countries. Genetic interactions between mutated genes play an important role in cancer development. They can be detected by searching for pairs of mutated genes that co-occur more (or less) often than expected. Co-occurrence suggests a cooperative role in cancer development, while mutual exclusivity points to synthetic lethality, a phenomenon of interest in cancer treatment research. Little is however known about genetic interactions in childhood cancer. Here, we apply a statistical pipeline to detect genetic interactions in a combined dataset comprising over 2,500 tumors from 23 cancer types. The resulting genetic interaction map of childhood cancers comprises 15 co-occurring and 27 mutually exclusive candidates. The biological mechanisms underlying most candidates are either tumor subtype, pathway epistasis or cooperation while synthetic lethality plays a much smaller role. Thus, other explanations beyond synthetic lethality should be considered when interpreting results of genetic interaction tests.

Citation Format: Josephine Daub, Saman Amini, Xiaotu Ma, Natalie Jager, Jinghui Zhang, Stefan Pfister, Frank Holstege, Patrick Kemmeren. A comprehensive map of genetic interactions in childhood cancer reveals multiple underlying biological mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2235.
Abstract 2242: Blood-based genome-wide copy number analysis of 500 cancer patients
Authors: Dai Chao , Wang Amy Xiaohong , Zhao Zhixin , Xie Feng , Zhou Kemin , Luo Shujun , Jia Shidong , Du Pan
Published: July 2021

Copy number variation (CNV) is an important characteristic in cancer genome. Blood-based low-pass whole genome sequencing (LP-WGS) has been increasingly used to identify copy number variations of large genomic ranges in cancer. Conventional LP-WGS data analysis lacks the identification of focal CNV of small genomic ranges and often includes biased estimation of copy-neutral baseline when unbalanced genome-wide copy number changes are present. In this study, we have developed a proprietary algorithm analysis pipeline and leverage PredicineCARE and PredicineATLAS panel-based sequencing platform to identify focal CNVs missed by LP-WGS, and accurately infer copy number neutral baseline for LP-WGS. Here we present plasma-based LP-WGS results from 500 cancer patients, including breast, prostate, pancreatic and lung cancers. Our study demonstrates a cancer type-specific pattern of copy number variation across chromosome arms. The CNV abnormality score we developed in this study can be used to distinguish healthy person from cancer patient, and monitor disease progression for longitudinal patient samples.

Citation Format: Chao Dai, Amy Xiaohong Wang, Zhixin Zhao, Feng Xie, Kemin Zhou, Shujun Luo, Shidong Jia, Pan Du. Blood-based genome-wide copy number analysis of 500 cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2242.
Abstract 2243: Comprehensive genomic profiling - does timing matter
Authors: Thapa Bicky , Ahmed Gulrayz , Lasowski Matthew , Thomas James P. , Reddi Honey V. , Zimmerman Michael T. , Urrutia Raul , Szabo Aniko , George Ben
Published: July 2021

Background: Comprehensive Genomic Profiling (CGP) is performed routinely in patients (pts) with metastatic solid tumors (MSTs) to guide treatment. However, there is variability in the interval between metastatic diagnosis (MDx) and performance of CGP based on histology and/or provider preference. We analyzed the CGP utilization patterns and its impact on outcomes at our academic medical center.

Methods: All MST pts with CGP data (January 2012 - April 2020), their date of MDx, and the date of CGP were identified by electronic medical record review. Pts who had CGP after MDx were divided into tertiles (T1-earliest, T3-latest) within each cancer type, while some pts had CGP performed prior to MDx (pre-mets). Overall survival (OS) was estimated from the time of MDx with left truncation at the CGP time. Cox regression model was used to estimate the impact of ‘timing of CGP' on survival for individual cancer (CA) types.

Results: Among 1,358 pts identified, 710 (52%) were female, 1,109 (82%) Caucasian, 186 (14%) Afro-Americans, and 1,320 (97%) non-Hispanic. Lung (254; 19%), colorectal (203; 15%), gynecologic (121; 8.9%), pancreatic (106; 7.8%) and connective tissue/soft tissue CAs (95; 7%) were the most frequently identified. Sex, race, and ethnicity had no impact on the time interval between MDx and CGP with 2 exceptions - Hispanics with lung CA and females with pancreas CA had delayed CGP compared to non-Hispanics and males respectively (p =0.019, p =0.025). The median time to CGP after MDx was shortest for urothelial CA (2.4 months) and longest for prostate CA (22 months). Pts with lung [T2 Hazard ratio (HR) of 2.25, p<0.001; T3 HR of 2.67, p<0.001], gastro-esophageal (T2 HR of 1.88, p=0.079; T3 HR of 2.49, p= 0.024), and gynecologic CAs (T2 HR of 2.58, p=0.012; T3 HR of 5.19, p=0.003) had better survival if they had CGP performed during the first tertile after MDx.

Conclusion: Early CGP after MDx may have a greater impact on OS in CA types with more actionable therapeutic targets. The inherent bias associated with limiting the analyses only to pts who had CGP performed hampers our ability to contrast these results with those who did not have CGP performed. The establishment of national quality metrics for CGP utilization by CA type is imperative.

Citation Format: Bicky Thapa, Gulrayz Ahmed, Matthew Lasowski, James P. Thomas, Honey V. Reddi, Michael T. Zimmerman, Raul Urrutia, Aniko Szabo, Ben George. Comprehensive genomic profiling - does timing matter [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2243.
Abstract 2250: Genomic and transcriptomic analyses of desmoid tumor reveals enrichment of transforming growth factor beta responsive signature
Authors: Park Changhee , Yun Kum-Hee , Song Sanghoon , Lee Jin Kyung , Ryu Jiyeon , Oh Bitna , Hwang Sunjin , Hahm Ki Baik , Kim Seung-Jin , Kim Seung Hyun , Ock Chan-Young , Kim Hyo-Song
Published: July 2021

Introduction: Desmoid tumor is a rare aggressive tumor where there is no satisfying systemic treatment. Previous studies showed increased expression of transforming growth factor-β (TGF-β) in the desmoid tumor. Here, we analyzed genomic and transcriptomic data of tumor samples from patients with desmoid tumor to evaluate therapeutic applicability of inhibition of TGF-β response.

Methods: We collected pre-treatment desmoid tumor samples from 31 patients in Yonsei cancer center, (YCC)-desmoid cohort and performed targeted next-generation sequencing and whole RNA sequencing. To compare the data with other cancer types, we used whole exome sequencing and whole RNA sequencing data from sarcoma patients from Yonsei Cancer Center (YCC-sarcoma cohort, n = 17 and n =53, respectively) and The Cancer Genome Atlas (TCGA, n = 9,235). Transcriptomic data was normalized throughout the three cohorts to reduce batch effect. To evaluate the enrichment of TGF-β responsive signature (TBRS) in tumor and microenvironment, we calculated the mean expression values of fibroblast-TBRS (F-TBRS) from previous study.

Results: In the two sarcoma cohorts (YCC-desmoid and YCC-sarcoma cohorts), desmoid tumor samples had the highest F-TBRS score among the various types of sarcoma. When compared with other cancer types in TCGA, desmoid tumor samples showed the higher F-TBRS than all other cancer types except for pancreatic adenocarcinoma. In the desmoid tumor samples, CTNNB1, GNAQ, and APC mutations were the top 3 frequent mutations (23, 19, and 2 samples, respectively). In the merged two sarcoma cohorts, CTNNB1/APC mutation and GNAQ mutation were both associated with higher enrichment in F-TBRS (p < 0.001, respectively).

Conclusion: Desmoid tumors are enriched with expression of genes associated with TGF-β response of fibroblast compared with other cancer types including other sarcomas. In addition, CTNNB1, APC and GNAQ mutations were associated with higher enrichment in TBRS. Therapeutic intervention to decrease the TGF-β response of fibroblast by using TGF-β receptor inhibitor may show clinical benefit in patients with desmoid tumors.

Citation Format: Changhee Park, Kum-Hee Yun, Sanghoon Song, Jin Kyung Lee, Jiyeon Ryu, Bitna Oh, Sunjin Hwang, Ki Baik Hahm, Seung-Jin Kim, Seung Hyun Kim, Chan-Young Ock, Hyo-Song Kim. Genomic and transcriptomic analyses of desmoid tumor reveals enrichment of transforming growth factor beta responsive signature [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2250.
Abstract 2272: Interrogating RAS isoform and mutational specificity for effectors with bioluminescence resonance energy transfer (BRET)
Authors: Rigby Megan , Columbus John , Wall Vanessa , Esposito Dominic , Turbyville Thomas
Published: July 2021

Mutations in the small GTPases HRAS, NRAS, and splice variants KRAS4a and KRAS4b occur in roughly 20% of all cancers1. Each of these four RAS isoforms share a high degree of homology, yet play distinct biological roles; mouse models devoid of KRAS die mid-gestation, whereas HRAS and NRAS null mice survive2. The occurrence of RAS isoform mutations and their specific oncogenic codon substitutions are non-uniform across cancer types, with KRAS mutations in the G12 position frequently driving colorectal cancer while NRAS Q61 mutations are commonly present in skin cancer1. Several explanations have been proposed for this, including differential regulation at the level of transcription, mRNA stability, translation, and protein stability, along with distinctions in post-translational modification, localization, and tissue-specific availability of effectors3. Subtle differences in the biochemical properties of amino acid substitutions may also influence the dominant mutational forms across cancer types. However, the question of whether RAS isoforms and their specific codon substitutions preferentially engage with certain effectors within a cellular context remains unclear, despite considerable efforts. Here, we utilize bioluminescence resonance energy transfer (BRET) between mVenus- and NanoLuc-tagged recombinant proteins to derive quantitative measurements of effector affinity across RAS isoforms and common mutants. By transiently expressing a fixed concentration of NanoLuc-tagged effectors while titrating increasing amounts of mVenus-tagged RAS in a cellular system, we generated saturation curves that reflect the nature of binding between the protein pair in vivo to help untangle this longstanding question. We further validated interactions by immunoprecipitation, and determined construct expression and colocalization via western blot and confocal microscopy.

1Prior IA, Hood FE, Hartley JL. The frequency of Ras mutations in cancer. Cancer Research 20202Malumbres M, Barbacid M. RAS oncogenes: the first 30 years. Nature Reviews Cancer 2003;3:459-653Li S, Balmain A, Counter CM. A model for RAS mutation patterns in cancers: finding the sweet spot. Nature Reviews Cancer 2018;18:767-77

Citation Format: Megan Rigby, John Columbus, Vanessa Wall, Dominic Esposito, Thomas Turbyville. Interrogating RAS isoform and mutational specificity for effectors with bioluminescence resonance energy transfer (BRET) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2272.
Abstract 2277: HER2 copy number variation detected by next-generation sequencing reveals HER2 expression heterogeneity in gastric cancer
Authors: Zhang Xiaotian , Chen Hui , Zhao Xiaochen , Wang Jie , Bai Yuezong
Published: July 2021

Purpose: Human epidermal growth factor receptor 2 (HER2) is an effective therapeutic target in gastric cancer (GC). Both HER2-positive and HER2-low GC could benefit from HER2 inhibitors including trastuzumab and trastuzumab deruxtecan. However, it is difficult to accurately evaluate HER2 status by immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH), owing to intra-tumor heterogeneity and the experience of the pathologist. Herein, we investigated whether HER2 copy number variation (CNV) detected by next-generation sequencing (NGS) could assist in accurately determining the HER2 status.

Methods: We analyzed HER2 CNV on tumor specimens from 212 GC patients using NGS in a CLIA-certified laboratory. The log ratio of HER2 >0.7 was defined as amplification and log ratio of 0.4 to 0.7 was defined as low amplification. HER2 expression was examined in all 212 GC patients by IHC and HER2 amplification was assessed in 22 patients by FISH.

Results: Of 212 patients, three had HER2 amplification and three had low HER2 amplification. Among three patients with HER2 amplification, all were found to have strong positive HER2 expression (IHC 3+). Among three patients with HER2 low amplification, two patients had HER2 IHC 2+ (including one HER2 FISH-negative and one HER2 FISH-unknown) and one patient had HER2 IHC 1+. Moreover, two patients were found HER2 IHC 3+ in whom without HER2 amplification. Of the two, one was most HER2 IHC 2+ with focal tumor IHC 3+, and the HER2 CNV was close to the threshold (log ratio of HER2: 0.2882). The reason for the discordance may be related to intra-tumor heterogeneity. HER2 copy number will be diluted in samples with focal 3+ and NGS reflects the relative global nature of the tumor specimens. No HER2 IHC-negative cases (N=99) showed HER2 CNV, suggesting that HER2 CNV detected by NGS has specificity of 100%.

Conclusions: HER2 CNV detected by NGS could predicts HER2 status in GC and more accurately stratified GC patients with either HER2-positive or HER2-low. Thus, we can screen out those who can truly benefit from trastuzumab and trastuzumab deruxtecan (eg. DS-8201). Prospective cohorts are needed to validate HER2 CNV detected by NGS for predicting response to anti-HER2 therapy.

Citation Format: Xiaotian Zhang, Hui Chen, Xiaochen Zhao, Jie Wang, Yuezong Bai. HER2 copy number variation detected by next-generation sequencing reveals HER2 expression heterogeneity in gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2277.
Abstract 2288: Identification of gene fusions in soft tissue sarcoma improved by integrative DNA and RNA sequencing
Authors: Liu Jiayong , Li Shu , Gao Tian , Wang Chunyang , He Qifan , Wang Xiaojuan , Ma Tonghui
Published: July 2021

Background: More than 50 different histologic subtypes of soft tissue sarcoma (STS) with mesenchymal origin have been recognized, and their overlapping morphology and histology make clinical diagnosis challenging. Gene fusion has been described as an important molecular biological feature of STS, which can assist in its diagnosis and treatment. Conventional DNAseq methods have limitations for gene fusion detection, while the RNAseq method might circumvent them. In this study, we evaluated the clinical value of integrated DNA and RNA sequencing in the detection of STS gene fusions.

Methods: Formalin-fixed and paraffin embedded (FFPE) tumor samples and matched blood of 142 Chinese STS patients were collected and tested by the next-generation sequencing (NGS)-based 825-gene DNA panel and 395-gene RNA panel at Genetronhealth, a laboratory accredited by College of American Pathologists and Clinical Laboratory Improvement Amendments.

Results: The genetic landscape of 75 male and 67 female Chinese patients with STS was analyzed. The median age of enrolled patients was 39 years (range, 1-82 years). Multiple histological subtypes were collected, including rhabdomyosarcoma (n = 15), liposarcoma (n = 15), myofibroblastic sarcoma (n = 11) and other types which were all less than 10 cases. Overall, 83 different fusions were detected in 60 patients. Of these, 25 fusions could be detected both by DNA and RNA panels in 18 patients, five fusions were detected only by the DNA panel in four patients, and 53 fusions only by the RNA panel in 39 patients. Compared to DNA-NGS individual testing, integrative panels increased the detection rate of fusion in patients with STS by 177% (53/30). The five gene fusions detected only by the DNA panel, including FOSL1-RELA, intergenic-RUNX2, ADAMTS16-TERT, NCR3LG1-KMT2A and YAP1-MAMLD1, remain clinical significance uncertain in STS. Fusion genes, such as PAX3-FOXO1, ASPSCR1-TFE3, COL1A1-PDGFB, EWSR1-ERG, were detected separately by the RNA panel, which could assist the diagnosis or targeted therapy. Additionally, unreported DIP2B-EWSR1 and AMLD1-SSX1 gene fusions were detected in a patient with clear cell sarcoma and a patient with synovial sarcoma respectively, which might be helpful in clinical diagnosis.

Conclusions: Our results showed that the integrated DNA and RNA sequencing can effectively improve the detection rate of STS gene fusions, which might benefit more STS patients.

Citation Format: Jiayong Liu, Shu Li, Tian Gao, Chunyang Wang, Qifan He, Xiaojuan Wang, Tonghui Ma. Identification of gene fusions in soft tissue sarcoma improved by integrative DNA and RNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2288.
Abstract 2295: SGK2, 14-3-3, and HUWE1 coordinately regulate the localization and stability of PTOV1
Authors: Pennington Katie L. , Woods James , Muir Colin , McEwan Colten M. , Gamage Pramoda S. Aththota , Eastmond Riley J. , Egbert Crissy M. , Heaton Tyler , Piccolo Stephen R. , Andersen Joshua L.
Published: July 2021

PTOV1 is an oncogenic protein, initially identified in prostate cancer, that promotes proliferation, cell motility, and invasiveness. However, the mechanism of PTOV1 regulation is poorly understood. To understand these mechanisms, we identify 14-3-3 as a PTOV1 interactor and show that high levels of 14-3-3 expression, like PTOV1, correlate with prostate cancer progression. Further, we found that SGK2-mediated phosphorylation of PTOV1 is required for 14-3-3 binding. This phosphorylation occurs in a cell cycle-dependent manner and peaks in the G1 phase. Disruption of the PTOV1-14-3-3 interaction results in an accumulation of PTOV1 in the nucleus and a proteasome-dependent reduction in PTOV1 protein levels. To understand the effect of 14-3-3 on PTOV1 stability, we found that loss of 14-3-3 binding leads to an increase in PTOV1 binding to the E3 ubiquitin ligase HUWE1, which promotes proteasomal degradation of PTOV1. Conversely, our data suggest that 14-3-3 stabilizes PTOV1 protein by sequestering PTOV1 in the cytosol and inhibiting its interaction with HUWE1. Finally, our data suggest that stabilization of the 14-3-3-bound form of PTOV1 promotes PTOV1-mediated expression of cJun. Together, these data provide a first mechanism to understand the regulation of PTOV1 stability, localization, and function within the cell.

Citation Format: Katie L. Pennington, James Woods, Colin Muir, Colten M. McEwan, Pramoda S. Aththota Gamage, Riley J. Eastmond, Crissy M. Egbert, Tyler Heaton, Stephen R. Piccolo, Joshua L. Andersen. SGK2, 14-3-3, and HUWE1 coordinately regulate the localization and stability of PTOV1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2295.
Abstract 2297: Regulatory role of MRCK gamma in ovarian cancer metastasis
Authors: Toledo-Jacobo Leslie
Published: July 2021

In ovarian cancer, compacted cell aggregates known as spheroids detach from the primary tumor and enable metastasis within the peritoneum. Targeting this ovarian metastatic cascade motivates a delineation of the morphogenetic pathways governing spheroid shedding and invasion. Here we analyze the role of one of three related Myotonic Dystrophy Kinase-Related CDC42-Binding Kinases (MRCKγ) in ovarian cancer metastasis, and test its potential as a therapeutic target. MRCKs are downstream effectors of Cdc42 and Rac1 GTPases and through activation of myosin-II could produce the mechanical force required during cell invasion. MRCKγ is amplified or mutant in 12.5% of 1680 serous ovarian cancer patient samples in TCGA. Analyses of ovarian cancer SKOV3ip cells with 4-fold overexpression of GFP-Rac1 and increased GTPase activation showed a 1.5-fold increase in MRCKγ protein and a concomitant increase in the phosphorylation of myosin required for contractile force generation. A similar increase in myosin phosphorylation was observed in two OVCAR8 cell lines with overexpression of GFP-Rac1 and GFP-Cdc42, respectively. Analyses of the effects MRCKγ knockdown on ovarian spheroid formation and in mesothelial clearance are in progress. To evaluate the therapeutic potential of MRCK/Cdc42BPs we are also testing their pharmacological inhibition with BDP9066 and SD208 during spheroid formation and mesothelial clearance. Our findings are supported by a recent report showing that inhibition of the related MRCKα kinase blocks ovarian cancer cell spheroid formation in vitro. By the end of these studies we will have a better understanding of the role of MRCK/Cdc42BPs in ovarian cancer metastatic pathway, and a potential therapeutic target for ovarian cancer treatment.

Citation Format: Leslie Toledo-Jacobo. Regulatory role of MRCK gamma in ovarian cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2297.
Abstract 23: Validation of a 27-gene immuno-oncology algorithm in metastatic urothelial carcinoma treated with an immune checkpoint inhibitor
Authors: Seitz Robert S. , Ross Douglas T. , Nielsen Tyler J. , Hout David R. , Schweitzer Brock L.
Published: July 2021

Background

Prognosis for patients with metastatic urothelial carcinoma (mUC) remains poor with fewer than 10% of patients surviving two years after diagnosis. The IMvigor210 was a multicenter, single-arm, phase 2 trial in patients with mUC treated by the immune checkpoint inhibitor (ICI) atezolizumab. RNA expression, overall survival, tumor mutation burden (TMB), and PD-L1 IHC data from this trial are publicly available.The 27-gene immuno-oncology (IO) algorithm has previously demonstrated significant association with ICI response in NSCLC and TNBC using three different ICI agents. Importantly, the algorithm and threshold for positivity was established prior to testing in ICI treated cohorts.

Methods

The prospectively defined 27-gene IO algorithm and threshold (IO Score) were applied to classify patients as likely responders or non-responders using available RNA expression data from 348 patients in the IMvigor210 trial. Cox proportional hazard models for overall survival was performed and the coefficient for the IO Score was determined in both a univariate and a multivariate equation with PD-L1 IHC and TMB.

Results

In total, 142 patients were positive by the IO Score (41%). Positivity was significantly associated with response (HR=0.61; 95% CI = 0.46 to 0.80; p < 0.001) and was significant in multivariate analysis with PD-L1 and TMB (HR=0.64; 95% CI = 0.45 to 0.92; p < 0.02). While both PD-L1 IHC staining and TMB were significant in univariate analysis, only TMB maintained significance in the multivariate equation.

Conclusions

These data demonstrate the association of the 27-gene IO algorithm and binary IO Score with response to ICI treatment in a third tissue indication (TNBC, NSCLC, and mUC) including four different ICI agents (two anti-PD-L1 and two anti-PD1). The algorithm and classification threshold were established prior to testing in all three studies and was not changed between the different tissue indications. Furthermore, in all three indications, only the IO Score consistently maintained significance in multivariate analysis with PD-L1 IHC and TMB. Taken together, these data begin to establish the 27-gene IO signature as a pan-cancer predictor of response to ICI therapy.

Citation Format: Robert S. Seitz, Douglas T. Ross, Tyler J. Nielsen, David R. Hout, Brock L. Schweitzer. Validation of a 27-gene immuno-oncology algorithm in metastatic urothelial carcinoma treated with an immune checkpoint inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 23.