bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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 &gt;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

Abstract
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

Abstract
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

Abstract
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

Abstract
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 &lt; 0.001) and was significant in multivariate analysis with PD-L1 and TMB (HR=0.64; 95% CI = 0.45 to 0.92; p &lt; 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.
Abstract 2301: Atomic-level insights into PI3K activation
Authors: Zhang Mingzhen , Jang Hyunbum , Nussinov Ruth 
Published: July 2021

Abstract
PI3Kα (PIK3CA) is the second highly mutated oncogene in cancer. It is activated by the receptor tyrosine kinases (RTKs) and Ras on the membrane, regulating the PI3K/Akt/mTOR pathway for the cell growth and proliferation. PI3Kα is an obligate dimer with p110α catalytic subunit and p85α regulatory subunit. Their interactions stabilize and maintain PI3Kα in the inactive state. At the molecular level, the activation of PI3Kα requires two events, (i) the release of nSH2 by phosphorylated tyrosine (pY) motif in the RTK and (ii) the membrane localization facilitated by Ras. The mechanism of PI3Kα activation at the atomic level suggests that PI3Kα undergoes the significant conformational change upon nSH2 release. The iSH2 in p85α subunit moves, which facilitates the membrane interactions and catalysis. The activation loop (a-loop) in the kinase domain becomes more flexible, exposing the basic residues for the substrate binding. The activation mechanism expedites our understanding of the PI3K autoinhibition, activation, and catalysis. By collecting and analyzing the available PI3K structures, we have identified the structural features that distinguish the inactive and active class IA PI3Ks. The a-loop is “collapsed” with kα11 in the regulatory arch “IN” in the inactive PI3Ks. Upon activation, the a-loop becomes “extended” and kα11 moves “OUT”. These features provide the functional explanations for both hotspot and weak oncogenic mutations and indicate their additive effects. The mechanism reveals a principle for PI3K allosteric drug discovery. The inhibitors that may modulate the iSH2 dynamics can allosterically prevent PI3K activation in the signaling pathways. Funded by Frederick National Laboratory for Cancer Research, National Institutes of Health, under contract HHSN261200800001E.
Citation Format: Mingzhen Zhang, Hyunbum Jang, Ruth Nussinov. Atomic-level insights into PI3K activation [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 2301.
Abstract 2308: The protein interaction landscape of breast cancer
Authors: Kim Minkyu , Park Jisoo , Bouhaddou Mehdi , Kim Kyumin , Rojc Ajda , Modak Maya , Soucheray Margaret , O'Leary Patrick , Wolf Denise , Mitchell Dominique C. , Zheng Fan , Gordan John D. , Coppé Jean-Philippe , Swaney Danielle L. , van' t Veer Laura , Ashworth Alan , Ideker Trey , Krogan Nevan J. 
Published: July 2021

Abstract
Cancers have been associated with a diverse array of genomic alterations, many of which are rare with unknown significance. To understand the cellular mechanisms impacted by such alterations in breast invasive carcinoma, we have applied affinity-purification mass spectrometry to delineate comprehensive biophysical interaction networks for 40 frequently altered breast cancer proteins across three human breast cell lines, providing a novel resource of context-specific and shared protein-protein interaction networks in breast cancer cells. These networks interconnect and enrich for common and rare cancer mutations, and are substantially rewired by mutations. Our analysis identifies novel PIK3CA-interacting proteins which repress AKT signaling, and UBE2N emerges as a BRCA1 interactor predictive of clinical response to PARP inhibition. We also show that Spinophilin interacts with and dephosphorylates BRCA1 to promote DNA double-strand break repair. Thus, cancer protein interaction landscapes provide a framework for recognizing oncogenic drivers and drug vulnerabilities.
Citation Format: Minkyu Kim, Jisoo Park, Mehdi Bouhaddou, Kyumin Kim, Ajda Rojc, Maya Modak, Margaret Soucheray, Patrick O'Leary, Denise Wolf, Dominique C. Mitchell, Fan Zheng, John D. Gordan, Jean-Philippe Coppé, Danielle L. Swaney, Laura van' t Veer, Alan Ashworth, Trey Ideker, Nevan J. Krogan. The protein interaction landscape of breast 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 2308.
Abstract 2313: The characteristics of ERBB2 exon 20 insertion in a large cohort of Chinese NSCLC patients
Authors: Wang Danhua , Yuan Hongling , Zhu Honglin 
Published: July 2021

Abstract
Background: ERBB2 mutations, especially exon 20 insertion (ERBB2ex20ins) had been extensively reported in NSCLC as classical driver factors. Previous researches indicate that NSCLC pts with ERBB2ex20ins are drug-resistant to afatinib, gefitinib and erlotinib. Up to now, approvals of targeted therapy of ERBB2ex20ins are still in process. Therefore, the objective of this study is to discover the features of ERBB2ex20ins in Chinese NSCLC patients, which could lead to more effective and personalized diagnosis and treatment.
Methods: 20656 Chinese NSCLC cases who had undergone molecular profiling at a Clinical Laboratory Improvement Amendments (CLIA) certified genomics laboratory in China between January 2017 to May 2020 were screened for our study. Some patients' clinical characteristics and treatment history were retrieved from the database for further evaluation.
Results: 11492 males and 9134 females were included in our cohort. ERBB2 gene mutation rate was 5.94% (1226/20656). Among them, 290 patients (1.4%), including 114 males and 176 females, harbored with ERBB2ex20ins, which include with p. Tyr772_Ala775dup (84.56%), p.Gly778_Pro780dup (10.74%), p.Ala775_Gly776insLeu(1.01%), p.Ala775_Gly776insVal(1.01%) and others(2.68%). Additionally, ERBB2ex20ins occurred more frequently in female patients (61% vs 39%, p&lt;0.005, fisher exact test), and had a relatively young age (p&lt;0.005, wilcoxon test) compared with others. Moreover co-variations of 290 pts are occurring with EGFR(4, 1.38%), KRAS(3, 1.03%), TP53(156, 53.79%), ERBB2 amp(21, 7.24%), MET amp (2, 0.69%), ALK amp (1, 0.34%) and RET fusion (1, 0.34%). Besides, a relatively lower TMB (p&lt;0.005, wilcoxon test) is shown on the patients with ERBB2ex20ins. We followed up 5 patients with ERBB2ex20ins mutations, who were all insensitive to traditional radiotherapy and chemotherapy and had poor prognosis with short PFS (1.5-12.4 months) and short OS (3.9-13.7 months).
Conclusion: Our results showed that the ERBB2ex20ins mutation tended to occur in younger, female patients. Additionally, ERBB2ex20ins mutated samples exhibited lower levels of TMB compared to wildtype tumors, which may not benefit from anti-PD1 treatment. We also found patients with ERBB2ex20ins mutation have been associated with short PFS and short OS. The detail mechanism of resistance and appropriate therapeutic strategies remain to be further study.
Citation Format: Danhua Wang, Hongling Yuan, Honglin Zhu. The characteristics of ERBB2 exon 20 insertion in a large cohort of Chinese NSCLC 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 2313.
Abstract 2316: Analysis of APC-1B promoter region responsible for familial adenomatous polyposis
Authors: Nakagawa Saya , Yamaguchi Kiyoshi , Saito Kimiko , Takane Kiyoko , Ikenoue Tsuneo , Furukawa Yoichi 
Published: July 2021

Abstract
APC (APC regulator of WNT signaling pathway) is not only a gene responsible for familial adenomatous polyposis (FAP), a hereditary disease characterized by hundreds or thousands adenomatous polyps in the colon, but also plays a crucial role in sporadic human cancers. Although most of FAP cases are caused by germline mutations in the coding region of APC, deletions or point mutations in the promoter regions are involved in a limited number of cases. Previously, we reported an FAP case with a large deletion of approximately 10 kb encompassing APC promoter 1B and exon1B of the APC gene. Since precise regulatory mechanism(s) of the transcription of APC remains to be clarified, we searched in this study the regulatory domain(s) in the deleted region. First, we performed cap analysis of gene expression (CAGE) analysis, and compared the amount of APC-1A and APC-1B transcripts in the peripheral blood cells of the patient with that of healthy volunteers. As a result, we found that the deletion decreased the amount of APC-1B to 39% - 45% in the patient compared to the healthy controls, and that it did not change the amount of APC-1A in the patient. In addition, an allele-specific expression analysis by deep cDNA sequencing revealed that the amount of APC transcripts from the mutated APC allele is reduced to 11.2% by the deletion in the patient, suggesting that the deletion resulted in the marked decrease of the transcription of the affected allele and that the remaining expression of deleted allele may be driven by other regulatory region(s) such as promoter 1A. Consistently, CAGE analysis demonstrated that APC-1B transcripts are more abundantly expressed than APC-1A transcripts in all tissues tested except for the brain, suggesting that promoter 1B plays a crucial role in the expression of APC transcription. Analysis of promoter 1B by reporter assay identified a critical region for the transcriptional activation between -117 bp and -49 bp of promoter 1B. These data will contribute to the better understanding of regulatory mechanisms of APC transcription and the evaluation of genetic variants located in promoter 1B.
Citation Format: Saya Nakagawa, Kiyoshi Yamaguchi, Kimiko Saito, Kiyoko Takane, Tsuneo Ikenoue, Yoichi Furukawa. Analysis of APC-1B promoter region responsible for familial adenomatous polyposis [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 2316.