bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5058: Recurrence risk prediction based on automatic histopathologic analysis of breast cancer using whole slide images
Authors: Lee Geongyu , Kim Chungyeul , Kwak Tae-Yeong , Kim Sun Woo , Chang Hyeyoon
Published: June 2022

The RS (Recurrence Score) is the results of a 21-gene test assessing the likelihood of breast cancer recurrence for hormone-positive, HER2-negative, and node-negative breast cancer patients. We conducted an experiment to find out whether there is a correlation between the RS value derived through genetic testing and specific morphological characteristics of breast cancer tissues with the expectation that these morphological features could predict RS values. Deep learning was utilized to assess the morphology of the hematoxylin-eosin (H&E) stained whole slide images (WSIs) of breast cancer. In this study, we used 125 breast cancer cases associated with H&E stained WSIs and RS scores which were divided into 3 risk groups based on the RS values: the low-risk group with 49 cases, the intermediate-risk group with 59 cases, and the high-risk group with 17 cases (low-risk for RS < 18, high-risk for RS > 31, and intermediate-risk for RS in between). On each WSI, an expert pathologist has annotated invasive breast tumor regions. We divided WSIs into 512x512 patches and trained a deep CNN model to classify the patches as benign (including DCIS), low-risk, intermediate-risk, or high-risk. In determining the risk group of each WSI, all patches from the WSI were classified by the model first, and then their majority class was assigned to the WSI. A nested cross validation was adopted to evaluate how well the model generalizes. The performance of the algorithm is shown in Table 1. According to the results, our model was able to distinguish between the low-risk group and the high-risk group to some extent. In particular, there was no case of misclassifying the low-risk group as high-risk. Since these high-risk patients require radiological examination, there is an advantage that the 21-gene test is not required. Although our model has yielded modest results, we believe that future studies through the integration of additional data with other clinical and pathological data will yield better results.

Result Table 21-gene test result (*ground truth) Low Intermediate High Prediction Low 42 14 0 Intermediate 5 44 8 High 2 1 9 Accuracy 0.932 0.776 0.912 Sensitivity 0.857 0.746 0.529 Specificity 0.816 0.803 0.972 PPV 0.851 0.772 0.750

Citation Format: Geongyu Lee, Chungyeul Kim, Tae-Yeong Kwak, Sun Woo Kim, Hyeyoon Chang. Recurrence risk prediction based on automatic histopathologic analysis of breast cancer using whole slide images [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 5058.
Abstract 5063: Predicting target driven toxicity for small molecule inhibitors to aid in drug development
Authors: Garcia-Quismondo Manuel , Parikh Mukti , Madhukar Neel , Gilvary Coryandar
Published: June 2022

Adverse events and toxicity concerns account for roughly 50% of clinical trial failures and the majority of drug withdrawals. A large part of these toxicity effects can be explained by a drug’s molecular target, known off targets or a drug’s lack of specificity. Therefore, the understanding of a target’s potential toxicity is crucial in the drug development process, potentially informing therapeutic hypotheses and/or chemical design. Here, we introduce a machine learning model to predict a gene’s likelihood to result in patient toxicity when inhibited, independent of chemical compound information. We used information on drug approvals, discontinuations and withdrawals from the FDA to define “toxic” and “safe” targets, to be used as training data. Our model leveraged preclinical, gene-specific features that can be easily collected such as tissue expression, pathway involvement, and loss of function data, and achieves significant predictive performance (ROC = 0.80). We validated our model’s ability to discriminate between successful and unsuccessful drug candidates based on their predicted target toxicity. Furthermore, our model was able to predict differences in toxicity between gene isoforms, which were in agreement with published in vivo evidence, further highlighting its ability to be applied to guide drug development and lead optimization. By applying our model, the prediction of target-specific toxicity can guide drug screenings, prioritize candidates and avoid costly and dangerous drug failures.

Citation Format: Manuel Garcia-Quismondo, Mukti Parikh, Neel Madhukar, Coryandar Gilvary. Predicting target driven toxicity for small molecule inhibitors to aid in drug development [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 5063.
Abstract 5079: Comparative proteome analysis for predicting the prognosis of trastuzumab-based therapy
Authors: Park Juin , Kwon Woo Sun , Kang Sun Kyoung , Kim Tae Soo , Hwang Jihyun , Cho Sang Woo , Kim Kyunggon , Chung Hyun Cheol , Rha Sun Young
Published: June 2022

Trastuzumab, a HER2-targeting antibody, has markedly altered the clinical course of the disease in HER2 + gastric cancer, which is 10-15% of metastatic GC. However, the majority of patients develop resistance within one year of treatment. Therefore, understanding the mechanisms of trastuzumab resistance is urgently needed to overcome trastuzumab resistance. This study explored the characteristics of trastuzumab resistant cell lines through comparative proteome analysis.

We previously reported establishment of four trastuzumab resistant cell lines from HER2 amplified GC cell lines by trastuzumab dose-escalation treatment; YCC-33TR, YCC-38TR, NCI-N87TR, and SNU-216TR. Formalin-fixed paraffin-embedded tissue samples were obtained 10 GC patients prior to trastuzumab therapy. The patients were first stratified into poor and good responders based on whether their tumors had or had not progressed. For analysis of differentially expressed proteins (DEPs), label-free quantitative proteomic profiling was performed using high-resolution LC-MS system. Gene ontology (GO) and KEGG pathway enrichment analyses were conducted using DAVID database.

Consistent with the previous results, we found that HER2 expression in TR cell lines remained as high as parental cell lines, also in proteomic profiling. As a result of proteomic analysis, total 5285 proteins were identified in 4 parental and 4 TR cell lines; 4854 common proteins, while 55 proteins unique to parental cell lines and 58 proteins unique to TR cell lines. Then, we did the hierarchical clustering with these DEPs to identify protein expression patterns. We observed that 129 and 62 proteins were upregulated in parental and TR cell lines, respectively (p<0.05). We identified C5orf51 and CENP-E, poor prognostic factors, were upregulated 200-fold in TR cell lines. Interestingly, we found that HLA-B, ITM2C, and PPP1R3D were highly expressed in TR cell lines and trastuzumab poor responders.

In conclusion, we performed comparative proteome analysis in parental and TR cell lines and investigated the corresponding expression change. It may gain further novel insights into the mechanisms of trastuzuamb resistance.

Citation Format: Juin Park, Woo Sun Kwon, Sun Kyoung Kang, Tae Soo Kim, Jihyun Hwang, Sang Woo Cho, Kyunggon Kim, Hyun Cheol Chung, Sun Young Rha. Comparative proteome analysis for predicting the prognosis of trastuzumab-based therapy [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 5079.
Abstract 5109: Development of cfDNA reference standards for methylation-sequencing tests
Authors: Li Bingsi , Su Jing , Xu Jiayue , Zhang Guangliang , Li Xiaoling , Zhou Ya , Wang Hao , Fang Shuai , Zhang Zhihong
Published: June 2022

Introduction: Recently, methylation sequencing has drawn significant attention as it has shown great promise for cancer detection and relapse surveillance. However, as with any low-input sequencing method, quality control is critical for implementation into the clinic, and it is difficult to obtain a sustainable source of patient samples for validation activities. To address these unmet needs, here we describe a design of fit-for-purpose cfDNA Methylation Reference Standards (MRS) to evaluate the performance of cfDNA-based methylation tests for oncology.

Methods: We analyzed the genome-wide methylation landscape of 6 human cancer cell lines, 4 normal human lymphocyte cell lines, and 24 healthy donor cfDNA samples via whole genome bisulfite sequencing (WGBS), the gold standard of methylation analysis. Using cancer cell line genomic DNA cleaved by double-stranded DNA endonuclease (Zymo), we developed a range of cfDNA MRS spanning clinically relevant tumor fractions. DNA fragmentation were validated using the Labchip system (Perkin Elmer) and tumor fractions were independently verified by droplet digital PCR (Biorad).

Results: The MRS series represent surrogates for lung, colorectal, liver, ovarian, pancreatic, and esophageal cancers. They display a size distribution comparable to cfDNA extracted from plasma, and represent a broad range of tumor fractions from 10% to 0.01%. In addition, the assembly accuracy was confirmed by digital droplet PCR (ddPCR) and ultra-deep mutation sequencing.

Conclusions: These results demonstrated that the analytical feature and clinical relevance of MRS provides a versatile tool for assay optimization, validation, and cross-platform comparison.

Citation Format: Bingsi Li, Jing Su, Jiayue Xu, Guangliang Zhang, Xiaoling Li, Ya Zhou, Hao Wang, Shuai Fang, Zhihong Zhang. Development of cfDNA reference standards for methylation-sequencing tests [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 5109.
Abstract 5156: Multiplexed EGFR mutation detection with C797S and T790M allelic context using six-color digital PCR
Authors: Yang Wei , Christensen Mari , Chan Jennifer K. , Tsai Julie , Patten Nancy , Tran Ha B. , Hillman Grant R. , Tai Yu Chuan , Bogard Patrick , Litterst Claudia M. , Brophy Victoria H. , Newton Nick , Nelson Christopher D. , Pattje Wouter J.
Published: June 2022

Non-small cell lung cancer (NSCLC) patients harboring activating mutations in epidermal growth factor receptor (EGFR) are benefited from Tyrosine Kinase Inhibitor (TKI) targeted therapy. However, more than 50% of patients receiving the first or second generations of TKI develop a resistance mutation, EGFR-T790M, and they will need to switch to the third-generation TKI (Osimertinib). Upon treatment, a second acquired mutation, EGFR-C797S, leads to the resistance to Osimertinib. If the C797S and T790M mutations are located in trans, a combination of the first and third-generation of TKI(s) may offer some benefit to the patient. The impact of the allelic context to the subsequent treatment is yet to be established and thus an assay identifying C797S and T790M allelic context may serve as a useful research tool. In recent years, digital PCR has emerged to be an ultra-sensitive method in non-invasive identification and monitoring of cancer mutations. However, compared to qPCR and NGS methods, current digital PCR assays are limited by the number of biomarkers that can be incorporated in a single assay and the maximum sample volume that can be screened in one test. In this study, we describe a multiplex digital PCR assay for quantitative detection of EGFR sensitizing and resistance mutations, and identification of C797S and T790M allelic context, using a 6-color digital PCR system that allows high sample volume utilization. The sensitivity and specificity of this multiplex dPCR assay were tested using a panel of contrived cell-free DNA samples. Individual mutations can be detected at as low as 0.2% fractional abundance level. Furthermore, we compared the performance of the multiplex with the 2-color droplet digital PCR Expert Design Assays on the Bio-Rad QX200 ddPCR system, using a commercial multiplex cfDNA reference standard set. The multiplexed EGFR mutation assay on the 6-color Digital LightCycler® System is a promising method for rapid and sensitive monitoring of EGFR mutations in cell-free DNA.

Citation Format: Wei Yang, Mari Christensen, Jennifer K. Chan, Julie Tsai, Nancy Patten, Ha B. Tran, Grant R. Hillman, Yu Chuan Tai, Patrick Bogard, Claudia M. Litterst, Victoria H. Brophy, Nick Newton, Christopher D. Nelson, Wouter J. Pattje. Multiplexed EGFR mutation detection with C797S and T790M allelic context using six-color digital PCR [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 5156.
Abstract 5170: Coding and non-coding gene meta-features predict outcome in pediatric rhabdomyosarcomas
Authors: Mitra Anirban P. , Mitra Sheetal A. , Buckley Jonathan D. , Skapek Stephen X. , Hawkins Douglas S. , Triche Timothy J.
Published: June 2022

INTRODUCTION: Pediatric rhabdomyosarcoma (RMS) has varying outcomes, particularly in intermediate-risk disease (IR-RMS) due to the limited ability of clinical staging to accurately risk-stratify a large proportion of patients. This study aimed to identify prognostic signatures in IR-RMS, the clinical subgroup with the most heterogeneous outcomes, which can potentially improve risk stratification compared with routine clinicopathologic metrics. Signature performance was validated on an independent set of RMS patients.

METHODS: Prospectively obtained primary tumor specimens from 80 IR-RMS patients on Children’s Oncology Group clinical trial protocols formed the training set. Tumors from 54 RMS patients across all clinical risk groups formed the validation set. Whole transcriptome profiling was performed using oligonucleotide microarrays employing nearly 1.4 million probe selection regions (PSRs) and used to derive weighted meta-features. Accuracies of protein-coding and non-coding meta-features to predict overall (OS) and event-free (EFS) survival were compared using areas under receiver operating characteristic curves. Associated biological processes were analyzed using curated pathway analysis tools.

RESULTS: PAX-FKHR status was able to predict OS (p=0.041) and EFS (p=0.008) in the validation set, but not in the training set. Histologic subtype followed a similar predictive pattern. Cox regression on over 17,000 coding genes on the training set identified a prognostic 30-coding gene meta-feature (gMF; OS p=0.001, EFS p=0.012). A similar analysis on non-coding transcripts identified a 39-PSR meta-feature (ncMF; OS, EFS p<0.001). Both gMF and ncMF were able to predict OS and EFS (p≤0.023) in the validation cohort. Based on OS, predictive accuracy of ncMF was higher than gMF (96% vs. 71%, p<0.001). Analysis of biological processes using gMF showed enrichment for functions associated with musculoskeletal development and signaling pathways. Similar analysis of non-coding meta-features revealed enrichment for cellular assembly, cell cycle, apoptosis, and cancer-associated functions.

CONCLUSIONS: A non-coding RNA meta-feature was able to better predict outcome in IR-RMS than a coding gene meta-feature, where most standard clinical prognosticators failed. The meta-features were independently validated in IR and non-IR RMS. This suggests that non-coding transcripts can regulate and determine RMS biology and aggressiveness, and be used as novel prognostic indicators.

Citation Format: Anirban P. Mitra, Sheetal A. Mitra, Jonathan D. Buckley, Stephen X. Skapek, Douglas S. Hawkins, Timothy J. Triche. Coding and non-coding gene meta-features predict outcome in pediatric rhabdomyosarcomas [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 5170.
Abstract 5214: Copper chelation overcomes the immunosuppressive tumor microenvironment in neuroblastoma
Authors: Rouaen Jourdin R. , Mercatelli Daniele , Saletta Federica , Poursani Ensieh M. , Murray Jayne E. , Tedla Nicodemus , Giorgi Federico M. , Vittorio Orazio
Published: June 2022

Immunotherapy remains a promising approach in the treatment of high-risk neuroblastoma, however efficacy is hampered by the immunosuppressive tumor microenvironment. We previously reported a link between intratumoral copper levels and Programmed Death-Ligand 1 (PD-L1) expression and therefore sought to elucidate the wider impact of copper chelation on immune evasion strategies (Voli et al 2020). Here we profile key elements of the neuroblastoma tumor microenvironment which work in concert to promote immunosuppression and tumor progression. Using the murine TH-MYCN model, animals were treated daily with the copper chelation agent tetraethylenepentamine (TEPA) for seven days before tumor resection and processing. Transcriptome analyses using single-cell RNA-sequencing revealed copper chelation positively skewed the functional status of tumor, immune and stromal compartments to enhance the anti-tumor immune response. This was supported by a tissue microarray screen using NanoString Digital Spatial Profiling which identified increased immune cell infiltration and regions of active tumor killing. High-resolution mass-spectrometry detected upregulation of major histocompatibility complex (MHC) proteins and exclusive antigenic signatures in peptide repertoires. A multiplex cytokine array indicated an improved anti-tumorigenic response underscored by T cell and Natural Killer cell activation. Importantly, combination of copper chelation and anti-GD2 antibody therapy led to tumor regression and significantly improved survival in vivo. Collectively, this study demonstrates the ability of copper chelation to successfully mitigate tumoral immune evasion strategies while providing remarkable insight into neuroblastoma biology. Findings provide crucial evidence in support of combining clinically approved copper chelators with immunotherapy to improve outcomes for neuroblastoma patients.

Citation Format: Jourdin R. Rouaen, Daniele Mercatelli, Federica Saletta, Ensieh M. Poursani, Jayne E. Murray, Nicodemus Tedla, Federico M. Giorgi, Orazio Vittorio. Copper chelation overcomes the immunosuppressive tumor microenvironment in neuroblastoma [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 5214.
Abstract 5225: The PI3K inhibitor Paxalisib combines with the novel HDAC1/3 inhibitor RG2833 to improve survival in mice bearing orthotopic xenografts of atypical teratoid/rhabdoid tumors
Authors: Findlay Tyler , Malebranche Kristen , Eberhart Charles , Raabe Eric , Rubens Jeffrey
Published: June 2022

Atypical teratoid/rhabdoid tumors (AT/RT) are the most common malignant brain tumors of infancy with a four-year event-free survival of 37%. Previously, we have identified high activation of both mTORC1 and mTORC2 through immunohistochemistry of 18 primary human AT/RT. The PI3K-Akt-mTOR signaling pathway drives tumorigenicity by promoting cancer cell growth and survival. Paxalisib is a highly brain-penetrant PI3K inhibitor acting upstream of mTORC1/2 to fully inhibit the activation of both complexes. Ongoing pediatric clinical trials have reported Paxalisib as safe and well-tolerated, with minimal dose limiting toxicities. Paxalisib treatment in mice bearing orthotopic xenografts of AT/RT slowed tumor growth and significantly extended survival from 40 to 54 days (bioluminescent imaging, log rank test p=0.0011). However, due to limited durability of single agent therapy, we conducted pilot studies to identify rational combination therapies to enhance Paxalisib survival benefits in AT/RT. RG2833 is a novel, highly brain penetrant, histone deacetylase 1/3 (HDAC1/3) inhibitor. Our preliminary data has shown that Paxalisib and RG2833 combine synergistically to decrease AT/RT cell growth (SynergyFinder ZIP score 11.1; CellTiter-Blue Cell Viability Assay, p<0.0001), and increase apoptosis (Western blot cPARP, MUSE Annexin V Assay, ANOVA p<0.001) compared to each agent alone and DMSO control. Additionally, our pilot combination study in orthotopic xenograft models of AT/RT demonstrated that combination therapy slows tumor growth more significantly than each agent alone and vehicle control (bioluminescent imaging). This novel combination therapy will readily translate into a new clinical trial aimed at improving survival in this deadly pediatric brain tumor.

Citation Format: Tyler Findlay, Kristen Malebranche, Charles Eberhart, Eric Raabe, Jeffrey Rubens. The PI3K inhibitor Paxalisib combines with the novel HDAC1/3 inhibitor RG2833 to improve survival in mice bearing orthotopic xenografts of atypical teratoid/rhabdoid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5225.
Abstract 5235: The role of transient single MET inhibition in MET-amplified and EGFR-mutant nonsmall cell lung cancer resistant to EGFR inhibitors
Authors: Lee Youngjoo , Choi Yu-Ra , Kang Eun Hye , Kim Sunshin , Park SeogYun , Han Ji-Youn
Published: June 2022

Background: In recent clinical trials for EGFR-mutant lung cancer acquiring MET amplification as resistance to EGFR inhibitor, two-drug combination treatment showed promising anti-tumor activity. However, these combination treatments also resulted in increased toxicity with intolerability. Thus, this study evaluated the possible role of single MET inhibition in these distinct tumors.

Methods: Using gefitinib-resistant MET-amplified lung cancer cells (HCC827GR), we tested the sensitivity to single MET inhibitor with various conditions. Supporting preclinical data with cell lines, the matched case reports and drug-sensitivity tests using patient-derived cells were presented. Furthermore, we chronically treated HCC827GR with single MET inhibitor to establish MET inhibitor-resistant cell line (HCC827GR_PR). And then, we explored putative resistance mechanisms of the HCC827GR_PR cells.

Results: The HCC827GR cells were partially inhibited by single MET inhibitor regardless of gefitinib-free duration or drug exposure time. Three patients with stage IV MET-amplified and EGFR-mutant lung cancer resistant to EGFR inhibitor showed initially definite response to single crizotinib treatment but their disease progressed within two or three months. The copy number of MET gene in plasma circulating tumor DNA was decreased significantly during crizotinib treatment and not increased even after progression to crizotinib. In their post-crizotinib tumor, MET amplification was disappeared in fluorescence in situ hybridization test. In vitro drug test using patient-derived cells revealed the sensitivity to EGFR inhibitor was recovered after single crizotinib treatment. We established HCC827GR_PR resistant to single MET inhibitor. In the major clones of HCC827GR_PR cells, EGFR signaling pathway was reactivated and gefitinib successfully suppressed their survival. Furthermore, increased MET gene copy number or bypass activation of FGFR1 were observed as resistance mechanism in the minor clones of HCC827GR_PR cells.

Conclusions: Single MET inhibitor could be effective but its efficacy could not durable in patients with MET-amplified and EGFR-mutant lung cancer resistant to EGFR inhibitors because these resistant cells might be subclones. A novel combination strategy is needed to get both long-term efficacy and less toxicity in these lung cancer patients.

Citation Format: Youngjoo Lee, Yu-Ra Choi, Eun Hye Kang, Sunshin Kim, SeogYun Park, Ji-Youn Han. The role of transient single MET inhibition in MET-amplified and EGFR-mutant nonsmall cell lung cancer resistant to EGFR 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 5235.
Abstract 5240: S-phase cyclinA associated protein in the ER(SCAPER)rs3812908 T>C promotes the nuclear translocation of CyclinA2 and enhances DNA damage repair in radioresistance of colorectal cancer
Authors: Yu Hai-na , Jiang Ting , Liu Shuang , Yuan Yan , Xi Shao-yan , Guo Zhi-wei , Yuan Yuan-hong , Li Yan , Xiao Wei-wei
Published: June 2022

Radiotherapy resistance is still an obstacle of improving the survival of patients with locally advanced colorectal cancer. In this study, whole-exome sequencing and targeted sequencing were preformed on colorectal cancer tumor tissue samples which were colloected from multiple centers, and the pathologic complete response predictive model PGS-LARC(Prediction Genotype Signature for Locally Advanced Rectal Cancer) was established. A candidate SNV-SCAPER rs3812908 T>C was screened using this model. To investigate the relationship between SCAPER rs3812908 T>C and radiosensitivity of colorectal cancer, targeted sequencing was performed and the results revealed that proportion of CC genotype was significantly higher in resistant sequencing cohort than in sensitive ones (30% vs. 22%). And Immunohistochemistry (IHC) results revealed that SCAPER protein expressed less in CC genotype colorectal cancer tissues than in TT genotype. Here, the cell proliferation results showed that SCAPER-KD cells and SCAPER rs3812908 CC cells were more radioresistant than SCAPER-NC and TT cells. Furthermore, the immunofluorescence assay showed SCAPER rs3812908 T>C promoted translocation of S phase associated protein-Cyclin A2 into nucleus and western blotting results showed that the phosphorylation of ERK and JNK(p-ERK and p-JNK) increased significantly in SCAPER CC cells, and the protein p-ATR, p-ATM, p-CDC25C and CDC25A related to homologous recombination repair were also increased in SCAPER-KD and SCAPER CC cells.Taken together, the SCAPER gene rs3812908 T>C plays an important role in radioresistance of colorectal cancer. The SNV of SCAPER rs3812908 T>C significantly promotes Cyclin A2 nuclear translocation, activates the MAPKs pathway, and increases homologous recombination repair, and finally leads to radioresistance.

Citation Format: Hai-na Yu, Ting Jiang, Shuang Liu, Yan Yuan, Shao-yan Xi, Zhi-wei Guo, Yuan-hong Yuan, Yan Li, Wei-wei Xiao. S-phase cyclinA associated protein in the ER(SCAPER)rs3812908 T>C promotes the nuclear translocation of CyclinA2 and enhances DNA damage repair in radioresistance of 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 5240.
Abstract 5251: GRIN2A mutations as potential positive predictor for response of immune checkpoint inhibitors in melanoma
Authors: Ye Ling , Fan Dandan , Chen Yaoxu , Huang Mengli
Published: June 2022

Background: Melanoma is a serious skin cancer. Immune checkpoint inhibitors (ICIs) including atezolizumab, pembrolizumab, nivolumab, ipilimumab have shown durable responses and have been approved by FDA. However, ICIs demonstrate antitumor effects only in a fraction of patients, and research exploring the association between gene mutation and clinical benefit is limited. Studies have shown that Tumor Mutation Burden (TMB) was significantly (p < 0.001) associated with mutations in genes like GRIN2A in Non-Small Cell Lung Cancer (NSCLC), which means that the mutation of GRIN2A gene may be related to the efficacy of immunotherapy in patients with NSCLC, but the association between GRIN2A mutation and TMB or survival in melanoma is unknown.

Methods: The association between GRIN2A mutation with TMB and survival data was analyzed in melanoma patients from the public immunotherapy-treated cohort called Miao2018.Pancancer.249.WES, which worked as training cohort while the validation cohort was retrieved from Melanoma.Allen2015.WES.110. Wilcoxon test was used for the comparison of TMB and Tumor Neoantigen Burden (TNB). Progress Free Survival (PFS):Overall survival (OS) analyses were conducted in the public cohort using Kaplan-Meier curves and log-rank tests. Statistical significance was set at p=0.05.

Results: In the training cohort, 33.8% (51/151) melanoma patients harbored GRIN2A mutation. GRIN2A mutation is associated with higher TMB (p<0.001) and higher TNB (p<0.001). Survival analysis demonstrated that GRIN2A mutation resulted in significantly longer PFS (5.6 vs 3.3months; HR, 0.58; p=0.027) and longer OS (22.5 vs 12.8 months; HR, 0.61; p=0.039) in melanoma patients treated with ICIs. While validation cohort1 showed that 22.7% (25/110) melanoma patients harbored GRIN2A mutation and GRIN2A mutation resulted in an increasing trend on TMB with strongly significant difference (p<0.001) and significantly longer OS (22.5 vs 8.3months; HR, 0.53; p=0.025).

Conclusions: This study shows that GRIN2A mutation is correlated with higher TMB and TNB in melanoma and serve as a predictive biomarker of ICI benefit in melanoma.

Citation Format: Ling Ye, Dandan Fan, Yaoxu Chen, Mengli Huang. GRIN2A mutations as potential positive predictor for response of immune checkpoint inhibitors in melanoma [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 5251.
Abstract 5280: TERT promoter mutations are an independent predictor of distant metastasis in Middle Eastern papillary thyroid microcarcinoma
Authors: Ahmed Saeeda Omer , Siraj Abdul K. , Parvathareddy Sandeep K. , Iqbal Kaleem , Qadri Zeeshan , Al-Rasheed Maha , Siraj Sarah , Thangavel Saravanan , Diaz Roxanne , Benito Allianah , Victoria Ingrid F. , AlKuraya Khawla S.
Published: June 2022

Background: Papillary thyroid microcarcinomas (PTMCs) have been attributed to the recent increased incidence of thyroid cancer. Although indolent, a subset of PTMC could potentially develop distant metastasis (DM). This study aimed to evaluate the clinico-pathological features and molecular characteristics of PTMC and identify the risk factors for DM in PTMC patients from Middle Eastern ethnicity.

Methods: We retrospectively analyzed 210 patients with histologically confirmed PTMC. Clinico-pathological associations for DM, BRAF mutation and TERT mutation were analyzed successfully in 184 patients. Multivariate analysis was performed using Cox proportional hazards model and logistic regression analysis.

Results: Among the PTMC patients included in this cohort, DM was noted in 6.0%(11/184), whereas tumor relapse occurred in 29/184 (15.8%). Of the 11 cases with DM, lung metastasis occurred in 8 cases, bone metastasis in 2 cases and brain metastasis in 1 case. Presence of extrathyroidal extension and older age were significantly associated with DM. Molecular analysis showed BRAF V600E mutations to be the most frequent, being detected in 45.7% (84/184). TERT promoter mutations were detected in 16 (8.7%) cases and were significantly associated with DM and shorter metastasis-free survival in multivariate analysis.

Conclusions: Our study indicates a surprisingly high frequency of TERT promoter mutation in Saudi patients with PTMC. Identifying TERT promoter mutations as an independent predictor of DM in patients with microcarcinoma could explain the inherent aggressive nature of PTMC from Middle Eastern ethnicity and magnify its role in patient risk stratification, which might help in improving therapeutic strategy for these patients.

Citation Format: Saeeda Omer Ahmed, Abdul K. Siraj, Sandeep K. Parvathareddy, Kaleem Iqbal, Zeeshan Qadri, Maha Al-Rasheed, Sarah Siraj, Saravanan Thangavel, Roxanne Diaz, Allianah Benito, Ingrid F. Victoria, Khawla S. AlKuraya. TERT promoter mutations are an independent predictor of distant metastasis in Middle Eastern papillary thyroid microcarcinoma [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 5280.
Abstract 5313: A BCL-XL PROTAC degrader DT2216 synergizes with KRASG12C inhibitors for effectively treating KRASG12C-mutated cancers
Authors: Khan Sajid , Wiegand Janet , Zhang Peiyi , Hu Wanyi , Thummuri Dinesh , Budamagunta Vivekananda , Hua Nan , Jin Lingtao , Allegra Carmen J. , Kopetz Edmund S. , Zajac-Kaye Maria , Kaye Frederic J. , Zheng Guangrong , Zhou Daohong
Published: June 2022

Purpose: Mutations in KRAS are the most common oncogenic drivers. Sotorasib (AMG510), a covalent inhibitor selectively targeting KRASG12C, was recently approved for the treatment of KRASG12C-mutated non-small cell lung cancer (NSCLC). However, the clinical efficacy of sotorasib and other KRASG12C inhibitors is limited by intrinsic resistance in colorectal cancer (CRC) and by the rapid emergence of acquired resistance in all treated solid tumors. Therefore, there is an urgent need to develop novel combination therapies to overcome sotorasib resistance and to maximize its efficacy.

Experimental Design: A panel of KRASG12C-mutated cell lines from NSCLC, CRC and pancreatic cancer (PC) were treated with sotorasib alone or in combination with BCL-XL proteolysis targeting chimera (PROTAC, such as DT2216) to assess effects on cell viability, colony formation and apoptosis. To identify mechanisms underlying sotorasib+DT2216 combination responses, we analyzed KRAS downstream signaling and expression of BCL-2 family proteins, and performed co-immunoprecipitation of BCL-XL to evaluate its interaction with pro-apoptotic BH3-only proteins. Finally, therapeutic efficacy of sotorasib alone and in combination with DT2216 was evaluated in vivo using different tumor xenograft models.

Results: We observed heterogeneous responses to sotorasib alone, whereas its combination with DT2216 strongly inhibited viability of KRASG12C cell lines that partially responded to sotorasib treatment. Mechanistically, co-treatment with DT2216 inhibited sotorasib-induced BCL-XL/BIM interaction leading to enhanced apoptosis. Furthermore, DT2216 co-treatment significantly improved the antitumor efficacy of sotorasib in vivo.

Conclusions: Our findings suggest that due to cytostatic activity, the efficacy of sotorasib is limited, and therefore its combination with a pro-apoptotic agent DT2216 shows synergistic responses and can potentially overcome resistance.

Citation Format: Sajid Khan, Janet Wiegand, Peiyi Zhang, Wanyi Hu, Dinesh Thummuri, Vivekananda Budamagunta, Nan Hua, Lingtao Jin, Carmen J. Allegra, Edmund S. Kopetz, Maria Zajac-Kaye, Frederic J. Kaye, Guangrong Zheng, Daohong Zhou. A BCL-XL PROTAC degrader DT2216 synergizes with KRASG12C inhibitors for effectively treating KRASG12C-mutated cancers [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 5313.
Abstract 5355: Mechanisms of resistance to CLN-081 (TAS6417) in non-small cell lung cancer with EGFR exon 20 insertions
Authors: Hayashida Takuma , Kagawa Yosuke , Mori Shunta , jie Liu , Kashima Yukie , Tanaka Kosuke , Udagawa Hibiki , Izumi Hiroki , Kobayashi Susumu
Published: June 2022

Background: EGFR exon 20 insertions are detected in approximately 10% of EGFR mutant non-small cell lung cancer (NSCLC). NSCLC with EGFR exon 20 insertions is resistance to conventional epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) such as osimertinib. CLN-081 is a novel EGFR-TKI which shows promising anti-tumor activity for EGFR exon 20 insertions in an ongoing clinical trial. However, previous studies of other EGFR-TKIs prompted us to hypothesize that tumors would acquire resistance to CLN-081 over time. Investigation of the mechanisms of resistance to CLN-081 will provide novel therapeutic strategies for patients with CLN-081-resistant NSCLC.

Methods: We first generated Ba/F3 cells stably expressing EGFR exon 20 insertions (Ba/F3-A767_S768insSVD and Ba/F3-Y764_V765insHH) and human patient-derived cells (PDCs), BID007 and BID019 harboring A763_Y764insFQEA and N771_P772insH, respectively. These cells were treated with increasing concentrations of CLN-081 to establish resistant cells. EGFR kinase domain was sequenced for parent Ba/F3 cell and resistant Ba/F3 clones to identify acquired EGFR mutations in resistant clones. PDC cells resistant to CLN-081 were subjected to whole exome sequencing (WES) and RNA sequencing (RNA-Seq) to examine whether resistant cells harbor acquired mutations and/or show changes in gene expression.

Results: Sequencing of the EGFR kinase domain revealed the Cys797Ser (C797S) mutations in all resistant clones of Ba/F3-A767_S768insSVD and Ba/F3-Y764_V765insHH cells. WES of resistant PDC cells showed that both BID007 and BID019 cells acquired mutations in KMT2C, a gene involved in histone methylation. In addition, acquired mutations were found in several kinases such as DGKZ, PAK2, and ROCK1. RNA-Seq showed that several genes involved in inflammatory responses and antigen presentation were upregulated in PDC cells resistant to CLN-081.

Conclusion: Our preclinical study identified several mechanisms of resistance to CLN-081 including acquired mutations and inflammatory responses. These results will provide new insights into development of a novel strategy to overcome or prevent resistance to CLN-081.

Citation Format: Takuma Hayashida, Yosuke Kagawa, Shunta Mori, Liu jie, Yukie Kashima, Kosuke Tanaka, Hibiki Udagawa, Hiroki Izumi, Susumu Kobayashi. Mechanisms of resistance to CLN-081 (TAS6417) in non-small cell lung cancer with EGFR exon 20 insertions [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 5355.
Abstract 5375: Precision run-on sequencing (PRO-seq) analysis of a treatment time course in ER+ breast cancer cell lines reveals the transcriptional changes underlying response to complete estrogen receptor antagonist (CERAN) OP-1250
Authors: Parisian Alison D. , Miller Caitlin , Ortega Fabian , Hodges-Gallagher Leslie , Barratt Susanna , Azofeifa Joey , Kushner Peter J. , Kulp David , Harmon Cyrus L.
Published: June 2022

OP-1250 is an orally-bioavailable complete estrogen receptor antagonist (CERAN) previously shown to shrink wild-type and Y537S mutant estrogen receptor-positive (ER+) tumors in multiple preclinical xenograft models. To better understand the effects of OP-1250 treatment on ER+ breast cancer cells, we used precision run-on sequencing (PRO-seq) to profile the direct transcriptional effects of OP-1250 in two commonly used breast cancer cell lines, MCF7 and CAMA-1. PRO-seq detects nascent RNA, and thus can detect changes at shorter timescales than traditional RNA-seq methods. We conducted PRO-seq 15 minutes, 1 hour, 6 hours and 24 hours after administration of OP-1250, estradiol, fulvestrant and tamoxifen to compare the effects of these compounds across the two cell lines. OP-1250 was administered in the absence of estradiol and after estradiol pretreatment to generate a detailed profile of the time course of its activity. We identified genes that display early transcriptional changes in response to the compounds tested, many of which have been previously identified as estrogen response genes. At later time points we observed transcriptional changes consistent with modulation of pathways involved in cell cycle progression. We show that OP-1250 treatment reverses the estradiol-induced transcriptional changes associated with estrogen receptor activation and chronicle the time course of these changes. Finally, we show greater similarity in the transcriptional changes induced by CERANs OP-1250 and fulvestrant compared to tamoxifen, as well as cell line-specific differences in estrogen response and response to anti-estrogen treatment. These data provide additional insights into the mechanisms of OP-1250 action on ER+ cell lines and patient tumors. OP-1250 is currently in a Phase I/II clinical trial for the treatment of ER+ breast cancer.

Citation Format: Alison D. Parisian, Caitlin Miller, Fabian Ortega, Leslie Hodges-Gallagher, Susanna Barratt, Joey Azofeifa, Peter J. Kushner, David Kulp, Cyrus L. Harmon. Precision run-on sequencing (PRO-seq) analysis of a treatment time course in ER+ breast cancer cell lines reveals the transcriptional changes underlying response to complete estrogen receptor antagonist (CERAN) OP-1250 [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 5375.
Abstract 5423: Translational PK/PD/efficacy modeling and efficacious human dose prediction for a first-in-class MUC1-EGFR (M1231) bispecific antibody drug conjugate
Authors: Zutshi Anup , Neuteboom Berend , Kumar Seema , Sloot Willem , Knuehl Christine , Dotterweich Julia , Ma Jianguo , Amendt Christiane , Venkatakrishnan Karthik , Park Taeshin , Pappas John , Kim Kyoung-Ae
Published: June 2022

Introduction: M1231 is a first-in-class bispecific antibody drug conjugate (ADC) targeting mucin-1 (MUC1) and epidermal growth factor receptor (EGFR), that is conjugated with a novel hemiasterlin-related microtubule inhibitor payload. Following dose, M1231 binds to EGFR and co-binds to tumor-associated hypoglycosylated MUC1, internalizes into the tumor cell and traffics to lysosomes where the payload is enzymatically released to affect cell viability.

Methods: A Multi-scale Systems Pharmacology model was developed to account for the ADC’s disposition and interactions with the underlying physiologic system, resulting in intracellular payload release in tumor cells to drive tumor growth inhibition (TGI). An in vitro model quantified ADC internalization and lysosomal trafficking in the MUC1 and EGFR-expressing cancer cell lines MDA-MB-468 and OVCAR-3. TGI was assessed in mice bearing MUC1-tumors from the squamous NSCLC patient-derived xenograft model, LUX003. Pharmacokinetics in cynomolgus monkeys was modeled using a Target Mediated Drug Disposition model and was allometrically scaled to humans.

Data Summary: All preclinical modeling results were integrated and scaled to simulate plasma M1231 concentrations to predict the human dose and corresponding exposures. Tumor stasis was estimated to begin at a dose of 2.4 mg/kg every 3 weeks (Q3W) with a maximum tumor regression achieved at a dose of 4.3 mg/kg Q3W.

Conclusions: The quantitative systems pharmacology model-based efficacious dose prediction range of 2.4 mg/kg to 4.3 mg/kg dosed Q3W informed the design of the ongoing M1231 first-in-human trial (NCT04695847).

Citation Format: Anup Zutshi, Berend Neuteboom, Seema Kumar, Willem Sloot, Christine Knuehl, Julia Dotterweich, Jianguo Ma, Christiane Amendt, Karthik Venkatakrishnan, Taeshin Park, John Pappas, Kyoung-Ae Kim. Translational PK/PD/efficacy modeling and efficacious human dose prediction for a first-in-class MUC1-EGFR (M1231) bispecific antibody drug conjugate [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 5423.
Abstract 5462: BPI-361175, a 4th generation EGFR-TKI for the treatment of non-small cell lung cancer (NSCLC)
Authors: Liu Lijia , Qiu Changyong , Liu Xiangyong , Lian Yuanyan , Chen Haibo , Song Xiaodong , Shen Qichao , Du Guolong , Guo Jing , Yan Dan , Lan Hong , Ding Lieming , Wang Jiabing
Published: June 2022

EGFR-activating mutations (Del19 or L858R) are major drivers in NSCLC (~40% in Asian and 10-20% in non-Asian). EGFR-TKIs have brought benefit to NSCLC patients with EGFR mutations, prolonging PFS and increasing quantity of life. Nevertheless, resistance inevitably emerges and leads to disease progression. Acquired EGFR C797S mutation is the most common event underlying resistance to the 3rd generation EGFR-TKIs, and there are no therapies. Herein, we report the discovery of BPI-361175, a 4th generation EGFR-TKI that overcomes EGFR resistant mutations. In vitro, BPI-361175 potently inhibited the activity of a variety of EGFR kinases, including triple (EGFRdel19 or L858R/T790M/C797S), double (EGFRdel19 or L858R/T790M, EGFRdel19 or L858R/C797S) and single (EGFRdel19 or L858R) mutations. Accordingly, BPI-361175 dose-dependently inhibited the phosphorylation of EGFR and the proliferation of cell lines harboring the above-mentioned mutations. Meanwhile, BPI-361175 were not active towards EGFRWT and IGF1R, therefore displayed good selectivity, both in kinase assays and in cell-based assays. In vivo, oral administration of BPI-361175 led to tumor suppression and regression in multiple EGFR mutant models, such as BaF3 EGFRDel19 or L858R/T790M/C797S, BaF3 EGFRDel19/C797S allograft models, and PC9 EGFRDel19/T790M/C797S, NCI-H1975 EGFRDel19/T790M/C797S, NCI-H1975 (EGFRL858R/T790M), HCC827 (EGFRDel19) CDX models, as well as a LDI-0025-200717 (EGFRDel19/T790M/C797S) PDX model. Remarkably, BPI-361175 significantly prolonged the life span of brain orthotropic BaF3 EGFRDel19/T790M/C797S allograft mice, demonstrating activity towards brain metastasis. In conclusion, BPI-361175 is a potent, selective, and orally bioavailable 4th generation EGFR-TKI which can potentially be used to treat NSCLC resistant mutations as well as at front line. Phase I clinical trial of BPI-361175 is enrolling patients in China, and US Phase I trial is expected to initiate in Q1 2022.

Citation Format: Lijia Liu, Changyong Qiu, Xiangyong Liu, Yuanyan Lian, Haibo Chen, Xiaodong Song, Qichao Shen, Guolong Du, Jing Guo, Dan Yan, Hong Lan, Lieming Ding, Jiabing Wang. BPI-361175, a 4th generation EGFR-TKI for the treatment of non-small cell lung cancer (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 5462.
Abstract 5490: Comparative activation of cellular ISR and cell death induction by p53 pathway restoring small molecules
Authors: Tian Xiaobing , El-Deiry Wafik S.
Published: June 2022

Restoration of the p53 pathway has been a long-term goal of the field of cancer research as an approach to treat tumors with mutated p53 and aggressive clinical behavior. In general, p53- pathway-restoring can be achieved by small molecules through p53-dependent or p53-independent ways. For short, hereafter p53-independent restoration of p53-pathway-signaling is also referred as ‘restoration of p53 pathway’. To perform a comparative activation of p53 target genes, novel compounds PG3 and PG3-Oc that activate a subset of p53-target genes in a p53-independent manner, and four known mutant p53-activating compounds were included (ZMC1, APR-246, CP-31398 and Ellipticine). Nutlin-3a was used as a negative control. PG3 and PG3-Oc induced significant upregulation of p21, PUMA (p53 upregulated modulator of apoptosis), and DR5 consistently in five tested cancer cell lines with various p53 status through ATF4 (Activating transcriptional factor 4) via the ISR in a p53-independent manner. However, mutant p53-targeting compounds induced the expression of the three p53 target genes and ATF4 in a highly variable and cell type-dependent manner. PG3 treatment activated ATF4 through the ISR via kinase HRI (Heme-regulated inhibitor). ATF4 mediated the upregulation of PUMA, p21 and NAG-1 (Nonsteroidal anti-inflammatory drug-activated gene 1). We identified PUMA-mediated cell apoptosis through activation of caspase-8 in HT29 cells and possibly caspase-10 in SW480 cells. In summary, we provide a new mechanism that PG3 induced cell death via an HRI/ATF4/PUMA axis that may be helpful in understanding drug efficacy.

Citation Format: Xiaobing Tian, Wafik S. El-Deiry. Comparative activation of cellular ISR and cell death induction by p53 pathway restoring small molecules [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 5490.