bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4239: Development of multi-targeting immunomodulatory SeekR RNA therapeutics to overcome resistance to PD-1 blockade
Authors: O'ketch Marvin , Love Victoria A. , Kiefer Jeffrey A. , Lee David W. , Castaño Lizette A. , Mousses Spyro , Azorsa David O.
Published: June 2022

T-cell exhaustion describes the dysfunctional state of effector T cells in the tumor microenvironment that results from chronic and prolonged exposure to antigen. It also represents an important mechanism of clinical resistance to immune checkpoint blockade. Recently, the transcription factor NR4A1 has been shown to be upregulated in tumor-specific T cells and plays a role in driving exhaustion during chronic antigen stimulation of T cells. Pro-oncogenic activities of NR4A1 have long been observed in various solid tumors including colorectal and breast cancers, and co-expression of NR4A1 with known immune checkpoint markers such as PD-L1 have also been observed in various cancer cell lines. These findings have identified NR4A1 as an important target for overcoming resistance to cancer immunotherapy. We hypothesize that multi-targeting to simultaneously block PD-1 signaling and silence NR4A1 gene expression can reverse T-cell exhaustion and expand the clinical benefit of PD-1 blockade in immune therapy resistant solid tumors. Using our SeekR™ RNA therapeutics platform, we combined aptamer binders to PD-1 with siRNA against NR4A1, andNR4A1 and evaluated their ability to reverse T-cell exhaustion and re-activate T-cell based anticancer immunity in solid tumors. Specifically, we created SeekR™ therapeutic RNA molecules with dual flanking RNA aptamers binders to PD-1 and other checkpoint inhibitors, connected by a double stranded bridge that encodes for siRNA silencers that target multiple immunomodulatory genes, such as NR4A1. The novel anti-PD-1 RNA aptamer component serve to: A) direct and deliver the SeekR™ RNA oligo therapeutics to exhausted T-cells that express PD-1 receptors; and B) internalize the siRNA component into the T-cells. The siRNA components of the SeekR™ serve to silence NR4A1 which lead to reversal of the cytotoxic T-cell exhausted phenotype following chronic in-vitro stimulation. These results demonstrate that dual targeting of PD-1 and NR4A1 has the potential to reverse T-cell exhaustion and the potential to overcome cancer immunotherapy resistance in the clinic.

Citation Format: Marvin O'ketch, Victoria A. Love, Jeffrey A. Kiefer, David W. Lee, Lizette A. Castaño, Spyro Mousses, David O. Azorsa. Development of multi-targeting immunomodulatory SeekR RNA therapeutics to overcome resistance to PD-1 blockade [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 4239.
Abstract 424: Development of HJC0152-based proteolysis-targeting chimera degraders for breast cancer therapy
Authors: Xu Junhai , Xu Jimin , Ma Ruixia , Zhou Mingxiang , Fricke Doerte R. , Chen Haiying , Kim Hyejin , Liu Xi , Zhou Jia , Shen Qiang
Published: June 2022

Signal transducer and activator of transcription 3 (STAT3), a member of the STAT family, is constitutively activated in various human cancers, and has been recognized as an attractive therapeutic target in cancer. STAT3 protein dimerizes and translocates to the nucleus to eventually transactivate downstream target genes. Despite some progress has been made in the past two decades, to date there is still lack of FDA-approved STAT3 inhibitors available for clinical use. Recently, proteolysis-targeting chimera (PROTAC) technology has dramatically advanced the development of therapeutics by introducing targeted protein degradation. Previously, our team has developed HJC0152, a promising STAT3 inhibitor, via structure- and fragment-based drug design strategies and in silico molecular modeling and docking. HJC0152 has demonstrated an attractive cancer therapeutic and preventive efficacy by targeting the non- estrogen receptor (ER)-based STAT3 signaling pathway. To achieve better potency and inhibition of STAT3 signaling, we therefore developed a series of HJC0152-based PROTAC protein degraders. These potential anticancer agents have been initially evaluated and several showed favorable potency in inhibiting the proliferation in a panel of breast cancer cell lines. We found that compounds JMX1122, JMX1123, and JMX1124 significantly inhibited proliferation and colony formation of a highly aggressive triple-negative breast cancer (TNBC) cell line, MDA-MB-231, and the ER-positive breast cancer cell lines. Different from the lead compound HJC0152, which showed an early inhibition on the phosphorylation of STAT3 at the Tyr705 and Ser727 residues, the newly developed HJC0152-PROTACs showed a significantly late differential inhibition of STAT3 phosphorylation at the Tyr705 and Ser727 residues, and reduced the total STAT3 protein level at 72 hours of treatment. Our current results support the notion that HJC0152-based PROTAC degraders potently suppress breast cancer cell proliferation and induce apoptosis, via direct targeting of STAT3 and its protein degradation. These compounds are currently being investigated for breast cancer cell migration and invasion, and will be evaluated for the in vivo inhibition of tumor growth and metastasis in different mouse models. This project is supported by NIH/NCI Awards R01CA226001 and R01CA231150 to Q.S. and J.Z.

Citation Format: Junhai Xu, Jimin Xu, Ruixia Ma, Mingxiang Zhou, Doerte R. Fricke, Haiying Chen, Hyejin Kim, Xi Liu, Jia Zhou, Qiang Shen. Development of HJC0152-based proteolysis-targeting chimera degraders for breast cancer 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 424.
Abstract 436: Rapid flow cytometric whole blood assay for assessment of SARS-CoV-2-reactive T cell immunity
Authors: Fülle Lorenz , Gert Philipp David , Traska Verena , Chatzopoulou Sofia , Dose Christian , Richter Anne , Schuster Marc
Published: June 2022

As of November 2021, the viral pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19), has infected more than 250 million individuals worldwide and killed over 5 million people. In addition to known risk groups, also cancer patients are at increased risk for severe disease progression. Therefore, understanding the nature of the accompanying immune response is essential, especially the role of T cells for successful virus defense but also during immunopathology leading to severe disease outcomes. Furthermore, as neutralizing antibodies are reported to decay within months post infection or vaccination or are even absent due to cancer treatment, SARS-CoV-2-specific T cell persistence is discussed as an indicator of long-term protective immunity. Especially, in immunocompromised cancer patients, levels of SARS-CoV-2-specifc antibodies may not be efficiently detected. Therefore, we developed a rapid and easy flow cytometric assay for the analysis of SARS-CoV-2-reactive CD4+ and CD8+ T cells directly from whole blood.

Citation Format: Lorenz Fülle, Philipp David Gert, Verena Traska, Sofia Chatzopoulou, Christian Dose, Anne Richter, Marc Schuster. Rapid flow cytometric whole blood assay for assessment of SARS-CoV-2-reactive T cell immunity [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 436.
Abstract 5043: Predicting melanoma staging using targeted RNA sequencing data using machine learning
Authors: Ahmed Fahad Shabbir , Irfan Furqan Bin
Published: June 2022

Introduction: Cancer staging can take essential time and expenses away from patients, both of which should be patients’ management. In this current study, we aim to develop a machine learning-based early TNM staging model.

Methods: Normalized ribonucleic acid sequencing (RNA-seq) counts data for melanoma patients was extracted from The Cancer Genome Atlas (TCGA). Six different experiments were run to produce machine learning algorithms for nodal metastasis, distant metastasis, combine (nodal or distant) metastasis, and higher vs lower tumor stage (T4/T3 vs T2/T1/Tis). All datasets were split using 80/20 for training and test sets. Synthetic Minority Oversampling Technique (SMOTE) was used to address the imbalanced distribution of the outcome. The algorithm accuracies were determined by a percent of sensitivity, specificity, predictive values (positive and negative: PPV and NPV), and area under the receiver-operator curve (AUROC).

Results: The best model for nodal metastasis was a random forest classifier (RF) with targeted gene expression (TE) showed higher sensitivity (98), specificity (100), PPV (100), NPV (94), and AUROC (1.00, 95%CI 0.91-0.99). TE for distant metastasis with RF, showed sensitivity (0), specificity (100), PPV (0), NPV (100), and AUROC (1.00, 95%CI 0.91-1.00). While TE for combined metastasis (nodal or distant) staging algorithm; Nodal or Distant Metastasis (TE) RF, showed sensitivity (98), specificity (100), PPV (100), NPV (99), and AUROC (1.00, 95%CI 0.88-0.98). The tumor staging (DEG and predicting higher stage i.e stage 3 or higher) algorithm; Tumor Staging (TE) RF, showed sensitivity (100), specificity (100), PPV (100), NPV (100), and AUROC (1.00, 95%CI 0.69-0.89) (Table 1).

Conclusion: Our machine learning models can predict tumor staging including higher vs lower stage tumor, nodal metastasis, and combined metastasis with high accuracy. However, these results need to be further validated.

Table 1. Machine learning models Experiment Sensitivity Specificity PPV NPV AUROC 95%CI Test Set Accuracy N Nodal Metastasis (Pan-Expression) DNN 66.22 16.98 52.69 26.47 0.495 0.25-0.47 54.55 479 Nodal Metastasis (Targeted Expression) DNN 81.13 100.0 100.0 88.10 0.982 0.62-0.83 90.21 479 Nodal Metastasis (Targeted Expression) RF 97.89 100.00 100.00 94 1.00 0.91-0.99 96.74 458 Distant Metastasis (Targeted Expression) RF 0.00 100.00 0.00 100 1.00 0.91-1.00 94.44 450* Nodal or Distant Metastasis (Targeted Expression) RF 97.56 100.00 100.00 98.56 1.00 0.88-0.98 98.91 458 Tumor Staging (Targeted Expression) RF 100.00 100.00 100.00 100.00 1.00 0.69-0.89 100.00 395 *27 cases with distant metastasis

Citation Format: Fahad Shabbir Ahmed, Furqan Bin Irfan. Predicting melanoma staging using targeted RNA sequencing data using machine learning [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 5043.
Abstract 5067: Identify the combination efficacy and immune regulation of Abraxane combines with human IL-15 albumin binding domain fusion protein on pancreatic ductal adenocarcinoma animal model
Authors: Yueh Po-Fu , Hsu Fei-Ting , Lan Keng-Li
Published: June 2022

Pancreatic ductal adenocarcinoma (PDAC) is one of the hardest medical challenge in the world. Nab-paclitaxel is significantly more effective chemotherapy drugs than paclitaxel formulated as Cremophor EL. In this study, we reported the immune effect of Abraxane to combine with our new design recombinant human IL-15 fused with albumin binding domain (hIL-15-ABD) on subcutaneously Panc02 and orthotopically KPC PDAC animal models. In our results, the combination treatment greatly reduced the subcutaneous tumor growth in Panc02 and KPC bearing models, compared with vehicle group. Furthermore, the combinational therapy successfully buildup the anticancer immunity microenvironment (TME) through increasing the activation of effector cells, such as of NK cells (CD3-/CD49b+/NK1.1+) and CD8+ T (CD8+/IFN-γ+/IL-2+) cells. Moreover, combination therapy may also decrease the accumulation of immunosuppressvie cells such as MDSCs (CD11b+/Gr-1+) and Tregs (CD4+/CD25+/Foxp3+). The combination of Abraxane and hIL-15-ABD were also reduced the NF-κB-mediated immunosuppressive markers, including IDO, Foxp3 and VEGF. In conclusion, Abraxane combined with hIL-15-ABD enhanced immue effector cells involved in both innate and adaptive immunities, reduced the TME’s immunosuppressive cells, and displayed superior inhibitory effect on both subcutaneous and orthotopic syngeneic murine pancreatic ductal adenocarcinoma models than that of either monotherapy. These results suggest that combinational therapy of Abraxane and hIL-15-ABD could be a promising treatment stratedgy for PDAC.

Citation Format: Po-Fu Yueh, Fei-Ting Hsu, Keng-Li Lan. Identify the combination efficacy and immune regulation of Abraxane combines with human IL-15 albumin binding domain fusion protein on pancreatic ductal adenocarcinoma animal model [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 5067.
Abstract 5089: RNF43 mutation as a predictor of immunotherapeutic efficacy in colorectal cancer
Authors: Yu Changjun , Kang Weibiao , Yuan Yu , Zhang Junling , Huang Mengli , Chen Yanan , Xia Xihua , Bai Yuezong
Published: June 2022

Background: RNF43, a single transmembrane circular E3 ubiquitin ligase, has been identified as a tumor suppressor for a variety of cancers, including ovarian cancer, gastric cancer, pancreatic cancer, endometrial cancer and colorectal cancer. It is even considered to be carcinogenic driver mutations in cholangiocarcinoma, ovarian cancer, gastric cancer, endometrial cancer and colorectal cancer (CRC). However, the correlation between RNF43 mutation and CRC immunotherapy has not been reported yet.

Methods: We evaluated the role of RNF43 in CRC using publicly available data from The Cancer Genome Atlas (TCGA) and Memorial Sloan Kettering Cancer Center (MSKCC). An in-house Chinese CRC cohort (n=2290) was used for the analysis of immune-related markers. The relationship between clinical pathologic features and RNF43 were analyzed with using the two-sided chi-squared test or the Fisher exact test. Clinicopathologic characteristics associated with overall survival using Cox regression and the Kaplan-Meier method.

Results: In the MSKCC cohort, a total of 108 CRC patients receiving immunotherapy were enrolled, of which 38 (34.9%) were over 60-year-old and 61 (56.0%) were male. RNF43 mutation was significantly associated with high TMB and high MSI score (all p <0.05). Besides these, RNF43 mutation was discovered to be enriched in MSI instable. Kaplan-Meier survival analysis showed that patients with RNF43 mutation obtained better OS compared to RNF43 wild-type (not reach vs. 13 months, HR, 0.12; 95% CI 0.03-0.49; p=0.0034). In the TCGA cohort, CRC patients of stage I-IV were 16.6%, 38.5%, 28.2% and 14.2%, respectively. All of these patients received radiation therapy. No association was observed between RNF43 and OS (HR, 1.83; 95% CI 0.66-5.07; p=0.2479). In the in-house Chinese CRC cohorts, 210 (9.2%) patients carried RNF 43 mutations, of which 123 patients (58.6%) were male. RNF43 mutations were significantly associated with higher TMB levels (p<0.0001) and PD-L1 TPS> 1% (p=0.0110) in the in-house Chinese RCC cohorts.

Citation Format: Changjun Yu, Weibiao Kang, Yu Yuan, Junling Zhang, Mengli Huang, Yanan Chen, Xihua Xia, Yuezong Bai. RNF43 mutation as a predictor of immunotherapeutic efficacy in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5089.
Abstract 5123: Establishing circulating tumor cell-derived xenografts following a period of in vitro culture
Authors: Xiao Jerry , Schlegel Richard , Agarwal Seema
Published: June 2022

Cancer metastasis—the spread of cancer cells from a primary node to a distant site—is responsible for as much as 90% of all cancer-associated deaths due to treatment resistance and increased tumor burden. Once established, metastatic nodules oftentimes exhibit distinct molecular phenotypes from their original primary tumor, undermining gold-standard methods for determining treatments for patients, which typically rely on molecular characterization of the primary tumor. Unfortunately, a lack of robust, scalable, and appropriate models for studying differences in patient-derived primary and metastatic tumors has hindered progress in identifying metastasis-specific therapies. Previously, we reported the ability to establish in vitro cultures of circulating tumor cells (CTCs), a unique precursor population of cells that exhibits an ability to escape the primary tumor but not yet fully complete metastasis. We have since expanded the application of this GU-CTC platform to culture CTCs from the blood of patients diagnosed with a variety of metastatic cancers, resulting in the successful culture of 31 unique patient-derived CTC cell lines. Furthermore, following an initial short-term culture period, we also performed subcutaneous injection of mixed CTC cultures into immunocompromised mice, resulting in not only primary tumor formation, but also systemic metastatic nodule formation in as short as 3 months. These resulting CTC-derived xenografts (CDXs) have been demonstrated using metastatic pancreatic, colorectal, and lung adenocarcinoma-derived CTCs. Encouragingly, all CDX models also exhibited replicable metastatic patterns upon reimplantation, reinforcing the important role of CTCs as precursors to metastasis. Bulk RNA-sequencing of patient-matched whole blood, cultured CTCs, and CDX-derived primary tumor and metastatic tissues further identified enrichment of an epithelial-mesenchymal transition as well as several cancer-specific gene signatures consistent with an invasive phenotype. This extended GU-CTC platform therefore enables not only the robust and rapid expansion of CTCs through both in vitro and in vivo methods, but also offers an avenue for personalized drug screens in the effort to target cancer metastasis.

Citation Format: Jerry Xiao, Richard Schlegel, Seema Agarwal. Establishing circulating tumor cell-derived xenografts following a period of in vitro culture [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 5123.
Abstract 5149: Autoantibodies to PAX5, PTCH1 and GNA11 as serological biomarkers in the detection of hepatocellular carcinoma in Hispanic Americans
Authors: Qiu Cuipeng , Wang Xiao , Wang Bofei , Ma Yangcheng , Zhang Xiaojun , Zhang Jian-Ying
Published: June 2022

Liver cancer, especially hepatocellular carcinoma (HCC), is the third cause of cancer death worldwide. In the United States, it remains higher incidence rates and worse survival in the Hispanic population than the other populations. Studies have demonstrated that autoantibodies to tumor-associated antigens (TAAs) could be biomarkers with low-cost, efficient, and highly sensitive characteristics. In this study, enzyme-linked immunosorbent assay (ELISA) was conducted to measure three autoantibodies to PAX5, PTCH1, and GNA11 in sera from 25 Hispanic Americans with HCC, 28 patients with liver cirrhosis (LC), and 27 patients with chronic hepatitis (CH) as well as sera from 85 healthy individuals. At the 95% specificity for healthy controls, 56%, 48%, and 44% of HCC sera (or patients) showed elevated levels of autoantibodies to PAX5, PTCH1, and GNA11 respectively. Among the patients with LC, frequencies for autoantibodies to PAX5, PTCH1, and GNA11 were 44%, 36%, and 25% respectively. In patients with CH, the frequencies of autoantibodies to PAX5, PTCH1, and GNA11 were 22%, 22%, and 15%, which were significantly lower than those in HCC (p<0.01). The area under the curves (AUCs) of autoantibodies to PAX5, PTCH1, and GNA11 for identifying HCC from healthy controls were 0.912, 0.915, and 0.915, respectively. The sensitivity could be improved to 68% when three of the autoantibodies were combined with the AUC of 0.932. Therefore, autoantibodies to PAX5, PTCH1, and GNA11 showed significantly higher levels in Hispanic HCC than those in the CH or healthy controls. Also, these three autoantibodies could enhance the detection of HCC if they were combined as the parallel test. In conclusion, autoantibodies to PAX5, PTCH1, and GNA11 could be potential biomarkers for the detection of HCC in Hispanic Americans. Large size of samples is needed to further determine their potential value in clinical application.

Citation Format: Cuipeng Qiu, Xiao Wang, Bofei Wang, Yangcheng Ma, Xiaojun Zhang, Jian-Ying Zhang. Autoantibodies to PAX5, PTCH1 and GNA11 as serological biomarkers in the detection of hepatocellular carcinoma in Hispanic Americans [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 5149.
Abstract 5162: TuFEst: a sensitive and cost-effective pan-cancer detection approach with accurate tumor fraction estimation
Authors: Lin Ziao , Stewart Chip , Martin Elizabeth E. , Danysh Brian P. , Jacobs Raquel A. , Slowik Kara , Lawton Lee , Lightbody Elizabeth , Rhrissorrakrai Kahn , Utro Filippo , Levovitz Chaya , Cibulskis Carrie , Ghobrial Irene M. , Shipp Margaret , Corcoran Ryan B. , Juric Dejan , Parida Laxmi , Parsons Heather A. , Getz Gad
Published: June 2022

Detecting cancer at early stages or upon recurrence is critical to decreasing cancer morbidity and mortality. We developed TuFEst (Tumor Fraction Estimator), a cost-effective computational approach for pan-cancer detection and tumor burden estimation from ultra-low coverage whole genome sequencing (~0.1x, ULP-WGS) of minimally invasive cell-free DNA (cfDNA). Current state-of-the-art methods estimate tumor fraction (TF) from ULP-WGS depending exclusively on total copy number variation, which loses tumor signal in either copy number-quiet tumors or tumors with copy-neutral loss-of-heterozygosity. Additionally, it is difficult in many cases to distinguish clonal from sub-clonal copy-number events, therefore complicating the ability to estimate tumor fraction. On the other hand, fragments shed into the blood from cancer cells, i.e., circulating tumor DNA (ctDNA), of various cancer types show significantly different length distribution than that from normal cells in healthy donors. By synergistically integrating both (i) copy number variation and (ii) altered fragment length signals, TuFEst successfully achieved higher sensitivity and more accurate TF estimation than current methods in >200 cfDNA samples across different cancer types, even in low tumor-fraction cases (TF < 0.1%). Application of TuFEst to serial cfDNA samples from blood biopsies demonstrate its utility in accurately estimating TF in ~100 cfDNAs, suggesting that TuFEst can be used to detect early cancer recurrence during different treatments. In one breast cancer patient receiving CDK4/6 therapy, TuFEst indicated disease progression 262 days earlier than routine imaging. Altogether, our work suggests that accurate TF estimation from cfDNA can not only aid in detecting cancer at early stages but also provide evidence of disease progression during treatment. We believe that such a non-invasive, cost-effective, pan-cancer detection method will benefit both initial cancer screening and monitoring of resistance to therapy in clinical applications.

Citation Format: Ziao Lin, Chip Stewart, Elizabeth E. Martin, Brian P. Danysh, Raquel A. Jacobs, Kara Slowik, Lee Lawton, Elizabeth Lightbody, Kahn Rhrissorrakrai, Filippo Utro, Chaya Levovitz, Carrie Cibulskis, Irene M. Ghobrial, Margaret Shipp, Ryan B. Corcoran, Dejan Juric, Laxmi Parida, Heather A. Parsons, Gad Getz. TuFEst: a sensitive and cost-effective pan-cancer detection approach with accurate tumor fraction estimation [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 5162.
Abstract 518: Association of CC chemokines with breast cancer disparity
Authors: Mir Hina , Brock Briana A. , Samant Rajeev , Singh Shailesh
Published: June 2022

Despite recent advances, breast cancer (BrCa) still affects many women, and the impact is disproportional in African Americans (AA) and European Americans (EA). Addressing socioeconomic and behavioral status has not been enough to reduce disparity, suggesting racial difference in BrCa biology. Our laboratory was the first to show the involvement of CC chemokines in BrCa. In this study, using ONCOMINE, TCGA, bc-GenExMiner, KMplotter, and antibody microarray, we examined the association of CC chemokines in BrCa outcomes and disparity. We show over-expression of CCL5, CCL7, CCL11, CCL17, CCL20, CCL22, and CCL25 in BrCa tissues. High mRNA levels of CCL7, CCL8, CCL17, CCL20, and CCL25 predicted a decrease in overall survival (OS). CCL7 and CCL8 were associated with decreased relapse-free survival. Expression of CCL17 and CCL25 was associated with decreased OS in AA. In EA, CCL8 was associated with decreased OS. Expression of CCL5, CCL7, CLC8, CCL17, CCL20, and CCL25 was highest in TNBC. The expression of CCL11 and CCL22 was associated with HER2 expression. CCL7, CCL8, CCL17, CCL20, and CCL25 were elevated in AAs. Since CCL25 showed a significant association with decreased OS in AA, we examined the expression of CCR9, which is the only receptor for CCL25, and CCR9-mediated signaling in BrCa cell lines derived from AA and EA. Our data show higher expression of CCR9 in AA than EA and distinct molecular cascade in cells derived from AA than EA. Furthermore, higher CCR9 expressing cells showed poor response to Carboplatin upon CCR9 activation. In conclusion, our data suggest the association of distinct CC-chemokines in BrCa progression, OS, and disparate disease outcome in AA compared to EA patients implying CCR9 signaling to be a potential target for improving chemotherapeutic response.

Citation Format: Hina Mir, Briana A. Brock, Rajeev Samant, Shailesh Singh. Association of CC chemokines with breast cancer disparity [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 518.
Abstract 5183: LGR5 CAR-T cells: A novel potential treatment against high grade serous ovarian cancer
Authors: Wang Wanqi , Bandara Veronika , Lokman Noor , Napoli Silvana , Gundsambuu Batjargal , Oehler Martin , Barry Simon C. , Ricciardelli Carmela
Published: June 2022

Ovarian cancer is second leading cause of cancer-related mortality among gynecological cancers in the Western world. Although initial responses to 1st line treatment is high, over 75% of patients eventually relapse and acquire chemotherapy resistance, which is the primary cause of ovarian cancer treatment failure. New therapies to improve patient outcome are therefore urgently required. Chimeric antigen receptor T (CAR-T) cell therapy is an adoptive immunotherapy that is currently being used to treat some blood cancers. CAR-T cell therapies have so far been less effective against solid cancers, due in part to the absence of suitable tumor-associated antigen (TAA).This study has investigated whether Leucine-rich repeat-containing G protein-coupled receptor 5, LGR5) is a suitable target for CAR-T cell therapy for ovarian cancer. We found that LGR5 is highly expressed in HGSOC cancer lines (COV318, COV362 and OAW28) and increased in HGSOC tissues following relapse with chemotherapy resistant disease. We assessed the cytotoxic effects of LGR5-CAR-T cells on a range of ovarian cancer cell lines and primary serous ovarian cancer cells derived from patient ascites in vitro by MTT and 3D spheroid assays. We demonstrated that LGR5-CAR-T cells were cytotoxic and significantly inhibited survival of ovarian cancer cell lines (COV318, COV362) that express high levels of LGR5 but not SKOV3 or OV90 that express lower LGR5 levels in monolayer culture. In addition, LGR5-CAR-T cells were cytotoxic and significantly inhibited survival of primary serous ovarian cancer cells compared to un-transduced CD3+ T cells. LGR5 CAR-T cells also exhibited anti-tumor activity against ovarian cancer cell lines (COV318, COV362 & OAW28) and primary serous ovarian cancer cells in vitro using 3D-spheroid culture assays. This study demonstrates that LGR5-CAR-T cells have great potential to be developed as a novel immunotherapy for ovarian cancer.

Citation Format: Wanqi Wang, Veronika Bandara, Noor Lokman, Silvana Napoli, Batjargal Gundsambuu, Martin Oehler, Simon C. Barry, Carmela Ricciardelli. LGR5 CAR-T cells: A novel potential treatment against high grade serous ovarian 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 5183.
Abstract 5193: Case report: Long-term response to Camrelizumab in a pretreated metastatic mixed testicular germ cell tumor patient
Authors: Zhang Hui , Jiang Da , Meng Erhong , Song Wenya , Zhang Xue
Published: June 2022

Introduction: To date, very limited information is available about the efficacy of immune checkpoint inhibitor (ICI) therapy in mixed testicular germ cell tumor (TGCT) or variations of DNA damage repair (DDR) genes as predicators for it.

Case presentation: We reported a 19-year-old male patient with pretreated metastatic mixed TGCT harboring 5 variations in the BRCA2, MSH6 and PMS2 genes detected using plasma-based circulating tumor DNA (ctDNA). He obtained a durable clinical benefit from single-agent Camrelizumab (a PD-1 inhibitor), with the progression-free survival (PFS) of over 19 months and overall survival (OS) of over 6 years.

Conclusion: To the best of our knowledge, this case is the first study of long-term benefit from ICI in a pretreated mixed metastatic TGCT patient harboring 5 variations of DDR genes detected using ctDNA.

Table 1. Genomic profile of the patient. Gene Transcript Exon Nucleotide change Alteration Mutant allele frequency/copy number (%) Sequencing depth (×) Medication guides CDH1 NM_004360 exon 15 c.2382delC p.V794fs 0.98 1018 Sensitive to bicalutamide FBXW7 NM_018315 exon 11 c.1761delG p.G587fs 1.88 1009 Sensitive to mTOR inhibitor BCR NM_004327 exon 19 c.3311C>G p.A1104G 1.92 1148 BCR NM_004327 exon 19 c.3316G>A p.D1106N 9.25 1124 BCR NM_004327 exon 22 c.3611C>G p.A1204G 2.29 918 BCR NM_004327 exon 22 c.3615G>A p.T1205T 2.05 926 BCR NM_004327 exon 22 c.3684T>C p.P1228P 2.3 1000 BRAF NM_004333 exon 1 c.64G>A p.D22N 54.15 301 BRCA2 NM_000059 exon 15 c.7522G>A p.G2508S 49.21 1138 CDH1 NM_004360 exon 2 c.144A>G p.R48R 0.7 1001 CYP2B6 NM_000767 exon 5 c.785A>G p.K262R 35.63 595 FCGR3A NM_000569 exon 4 c.634T>G p.F212V 99.75 810 FGFR1 NM_015850 exon 15 c.2017C>T p.R673W 0.84 958 FGFR1 NM_015850 exon 15 c.1991G>T p.W664L 0.25 815 LRIG3 NM_153377 exon 16 c.2589G>A p.T863T 48.91 1143 MSH6 NM_000179 exon 10 c.4006G>T p.V1336F 8.31 349 PMS2 NM_000535 exon 9 c.932A>G p.H311R 0.27 1109 PMS2 NM_000535 exon 9 c.934A>G p.M312V 0.44 1131 PMS2 NM_000535 exon 15 c.2570G>C p.G857A 69.81 573 ROS1 NM_002944 exon 29 c.4783T>C p.L1595L 50.62 1051 SMO NM_005631 exon 3 c.582A>G p.E194E 48.98 1223 TSC2 NM_000548 exon 41 c.5209C>A p.P1737T 1.04 866

Citation Format: Hui Zhang, Da Jiang, Erhong Meng, Wenya Song, Xue Zhang. Case report: Long-term response to Camrelizumab in a pretreated metastatic mixed testicular germ cell tumor patient [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 5193.
Abstract 5223: Pediatric cancer incidence among racial/ethnic groups living in rural/urban areas of the United States
Authors: Shetty Priya B. , Lupo Philip J. , Scheurer Michael E.
Published: June 2022

Background: The impact of urban/rural residence on pediatric cancer incidence has not been well studied. Additionally, the impact of race/ethnicity on pediatric cancer incidence by urban/rural status has not been evaluated, which could inform our understanding of the roles of shared genetic and environmental causes of these malignancies.

Methods: Using SEER18, we calculated pediatric cancer incidences for individuals diagnosed 2000-2018 by residence (urban/rural). Next we calculated incidence rate ratios (IRR) to evaluate the role of race/ethnicity on incidence stratified by urban vs. rural status.

Results: See Table. Overall, most incidences were similar by residence, i.e., lower or equal in rural versus urban areas, except the rural group having significantly lower incidences of leukemias and germ cell tumors (GCTs). Additionally, the incidence of most pediatric cancers was consistently higher among NHW in both urban and rural areas. Yet, incidence of some cancers differed by urban/rural residence within race/ethnicity: retinoblastoma (NHB, Hispanic, and API); soft tissue sarcomas (NHB and AI/AN); hepatic tumors (AI/AN); and GCTs (API).

Conclusions: In general, Hispanic, NHB, and AI/AN populations have similar incidence of pediatric cancers in urban or rural areas. These groups have some shared bio-geographical ancestry, suggesting a possible effect of genetics on risk. Further, differences in incidence by urban/rural residence within race/ethnicity suggest a possible role of environment for some cancers. Interestingly, for GCTs, NHB had a lower IRR in urban and rural areas, but Hispanic populations had a significantly higher IRR. This finding, consistent with a recent study in adults, suggest that African ancestry may confer a protective effect on risk of GCTs. Further, the GCT effect sizes were more protective in the rural group for each race/ethnicity group, suggesting the possible role of environmental factors and interactions of environment with ancestry.

Pediatric cancer incidence by race/ethnicity group and urban/rural residence

Citation Format: Priya B. Shetty, Philip J. Lupo, Michael E. Scheurer. Pediatric cancer incidence among racial/ethnic groups living in rural/urban areas of the United States [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 5223.
Abstract 5233: Evolution of therapy resistance through acquired KRAS amplification in ROS1 fusion KRAS G12C double positive NSCLC
Authors: Priest Katherine , Le Anh , Aisner Dara , Gebregzabheir Amanuail , Nijmeh Hala , Mandell Melanie , Davies Kurtis , O'Donnell Emily , Doebele Robert C. , Bao Liming , Schenk Erin L.
Published: June 2022

Patients with metastatic non-small cell lung cancer (NSCLC) positive for a ROS proto-oncogene 1 (ROS1) fusion usually experience significant disease response and long-term control while on treatment with a ROS1 targeting tyrosine kinase inhibitor (TKI) but significant clinical heterogeneity exists. The presence of co-occurring genomic alterations likely contribute to this diversity in clinical outcomes. Here, we report on a patient with metastatic NSCLC with a ROS1 fusion and Kirsten rat sarcoma viral oncogene homolog (KRAS) G12C mutation detected at diagnosis who experienced a short duration of disease control on targeted therapy. The patient was initially treated with entrectinib, a ROS1 TKI, and, at progression, also received sotorasib, a small molecule inhibitor of KRAS G12C, in combination. Using specimens from therapeutically relevant time points including at diagnosis, at time of resistance to entrectinib, and at time of resistance to entrectinib and concurrent sotorasib, we performed broad next generation sequencing and FISH studies to detail the development of therapy resistance. Variant allele frequency of KRAS G12C was increased at each time point (3.2%, 74.2%, and 97%, respectively). A cell line was derived from the patient at time of progression on entrectinib therapy. In vitro testing of the cell line demonstrated increased TKI responsiveness when treated with entrectinib and sotorasib. Signaling pathway analysis of the cell line showed entrectinib inhibited phosphorylation of ROS1 and AKT, but not ERK. Sotorasib alone or in combination with entrectinib resulted in decreased phosphorylation of ERK. In vitro testing suggested efficacy with the combination of entrectinib and sotorasib. However, in clinical follow up the patient’s disease demonstrated progression on the combination, likely related to KRAS G12C amplification. This case supports the need for broad molecular profiling for potential therapeutic and prognostic information to personalize therapy in patients with metastatic NSCLC.

Citation Format: Katherine Priest, Anh Le, Dara Aisner, Amanuail Gebregzabheir, Hala Nijmeh, Melanie Mandell, Kurtis Davies, Emily O'Donnell, Robert C. Doebele, Liming Bao, Erin L. Schenk. Evolution of therapy resistance through acquired KRAS amplification in ROS1 fusion KRAS G12C double positive 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 5233.
Abstract 5242: Rationally designing a radionuclide drug conjugate for heterogeneous genomically stable gastric cancer
Authors: Yang Le , Xu Rui , Guo Peng , Yi Heqing , Cheng Xiangdong
Published: June 2022

Background: Gastric cancer (GC) is one of common malignant tumors with a 5-year survival rate less than 10% for patients in advanced stages. Genomically stable gastric cancer (GSGC), featuring the worst prognosis of four subtypes of GC based on its molecular characteristics, receives limited benefits from recently approved HER2-targeted antibody drug conjugates (ADCs) due to the lack and heterogeneity of tumoral HER2 expression. Currently, radionuclide drug conjugates (RDCs) have attracted great attention in targeted therapy, owing to its unique advantages of radiation-associated direct DNA damages and relatively long radiation distances. These unique advantages enable RDCs to efficiently and broadly ablate both cancer cells and cancer-associated stromal cells in heterogeneous tumor microenvironment without being internalized by target cells, featuring a novel and more efficient “bystander killing” effect than linker-cleavable ADCs. Here, a RDC was developed by rationally screening GSGC-targeting antibodies and radionuclides for targeted treatment of GSGCs. Meanwhile, the “bystander killing” effect of the RDC will be quantitatively determined and compared with conventional linker-cleavable ADCs.

Results: First, ICAM1 was identified as a more preferable molecular target relatively to HER2 in human GSGCs via flow cytometric analyses. Next, a RDC was constructed by covalently conjugating anti-ICAM1 antibody with radionuclide 131I via indogen chemistry. 131I, the RDC warhead emitting β-particles with an emission range of approximately 0.8 mm, is a clinically-used radionuclide with FDA approval for treating several tumors. Then, the half maximum inhibitory concentrations (IC50s) of constructed 131I conjugated ICAM1 antibody (131I-ICAM1) was evaluated in human GSGC cell lines. Its inherent bystander killing effect was validated by measuring the viability of ICAM1 negative cells co-incubated with ICAM1 positive cells in the treatment of 131I-ICAM1, in comparison with ADC of the same target. Ultimately, the anti-tumor efficacy of 131I-ICAM1 was verified in heterogeneous GSGC models. Simultaneously, the histopathological damages to normal organs by 131I-ICAM1 was minimized by optimizing its dose.

Conclusions: In this study, we constructed a rationally designed 131I-ICAM1 by conjugating ICAM-1 antibody and clinical available radionuclide 131I and investigated the intrinsic bystander killing effect of this RDC in ablating heterogeneous GSGCs. Our research explored the potential of 131I-ICAM1 as a promising targeted therapeutic candidate for treating heterogeneous GSGCs.

Citation Format: Le Yang, Rui Xu, Peng Guo, Heqing Yi, Xiangdong Cheng. Rationally designing a radionuclide drug conjugate for heterogeneous genomically stable gastric 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 5242.
Abstract 5316: Risk of cognitive impairment associated with androgen deprivation therapy in prostate cancer
Authors: Verma Shiv , Shankar Eswar , Singh Viabhav , Gupta Sanjay
Published: June 2022

Androgen deprivation therapy (ADT) is a commonly used clinical treatment for non-metastatic and metastatic hormone-sensitive prostate cancer. Long-term ADT treatment results in adverse side-effects in patients including depression, frailty, cognitive impairment and dementia. Studies have reported increased levels of pro-inflammatory cytokines and inflammatory markers in older cancer patients, however, the relationship between inflammatory biomarkers and the severity of cognition in prostate cancer patients under ADT has not been investigated. We sought to identify peripheral biomarkers that could provide links between the mental changes and major pathological mechanisms responsible for the development of cognition in these patients. For these studies, gene expression data (GSE69223) of 30 matched malignant and non-malignant prostate tissue samples from 15 prostate cancer patients receiving neoadjuvant antiandrogen therapy before prostatectomy, were compared in parallel with postmortem brain tissue samples of Parkinson's and Alzheimer patients as additional neurological diagnosis. IPA analysis was performed in the context of known biological response and regulatory networks. Fisher’s exact test for each network was converted to a score of −log10 (p-value). Further validation was performed in BT142-neural cells and M059K-glial cells by qRT-PCR with and without antiandrogen (enzalutamide) treatment. A total of 1952 DEGs were identified in postmortem brain tissue specimens, and 101 DEGs were identified in prostate cancer patients receiving ADT before surgery. IPA analysis revealed 33 commonly expressed genes with changes in cytokine-cytokine signaling network overlapped in both patient cohorts. Pathway analysis showed that IL17 signaling pathway, regulation of cytokine production and changes in T-cell subsets by IL-17A and IL-17F were overrepresented. Furthermore, lipopolysaccharide, tumor necrosis factor and toll-like receptors were identified as upstream transcriptional regulators of these signaling pathways. Gene expression of pro-inflammatory cytokines viz. LIFR, IL1RN, IL6, IL10 and LIF were increased in both neural and glial cells treated with enzalutamide, compared to non-enzalutamide treated cells. Our results suggest that changes in cytokine signaling under the influence of ADT in prostate cancer patients may linked with cognitive impairment presenting new areas for diagnostic and therapeutic development in combating brain deficits.

Citation Format: Shiv Verma, Eswar Shankar, Viabhav Singh, Sanjay Gupta. Risk of cognitive impairment associated with androgen deprivation therapy in prostate 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 5316.
Abstract 5336: Dissecting the molecular mechanism of trastuzumab resistance in stage IV HER2-positive gastric cancer patients
Authors: Xu Qi , Li Jingjing , Tang Haimeng , Bao Hua , Yan Junrong , Wu Xue , Shao Yang , Jin Jianying , Luo Cong , Weng Haimin , Ying Jieer
Published: June 2022

Introduction: The effect of trastuzumab in targeted therapy for HER2-positive gastric cancer (GC) is limited by the eventual development of resistance within patients. Although numerous studies have been published on this topic, both the mechanism of innate and acquired trastuzumab resistance are still not fully understood. In this study, we compare the mutational landscape of paired solid tumor samples before and after treatment in an effort to identify acquired events associated with resistance.

Methods: We performed whole-exome sequencing on 46 tumor and 23 whole blood samples from patients with stage IV gastric cancer were obtained from before treatment (n = 23) and at disease progression (PD) (n = 23). HER2 status was checked using immunohistochemistry and validated with florescence in situ hybridization (FISH). Correlation analysis was then conducted between the mutational profile and clinical data of patients.

Results: Comparisons between innate resistance samples and acquired resistance samples at baseline revealed three copy number variation events (CDK12 amplification, ERBB2 amplification, MECOM amplification) that occurs in significantly different proportions (p < 0.05). In addition, for baseline samples, MECOM was shown to be associated with poor progression-free survival (PFS) (Hazard Ratio (HR), 12; 95% CI, 1.6 - 85; p = 0.027). Commonly acquired events (i.e., lacking in before treatment samples and present at PD) within patients include TP53 mutation, MYC amplification, MCL1 amplification, CDKN2A/2B deletion, and CCNE1 amplification. Of these, patients with MCL1 gene amplification had worse survival (HR, 4.8; 95% CI, 1.2 - 20; p = 0.050) than patients with wild-type MCL1. In addition, the NOTCH pathway acquired mutations in 4 of 23 patients and was found to be correlated with a worse PFS (HR, 5.1; 95% CI, 1.4 - 19; p = 0.023), indicating that this pathway is possibly involved with trastuzumab resistance to some degree.

Conclusion: Overall, our results show that comparisons of samples obtained before treatment and at PD can give insight about innate and acquired resistance mechanisms to trastuzumab in stage IV, HER2-positive GC patients.

Citation Format: Qi Xu, Jingjing Li, Haimeng Tang, Hua Bao, Junrong Yan, Xue Wu, Yang Shao, Jianying Jin, Cong Luo, Haimin Weng, Jieer Ying. Dissecting the molecular mechanism of trastuzumab resistance in stage IV HER2-positive gastric cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5336.