bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1866: D02, a novel, non-blocking antibody targeting IL2RA, exhibits significant anti-tumor activity in IL2RA-humanized mice
Authors: Cao Shuzhen , Zhang Wenjiao , Lin Qingcong
Published: June 2023

Regulatory T cells, or Tregs, are a subset of CD4+ T cells that negatively regulate immune responses to promote their resolution and protect against autoimmunity. Infiltration of Tregs in the tumor microenvironment (TME), and a low ratio of effector T cells to Tregs, is frequently associated with tumor progression and poor prognosis. The alpha subunit of the IL-2 cytokine receptor (IL2RA), a component of the high-affinity IL-2 receptor along with the β and γ subunits (IL2Rβγ), is constitutively expressed on Tregs and transiently expressed on effector T cells. IL-2 is a key cytokine for effector T cell survival and cytolytic responses. We aimed to discover an IL2RA-targeting antibody capable of depleting Tregs but permitting IL-2 stimulation of effector T cells in the TME. We developed a fully human IgG1 antibody specific to IL2RA, D02, from our proprietary RenMab™ mice, which contain the entire human immunoglobulin variable domain. D02 binds both human and cynomolgus monkey IL2RA with high affinity without hindering IL2RA-IL-2 binding or inhibiting IL-2 signaling. To evaluate the safety and efficacy of D02 in vivo, we established a syngeneic mouse tumor model in IL2RA-humanized mice. We observed that D02 potently inhibited MC38 (colon adenocarcinoma) tumor growth at 10 mg/kg. Further studies will aim to characterize the effect of D02 on the ratio of effector T cells to Tregs in the TME. These data indicate that D02 is a novel, IL2RA-specific monoclonal antibody that uniquely exhibits significant anti-tumor activity in vivo while preserving IL-2 signaling to effector T cells.

Citation Format: Shuzhen Cao, Wenjiao Zhang, Qingcong Lin. D02, a novel, non-blocking antibody targeting IL2RA, exhibits significant anti-tumor activity in IL2RA-humanized mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1866.
Abstract 2011: Polycondensate-epitope vaccine augments anti-cancer T lymphocyte responses and induces long-term immune memory
Authors: Hu Xiaomeng , Tang Li
Published: June 2023

Background: Personalized cancer vaccines are promising treatments to induce or augment antitumor responses. Despite the observed benefits in early-phase clinical studies, the clinical efficacy of cancer vaccines remains modest. Here, we aim to develop a vaccine delivery strategy to enhance the antitumor efficacy of cancer vaccines.

Method: We developed polycondensate-epitope vaccines (PEVs) for co-delivering of major histocompatibility complex (MHC) I and II-restricted peptides (OVA257-264 and OVA323-339) to elicit antigen-specific CD4+ and CD8+ T cells for long-term antitumor immunity. PEVs were prepared by polymerizing amino-functionalized MHC I and MHC II-restricted peptides with a TLR1/2 agonist, Pam3CSK4, using a responsive linker. We characterized the physical properties (size, MW) and responsiveness of the prepared PEVs. The immunogenicity was evaluated in mice via flow cytometry and ELISpot assay. We finally assessed the antitumor efficacy in both prophylactic and therapeutic tumor models.

Results: The prepared PEVs have an average size of 20 nm to 50 nm, >95% incorporating efficiency, and a remarkably high loading capacity of antigens and adjuvants (57.18~ 61.3 wt/wt %). PEVs consisting of both MHC I and MHC II-restricted OVA peptides induced robust antigen-specific CD4+ and CD8+ T cell responses and long-term memory immune response against tumors. The vaccine-induced CD8+ and CD4+ T cells exhibited high proliferative capacity and polyfunctionality upon antigen restimulation ex vivo. In a prophylactic model, mice immunized by PEVs completely rejected the first and the second challenge of YUMM1.7-OVA tumor cells with 100% rejection rate. In a therapeutic model, treatment with PEVs loaded OVA257-264 and OVA323-339 peptides induced marked tumor regression in mice bearing established YUMM1.7-OVA tumors showing enhanced anti-tumor efficacy as compared to PEVs loaded with CD8 epitope alone.

Conclusion: Our results demonstrate that PEV is a promising vaccine delivery strategy for eliciting highly effective and durable anti-cancer immune responses.

Citation Format: Xiaomeng Hu, Li Tang. Polycondensate-epitope vaccine augments anti-cancer T lymphocyte responses and induces long-term immune memory [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2011.
Abstract 2012: A novel antibody-drug conjugate platform enabling high drug-to-antibody ratios and greater payload flexibility
Authors: Juen Ludovic , Collier Adam J. , Tolcher Anthony W. , Ouberai Myriam M.
Published: June 2023

Historically, increasing the drug-to-antibody ratio (DAR) in an antibody-drug conjugate (ADC) significantly raises aggregation propensity as a result of the hydrophobicity of the payload. Consequently, DARs are commonly limited to 4, forcing developers to incorporate very high potency payloads to achieve the required efficacy. This, combined with chemical instability and off-target uptake, often results in dose-limiting toxicities and narrow therapeutic indexes.

In this study, we used a novel and flexible multivalent linker technology to construct two ADCs targeting HER-2 with the monoclonal antibody, trastuzumab and interchain cysteine bioconjugation. One ADC incorporated monomethyl auristatin E (MMAE) as the drug payload at average DAR 16 whilst the second incorporated the camptothecin analog, SN38, as the drug payload also at average DAR 16. The ADCs were characterized by liquid chromatography-mass spectrometry (LC-MS), size-exclusion chromatography (SEC), hydrophobic interaction chromatography (HIC) and SDS-PAGE and were then tested for efficacy in a range of HER-2 positive cell lines in vitro, and tumor growth inhibition studies using NCI-N87 cells in a mouse xenograft.

Both ADCs remained > 95% monomeric (no aggregation) and demonstrated greater chemical stability in ex-vivo serum stability studies compared to comparator ADC constructs utilizing a clinically validated linker and the same payload release chemistry. In in vitro cell killing studies, the ADCs demonstrated target-specific cell killing with the SN38 average DAR 16 ADC achieving a disproportionate 30-fold increase in IC50 (by ADC concentration) compared to a DAR 8 comparator. Dose dependent tumor growth inhibition was observed in an HER-2 positive NCI-N87 mouse xenograft model with no change in mouse body weight, and good systemic exposure.

These data demonstrate our capability, using a novel multivalent linker technology, to construct ADCs with DARs considerably greater than DAR 8 which are chemically stable, shield payloads from hydrophobic interactions (no aggregation), demonstrate good in vivo exposure profiles and which are highly efficacious in vitro and in vivo.

Higher DARs will permit the incorporation of lower potency and targeted small molecule payloads into ADCs which will result in targeted cancer therapeutics with wider therapeutic indexes through the delivery of greater concentrations of payload to the tumor microenvironment and lower, payload-associated, dose-limiting toxicity.

Citation Format: Ludovic Juen, Adam J. Collier, Anthony W. Tolcher, Myriam M. Ouberai. A novel antibody-drug conjugate platform enabling high drug-to-antibody ratios and greater payload flexibility [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2012.
Abstract 202: Perfused patient-derived tumor organoid models with autologous immune cells for preclinical drug development
Authors: Millard Melissa , Dance Natalie , DesRochers Teresa M.
Published: June 2023

The paradigm shift towards inclusion of primary patient samples in preclinical drug development bottlenecks at the tissue procurement step due to an on-going lack of ’research-ready’ tumor samples. Organoid technology was developed as a solution to this hurdle. Their ability to expand in culture makes them a renewable resource similar to cell lines while recapitulating key properties of the primary tissue, including tumor heterogeneity, structural organization and drug responses. As preclinical drug development continues to adopt organoid-based screening technology and immune-oncology agents continue to be advanced, there is high demand for more complex organoid-based models capable of more accurately predicting individual patient drug responses. Due to their development process, the vast majority of organoids do not contain immune cells, resulting in the need to utilize allogeneic immune cells for any immune cell involved interrogation of the models. Maintaining the immune cells for incorporation with the organoid model can overcome this hindrance. Additionally, perfused organoid models offer a complex, ex vivo model with the ability to replicate the mechanical forces imparted by blood flow and interstitial pressure. Compared to 2D and static 3D cultures, perfused 3D culture models show enhanced proliferative and migratory capacities and can be sustained as long-term cultures. In our previous studies, DNA methylation signatures in patient-derived breast microtumors grown in Kiyatec’s 3DKUBE™ perfusion bioreactor matched the primary tissues of derivation. Given the need for more complex biology when assessing immune-oncology agents, the physiological relevance in maintaining gene expression ex vivo, and the capability to sustain long-term viability, the impact of autologous immune cells and perfusion on the success of organotypic culture was investigated across a panel of primary patient tumors. Immune cells were profiled for status and activity and imaging and viability assays were used to evaluate static and perfused 3D organoid models for differences in viability and morphology. PCR was used to examine how mechanically transduced forces alter gene expression and DNA methylation signatures. Drug responses were measured using our KIYA-Predict™ platform, comparing organoid drug responses to primary tissue drug responses. Results of this study provide insight on alternative methods of organotypic culture and evidence for the utilization of more complex tissue modeling in preclinical drug development.

Citation Format: Melissa Millard, Natalie Dance, Teresa M. DesRochers. Perfused patient-derived tumor organoid models with autologous immune cells for preclinical drug development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 202.
Abstract 2025: Phosphoproteomic profiling following MAP3K1 kinase inhibition identifies NPM1 as a novel substrate
Authors: Boghean Lidia , Singh Sarbjit , Mangalaparthi Kiran , Shukla Surendra K. , Kizhake Smitha , Kizhake Amritha , Wishka Donn , Mallareddy Jayapal Reddy , Morris Joel , Grothaus Paul , Singh Pankaj K. , Pandey Akhilesh , Natarajan Amarnath
Published: June 2023

In response to diverse cellular cues, MAP3K1, a mitogen-activated protein kinase, participates in various cancer signaling networks including the NFκB, JNK, ERK, and p38 pathways. Functioning as a signaling kinase in these oncogenic pathways, MAP3K1 contributes to tumor growth and metastasis, thus making it an attractive therapeutic target for cancer. Structure-guided design using MAP3K1 AlphaFold and Schrödinger GLIDE led to the development of 51-106, a selective MAP3K1 small molecule inhibitor. Profiling using the KiNativTM platform in a cellular matrix revealed 51-106 as a selective ATP-competitive MAP3K1 inhibitor. 51-106 blocked TNFα-induced MAP3K1-IKKβ-mediated NFκB activity. Phosphoproteomics analysis following MAP3K1 inhibition by 51-106 showed a dose dependent decrease in NPM1 T199 phosphorylation indicating NPM1 as a novel substrate of MAP3K1. NPM1 plays a critical role in DNA damage repair; consistently we observed a dose dependent S-phase arrest upon MAP3K1 inhibition by 51-106, suggesting a dysfunctional DNA damage response. Higher MAP3K1 transcript level in pancreatic cancer patients is associated with poorer (50% vs. 15%) 5-year survival. Treatment of pancreatic cancer cell lines with the MAP3K1 inhibitor 51-106 inhibited cell growth and migration. In combination studies, 51-106 synergistically inhibited growth with gemcitabine in LSL-KrasG12D/+, LSL-Trp53R172H/+, Pdx1-Cre (KPC) cell lines in vitro and in KPC syngeneic orthotopic implantation mouse model of pancreatic cancer in vivo. Our study is the first to identify NPM1 as a potential substrate of MAP3K1, and these results warrant the investigation of MAP3K1 inhibition as a therapeutic option in cancer.

Citation Format: Lidia Boghean, Sarbjit Singh, Kiran Mangalaparthi, Surendra K. Shukla, Smitha Kizhake, Amritha Kizhake, Donn Wishka, Jayapal Reddy Mallareddy, Joel Morris, Paul Grothaus, Pankaj K. Singh, Akhilesh Pandey, Amarnath Natarajan. Phosphoproteomic profiling following MAP3K1 kinase inhibition identifies NPM1 as a novel substrate [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2025.
Abstract 2105: Implications of metastatic stage at presentation in docetaxel naïve metastatic castrate resistant prostate cancer
Authors: Malone Shawn , Wallis Christopher , Morgan Scott , Kishan Amar , Le Amy Tu Trinh , Malone Julia , Sun Yilun , Spratt Daniel , Saad Fred , Roy Soumyajit
Published: June 2023

Background: Studies on metastatic hormone sensitive prostate cancer have shown that metachronous presentation has a better prognosis compared to synchronous disease. However, it remains unknown if such association is pertinent in metastatic castrate resistant prostate cancer (mCRPC). We performed a secondary analysis of ACIS study to determine if the response to dual androgen receptor axis-targeted therapy (ARAT) in in docetaxel naïve metastatic castrate resistant prostate cancer (mCRPC) varies based on M-stage at diagnosis and if prior local therapy plays an effect modifying role in the association of M-stage at presentation with survival.

Patients and Methods: In this phase III randomized controlled trial, mCRPC patients with no prior exposure to androgen biosynthesis signaling inhibitors were randomly assigned to either apalutamide or placebo combined with abiraterone and prednisone. Cox regression models were applied for radiographic progression-free survival (rPFS), overall survival (OS) with interaction terms between M-stage and treatment regimen. Multivariable Cox regression analyses were performed to determine the adjusted association of M-stage with rPFS and OS after considering the effect modification by prior local therapy (LT).

Results: Among 972 evaluable patients -432 had M0, 334 had M1 at diagnosis while M-stage was unknown in 206. We did not find any statistically significant heterogeneity of treatment effect on rPFS (interaction p=0.13; HR for placebo in M0 group: 1.42 [1.13-1.79]; M1/unknown group: 1.11 [0.90-1.37]), and OS (interaction p=0.87; HR for placebo in M0 group: 1.02 [0.81-1.29], and M1/unknown group: 1.00 [0.82-1.23]) based on M-stage at diagnosis. There was no significant association of M-stage with rPFS (HR for LT group: 1.08 [0.84-1.40], HR for no LT: 0.91 [0.67-1.24]) and OS (HR for LT: 1.04 [0.81-1.33] and no LT: 0.95 [0.70-1.29]) with no significant heterogeneity depending on receipt of LT (interaction p-value of 0.94 and 0.93, respectively).

Conclusion: We did not find a statistically significant heterogeneity in efficacy of dual ARAT based on synchronous versus metachronous presentation. M-stage was not found to be a predictor for rPFS and OS after considering effect modification by prior LT.

Citation Format: Shawn Malone, Christopher Wallis, Scott Morgan, Amar Kishan, Amy Tu Trinh Le, Julia Malone, Yilun Sun, Daniel Spratt, Fred Saad, Soumyajit Roy. Implications of metastatic stage at presentation in docetaxel naïve metastatic castrate resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2105.
Abstract 2207: The prognostic role of γδ T cells in colorectal cancer and the establishment of related nomogram for predicting overall survival of the patients
Authors: Ma Rulan , Xue Dangcheng , Zhang Yong , Zhu Kun , Yuan Dawei , Sun Tuanhe , Mo Caijing , Deng Xiaoyuan , Qin Fujun , Li Kang
Published: June 2023

Objective: The aim of the present study was to explore the prognostic role of γδ T cells in colorectal cancer, and establish a nomogram for predicting the overall survival of the patients.

Methods: Immunohistochemistry was performed to analyze the infiltration degree of γδ T cells in tumor and normal tissues of colorectal cancer. The relationship between γδ T cells infiltration in tumor tissues and the prognosis of patients with colorectal cancer were determined by survival analysis. Cox regression analysis was performed to detect the factors related to the prognosis of patients with colorectal cancer. R software was used to establish and verify a nomogram for predicting the prognosis of patients with colorectal cancer.

Results: The degree of γδ T cell infiltration in tumor tissues and normal tissues of CRC was not different (t=0.35, P=0.731). However, the infiltration of γδ T cell was related to the survival status of the patients (x2=4.88, P=0.027). Besides, the infiltrating degree of γδ T cells in tumor tissue was obviously related to the prognostic improvement of the patients with colorectal cancer (Log-rank P=0.016) and could reflect the benefit of adjuvant chemotherapy (Log-rank P=0.003). Cox regression analysis showed that tumor stage (HR:3.14, 95%CI:1.25-7.89, P=0.015), serum CEA level (HR:3.67, 95%CI:1.48-9.10, P=0.005) and γδ T cell infiltration (HR:0.38, 95%CI:0.14-0.99, P=0.049) were independent prognostic factors of overall survival in patients with colorectal cancer. A nomogram based on tumor stage, serum CEA level and γδ T cell infiltration was established and showed a good prediction ability for survival of patients with colorectal cancer.

Conclusion: γδ T cell infiltration degree in tumor tissue was an important factor to improve the outcome of patients with colorectal cancer, and could predict the benefit of adjuvant chemotherapy. The nomogram had a good ability for predicting overall survival of the patients with colorectal cancer.

Citation Format: Rulan Ma, Dangcheng Xue, Yong Zhang, Kun Zhu, Dawei Yuan, Tuanhe Sun, Caijing Mo, Xiaoyuan Deng, Fujun Qin, Kang Li. The prognostic role of γδ T cells in colorectal cancer and the establishment of related nomogram for predicting overall survival of the patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2207.
Abstract 2214: NEDD9 as a prognostic biomarker and its immune landscape in lung adenocarcinoma
Authors: Al-Kraimeen Leen M. , Al-Kraimeen Yaqeen M.
Published: June 2023

Introduction: Lung adenocarcinoma (LUAD) is the deadliest cancer worldwide. Many efforts are made to search for new biomarkers to screen for immunotherapy candidates and predict the response. Neural Precursor Cell Expressed, developmentally down-Regulated 9 (NEDD9), is predominantly expressed in many cancer types but has not been studied yet in lung adenocarcinoma. Herein, we analyzed the association of NEDD9 with immune inhibitory components to understand its immune landscape in lung adenocarcinoma.

Methods: Gene expression profiles were retrieved from The Cancer Genomic Atlas Lung Adenocarcinoma cohort (n = 567). We used TIMER 2.0 for immune inhibitory cell infiltrates analysis. Tumor mutational burden (TMB) was measured using the cBioPortal tool. The enrichment analysis of function and signaling pathways of DEGs in LUAD was done by gene ontology (GO) using Enrichr.

Results: NEDD9 is differentially expressed in LUAD tissues (P < 0.00). High NEDD9 expression had better overall survival prognostic value in LUAD patients (HR: 0.66, 95% CI: 0.49 - 0.89, P = 0.0221) compared to low expression. NEDD9 expression was positively correlated with the infiltration of cancer-associated fibroblasts and macrophage M2 cells (spearman’s ρ = 0.257, P < 0.001, ρ = 0.266, P < 0.001, respectively), but negatively with myeloid-derived suppressor cells (MDSC) (ρ = -0.344, P < 0.001). Moreover, survival analysis based on NEDD9 expression and MDSC levels revealed a better OS group identified by low MDSC levels and low NEDD9 expression after adjustment for age, stage, and purity. In terms of immune checkpoint genes’ expression, NEDD9 expression was directly correlated with CTLA-4, PD-1, PD-L1, VSIR, and LAG-3 (ρ > 0.2, Q value < 0.05). TMB was inversely associated with NEDD9 expression (ρ = -0.1, P < 0.001). GO analysis showed that genes co-expressed with NEDD9 were mainly in the phagocytic vesicles and participated in biological processes of cellular response to interferon-gamma by molecular function such as cysteine-type endopeptidase activity involved in apoptotic signaling pathways.

Conclusion: We found that NEDD9 expression is a useful biomarker of immunosuppression in LUAD patients and can predict the response to immunotherapy. Our results suggest that NEDD9 is a favorable prognostic biomarker, which could be explained by low MDSC. Further studies are needed for a better understanding of the NEDD9 value in LAUD.

Citation Format: Leen M. Al-Kraimeen, Yaqeen M. Al-Kraimeen. NEDD9 as a prognostic biomarker and its immune landscape in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2214.
Abstract 2282: Immune modulation of the T cell repertoire in mice following immunotherapy and chemotherapy combination treatments
Authors: Elhanati Yuval , George Mariam M. , Choi Hyejin , Maniyar Rachana , Hamadane Linda , Mohibullah Neeman , Greenbaum Benjamin D. , Merghoub Taha
Published: June 2023

Background: Immune checkpoint blockade therapeutics have revolutionized cancer therapy. However, most patients are either unresponsive or develop acquired resistance. Understanding patient-specific temporal T cell repertoires in the context of immune interventions will contribute to a better understanding of potential improvement strategies for better T cell anti-tumor immunity. Current methods to understand the T cell repertoire changes over time are limited due to the limited amount of material and prohibitive cost. In this study, we designed and performed longitudinal TCR sequencing in mice treated with multiple therapies.

Methods: C57BL/6 mice were used in each treatment group, with blood drawn overtime before, during and after treatment. Mice were treated with a combination of immunotherapeutic agents and OVA peptide immunization, 100µl blood was drawn at multiple pre-, on- and post-treatment time points followed subsequently by TCR sequencing. Cyclophosphamide (CTX) is known to cause lymphodepletion followed by homeostatic proliferation. Thus, we also treated B16-F10 tumor bearing mice with CTX, and performed TCR sequencing on blood draws pre-, on-, and post-treatment to track TCR clone diversity and clonality over time.

Results: We find that our method is sensitive enough to detect effects of immunotherapies on TCR diversity in small sample quantities. Using our method, we discovered that certain immunotherapeutic agents, most evidently CD40, have a significant but transient effect on the diversity of the T cell repertoire. We observed an initial increase in repertoire clonality, seven days post CD40 treatment followed by contraction. We show how we can identify antigen specific T cells and follow reacting T cell clones. In addition, we find that CTX treatment is associated with increased clonality in tumor bearing mice particularly in the week following treatment reflecting changes in the TCR repertoire.

Conclusion: We have developed a method by which we can follow the TCR repertoire in mice treated with immunotherapy or chemotherapy. This enabled us to isolate and study the effects of different immune modulatory drugs of the endogenous T cell repertoire overtime.

Citation Format: Yuval Elhanati, Mariam M. George, Hyejin Choi, Rachana Maniyar, Linda Hamadane, Neeman Mohibullah, Benjamin D. Greenbaum, Taha Merghoub. Immune modulation of the T cell repertoire in mice following immunotherapy and chemotherapy combination treatments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2282.
Abstract 2291: Dynamics of genomic instability of circulating tumor DNA in pancreatic cancer patients
Authors: Heo SooBeen , Chun Jung Won , Cho Eun-Hae , Lee Tae-Rim , Ki Chang-Seok , Kim Yun-Hee , Woo Sang Myung , Kong Sun-Young
Published: June 2023

Background: Genomic instability of circulating tumor DNA (ctDNA) has been evaluated as a prognostic biomarker in pancreatic ductal adenocarcinoma (PDAC). However, we did not investigated the association of dynamics between baseline and follow-up genomic instability level and patients outcome.

Methods: CtDNA I-score which low-depth whole-genome wide copy number alterations calculated by Z-score comparing the relative frequency for each bin with healthy control were investigated in total 87 PDAC patients (N=32 in resectable stage and N=55 in metastatic stage). Follow-up period for resectable and metastatic patients was different after one month, and 2 and 4 months, respectively. Then the association between I-score dynamics at follow-up and survivals (progression free survival (PFS) and overall survival (OS)) were analyzed.

Results: The mean I-score represented as 7.212 (6.887 ± 0.073 in 32 resectable patients and 7.536 ± 0.123 in 55 metastatic patients, p < 0.01) at baseline. In recetable patients, I-score decreased upto 6.710±0.03 (p=0.03) after 1 month and dynamics (decrease or increase) of I-score did not showed significant association with PFS and OS with hazard ratio (HR) of 3.6 (range 0.16-79.2 95% Cl) and 3.9 (range 0.3-50.7), respectively. I-score of metastatic patients at 2 and 4 moths were decresed to 7.180±0.062 (p= 0.01) and 7.029±0.056 (p < 0.01). The change of I-score represented association with PFS and OS as HR 2.8 (range 0.9-8.5) and 0.5 (range 0.11-2.20) at 2 months and 1.1 (range 0.2-5.5) and 3.3 (range 0.07-142.7) at 4 months, respectively.

Conclusion: Overall I-score decreased after treatment in both resectable and metastatic patients. To investigate impact for outcome of dynamics of genomic instability in ctDNA, we will continue to analyze follow-up data for long term results.

Citation Format: SooBeen Heo, Jung Won Chun, Eun-Hae Cho, Tae-Rim Lee, Chang-Seok Ki, Yun-Hee Kim, Sang Myung Woo, Sun-Young Kong. Dynamics of genomic instability of circulating tumor DNA in pancreatic cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2291.
Abstract 2293: Tumor-informed fixed and patient-specific panels for minimal residual disease (MRD) detection in early-stage NSCLC:a head-to-head comparison
Authors: Zhang Pengpeng , Gong Zetian , Yu Yue , Wang Xiaoxuan , Ye Lei , Wang Xiaoqiang , Tang Xuan , Zhang Chao , Deng Wanglong , Song Chao , Xu Qing , Li Yansong , Wang Wei
Published: June 2023

Introduction: Detection of minimal residual disease (MRD) by ctDNA based on tumor-informed or tumor-naive strategy could be used as an effective method to predict the relapse of NSCLC. As for tumor-informed strategy,both fixed panel and patient-specific panel are promising methods in MRD monitoring. Patient-specific panel can be used to monitor tissue specific somatic mutations individually. Besides, fixed panel can make up for the deficiency caused by organizational heterogeneity. In this study, we compared the monitoring effect of novel tumor-informed fixed and patient-specific panels.

Methods: 81 patients with stage I-III resected NSCLC were analyzed, including 45 patients (55.6%) with stage I, 15 (18.5%) with stage II and 21 (25.9%) with stage III. Tumor samples were obtained at surgery. Preoperative blood samples (baseline) were analyzed by both tumor-informed fixed and patient-specific panels based on hybrid capture. Tumor-informed fixed panel was performed by using ultra-deep (60000X) next-generation sequencing with 158 gene panel spanning 118 kb of human genome. Patient-specific panel was also performed by using ultra-deep (100000X) next-generation sequencing with customized 40 single nucleotide variants identified using whole-exome sequencing.

Results: Tumor-informed fixed panel monitored 212 mutations (median, 3; range, 0-7). Most of them (95.3%) were matched in the corresponding tumor tissues. For patient-specific panels, 91% of patients were customized design 40 mutations, affected by the detection of tissue somatic mutations. Based on fixed or patient-specific panel, ctDNA mutations were detected in 46.9% vs 49.4% (P=0.75) at baseline, respectively (Stage I: 35.6% vs 37.8%, P= 0.83; Stage II: 53.3% vs 60%, P=0.71; Stage III: 66.7% vs 66.7%).

Conclusions: Both tumor-informed fixed and patient-specific panel NGS assay can detect the presence of ctDNA in early-stage NSCLC. However, the detection rate of preoperative ctDNA mutations was slightly higher based on patient-specific panel.

Citation Format: Pengpeng Zhang, Zetian Gong, Yue Yu, Xiaoxuan Wang, Lei Ye, Xiaoqiang Wang, Xuan Tang, Chao Zhang, Wanglong Deng, Chao Song, Qing Xu, Yansong Li, Wei Wang. Tumor-informed fixed and patient-specific panels for minimal residual disease (MRD) detection in early-stage NSCLC:a head-to-head comparison [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2293.
Abstract 2294: The development of 3D deformable microfilter with a DNA aptamer for detecting circulating tumor cell
Authors: Iwatsuki Masaaki , Nakashima Yuta , Kitamura Yusuke , Yasuda Keiichiro , Baba Hideo
Published: June 2023

Introduction: The analysis of blood for circulating tumor cells (CTCs) has opened new avenues for cancer diagnostics, including early detection, risk assessment and staging. However, research about CTCs has been challenging due to the rarity of CTCs in bloodstream. We develop a three-dimensional deformable microfilter with a EpCAM aptamer for detecting CTCs and conduct a pilot study to evaluate the efficacy of our novel detection devise.

Methods: The cancer cell suspension with blood from healthy volunteers and human blood sample from cancer patients are passed through the microfilter and counted by fluorescence microscope. We also countered the number of cancer cells by CellSearch eq \o\ac(○,R)R. The peripheral blood sample from upper gastrointestinal cancer patients are also passed through the microfilter.

Results: Even in the presence of 100 times normal cell, cancer cells were captured on the substrate successfully from cell suspensions with several mixing ratios. We can capture cancer cells suspended with PB from healthy volunteer more effectively compared with CellSerach®. A total of 15 patients and 40 samples were enrolled (Stage I: II: III: IV: recurrence=1:1:3:4:6). The average number of CTCs was 3.1 cells/ml (0-6.3 cells). Among the 15 patients with GC, CTCs were detected by our system in 13 patients. Even in GC patients suspected with peritoneal dissemination without definitive mass by imaging, CTCs were successfully detected. For the patients who were measured multiple times with clinical time course, we found a close correlation between CTC number and CEA level or image assessment.

Conclusion: We successfully detected CTCs in the patients with upper gastrointestinal cancer patients. Although our pilot study indicates the potential of a novel devise to capture CTC effectively, a large scale of validation is needed to confirm the clinical utility.

Citation Format: Masaaki Iwatsuki, Yuta Nakashima, Yusuke Kitamura, Keiichiro Yasuda, Hideo Baba. The development of 3D deformable microfilter with a DNA aptamer for detecting circulating tumor cell [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2294.
Abstract 23: Development of a biallelicDicer1mutant mouse strain for studying the pathogenesis of DICER1 syndrome-associated cancer
Authors: Wang Yemin , Chen Shary , Senz Janine , Douglas Maxwell , Thornton Shelby , Moscovitz Yana , Gilks C. Blake , Huntsman David , Morin Gregg
Published: June 2023

DICER1 encodes a RNase III enzyme that post-transcriptionally controls gene expression through governing microRNA (miRNA) biogenesis. We and others have demonstrated that somatic mutations of DICER1 at its RNase IIIb domain metal binding sites, impairing its capability to produce mature miRNAs from the 5P strand of miRNA precursors, occur recurrently in a broad spectrum of cancers associated with the DICER1 syndrome that affects children and youths predominantly. The biallelic DICER1 mutations in these cancers challenge the two-hit hypothesis theory of traditional tumour suppressors, but it remains unproven whether these mutations are sufficient to drive tumorigenesis. The lack of biology relevant preclinical models has also hindered the understanding the pathogenesis. Here, we developed a genetically engineered mouse strain that expresses an inducible knockin Dicer1 missense mutation (Dicer1+/fl-D1693N), equivalent to the DICER1 RNase IIIb hotspot mutation D1709N in human cancers. This conditional strain behaves as a null allele due to an aberrant splicing event without Cre-mediated recombination. When crossed with a well-characterized conditional null Dicer1 strain (Dicer1fl/fl), the resulting compound heterozygous strain (Dicer1fl/fl-D1693N), acts as a hemizygous wildtype allele that is converted to a hemizygous missense mutation allele upon Cre-mediated recombination, reflecting the genetic status of DICER1 in DICER1 syndrome-associated cancer. When crossing with the anti-Mullerian hormone receptor 2 (Amhr2) driven cre strain (Amhr2+/cre), the biallelic Dicer1 mutation resulted in infertility in females by impairing the development of oviduct and endometrium and ultimately drove the development of multicystic tubal and intra-uterine tumours. Histologically, these murine tumors resemble human Müllerian adenosarcoma and other DICER1 syndrome-associated sarcomas. Molecular analysis of these murine tumours validated the miRNA biogenesis defects in 5P-miRNA production, uncovered the activation of the myc signaling and identified that loss of let-7 family miRNAs may drive the transcriptomic rewiring and malignant transformation. Thus, this first DICER1 syndrome-associated murine cancer model faithfully recapitulates the biology of human cancer and provides a unique tool for future investigation and therapeutic development.

Citation Format: Yemin Wang, Shary Chen, Janine Senz, Maxwell Douglas, Shelby Thornton, Yana Moscovitz, C. Blake Gilks, David Huntsman, Gregg Morin. Development of a biallelicDicer1mutant mouse strain for studying the pathogenesis of DICER1 syndrome-associated cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 23.
Abstract 2312: Single-cell low pass whole genome sequencing for copy-number profiling in circulating tumor cells from prostate, non-small cell lung and breast cancers
Authors: Wang Danyi , Locatelli Giuseppe , Gounaris Ioannis , Scheuenpflug Juergen , Feng Zheng
Published: June 2023

Background: Circulating tumor cells (CTCs) have been considered as an alternative to tissue biopsy for providing both germline-specific and tumor-derived genetic variants. Copy number variations (CNVs) play an important role in molding the genomes of cancers and have been shown the clinical value for prognostic signature and therapeutic target. The current study aimed to evaluate CNVs at single-cell resolution and explore the potential clinical utility of tracking this key mechanism of cancer progression.

Methods: Blood samples were collected in Streck tubes from 40 stage II-IV cancer patients (5 prostate cancer, 15 non-small lung cancer (NSCLC), 20 breast cancer (BC)) before treatment. CTCs was identified as cells containing an intact nucleus, without CD45 expression, and with cytokeratin expression. Genomic analysis of chromosomal CNVs by low pass whole genome sequencing (Lp-WGS) and number of large-scale transitions (LSTs) calculation was performed in the CTCs.

Results: A total of 9 CTCs from 4 prostate cancer, 70 CTCs from 7 NSCLC, 22 CTCs from 9 breast cancer patients, representing a range of sizes, shapes, and protein expression levels of cytokeratin were identified. A total of 84 individual CTCs were successfully sequenced from 20 patients (1-6 CTCs/patient). The selected highlights for gene CNVs include: 1) CXCR4 and ATM were detected as loss on single cell CTC (scCTC) level in BC; 2) MED12, an important regulator for maintaining accurate cytokinesis and survival, was detected as loss on scCTC level in NSCLC. A wide range of LST scores were observed among the 20 patient samples. Cell morphology analysis, phenotypic heterogeneity biomarker analysis and homologous recombination deficiency (HRD) biomarker analysis using a previously developed HRD classifier1 trained on genomic markers is still ongoing.

Conclusion: Our data demonstrated that Lp-WGS of DNA from CTCs can detect CNVs loss and assess disease heterogeneity at the single-cell level. Since genome-wide CNV profiles can be used to characterize genomic instability, it is anticipated that the integrative analysis of morphology and genomics in CTCs can potentially complement tissue and/or ctDNA analysis to determine HRD, enabling in-depth investigation of tumor heterogeneity and individualized clinical assessment.

Citation Format: Danyi Wang, Giuseppe Locatelli, Ioannis Gounaris, Juergen Scheuenpflug, Zheng Feng. Single-cell low pass whole genome sequencing for copy-number profiling in circulating tumor cells from prostate, non-small cell lung and breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2312.
Abstract 2657: Preclinical model to evaluate the safety and efficacy of PODO83: A monoclonal antibody against podocalyxin that targets tumor growth and metastasis
Authors: Brassard Julyanne , Hughes Michael R. , Dean Pamela , Hernaez Diana Canals , Schwab Janella , Lau Yasmine , Roskelley Calvin D. , McNagny Kelly M.
Published: June 2023

Podocalyxin (PODXL) is a highly glycosylated transmembrane sialomucin normally found on the apical free surface of mesothelial, vascular endothelial, luminal mammary epithelial cells, kidney podocytes and pluripotent and hematopoietic stem cells. We were the first to show that PODXL is upregulated on human cancers and an independent predictor of poor prognosis in breast and high-grade serous ovarian carcinoma (HGSOC). We also demonstrated that PODXL expression is crucial for primary tumor growth, local invasion, and experimental metastasis to distant organs. Subsequently, these results were extended to a wide range of other tumor types. We next developed a large series of high-affinity monoclonal antibodies (mAb) to human PODXL and evaluated these for therapeutic activity against the PODXL+ metastatic breast cancer cell line, MDA-MB-231, in xenografted NOD-SCID IL2Rγ-/- (NSG) mice. One of these, PODO83, potently attenuated primary tumor growth and formation of distal metastases. The PODO83 reactive epitope maps to the juxtamembrane stalk domain (non-glycosylated region) of the PODXL core protein. As a promising therapeutic it is imperative to perform toxicity studies and determine if PODO83 adversely affects the function of PODXL on normal tissues. Accordingly, we generated a transgenic mouse strain (C57Bl/6 congenic) replacing 4 of the 8 mouse PODXL-encoding exons with the orthologous human exons (including those encoding the PODO83 epitope). These mice were healthy and we confirmed by immunohistochemistry that they exhibit appropriate PODO83 immunoreactivity in all expected tissues (podocytes, endothelia, etc). Strikingly, administration of PODO83 in vivo at high doses (4 treatments of 5 mg/kg over 14 days) resulted in no overt signs of toxicity. To now fully assess the safety and efficacy profile of the PODO83 mAb in this preclinical humanized mouse model we have developed mouse metastatic tumor cell line expressing human PODXL and will evaluate the ability of PODO83 to inhibit tumor growth and metastasis while sparing normal tissues in vivo. The results from this study will help us advance PODO83 mAb as a safe and effective approach to treating the wide variety of cancer subtypes that express PODXL.

Citation Format: Julyanne Brassard, Michael R. Hughes, Pamela Dean, Diana Canals Hernaez, Janella Schwab, Yasmine Lau, Calvin D. Roskelley, Kelly M. McNagny. Preclinical model to evaluate the safety and efficacy of PODO83: A monoclonal antibody against podocalyxin that targets tumor growth and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2657.
Abstract 2670: Drug combinations against Barrett's stem cells show efficacy across advanced lesions in esophageal cancer
Authors: Xian Wa , Lin Jennifer , Oraei Mona , McKeon Frank , Wang Shan , Ajani Jaffer , Crum Christopher , Bachovchin William , Khorrami Melina , Su Amber , Khorrami Melika , Song Shumei , Siegelman Jeremy , Vincent Matt , Ho Khek Yu , Yamamoto Yusuke
Published: June 2023

We have applied a single cell cloning technology to patient-matched endoscopic biopsies of Barrett's esophagus and co-existing lesions of low-grade dysplasia (LGD), high-grade dysplasia (HGD), and esophageal adenocarcinoma (EAC). In vitro differentiation and xenografting of these clones yields epithelia with histology corresponding to the origin of these clones, and the EAC clones yield aggressive tumors in vivo. In addition, genomic analyses of these clones reveals their phylogenetic relationships based on common and accumulating mutations. In efforts to identify drugs that would target the Barrett's stem cells for preemptive therapeutics, we performed parallel screens of small molecule libraries against Barrett's stem cells and patient-matched normal esophageal stem cells. Synthetic lethal strategies ultimately yielded drug combinations that showed low nanomolar efficacy against Barrett's stem cells that spared normal esophageal stem cells even at micromolar concentrations. The synthesis of new compositions of matter corresponding to these leads has identified powerful analogs that not only selectively eliminate stem cells of Barrett's esophagus but show similar efficacy in vitro against stem cells of LGD, HGD, and EAC. In vitro, these drug combinations show broad efficacy against Barrett's and EAC, with nanomolar elimination of 20 of 23 Barrett's cases and 6 of 7 EAC cases. In tumors derived from xenografting EAC clones, these new drug combinations show robust activity marked by tumor shrinkage and a profound loss of tumor cell clonogenicity. We foresee the potential of these synthetic lethal drug combination both as topical delivery for premetastatic lesions in the distal esophagus and perhaps as systemic applications for advanced EAC cases.

Citation Format: Wa Xian, Jennifer Lin, Mona Oraei, Frank McKeon, Shan Wang, Jaffer Ajani, Christopher Crum, William Bachovchin, Melina Khorrami, Amber Su, Melika Khorrami, Shumei Song, Jeremy Siegelman, Matt Vincent, Khek Yu Ho, Yusuke Yamamoto. Drug combinations against Barrett's stem cells show efficacy across advanced lesions in esophageal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2670.
Abstract 2676: Gender-associated improvement in gemcitabine’s therapeutic outcome by Palmatine
Authors: Ybarra Meagan Marie , Yang Xiaoyu , Munoz Amanda , Villarreal Michelle , Michalek Joel , Wang Li-Ju , Chen Yidong , Yuji Ikeno , Halff Glenn , Weintraub Susan , Gosh Rita , Kumar Addanki P.
Published: June 2023

Despite a plethora of therapeutic strategies, improved survival is only modest for patients diagnosed with pancreatic ductal adenocarcinoma (PDAC). Additionally, between 2000 and 2018, pancreatic cancer incidence significantly increased with the greatest increase among women ages 15-35 years. We identified a protoberberine alkaloid, Palmatine (PMT), that was effective in slowing tumor growth and improving therapeutic outcome of gemcitabine (GEM) in pancreatic tumor bearing mice. Interestingly, the improved therapeutic outcome with the combination was observed in a sex-associated manner in mice. Intriguingly, PMT reduced proliferation of cells isolated from surgically resected tumor samples in 71% of female and 33% of male pancreatic cancer patients. We also observed that the correlation between PMT effects on cancer-related biological functions was associated with downregulation of STAT3 signaling. RNA-seq data from STAT3-KD pancreatic cancer cells revealed enrichment of genes associated with fatty acid metabolism. Of these, mRNA expression of ELOVL2 (Elongation of Very Long Chain Fatty Acids-Like 2) was most significantly increased suggesting a negative regulatory role for STAT3 in ELOVL2 expression. In silico analysis of the pancreatic cancer UalcanPan database shows that ELOVL2 is significantly reduced in human pancreatic tumors relative to normal pancreas and that high expression of ELOVL2 is associated with increased survival. The fatty acid elongase, ELOVL2, is involved in the production of docahexaenoic acid (DHA). Our experimental data show that PMT increased ELOVL2 expression. Taken together, these findings suggest the potential utility of PMT in therapeutic sensitization of GEM through deregulation of STAT3-mediated ELOVL2 signaling. These observations further suggest a sex-associated role for PMT in improving outcomes that may in part involve ELOVL2 function. Supported in part through VA Merit Award BX003876 and Owens Foundation pilot (APK).

Citation Format: Meagan Marie Ybarra, Xiaoyu Yang, Amanda Munoz, Michelle Villarreal, Joel Michalek, Li-Ju Wang, Yidong Chen, Ikeno Yuji, Glenn Halff, Susan Weintraub, Rita Gosh, Addanki P. Kumar. Gender-associated improvement in gemcitabine’s therapeutic outcome by Palmatine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2676.