bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3712: The C-terminal HSP90 inhibitor, a novel deguelin derivative, exerts anti-metastatic effects in triple-negative breast cancer by targeting cancer stem-like properties
Authors: Park Minsu , Cho Tae-Min , Park Soeun , Park Jung Min , Seo Juyeon , Ko Dongmi , Kim Seongjae , Seuk So Ra , Kang Yong Gu , Nam Kee Dal , Kim Yoon-Jae , Kim Ji Young , Seo Jae Hong
Published: June 2022

Purpose: Triple-negative breast cancer (TNBC) still relies on non-selective cytotoxic anticancer agents due to the absence of established molecular targets for the phenotype. The heat shock protein 90 (HSP90) is a promising therapeutic target because it affects the overall progression of cancer, including cell proliferation, angiogenesis and metastasis. A variety of N-terminal HSP90 inhibitors have been tried several times in clinical trials, but none have been approved for clinical use to date due to issues including heat shock response (HSR) induction, undesirable effects, and clinical toxicity. In this study, we sought to investigate whether a novel C-terminal HSP90 inhibitor SL-145 could resolve metastasis in TNBC through inhibition of cancer stem-like properties.

Experimental Design: The effects of SL-145 on TNBC cell lines in vitro were evaluated in terms of cell proliferation, apoptosis, caspase-3 activity, breast cancer stem cell (BCSC)-like properties and heat shock response. An orthotopic allograft model with 4T1 mammospheres was used to examine the effect of SL-145 on tumor growth and metastasis in vivo.

Results: SL-145 induces apoptosis without triggering the HSR and simultaneously inhibits several oncogenic signaling pathways including AKT, MEK/ERK and JAK2/STAT3. SL-145 effectively targets BCSC-like properties with significant reductions in CD44, CD49f and ALDH1 expression as well as impairment of mammosphere-forming ability. To confirm the physiological relevance of our in vitro observations, we investigated the effects of SL-145 on tumor growth, angiogenesis and metastasis in mammosphere-derived allograft tumors with self-renewal capacity. SL-145 administration reduced tumor burden and angiogenesis, which were enriched in BCSCs, and it resulted in significant reductions in lung and liver metastases. In addition, no toxic effects of inhibitors on markers of liver or renal function were observed.

Conclusion: Our findings suggest that SL-145 may represent an effective therapeutic approach for targeting cancer stem cells and simultaneous inhibition of the HSP90 client oncoprotein to treat TNBC with a heterogeneous and aggressive nature.

Citation Format: Minsu Park, Tae-Min Cho, Soeun Park, Jung Min Park, Juyeon Seo, Dongmi Ko, Seongjae Kim, So Ra Seuk, Yong Gu Kang, Kee Dal Nam, Yoon-Jae Kim, Ji Young Kim, Jae Hong Seo. The C-terminal HSP90 inhibitor, a novel deguelin derivative, exerts anti-metastatic effects in triple-negative breast cancer by targeting cancer stem-like properties [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 3712.
Abstract 3804: Interferon gamma induces NOS2 and COX2 expression in estrogen receptor negative breast cancer leading to immunosuppressive tumor microenvironment
Authors: Cheng Yuk Sing Robert , Ridnour Lisa , Somasundaram Veena , Bhattacharyya Dana , McGinity Christopher , McVicar Daniel , Anderson Stephen , Lockett Stephen , Wink David
Published: June 2022

Breast cancer is the second leading cause of cancer death among U.S. women although the mortality is on a steadily decreasing trend since early 90s. We previously demonstrated a strong correlation between elevated NOS2 and COX2 expressions suggesting these genes can serve as markers of poor prognosis in estrogen receptor negative (ER-) breast cancer. In other words, NOS2 and COX2 is generally associated with the immune response. Induction of NOS2 and COX2 has also been shown to orchestrate multiple pro-oncogenic pathways that may contribute to the immunosuppressive nature of cancer cells. To better understand the interactions between cytokines and breast cancer cells and develop effective therapeutics for breast cancer, we examined the effects of selected cytokines on MDA-MB-231, a human (ER-) breast adenocarcinoma cell line. We found that in combination with cytokines, such as IFNG plus TNF, IL1B, or IL17, significantly induced NOS2 and COX2. IFNG plus TNF or IL1B most strongly induced NOS2 and COX2 where IFNG or IL17 to a lesser extent. It indicates that expressions of NOS2 and COX2 required IFNG but at a low dose in presence of other cytokines. Single-cell RNAseq analysis shows that cells treated with IFNG plus TNF or IL1B clustered with those expressed NOS2 and COX2 as revealed in tSNE plots. Expression of other factors such as IL8 and IL6 (suggested markers for prognosis of breast cancer) or PDL1 and IDO1 (suggested cancer therapeutic targets) also co-clustered with NOS2 and COX2 expressions. In addition, we found increased IL1A and IL1B expressions provide fortification to NOS2 and COX2 expressions. Taken together, our current findings indicate the interactions between breast cancer cells and cytokines. We believe further spatial transcriptomic and proteomic studies may be beneficial for clarifying the complex networks of the immunosuppressive tumor microenvironment.

Citation Format: Yuk Sing Robert Cheng, Lisa Ridnour, Veena Somasundaram, Dana Bhattacharyya, Christopher McGinity, Daniel McVicar, Stephen Anderson, Stephen Lockett, David Wink. Interferon gamma induces NOS2 and COX2 expression in estrogen receptor negative breast cancer leading to immunosuppressive tumor microenvironment [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 3804.
Abstract 3848: Neuronal mimicry promotes breast cancer leptomeningeal metastasis from bone marrow
Authors: Whiteley Andrew E. , Price Trevor T. , Simon Brennan G. , Xu Katie R. , Sipkins Dorothy A.
Published: June 2022

Breast cancer cell (BCC) metastasis to the leptomeninges (LM) is an increasingly common disease complication with a grim prognosis of weeks to months. There are currently few therapeutic options to prevent or treat leptomeningeal disease (LMD), in part due to our limited knowledge of the molecular pathways involved in tumor invasion and survival within this unique niche. Here we show that BCCs in mice can bypass the restrictive blood-brain barrier and invade the LM by migrating along the abluminal surface of emissary vessels that connect the vertebral/calvarial bone marrow and meninges. This is mediated by tumor cell integrin α6 engaging extracellular matrix laminin on the vascular basement membrane. Upon invasion of the LM, BCCs co-localize with CSF1R+ meningeal macrophages/microglia in the perivascular space. We demonstrate that ablation of these myeloid cells by CSF1R inhibition leads to prolonged disease-free survival due to decreased LMD burden. Importantly, we show that CSF1R+ cell depletion does not prevent tumor cell LM colonization, but instead limits disease expansion within the LM, highlighting the pro-tumor phenotype of these meningeal macrophages/microglia. Our data suggest that meningeal macrophages/microglia support BCC proliferation/survival by up-regulating glial cell line-derived neurotrophic factor (GDNF), a key neurotrophic factor released by macrophages/microglia in response to neuronal injury. In vitro, GDNF protects BCCs from cell death induced by glucose deprivation, suggesting that tumor cells may hijack a macrophage neuronal injury response program to thrive within the nutrient-poor LM niche. Unexpectedly, we found that integrin α6 deletion or antibody blockade eliminates the protective role of GDNF by modulating GDNF/NCAM receptor signaling in BCCs. Taken together, our data suggest that BCCs co-opt neuronal pathfinding mechanisms and resident macrophages/glia to efficiently invade and thrive within the LM niche. Integrin α6 appears to be a master regulator of this neuronal mimicry through its ability to promote abluminal vessel trafficking and mediate responsiveness to GDNF. Finally, a case-control study of bone-metastatic breast cancer patients reveals a significant correlation between integrin α6 expression and incidence of dural-based meningeal metastasis, suggesting the clinical relevance of this pathway and potential role of α6 integrin as a biomarker of LMD risk and therapeutic target.

Citation Format: Andrew E. Whiteley, Trevor T. Price, Brennan G. Simon, Katie R. Xu, Dorothy A. Sipkins. Neuronal mimicry promotes breast cancer leptomeningeal metastasis from bone marrow [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 3848.
Abstract 387: Blood brain barrier (BBB) disruption by tumor treating fields (TTFields) in a human 3D in vitro model
Authors: Salvador Ellaine , Kessler Almuth F. , Köppl Theresa , Schönhärl Sebastian , Burek Malgorzata , Brami Catherine Tempel , Voloshin Tali , Giladi Moshe , Ernestus Ralf-Ingo , Löhr Mario , Förster Carola Y. , Hagemann Carsten
Published: June 2022

The clinical translatability of novel drug delivery systems begins with basic scientific breakthroughs. Our recent discovery of the ability of Tumor Treating Fields (TTFields) to potentially and transiently disrupt the blood brain barrier (BBB) using our murine in vitro and in vivo models, led us to validate our findings in a human 3D in vitro model established in our lab. The model consists of primary brain microvascular endothelial cells co-cultured with immortalized perciytes in a transwell system. TTFields are alternating electric fields of low intensity (1-3V/cm) and intermediate frequency (100-300kHz), which are effective and approved for the treatment of glioblastoma (GBM) using 200kHz frequency. Our murine data point out that TTFields could disrupt the BBB optimally at 100kHz. To investigate if TTFields exhibit similar effects in the human cell-based in vitro model, it was subjected to TTFields at various frequencies for 24-96h. Cells were afterwards made to recover for 24-96h. To assess BBB integrity and compromise, transendothelial electrical resistance (TEER) was measured before start of TTFields, immediately after end of TTFields, as well as 24-96h after TTFields. In addition, a permeability assay was performed. Finally, immunofluorescence (IF) staining visualized the effects of TTFields on tight junction protein claudin-5 localization. TTFields application of all investigated frequencies significantly decreased TEER. However, the strongest effects were observed with 100kHz after 72h. IF staining revealed delocalization of claudin-5 from the cell boundaries to the cytoplasm. Restoration of cell integrity was already evident as early as 24h, with complete recovery after 48h. Results using our human 3D in vitro model validated our previous observations from murine in vitro and in vivo models that TTFields could transiently disrupt the BBB. These findings provide fundamental pre-clinical data for translation from bench to bedside. Accordingly, TTFields demonstrate to be a promising novel approach in opening the BBB to facilitate drug delivery for improved treatment of central nervous system diseases including devastating brain tumors such as GBM.

Citation Format: Ellaine Salvador, Almuth F. Kessler, Theresa Köppl, Sebastian Schönhärl, Malgorzata Burek, Catherine Tempel Brami, Tali Voloshin, Moshe Giladi, Ralf-Ingo Ernestus, Mario Löhr, Carola Y. Förster, Carsten Hagemann. Blood brain barrier (BBB) disruption by tumor treating fields (TTFields) in a human 3D in vitro 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 387.
Abstract 391: Identifying molecular drivers of olaparib resistance through genome-wide sgRNA screening in prostate organoids
Authors: Pappas Kyrie Jean , Karthaus Wouter , Laclair Justin , Russo Marco , Sawyers Charles
Published: June 2022

Cancers harboring bi-allelic loss of the breast cancer genes (BRCA1 and BRCA2) are sensitive to poly(ADP-ribose) polymerase inhibitors (PARPi), which are clinically approved in breast, ovarian, and more recently prostate cancer. Genetic alteration of BRCA2 is frequent in metastatic castration-resistant prostate cancer (mCRPC), and confers sensitivity to the PARPi olaparib; however, resistance is anticipated. mCRPC has a unique genetic landscape, and is likely to present different mechanisms of resistance compared to breast and ovarian cancer because loss of BRCA2 in prostate cancer occurs primarily through a large deletion of 13q that frequently includes Rb1; a setting in which reversion mutations of Brca2 are not possible.

We have developed Brca2-deficient olaparib-sensitive murine prostate organoid models in clinically relevant genetic backgrounds (Brca2∆/∆Trp53∆/∆Pten∆/∆, Brca2∆/∆Trp53∆/∆, and Brca2∆/∆ sgRb1), as well as cell lines and patient-derived xenografts (PDX) to identify molecular mechanisms of olaparib resistance. We employed a genome-wide sgRNA positive selection screen to identify gene drivers of olaparib resistance in Brca2-deficient murine prostate organoid models. Putative resistance drivers are involved in many relevant pathways including DNA replication and repair, PARP1 substrate NAD+ metabolism, and androgen receptor signaling. While some pathways are genotype-specific, some are driving resistance in a pan-genotype manner. We are currently using our olaparib-sensitive model systems to validate specific resistance drivers in vitro and in vivo, determine their specificity to the BRCA1 or BRCA2 loss settings, and unravel the precise molecular mechanisms behind these resistance drivers.

Citation Format: Kyrie Jean Pappas, Wouter Karthaus, Justin Laclair, Marco Russo, Charles Sawyers. Identifying molecular drivers of olaparib resistance through genome-wide sgRNA screening in prostate organoids [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 391.
Abstract 395: Characterizing the role of chaperone-mediated autophagy in prostate cancer treatment resistance
Authors: Nikesitch Nicholas , Beraldi Eliana , Zhang Fan , Adomat Hans , Bell Robert , Fazli Ladan , Wells Christopher , Pinette Nicholas , Wang Yuzhuo , Gleave Martin
Published: June 2022

Androgen deprivation therapy (ADT) and androgen receptor pathway inhibition (ARPI) remains the standard of care for advanced prostate cancer (PCa). As part of its canonical activities, the androgen receptor (AR) plays an important role in PCa metabolism. AR inhibition with ARPI subjects PCa cells to acute metabolic stress caused by reduced biosynthesis and energy production. The upregulation of ARPI-induced stress response mechanisms is essential adaptive mechanism for cell proliferation and survival. This process requires PCa cells undergoing rapid phenotypic changes to adapt to their environment and circumvent lethal outcomes. By profiling the proteomic pathway alterations associated with the ARPI stress response in LNCaP cells, we noted a significant upregulation of chaperone mediated autophagy (CMA), a stress response mechanism yet to be defined in PCa. CMA, a selective protein degradation pathway, specifically targets protein substrates via a CMA recognition motif and is an essential survival mechanism in cancer cells during energy depleted metabolic stress. Within in-vitro and in-vivo PCa models, ARPI induced CMA is reflected through the increased activity of CMA lysosomes and specifically by the increased expression of the CMA marker, lysosomal associated membrane protein 2a (L2A). L2A knockdown using shRNA not only elicited a strong anti-proliferative effect in PCa cells, but also compromised PCa metabolism with decreases in ATP levels and mTORC1 signaling. Proteomic analysis by mass spectrometry further identified that CMA promotes chromatin silencing, and the suppression of pathways associated with transcription. Conversely, L2A overexpression not only promoted PCa cell proliferation during Enza treatment, but upregulated of hallmark target genes of AR-indifferent PCa growth. The upregulation of CMA facilitated proteome remodeling during ARPI, leading to increased mTORC1 signaling and biosynthesis. In summary, our data illustrates the importance of CMA in mediating the ARPI stress response in PCa, providing novel insights into the mechanisms of ARPI treatment resistance.

Citation Format: Nicholas Nikesitch, Eliana Beraldi, Fan Zhang, Hans Adomat, Robert Bell, Ladan Fazli, Christopher Wells, Nicholas Pinette, Yuzhuo Wang, Martin Gleave. Characterizing the role of chaperone-mediated autophagy in prostate cancer treatment resistance [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 395.
Abstract 398: Tribbles 2 confers resistance to anti-androgenic therapy in prostate cancer via lineage switching
Authors: Monga Jitender , Adrianto Indra , Rogers Craig , Gadgeel Shirish , Chitale Dhananjay , Ghosh Jagadananda
Published: June 2022

Background: About 33,000 men will die due to prostate cancer in the US in the year 2021. Prostate cancer initially responds to androgen receptor (AR) targeted therapies (e.g., enzalutamide, darolutamide). However, therapy-resistant, aggressive, lethal malignancy invariably develops for which no effective, targeted treatment options are available. Though failures of AR-targeted therapies remain as major cause for mortality among prostate cancer patients, molecular mechanisms underlying the emergence of resistance are still to be fully characterized.

Methods: To understand the molecular basis of enzalutamide resistance, we developed a prostate cancer cell model to mimic the clinical conditions in enzalutamide-resistant disease. These cells were transcriptionally profiled for gene expression analysis by Illumina Hi-Seq whole genome gene-expression array. Hits were validated by RT-qPCR and Western blot. For clinical correlation, samples from enzalutamide treated prostate PDX models as well as surgical prostate tumors from patients were comprehensively analyzed. Role of new hits were determined by lentiviral shRNAs and analysis of cell viability, apoptosis, and downstream targets. Pro-cancer effects were analyzed by cell proliferation, invasion, and soft-agar colony formation.

Results: We identified that the Tribbles 2 (TRIB2) pseudokinase is overexpressed in enzalutamide resistant prostate cancer (ERPC) cells. Elevated level of TRIB2 was also observed in enzalutamide treated PDX tumors in mice, and in prostate tumors from patients who were treated with enzalutamide. We found that TRIB2 protein level is especially higher in prostate cancer cells where the AR activity is low, or absent due to genetic changes. Forced overexpression of TRIB2 results in aggressive prostate cancer cell growth and makes the cells resistant to enzalutamide. Conversely, inhibition of TRIB2 by shRNA or chemical inhibitor decreases viability and re-sensitizes ERPC cells back to enzalutamide, suggesting that TRIB2 plays an important role as a driver in the resistance mechanism. Interestingly, TRIB2 downregulates luminal markers, but upregulates neuroendocrine markers via the master neuronal transcription factor, BRN2, and the reprogramming factor, SOX2. Inhibition of either BRN2 or SOX2 also re-sensitizes ERPC cells to enzalutamide.

Conclusion: These findings suggest that TRIB2 confers resistance to enzalutamide therapy through lineage switching from luminal to neuroendocrine type, involving BRN2 and SOX2.

Citation Format: Jitender Monga, Indra Adrianto, Craig Rogers, Shirish Gadgeel, Dhananjay Chitale, Jagadananda Ghosh. Tribbles 2 confers resistance to anti-androgenic therapy in prostate cancer via lineage switching [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 398.
Abstract 3997: Inhibiting ribosomal proteins with a small molecule: Therapeutic strategy for triple negative breast cancer
Authors: Dheeraj Arpit , Tailor Dhanir , Resendez Angel , Marques Fernando Jose , Bermudez Abel , Pitteri Sharon , Malhotra Sanjay
Published: June 2022

Aberration in the protein translation can lead to changes in the protein expression that can serve as the drivers of tumor progression. Ribosomes are a molecular machine that acts as a hub for protein synthesis, and dysregulation of ribosome function is causative for cancer formation. Our investigation on the causes of breast cancer progression has identified a small molecule ‘SU056’ that shows efficacy against TNBC models. SU056 treatment inhibits growth and clonogenic potential of TNBC cells (MDA-MB-231, MDA-MB-468, SUM159, 4T1, EMT6 and E0771), by arresting the cell cycle progression through G2/M phase. Proteomics analysis suggested translational process as a target of SU056 in these cells. We found that its treatment modulated expression of several molecules of translational complex such as RPL (RPL9, RPL11, RPL15), RPS (RPSA, RPS9, RPS16, RPS20), and translation initiation factors (eIF6, eIF5, eIF4A, eIF4G), which leads to overall inhibition. This was further confirmed by tumor xenograft study with different TNBC models, which also showed that metastatic nodules in the lungs were inhibited by SU056 compared to control group. The results were further confirmed in a Patient Derived Xenograft (PDX) model SUTI151. Overall, our study has identified a lead candidate SU056, and provides strong foundation to further develop a new therapy for treatment of patients with TNBCs.

Citation Format: Arpit Dheeraj, Dhanir Tailor, Angel Resendez, Fernando Jose Marques, Abel Bermudez, Sharon Pitteri, Sanjay Malhotra. Inhibiting ribosomal proteins with a small molecule: Therapeutic strategy for triple negative breast 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 3997.
Abstract 4010: Analytical concordance of 3 independent diagnostic assays for the detection of FGFR alterations in urothelial carcinoma tumor tissue
Authors: Major Christopher , Wang Songbai
Published: June 2022

Background: The Qiagen therascreen® companion diagnostic is FDA approved to aid identifying patients with urothelial carcinoma who harbor susceptible fibroblast growth factor receptor (FGFR) gene alterations and are therefore eligible for treatment with erdafitinib, an FGFR inhibitor. We examined analytical concordance between the Qiagen assay against 2 next-generation sequencing (NGS) platforms used to identify molecular targets for tailored treatment, including FGFR alterations.

Methods: Formalin-fixed paraffin-embedded tumor tissue samples (N = 54: muscle-invasive bladder cancer [n = 18], non-muscle-invasive bladder cancer [n = 23], cholangiocarcinoma [n = 12], non-small-cell lung cancer [n = 1]) were obtained commercially. FGFR alterations were detected using the Qiagen therascreen FGFR RGQ RT-PCR Kit and tested for concordance vs NGS platforms from Thermo Fisher Scientific (Oncomine Comprehensive™ assay) and Illumina (TruSight™ Oncology 500 [TSO500]). Concordance assessment of positive, negative, and overall agreement was done.

Results: 54 samples yielded valid results using the Qiagen assay. 51 met quality control metrics with the Thermo Fisher assay, and 47 with the Illumina assay. FGFR alterations were found in 17 samples, including 16 with single nucleotide variants (SNVs): R248C (n = 1), S249C (n = 7), and Y373C (n = 8), 1 with an FGFR3:TACC3 fusion and 1 with both FGFR3:TACC3 fusion and S249C mutation. Qualitative positive agreement (100%), negative agreement (100%), and overall agreement (100%) between the Thermo Fisher NGS assay and the Illumina NGS assay vs the Qiagen assay for SNVs was observed (Table). 2 fusions detected as positive by the Qiagen assay were not identified as the TACC3v1 fusion by NGS assays.

Conclusions: There was a high level of analytical concordance in detection of FGFR alterations indicated for erdafitinib between the Qiagen companion diagnostic assay and 2 commercially available NGS platforms.

Table. Concordance in detection of FGFR alterations Qiagen therascreen RT-PCR Positive Negative NGS Thermo Fisher Oncomine Dx Positive 17/17 (100%); 95% CI, 86.3%-100% 0/34 (0) Negative 0/17 (0) 34/34 (100%); 95% CI, 92.6%-100% Overall 51/51 (100%); 95% CI, 95.0%-100% NGS Illumina TSO500 Positive 17/17 (100%); 95% CI, 86.3%-100% 0/30 (0) Negative 0/17 (0) 30/30 (100%); 95% CI, 91.7%-100% Overall 47/47 (100%); 95% CI, 94.6%-100%

Citation Format: Christopher Major, Songbai Wang. Analytical concordance of 3 independent diagnostic assays for the detection of FGFR alterations in urothelial carcinoma tumor tissue [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 4010.
Abstract 4102: Vulnerability signature guided glioblastoma umbrella trial
Authors: Berens Michael E. , Peng Sen , Lee Matthew , Tang Nanyun , Ahluwalia Manmeet S. , Fonkem Ekokobe , Fink Karen L. , Raizer Jeffrey , Walker Christopher , Dhruv Harshil
Published: June 2022

Glioblastoma is characterized by intra- and inter-tumoral heterogeneity. A glioblastoma umbrella signature trial (GUST) posits multiple investigational treatment arms based on corresponding biomarker signatures. One contingency for an efficient umbrella trial is a suite of orthogonal signatures to classify patients into the likely most-beneficial arm. Assigning optimal thresholds of vulnerability signatures to classify patients as “most-likely responders” for each specific treatment arm is a crucial task. We utilized relative expression orderings (REO), entropy-regularized logistic regression (ERLR) and random forest classifier, to predict vulnerability classification. By applying semi-supervised algorithms to the TCGA GBM cohort, we were able to transform the samples with the highest certainty of predicted response into a self-labeled dataset and thus augment the training data. In this case, we developed a predictive model with a larger sample size and potentially better performance. Our GUST design currently includes four treatment arms for GBM patients: Arsenic Trioxide, Methoxyamine, Selinexor and Pevonedistat. Each treatment arm manifests its own signature developed by the customized machine learning pipelines based on selected gene mutation status, whole transcriptome data and real world outcomes from clinical trials. In order to increase the robustness and scalability, we also developed a multi-class/label classification ensemble model that’s capable of predicting a probability of “fitness” of each novel therapeutic agent for each patient. Such a multi-class model would also enable us to rank each arm and provide sequential treatment planning. By expansion to four independent treatment arms within a single umbrella trial, a “mock” stratification of TCGA GBM patients labeled 56% of all cases into at least one “high likelihood of response” arm. Predicted vulnerability using genomic data from preclinical PDX models correctly placed 4 out of 6 models into the “responder” group. Our utilization of multiple vulnerability signatures in a GUST trial demonstrates how a precision medicine model can support an efficient clinical trial for heterogeneous diseases such as GBM.

Citation Format: Michael E. Berens, Sen Peng, Matthew Lee, Nanyun Tang, Manmeet S. Ahluwalia, Ekokobe Fonkem, Karen L. Fink, Jeffrey Raizer, Christopher Walker, Harshil Dhruv. Vulnerability signature guided glioblastoma umbrella trial [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 4102.
Abstract 4232: TLR2 agonist as a novel therapeutic approach to treat pancreatic adenocarcinoma
Authors: Dheeraj Arpit , Shukla Chandreshwar , Tailor Dhanir , Jain Nayan K. , Stefan Kirsten , Patel Chintan D. , Modi Rajiv , Khamar Bakulesh M. , Malhotra Sanjay V.
Published: June 2022

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with an overall 5-year survival rate of <10% due to late stage diagnosis and poor clinical outcome with existing therapies. PDAC displays a high degree of tumor heterogeneity and immunosuppressive tumor microenvironment with lower tumor infiltrating lymphocytes (TIL). These factors contribute to resistance against chemotherapies and immunotherapies. Immunotherapies have shown activities across different tumor types including chemotherapy or targeted therapy resistant cancers however these options have little efficacy in the PDAC tumor. Here, in this study we tested the efficacy of gemcitabine in combination with Cadi-05 (TLR2 agonist) against established murine PDAC tumor models (Pan02 in C57/BL6 and 688M in B6129SF1/J). Animals were randomized to receive gemcitabine, Cadi-05, their combination or no treatment when they had tumor size ≈ 50 mm3, 65mm3 and 100 mm3. The weekly treatment of gemcitabine, Cadi-05 and their combination inhibited the tumor progression across all tumor sizes. At the end of study, PBMC and tumors were collected and analyzed for different immune parameters. Results revealed that Cadi-05 treatment alone was associated with increase in CD4+ and CD8+ T cells in PBMC as well as amongst TIL with significant decrease in their expression of immunosuppressive markers like FOXP3 and PD-1. Its combination with gemcitabine synergized the effect of each other. There was further increase in absolute TIL as well as TIL expressing CD4+ and CD8+ markers with decrease in FOXP3 and PD-1 expressing CD4+ and CD8+ TIL. Inhibition of tumor progression was associated with improved effector function of PBMC. Synergy between Cadi-05 and gemcitabine was also evident in effector function. In presence of established tumor, TLR2 agonist Cadi-05 improves effector function, increases CD4+ and CD8+ expressing TIL, decreases immune suppressive TIL and retards tumor growth. Our study suggests that combination of gemcitabine and Cadi-05 inhibits the tumor growth irrespective of its size and it is coupled with increased anti-tumor response and decreased immunosuppressive function

Citation Format: Arpit Dheeraj, Chandreshwar Shukla, Dhanir Tailor, Nayan K. Jain, Kirsten Stefan, Chintan D. Patel, Rajiv Modi, Bakulesh M. Khamar, Sanjay V. Malhotra. TLR2 agonist as a novel therapeutic approach to treat pancreatic adenocarcinoma [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 4232.
Abstract 4251: Development and characterization of an epiregulin antibody-drug conjugate for targeting colorectal cancer cell plasticity
Authors: Jacob Joan , Liang Zhengdong , Carmon Kendra
Published: June 2022

Colorectal cancer (CRC) is the second leading cause of cancer related deaths in the United States. This is largely due to metastasis, tumor relapse, and the vast heterogeneity of CRC tumors leading to treatment failure. Cancer stem cells (CSCs) are a small population of tumor-initiating cells thought to act as immortal seeds that can form metastases and contribute to tumor relapse. CSCs have been shown to exhibit plasticity or the ability to transition between differentiated and undifferentiated states to evade treatment and to promote tumor progression. Epiregulin (EREG) is an EGFR family ligand that is highly expressed in both states, as well as in treatment resistant CRCs of various mutation statuses. We showed that knock-out of EREG in a CRC cell line resulted in significant tumor inhibition in vivo, suggesting EREG is a promising target for therapeutic development. Therefore, we generated EREG-targeted antibody-drug conjugates (ADCs) to act as guided missiles for the delivery of cytotoxic drugs into EREG-expressing tumors to overcome plasticity and resistance in CRC. To develop a novel EREG ADC, we cloned and produced three separate EREG monoclonal antibody (mAbs) and tested them for binding, the ability to internalize into CRC cells, and to neutralize EREG activity. All three EREG mAbs were shown to bind with high affinity to EREG tethered to the surface of CRC cells and internalize to the lysosome, which is important for processing the release of drug from the ADC. We then conjugated the highest affinity EREG mAb and a non-targeting isotype control antibody to a highly cytotoxic drug via a cleavable peptide linker. EREG ADCs were evaluated in vitro against a wide panel of CRC cell lines of various Kras, Braf, and PI3CKA mutational statuses and different levels of EREG expression. Drug efficacy was determined using cytotoxicity assays to measure changes in CRC cell survival with escalating doses of unconjugated control antibody and EREG mAb, as well as control ADC (cADC) and EREG ADC. EREG mAb alone did not result in significant CRC cell death. However, EREG ADCs exhibited potent cell-killing in EREG-expressing CRC cells, whereas minimal effects were observed with cADC. Future progress will involve testing the safety and efficacy of EREG ADCs against patient-derived tumor xenograft models of CRC in vivo. These preliminary results demonstrate the therapeutic potential of EREG ADCs for targeting plasticity and drug resistance in CRC.

Citation Format: Joan Jacob, Zhengdong Liang, Kendra Carmon. Development and characterization of an epiregulin antibody-drug conjugate for targeting colorectal cancer cell plasticity [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 4251.
Abstract 4263: A novel pegylated biparatopic antibody-drug conjugate (pb-adc) targeting cancers with low HER2+ expression
Authors: Liu Shumin , Yin Shuqiang , Lyu Weidong , Lei Yang , Zhuo Qiudong , Wu Zibin , Tan Shuangyu , Zheng Liling , Wen Yu (Yvonne) , Wu David
Published: June 2022

ADCs have demonstrated much improved target selectivity and efficacy comparing to the nonspecific cytotoxic small molecule drug. The goal of ADC technology is to resolve the toxicity issue inherent in potent small molecule drugs. Yet, the main problem facing current ADC technology is still a toxicity issue, evidenced by 9 out of 12 FDA approved ADCs carrying black box warning labels and many failed clinical programs due to their toxicities. Many factors contribute to the ADC’s toxicity including but not limited to random conjugation of payloads to the antibody, premature release of payload, Fc related toxicity, on-target/off-tumor toxicity etc. In this study, we developed a novel pegylated BsAb-ADC formed by site-specific conjugating a fusion protein of two scFvs that target at two different epitopes of Her2, with PEG-MMAE, a pegylated cytotoxic payload MMAE. As expected, the compound is homogeneous without any Fc related toxicity. Although the compound showed lower affinity to Her2 positive cells, it demonstrated higher in vitro cytotoxicity than T-DM1, especially for Her2 low expressing cell lines when its DAR is 4. Furthermore, the compound was comparable to or better than T-DM1 or DS-8201 in inhibiting xenograft tumor models (including Her2+ low expressing models) even when DAR is only 2. The compound also demonstrated efficient internalization without detectable efflux, suggesting improved endosome and lysosome trafficking, most probably due to the lack of Fc promoted efflux mechanism and formation of complex between biparatopic Her2 antibody and Her2. In addition, unlike T-DM1 and DS-8201, the compound did not generate cytotoxicity to megakaryocyte cell line Dami, and is less toxic to the non-cancerous HaCaT cells than T-DM1 or DS-8201. The compound is stable with no detectable release of the payload when incubating with human Plasma for a week at 37°C. The circulation T1/2 of the compound in rat is about 30 hours. In conclusion, our pegylated BsAb-ADC compound demonstrated improved efficacy with better safety profile than T-DM1 and DS-8201.

Citation Format: Shumin Liu, Shuqiang Yin, Weidong Lyu, Yang Lei, Qiudong Zhuo, Zibin Wu, Shuangyu Tan, Liling Zheng, Yu (Yvonne) Wen, David Wu. A novel pegylated biparatopic antibody-drug conjugate (pb-adc) targeting cancers with low HER2+ expression [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 4263.
Abstract 474: Integrating imaging and multi-omics data to elucidate racial differences in breast tumor biology to optimize precision oncology approaches and patient outcome
Authors: Liadis Nicole , Earnest Tyler , Braun Eduardo , Antony Anu , Munn Lance , Hallock Michael , Cook Daniel ,   The SimBioSys Team
Published: June 2022

Background: Racial disparities in breast cancer incidence and clinical outcome have been well characterized. In particular, African American (AA) patients have higher mortality rates than other racial groups. Research into these racial disparities has primarily focused on socioeconomic determinants, with some studies exploring potential molecular determinants and limited biological differences found between AA and Caucasian patient tumors. Tumor intrinsic and extrinsic factors that promote racial differences in breast cancer development and patient outcome are not fully understood and strategies to address this are scarce. As a result, we have developed a platform that combines patient-specific imaging and multi-omics data to elucidate how biological differences integrate to promote racial disparities in tumor behavior and patient outcome.

Methods: Imaging and transcriptomic data from over 500 patients were integrated within the SimBioSys TumoScope biophysical modeling software to understand racial differences in tumor biology and coordinated tumor behavior.

Results: AA patients have tumors that display higher growth rates, characteristically have higher adipose tissue around the tumor, higher spatial variation in drug secretion, lower spatial variation in blood flow/and increased tumor stiffness.

Conclusion: Using a transdisciplinary approach, our results show that metabolic and structural tumor features are associated with the disproportionately poor survival rates observed in AA breast cancer patients. By characterizing racial-specific tumor intrinsic and extrinsic biological factors and their potential interactions, strategies may emerge to personalize clinical management based on racial differences. In this way, precision oncology approaches can be applied to increase life-expectancy for racial minorities with breast cancer.

Citation Format: Nicole Liadis, Tyler Earnest, Eduardo Braun, Anu Antony, Lance Munn, Michael Hallock, Daniel Cook, The SimBioSys Team. Integrating imaging and multi-omics data to elucidate racial differences in breast tumor biology to optimize precision oncology approaches and patient outcome [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 474.
Abstract 50: Multi-omics and immune cell profiling of metastatic uveal melanomas
Authors: Moser Justin C. , Shao Yusra F. , Xiu Joanne , Baca Yasmine , Sato Takami , Dalvin Lauren A. , Darabi Sourat , Korn Michael , Eisenberg Burton , Gibney Geoff , Domingo-Musibay Evidio , In Gino , Hoon Dave , Gordon Michael S.
Published: June 2022

Background: Uveal melanoma (UM) is a rare tumor of the eye which is biologically distinct from cutaneous melanoma (CM) and carries a poor prognosis once metastatic. We aimed to examine a multi-omics profile of UM as compared to CM.

Methods: A total of 277 UM and 1,297 CM metastatic or primary samples were analyzed using next-generation sequencing (NextSeq, 592 genes and WES, NovaSeq, >700 genes) and whole transcriptome sequencing (WTS; NovaSeq) (Caris Life Sciences). Tumor mutational burden (TMB) was measured by totaling somatic mutations per tumor (TMB-high cutoff >10 mutations per MB). Immune cell fraction was calculated by QuantiSeq. T- cell inflamed score was calculated using gene expression data. Pathway gene enrichment analysis using WTS data was performed using GSEA. Biostatistical significance was determined using chi-square/Fisher-Exact or Wilcoxon rank sum test and adjusted for multiple comparisons.

Results: For all cases (primary and metastatic), UM compared to CM had a higher rate of GNAQ/11 (93.8% vs. 2.1% p≤0.001), SF3B1 (20.4% vs 3% p≤0.001), and BAP1 (52.9% vs. 1.5% p≤0.001) mutations. UM also had higher levels of MYC (7% vs 0.9% p≤0.001), NCOA2 (3.1% vs 0.1% p≤0.001), and RUNX1T1 genomic amplifications (2.3% vs 0.2% p≤0.001). Assessing only samples of liver metastases, UM was shown to have higher abundance of M2 macrophages (P≤0.0001) and less abundance of M1 macrophages(P≤0.0001), monocytes(P≤0.0001), CD4 T-cells(P≤0.0001), and regulatory T-cells (p = 0.0003) as compared to CM. GSEA comparison between liver metastases of UM and CM samples showed G2M checkpoint (NES score, 1.60 p≤0.0001) and E2F targets (NES score, 1.58 p=0.002) to be higher in metastatic CM. When comparing T-cell inflamed, intermediate, and non-inflamed tumors from any site, CM or UM, the average Z scores for both G2M and E2F were highest for inflamed and lowest for non-inflamed, P≤0.0001. A similar trend of higher Z score was seen for TMB high vs TMB low tumors, p≤0.0001.

Conclusions: UM and CM are characterized by significantly different genomic and transcriptomic alterations, and cellular composition of TME. Further understanding of these characteristics may lead to better treatment strategies for metastatic UM.

Citation Format: Justin C. Moser, Yusra F. Shao, Joanne Xiu, Yasmine Baca, Takami Sato, Lauren A. Dalvin, Sourat Darabi, Michael Korn, Burton Eisenberg, Geoff Gibney, Evidio Domingo-Musibay, Gino In, Dave Hoon, Michael S. Gordon. Multi-omics and immune cell profiling of metastatic uveal melanomas [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 50.
Abstract 5007: Discovery of stromal targets in pancreatic cancer
Authors: Li Shengjun , Park Jeong-Bin , Im Hyung-Jun
Published: June 2022

Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies with limited treatment options. Development of stroma targeting therapeutics for PDAC is gaining attention because PDAC has a unique tumor microenvironment with dense tumor stroma and the tumor stroma is a critical mediator of PDAC progression. Herein, we discovered pancreatic cancer stroma-specific cell surface markers by integrative analysis of single cell RNA sequencing and cell surface marker database.

Methods: Single cell RNA sequencing data of PDAC tissue (n = 3, GSE154778) and normal pancreas tissue (n = 3, GSE131886) was obtained from Gene Expression Omnibus database. Using Seurat package, the data from each sample integrated and the cells were clustered. We selected stroma cell cluster for differential analysis to obtain the genes enriched in PDAC stroma. Then, the intersection of the PDAC stroma specific genes with the gene set of SurfaceomeDB was obtained, which allowed us to obtain the stroma cell surface markers that are highly expressed in PDAC. The marker genes were validated in 1) 36 pairs of PDAC and normal tissue samples from a RNA sequencing data (GSE15471), and 2) 143 PDAC samples in The Cancer Genome Atlas (TCGA), 328 normal pancreatic tissues in Genotype-Tissue Expression (GTEx) database (https://www.gtexportal.org).

Results: The cells from PDAC and normal pancreas were clustered into ductal/tumor, stromal and immune cell clusters according to the expression of cell-type specific marker genes. We identified variably expressed genes between PDAC and normal cells within the stromal cell cluster. Among the PDAC stroma-specific genes, we could obtain 360 cell surface markers using SurfaceomeDB. The top ten PDAC stroma-specific cell surface marker genes were MXRA8, ANTXR1, THY1, SCD1, LY6E, BST2, GPNMB, CDH11, GJB2, and CD55. To validate the results, we compared the expression levels of the top 10 genes between pancreatic cancer tissue and adjacent normal pancreatic tissue. We found that the expression levels of the genes were significantly higher in the cancer tissue compared to the normal pancreatic tissue. We also confirmed that the expression levels of 10 genes were significantly higher in all stages of PDAC compared to normal tissues in a combined RNA sequencing dataset from healthy human pancreatic tissue from GTEx and pancreatic cancer patients from TCGA.

Conclusion: We identified pancreatic cancer stroma-specific cell surface markers using single-cell RNA sequencing data and SurfaceomeDB. The markers can be utilized in development of various pancreatic cancer stroma targeted therapeutics including antibodies, antibody-drug conjugates, peptides, cell therapeutic and nanoparticles.

Citation Format: Shengjun Li, Jeong-Bin Park, Hyung-Jun Im. Discovery of stromal targets in pancreatic 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 5007.
Abstract 5056: Automated Gleason grading of digitized frozen section prostate tissue slide images
Authors: Cho Joonyoung , Kwak Tae-Yeong , Kim Sun Woo , Chang Hyeyoon
Published: June 2022

Frozen sections are used in intraoperative consultations which need rapid microscopic analysis and in certain pathological procedures that require fresh tissue. Due to the various artifacts present on frozen section tissue slides, it is difficult to automatically analyze them. We tried automatic analysis of frozen sections.

Two types of segmentation deep learning models detecting Gleason patterns were used. Both models were trained from hematoxylin and eosin (H&E) stained formalin-fixed, paraffin-embedded prostate tissue slide images. Each slide image was reviewed by an experienced pathologist, and all prostate cancer lesions were annotated with corresponding Gleason grades. One model was trained with H&E stained images (RS model), and the other model was trained with Hematoxylin-only (H-only) stained images (H-only model). A color deconvolution method was used to generate H-only stained images from original H&E stained images.

In evaluation, frozen section prostate cancer slide images from The Cancer Genome Atlas (TCGA) were used. To diagnose the slide, we splitted whole slide images (WSI) into patches and analyze those patches to segment the Gleason pattern area. For the WSI result, we reconstructed the result as a whole size heatmap, then we counted the Gleason pattern to diagnose the slide as the prostate grade group.

In detecting malignant cases, the RS model achieved a sensitivity of 98% and the H only model of 97%, respectively. In detecting clinically significant risk cases (grade group 2 or over), sensitivities of 99% and 96% were achieved, respectively. Most of the errors were all false-positive cases. In particular, the RS model mainly had false positives because of the ice crystal artifact, and the H-only model had many false positives for the folded part and the part suspected of being a prostatic intraepithelial neoplasia (PIN). False negatives were common in the compression artifacts for both models.

We confirmed that both models showed high performance in cancer detection. In addition, they showed high accuracy in the classification of high-risk and low-risk groups of cancer. Further performance improvement can be expected with additional training of data related to artifacts or PIN.

Citation Format: Joonyoung Cho, Tae-Yeong Kwak, Sun Woo Kim, Hyeyoon Chang. Automated Gleason grading of digitized frozen section prostate tissue slide images [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5056.