bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3697: Proof-of-concept study to enumerate large oncosomes using the RareCyte CTC platform
Authors: Papp Eszter , Vandesompele Jo , Vermeulen Peter B. , Dirix Luc Y. , Kockx Mark
Published: March 2024

Introduction: Large oncosomes (LO) are produced by tumor cells and can be detected in blood from cancer patients. The clinical utility of enumerating and characterizing LOs along with CTCs has been demonstrated, especially in settings where CTC counts are low. The RareCyte CTC platform has the potential to capture LOs along with CTCs. We performed a pilot study to evaluate the RareCyte CTC platform’s potential to analyze LOs using established preanalytical procedures.

Methods: Metastatic breast cancer patients’ (N=10) blood smears labelled with RarePlex® Enumeration panel kit were re-evaluated to identify objects with LO-like characteristics at 10x magnification, along with negative control slides (N=5). LO-like objects were annotated and re-scanned at 40x magnification using the CyteFinder® imaging instrument. After establishing the criteria for LO identification, LO enumeration was performed on a cohort of MBC patients (N=6). Sets of five blood smear slides stained with the RarePlex® Enumeration panel kit were reviewed and LO counted. Total LO counts were established by extrapolating LO counts to 7.5 mL plasma. Pearson correlation was used to determine the level of correlation between LO counts and previously obtained CTC counts.

Results: The established identification criteria enabled the consistent enumeration of LOs at 10X magnification. Total LO count was 9.6 on the negative control slides. In MBC patients the mean total LO count was 306.2 (range 3.2 - 792). There was a significant positive correlation between LO and CTC count (r=0.855, p=0.3). In samples with CTC>0 (N=3), the average total LOs count was 588, about six times higher than CTC count. In CTC=0 patient samples (N=3) the mean total LO count was 24.3 (range 3.2-36).

Conclusions: We report a novel protocol to quantify large oncosomes using the RareCyte CTC platform using established preanalytical workflows. The strong CK/EpCam staining in LOs and the strong correlation of LO count with CTC count indicates their tumoral origin. Due to their higher abundance, LOs combined with CTCs offer a more sensitive tool for treatment response monitoring. Due to its broad range, LO counts in patients with CTC=0 may reveal therapy response dynamics undetectable with CTC enumeration alone. Ongoing work focuses on the parallel detection and integrated evaluation of HER2 by immunofluorescent staining of CTCs and LOs, along with digital PCR based HER2 quantification using cfDNA from matched blood plasma samples.

Citation Format: Eszter Papp, Jo Vandesompele, Peter B. Vermeulen, Luc Y. Dirix, Mark Kockx. Proof-of-concept study to enumerate large oncosomes using the RareCyte CTC platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3697.
Abstract 376: Targeting the convergence on HIF-1α of CDK4/6 and MAPK pathway: Implications for enhanced anticancer strategies
Authors: Zhao Shuai , Zhou Lanlan , Zhang Shengliang , El-Deiry Wafik S.
Published: March 2024

Hypoxia-inducible factor 1-alpha (HIF-1α) plays a pivotal role in orchestrating cellular responses to hypoxia, influencing cancer cell survival and progression. Our previous work identified a non-canonical mechanism wherein Smurf2 mediates HIF-1α degradation under CDK4/6 inhibition. Through proteomic analysis, we discovered that serine 451 phosphorylation occurs on HIF-1α but not in palbociclib-treated samples. Point mutations at this site, substituting serine with alanine, resulted in decreased HIF-1α levels and enhanced interaction with Smurf2. Intriguingly, under palbociclib treatment, we observed phosphorylation at the serine 643 site. This site has been previously associated with MAPK-dependent regulation of HIF-1α localization and activity (Ilias Mylonis, et al., 2006), particularly relevant given the reported MAPK reliance in acquired CDK4/6 inhibitor-resistant scenarios (Renée de Leeuw, et al., 2018). To explore therapeutic implications, we investigated the impact of combined CDK4/6 (palbociclib) and MEK1/2 inhibition (trametinib, selumetinib, PD98059, U0126). Dual inhibition robustly reduced HIF-1α expression in colorectal cancer cells (HCT116, SW480) and suppressed HIF-1α activity in luciferase reporter assays. This effect extended to synergistic inhibition of cell viability under both normoxia and hypoxia in HCT116 and SW480 cells. Such effect is also applicable to other cancer types and cell lines (e.g. U251). In summary, our findings unveil a phosphorylation site on HIF-1α associated with CDK4/6 activity, influencing its protein stabilization. This discovery supports the rationale for combining CDK4/6 and MEK1/2 inhibition as a promising strategy in the treatment of solid tumors.

Citation Format: Shuai Zhao, Lanlan Zhou, Shengliang Zhang, Wafik S. El-Deiry. Targeting the convergence on HIF-1α of CDK4/6 and MAPK pathway: Implications for enhanced anticancer strategies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 376.
Abstract 3769: Spatial biology in situ hybridization and multiplexed immunohistochemistry detection compatibility using a modified protocol
Authors: Clarke Scott T. , Voeun Mae , Montoya Leticia , Vonnegut Chris , Mandavilli Bhaskar
Published: March 2024

In the field of spatial-omics imaging, combining mRNA in situ hybridization (ISH) detection with multiplexed protein immunohistochemistry detection (IHC) is desirable. We present a simplified workflow in FFPE tissue sections where ISH is detected using branched ssDNA signal amplification visible by brightfield imaging combined with multiplexed IHC using directly labeled antibodies detected by fluorescence. In multiple studies mRNA expression of PCNA (Proliferating Cell Nuclear Antigen) shows moderate to high nuclear positivity observed in most cancer cells, with gliomas and lymphomas being the few negative exceptions. In contrast, expression of PCNA in adult non-cancerous tissue has low to no expression, with tonsil and bone marrow being the exceptions. We first show the relationship between proliferation as measured by EdU detection, PCNA antibody and PCNA mRNA expression in the embryonic mouse model where PCNA expression is prevalent in developing tissue. Then we demonstrate a simplified working protocol for combining ISH and IHC in FFPE human cancer tissue sections for the co-detection of PCNA mRNA together with IHC using a panel of six protein markers relevant to the tumor microenvironment. For IHC, we directly labeled validated unconjugated antibodies with fluorophores using amine-reactive chemistry and select the degree of labeling (DOL) and titer for optimal signal/background most useful for multiplexing on FFPE tissue. We found important protocol steps to consider for compatibility between IHC and ISH detection method. Loss of IHC protein epitope due to ISH protocol use of proteases and loss of ISH signal due to presence of RNase commonly present in IHC antibody relevant reagents can prevent combining IHC with ISH. Stabilizing IHC through refixation prior to ISH workflow is also required. Modifying the protocols to avoid these incompatible treatments and using directly labeled antibodies provides useful strategies for multiplexing IHC with ISH.

Citation Format: Scott T. Clarke, Mae Voeun, Leticia Montoya, Chris Vonnegut, Bhaskar Mandavilli. Spatial biology in situ hybridization and multiplexed immunohistochemistry detection compatibility using a modified protocol [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3769.
Abstract 3823: Clinical outcomes of uveal melanoma patients in the emergency department
Authors: Beneke Alice A. , Taneja Kamil , Ladehoff Lauren , Root Kevin , Toloza Eric
Published: March 2024

Purpose: Uveal melanoma is a rare ocular malignancy that has not been well characterized at a large scale. Specifically, uveal melanoma diagnosis and outcomes in the emergency department (ED) has not been characterized.

Methods: The Nationwide Emergency Department Sample was queried from the last quarter of 2015 to 2019 to identify patients with a primary diagnosis of uveal melanoma. Multivariable logistic regression, with patient- and hospital-level characteristics as covariates, was used to identify factors associated with increased risk of inpatient admission.

Results: From the last quarter of 2015 to 2019, there were 1,274 ED encounters with a primary diagnosis of uveal melanoma. Most patients were less than 11 years old (43.4%), male (51.1%), or a Medicaid beneficiary (37.8%), and most belonged to a family in the lowest income quartile (32.0%). The median age of these patients was 35 years (IQR: 2-64). Most patients presented to hospitals in the South (53.9%), with a Trauma Level I designation (51.4%), and most to a metropolitan teaching hospital (89.1%). The most common ED outcomes were same-day discharge (61.6%) and admission to the inpatient setting (31.2%). Patients presenting to Trauma Level I hospitals were most likely to be admitted (odds ratio [OR]=2.21; p=0.031). The factors that were most significantly associated with decreased odds of inpatient admission were: patients who were not charged for services (often due to charity) (OR=0.13; p=0.040), Medicaid beneficiaries (OR=0.27; p=0.031), and private insurance beneficiaries (OR=0.34; p=0.047). Among the admitted patients, patients can be discharged to home with self-care (76.2%) or with home-health care (14.9%) or can be transferred to an intermediate-care facility (8.1%). The mean hospital length of stay was 5.7±0.6 days. In-hospital mortality rate for admitted patients was very low (0.8%).

Conclusion: Uveal melanoma patient outcomes are closely related to insurance status, indicating socioeconomic factors as a modulator of patient outcomes.

Citation Format: Alice A. Beneke, Kamil Taneja, Lauren Ladehoff, Kevin Root, Eric Toloza. Clinical outcomes of uveal melanoma patients in the emergency department [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3823.
Abstract 3862: Identification, profiling and clonotypic tracking of tumor-reactive T cells derived from bronchoalveolar lavage in lung cancer patients
Authors: Ryu Heeju , Sun Wei , Wurscher Michelle A. , Nair Viswam S. , Newell Evan W.
Published: March 2024

Immunotherapeutic strategies for disinhibiting T cell responses have revolutionized lung cancer treatment. However, the identification of tumor-reactive T cells and the acquisition of adequate tissue for molecular and immune profiling remains a challenge that hinders our ability to adequately characterize the mechanisms of immunotherapy response versus resistance. To address this gap, we are investigating the use of bronchoalveolar lavage (BAL) as an alternative to blood or tumor biopsy samples to identify tumor reactive T cells.

We collected cells from a prospective bronchoscopic biorepository of patients undergoing lung cancer evaluation that were subjected to bilateral BAL, phlebotomy, and tissue sampling. We then employed flow cytometry and single-cell multi-omic analyses to identify, characterize and clonotypically track tumor-reactive T cells obtained from BAL, blood and tumor samples from lung cancer patients. Analysis of BAL samples revealed a significant enrichment of terminally exhausted CD8+CD39+CD103+ T cells in BAL from tumor-bearing lungs compared to non-tumor bearing lung BAL and blood PBMCs in 14 patients. We then used single-cell sequencing-based multi-omics to deeply profile bilateral BAL cells, blood PBMCs and tumor tissues from 5 of these patients.

By tracking T cell receptor (TCR) sequences across patient-matched samples, we found BAL derived T cell clonotypes that expressed markers of terminal exhaustion, such as CD39 and CXCL13 in the tumor, which strongly implicates them as being tumor reactive and relatively abundant in BAL. Further validation through functional assays is being used to confirm the tumor reactivity of these clones.

These data demonstrate the feasibility of capturing tumor-specific T cells during bronchoscopy, providing promising opportunities for patient outcome characterization and exploration of novel therapies. This relatively non-invasive and practical test during routine bronchoscopy offers a cost-effective and safe alternative to identifying tumor-reactive T cells from surgical specimens or biopsies.

Citation Format: Heeju Ryu, Wei Sun, Michelle A. Wurscher, Viswam S. Nair, Evan W. Newell. Identification, profiling and clonotypic tracking of tumor-reactive T cells derived from bronchoalveolar lavage in lung cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3862.
Abstract 3875: Glioblastoma mutational profiles drive cancer cell signaling and immune evasion
Authors: Pourmaleki Maryam , Greenstein Brian D. , Jones Caitlin J. , Nandakumar Subhiksha , Navarrete Daniel A. , Mehta Smrutiben , Campos Carl , Hollmann Travis J. , Socci Nicholas D. , Bale Tejus , Shah Sohrab P. , Mellinghoff Ingo K.
Published: March 2024

Glioblastoma multiforme (GBM) is the most common malignant brain tumor in adults with a median survival below two years. Characterization of GBM through gene expression profiling and DNA sequencing has identified disease subgroups and commonly altered genes and pathways, including alterations in the genes encoding neurofibromin-1 (NF1) and the epidermal growth factor receptor (EGFR). NF1 and EGFR are involved in receptor tyrosine kinase (RTK), RAS/MEK/ERK, and PI3K signaling, and together, are genetically altered in over 60% of adult GBMs. Interestingly, NF1 and EGFR alterations in GBM are almost always mutually exclusive. Here, we designed a multimodal approach integrating spatial proteomics, transcriptomics, and genomics to measure cell composition, immune cell function, cancer cell signaling, cellular spatial organization, gene expression, transcriptional subtypes, and genome alterations in 80 NF1 and EGFR altered human GBMs with extensively curated treatment and survival data. We quantified the spatial expression of 42 proteins in over 31 million single cells measuring RTK/RAS/PI3K and Rb signaling and features of the TME, including 23 cell types covering tumor cells, immune cells, and brain resident cells. In addition to tumor genotype labels, we classified each GBM tumor by its transcriptional subtype (i.e., mesenchymal, classical, or proneural). We identified genotype-phenotype associations in GBM including hyperactive RAS signaling cellular niches, a macrophage-rich TME, and an epithelial-mesenchymal signature in NF1 altered tumors and hyperactive RTK signaling and an immune desert TME in EGFR amplified tumors. Furthermore, we observed spatial heterogeneity in cancer cell signaling patterns suggestive of the presence of different tumor cell clones within different regions of each GBM tumor. Together, we identify several genotype-associated features of GBMs, reinforcing the value of integrating spatial multi-omic data for generation of genotype-driven therapeutic hypotheses, with implications for GBM genotype-based therapeutic stratification.

Citation Format: Maryam Pourmaleki, Brian D. Greenstein, Caitlin J. Jones, Subhiksha Nandakumar, Daniel A. Navarrete, Smrutiben Mehta, Carl Campos, Travis J. Hollmann, Nicholas D. Socci, Tejus Bale, Sohrab P. Shah, Ingo K. Mellinghoff. Glioblastoma mutational profiles drive cancer cell signaling and immune evasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3875.
Abstract 4009: Discovery of inhibitory CAR target DSG1 for damping NECTIN4 on-target off-tumor toxicity in iPSC-derived CAR-T cell therapy
Authors: Hall Matthew S. , Dower Christopher M. , Miller Michael , Wheeler John , Carton Jill , Manor Ohad , Levitsky Hyam
Published: March 2024

Century Therapeutics is developing NECTIN4 targeted induced Pluripotent Stem Cell (iPSC) derived Chimeric Antigen Receptor (CAR) T cell therapy. NECTIN4 targeted antibody drug conjugate enfortumab vedotin, while generally well tolerated, causes severe skin adverse events in some patients, thought to be driven by on-target off-tumor toxicity against NECTIN4 displaying skin keratinocytes. We include a safety switch in our first clinical-stage iPSC-derived CAR-NK cell therapy, CNTY-101, which provides an antibody target for elimination of the engineered cells should that be necessary. An additional method for reducing the incidence and severity of this type of adverse event is through the incorporation of an inhibitory CAR, also known as a NOT-gate, directed against antigen expressed on normal skin keratinocytes, but the optimal surface protein to target with such an inhibitory CAR for a NECTIN4 targeted therapy is unknown. Here, we identify DSG1 (Desmoglein-1) as a top inhibitory CAR target for NECTIN4 targeted CAR-T cell therapy by conducting a multi-omics analysis of public single-cell RNAseq, bulk RNAseq, and protein microarray immunohistochemistry datasets. We find that DSG1 is constitutively and uniformly displayed on the surface of skin keratinocytes in the layers of epidermis where they display NECTIN4, and DSG1 gene expression in normal skin is uniformly high across individuals. Conversely, DSG1 mRNA and protein are rarely expressed in NECTIN4 expressing cancer indications including bladder, breast, non-small cell lung, ovarian, and pancreatic. Further, autoimmune antibodies specific to DSG1 have been described, suggesting that DSG1 is targetable by a CAR in situ. Finally, DSG1 is not expressed by our iPSC-derived CAR-T cells. While NECTIN4 expression is greatest in skin keratinocytes, epithelial cells in other tissues express NECTIN4 at lower levels. In this study, we compare the expression levels of NECTIN4 to targets associated with tissue and cell-type specific on-target off-tumor toxicity in primary CAR-T cell clinical trials. Our findings support the strategy of DSG1-directed inhibitory CAR incorporation into NECTIN4 specific CAR-T cell therapeutic candidates.

Citation Format: Matthew S. Hall, Christopher M. Dower, Michael Miller, John Wheeler, Jill Carton, Ohad Manor, Hyam Levitsky. Discovery of inhibitory CAR target DSG1 for damping NECTIN4 on-target off-tumor toxicity in iPSC-derived CAR-T cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4009.
Abstract 409: Deciphering chromosomal instability in consensus molecular subtypes (CMS) in CRC: Insights from an integrative multi-omics approach
Authors: Bischof Julia , Woodsmith Jonathan , Church David
Published: March 2024

CRC is a heterogeneous disease with different molecular subtypes, which can have a profound impact on treatment response and patient outcomes. CMS classification based on gene expression profiles has been shown to differentiate patients into clinically relevant sub-groups. However, deep multi-omics characterization of the CMS classes based on high quality patient data is lacking. Through the integration of multi-omics data, we aim to enhance our understanding of CRC’s molecular heterogeneity and thereby facilitate the development of personalized therapeutic strategies.

We performed a multi-omics analysis of CRC patients to identify potential new features of CMS groups. 890 fresh-frozen, surgically resected CRC tumor and adjacent normal samples were used to analyze whole genome and RNA sequencing data. DNA and RNA was prepared using Qiagen AllPrep Universal and KAPA Hyper Prep kit (DNA), as well as TruSeq Stranded Total mRNA kits and sequenced on a NovaSeq6000 system. We identified CMS subtypes based on RNA-Seq data and performed all statistical analyses using R.

Our analysis revealed distinct molecular characteristics across the four CMS subtypes, including unique driver mutations, signaling cascades, and immune cell infiltration profiles. The poor prognosis associated with CMS4 patients was corroborated by our clinical data. Notably, we observed high global chromosomal instability (CIN) profiles for both CMS2 and CMS4 and identified recurrent global aneuploidy patterns within these subtypes that link alterations of known cancer genes to these large-scale structural events. We found higher levels of CIN in CMS2 compared to CMS4, which appears to be predominantly driven by numerical, rather than structural CIN. Specifically, in CMS2, SMAD2/4 is commonly impacted by deletion on chromosome arm 18q, while PLCG1 is more influenced by amplifications on 20q respectively, suggesting potential values as CRC CMS biomarkers.

In conclusion, our integrative multi-omics analysis offers a comprehensive understanding of CRC molecular subtypes, which can inform personalized treatment strategies. Our findings underscore the importance of considering not only specific driver mutations but also large-scale structural rearrangements in the context of CMS subtypes.

Citation Format: Julia Bischof, Jonathan Woodsmith, David Church. Deciphering chromosomal instability in consensus molecular subtypes (CMS) in CRC: Insights from an integrative multi-omics approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 409.
Abstract 4137: Feasibility of a novel image guided injection tool for non-surgical implantation of orthotopic tumors
Authors: Kierski Thomas M. , Rojas Juan D. , Beaumont Nathan , Charity Theresa , Marek Robert D. , Young Kenneth H. , Palmer Gregory M. , Gessner Ryan C. , Czernuszewicz Tomek J.
Published: March 2024

The purpose of this study was to evaluate a novel device for non-surgical implantation of tumor cells using ultrasonic (US) image guidance. There are a variety of mouse model cancer types (e.g. sub-cu, orthotopic, genetically engineered). Orthotopic tumors are increasingly prevalent but usually require surgery, which reduces throughput and injures the surrounding anatomy. Injections are an alternative to surgery, but usually require image guidance or extensive training. US guided injection systems exist, but are suboptimal because they require significant training, as the US beam is not necessarily coplanar with needle location or trajectory, reducing accuracy and throughput. We tested a new approach to image guided injection which ensures that the US beam is coplanar with the needle. To test the efficacy of the image guided injection device across a variety of common orthotopic tumors, we delivered luc-tagged cells to the prostate (2.5e5 cells in 40 µL, PC3, N=8), liver (2e6 cells in 100 µL, Hep G2, N=5), and brain (1.75e5 cells in 100 µL, U87-MG, N=3). The brain tumor model was introduced via intracardiac injection to simulate metastases. Between 3 and 8 mice were injected for each tumor model. For injection, animals were anesthetized and positioned on motion stage. A 1 mL syringe was mounted to the adjustable injection gantry with the needle co-planar with the US beam, and the target organ was visualized with US. Cells were delivered to the targets using the US live stream as a guide. Between 1 to 3 weeks after the injections, tumors were confirmed via BLI with an IVIS (Revvity, Waltham, MA, USA). For each of the three tumor cell lines, animal preparation and injections could be performed in 10 mins by recently-trained novice users. All three cell lines could be effectively delivered to the orthotopic host tissues, and this was confirmed by using BLI of the cells. This study represents the first time a co-planar US beam and needle delivery mechanism was used for the purpose of non-surgical implantation of orthotopic tumors. Future developments of this platform could include improvements to automation of needle placement and trajectory to ensure successful payload delivery by novice users.

Citation Format: Thomas M. Kierski, Juan D. Rojas, Nathan Beaumont, Theresa Charity, Robert D. Marek, Kenneth H. Young, Gregory M. Palmer, Ryan C. Gessner, Tomek J. Czernuszewicz. Feasibility of a novel image guided injection tool for non-surgical implantation of orthotopic tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4137.
Abstract 418: BLM helicase unwinds lagging strand substrates to assemble the ALT telomere damage response
Authors: Krishnan Aravind M. , Jiang Haoyang , Zhang Tianpeng , Kaur Hardeep , Shi Tao , Kwon Youngho , Sung Patrick , Greenberg Roger A.
Published: March 2024

The Bloom Syndrome helicase (BLM) is critical for Alternative Lengthening of Telomeres (ALT), a homology directed repair mediated telomere maintenance mechanism that is prevalent in cancers of mesenchymal origin. The DNA substrates that BLM engages to direct telomere recombination during ALT remain unknown. Here, we determine that BLM helicase acts on lagging strand telomere intermediates that occur specifically in ALT positive cells to assemble a replication stress associated DNA damage response. Loss of ATRX was permissive for BLM localization to ALT telomeres in S and G2 commensurate with the appearance of telomere C-strand specific single-stranded DNA. Moreover, DNA2 nuclease deficiency increased 5’-lagging strand flap formation and ALT in a BLM dependent manner, and BLM promoted ALT in response to telomere C-strand, but not G-strand, single-stranded nicks. These findings define the seminal events in the ALT DNA damage response, linking aberrant lagging strand DNA replication with a BLM directed HDR mechanism that sustains telomere length in a subset of human cancers.

Citation Format: Aravind M. Krishnan, Haoyang Jiang, Tianpeng Zhang, Hardeep Kaur, Tao Shi, Youngho Kwon, Patrick Sung, Roger A. Greenberg. BLM helicase unwinds lagging strand substrates to assemble the ALT telomere damage response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 418.
Abstract 4202: A novel 3D model investigating the pathophysiology of prostate cancer bone marrow metastasis
Authors: Yang Jianhui
Published: March 2024

Our study is aimed to apply a 3-dimensional (3-D) in vitro model emulating the extracellular matrix (ECM) of the bone marrow microenvironment (BMM) to explore the interaction of disseminated Prostate Cancer (PC) cells and ECM. Wharton's Jelly (WJ), which histologically and biochemically resembles the ECM part of the hematopoietic stem cell (HSC) niche, was decellularized as a novel 3-D culture platform, named as decellularized WJ matrix (DWJM). CD133, a critical marker of PC stem cells (PCSC), was chosen to initially evaluate the PCSC phenotype of DU-145 cells cultured using DWJM by flow cytometry and Image-Stream. DWJM was used to culture PC Cell line DU-145 cells. Enriched CD133(+) cells by Fluorescence-Activated Cell Sorting (FACS) were further analyzed for functional phenotypes of PCSC, and the mechanism of reactivated expression of CD133 was also investigated. A small percentage (about 2-5%) of CD133(+) DU-145 cells were detected after DU-145 cell culturing using DWJM for 3-7 days. Sorted CD133+ cells formed more colonies in vitro and manifested some characteristics of Epithelial-to-Mesenchymal Transition (EMT), including increased nuclear to cytoplasmic ratio and spindle-cell morphology. The undetectable expression of CD133 mRNA and protein in parental DU-145 cells was at least partly caused by promotor methylation, while culturing using DWJM reactivated the expression of CD133 by demethylating the CD133 DNA promotor. Taken together, our in vitro findings provide preliminary findings to support the possible conversion of disseminated PC cells to PCSC by epigenetic modulation in the BMM, and these early findings warrant further validation using an in vivo mouse model.

Citation Format: Jianhui Yang. A novel 3D model investigating the pathophysiology of prostate cancer bone marrow metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4202.
Abstract 4216: Indication agnostic evaluation of CAR T cell function using patient-derived immunocompetent tumoroid modelling platform
Authors: Ochola Damieanus O. , Mundo Huckie Dell , Samuel Preethi , Korkorina Natalia , Dave Bhuvanesh
Published: March 2024

Introduction: Engineered T cells redirected towards tumor-specific cytotoxicity is a promising immunotherapeutic modality that has been well characterized for efficacy against B cell malignancies and evaluated in multiple tumor types. However, the development and optimization of CAR T cell therapies requires a rigorous preclinical model for the evaluation of CAR T cell function, tumor killing, cytokine production, and memory responses.

Experimental Procedure: We are evaluating our model platform Custom Organoid Modelling Platform for Accurate and Speedy SolutionS (COMPASS 2) as a comprehensive platform for testing developmental and functional stages of CAR T cells including activation, memory, and exhaustion. We are performing qualitative and quantitative analyses of surface markers to recapitulate the complexity of human cancer. Additionally, since CAR T cells mediate crosstalk with other immune components in the TME, we also evaluate and monitor the presence of B cells, NK cells, macrophages, and endogenous T cells. Triple Negative Breast Cancer (TNBC); Immunophenotyping (IP); Immunofluorescence (IF); Fluorescence Activated Cell Sorting (FACS); T regulatory (Treg).

Summary of Results: Our evaluation of COMPASS 2 for functional testing of CAR T cells demonstrates the feasibility of the platform in preclinical CAR T cell evaluation. We showed T cell infiltration and analyzed cytokine production that may alter tumor cells and TME. Crosstalk with other immune cells will be evaluated. We are currently evaluating the tumor volume changes using an EGFRvIII-targeted CART cell therapy on TNBC model systems, followed by apoptosis and EGFR analysis using FACS.

Conclusion: Our COMPASS 2 model platform enables studies that require recapitulating hurdles to CAR therapy, including antigen escape, T cell dysfunction and trafficking; to reveal an essential role of the endogenous immune response mediating the antitumor effect following CAR therapy.

Citation Format: Damieanus O. Ochola, Huckie Dell Mundo, Preethi Samuel, Natalia Korkorina, Bhuvanesh Dave. Indication agnostic evaluation of CAR T cell function using patient-derived immunocompetent tumoroid modelling platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4216.
Abstract 4244: Clinical response assessment of immune checkpoint inhibitors in mismatch repair-deficient endometrial cancer using a T cell organoid coculture system
Authors: Oh Ju Hee , Choi Eun Hye , Lee Ji Eun , Nam Eun Ji
Published: March 2024

Endometrial cancers with the mismatch repair deficiency (MMR-D) phenotype exhibit characteristics such as an increased burden of tumor mutations and the presence of tumor-infiltrating lymphocytes (TILs) involved in tumor invasion. While monotherapy using immune checkpoint inhibitors (ICIs) has shown clinical improvement in MMR-D endometrial cancer (EC), observed response rates ranging from 30% to 50% suggest the existence of inherent resistance mechanisms. One notable feature of MMR-D tumors is the high proportion of tumor-infiltrating lymphocytes (TILs) encompassing various lymphocytes with diverse effects on immune interactions. Therefore, we aim to assess the feasibility of a self T-cell-tumor organoid co-culture platform for individual MMR-D endometrial cancer patients. We provide evidence that co-culturing self-tumor organoids with peripheral blood lymphocytes can be utilized to evaluate ICI responsiveness in MMR-D endometrial cancer patients. The application of a specific T-cell organoid co-culture platform to a cohort of patient resistant to monotherapy ICIs offers a means to anticipate the timing for minimal immunotherapeutic intervention and the appropriate timing for combination therapy.

Citation Format: Ju Hee Oh, Eun Hye Choi, Ji Eun Lee, Eun Ji Nam. Clinical response assessment of immune checkpoint inhibitors in mismatch repair-deficient endometrial cancer using a T cell organoid coculture system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4244.
Abstract 4302: ONECUT2 activates diverse resistance drivers of androgen receptor-independent heterogeneity in prostate cancer
Authors: Qian Chen , Yang Qian , Rotinen Mirja , Huang Rongrong , Kim Hyoyoung , Gallent Brad , Yan Yiwu , Cadaneanu Radu M. , Zhang Baohui , Kaochar Salma , Freedland Stephen J. , Posadas Edwin M. , Ellis Leigh , Vizio Dolores Di , Morrissey Colm , Nelson Peter S. , Brady Lauren , Murali Ramachandran , Campbell Moray J. , Yang Wei , Knudsen Beatrice S. , Mostaghel Elahe A. , Ye Huihui , Garraway Isla P. , You Sungyong , Freeman Michael R.
Published: March 2024

Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 targets include the glucocorticoid receptor (GR) and the NE splicing factor SRRM4, which are key drivers of lineage plasticity. Thus, OC2, despite its previously described NEPC driver function, can indirectly activate a portion of the AR cistrome through epigenetic activation of GR. Mechanisms by which OC2 regulates gene expression include promoter binding, enhancement of genome-wide chromatin accessibility, and super-enhancer reprogramming. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC and support enhanced efforts to therapeutically target OC2 as a means of suppressing treatment-resistant disease.

Citation Format: Chen Qian, Qian Yang, Mirja Rotinen, Rongrong Huang, Hyoyoung Kim, Brad Gallent, Yiwu Yan, Radu M. Cadaneanu, Baohui Zhang, Salma Kaochar, Stephen J. Freedland, Edwin M. Posadas, Leigh Ellis, Dolores Di Vizio, Colm Morrissey, Peter S. Nelson, Lauren Brady, Ramachandran Murali, Moray J. Campbell, Wei Yang, Beatrice S. Knudsen, Elahe A. Mostaghel, Huihui Ye, Isla P. Garraway, Sungyong You, Michael R. Freeman. ONECUT2 activates diverse resistance drivers of androgen receptor-independent heterogeneity in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4302.
Abstract 4342: Breast cancer multi-omic single cell profiling identifies key progressive disease markers
Authors: Russell Hugh , Rao Manisha , Duclos Grant , Aguilar Rogelio , Barkas Nick , Callahan Megan , Chaudhary Ojasvi , Gathungu Peter , Rands Chris , Shankarappa Varsha , Stetson Daniel , Rotem Asaf , Scaltriti Maurizio , Dougherty Brian
Published: March 2024

Breast cancer is one of the most diagnosed cancers and has a complex tumor microenvironment (TME). Breast tumors are subtyped by receptor expression, and all have a high degree of cellular heterogeneity. We analyzed tumors from 8 individuals with early-stage breast cancer. The patients had either triple negative breast (TNBC) or an estrogen receptor (ER) positive cancer. The tumors and normal adjacent tissue were profiled by single-nuclei gene expression (GEX) and ATAC data using the 10X multi-ome methodology. Gene set analysis identified specific epithelial clusters associated with the estrogen early/late response, epithelial mesenchymal transition, and several key cytokine pathways. From those epithelial cells, a subset highly proliferative in nature emerged. It consists of both ER positive and TNBC tumor types enriched for specific DNA transcriptional motifs including those for stem cell (Yamanaka) factors and other cellular proliferation motifs. GEX proliferation markers such as MKi-67 were also highly expressed. Overlaying GEX and ATAC data, it was possible to filter the numerous differentially expressed genes and peaks into a subset of genes specific to progressive breast cancer within the proliferative cluster. Those genes included ESRP1, POP4, CCNE1, and AAMDC all of which are associated with progressive breast cancer. To further elucidate the complexity of the TME, we examined clusters of fibroblasts from our dataset. A difference in cancer associated fibroblast marker gene expression was related to the level of ER expression expressed in the tumor epithelium. In general, ER-low tumor fibroblasts had higher expression of immune cancer associated fibroblasts (iCAFs) markers while ER-positive and TNBC tumors had greater expression of extracellular matrix associated markers (emCAFs). Specific clusters were enriched for emCAFs and iCAFs representing another critical part of the TME. In conclusion, using a multi-modal single-cell approach to the TME allowed the identification of an aggressive cluster of epithelial cells marked by genes for cellular proliferation and noted therapeutic targets while also characterizing other critical TME components especially, CAFs.

Citation Format: Hugh Russell, Manisha Rao, Grant Duclos, Rogelio Aguilar, Nick Barkas, Megan Callahan, Ojasvi Chaudhary, Peter Gathungu, Chris Rands, Varsha Shankarappa, Daniel Stetson, Asaf Rotem, Maurizio Scaltriti, Brian Dougherty. Breast cancer multi-omic single cell profiling identifies key progressive disease markers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4342.
Abstract 4423: Cholesterol and arachidonic acid promote the tumor growth of epithelial ovarian cancer via MAPK signaling pathway
Authors: Sakaguchi-Mukaida Hitomi , Hiramatsu Kosuke , Kakuda Mamoru , Nakagawa Satoshi , Kimura Toshihiro , Ueda Yutaka , Kimura Tadashi
Published: March 2024

Introduction: Previously, we reported that VLDL promoted cell proliferation of epithelial ovarian cancer (EOC) cells in vitro. In vivo, we also confirmed that High-Fat Diet (HFD) strongly promoted the tumor growth of EOC. These results suggest that lipid molecules in HFD might contribute to cell proliferation of EOC cell. In this study, we performed metabolome analysis and analyzed the metabolomic profile of lipid molecules of HFD fed mouse serum. Finally, we demonstrated that some lipid molecules promoted the cell proliferation of EOC cells in vitro and vivo.

Methods: We obtained the serum of HFD and normal diet (ND) fed mouse (non-tumor bearing) and performed metabolome analysis to identify the lipid molecules which associate with cell proliferation. In addition, we demonstrated that the lipid molecules promoted cell proliferation and activated signaling pathway of EOC cells in vitro. Moreover, we evaluated that the lipid molecules-rich diet promoted the tumor growth of EOC in vivo.

Results: The tumor growth of EOC (EOC cell line; KURAMOCHI and RMG-I) was significantly promoted by HFD compared to ND in vivo (p < 0.05, respectively). Metabolome analysis using the serum of HFD and ND fed mouse (non-tumor bearing) detected 210 metabolites, and principal component analysis showed obvious different metabolic profiles of HFD fed mouse serum compared to ND. Partial least squares-discriminant analysis revealed cholesterol and arachidonic acid (AA) as the lipid molecules with high VIP score in the serum of HFD fed mouse. In vitro, cholesterol and AA significantly promoted cell proliferation, respectively (p < 0.05) through the activation of MAPK signaling pathway. In vivo, we also confirmed that cholesterol and AA-rich feed promoted the tumor growth of EOC, respectively (p < 0.05).

Conclusions: Cholesterol and AA significantly promoted the tumor growth of epithelial ovarian cancer through the activation of MAPK signaling pathway.

Citation Format: Hitomi Sakaguchi-Mukaida, Kosuke Hiramatsu, Mamoru Kakuda, Satoshi Nakagawa, Toshihiro Kimura, Yutaka Ueda, Tadashi Kimura. Cholesterol and arachidonic acid promote the tumor growth of epithelial ovarian cancer via MAPK signaling pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4423.
Abstract 4466: Omega-3 fatty acid-induced ferroptosis in 4T1 breast cancer through CD36/FABP5 axis
Authors: Avellino Anthony , Hao Jiaqing , Yorek Matthew , yu Jian , Li Bing
Published: March 2024

Mammalian cells utilize energy from many different sources, and fatty acids are one of these sources. Dietary fats contain various structures of fatty acids, each impacting cell lipid metabolism in unique ways. Omega-3 fatty acids are known to induce breast cancer cell death through ferroptosis. However, the specific molecular mechanisms by which omega-3 fatty acids trigger ferroptosis have yet to be fully elucidated. Fatty acid binding proteins (FABPs) constitute a family of evolutionarily conserved lipid chaperones, facilitating the transport and utilization of fatty acids within cells. Notably, FABP5 is highly expressed in breast cancer, especially in the most aggressive form, triple-negative breast cancer. We hypothesized that FABP5 acts as a lipid sensor, mediating the ferroptosis induced by omega-3 fatty acids in triple-negative breast cancer cells. To test this, we created Fabp5 stable knockout cell lines in 4T1 and MDA-MB-231, two commonly used triple-negative breast cancer cell lines, using CRISPR/Cas9 technology. When treated with docosapentaenoic acid (DPA), these Fabp5-knockout cells exhibited reduced ferroptosis compared to their wild-type counterparts. Interestingly, blocking the surface protein CD36, either with inhibitors or antibodies, also reduced DPA-induced ferroptosis. Furthermore, mutations in Fabp5 decreased maximal mitochondrial respiration in both 4T1 and MDA-MB-231 cells, suggesting a crucial role for FABP5 in mediating oxygen consumption and reactive oxygen species (ROS) production during DPA-induced ferroptosis. Additionally, mice fed a high-fat diet rich in omega-3 fatty acids showed reduced tumor size and lung metastasis. Collectively, our data indicate that FABP5 is a key molecular sensor mediating oxygen consumption and ROS production, thus contributing to ferroptosis induced by omega-3 fatty acids in triple-negative breast cancer.

Citation Format: Anthony Avellino, Jiaqing Hao, Matthew Yorek, Jian yu, Bing Li. Omega-3 fatty acid-induced ferroptosis in 4T1 breast cancer through CD36/FABP5 axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4466.
Abstract 4513: Exploration degradation of intrinsically disordered protein YAP induced by PROTACs
Authors: Zhou Chen , Sun Chunbao , Pi Liya , Li Chenglong
Published: March 2024

Yes-associated protein (YAP), a potent oncogene and a key player in the Hippo tumor suppression pathway, has long been considered challenging to target due to its partially intrinsically disordered nature. However, recent advancements in High-throughput Screening (HTS) have yielded a breakthrough, as several YAP binders have been identified, igniting new possibilities in the quest to combat YAP-driven malignancies. Building upon this progress, a novel approach utilizing Proteolysis-Targeting Chimera (PROTAC) technology was employed to design and synthesize a series of YAP degraders. Here, our degraders were created by linking NSC682769, a previously reported YAP binder, with either VHL ligand 2 or pomalidomide using various linkers of different lengths and types. Among these degraders, YZ-6 emerges as the most promising, inducing rapid and sustained YAP degradation via promoting its ubiquitination-proteasome-dependent proteolysis. This process effectively suppressed YAP/TEAD-led transcription in both YAP-dependent NCI-H226 and Huh7 cancer cell lines. In addition to its degradation capabilities, YZ-6 also exhibited antiproliferative activity in both cell lines. Importantly, YZ-6 efficiently suppressed tumor development in the Huh7 xenograft mouse model, accompanied by a remarkable decrease in YAP levels, without adverse effects on the mice. These findings highlight the potential of PROTAC-mediated degradation as a viable strategy for reducing oncogenic YAP levels and attenuating downstream signaling in cancer cells. Moreover, the development of PROTACs based on NSC672869 holds promise for treating YAP-driven malignancies, opening new avenues for cancer therapy.

Citation Format: Chen Zhou, Chunbao Sun, Liya Pi, Chenglong Li. Exploration degradation of intrinsically disordered protein YAP induced by PROTACs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4513.
Abstract 4516: Inhibiting YAP activity in cancers by targeted degradation of TEAD
Authors: Chen Hui , Gridnev Artem , Schlamowitz Netanya , Zheng Guangrong , Misra Jyoti R.
Published: March 2024

The oncogenic transcriptional coactivators YAP/TAZ function as the terminal effectors of the Hippo signaling pathway and are dysregulated in many human cancers, where they promote cancer cell proliferation, survival, stemness, and resistance to targeted therapies, and thus provide a critical point for therapeutic targeting. YAP/TAZ activity is regulated by phosphorylation mediated by the kinase cascade of the Hippo signaling pathway, where phosphorylation causes cytoplasmic retention. Aberrantly activated Hypo/unphosphorylated YAP/TAZ translocates into the nucleus, where it exerts its oncogenic activity by associating with the TEAD1-4 transcription factors and inducing expression of genes encoding pro-proliferative and antiapoptotic factors. Since YAP/TAZ cannot be directly therapeutically targeted, its oncogenic transcriptional activity can be controlled indirectly by targeted degradation of TEAD. Here we report on the development of Proteolysis Targeting Chimeras that potently induces degradation of TEAD and inhibits YAP transcriptional activity and cell proliferation in YAP-dependent cancers.

Citation Format: Hui Chen, Artem Gridnev, Netanya Schlamowitz, Guangrong Zheng, Jyoti R. Misra. Inhibiting YAP activity in cancers by targeted degradation of TEAD [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4516.