bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A005: Androgen receptor variants mRNA absolute quantification in prostate cancer cell models
Authors: Larson Gabrianne , Sychev Zoi , Plymate Stephen , Corey Eva , Drake Justin M. 
Published: June 2023

Abstract
Background: Patients treated with Androgen Deprivation Therapy (ADT) have been shown to increase the expression of constitutively active Androgen Receptor (AR) splice variants (AR-Vs). These splice variants lack the ligand binding domain at the C-terminus of AR, required for binding to antiandrogen therapies. AR-V7 has also been correlated to the development and progression of castration resistant prostate cancer (CRPC). As not all circulating tumor cells (CTCs) contain AR-V7, we hypothesized that other AR-Vs are involved in the mechanism of resistance to ADT commonly seen in CRPC. To test this, we developed an mRNA quantitative assay targeting AR-Vs and then correlated our results with a targeted mass spectrometry (MS) based protein assay. This work will provide a feasible quantification of AR-V transcripts and that may provide a stratification for predicted responses to ADT treatment in patients that could be useful to clinicians. Methods: The absolute copy number of total AR, AR-V2, AR-V7, AR-V12, and AR-V23 were determined in eight different PCa cell lines and 48 patient derived xenografts (PDXs) using qRT-PCR assays. We performed siRNA targeting of these variants to evaluate primer specificity by evaluating knockdown efficiencies. These results will be correlated to targeted MS quantification of AR-Vs in each cell model. Results: We found that the most highly expressed variants in PCa cell lines were AR-V7 and AR-V12. In the LuCaP PDX model, AR-V12 was shown to have the highest expression of the AR-Vs tested. Specificity of AR-V knockdown was tested using AD-1 (which only expresses the full- length AR transcript) and R1-D567 (which only expresses AR-V567es, an AR-V12-like variant) cell lines. Conclusions: We were able to determine the landscape of AR-V mRNA expression in eight PCa cell lines and in 48 PDX tumor samples. This data will be correlated to protein expression currently being analyzed using a targeted MS method developed in our lab. Our work will be useful to help clinicians stratify PCa patients based on their AR-V expression profiles. This will establish a prognostic biomarker program that measures AR-V proteins in real time from clinical biopsy tissues, circulating tumor cells, or exosomes and informs the clinician on which course of treatment may be effective for each patient. Establishing a CRPC biomarker other than AR-V7 that can help explain the AR-V7 negative CRPC patients could eventually improve clinical application and predictive treatment outcomes.
Citation Format: Gabrianne Larson, Zoi Sychev, Stephen Plymate, Eva Corey, Justin M. Drake. Androgen receptor variants mRNA absolute quantification in prostate cancer cell models [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A005.
Abstract A012: Adaptive and non-adaptive gene expression responses in prostate cancer during androgen deprivation
Authors: Nätkin Reetta , Pennanen Pasi , Syvälä Heimo , Bläuer Merja , Kesseli Juha , Tammela Teuvo L.J. , Nykter Matti , Murtola Teemu J. 
Published: June 2023

Abstract
Development of novel and efficient treatments for advanced prostate cancer (PCa) requires better understanding of the cellular mechanisms behind the transition to castration resistant prostate cancer (CRPC). We created long-term cell cultures to model the development of castration resistance. Using a low passage VCaP cells as an initial model, we first created a highly testosterone-dependent PCa cell line (VCaP-T) and then a subclone cell line developing the ability to grow at low testosterone concentration (VCaP-CT). Adaptation to low testosterone was solely due to long term culturing and experimental work confirmed for example higher AR expression and antiandrogen resistance in VCaP-CT compared to VCaP-T. With the developed models we aimed to uncover persistent and adaptive responses to testosterone level and to identify genes that potentially contribute to transition and proliferation of the castration resistant cells through androgen receptor (AR) regulation. Expression levels were measured using RNA-seq. We defined AR-associated genes as the ones with changes due to testosterone depletion in VCaP-T (418 genes) and further adaptive genes as the ones that restored expression level in VCaP-CT (134 genes). Interestingly, we identified 151 genes that were non-AR-associated in VCaP-T but gained the association in VCaP-CT cells. Genes gaining the AR-association were also hypothesized to be important for CRPC progression and castration resistant cells. We validated and assessed the clinical significance of the model and the findings using The Cancer Genome Atlas Prostate Adenocarcinoma data and multivariate Cox regression analysis. Expressions of 47 AR-associated or association gaining genes were statistically significant markers for progression-free survival. These included genes related to immune response, adhesion and transport. Genes ABCC5, SPRED3, TMPRSS11F, SPARC, SLC1A1, SATB1, PDGFRB and C1QTNF6 showed strong evidence being associated with tumor stage and aggressiveness in addition to progression-free survival. Taken together, we identified and validated multiple genes being linked with progression of prostate cancer and proposed several novel risk genes. These findings increase knowledge on mechanisms of castration resistance and may open new possibilities for treatments. Identified genes have potential to be used as biomarkers or therapeutic targets after further studies.
Citation Format: Reetta Nätkin, Pasi Pennanen, Heimo Syvälä, Merja Bläuer, Juha Kesseli, Teuvo L.J. Tammela, Matti Nykter, Teemu J. Murtola. Adaptive and non-adaptive gene expression responses in prostate cancer during androgen deprivation [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A012.
Abstract A022: Alternative polyadenylation as a therapeutic vulnerability in prostate cancer
Authors: Tietz Kiel T. , McClukey Braedan M. , Munro Sarah A. , Miller Conor R. , Dehm Scott M. 
Published: June 2023

Abstract
Prostate cancer is the second leading cause of male cancer death in the United States. While localized disease can be cured by radiation or surgery, metastatic prostate cancer presents a clinical challenge. Metastatic prostate cancer can initially be controlled by endocrine therapies that target the androgen receptor (AR), however, these tumors will inevitably develop resistance. This stage of the disease, termed castration-resistant prostate cancer (CRPC), is responsible for the majority of prostate cancer-specific deaths. Current treatment options for CRPC patients are not curable and highlight the need to develop novel therapeutic options that will more effectively treat the disease. Spliced mRNA molecules undergo cleavage and polyadenylation ~25 base pair downstream from a canonical 5’AAUAAA poly(A) site located within the 3’ untranslated region (UTR). Shortening of mRNA 3’UTRs through alternative polyadenylation has been found in numerous cancers leading to downregulation of tumor suppressor genes and upregulation of oncogenes. To investigate the function of alternative polyadenylation in CRPC, we conducted a loss-of-function screen of mRNA polyadenylation factors in hormone-sensitive LNCaP cells and hormone-insensitive LNCaP95 and 22Rv1 cells. We found that knockdown of the cleavage and polyadenylation specificity factor (CPSF) component, CPSF1, inhibited growth of all cell lines. To define pathways that are regulated by CPSF1 in prostate cancer, we identified CPSF1-dependent gene expression using RNA-seq and CPSF1-dependent poly(A) sites using poly(A)-ClickSeq (PAC-Seq). Gene set enrichment analysis of RNA-seq data revealed the Glycolysis Hallmark and Hypoxia Hallmark gene sets were positively regulated by CPSF1. Analysis of PAC-seq data revealed global induction of poly(A) sites distal to 3’ UTRs upon CPSF1 knockdown. By integrating these RNA-seq and PAC-seq datasets, we have identified AR-independent pathways that may be attractive for therapeutic targeting in prostate cancer. This study has revealed post-transcriptional gene regulation by CPSF1 as an important pathway used in CRPC.
Citation Format: Kiel T. Tietz, Braedan M. McClukey, Sarah A. Munro, Conor R. Miller, Scott M. Dehm. Alternative polyadenylation as a therapeutic vulnerability in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A022.
Abstract A023: RNF185 modulates prostate cancer metastatic potential through regulation of epithelial-mesenchymal transition
Authors: Van Espen Benjamin , Fazli Ladan , Oo Htoo Z. , Murad Rabi , Gleave Martin , Ronai Ze'ev A. 
Published: June 2023

Abstract
RNF185 is a RING finger domain-containing ubiquitin ligase which is anchored to the ER and resemble RNF5, a ubiquitin ligase implicated in ER associated degradation. In prostate cancer, deregulation of the expression or activity of several ubiquitin ligases has been shown to contribute to disease progression (e.g., Siah2, SPOP, RNF6). Analysis of prostate tumor patient data revealed a negative correlation between RNF185 expression and prostate adenocarcinoma progression and metastasis. Supporting these observations, several prostate cancer cell lines exhibited greater migration and invasion capabilities upon RNF185 depletion, in vitro. Subcutaneous inoculation of mouse prostate cancer MPC3 cells, stably expressing shRNA against RNF185, resulted in larger tumors and more frequent lung metastases in NSG mice. These results suggest that the increased metastatic potential associated with lower RNF185 levels may depend on molecular changes intrinsic to the tumors cells. RNA-sequencing and Ingenuity Pathway Analysis of RNF185-depleted compared to control MPC3 cells identified wound healing and cellular movement among the most significantly upregulated pathways in RNF185-depleted cells. Transcription regulators of Epithelial-Mesenchymal Transition (EMT) Snai2 and Zeb1 were among the most upregulated genes that were predicted to be activated based on the expression of their target genes. Comparison between differentially expressed genes in patients with low RNF185 expression, and RNF185-depleted cell lines (from mouse and human prostate tumors) confirmed deregulation of genes implicated in EMT. Taken together, our results identify RNF185 as gatekeeper of prostate cancer metastasis, via its control of EMT genes implicated in cell motility and metastasis.
Citation Format: Benjamin Van Espen, Ladan Fazli, Htoo Z. Oo, Rabi Murad, Martin Gleave, Ze'ev A. Ronai. RNF185 modulates prostate cancer metastatic potential through regulation of epithelial-mesenchymal transition [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A023.
Abstract A027: Identification and characterization of PLUTO-201, a novel lncRNA associated with prostate cancer metastasis
Authors: Li Haolong , Younger Noah , Shin Hyun Jin , Malik Bhavna , Zhao Shuang G. , Pitchiaya Sethuramasundaram , Calvert Marsha , Zhang Meng , Chang Laura , Chesner Lisa , Hua Junjie , Li Kathy , Kothari Vishal , Egusa Emily , Chou Jonathan , Das Rajdeep , Burlingame Alma , Chinnaiyan Arul M. , Li Hui , Feng Felix Y. 
Published: June 2023

Abstract
Prostate cancer is the most common non-cutaneous malignancy in men, accounting for approximately 268,000 cases and 35,000 deaths in the United States each year. This disease is a heterogeneous entity with a wide spectrum of clinical behaviors and outcomes - while a majority of men will be cured of early-stage prostate cancer, approximately 20% will develop metastatic disease, which is incurable and ultimately fatal. Despite extensive investigation, the factors promoting aggressive prostate cancer are incompletely understood. Using recently reported microarray data representing a comprehensive analysis of lncRNA prevalence across thousands of patients with prostate cancer, we now report the identification of a novel lncRNA, Prostate Locus of Uncharacterized Transcript Outlier 201 (PLUTO-201), which is strongly associated with metastasis and poor overall survival in men with prostate cancer. We find that in vitro manipulation of PLUTO-201 expression levels in prostate cancer cell lines modulates proliferation rates and markers of aggressive phenotype. Further investigation shows that PLUTO-201 localizes to the nucleus and regulates transcription of multiple genes including those responsible for steroid biosynthesis and the MHC class 1 complex, driving increased growth in androgen-depleted conditions and decreased susceptibility to T cell-mediated cytotoxicity. Overall, our findings nominate PLUTO-201 as a driver of aggressive prostate cancer phenotypes and poor clinical outcomes and suggest possible mechanisms accounting for this activity.
Citation Format: Haolong Li, Noah Younger, Hyun Jin Shin, Bhavna Malik, Shuang G. Zhao, Sethuramasundaram Pitchiaya, Marsha Calvert, Meng Zhang, Laura Chang, Lisa Chesner, Junjie Hua, Kathy Li, Vishal Kothari, Emily Egusa, Jonathan Chou, Rajdeep Das, Alma Burlingame, Arul M. Chinnaiyan, Hui Li, Felix Y. Feng. Identification and characterization of PLUTO-201, a novel lncRNA associated with prostate cancer metastasis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A027.
Abstract A033: Exploring synthetic lethality of targeting miR346-unfolded protein response dependent DNA damage response mechanisms in treatment-resistant prostate cancer
Authors: Doultsinos Dimitrios , Mills Ian , Fletcher Claire 
Published: June 2023

Abstract
Background: The Unfolded Protein Response (UPR) is a key homeostatic mechanism that is activated during endoplasmic reticulum (ER) stress caused by both intrinsic (genomic instability, metabolic demand) and extrinsic (chemo/radiotherapy, nutrient deprivation, hypoxia) factors. IRE1 is the main UPR transducer, signalling the transcription factor XBP1, and IRE1 Regulated Dependent Decay (RIDD) to resolve ER stress by controlling the expression of mRNA and miRNAs. IRE1 also regulates aspects of the DNA damage response (DDR) and IRE1-binding drugs have clinical effects as monotherapies or as adjuvants to chemotherapeutics. One miRNA involved in both the DDR and IRE1 biology is miR-346, which we have shown to cause widespread DNA damage in prostate cancer (PCa), sensitising PCa to DNA damaging drugs and associating with improved PCa outcomes. Rationale: In RNAseq data datasets we have shown that miR-346 causes a widespread transcriptional downregulation of DDR markers whilst we observed the opposite in IRE1-CRISPR-KO PCa cells. We have also developed novel IRE1 modulators that sensitise cancers to chemotherapy in vivo. These findings offer a strong rationale to explore co-targeting of miR-346 and IRE1 in the presence of DNA damaging agents to treat aggressive forms of PCa. Consequently, we want to elucidate the exact biology underpinning the miR346-IRE1/XBP1/RIDD-DDR axis to prognosticate treatment groups with gene signatures as proxies of PARPi/chemotherapeutic susceptibility. Impact: If miR-346 is a downstream effector of IRE1 activity, then an IRE1 prognostic signature can act as proxy for stratification and selection of patients for miR-346 treatment as sensitiser to DNA damaging agents whilst if miR-346 and IRE1 work in parallel, we could achieve clinically significant results by exploiting synthetic lethality. By stratifying large cohorts through IRE1/miR-346/DDR signatures (personalised precision medicine) we can increase the pool of patients for whom DNA damaging agents are effective by inducing a BRCAness phenotype, improving treatment responses and quality of life.
Citation Format: Dimitrios Doultsinos, Ian Mills, Claire Fletcher. Exploring synthetic lethality of targeting miR346-unfolded protein response dependent DNA damage response mechanisms in treatment-resistant prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A033.
Abstract A045: Whole transcriptome analysis of paired African American prostate cancer cell lines
Authors: Lee Kristi Y. , Beatson Erica L. , Chau Cindy H. , Price Douglas K. , Figg William D. 
Published: June 2023

Abstract
Recent investigations on patient race have begun to characterize biological differences in prostate cancer, particularly among patients of African ancestry. Despite clinical trends continuously demonstrating this health disparity, very few African American cell line models exist for downstream molecular investigations, and even fewer have undergone proper characterization of their expression profiles. Here, we characterize the transcriptome of the non-malignant RC-77 N/E and malignant RC-77 T/E prostate epithelial cell lines previously established from prostate specimens from the same African American patient with early-stage primary prostate cancer. Total RNA sequencing was performed on the paired cell lines using Illumina NextSeq 2000 P2 to build transcriptomic profiles that have previously been undetermined. Following data analysis and normalization, we identified 369 genes with significant upregulation in the RC-77 T/E cell line in comparison to its normal counterpart. Among the top 15 upregulated genes, half of them were previously characterized in prostate cancer but not in the context of patient race. We further compared the transcriptome of RC-77 T/E to that of the African American metastatic MDA-PCa-2b. Finally, we analyzed differential gene expression by race among prostate cancer patients in The Cancer Genome Atlas (TCGA) to correlate our transcriptomics findings on the cell line level with that on the population level. These findings may allow for more targeted assessments of genes that are dependent on race as molecular tools are established to narrow the health disparities gap in prostate cancer.
Citation Format: Kristi Y. Lee, Erica L. Beatson, Cindy H. Chau, Douglas K. Price, William D. Figg. Whole transcriptome analysis of paired African American prostate cancer cell lines [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A045.
Abstract A068: Prostate luminal progenitors as the cell-of-origin for androgen receptor-independent prostate cancer
Authors: Chua Chee Wai 
Published: June 2023

Abstract
In the recent years, we have witnessed the emergence of androgen receptor (AR)-independent prostate cancer (AIPC) with the clinical use of second-generation androgen deprivation therapy, namely Enzalutamide and Abiraterone. Unluckily, treatment options for the end-stage AIPC patients are mainly palliative but not curable. However, the cellular origin and mechanisms involved in the evolution of AIPCs remain unclear. Previously, we have discovered that AR is not required for the survival and maintenance of progenitor property of CA stration- R esistant N kx3.1-expressing cells (CARNs), thus highlighting the AR-independent nature of this luminal progenitor subset. Interestingly, AR-deleted CARNs demonstrate gene expression profile that is highly similar to human neuroendocrine prostate cancer (NEPC), a subtype of AIPC. Moreover, upon Pten deletion and mutated Kras activation, AR-deleted CARNs can generate tumors exhibiting focal neuroendocrine differentiation, indicating the ability of CARNs to serve as a cell-of-origin for NEPC. Based on these observations, we hypothesize that AR-independent prostate luminal progenitor subsets are capable of initiating AIPC upon oncogenic transformation, while the transformed cells represent distinct subsets in AIPC that possess cancer stem cell property. In our latest assessments, we have validated the ability of CARNs to initiate NEPC using a novel genetically-engineered mouse model of prostate cancer. Moreover, we have established tumor organoids from CARNs-initiated AIPC, which are capable of generating allografts in both immunodeficient and immunocompetent mice, implying their immune-evading capability. Lastly, we have performed small molecule library screening on the transformed CARNs-derived tumor organoids to identify effective treatment options for AIPC. Taken together, our study has provided novel insights into the cellular origin of AIPCs. Consequently, targeting these prostate luminal progenitors-initiated tumor cells as well as their molecular property may serve as novel therapeutic strategies to overcome AR independence in prostate cancer.
Citation Format: Chee Wai Chua. Prostate luminal progenitors as the cell-of-origin for androgen receptor-independent prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A068.
Abstract A074: In vivo modeling of castration-resistant prostate cancer in the immunodeficient SRG OncoRat
Authors: Walton R. Grace , Begemann Diane , Dunn Cynthia , Steffey Valeriya , Ross Abigail , Haque Razoanul , Noto Fallon K. 
Published: June 2023

Abstract
Prostate cancer is the second most common cause of cancer-related deaths in American men. When locally targeted approaches fail, androgen deprivation therapy is administered to block androgen stimulated prostate cancer growth signals. Most tumors initially exhibit rapid and dramatic regression following androgen deprivation therapy. However, many patients treated with androgen deprivation therapy will have disease recurrence and develop castration-resistant prostate cancer (CRPC), which is highly metastatic with poor survival rates. To improve clinical options for CRPC, pre-clinical animal models that closely recapitulate the human disease course are an essential component of drug development. SRG OncoRats are highly immunocompromised Rag2/Il2rg double knockouts that lack mature B cells, T cells, and circulating NK cells. To establish an in vivo model of CRPC, we inoculated VCaP cells subcutaneously into the hind-flank of SRG OncoRats and monitored tumor growth. On Day 24 rats underwent orchiectomy and tumor growth was further monitored through Day 46. As seen with androgen deprivation therapy in humans, VCaP tumors initially regressed in the SRG OncoRats. However, VCaP tumors resumed growth 14 days after castration, faithfully modeling the progression of CRPC. After tumor regrowth, animals were enrolled into a therapeutic efficacy study that mimics the current clinical challenges in prostate cancer treatment.
Citation Format: R. Grace Walton, Diane Begemann, Cynthia Dunn, Valeriya Steffey, Abigail Ross, Razoanul Haque, Fallon K. Noto. In vivo modeling of castration-resistant prostate cancer in the immunodeficient SRG OncoRat [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A074.