bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating Facilitators’ Experience Delivering a Stress-Reducing Intervention for Indigenous Women with and without HIV
Authors: Quelch Jenna , Jackson Randy , Toombs Elaine , Robinson Margaret , Serghides Lena , Aker Amira , Gauvin Holly , Sinoway Candida , Barkman Linda , Mushquash Christopher , Gesink Dionne , Amirault Marni , Benoit Anita C.
Published: June 2023

Indigenous women encounter increased stressful life experiences such as socioeconomic insecurities as well as inequities in health services and outcomes. These stress inequities, which stem from the historical and ongoing effects of settler colonialism, also worsen health outcomes for those women living with HIV. As a part of a broader research project on the impacts of stress-reducing interventions for indigenous women, this study examines the experiences of the women who facilitated the intervention. This research was conducted to evaluate the impacts of a biweekly stress-reducing intervention conducted in Thunder Bay, Ontario. The facilitators of the intervention participated in a focus group in 2019 where they detailed the reach, effectiveness, adoption, and implementation of the intervention. The results suggest that effective stress-reducing interventions should strive to be accessible and inclusive and that doing so can increase program engagement with the service organization hosting the intervention. Further, the results highlight the strengths and challenges of the intervention, including how it helped foster leadership skills and increased indigenous cultural learning among facilitators. These findings demonstrate the strength of community-led interventions and subsequent opportunities for facilitators to grow as leaders. Further, the study highlights how this style of intervention can also encourage participants to engage in other health and wellbeing programs offered by the community partner hosting the intervention. These findings suggest that interventions aimed at reducing stress among indigenous women facing socioeconomic insecurities, including those living with HIV, are both feasible and beneficial for participants, facilitators, and the nonprofit service organizations delivering them.
Optimization of Machining Parameters of Natural/Glass Fiber with Nanoclay Polymer Composite Using Response Surface Methodology
Authors: Ragunath S. , Rathod Meenakshi L. , Saravanan K. G. , Rakesh N. , Kifetew Melkamu
Published: June 2023

Machining processes are one of the most important finishing operations in the fabrication of composites, which contain natural fibers. However, it is difficult to attain a better fishing on the final components. Hence, an attempt has been made in the work to achieve a good surface finish in compression-molded hybrid fiber composites containing nanoclay particles by optimizing the milling parameters. Experiments were conducted by using Box–Behnken design (response surface methodology (RSM)) to optimize the milling process parameters such as spindle speed (16, 24, and 32 rpm), feed rate (0.1, 0.2, and 0.3 mm/rev.), and depth of cut (1, 1.5, 2 mm) along with different vol% of nanoclay content (3%, 6%, and 9%). The surface roughness of machined fiber composite was measured, and the most influential parameters were analyzed by analysis of variance, evaluation of signal-to-noise ratio, and mathematical models of responses were developed by RSM. The experimental results (A2B1C4D3) indicated that the feed rate is one of the most significant parameters, followed by nanoclay content, depth of cut, and spindle speed. Surface roughness was found to decrease continuously (2.18–2.08 µm) with increasing nanoclay content (up to 6%) at a certain limit and further addition of clay content (above 6%); the results were declined (2.42 µm) for the same levels of other parameters.
Supplementary Figures from Terminally Exhausted CD8+ T Cells Resistant to PD-1 Blockade Promote Generation and Maintenance of Aggressive Cancer Stem Cells
Authors: Chakravarti Mohona , Dhar Sukanya , Bera Saurav , Sinha Abhipsa , Roy Kamalika , Sarkar Anirban , Dasgupta Shayani , Bhuniya Avishek , Saha Akata , Das Juhina , Banerjee Saptak , Vernekar Manisha , Pal Chiranjib , Alam Neyaz , Datta Dipak , Baral Rathindranath , Bose Anamika
Published: June 2023

Contains supplementary figure S1, S2, S3, S4, S5 and S6.
Supplementary Data from A Self-Propagating c-Met–SOX2 Axis Drives Cancer-Derived IgG Signaling That Promotes Lung Cancer Cell Stemness
Authors: Huang Xinmei , Zhang Shenghua , Tang Jingshu , Tian Tian , Pan Yilin , Wu Lina , Zhang Jingxuan , Liu Yang , Huang Jing , Dai Hui , Xu Weiyan , Zhang Youhui , Chen Jinfeng , Cao Mengshu , Zhang Liang , Qiu Xiaoyan
Published: June 2023

Supplementary figures and tables.
Supplementary Data from Large B-cell Lymphomas of Immune-Privileged Sites Relapse via Parallel Clonal Evolution from a Common Progenitor B Cell
Authors: Los-de Vries G. Tjitske , Stathi Phylicia , Rutkens Ryanne , Hijmering Nathalie J. , Luijks Jeroen A.C.W. , Groenen Patricia J.T.A. , de Jong Daphne , Ylstra Bauke , Roemer Margaretha G.M.
Published: June 2023

Supplementary Data
Supplementary Data from BCA101 Is a Tumor-Targeted Bifunctional Fusion Antibody That Simultaneously Inhibits EGFR and TGFβ Signaling to Durably Suppress Tumor Growth
Authors: Boreddy Srinivas Reddy , Nair Reshmi , Pandey Prashant Kumar , Kuriakose Anshu , Marigowda Shivakumar Bhadravathi , Dey Chaitali , Banerjee Arindam , Kulkarni Hanumant , Sagar Milind , Krishn Shiv Ram , Rao Shruthi , AR Madhukara , Tiwari Vinita , Alke Bhavna , MV Prashantha Kumar , Shri Meena , Dhamne Chaitrali , Patel Sonal , Sharma Pinky , Periyasamy Sankar , Bhatnagar Jaya , Kuriakose Moni Abraham , Reddy Ram Bhupal , Suresh Amritha , Sreenivas Suma , Govindappa Nagaraja , Moole Praveen Reddy , Bughani Usha , Tan Seng-Lai , Nair Pradip
Published: June 2023

Supplementary data
Table S1, S2 from DAB2IP Is a Bifunctional Tumor Suppressor That Regulates Wild-Type RAS and Inflammatory Cascades in KRAS Mutant Colon Cancer
Authors: Miller Abigail L. , Perurena Naiara , Gardner Alycia , Hinoue Toshinori , Loi Patrick , Laird Peter W. , Cichowski Karen
Published: June 2023

Table S1: Genes enriched in tumor macrophages, Table S2: The methylation of RASGAPs in human colorectal cancer (TCGA)
Supplementary Data from The m6A Reader YTHDF2 Promotes Bladder Cancer Progression by Suppressing RIG-I–Mediated Immune Response
Authors: Zhang Lei , Li Yuqing , Zhou Lingli , Zhou Houhong , Ye Liefu , Ou Tong , Hong Huaishan , Zheng Shiwen , Zhou Ziyu , Wu Kang , Yan Zeqin , Thiery Jean Paul , Cui Jun , Wu Song
Published: June 2023

Supplementary table ST3
Data from BCA101 Is a Tumor-Targeted Bifunctional Fusion Antibody That Simultaneously Inhibits EGFR and TGFβ Signaling to Durably Suppress Tumor Growth
Authors: Boreddy Srinivas Reddy , Nair Reshmi , Pandey Prashant Kumar , Kuriakose Anshu , Marigowda Shivakumar Bhadravathi , Dey Chaitali , Banerjee Arindam , Kulkarni Hanumant , Sagar Milind , Krishn Shiv Ram , Rao Shruthi , AR Madhukara , Tiwari Vinita , Alke Bhavna , MV Prashantha Kumar , Shri Meena , Dhamne Chaitrali , Patel Sonal , Sharma Pinky , Periyasamy Sankar , Bhatnagar Jaya , Kuriakose Moni Abraham , Reddy Ram Bhupal , Suresh Amritha , Sreenivas Suma , Govindappa Nagaraja , Moole Praveen Reddy , Bughani Usha , Tan Seng-Lai , Nair Pradip
Published: June 2023

Abstract
The EGFR and TGFβ signaling pathways are important mediators of tumorigenesis, and cross-talk between them contributes to cancer progression and drug resistance. Therapies capable of simultaneously targeting EGFR and TGFβ could help improve patient outcomes across various cancer types. Here, we developed BCA101, an anti-EGFR IgG1 mAb linked to an extracellular domain of human TGFβRII. The TGFβ “trap” fused to the light chain in BCA101 did not sterically interfere with its ability to bind EGFR, inhibit cell proliferation, or mediate antibody-dependent cellular cytotoxicity. Functional neutralization of TGFβ by BCA101 was demonstrated by several in vitro assays. BCA101 increased production of proinflammatory cytokines and key markers associated with T-cell and natural killer–cell activation, while suppressing VEGF secretion. In addition, BCA101 inhibited differentiation of naïve CD4+ T cells to inducible regulatory T cells (iTreg) more strongly than the anti-EGFR antibody cetuximab. BCA101 localized to tumor tissues in xenograft mouse models with comparable kinetics to cetuximab, both having better tumor tissue retention over TGFβ “trap.” TGFβ in tumors was neutralized by approximately 90% in animals dosed with 10 mg/kg of BCA101 compared with 54% in animals dosed with equimolar TGFβRII-Fc. In patient-derived xenograft mouse models of head and neck squamous cell carcinoma, BCA101 showed durable response after dose cessation. The combination of BCA101 and anti-PD1 antibody improved tumor inhibition in both B16-hEGFR–expressing syngeneic mouse models and in humanized HuNOG-EXL mice bearing human PC-3 xenografts. Together, these results support the clinical development of BCA101 as a monotherapy and in combination with immune checkpoint therapy.
Significance:
The bifunctional mAb fusion design of BCA101 targets it to the tumor microenvironment where it inhibits EGFR and neutralizes TGFβ to induce immune activation and to suppress tumor growth.
Data from ANO1 Reprograms Cholesterol Metabolism and the Tumor Microenvironment to Promote Cancer Metastasis
Authors: Deng Chun-Miao , Zhang Guo-Geng , Liu Qin-Wen , Xu Jiao-Jiao , Liu Zhi-Chao , Yang Jing , Xu Tao-Yang , Li Zhi-Gang , Zhang Fan , Li Bin
Published: June 2023

Abstract
Tumor metastasis is a complex process. A better understanding of the mechanistic underpinnings of the metastatic cascade could uncover approaches to better prevent and target metastases. Here, we integrated transcriptomic profiling in primary esophageal squamous cell carcinoma (ESCC) and matched lymph node metastatic tissues and genome-wide CRISPR/Cas9 functional screening to identify the key drivers of cancer metastasis. Anoctamin 1 (ANO1) expression was found to be elevated in primary tumors and further increased in metastatic tissues. High expression of ANO1 was associated with poor patient survival, and ANO1 overexpression promoted cancer invasion and metastasis. Mechanistically, ANO1 inactivated the LXR pathway and increased intracellular cholesterol accumulation by interacting with JUN to repress the transcription of cholesterol hydroxylase, CYP27A1. In a paracrine manner, IL1β secreted from ANO1-expressing ESCC cancer cells activated NF-κB signaling in fibroblasts to stimulate production of the chemokine CCL1, which in turn enhanced invasion of ESCC cancer cells. Furthermore, molecular docking and in silico screening of 1,500,000 small molecules identified K786–4469 as a lead compound that targeted ANO1 and suppressed cancer metastasis in vitro and in vivo. Overall, these findings uncover a noncanonical function of ANO1 in regulating cholesterol metabolism and fibroblast function, revealing ANO1 as a potential prognostic biomarker and therapeutic target for metastatic ESCC.
Significance:
Metastatic cancer cells upregulate ANO1 to activate cell-intrinsic and -extrinsic mechanisms that alter cholesterol metabolism and stimulate fibroblasts, which can be targeted with ANO1 inhibitors to inhibit metastatic growth.

See related commentary by Singh and Mehla, p. 1759
Data from ZDHHC2-mediated AGK palmitoylation activates AKT/mTOR signaling to reduce sunitinib sensitivity in renal cell carcinoma
Authors: Sun Yan , Zhu Liang , Liu Pian , Zhang Huan , Guo Feng , Jin Xin
Published: June 2023

Abstract
Tyrosine kinase inhibitors (TKIs) that can suppress the VEGF signaling pathway and angiogenesis have been developed to impede the progression of malignant tumors and have been approved as first-line targeted agents for clear cell renal cell carcinoma (ccRCC). Dysregulation of lipid metabolism is a major driver of TKI resistance in renal cancer. In this study, we showed that the palmitoyl acyltransferase ZDHHC2 is abnormally upregulated in tissues and cell lines resistant to TKIs, such as sunitinib. Upregulation of ZDHHC2 contributed to sunitinib resistance in cells and mice, and ZDHHC2 regulated angiogenesis and cell proliferation in ccRCC. Mechanistically, ZDHHC2 mediated AGK S-palmitoylation to promote translocation of AGK into the plasma membrane and activation of the PI3K-AKT-mTOR signaling pathway in ccRCC, which modulated sunitinib sensitivity. In conclusion, these results identify a ZDHHC2-AGK signaling axis and suggest that ZDHHC2 is a targetable candidate for improving the anti-tumor efficacy of sunitinib in ccRCC.
Data from Distinct Nrf2 Signaling Thresholds Mediate Lung Tumor Initiation and Progression
Authors: DeBlasi Janine M. , Falzone Aimee , Caldwell Samantha , Prieto-Farigua Nicolas , Prigge Justin R. , Schmidt Edward E. , Chio Iok In Christine , Karreth Florian A. , DeNicola Gina M.
Published: June 2023

Abstract
Mutations in the KEAP1-NRF2 pathway occur in up to a third of non-small cell lung cancer (NSCLC) cases and often confer resistance to therapy and poor outcomes. Here, we developed murine alleles of the KEAP1 and NRF2 mutations found in human NSCLC and comprehensively interrogated their impact on tumor initiation and progression. Chronic NRF2 stabilization by Keap1 or Nrf2 mutation was not sufficient to induce tumorigenesis, even in the absence of tumor suppressors p53 or LKB1. When combined with KrasG12D/+, constitutive NRF2 activation promoted lung tumor initiation and early progression of hyperplasia to low-grade tumors but impaired their progression to advanced-grade tumors, which was reversed by NRF2 deletion. Finally, NRF2 overexpression in KEAP1 mutant human NSCLC cell lines was detrimental to cell proliferation, viability, and anchorage-independent colony formation. Collectively, these results establish the context-dependence and activity threshold for NRF2 during the lung tumorigenic process.
Trial protocol 1 from Efficacy of Nivolumab in Pediatric Cancers with High Mutation Burden and Mismatch Repair Deficiency
Authors: Das Anirban , Tabori Uri , Sambira Nahum Lauren C. , Collins Natalie B. , Deyell Rebecca , Dvir Rina , Faure-Conter Cecile , Hassall Timothy E. , Minturn Jane E. , Edwards Melissa , Brookes Elissa , Bianchi Vanessa , Levine Adrian , Stone Simone C. , Sudhaman Sumedha , Sanchez Ramirez Santiago , Ercan Ayse B. , Stengs Lucie , Chung Jill , Negm Logine , Getz Gad , Maruvka Yosef E. , Ertl-Wagner Birgit , Ohashi Pamela S. , Pugh Trevor , Hawkins Cynthia , Bouffet Eric , Morgenstern Daniel A.
Published: June 2023

Full trial protocol NCT02992964
Supplementary Table S1 from Efficacy of Nivolumab in Pediatric Cancers with High Mutation Burden and Mismatch Repair Deficiency
Authors: Das Anirban , Tabori Uri , Sambira Nahum Lauren C. , Collins Natalie B. , Deyell Rebecca , Dvir Rina , Faure-Conter Cecile , Hassall Timothy E. , Minturn Jane E. , Edwards Melissa , Brookes Elissa , Bianchi Vanessa , Levine Adrian , Stone Simone C. , Sudhaman Sumedha , Sanchez Ramirez Santiago , Ercan Ayse B. , Stengs Lucie , Chung Jill , Negm Logine , Getz Gad , Maruvka Yosef E. , Ertl-Wagner Birgit , Ohashi Pamela S. , Pugh Trevor , Hawkins Cynthia , Bouffet Eric , Morgenstern Daniel A.
Published: June 2023

Representativeness of Study Participants
Supplementary Data 1 from Monitoring Sarcoma Response to Immune Checkpoint Inhibition and Local Cryotherapy with Circulating Tumor DNA Analysis
Authors: Bui Nam Q. , Nemat-Gorgani Neda , Subramanian Ajay , Torres Ileana A. , Lohman Marta , Sears Timothy J. , van de Rijn Matt , Charville Gregory W. , Becker Hans-Christoph , Wang David S. , Hwang Gloria L. , Ganjoo Kristen N. , Moding Everett J.
Published: June 2023

Supplementary Tables S1-S5
Suppl Figure S1 from Efficacy of Nivolumab in Pediatric Cancers with High Mutation Burden and Mismatch Repair Deficiency
Authors: Das Anirban , Tabori Uri , Sambira Nahum Lauren C. , Collins Natalie B. , Deyell Rebecca , Dvir Rina , Faure-Conter Cecile , Hassall Timothy E. , Minturn Jane E. , Edwards Melissa , Brookes Elissa , Bianchi Vanessa , Levine Adrian , Stone Simone C. , Sudhaman Sumedha , Sanchez Ramirez Santiago , Ercan Ayse B. , Stengs Lucie , Chung Jill , Negm Logine , Getz Gad , Maruvka Yosef E. , Ertl-Wagner Birgit , Ohashi Pamela S. , Pugh Trevor , Hawkins Cynthia , Bouffet Eric , Morgenstern Daniel A.
Published: June 2023

Pathological complete remission in metastatic colorectal adenocarcinoma. (A) Baseline (hematoxylin-eosin, CD8 and PD-L1). (B) Post-nivolumab: no detectable tumor cells, increased inflammation, and increase in CD8 and PD-L1 expression. All IHC images are 100X.
Data from Efficacy of Nivolumab in Pediatric Cancers with High Mutation Burden and Mismatch Repair Deficiency
Authors: Das Anirban , Tabori Uri , Sambira Nahum Lauren C. , Collins Natalie B. , Deyell Rebecca , Dvir Rina , Faure-Conter Cecile , Hassall Timothy E. , Minturn Jane E. , Edwards Melissa , Brookes Elissa , Bianchi Vanessa , Levine Adrian , Stone Simone C. , Sudhaman Sumedha , Sanchez Ramirez Santiago , Ercan Ayse B. , Stengs Lucie , Chung Jill , Negm Logine , Getz Gad , Maruvka Yosef E. , Ertl-Wagner Birgit , Ohashi Pamela S. , Pugh Trevor , Hawkins Cynthia , Bouffet Eric , Morgenstern Daniel A.
Published: June 2023

AbstractPurpose:
Checkpoint inhibitors have limited efficacy for children with unselected solid and brain tumors. We report the first prospective pediatric trial (NCT02992964) using nivolumab exclusively for refractory nonhematologic cancers harboring tumor mutation burden (TMB) ≥5 mutations/megabase (mut/Mb) and/or mismatch repair deficiency (MMRD).
Patients and Methods:
Twenty patients were screened, and 10 were ultimately included in the response cohort of whom nine had TMB >10 mut/Mb (three initially eligible based on MMRD) and one patient had TMB between 5 and 10 mut/Mb.
Results:
Delayed immune responses contributed to best overall response of 50%, improving on initial objective responses (20%) and leading to 2-year overall survival (OS) of 50% [95% confidence interval (CI), 27–93]. Four children, including three with refractory malignant gliomas are in complete remission at a median follow-up of 37 months (range, 32.4–60), culminating in 2-year OS of 43% (95% CI, 18.2–100). Biomarker analyses confirmed benefit in children with germline MMRD, microsatellite instability, higher activated and lower regulatory circulating T cells. Stochastic mutation accumulation driven by underlying germline MMRD impacted the tumor microenvironment, contributing to delayed responses. No benefit was observed in the single patient with an MMR-proficient tumor and TMB 7.4 mut/Mb.
Conclusions:
Nivolumab resulted in durable responses and prolonged survival for the first time in a pediatric trial of refractory hypermutated cancers including malignant gliomas. Novel biomarkers identified here need to be translated rapidly to clinical care to identify children who can benefit from checkpoint inhibitors, including upfront management of cancer.
Abstract A013: Minor intron splicing is critical for survival of lethal prostate cancer
Authors: Augspach Anke , Rubin Mark Andrew , Kanadia Rahul
Published: June 2023

The role of major intron splicing in PCa is well established and highly investigated. However, the equally important and impactful minor spliceosome (MiS) and minor intron splicing have remained underexplored in PCa. Here for the first time, we show that minor intron containing genes (MIGs) are enriched as direct interactors of PCa-causing genes and that their expression levels correspond to different stages of PCa progression. Accordingly, we show that U6atac expression and MiS activity reinforces cell growth and correlates with PCa progression. Consequently, highly proliferative PCa cells are strongly susceptible to siU6atac-mediated MiS inhibition. In this sense, siU6atac is significantly more efficient in lowering the tumor burden of castration resistant prostate cancer (CRPC) cells and organoids than the current state-of-the-art combination therapy. Mechanistically, we show that inhibition of the MiS through siU6atac causes minor and major intron mis-splicing and aberrant expression of MIG and non-MIG transcripts and encoded proteins, which enriches for MAPK activity, DNA repair, and cell cycle. Single cell-RNAseq confirms cell cycle defects and lineage dependency on the MiS from primary to CRPC and neuroendocrine PCa. Finally, our data provides strong evidence that Androgen receptor signaling functions as a regulator of MiS activity throughout PCa disease progression to CRPC while p38MAPK influences MiS activity in neuroendocrine PCa. Furthermore, we discovered that MiS inhibition in neuroendocrine PCa shifts alternative splicing in favor of canonical REST1 isoform thereby blocking lineage plasticity and progression to lethal therapy resistant PCa. This finding positions the MiS as yet another disruptor of a crucial molecular pathway underpinning the emergence of CRPC and neuroendocrine PCa. Based on these findings we posit that the MiS may be a common denominator of prominent PCa driver genes and a driving factor of advanced lethal PCa. We hypothesize that the MiS represents a point of vulnerability in therapy-resistant PCa.

Citation Format: Anke Augspach, Mark Andrew Rubin, Rahul Kanadia. Minor intron splicing is critical for survival of lethal 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 A013.
Abstract A026: BMX inhibition reverses HSD3B1-driven resistance in prostate cancer
Authors: Li Xiuxiu , Berk Michael , Goins Christopher , Alyamani Mohammad , Chung Yoon-Mi , Wang Chenyao , Patel Monaben , Rathi Nityam , Zhu Ziqi , Willard Belinda , Stauffer Shaun , Klein Eric , Sharifi Nima
Published: June 2023

Background: Prostate cancer is the second leading cause of cancer-related death in men in the United States and is dependent on androgens and androgen receptor (AR) activation. Androgen deprivation therapy (ADT) is the mainstay treatment, but it as well as next-generation treatments eventually fail. Disease then progresses as castration-resistant prostate cancer (CRPC), which is driven by reactivation of the androgen-AR axis. 3β-hydroxysteroid dehydrogenase-1 (3βHSD1) catalyzes the rate-limiting step for potent androgen synthesis from adrenal-derived precursors, thereby stimulating CRPC. HSD3B1, which encodes for 3βHSD1, has a common missense-encoding germline variation that enhances conversion from adrenal DHEA to potent androgens. Clinical studies demonstrate that this “adrenal-permissive” HSD3B1 genotype confers more rapid progression on ADT, and recent studies show that overall survival is shorter in patients with the adrenal-permissive genotype who are treated with ADT + enzalutamide. The Etk/BMX kinase may be involved in the development and progression of CRPC. We sought to determine whether phosphorylation of 3βHSD1 is required for its activation and that the necessary kinase could be a potential target. Methods: In prostate cancer lines, mouse xenograft models, and fresh patient prostatectomy tissues, mass spectrometry and HPLC were used to identify steroid metabolites. Genetic and pharmacological methods were used to identify inhibition of BMX-mediated 3βHSD1 phosphorylation in CRPC. Results: BMX inhibition suppressed castration-resistant prostate cancer through targeting 3βHSD1 phosphorylation. 3βHSD1 transcription level and enzyme activity were induced in enzalutamide-resistant prostate cancer cell lines. 3βHSD1 and SF-1 transcription levels were positively correlated in prostate adenocarcinoma (TCGA database). BMX inhibition by zanubrutinib suppressed enzalutamide resistance induced 3βHSD1 enzyme activity. Conclusions: BMX promotes CRPC by regulating 3βHSD1 phosphorylation. BMX inhibition has potential as a new therapy to optimize CRPC treatment.

Citation Format: Xiuxiu Li, Michael Berk, Christopher Goins, Mohammad Alyamani, Yoon-Mi Chung, Chenyao Wang, Monaben Patel, Nityam Rathi, Ziqi Zhu, Belinda Willard, Shaun Stauffer, Eric Klein, Nima Sharifi. BMX inhibition reverses HSD3B1-driven resistance 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 A026.
Abstract A070: Determining gene expression regulated by androgen receptor variant 7 in co-loss of MAP3K7/CHD1 prostate cancer
Authors: Gillette Claire , Jillson Lauren , Cramer Scott
Published: June 2023

Prostate cancer (PCa) is the second leading cancer diagnosis in men. The ACS estimates 268,490 new cases of PCa and 34,500 deaths in 2022. Most patients with local PCa are disease free at the 5-year mark. Patients with metastatic PCa only have a 31% 5-year disease-free survival rate. While these patients may initially respond to androgen deprivation therapy, many will progress to castration-resistant prostate cancer (CRPC) and fail treatment. There is a need to develop new therapies to treat CRPC. The Cramer lab studies the dual deletion of MAP3K7 and CHD1 PCa subtype. In MAP3K7/CHD1-depleted PCa cell lines the ratio of AR splicing variants shifts to enrich for the constitutively active variant AR-v7, a known driver of CRPC. Other studies demonstrated that AR-v7 has unique target genes and can alter canonical AR target gene expression. I hypothesize that gain of AR-v7 signaling activates atypical gene targets which alter the gene expression of MAP3K7/CHD1-depleted PCa. I will determine the chromatin-binding targets and identify AR-v7 specific candidate genes. Patients with loss of MAP3K7 and CHD1 also enrich in the spliceosome protein U2AF2, therefore I will also perform transcriptomics with/without AR-FL and AR-v7 to characterize the larger impacts of AR-variant signaling at the RNA level. To this end, I will develop an inducible knockdown system in dual shMAP3K7/shCHD1 cells targeting AR-FL, AR-v7, and AR-Total. This will provide insight into the role of AR-v7 in two stages of gene expression and identify candidate therapeutic genes/pathways in loss of MAP3K7 and CHD1 PCa.

Citation Format: Claire Gillette, Lauren Jillson, Scott Cramer. Determining gene expression regulated by androgen receptor variant 7 in co-loss of MAP3K7/CHD1 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 A070.
Abstract A085: A luminal intermediate cell state maintains long-term prostate homeostasis and contributes to tumorigenesis
Authors: Luo Fu , Tshering Lara F. , Tutuska Karis , Szenk Mariola , Rubel Diana , Rail James G. , Russ Savanah , Liu Jingxuan , Nemajerova Alice , Balázsi Gábor , Talos Flaminia
Published: June 2023

Cellular heterogeneity poses tremendous challenges for developing cell-targeted therapies and biomarkers of clinically significant prostate cancer. The origins of this heterogeneity within the cellular complexities of normal adult and aging tissue remain unknown leaving important cellular states and transcriptional programs that allow the expansion of malignant clones in early cancer unidentified. These unresolved questions hamper the development of novel therapies designed to block the deregulated proliferation of prostate epithelial cells. To define cell states that contribute to early cancer development, we performed in vivo lineage tracing with multicolor reporters, whole organ mapping and single cell transcriptomics of normal and malignant prostate from genetically-engineered mouse models. We show here that the long-term luminal homeostasis is maintained by multiple clones with various fitness levels. Long-term clonal expansions are enabled by a luminal transcriptional state harboring basal markers (Luminal Intermediate, LumI) and controlled by Wnt/p63 signaling. Moreover, LumI cells greatly expand during early stages of tumorigenesis in several mouse models of prostate cancer. Specific genetic ablation of p63 from luminal cells in vivo decreases clonal activity in homeostasis and reduces the formation of aggressive clones in prostate tumor models. Finally, the LumI cells and Wnt signaling appear to significantly increase in human aging prostate and prostate cancer samples, highlighting the importance of this hybrid cell state for human pathologies with potential translational impact. Our models reveal a continuity of this cell state from normal homeostasis to aging and early cancer with specific alterations at each stage. Understanding how the luminal intermediate cell state is regulated in homeostasis and deregulated in hyperproliferative contexts is crucial for the development of prognostic markers and new therapeutic interventions for prostate diseases.

Citation Format: Fu Luo, Lara F. Tshering, Karis Tutuska, Mariola Szenk, Diana Rubel, James G. Rail, Savanah Russ, Jingxuan Liu, Alice Nemajerova, Gábor Balázsi, Flaminia Talos. A luminal intermediate cell state maintains long-term prostate homeostasis and contributes to tumorigenesis [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 A085.
Abstract B012: Genomic and epigenomic drivers of double-negative metastatic prostate cancer
Authors: Lundberg Arian , Zhang Meng , Aggarwal Rahul R. , Li Haolong , Zhang Li , Foye Adam , Sjöström Martin , Chou Jonathan , Chang Kevin , Moreno-Rodriguez Thaidy , Shrestha Raunak , Baskin Avi , Zhu Xiaolin , Weinstein Alana S. , Younger Noah , Alumkal Joshi J. , Beer Tomasz M. , Chi Kim N. , Evans Christopher P. , Gleave Martin , Lara Primo N. , Reiter Robert E. , Rettig Matthew B. , Witte Owen N. , Wyatt Alexander W. , Feng Felix Y. , Small Eric J. , Quigley David A.
Published: June 2023

Systemic targeted therapy in prostate cancer is primarily focused on ablating androgen receptor (AR) signaling. Androgen deprivation therapy and second-generation AR-targeted therapy selectively favor the development of treatment-resistant subtypes of metastatic castration-resistant prostate cancer (mCRPC), defined by whether the tumor expresses either AR or neuroendocrine (NE) markers. Among the subtypes of mCRPC, the molecular drivers of double-negative (AR-/NE-) mCRPC are poorly defined. In this study, we comprehensively characterize genomic and epigenomic features of treatment-emergent mCRPC subtypes in 210 tumors by integrating matched RNA sequencing, whole-genome sequencing, and whole-genome bisulfite sequencing. We show that AR-/NE- tumors exhibit a clinically and molecularly distinct phenotype. Patients with AR-/NE- mCRPC tumors have the shortest survival, and these tumors preferentially harbor amplification of the chromatin remodeler CHD7 and loss of PTEN. We demonstrate that methylation changes in CHD7 candidate enhancers are linked to elevated CHD7 expression in AR-/NE+ tumors. Moreover, we use genome-wide methylation analysis to nominate the Krüppel-like factor gene KLF5 as a driver of the AR-/NE- phenotype and link its activity to loss of the tumor suppressor RB1. These observations reveal the aggressiveness of the AR-/NE- tumors and elucidate genomic and epigenomic drivers of mCRPC subtypes, which may facilitate the identification of novel therapeutic targets in this highly aggressive disease.

Citation Format: Arian Lundberg, Meng Zhang, Rahul R. Aggarwal, Haolong Li, Li Zhang, Adam Foye, Martin Sjöström, Jonathan Chou, Kevin Chang, Thaidy Moreno-Rodriguez, Raunak Shrestha, Avi Baskin, Xiaolin Zhu, Alana S. Weinstein, Noah Younger, Joshi J. Alumkal, Tomasz M. Beer, Kim N. Chi, Christopher P. Evans, Martin Gleave, Primo N. Lara, Robert E. Reiter, Matthew B. Rettig, Owen N. Witte, Alexander W. Wyatt, Felix Y. Feng, Eric J. Small, David A. Quigley. Genomic and epigenomic drivers of double-negative metastatic 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 B012.
Abstract B063: Interplay between PARP and the RB/E2F axis in prostate cancer
Authors: Evans Latese , Cunningham Moriah , Gonzalez Jasibel Vasquez , Schiewer Matthew
Published: June 2023

Retinoblastoma (RB) protein is a tumor suppressor that represses the transcriptional activity of E2Fs by forming an RB-E2F repressor complex. The phosphorylation of RB by CDK4/6 results in dissociation of the complex and subsequent E2F transcriptional activity, leading to cell cycle progression. RB loss occurs in 10-15% of castration-resistant prostate cancer (CRPC) which is associated tumor aggressiveness and poor clinical outcomes. RB loss is also associated differential treatment response to an array of treatment modalities, including hormone therapy and DNA damage inducing chemotherapy. RB depletion leads to enhanced expression of DNA repair proteins due to increased transcriptional activity of E2F1. PARP-1 is an enzyme that plays a role in multiple nuclear processes including DNA repair, transcriptional regulation, and chromatin dynamics. Increased PARP-1 activity is associated with and correlates to poor clinical outcomes in CRPC. E2F1 transcriptional activity is supported by PARP enzymatic activity, but the consequences of the functional interaction between the RB/E2F axis and PARP remains an open line of inquiry, which may yield novel treatment strategies and/or biomarkers of response. Isogenic models of RB1 knockdown were used to evaluate the impact of RB loss on PARP enzymatic activity. PARP-1 protein increases upon RB1 depletion with a concomitant increase in PARP activity. Growth curve assays were conducted to examine the biological response to PARP inhibition in the isogenic models. Results suggest a differential response between control and RB1 depleted cells when treated with Olaparib. RB1depleted cells also exhibit differential PARP activity in response to treatment with the IC50 dose of Olaparib. Future studies have been designed to evaluate the impact of RB alteration and manipulation of PARP activity on biological and molecular processes that are governed by RB/E2F and PARP.

Citation Format: Latese Evans, Moriah Cunningham, Jasibel Vasquez Gonzalez, Matthew Schiewer. Interplay between PARP and the RB/E2F axis 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 B063.
Abstract B076: IGFBP3 promotes resistance to olaparib via modulating EGFR signaling in advanced prostate cancer
Authors: Leslie Amy R. , Gao Allen C. , Lombard Alan P. , Ning Shu
Published: June 2023

Background: Castration-resistant prostate cancer (CRPC) is an incurable disease and a leading cause of cancer death in men worldwide. Olaparib (Lynparza) was among the first PARP inhibitors (PARPi) approved for the treatment of CRPC tumors harboring DNA repair defects. However, clinical resistance to PARPi’s has been documented. The mechanisms underlying resistance to PARPi’s remain elusive. To study acquired resistance, we developed olaparib-resistant LN-OlapR and 2B-OlapR cell lines generated through chronic olaparib treatment of the olaparib-sensitive cell lines LNCaP and C4-2B, respectively. RNA-seq revealed IGFBP3 is overexpressed in both OlapR cell lines. IGFBP3 overexpression is correlated with poor clinical outcome and is thought to participate in DNA repair pathways. IGFBP3 plays a key role in nonhomologous end joining (NHEJ) repair through a ternary complex with EGFR and DNA-PKcs. The IGFBP3/EGFR signaling axis is thought to modulate NHEJ repair and could have implications for PARPi sensitivity. We hypothesize that increased IGFBP3 expression promotes PARPi resistance by enhancing DNA repair capacity. Methods: RNA-sequencing and gene set enrichment analysis were used to determine the expression profile changes in resistant cells compared to parental cells. Real time PCR and western blots confirmed the expression of DNA damage repair genes such as γH2AX, EGFR, and DNA-PKcs. ELISA was used to determine IGFBP3 secretion. RNAi was used to inhibit IGFBP3 and EGFR expression. Gefitinib was used to inhibit EGFR activity. Cell viability assays were used to assess cell growth. Results: Transcriptomic profiling revealed that IGFBP3 is highly expressed in resistant models. We verified increased levels of IGFBP3 RNA and protein in both OlapR models. We found that RNAi inhibition of IGFBP3 increases γH2AX and cleaved-PARP protein levels in the resistant models, which suggests accumulation of DNA double strand breaks (DSBs) leading to genomic instability and cell death. We discovered increased phosphorylation of EGFR and DNA-PKcs in the resistant cells. Furthermore, silencing/inhibiting IGFBP3 and EGFR reduces OlapR cell viability and resensitizes resistant cells to treatment. Conclusions: Our findings demonstrated that inhibiting IGFBP3 and EGFR aids in PARPi sensitivity in the resistant setting. Future work will utilize OlapR models to study how the IGFBP3/EGFR/DNA-PKcs protein complex promotes the development of resistance. Understanding the role of IGFBP3 in PARPi resistance will enhance our ability to re-sensitize resistant CRPC to PARPi therapeutics.

Citation Format: Amy R. Leslie, Allen C. Gao, Alan P. Lombard, Shu Ning. IGFBP3 promotes resistance to olaparib via modulating EGFR signaling in advanced 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 B076.
Abstract PR005: Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3’ untranslated region mutations
Authors: Schuster Samantha L. , Arora Sonali , Wladyka Cynthia L. , Corey Lukas , Stackhouse Bethany L. , Kollath Lori , Corey Eva , True Lawrence D. , Young Dave , Paddison Patrick J. , Hsieh Andrew C.
Published: June 2023

It is clear from the high mortality rate in advanced cancers that we need a more complete understanding of the many sources of oncogenic dysregulation in tumors. The importance of the non-coding genome in disease has recently begun to be revealed through expanded use of whole genome sequencing. In particular, 3’ untranslated region (3’UTR) somatic mutations represent an important but largely unexplored avenue of alternative oncogenic gene dysregulation. Individual instances of 3’UTR-mediated oncogenicity are known, including oncogenic RNA binding proteins and microRNAs. However, a comprehensive, high-throughput study of patient-based 3’UTR mutations and their effect on post-transcriptional gene regulation in cancer has yet to be undertaken. To determine the significance of 3’UTR mutations in advanced disease, we identify 3’UTR somatic variants across 185 metastatic castration-resistant prostate tumors, discovering 14,497 single-nucleotide mutations, which are enriched in oncogenic pathways and 3’UTR regulatory elements. We develop two complementary massively parallel reporter assays (MPRAs) to measure how thousands of these patient-based mutations affect two distinct levels of post-transcriptional gene regulation: mRNA translation and stability. These MPRAs identify hundreds of functional variants that allow us to define three determinants of mutation significance: sequence conservation, known regulatory elements, and RNA structure. Furthermore, we demonstrate the clinical relevance of these mutations, observing that CRISPR-Cas9 base editing of distinct patient 3’UTR mutations into endogenous cellular loci increases oncogenic mRNA translation and cellular stress resistance. Finally, we go back to patients, illustrating that those harboring oncogenic 3’UTR mutations discovered by our methods display particularly poor prognosis. This work represents an unprecedented view of the extent to which disease-relevant 3’UTR mutations affect mRNA stability, translation, and cancer progression, uncovering principles of regulatory functionality and potential therapeutic targets in previously unexplored regulatory regions.

Citation Format: Samantha L. Schuster, Sonali Arora, Cynthia L. Wladyka, Lukas Corey, Bethany L. Stackhouse, Lori Kollath, Eva Corey, Lawrence D. True, Dave Young, Patrick J. Paddison, Andrew C. Hsieh. Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3’ untranslated region mutations [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 PR005.
Abstract PR007: ERG-driven luminal prostate cancers emerge from Ck5+/Nkx3.1+ basal cells
Authors: Feng Weiran , Ladewig Erik , Salsabeel Nazifa , Zhao Huiyong , Lee Young Sun , Gopalan Anuradha , Luo Hanzhi , Kang Wenfei , Fan Ning , Rosiek Eric , Masilionis Ignas , Manova-Todorova Katia , Chaligné Ronan , de Stanchina Elisa , Carver Brett S. , Chen Yu , Gao Dong , Leslie Christina S. , Sawyers Charles L.
Published: June 2023

TMPRSS2-ERG translocations are initiating lesions in nearly 50% of human prostate adenocarcinomas, often in conjunction with PTEN loss. In mice, prostate-specific expression of ERG using a Probasin-Cre driver (Pb-Cre4) is sufficient to induce invasive Ck8+ luminal adenocarcinoma with high penetrance in the context of Pten loss. Because TMPRSS2 expression in the human prostate is androgen-regulated and thereby largely restricted to luminal epithelial cells, it has been assumed that luminal cells are the likely cell of origin for TMPRSS2-ERG positive prostate cancers. To gain further support for this hypothesis, we examined the early stages of luminal adenocarcinoma initiation in the Pb-Cre ERG/Pten model at a single cell level. To our surprise, we found a highly proliferative population of ERG+ Ck5+ (a putative basal marker) cells that are enriched at the invasive front in a background of more canonical ERG+/Ck8+/Ck5- luminal tumor cells. We next performed lineage tracing experiments using Ck5-, Ck8- as well as Nkx3.1-Cre drivers, introduced via viral injection or tamoxifen induction, which collectively support the hypothesis that ERG-driven tumors originate in a subset of basal cells defined by Ck5+/Nkx3.1+. This conclusion is further supported by orthotopic transplantation of freshly isolated primary mouse prostate basal (Cd49f high) or luminal (Cd24 high) cells showing that ERG+/Ck8+ tumors arise preferentially from basal cells following ex vivo ERG/Pten activation. Time course experiments in organoids and in vivo show that ERG promotes Ck8+ luminal differentiation from highly proliferative Ck5+ cells, progressing through a Ck5+/Ck8+ intermediate cell state. Collectively, these data implicate a tumor initiating cell population defined by a mix of basal (Ck5) and luminal (Nkx3.1) markers that, under the influence of ERG expression, can expand and invade while retaining full luminal differentiation potential. Our results also suggest that widely held assumptions regarding luminal-specific expression of canonical markers such as Nkx3.1 and Probasin may need revision.

Citation Format: Weiran Feng, Erik Ladewig, Nazifa Salsabeel, Huiyong Zhao, Young Sun Lee, Anuradha Gopalan, Hanzhi Luo, Wenfei Kang, Ning Fan, Eric Rosiek, Ignas Masilionis, Katia Manova-Todorova, Ronan Chaligné, Elisa de Stanchina, Brett S. Carver, Yu Chen, Dong Gao, Christina S. Leslie, Charles L. Sawyers. ERG-driven luminal prostate cancers emerge from Ck5+/Nkx3.1+ basal cells [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 PR007.
Abstract PR013: Unlocking the proteome of metastatic prostate cancer circulating tumor cells
Authors: Drake Justin M. , Sychev Zoi , Horrmann Alec , Smith Kaylee Judith , Galeano-Garces Catalina , Arafa Ali , Heller Nicholas , Ahmadi Mahdi , Hong Jiarong , Ludwig Megan , Hwang Justin , Antonarakis Emmanuel S. , Parthasarathy Jayant
Published: June 2023

In recent years, liquid biopsies have emerged to provide improved insights on the current disease state of a patient, but they generally rely on a small number of protein markers from immunofluorescent staining or cell-free DNA, which provides limited information especially around drug targets. As more targeted therapies and immunotherapies enter the market, selecting the optimal drug target could improve patient outcomes drastically. One way to achieve this goal is to generate multi-omic datasets from the cancer cells in circulation, known as circulating tumor cells (CTCs). In this study, we collaborated with Astrin Biosciences and used their patented isolation technology to enrich CTCs with high purity from the blood of 15 metastatic castration resistant prostate cancer (mCRPC) patients. The enriched CTCs and a patient matched control sample consisting primarily of white blood cells were divided such that RNA and protein could be interrogated from the same patient. Label free unbiased mass spectrometry-based proteomics was used to identify the CTC-enriched proteins and marks the first time a global proteomic assessment has been performed on CTCs from cancer patients. Initial analysis identified over 1,500 peptides corresponding to greater than 500 proteins from each patients’ CTCs; including increased epithelial cell markers in the CTC-enriched sample and increased WBC markers in the control sample. Hallmarks of androgen response and detection of the androgen receptor were also identified in the CTC-enriched proteome. Overall, this study was designed to show the feasibility of obtaining large scale proteomic data from a liquid biopsy and future studies will provide more insight into the clinical utility of such data with a focus on cancer signaling mechanisms and biomarkers. Importantly, as we analyze more patients, we plan to compare the proteomic data with future RNA signatures across mCRPC patients to eventually be able to correlate them with drug response with the overall goal to improve treatment selection and patient outcomes.

Citation Format: Justin M. Drake, Zoi Sychev, Alec Horrmann, Kaylee Judith Smith, Catalina Galeano-Garces, Ali Arafa, Nicholas Heller, Mahdi Ahmadi, Jiarong Hong, Megan Ludwig, Justin Hwang, Emmanuel S. Antonarakis, Jayant Parthasarathy. Unlocking the proteome of metastatic prostate cancer circulating tumor cells [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 PR013.
Table S8 from A Transcriptome-Based Precision Oncology Platform for Patient–Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies
Authors: Mundi Prabhjot S. , Dela Cruz Filemon S. , Grunn Adina , Diolaiti Daniel , Mauguen Audrey , Rainey Allison R. , Guillan Kristina , Siddiquee Armaan , You Daoqi , Realubit Ronald , Karan Charles , Ortiz Michael V. , Douglass Eugene F. , Accordino Melissa , Mistretta Suzanne , Brogan Frances , Bruce Jeffrey N. , Caescu Cristina I. , Carvajal Richard D. , Crew Katherine D. , Decastro Guarionex , Heaney Mark , Henick Brian S. , Hershman Dawn L. , Hou June Y. , Iwamoto Fabio M. , Jurcic Joseph G. , Kiran Ravi P. , Kluger Michael D. , Kreisl Teri , Lamanna Nicole , Lassman Andrew B. , Lim Emerson A. , Manji Gulam A. , McKhann Guy M. , McKiernan James M. , Neugut Alfred I. , Olive Kenneth P. , Rosenblat Todd , Schwartz Gary K. , Shu Catherine A. , Sisti Michael B. , Tergas Ana , Vattakalam Reena M. , Welch Mary , Wenske Sven , Wright Jason D. , Canoll Peter , Hibshoosh Hanina , Kalinsky Kevin , Aburi Mahalaxmi , Sims Peter A. , Alvarez Mariano J. , Kung Andrew L. , Califano Andrea
Published: June 2023

List of available interactomes (gene regulatory networks) that have been generated from RNASeq datasets of patient tumor samples using the ARACNe algorithm.