bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S5 from Glucose Deprivation Promotes Pseudohypoxia and Dedifferentiation in Lung Adenocarcinoma
Authors: Saggese Pasquale , Pandey Aparamita , Alcaraz Martín , Fung Eileen , Hall Abbie , Yanagawa Jane , Rodriguez Erika F. , Grogan Tristan R. , Giurato Giorgio , Nassa Giovanni , Salvati Annamaria , Shirihai Orian S. , Weisz Alessandro , Dubinett Steven M. , Scafoglio Claudio
Published: January 2024

Figure S5
Supplementary Table 4 from Integration of Pan-Cancer Single-Cell and Spatial Transcriptomics Reveals Stromal Cell Features and Therapeutic Targets in Tumor Microenvironment
Authors: Du Yanhua , Shi Jintong , Wang Jiaxin , Xun Zhenzhen , Yu Zhuo , Sun Hongxiang , Bao Rujuan , Zheng Junke , Li Zhigang , Ye Youqiong
Published: January 2024

Supplementary Table 4
Supplementary Table 6 from Small Cell Lung Cancer Plasticity Enables NFIB-Independent Metastasis
Authors: Ko Julie H. , Lambert Kyle E. , Bhattacharya Debadrita , Lee Myung Chang , Colón Caterina I. , Hauser Haley , Sage Julien
Published: January 2024

HOMER analysis CUT and RUN
Supplementary Table 2 from Small Cell Lung Cancer Plasticity Enables NFIB-Independent Metastasis
Authors: Ko Julie H. , Lambert Kyle E. , Bhattacharya Debadrita , Lee Myung Chang , Colón Caterina I. , Hauser Haley , Sage Julien
Published: January 2024

Differentially expressed genes RNA-seq
Supplementary Information from CircMMP2(6,7) Cooperates with β-Catenin and PRMT5 to Disrupt Bone Homeostasis and Promote Breast Cancer Bone Metastasis
Authors: Xu Yingru , Li Xincheng , Zhang Shuxia , Tang Miaoling , Yu Ruyuan , Liao Xinyi , Li Ziwen , Li Man , Chen Suwen , Qian Wanying , Song Libing , Ke Zunfu , Li Jun
Published: January 2024

Supplementary Materials and Methods and Supplemental Figures and Figure legends
Data from Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer
Authors: Ahn Songyeon , Park Jun Hyoung , Grimm Sandra L. , Piyarathna Danthasinghe Waduge Badrajee , Samanta Tagari , Putluri Vasanta , Mezquita Dereck , Fuqua Suzanne A.W. , Putluri Nagireddy , Coarfa Cristian , Kaipparettu Benny Abraham
Published: January 2024

Abstract
Approximately one-third of endocrine-treated women with estrogen receptor alpha–positive (ER+) breast cancers are at risk of recurrence due to intrinsic or acquired resistance. Thus, it is vital to understand the mechanisms underlying endocrine therapy resistance in ER+ breast cancer to improve patient treatment. Mitochondrial fatty acid β-oxidation (FAO) has been shown to be a major metabolic pathway in triple-negative breast cancer (TNBC) that can activate Src signaling. Here, we found metabolic reprogramming that increases FAO in ER+ breast cancer as a mechanism of resistance to endocrine therapy. A metabolically relevant, integrated gene signature was derived from transcriptomic, metabolomic, and lipidomic analyses in TNBC cells following inhibition of the FAO rate-limiting enzyme carnitine palmitoyl transferase 1 (CPT1), and this TNBC-derived signature was significantly associated with endocrine resistance in patients with ER+ breast cancer. Molecular, genetic, and metabolomic experiments identified activation of AMPK-FAO-oxidative phosphorylation (OXPHOS) signaling in endocrine-resistant ER+ breast cancer. CPT1 knockdown or treatment with FAO inhibitors in vitro and in vivo significantly enhanced the response of ER+ breast cancer cells to endocrine therapy. Consistent with the previous findings in TNBC, endocrine therapy–induced FAO activated the Src pathway in ER+ breast cancer. Src inhibitors suppressed the growth of endocrine-resistant tumors, and the efficacy could be further enhanced by metabolic priming with CPT1 inhibition. Collectively, this study developed and applied a TNBC-derived signature to reveal that metabolic reprogramming to FAO activates the Src pathway to drive endocrine resistance in ER+ breast cancer.
Significance:
Increased fatty acid oxidation induced by endocrine therapy activates Src signaling to promote endocrine resistance in breast cancer, which can be overcome using clinically approved therapies targeting FAO and Src.
Integration of Pan-Cancer Single-Cell and Spatial Transcriptomics Reveals Stromal Cell Features and Therapeutic Targets in Tumor Microenvironment
Authors: Du Yanhua , Shi Jintong , Wang Jiaxin , Xun Zhenzhen , Yu Zhuo , Sun Hongxiang , Bao Rujuan , Zheng Junke , Li Zhigang , Ye Youqiong
Published: January 2024

Stromal cells are physiologically essential components of the tumor microenvironment (TME) that mediates tumor development and therapeutic resistance. Development of a logical and unified system for stromal cell type identification and characterization of corresponding functional properties could help design antitumor strategies that target stromal cells. Here, we performed a pan-cancer analysis of 214,972 nonimmune stromal cells using single-cell RNA sequencing from 258 patients across 16 cancer types and analyzed spatial transcriptomics from 16 patients across seven cancer types, including six patients receiving anti–PD-1 treatment. This analysis uncovered distinct features of 39 stromal subsets across cancer types, including various functional modules, spatial locations, and clinical and therapeutic relevance. Tumor-associated PGF+ endothelial tip cells with elevated epithelial–mesenchymal transition features were enriched in immune-depleted TME and associated with poor prognosis. Fibrogenic and vascular pericytes (PC) derived from FABP4+ progenitors were two distinct tumor-associated PC subpopulations that strongly interacted with PGF+ tips, resulting in excess extracellular matrix (ECM) abundance and dysfunctional vasculature. Importantly, ECM-related cancer-associated fibroblasts enriched at the tumor boundary acted as a barrier to exclude immune cells, interacted with malignant cells to promote tumor progression, and regulated exhausted CD8+ T cells via immune checkpoint ligand–receptors (e.g., LGALS9/TIM-3) to promote immune escape. In addition, an interactive web-based tool (http://www.scpanstroma.yelab.site/) was developed for accessing, visualizing, and analyzing stromal data. Taken together, this study provides a systematic view of the highly heterogeneous stromal populations across cancer types and suggests future avenues for designing therapies to overcome the tumor-promoting functions of stromal cells.

Significance:

Comprehensive characterization of tumor-associated nonimmune stromal cells provides a robust resource for dissecting tumor microenvironment complexity and guiding stroma-targeted therapy development across multiple human cancer types.
Phase I Study of ORIC-101, a Glucocorticoid Receptor Antagonist, in Combination with Enzalutamide in Patients with Metastatic Castration-resistant Prostate Cancer Progressing on Enzalutamide
Authors: Abida Wassim , Hahn Andrew W. , Shore Neal , Agarwal Neeraj , Sieber Paul , Smith Matthew R. , Dorff Tanya , Monk Paul , Rettig Matthew , Patel Rupal , Page Anne , Duff Maureen , Xu Rongda , Wang Jian , Barkund Shravani , Pankov Aleksandr , Wang Amber , Junttila Melissa R. , Multani Pratik S. , Daemen Anneleen , Chow Maneval Edna , Logothetis Christopher J. , Morris Michael J.
Published: January 2024

Purpose:

Increased glucocorticoid receptor (GR) signaling is a proposed compensatory mechanism of resistance to androgen receptor (AR) inhibition in metastatic castration-resistant prostate cancer (mCRPC). ORIC-101 is a potent and selective orally-bioavailable GR antagonist.

Patients and Methods:

Safety, pharmacokinetic/pharmacodynamic, and antitumor activity of ORIC-101 in combination with enzalutamide were studied in patients with mCRPC progressing on enzalutamide. ORIC-101 doses ranging from 80 to 240 mg once daily were tested in combination with enzalutamide 160 mg once daily. Pharmacokinetics/pharmacodynamics was assessed after a single dose and at steady state. Disease control rate (DCR) at 12 weeks was evaluated at the recommended phase 2 dose (RP2D).

Results:

A total of 41 patients were enrolled. There were no dose-limiting toxicities and the RP2D was selected as 240 mg of ORIC-101 and 160 mg of enzalutamide daily. At the RP2D, the most common treatment-related adverse events were fatigue (38.7%), nausea (29.0%), decreased appetite (19.4%), and constipation (12.9%). Pharmacokinetic/pharmacodynamic data confirmed ORIC-101 achieved exposures necessary for GR target engagement. Overall, for 31 patients treated at the RP2D, there was insufficient clinical benefit based on DCR (25.8%; 80% confidence interval: 15.65–38.52) which did not meet the prespecified target rate, leading to termination of the study. Exploratory subgroup analyses based on baseline GR expression, presence of AR resistance variants, and molecular features of aggressive variant prostate cancer suggested possible benefit in patients with high GR expression and no other resistance markers, although this would require confirmation.

Conclusions:

Although the combination of ORIC-101 and enzalutamide demonstrated an acceptable tolerability profile, GR target inhibition with ORIC-101 did not produce clinical benefit in men with metastatic prostate cancer resistant to enzalutamide.
Abstract A007: Expression and activity of Rac, Cdc42, and their downstream effector PAK in Puerto Rican pancreatic cancer patients
Authors: Torres-Sanchez Anamaris , Berrios-Rodriguez Jahdiel , Cruz-Rodriguez Jerry , Contreras-Santini Jasmin , Carlo Victor , Dharmawardhane Suranganie
Published: January 2024

Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed after the localized tumor has metastasized, which decreases its survival rate to a grim 3%. Mortality from PDAC is also increasing in Puerto Rico with lower survival rates than in the US. Therefore, it is pivotal to identify viable targets for the late stages of PDAC. The small GTPase Ras is the most mutated oncogene in PDAC. Oncogenic Ras, as well as multiple oncogenic cell surface receptors, activate the related GTPases Rac and Cdc42, which in turn activate p21-activated kinase (PAK) by autophosphorylation (p-PAK), to drive cancer cell invasion, and thus metastasis. Rac and Cdc42 are overexpressed in 21% of PDAC patients and contribute to poor prognosis. To determine the feasibility of treating PDAC with Rac/Cdc42 inhibitors that we are developing, this study aims to identify the p-PAK levels and Rac/Cdc42 expression in PDAC tissue from Puerto Rican patients. The hypothesis is that p-PAK levels, as well as Rac/Cdc42 expression, are selectively elevated in high-grade invasive PDAC. Immunohistochemistry for p-PAK and immunofluorescence for Rac/Cdc42 were conducted in fixed, paraffin-embedded PDAC biopsy samples of Puerto Rican patients. Preliminary results demonstrate that higher p-PAK levels are correlated with stage 3 and stage 4 tissue, and Rac and Cdc42 are expressed in ductal regions of PDAC tissue. Taken together, p-PAK has potential as a diagnostic biomarker for high-grade PDAC and will aid patient stratification in the planned clinical trials for our lead Rac/Cdc42 inhibitor, MBQ-167.

Citation Format: Anamaris Torres-Sanchez, Jahdiel Berrios-Rodriguez, Jerry Cruz-Rodriguez, Jasmin Contreras-Santini, Victor Carlo, Suranganie Dharmawardhane. Expression and activity of Rac, Cdc42, and their downstream effector PAK in Puerto Rican pancreatic cancer patients [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A007.
Abstract A023: Cytokine loss leads to decreased tumor differentiation and a more aggressive phenotype
Authors: Bell Whitney J. , Kren Nancy , Wang Yan , Modliszewski Jennifer , Xu Yi , Guan Meijiang , DelGiorno Kathleen , Yeh Jen Jen , Pylayeva-Gupta Yuliya
Published: January 2024

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers with a 5-year survival rate of only 11% and approximately half the patients present with distant metastasis at the time of diagnosis. PDAC is accompanied by pronounced alterations in stromal responses and immune surveillance programs, which are now recognized as some of the major drivers in PDAC tumor evolution. The role of immune modulators in driving aggressiveness of PDAC is poorly understood. We investigate how the loss of host-derived IL-12 and IL-23 in murine models of pancreatic cancer can lead to changes in changes in tumor morphology, cellular differentiation, and tumor immune microenvironment. In orthotopic tumors isolated from IL-12 and IL-23 knockout mice tumor morphology is altered and appears to be less differentiated. Noticeably, ductal area decreases in tumors from IL-23 and IL-12 knockout mice. Single cell RNA sequencing of tumors isolated from IL-12 and IL-23 knockout mice reveals a cluster of tumor cells with decreased gastric gene expression. Gastric genes such as TFF1, TFF2, MUC5AC, GKN1, and GKN2 have been implicated in pancreatic cancer development, progression, and tumor subtype. The classical pancreatic tumor subtype designation correlates with better differentiated pancreatic tumors as opposed to the more poorly differentiated tumors in the basal subtype. The classical expression signature is characterized by the expression of GATA6 and other epithelial cell terminal differentiation genes and includes several of these gastric genes. We hypothesize that loss of IL-12 and IL-23 leads to loss of tumor differentiation and to a more aggressive phenotype.

Citation Format: Whitney J. Bell, Nancy Kren, Yan Wang, Jennifer Modliszewski, Yi Xu, Meijiang Guan, Kathleen DelGiorno, Jen Jen Yeh, Yuliya Pylayeva-Gupta. Cytokine loss leads to decreased tumor differentiation and a more aggressive phenotype [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A023.
Abstract A026: Senescence driven by pharmacological RAS inhibition potentiates anti-tumor activity of combination therapies in pancreatic cancer
Authors: Broderick Caroline , Mezzadra Riccardo , Jiminez-Sanchez Alejando , Chaves-Perez Almudena , Simon Janelle , Ho Yu-Jui , Sisso Exequiel , Tian Sha , Kulick Amanda , DeStanchina Elisa , Lowe Scott W.
Published: January 2024

Senescence is a form of stable proliferative arrest that occurs in response to various forms of cellular stress. In established cancer, these include unresolved DNA damage triggered by chemotherapeutic agents or irradiation, re-establishment of tumor suppressive programs, and by drugs that target cell cycle progression. Senescent cells take on a “Senescence Associated Secretory Phenotype” or SASP, characterized by increased expression of proinflammatory cytokines and other factors that modulate the tissue environment. The SASP triggers immune cell infiltration and, in the context of cancer, potent antitumor immunity. This implicates the use of senescence-inducing agents clinically and suggests that senescence biology may be harnessed to increase the fraction of patients that respond to immunotherapy. RAS is mutated in over 90% of pancreatic cancers, but until recently, has been considered to be “undruggable” due to its small size and lack of drug binding pockets. Recent advances in chemical biology have led to the development of several mutant isoform-specific and broad-spectrum RAS-GTP inhibitors, which hold great clinical promise. We have found that, in mouse models of pancreatic cancer, the non-covalent broad-spectrum inhibitor RM-042 and the covalent KRASG12D specific inhibitor RM-044 trigger a senescence-like phenotype characterized by cell cycle arrest and increased SASP expression. RAS inhibitor-mediated senescence enhances the immune surveillance of tumor cells, and this effect is potentiated by certain combination agents. Our results suggest that senescence contributes to RAS inhibitor efficacy in PDAC and reveal strategies to harness the immune system to improve therapy outcomes and circumvent resistance.

Citation Format: Caroline Broderick, Riccardo Mezzadra, Alejando Jiminez-Sanchez, Almudena Chaves-Perez, Janelle Simon, Yu-Jui Ho, Exequiel Sisso, Sha Tian, Amanda Kulick, Elisa DeStanchina, Scott W. Lowe. Senescence driven by pharmacological RAS inhibition potentiates anti-tumor activity of combination therapies in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A026.
Abstract A047: ARID1A mutations drive metastasis of pancreatic neuroendocrine tumors and pancreatic adenocarcinomas by activation of NTN1/UNC5B signaling
Authors: Harris Chris , Nezhad Muhammad Sadeqi , Asad Asra , Narrow Wade , Prela Orjola , Carpizo Darren
Published: January 2024

ARID1A, a component of the SWI/SNF DNA chromatin remodeling complex, is recurrently mutated in many types of cancer. In pancreatic ductal adenocarcinomas (PDACs), mutations in ARID1A are found in 6-15% of cases, and ARID1A expression has previously been shown to associate with poor patient outcome. But the effect of ARID1A mutations on pancreatic neuroendocrine tumors (PNETs) has not been previously studied, and we observed that ARID1A mutations were 15-fold more common in patients with metastatic PNETs than in patients with localized disease, indicating the importance of ARID1A mutations in driving the progression of what is normally an indolent disease. We have studied ARID1A mutations in models of both PDACs and PNETs and observe that in both diseases ARID1A mutations associated with several properties common to metastatic cells including epithelial-mesenchymal transition, in vitro invasiveness, and insensitivity to anoikis. Mutation of ARID1A activated expression of the axonal guidance protein NTN1 in both PDACs and PNETs, and interaction between the NTN1 ligand and its dependence receptor UNC5b were required for the metastatic properties of ARID1A mutant cells. Treatment with a NTN1 inhibitor, NP137, overcame insensitivity to anoikis, while deletion or knockdown of UNC5b caused ARID1A mutant cells to undergo a mesenchymal-epithelial transition. In vivo, metastasis of PDACs was blocked by NP137 treatment, or by deletion of UNC5b. NP137 is currently in clinical trials for many tumor types including PDACs, and our data strongly indicate that NP137 should also be tested in patients with metastatic PNETs.

Citation Format: Chris Harris, Muhammad Sadeqi Nezhad, Asra Asad, Wade Narrow, Orjola Prela, Darren Carpizo. ARID1A mutations drive metastasis of pancreatic neuroendocrine tumors and pancreatic adenocarcinomas by activation of NTN1/UNC5B signaling [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A047.
Abstract A053: The effects of chemotherapy on B cells and T cells in blood and tumor tissue in patients with pancreatic cancer – from diagnosis to terminal disease
Authors: Jacobsen Hedda
Published: January 2024

Pancreatic cancer (PC) is a devastating disease and is almost always synonymous with a poor outcome. Chemotherapy is the standard treatment and is administered in either an adjuvant or palliative setting. However, nearly all patients, regardless of treatment intent, eventually develop chemoresistance. Little is known about the events causing chemoresistance, but increased knowledge is essential for improving patient outcomes. The aim of this study was to increase the knowledge of how the immune system, locally and systemically, is affected by chemotherapy and how this influences patient outcomes. Hence, immunohistochemical analysis of T and B cell prevalence in post-mortem tumor tissue was performed and combined with flow cytometric analysis of the dynamics of circulating T and B cell subsets during chemotherapy in nine PC patients enrolled in a clinical study. Despite the small number of patients included in this study, some interesting results were found. A high number of tertiary lymphoid-like structures (TLLSs) in the primary tumor was associated with shorter survival, which is contradictory to previous findings and possibly indicates a negative effect of chemotherapy on TLLSs. Certain subpopulations of T and B cells exhibited variations during treatment, possibly in response to chemotherapy. The frequency of T cells in blood also tended to correlate inversely with the frequency in primary tumor and liver metastases. Overall, this exploratory study provides insights into how the immune system in PC is affected by chemotherapy. Further study is warranted to shed more light on the intrinsic chemoresistance of PC and to identify new therapeutic strategies.

Citation Format: Hedda Jacobsen. The effects of chemotherapy on B cells and T cells in blood and tumor tissue in patients with pancreatic cancer – from diagnosis to terminal disease [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A053.
Abstract A059: Targeting pancreatic cancer metabolic dependencies through glutamine antagonism
Authors: Encarnacion-Rosado Joel , Kimmelman Alec C. , Wild Robert
Published: January 2024

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest types of cancer. A factor that contributes to the poor prognosis of the disease is the complex tumor microenvironment (TME). The PDAC TME is composed of excessive fibrosis and desmoplasia, which creates a harsh environment resulting in hypoxia and altered nutrient availability. To promote survival and proliferation in this environment, PDAC cells can reprogram glutamine (Gln) metabolism. Previous studies have demonstrated that PDAC cells use Gln to support proliferation and redox balance. However, earlier attempts to inhibit Gln metabolism using glutaminase inhibitors resulted in rapid metabolic reprogramming and therapeutic resistance. We hypothesized that a Gln analogue, such as 6-Diazo-5-oxo-L-norleucine (DON), could broadly target Gln metabolism in PDAC and prevent rapid adaptation. Indeed, DON treatment led to a significant decrease in PDAC proliferation and a profound reduction of various metabolites involved in central carbon and nucleotide metabolism, suggesting that DON creates a metabolic crisis. In addition, we observed a significant decrease in tumor growth in various in vivo models (syngeneic, immunodeficient and PDXs) using DRP-104 (sirpiglenastat), a novel pro-drug version of DON that was designed to circumvent DON associated GI toxicity and allow the therapeutic exploration of broad Gln antagonism. Mechanistically, we found that ERK signaling is increased as a compensatory mechanism through the increased activity of receptor tyrosine kinases (RTKs). Combinatorial treatment of DRP-104 and Trametinib (MEK1/2) inhibitor led to a significant increase in survival in a syngeneic model PDAC. Taken together, these pre-clinical results suggest that broadly targeting Gln metabolism could provide a new therapeutic avenue for PDAC and that the combination with an ERK signaling pathway inhibitor could further improve the therapeutic outcome.

Citation Format: Joel Encarnacion-Rosado, Alec C. Kimmelman, Robert Wild. Targeting pancreatic cancer metabolic dependencies through glutamine antagonism [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A059.
Abstract A095: ZNF274 suppresses the mesenchymal state, thereby causing intrinsic resistance to CDK7 inhibition
Authors: Gianopulos Jessica , Wallace-Povirk Adrianne , Kugel Sita
Published: January 2024

Pancreatic Ductal Adenocarcinoma (PDA) can be characterized by two distinct transcriptional subtypes: classical and basal. The basal PDA subtype is more aggressive and has the worst overall survival. We have previously shown that the histone deacetylase (HDAC) Sirtuin 6 (SIRT6), a marker of the classical PDA subtype, can control sensitivity to CDK7 inhibitors. Interestingly, SIRT6 is part of the KAP1 repressive complex where it functions as an HDAC. This complex functions to maintain heterochromatin at specific regions of the genome by removing marks of open chromatin and installing marks of repressive chromatin with histone methyltransferases (HMT) and DNA methyltransferases (DNMT). The complex relies on a KRAB-Zinc Finger protein to bind DNA directly and modify chromatin at those regions. Since we found that SIRT6 can control sensitivity to CDK7 inhibition, we hypothesized that the KAP1 repressive complex is crucial for maintaining subtype-specific chromatin states and that manipulation of any part of this complex could alter subtype, thereby changing sensitivity to CDK7 inhibition. In a survey of basal and classical PDA cell lines, we found that the KRAB-Zinc Finger ZNF274 showed substantial differential expression, similar to SIRT6, and correlated with overall patient survival. We validated ZNF274 expression in PDA cell lines and organoids by western blot and immunofluorescence and found that classical PDA expressed high levels of ZNF274. Next, we investigated how loss of ZNF274 would affect classical PDA cells and found that knockdown of this protein induced an epithelial-to-mesenchymal (EMT) transition through increased ZEB1 expression. We analyzed protein and RNA expression of more EMT regulators and identified morphological changes representative of EMT. Therefore, this induction of EMT upon loss of ZNF274 could be initiating a subtype switch from classical PDA to basal. To determine if loss of ZNF274 and induction of the mesenchymal state could sensitize cells to CDK7 inhibition as we have previously shown, we performed ZNF274 knockdown in classical PDA and saw a dramatic increase in sensitivity to CDK7 inhibitors. Therefore, we have shown the KAP1 repressive complex to be important in regulating cell state and sensitivity of classical PDA to CDK7 inhibitors which we hope to exploit to improve patient responses to CDK7 inhibition therapy.

Citation Format: Jessica Gianopulos, Adrianne Wallace-Povirk, Sita Kugel. ZNF274 suppresses the mesenchymal state, thereby causing intrinsic resistance to CDK7 inhibition [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A095.
Abstract A100: KRAS inhibition targets and depends on pro-oncogenic HuR in PDAC cells
Authors: Halamish Hen , Bush Michaela , Smith Alexander , Sears Rosalie , Brody Jonathan
Published: January 2024

The Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation is found in more than 90% of patients with pancreatic ductal adenocarcinomas (PDACs), making it a prime target for therapeutic drug development. HuR (ELAVL1) has been extensively studied in the context of PDAC and also plays a key role in PDAC progression and chemoresistance. In recent years, researchers have shed light on the specific role of the HuR protein in PDAC and its relationship with KRAS signaling. Using in KRASG12D – mutant patient derived models, cell lines derived from GEMM models, and conventional cell lines, we found that HuR CRISPR knock out lines showed more than 80-fold resistance to MRTX1133 (a KRAS inhibitor targeted against G12D mutation) compared to wild type cells. Furthermore, western blot and immunofluorescence studies demonstrated that therapeutic inhibition of KRAS, inhibited HuR protein expression and subcellular localization in as early as 3 hours post-treatment. Furthermore, HuR protein levels decreased post-treatment even under nutrient starvation. Herein, we show that the presence of HuR is necessary for the efficacy of KRAS targeting and Kras inhibition can rapidly degrade HuR protein levels and its active subcellular localization. Mechanistic studies determining the molecular interaction between HuR and KRAS and KRAS related proteins and mRNAs are underway. Taken together with ongoing studies, we are exploring the importance of HuR as a key downstream target of KRAS’ oncogenic activity and if the loss of HuR may be a potent, PDAC therapeutic resistance mechanism. Understanding the interplay between KRAS and HuR could offer a novel strategy to disrupt the oncogenic KRAS signaling cascade and overcome the potential inherent resistance of KRAS-mutant PDACs to promising, KRAS-targeted therapies.

Citation Format: Hen Halamish, Michaela Bush, Alexander Smith, Rosalie Sears, Jonathan Brody. KRAS inhibition targets and depends on pro-oncogenic HuR in PDAC cells [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A100.
Abstract A102: Secreted frizzled related-protein 2 is prognostic for survival in pancreatic cancer
Authors: Hsu Lillian , Siegel Julie , Nasarre Patrick , Mukherjee Rupak , Gormley Meghan , Richardson Bailey , Morningstar Jordan , Khan Imran , Hilliard Eleanor , O’Bryan John , Helke Krist , Spruill Laura , Dolloff Nathan , Klauber-Demore Nancy
Published: January 2024

INTRODUCTION: Secreted frizzled-related protein 2 (SFRP2) is overexpressed in several tumor types and blocks tumor apoptosis, increases angiogenesis, and promotes T-cell exhaustion. It has also been shown to be associated with fibrosis in non-neoplastic pathologies. We hypothesize SFRP2 is prognostic for survival and associated with PDAC fibrosis and mesenchymal transformation. METHODS: SFRP2 gene expression and protein levels in patients with PDAC were analyzed using NCI’s The Cancer Genome Atlas (TCGA) data and data from resected tumors analyzed for protein levels by western blot. Disease free survival (DFS) and overall survival (OS) were analyzed using Kaplan Meier test. The association of stroma content and SFPR2 RNA expression in human PDAC was studied using Spearman correlation between the ESTIMATE algorithm stromal score and TCGA data. The GEPIA tool was used to compare SFRP2 mRNA levels between PDAC and normal pancreas tissue. Immunohistochemistry (IHC) for SFRP2 in KPC PDAC tumors were correlated with fibrosis stains Picrosirus red and Massone trichome. The role of SFRP2 in mesenchymal transformation was assessed by western blot in fibroblasts. RESULTS: TCGA RNAseq analysis of SFRP2 expression showed highest SFRP2 mRNA levels in pancreatic cancer out of 32 cancer types. GEPIA analysis of PDAC (n=179) and normal pancreas (n=177) mRNA data showed higher levels of SFRP2 mRNA in PDAC compared to normal pancreas (p<.01). High SFRP2 mRNA levels were associated with decreased disease-free survival hazard ratio = 2.6; p=0.0097). PDAC tissue showed higher SFRP2 protein compared to matched normal-adjacent tissue (n=24, p=0.0003). High SFRP2 expression was associated with decreased OS (p=0.0158. The ESTIMATE stromal score correlated with SFRP2 expression in human PDAC (Spearman correlation coefficient 0.81). Fibrosis levels in KPC PDAC tumors correlated with SFRP2 IHC (Spearman correlation coefficient 0.75). Fibroblasts treated with SFRP2 and TGFβ showed higher mesenchymal markers compared to untreated control. CONCLUSIONS: SFRP2 is increased in PDAC, associated with tumor fibrosis, and prognostic for survival. SFRP2 is a novel therapeutic target in PDAC.

Citation Format: Lillian Hsu, Julie Siegel, Patrick Nasarre, Rupak Mukherjee, Meghan Gormley, Bailey Richardson, Jordan Morningstar, Imran Khan, Eleanor Hilliard, John O’Bryan, Krist Helke, Laura Spruill, Nathan Dolloff, Nancy Klauber-Demore. Secreted frizzled related-protein 2 is prognostic for survival in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A102.
Abstract B013: Effect of aging on pancreatic cancer progression
Authors: Bhullar Deepika , Maganti Swetha , Zhang Yijuan , Galapate Cheska Marie , Murad Rabi , Adams Peter D. , Commisso Cosimo
Published: January 2024

Pancreatic ductal adenocarcinoma (PDAC) is a highly invasive disease mainly seen in older adults. Most pancreatic cancer cases occur in individuals who are over the age of 60, and the risk continues to increase with each decade of life, with the median age at diagnosis for PDAC being around 70 years old. Why age is a significant risk factor in PDAC remains unanswered question. To examine the impact of organismal age on PDAC progression, we used a syngeneic orthotopic mouse model of PDAC in young and old animals. We found that the growth of primary tumors was significantly enhanced in the older mice indicating that organismal age can influence tumor progression. We also found that older mice had increased metastatic tumor burden in the liver, intestines and diaphragm. To gain a comprehensive view of how age might be affecting PDAC progression, we performed transcriptomics on the tumors derived from young or old animals. Strikingly, using gene set enrichment analysis (GSEA), we found that epithelial-mesenchymal transition (EMT) and extracellular matrix (ECM) molecule deposition-related signatures were enriched in the old mice, suggesting that the enhanced metastasis that we observed in old animals could be related to changes in the ECM. Moreover, we also identified various immune cell signatures that were enriched in the old or young mice, suggesting that the immune contexture dramatically changes depending on the age of the organism. These ECM and immune cell signatures were validated histologically. Based on these preliminary data, our working hypothesis is that the tumor stroma in old versus young organisms plays a critical role in PDAC progression, and we are employing various in vitro and in vivo techniques to test this idea.

Citation Format: Deepika Bhullar, Swetha Maganti, Yijuan Zhang, Cheska Marie Galapate, Rabi Murad, Peter D. Adams, Cosimo Commisso. Effect of aging on pancreatic cancer progression [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B013.
Abstract B024: Hypoxia at 3D organoid establishment selects essential subclone within heterogenous pancreatic cancer
Authors: Kumano Koichiro , Nakahashi Hiromitsu , Louphrasitthiphol Pakavarin , Kuroda Yukihito , Miyazaki Yoshihiro , Shimomura Osamu , Hashimoto Shinji , Akashi Yoshimasa , Mathis Bryan James , Kim Jaejeong , Owada Yohei , Oda Tatsuya
Published: January 2024

Hypoxia is a key microenvironment associated with malignant traits, including epithelial-mesenchymal transition (EMT) and chemotherapy resistance. Pancreatic ductal adenocarcinoma (PDAC) is extremely hypoxic due to hypovascularity and abundant stromal proliferation. This severe condition accelerates the emergence of hypoxia-adapted cells, which contaminate PDAC as a heterogeneous population. Thus, analyzing hypoxia-adapted cells should be prioritized in analyzing/developing PDAC therapeutic strategies. Recently, 3D organoid culture has been widely used to simulate various organ cancers, featuring precise control with respect to cellular selection through diverse culture conditions. However, as the technology of single-cell analysis has revealed more details of the heterogeneity, the current 3D organoid culture system was also known to have limitation that the system has some potential selection bias. Although several selection biases have been identified, very few reports have focused on oxygen concentrations as a selection bias, leaving room for intervention. To overcome the potential selection bias, we focused on oxygen concentration during the establishment of 3D organoids. We subjected identical PDAC surgical samples to normoxia (O2 20%) or hypoxia (O2 1%) from primary culture, yielding glandular and solid organoid morphology, respectively. Pancreatic cancer organoids established under hypoxia displayed higher expression of EMT-related proteins, a Moffitt basil-like subtype transcriptome, and higher 5-FU resistance in contrast to established organoids under normoxia. We suggest that hypoxia during organoid establishment efficiently selects for hypoxia-adapted cells possibly responsible for PDAC malignant traits, facilitating a fundamental source for elucidating and developing new treatment strategies against recalcitrant PDAC.

Citation Format: Koichiro Kumano, Hiromitsu Nakahashi, Pakavarin Louphrasitthiphol, Yukihito Kuroda, Yoshihiro Miyazaki, Osamu Shimomura, Shinji Hashimoto, Yoshimasa Akashi, Bryan James Mathis, Jaejeong Kim, Yohei Owada, Tatsuya Oda. Hypoxia at 3D organoid establishment selects essential subclone within heterogenous pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B024.
Abstract B026: αvβ5 Integrin serves as a tumor-specific marker for immunosuppressive regulatory T cells in pancreatic cancer
Authors: Kunisada Yuki , Suzuki Kodai , Miyamura Norio , Eikawa Shingo , de Mendoza Tatiana Hurtado , Mose Evangeline S. , Lu Caisheng , Kuroda Yukihito , Ruoslahti Erkki , Lowy Andrew M. , Sugahara Kazuki N.
Published: January 2024

Regulatory T cells (Tregs) contribute to the immunosuppressive nature of pancreatic ductal adenocarcinoma (PDAC). Systemic depletion of Tregs can enhance anti-tumor T cell immunity, but can also cause unwanted autoimmune complications. A tumor-specific Treg-targeted therapy that effectively and safely enhances anti-tumor immunity for PDAC treatment remains an unmet need. We have recently found that αvβ5 integrin is expressed on Tregs that reside in the PDAC, but not those in the spleen, suggesting that the integrin can serve as a targetable marker for tumor-resident Tregs. Indeed, long-term treatment with the iRGD tumor-penetrating peptide, which effectively targets αvβ5+ cells in PDAC tissue, depleted Tregs in a tumor-specific manner leading to a significant expansion of CD8+ T cells in transgenic and syngeneic PDAC mouse models. αvβ5+ Tregs were induced from both naïve CD4+ T cells and naturally occurring Tregs. T cell receptor stimulation was found to be the common inducer of αvβ5+ Tregs. αvβ5+ Tregs formed a subpopulation of CCR8+ Tregs, which are preferentially found in the tumor tissue of various cancer types. Our most recent data show that the αvβ5 integrin marks a highly immunosuppressive fraction of the CCR8+ Tregs, suggesting that targeting αvβ5+ Tregs can lead to effective depletion of immunosuppressive Tregs in a tumor-specific manner.

Citation Format: Yuki Kunisada, Kodai Suzuki, Norio Miyamura, Shingo Eikawa, Tatiana Hurtado de Mendoza, Evangeline S. Mose, Caisheng Lu, Yukihito Kuroda, Erkki Ruoslahti, Andrew M. Lowy, Kazuki N. Sugahara. αvβ5 Integrin serves as a tumor-specific marker for immunosuppressive regulatory T cells in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B026.
Abstract B030: Spatial coupling of microbes and immune cells shapes the tumor microenvironment in human cancers
Authors: Li Yan , Chang Renee B. , Stone Meredith L. , Xue Yuqing , Coho Heather , Markowitz Kelly , Patel Dhruv , Herrera Veronica M. , Li Joey H. , Delman Devora , Zhang Liti , Choi-Bose Shaanti , Giannone Michael , Lee Jae W. , Beatty Gregory
Published: January 2024

Microbes play a crucial role in the tumor microenvironment, yet the factors governing their presence within tumors remain poorly understood. In this study, we employed advanced in situ spatial-profiling technologies to investigate the relationship between microbial and immune cell heterogeneity in human lung and pancreas cancers. We observed a spatial coupling between microbes and immune cells, which was also replicated in mouse models of pancreatic cancer. Within the tumor, distinct niches characterized by T cell abundance or scarcity exhibited varied microbial diversity and compositions associated with immunologically active and quiescent phenotypes. Interestingly, gut microbiome are similar between mice bearing T cell- enriched or T cell-poor pancreas tumors. Depletion of intra-tumoral bacteria resulted in reduced tumor growth specifically in T cell-poor tumors and altered the phenotype and presence of myeloid and B cells in T cell-enriched tumors, without affecting T cell infiltration. Conversely, depletion of T cells disrupted the immunological state of tumors and led to a decrease in intra-tumoral bacteria. Our findings highlight a tight interplay between microbes and T cells in the tumor microenvironment, where spatially defined immune-microbial communities differentially influence tumor biology.

Citation Format: Yan Li, Renee B. Chang, Meredith L. Stone, Yuqing Xue, Heather Coho, Kelly Markowitz, Dhruv Patel, Veronica M. Herrera, Joey H. Li, Devora Delman, Liti Zhang, Shaanti Choi-Bose, Michael Giannone, Jae W. Lee, Gregory Beatty. Spatial coupling of microbes and immune cells shapes the tumor microenvironment in human cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B030.
Abstract B035: Investigating the roles of GLI transcription factors in the pancreatic cancer microenvironment
Authors: Medina-Cabrera Paola Isabel , Scales Michael , Steele Nina , Allen Benjamin , di Magliano Marina Pasca
Published: January 2024

Pancreatic ductal adenocarcinoma (PDA) remains a difficult cancer to treat due to an extensive and complex tumor microenvironment. In particular, intercellular signaling between tumor cells, fibroblasts and immune cells is a key contributor to pancreatic tumor growth. One of these signals, the Hedgehog (HH) pathway, is a known feature of PDA. Pancreatic tumor cells secrete HH ligands, which signal in a paracrine fashion to fibroblasts in the tumor microenvironment. Notably, the role of HH signaling is complicated, with reports suggesting both tumor-promoting and tumor-restraining functions in pancreatic cancer. GLI proteins (GLI1-3) are the transcriptional effectors of the HH pathway; their contribution to pancreatic tumor growth is equally complex. This study seeks to investigate the contribution of GLI1-3 in PDA progression. Our lab has demonstrated that Gli1-3 are expressed in pancreatic fibroblasts and that all three Glis functionally contribute to pancreatic cancer progression through effects on immune cell infiltration. To further explore the mechanisms of GLI function, we have generated a novel mouse model carrying endogenous, epitope-tagged Gli alleles (Gli1FLAG/FLAG;Gli2HA/HA;Gli3V5/V5). This model will allow us to define GLI protein processing and localization as well as the identification of target genes to elucidate the contribution of GLI-driven transcriptional programs that regulate tumor immune infiltration in PDA.

Citation Format: Paola Isabel Medina-Cabrera, Michael Scales, Nina Steele, Benjamin Allen, Marina Pasca di Magliano. Investigating the roles of GLI transcription factors in the pancreatic cancer microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B035.
Abstract B037: Anti-fibrotic FAK ‘priming’ to improve contemporary chemotherapy in pancreatic cancer
Authors: Murphy Kendelle J. , Reed Daniel A. , Chambers Cecilia R. , Channon Lily M. , Pajic Marina , Herrmann David , Timpson Paul
Published: January 2024

Pancreatic ductal adenocarcinoma (PDAC) is a highly metastatic, chemo-resistant malignancy and is characterized by a dense, desmoplastic stroma that increases the biomechanical force load on cancer cells and is thought to both promote and restrict disease advancement. Using the p53 mutant KPC mouse model of PDAC, we visualized transient manipulation of focal adhesion kinase (FAK), which integrates bidirectional cell-environment signalling. The fluorescent ubiquitination-based cell cycle indicator (FUCCI) cell cycle reporter was used during intravital (in vivo) imaging to monitor dynamic changes in FAK activity, stromal biomechanics and gemcitabine/Abraxane-induced effects. Critically, micropatterned pillar plates and stiffness-tuneable matrices were used to pinpoint the contribution of mechanical environmental cues to chemo-sensitization, while fluid flow– induced shear stress assessment, patient-derived matrices, and personalized in vivo models allowed us to deconstruct how FAK inhibition can reduce PDAC spread. In a precision medicine approach, stratification of PDAC patient samples via Merlin status revealed a subset of patients that are likely to respond to FAK priming before chemotherapy. This dataset has led to the establishment of a Phase II clinical trial of first- line FAK inhibition in combination with Gemcitabine/Abraxane in PDAC Patients (NCT05355298).

Citation Format: Kendelle J. Murphy, Daniel A. Reed, Cecilia R. Chambers, Lily M. Channon, Marina Pajic, David Herrmann, Paul Timpson. Anti-fibrotic FAK ‘priming’ to improve contemporary chemotherapy in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B037.