Drivers Of Pancreatic Ductal Adenocarcinoma Research Articles

Abstract 3300: Dual inhibition of PIKfyve and KRAS/MAPK as a potential for therapeutic strategy for pancreatic ductal adenocarcinoma

Abstract Background: PIKfyve is a lipid kinase that serves as the single source for PI(3,5)P2, a critical molecule for lysosome functions, including autophagy. Pancreatic Ductal Adenocarcinoma (PDAC) is known to utilize autophagy as well as other lysosome functions to survive in its harsh microenvironment. Considering the role of PIKfyve in autophagy, we hypothesized that PIKfyve is important for PDAC pathophysiology. Indeed, we screened multiple cell lines of different cancer lineages and found that PDAC cell lines were highly sensitive to PIKfyve inhibitors apilimod and ESK981. Given these results, we aimed to establish PIKfyve inhibition as a therapeutic strategy for PDAC. Importantly, this idea is rapidly translatable as both apilimod and ESK981 have both cleared phase-1 clinical trials. Additionally, PDAC nearly ubiquitously harbors a mutation in KRAS, leading to the overactivation of the KRAS-RAF-MEK-ERK pathway, which is known to be the driver of PDAC. Recent reports showed that inhibition of this pathway results in induction of autophagic flux as a protective mechanism in PDAC. Thus, we aimed to investigate the therapeutic potential of PIKfyve inhibition in blocking protective autophagy induced by KRAS/MAPK inhibition. Methods and results: In order to determine the potential of PIKfyve inhibition as a therapeutic for PDAC treatment, we first established that PIKfyve inhibition disrupts the autophagic flux in cells. Specifically, we used PIKfyve inhibitors ESK981 and apilimod as well as CRISPRi-mediated knockdown and saw a decrease in autophagic flux through western blot and GFP-LC3-RFP-LC3∆G-based autophagic flux probe analyses. Finally, PIKfyve inhibition decreased cell viability with IC50s in the nanomolar range.To evaluate the potential of combined inhibition of KRAS/MAPK and PIKfyve, we first confirmed that genetic or pharmacological KRAS/MAPK perturbation indeed increases autophagic flux utilizing the autophagic flux probe. Importantly, we found that PIKfyve inhibition attenuates the autophagic flux induced by KRAS/MAPK inhibition. Moreover, we determined that dual inhibition of PIKfyve and KRAS/MAPK resulted in synergistic growth inhibition employing CellTiter-Glo-based synergy assays. Further, to investigate the in vivo potential of this combination, we utilized a syngeneic orthotopic model of PDAC. Surprisingly, most mice were cured when treated with both ESK981 and trametinib while each individual treatment only modestly decreased tumor burden. Additionally, we established a patient-derived xenograft model where mice treated with a combination of ESK981 and trametinib (MEK inhibitor) or ESK981 and MRTX-1133 (KRASG12D inhibitor) displayed substantial tumor regression in comparison to single treatment or control groups. Taken together, the dual inhibition of PIKfyve and KRAS holds promise as a therapeutic strategy for PDAC treatment. Citation Format: Jasmine P. Wisniewski, Caleb Cheng, Bailey Jackson, Ahmet Korkaya, Sydney Peters, Yuanyuan Qiao, Costas A. Lyssiotis, Arul M. Chinnaiyan. Dual inhibition of PIKfyve and KRAS/MAPK as a potential for therapeutic strategy for pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3300.

Abstract 1581: Colony-stimulating factor-1 receptor as a potential therapeutic target in pancreatic ductal adenocarcinoma

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is associated with poor prognosis, rising incidence and suffers from limited existing treatment options. Currently, salient features of PDAC are being investigated that can potentially predict immunotherapy outcomes, to identify small patient populations that can benefit from such strategies. Preliminary studies show that colony-stimulating factor-1 receptor (CSF1R), a surface receptor tyrosine kinase that drives survival, function, proliferation and differentiation of several myeloid lineage cell types can be a potentially interesting target for combination immunotherapy. Methods: PDAC patients from the TCGA PanCancer Atlas were stratified into CSF1Rhi and CSF1Rlo cohorts and clinically relevant characteristics were compared between the two. The mRNA expression of CSF1R and immunological markers of interest were evaluated and Gene Set Enrichment Analysis (GSEA) was run on the two groups to analyze differential expression of gene sets. Results: mRNA expression z-scores were used to classify 129 patient samples in the TCGA PanCancer Atlas dataset into CSF1Rhi (z-score>1, n=20) and CSF1Rlo (z-score<0, n=109) cohorts. Both have similar disease staging, MSI MANTIS scores, tumor mutation burden, median diagnosis age, sex and race distribution. However, the CSF1Rhi cohort has a distinct, non-conventional PDAC driver gene mutation profile (genomic alteration frequencies in CSF1Rhi vs CSF1Rlo cohorts respectively: a) KRAS: 30% vs 73% b) CDKN2A: 15% vs 57% and c) SMAD4: 5% vs 42%) (p-value<0.01 for each). CSF1R correlates with markers of CD8+ T-cell function (R2 values: CD8A: 0.683, GZMB: 0.508, PRF1: 0.673), CD8+ T-cell infiltration (CXCL9: 0.596, CXCL10: 0.483, CCL5: 0.666) and expression of immune checkpoint genes (PDCD1: 0.602, CD274: 0.544, CTLA4: 0.613). CD8A, GZMB, PRF1, CXCL9, CXCL10, CCL5, PDCD1, CD274, CTLA4 are significantly upregulated in the CSF1Rhi group (log2Fold changes respectively: 2.07, 1.57, 1.48, 2.51, 1.71, 1.75, 1.63, 1.34, 1.80). GSEA against the hallmark gene set database shows that KRAS signaling, Inflammatory response, IL6 JAK STAT3 and Interferon-gamma signaling are significantly upregulated in the CSF1R high patient group (FDR q-value <0.01 for each). Conclusion: Preliminary in silico analysis suggests that PDAC patients with higher levels of CSF1R may be more immune infiltrated. Future studies will evaluate the potential of CSF1R as a biomarker to identify an immune infiltrated subset of PDAC patients ex vivo and the mechanism of immune infiltration in CSF1Rhi PDACs in vivo. Citation Format: Somak Chaudhuri, Dustin A. Deming, Cheri A. Pasch, Katherine A. Johnson, Chelsie K. Sievers, Philip B. Emmerich. Colony-stimulating factor-1 receptor as a potential therapeutic target in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1581.

Abstract A065: Lineage tracing oncogenic isoforms of HER2 in a mouse model of pancreatic cancer

Abstract Among the numerous clinical challenges of pancreatic ductal adenocarcinoma (PDAC) is the eventual development of therapeutic resistance. Although previous studies report that only about 3% of PDAC cases are HER2 gene amplified, as many as 82% of PDAC tumors may have HER2 overexpressed. Anti-HER2 therapy with trastuzumab has yielded tremendous therapeutic success in breast cancer and multiple gastrointestinal malignancies, however minimal benefit is found in PDAC. Experimental mouse models have demonstrated initiation and acceleration of pancreatic tumorigenesis through overexpression of activated mutant HER2, yet the role of HER2 alone as a driver of PDAC and treatment resistance is still unknown. Multiple HER2 isoforms exist that are generated either via alternative splicing and loss of exon 16 (d16 HER2) or through N-terminal truncations (p95 HER2). These isoforms are implicated in differential responses to anti-HER2 therapy in the breast. Previously we described a HER2+ cancer rainbow mouse model in which human wild-type HER2 (WT HER2), d16 HER2, and p95 HER2 were expressed in the same mouse and lineage traced through co-expression of fluorescent protein reporters. Studies in the mammary gland revealed that each isoform drives distinct tumor phenotypes. Herein, we hypothesize that these isoforms drive HER2 positive PDAC. HER2 Crainbow mice were crossed with mice expressing PDX1-Cre recombinase to initiate recombination and expression of each fluorescently labelled HER2 isoform during pancreas development. PDX1-Cre/HER2 Crainbow (PHBOW) mice were followed for up to one year and sacrificed to lineage trace each isoform and register HER2 lineages with histopathology. Within our pilot cohort, early-stage pre-malignant pancreatic intraepithelial neoplasia (PanIN-1) was observed in 75% of PDAC HER2bow mice as early as five weeks. By one year, 50% demonstrated high grade PanIN (i.e. PanIN-3) and features of early invasion. Although WT HER2 was expressed abundantly throughout the pancreas, lineage tracing revealed WT HER2 was not found in pre-malignant lesions. Conversely, the pre-malignant PanIN lesions and early invasive histopathologic features traced to d16 HER2 expressing cells, while p95 HER2 traced with areas of acinar-to-ductal metaplasia, lesions known to be early initiators of pancreatic dysplasia. Our data show how the oncogenic HER2 isoforms, and not WT HER2, are able to drive PanIN lesions and, at lower frequency, invasive PDAC after one year. Future work seeks to complete HER2 Crainbow lineage tracing in PHBOW mice, test HER2 targeted therapy in PHBOW mice, and quantify HER2 isoforms in HER2+ human PDAC cases. Citation Format: Elishama N. Kanu, Joelle Sills, Rebecca Shelley, Joshua D. Ginzel, Joseph Fernandes, Ashley A. Fletcher, Peter J. Allen, Daniel P. Nussbaum, Joshua C. Snyder. Lineage tracing oncogenic isoforms of HER2 in a mouse model of 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 A065.

Abstract B092: CDK8 and CXCL2 remodel the tumor microenvironment to contribute to KRASG12D small molecule inhibition resistance in pancreatic ductal adenocarcinoma

Abstract Mutations in KRAS are a dominant driver of pancreatic ductal adenocarcinoma (PDAC), with over 50% of PDAC patients presenting with KRASG12D mutations. The recent development of small molecule inhibitors targeting KRASG12D has enabled effective targeting of mutant KRAS signaling and suppression of tumor growth; however, the contribution of the tumor microenvironment to the therapeutic efficacy of KRASG12D inhibition and mechanisms of resistance to KRASG12D suppression remain to be fully elucidated. Here, we employed spatial transcriptomics and proteomics to evaluate cancer cell intrinsic and extrinsic responses to KRASG12D inhibition with MRTX1133. MRTX1133 treatment was associated with increased antigen presenting cells (APCs), T cells, and putative tumor-restraining fibroblasts within proximity to cancer cells, suggesting that antigen presentation and remodeling of the local microenvironment facilitates an effective response to KRASG12D inhibition. In the context of relapsed MRTX1133 treated tumors, single cell RNA sequencing and validation identified CDK8 as an intrinsic mediator of resistance and CXCL2 as an extrinsic mediator of resistance. Together, these studies identify APCs and CDK8 as therapeutic targets for enabling long term responses to small molecule KRASG12D inhibition with MRTX1133. Citation Format: Kathleen M. McAndrews, Krishnan K. Mahadevan, Bingrui Li, Amari M. Sockwell, Sami J. Morse, Patience J. Kelly, Michelle L. Kirtley, Meagan R. Conner, Sarah I. Patel, Shreyasee V. Khumbar, Kent A. Arian, Yasaman Barekatain, Barbara A. Moreno Diaz, Hengyu Lyu, Hikaru Sugimoto, Lakshmi Kavitha Sthanam, Navid Sobhani, Francesca Paradiso, Vincent Bernard, Paola Guerrero, Haoqiang Ying, Anirban Maitra, Timothy P. Heffernan, Raghu Kalluri. CDK8 and CXCL2 remodel the tumor microenvironment to contribute to KRASG12D small molecule inhibition resistance in pancreatic ductal adenocarcinoma [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 B092.

Molecular characteristics of early-onset pancreatic ductal adenocarcinoma.

The median age of patients with pancreatic ductal adenocarcinoma (PDAC) at diagnosis is 71 years; however, around 10% present with early-onset pancreatic cancer (EOPC), i.e., before age 50. The molecular mechanisms underlying such an early onset are unknown. We assessed the role of common PDAC drivers (KRAS, TP53, CDKN2A and SMAD4) and determined their mutational status and protein expression in 90 formalin-fixed, paraffin-embedded tissues, including multiple primary and matched metastases, from 37 EOPC patients. KRAS was mutated in 88% of patients; p53 was altered in 94%, and p16 and SMAD4 were lost in 86% and 71% of patients, respectively. Meta-synthesis showed a higher rate of p53 alterations in EOPC than in late-onset PDAC (94% vs. 69%, P = 0.0009) and significantly higher loss of SMAD4 (71% vs. 44%, P = 0.0025). The majority of EOPC patients accumulated aberrations in all four drivers; in addition, high tumour heterogeneity was observed across all tissues. The cumulative effect of an exceptionally high rate of alterations in all common PDAC driver genes combined with high tumour heterogeneity suggests an important mechanism underlying the early onset of PDAC.

A pancreatic cancer organoid platform identifies an inhibitor specific to mutant KRAS

KRAS mutations, mainly G12D and G12V, are found in more than 90% of pancreatic ductal adenocarcinoma (PDAC) cases. The success of drugs targeting KRASG12C suggests the potential for drugs specifically targeting these alternative PDAC-associated KRAS mutations. Here, we report a high-throughput drug-screening platform using a series of isogenic murine pancreatic organoids that are wild type (WT) or contain common PDAC driver mutations, representing both classical and basal PDAC phenotypes. We screened over 6,000 compounds and identified perhexiline maleate, which can inhibit the growth and induce cell death of pancreatic organoids carrying the KrasG12D mutation both invitro and invivo and primary human PDAC organoids. scRNA-seq analysis suggests that the cholesterol synthesis pathway is upregulated specifically in the KRAS mutant organoids, including the key cholesterol synthesis regulator SREBP2. Perhexiline maleate decreases SREBP2 expression levels and reverses the KRAS mutant-induced upregulation of the cholesterol synthesis pathway.

Arachidonate 15-lipoxygenase-mediated production of Resolvin D5n-3 DPA abrogates pancreatic stellate cell-induced cancer cell invasion.

Activation of pancreatic stellate cells (PSCs) to cancer-associated fibroblasts (CAFs) is responsible for the extensive desmoplastic reaction observed in PDAC stroma: a key driver of pancreatic ductal adenocarcinoma (PDAC) chemoresistance leading to poor prognosis. Specialized pro-resolving mediators (SPMs) are prime modulators of inflammation and its resolution, traditionally thought to be produced by immune cells. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based lipid mediator profiling PSCs as well as primary human CAFs express enzymes and receptors to produce and respond to SPMs. Human PSC/CAF SPM secretion profile can be modulated by rendering these cells activated [transforming growth factor beta (TGF-β)] or quiescent [all-trans retinoic acid (ATRA)]. ATRA-induced nuclear translocation of arachidonate-15-lipoxygenase (ALOX15) was linked to increased production of n-3 docosapentaenoic acid-derived Resolvin D5 (RvD5n-3 DPA), among other SPMs. Inhibition of RvD5n-3 DPA formation increases cancer cell invasion, whereas addback of this molecule reduced activated PSC-mediated cancer cell invasion. We also observed that circulating concentrations of RvD5n-3 DPA levels were decreased in peripheral blood of metastatic PDAC patients when compared with those measured in plasma of non-metastatic PDAC patients. Together, these findings indicate that RvD5n-3 DPA may regulate cancer-stroma cross-talk and invasion.

Tetrandrine synergizes with MAPK inhibitors in treating KRAS-mutant pancreatic ductal adenocarcinoma via collaboratively modulating the TRAIL-death receptor axis

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal malignancies lacking effective therapies. KRAS mutations that occur in over 90% of PDAC are major oncogenic drivers of PDAC. The MAPK signaling pathway plays a central role in KRAS-driven oncogenic signaling. However, pharmacological inhibitors of the MAPK pathway are poorly responded in KRAS-mutant PDAC, raising a compelling need to understand the mechanism behind and to seek new therapeutic solutions. Herein, we perform a screen utilizing a library composed of 800 naturally-derived bioactive compounds to identify natural products that are able to sensitize KRAS-mutant PDAC cells to the MAPK inhibition. We discover that tetrandrine, a natural bisbenzylisoquinoline alkaloid, shows a synergistic effect with MAPK inhibitors in PDAC cells and xenograft models. Mechanistically, pharmacological inhibition of the MAPK pathway exhibits a double-edged impact on the TRAIL-death receptor axis, transcriptionally upregulating TRAIL yet downregulating its agonistic receptors DR4 and DR5, which may explain the limited therapeutic outcomes of MAPK inhibitors in KRAS-mutant PDAC. Of great interest, tetrandrine stabilizes DR4/DR5 protein via impairing ubiquitination-mediated protein degradation, thereby allowing a synergy with MAPK inhibition in inducing apoptosis in KRAS-mutant PDAC. Our findings identify a new combinatorial approach for treating KRAS-mutant PDAC and highlight the role of TRAIL-DR4/DR5 axis in dictating the therapeutic outcome in KRAS-mutant PDAC.

Comprehensive Genomic Analysis Stratified by KRAS Status in Patients with Pancreatic Adenocarcinoma and Its Prognostic Significance

KRAS mutations (MUT) are one of the major drivers in pancreatic ductal adenocarcinoma (PDA) with over 90% of patients having alterations. However, the genetic landscape of PDA based on KRAS status is not well studied. The aim of this study is to investigate genomic alterations based on KRAS status and to identify driver mutations in patients with KRAS wild type (WT). Next-generation sequencing with 324 pre-specified genes was performed on patients with histologically confirmed PDA. The landscape of somatic mutations was stratified by KRAS status. Outcomes of interest included overall survival (OS), local failure (LF) following radiotherapy, time to metastasis, and CA 19-9 level. All outcomes were stratified by KRAS status. Genetic alterations exclusive to patients with KRAS WT were analyzed. OS was calculated using the Kaplan-Meier estimates and log-rank test, and LF was measured using cumulative incidence. A multivariate cox-regression analysis (MVA) was performed to identify prognostic factors for survival. Gene ontology analysis of KRAS WT exclusive genes was performed via DAVID (Database for Annotation, Visualization, and Integrated Discovery). A total of 272 patients with metastatic PDA were included. The median age at diagnosis was 65.4 (range, 26.77-83.21) years. The median follow-up was 15.7 (0.06-136.7) months. 91% percent (n = 248) of patients were found to be KRAS MUT. The chi-square test showed that the primary tumor site (p = 0.027) and perineural invasion (p = 0.006) were associated with KRAS status. The median CA 19-9 was 143.6 (15.5-27996) U/ml and 341.15 (0-100000) U/ml for KRAS WT and KRAS MUT, respectively (p = 0.23). The median OS for KRAS WT and MUT was 31.4 (95% CI 25.1-NA) and 13.3 (95% CI 11.3-14.5) months, respectively (p = 0.0008). In patients with metachronous recurrence, the median time to metastasis was 22.4 (1.37-52.97) months and 12.8 (1.8-84.97) months for KRAS WT and KRAS MUT, respectively (p = 0.057). KRAS MUT types including G12 and Q21 were not associated with OS (p = 0.58). On MVA, including KRAS status, age, sex, and metastatic types (de novo vs. metachronous), only KRAS mutation was associated with worse OS [HR 2.64; 95% CI 1.53 to 4.56; p = 0.0004]. In patients treated with radiation, the LF rate at 12 months was 12.5% in patients with KRAS WT and 33.8% in KRAS MUT (p = 0.13). Heatmap analysis identified that RAD50, ALK, BCORL1, BRAF, CDC73, FAM123B, NF2, ERBB4, and ERCC4 were exclusively mutated in patients with KRAS WT. These genes were enriched in pathways associated with tyrosine kinase catalytic domain activity, ubiquitination, and nuclear localization signal. This study identified driver mutations in patients with KRAS WT. KRAS status was associated with pathologic features and disease prognosis after treatment. Further study leveraging more powered cohorts is warranted.

Abstract 6203: CTC1-STN1-TEN1 (CST) complex-independent roles for STN1 in DNA double-strand break repair in pancreatic ductal adenocarcinoma

Abstract KRAS mutation occurs in 90-95% of pancreatic ductal adenocarcinoma (PDAC) and is a driver of PDAC; however, the underlying molecular mechanisms by which KRAS mutation maintains survival and promotes progression of PDAC need further refinement. We herein report that KRAS mutations increase STN1 (also named OBFC1) expression leading to enhanced repair of DNA double strand breaks (DSBs) in PDAC. Analysis of The Cancer Genome Atlas databases reveal that STN1 is significantly upregulated in PDAC tissue and, is associated with KRAS mutation and poor survival. Silencing KRAS or pharmacologic inhibition of KRAS signaling decreased STN1 expression in PDAC cells. Canonically, STN1 forms a CST (CTC1-STN1-TEN1) complex, which is important for telomere duplication and maintenance. Intriguingly, siRNA-mediated depletion of STN1 (but not CTC1 or TEN1) sensitized PDAC cells to ionizing radiation and chemotherapy as assessed by radiation clonogenic assay and alamarBlue assay, respectively. Consistently, immunoblotting and immunofluorescence analyses of γH2AX (marker of DNA damage) demonstrated that depletion of STN1 (but not CTC1 or TEN1) resulted in DNA damage. To explore the underlying molecular mechanisms, we performed proteomic analysis and found that STN1 physically interacts with many proteins important for DNA repair, replication and cell cycle progression. Of note, we revealed unreported interactions of STN1 with ATM, ATR and DNA-PKcs, key components of DNA damage response signaling. Furthermore, homologous recombination and non-homologous end joining repair reporter assays demonstrated that STN1 silencing reduced both homologous recombination and non-homologous end joining repair of DSBs in U2OS and PDAC cells. Moreover, flow cytometry and immunofluorescence analyses showed that knockdown of STN1 by siRNA impaired cell cycle arrest at S and G2/M phases which was accompanied with mitotic catastrophe in response to ionizing radiation. Our findings have revealed novel CST complex-independent roles for STN1 in DSB repair and suggest STN1 is a novel biomarker for PDAC as well as potentially other cancers. Citation Format: Changxian Shen, Linlin Yang, Sergio Corrales-Guerrero, Sindhu Nair, Terence Williams. CTC1-STN1-TEN1 (CST) complex-independent roles for STN1 in DNA double-strand break repair in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6203.

Abstract 4757: Loss of KDM5A supports KRAS-driven pancreatic cancer

Abstract Objective: Mutant KRAS is a primary driver of pancreatic ductal adenocarcinoma (PDAC), which exhibits marked hypoxia. Despite the strong association of hypoxia and PDAC, the relationship between KRAS and hypoxia is still poorly understood. The oxygen-sensitive histone lysine demethylase, KDM5A, was recently reported to mediate epigenetic responses to hypoxia independent of the hypoxia-inducible factors. KDM5A epigenetically represses transcription via two mechanisms: by its demethylase activity on activating H3K4me3 marks, and through its interaction with deacetylase complexes containing HDAC1/2, which deacetylates activating H3K9ac and H4K16ac histone marks. Under hypoxic conditions, KDM5A loses its activity, leading to restoration of these H3K4me3 marks, thereby activating KDM5A target genes. The purpose of this study is to understand how KDM5A loss of function contributes to pathogenesis of mutant KRAS-driven pancreatic cancer. Methods: Cell lines derived from mice with pancreas-specific p53 deletion and doxycycline-inducible expression of KrasG12D (iKPC). Protein lysates were prepared using RIPA buffer. Histones were purified by acid extraction. Immunoblotting was used to probe for protein levels of Kdm5a, H3K4me3, H3K9ac, and H4K16ac. Genetic ablation of KrasG12D was performed by culturing iKPCs in tetracycline-free medium. Kras was induced by adding doxycycline to the culture medium. Pharmaceutical inhibition of MEK, proteasome, and Kdm5a were performed by treating iKPCs with mirdametinib, MG-132, and CPI-455, respectively. Knockdown of β-TrCP and FBXW7 were performed by stable expression of shRNA in iKPCs. Protein motif scanning was performed using the Eukaryotic Linear Motif (ELM) Prediction online software. Results: We discovered that Kdm5a protein levels were abrogated by induction of KrasG12D and stabilized by genetic ablation of Kras. Pharmaceutical inhibition of MEK or proteasome function stabilized Kdm5a, indicating that Kras induces Kdm5a proteasomal degradation through the MEK/ERK pathway. H3K4me3, H3K9ac, and H4K16ac histone marks were increased in Kras-on iKPC compared to Kras-off iKPC, consistent the expected effect of Kras-induced Kdm5a degradation. Pharmaceutical inhibition Kdm5a in the Kras-off setting restored H3K4me3, suggesting that Kdm5a contributes to demethylation of H3K4me3 in iKPC. We identified two phosphodegron sites corresponding to β-TrCP and FBXW7 of the ubiquitin ligase complex within the Kdm5a protein sequence. Knockdown of either β-TrCP or FBXW7 in iKPC both stabilized Kdm5a despite induction of Kras. Conclusion: We conclude that Kdm5a plays a tumor suppressor role in pancreatic cancer by epigenetically repressing transcriptional programs necessary for KRAS-driven oncogenesis. Citation Format: Jasper R. Chen, Jincheng Han, Cullen M. Taniguchi, Ronald A. DePinho. Loss of KDM5A supports KRAS-driven pancreatic cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4757.

Coadaptation fostered by the SLIT2-ROBO1 axis facilitates liver metastasis of pancreatic ductal adenocarcinoma

To explore the mechanism of coadaptation and the potential drivers of pancreatic ductal adenocarcinoma (PDAC) metastasis to the liver, we study key molecules involved in this process and their translational value. Premetastatic niche (PMN) and macrometastatic niche (MMN) formation in a mouse model is observed via CT combined with 3D organ reconstruction bioluminescence imaging, and then we screen slit guidance ligand 2 (SLIT2) and its receptor roundabout guidance receptor 1 (ROBO1) as important factors. After we confirm the expression and distribution of SLIT2 and ROBO1 in samples from PDAC patients and several mouse models, we discover that SLIT2-ROBO1-mediated coadaptation facilitated the implantation and outgrowth of PDAC disseminated tumour cells (DTCs) in the liver. We also demonstrate the dependence receptor (DR) characteristics of ROBO1 in a follow-up mechanistic study. A neutralizing antibody targeting ROBO1 significantly attenuate liver metastasis of PDAC by preventing the coadaptation effect. Thus, we demonstrate that coadaptation is supported by the DR characteristics in the PMN and MMN.

Clinical and molecular presentation of KRAS G12D-mutated pancreatic ductal adenocarcinoma in real-world settings.

738 Background: Pancreatic ductal adenocarcinoma (PDAC) remains a devastating diagnosis with an overall 5-year survival rate of ~10%. Therapies targeting KRAS G12D, a prevalent molecular driver of PDAC, represent an active area of investigation with many agents currently in clinical development. This study characterizes the real-world clinico-genomic landscape of patients with KRAS G12D-mutated PDAC to inform ongoing therapeutic development and clinical trial design. Methods: We conducted a retrospective, records-based analysis of 2,805 patients with PDAC from across 299 community-based oncology clinics. All patients had broad-panel next generation sequencing (NGS) from commercial vendors performed as standard of care. Patients were stratified into KRASWT (26%), KRASG12D (31%), and KRASnon-G12D (43%) cohorts according to NGS results and assessed for co-mutations, overall survival, and time to chemotherapy failure. Results: The KRASG12D and KRASnon-G12D cohorts exhibited similar mutational landscapes with frequent alterations in TP53, CDKN2A, and SMAD4 ( > 20% frequency occurrence) and infrequent actionable co-mutations (i.e. ATM, MTAP, BRCA1/2, PIK3CA, and MYC; < 5% frequency occurrence). KRASG12D exhibited significantly decreased overall survival compared to KRASWT (m (95% CI); 32.4 months (27.6-37.6 months) [ KRASWT], 20.1 months (17.0-22.7 months) [ KRASG12D], 21.7 months (20.0-25.0 months) [ KRASnon-G12D]; Cox model p-value < 0.001) as well as significantly shortened time to chemotherapy failure compared to both KRASnon-G12D and KRASWT (m (95% CI); 10.8 months (9.6-11.6 months) [ KRASWT], 7.8 months (7.3-8.7 months) [ KRASG12D], 9.8 months (8.8-11.1 months) [ KRASnon-G12D]; Cox model p-value < 0.01). Within the KRASG12D cohort, no co-mutations were significantly associated with overall survival. Conclusions: This study demonstrates the acute need for KRAS G12D-targeted agents in the clinic, as patients with KRAS G12D-driven PDAC experience particularly poor patient outcomes and lack alternative molecular targets.

Abstract B015: Systemic reprogramming of fibroblasts and immune cells precedes metastatic spread in pancreatic cancer

Abstract Oncogenic KRAS (Kras*) is a near-universal driver of pancreatic ductal adenocarcinoma (PDA), and its activity is required for the formation of the PDA precursor lesions, pancreatic intraepithelial neoplasia (PanIN). PanIN formation is accompanied by fibrosis and immune cell infiltration, creating a precursor tumor microenvironment (PME) that is maintained and evolves through the disease progression. In mice bearing overt pancreatic cancer, pancreatic cells secrete specific factors to prime the liver and lung, forming the premetastatic niche. Presently, it remains to be elucidated at what stage of PDA tumorigenesis the premetastatic niche is initiated, as well as the mechanisms underlying this formation. As PDA patients are commonly diagnosed with metastatic disease, it is imperative to understand the mechanism underlying formation of the premetastatic niche, as well as determinants of metastasis outgrowth. To determine whether Kras*-dependent signals are required for the formation of the premetastatic niche, we used an inducible and reversible murine model of pancreas-specific Kras* expression developed by our group known as the iKras* mouse. We expressed Kras* in the pancreatic epithelium of adult mice for 16 weeks and validated the presence of advanced PanIN lesions without overt malignancy. We then performed single cell RNA sequencing (scRNA-seq) on the pancreas, liver, and lung of these mice, with liver and lung being common sites of metastasis for pancreatic cancer. We have previously shown that pancreatic fibroblasts are reprogrammed early during carcinogenesis, a finding that holds true at this later timepoint. Interestingly, we observed parallel changes in gene expression in fibroblasts, macrophages, and T cells in the lungs of PanIN bearing mice. Ongoing studies aim to validate the changes seen in the scRNA-seq and functionally evaluate systemic activation of fibroblasts and immune cells within the premetastatic niche. Citation Format: Emily L. Lasse Opsahl, Ashley Velez-Delgado, Katelyn L. Donahue, Padma Kadiyala, Carlos Espinoza, Yaqing Zhang, Marina Pasca di Magliano. Systemic reprogramming of fibroblasts and immune cells precedes metastatic spread in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B015.

Preprint Highlight: Collagen remodeling dictates pancreatic cancer bioenergetics and outcome through DDR1 activation or degradation.

Aberrant desmoplasia (e.g., collagen deposition) is a prominent hallmark of pancreatic ductal adenocarcinoma (PDAC) pathogenesis. The mechanisms and signaling pathways impacted by the prevalent increase in collagen deposition are poorly understood. This study demonstrated opposing roles of fibrolytic stroma (cleaved type I collagen) and inert stroma (intact type I collagen) in driving PDAC tumorigenicity. Cleaved type I collagen activates discoidin domain receptor 1 (DDR1), leading to increased tumor growth and liver metastases, macropinocytosis, metabolism, mitochondrial biogenesis, and poor patient outcomes. These effects were inhibited by intact type I collagen. This study describes new roles of DDR1-mediated regulation of macropinocytosis and mitochondrial biogenesis, delineates stromal states as oncogenic drivers of PDAC, and advances our understanding of aberrant desmoplasia.

Genomic characterization of undifferentiated sarcomatoid carcinoma of the pancreas

Undifferentiated sarcomatoid carcinoma (USC) of the pancreas is a rare but especially aggressive variant of pancreatic ductal adenocarcinoma (PDAC), composed of at least 80% of sarcomatoid cells. This study aimed to elucidate its clinicopathological and molecular features. The study cohort included 10 patients with pancreatic USC. Clinicopathological parameters were determined for each patient. The molecular profile was investigated using next-generation sequencing (NGS). Histologically, all tumors were hypercellular neoplasms with spindle-shaped or sarcomatoid cells. All patients showed vascular and perineural invasion. Most patients had a poor prognosis. NGS showed important similarities with conventional PDAC, including frequent alterations in the classic PDAC drivers, KRAS (100% of cases), TP53 (90%), and CDKN2A (60%). There were also some important distinctions from conventional PDAC: 1) SMAD4, a typical PDAC driver gene, was mutated in only one case (10%); 2) Another distinctive molecular feature was the recurrent KRAS amplification (30% of cases), which is very rare in conventional PDAC. It has been previously reported in another subtype of pancreatic undifferentiated carcinoma, the rhabdoid variant, and may be a key event leading to the acquisition of an undifferentiated phenotype in a subgroup of cases; 3) Lastly, in two different cases, we detected two potentially actionable targets, not belonging to the typical PDAC molecular landscape, such as MCL1 amplification and POLQ mutation. Our study sheds light on this rare tumor type, which shows aggressive biological behavior and few druggable alterations. The most distinctive molecular features of pancreatic USC are the paucity of SMAD4 alterations and recurrent KRAS amplification.

TP53-Status-Dependent Oncogenic EZH2 Activity in Pancreatic Cancer

Simple SummaryEpigenetic alterations contribute to the aggressiveness and therapy resistance of Pancreatic Ductal Adenocarcinoma (PDAC). However, epigenetic regulators, including Enhancer of Zeste Homolog 2 (EZH2), reveal a strong context-dependent activity. Our study aimed to examine the context-defining molecular prerequisites of oncogenic EZH2 activity in PDAC to assess the therapeutic efficacy of targeting EZH2. Our preclinical study using diverse PDAC models demonstrates that the TP53 status determines oncogenic EZH2 activity. Only in TP53-wildtype (wt) PDAC subtypes was EZH2 blockade associated with a favorable PDAC prognosis mainly through cell-death response. We revealed that EZH2 depletion increases p53wt stability by the de-repression of CDKN2A. Therefore, our study provides preclinical evidence that an intact CDKN2A-p53wt axis is indispensable for a beneficial outcome of EZH2 depletion and highlights the significance of molecular stratification to improve epigenetic targeting in PDAC. Pancreatic Ductal Adenocarcinoma (PDAC) represents a lethal malignancy with a consistently poor outcome. Besides mutations in PDAC driver genes, the aggressive tumor biology of the disease and its remarkable therapy resistance are predominantly installed by potentially reversible epigenetic dysregulation. However, epigenetic regulators act in a context-dependent manner with opposing implication on tumor progression, thus critically determining the therapeutic efficacy of epigenetic targeting. Herein, we aimed at exploring the molecular prerequisites and underlying mechanisms of oncogenic Enhancer of Zeste Homolog 2 (EZH2) activity in PDAC progression. Preclinical studies in EZH2 proficient and deficient transgenic and orthotopic in vivo PDAC models and transcriptome analysis identified the TP53 status as a pivotal context-defining molecular cue determining oncogenic EZH2 activity in PDAC. Importantly, the induction of pro-apoptotic gene signatures and processes as well as a favorable PDAC prognosis upon EZH2 depletion were restricted to p53 wildtype (wt) PDAC subtypes. Mechanistically, we illustrate that EZH2 blockade de-represses CDKN2A transcription for the subsequent posttranslational stabilization of p53wt expression and function. Together, our findings suggest an intact CDKN2A-p53wt axis as a prerequisite for the anti-tumorigenic consequences of EZH2 depletion and emphasize the significance of molecular stratification for the successful implementation of epigenetic targeting in PDAC.

Longitudinal profiling of circulating tumour DNA for tracking tumour dynamics in pancreatic cancer

BackgroundThe utility of circulating tumour DNA (ctDNA) for longitudinal tumour monitoring in pancreatic ductal adenocarcinoma (PDAC) has not been explored beyond mutations in the KRAS proto-oncogene. Here, we aimed to characterise and track patient-specific somatic ctDNA variants, to assess longitudinal changes in disease burden and explore the landscape of actionable alterations.MethodsWe followed 3 patients with resectable disease and 4 patients with unresectable disease, including 4 patients with ≥ 3 serial follow-up samples, of whom 2 were rare long survivors (> 5 years). We performed whole exome sequencing of tumour gDNA and plasma ctDNA (n = 20) collected over a ~ 2-year period from diagnosis through treatment to death or final follow-up. Plasma from 3 chronic pancreatitis cases was used as a comparison for analysis of ctDNA mutations.ResultsWe detected > 55% concordance between somatic mutations in tumour tissues and matched serial plasma. Mutations in ctDNA were detected within known PDAC driver genes (KRAS, TP53, SMAD4, CDKN2A), in addition to patient-specific variants within alternative cancer drivers (NRAS, HRAS, MTOR, ERBB2, EGFR, PBRM1), with a trend towards higher overall mutation loads in advanced disease. ctDNA alterations with potential for therapeutic actionability were identified in all 7 patients, including DNA damage response (DDR) variants co-occurring with hypermutation signatures predictive of response to platinum chemotherapy. Longitudinal tracking in 4 patients with follow-up > 2 years demonstrated that ctDNA mutant allele fractions and clonal trends were consistent with CA19-9 measurements and/or clinically reported disease burden. The estimated prevalence of ‘stem clones’ was highest in an unresectable patient where changes in ctDNA dynamics preceded CA19-9 levels. Longitudinal evolutionary trajectories revealed ongoing subclonal evolution following chemotherapy.ConclusionThese results provide proof-of-concept for the use of exome sequencing of serial plasma to characterise patient-specific ctDNA profiles, and demonstrate the sensitivity of ctDNA in monitoring disease burden in PDAC even in unresectable cases without matched tumour genotyping. They reveal the value of tracking clonal evolution in serial ctDNA to monitor treatment response, establishing the potential of applied precision medicine to guide stratified care by identifying and evaluating actionable opportunities for intervention aimed at optimising patient outcomes for an otherwise intractable disease.

Development of PCR assays to detect signature circulating tumor DNA methylation markers and KRas mutations for pancreatic ductal adenocarcinoma (PDAC).

524 Background: PDAC is a cancer of high mortality. Accurate and cost-effective PCR assays detecting diagnostic and prognostic PDAC markers in blood are desirable for conducting PDAC screening in high-risk populations, evaluating treatments for patients and surveying for post-treatment relapse. Methods: We combined PDAC-diagnosing ctDNA methylation markers with PDAC-driving Kras mutations as targets to develop said PCR tests. Methylation markers were previously validated to classify PDAC plasma at a high accuracy by a targeted methylation sequencing assay. Seven known PDAC driver mutations in KRas exon2 were selected. Taqman-based quantitative methylation-specific PCR (MSP) and ARMS PCR were designed for methylation markers and KRas mutations, respectively, and were validated for technical performances. A step of pre-amplification of input DNA by conventional PCR was included prior to quantitative PCR to improve sensitivity. Over 200 clinical PDAC and control tissue and plasma samples were used to determine their analytical performances in classifying PDAC plasma. Results: All targets were detected at a limit-of-detection of 0.25% or better on standards DNA in PCR. To test clinical plasma samples, methylation markers were first filtered by comparing their levels in PDAC-, para-tumor tissues and whole blood cells. Twenty-four most discriminatory markers for PDAC tissues were selected and used to classify 110 PDAC plasma samples from equal number of normal samples. They were evaluated for their sensitivity at a pre-set specificity of 90%. The 4 best-performing markers were selected to build and cross-validate a general-linear-model (GLM) PDAC classifier, which achieved a sensitivity of 66% at 90% specificity (AUC = 0.829) in cross-validation. Adding status of KRas mutations further improved prediction accuracy by increasing sensitivity to 75% (AUC = 0.89), demonstrating the methylation markers and KRas mutations complement each other in detection PDAC plasma. Conclusions: Our results suggest that a small number of our DNA methylation markers can classify PDAC plasma at a reasonably high accuracy by MSP. Incorporating KRas driver mutations further improved classification accuracy. Together they are promising to be further translated into diagnostics for PDAC early screening, treatment assessment and postoperative surveillance.

Metabolic reprogramming by driver mutation-tumor microenvironment interplay in pancreatic cancer: new therapeutic targets.

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers globally with a mortality rate exceeding 95% and very limited therapeutic options. A hallmark of PDAC is its acidic tumor microenvironment, further characterized by excessive fibrosis and depletion of oxygen and nutrients due to poor vascularity. The combination of PDAC driver mutations and adaptation to this hostile environment drives extensive metabolic reprogramming of the cancer cells toward non-canonical metabolic pathways and increases reliance on scavenging mechanisms such as autophagy and macropinocytosis. In addition, the cancer cells benefit from metabolic crosstalk with nonmalignant cells within the tumor microenvironment, including pancreaticstellate cells, fibroblasts, and endothelial and immune cells. Increasing evidence shows that this metabolic rewiring is closely related to chemo- and radioresistance and immunosuppression, causing extensive treatment failure. Indeed, stratification of human PDAC tumors into subtypes based on their metabolic profiles was shown to predict disease outcome. Accordingly, an increasing number of clinical trials target pro-tumorigenic metabolic pathways, either as stand-alone treatment or in conjunction with chemotherapy. In this review, we highlight key findings and potential future directions of pancreatic cancer metabolism research, specifically focusing on novel therapeutic opportunities.