Subtypes Of Pancreatic Ductal Adenocarcinoma Research Articles

Tumor-intrinsic and Cancer-associated Fibroblast Subtypes Independently Predict Outcomes in Pancreatic Cancer.

To assess the utility of tumor-intrinsic and cancer-associated fibroblast (CAF) subtypes of pancreatic ductal adenocarcinoma (PDAC) in predicting response to neoadjuvant therapy (NAT) and overall survival. PDAC remains a deadly disease with limited treatment options, and both the tumor as well as the microenvironment play an important role in pathogenesis. Gene expression-based tumor-intrinsic subtypes (classical and basal-like) have been shown to predict outcomes, but tumor microenvironment subtypes are still evolving. RNA-sequencing was performed on 114 deidentified resected PDAC tumors. Clinical data were collected by retrospective chart review. Single sample classifiers (SSCs) were used to determine classical and basal-like subtypes as well as tumor-permissive permCAF and tumor-restraining restCAF subtypes. Survival was analyzed using log-rank test. Patients who received NAT had an increase in overall survival (OS), with median survival of 27.9 months compared to 20.1 months for those who did not receive NAT, but the difference did not reach statistical significance (HR 0.64, P=0.076). Either tumor-intrinsic or CAF subtypes alone were associated with OS regardless of NAT or no NAT, and patients with classical or restCAF subtype had the best outcomes. When evaluated together, patients with classical-restCAF subtype had the best OS and basal-permCAF the worst OS (P<0.0001). NAT patients with classical-restCAF subtype demonstrated the longest OS compared to the other groups (P=0.00041). CAF subtypes have an additive effect over tumor-intrinsic subtypes in predicting survival with or without neoadjuvant FOLFIRINOX in PDAC. Molecular subtyping of both tumor and CAF compartments of PDAC may be important steps in selecting first-line systemic therapy.

Deciphering fatty acid biosynthesis-driven molecular subtypes in pancreatic ductal adenocarcinoma with prognostic insights.

Pancreatic ductal adenocarcinoma (PDAC) poses a significant challenge due to its high heterogeneity and aggressiveness. Recognizing the urgency to delineate molecular subtypes, our study focused on the emerging field of lipid metabolism remodeling in PDAC, particularly exploring the prognostic potential and molecular classification associated with fatty acid biosynthesis. Gene set variation analysis (GSVA) and single-sample gene set enrichment analysis (ssGSEA) were performed to evaluate the dysregulation of lipid metabolism in PDAC. Univariate cox analysis and the LASSO module were used to build a prognostic risk score signature. The distinction of gene expression in different risk groups was explored by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Weighted Gene Co-expression Network Analysis (WGCNA). The biological function of Acyl-CoA Synthetase Long Chain Family Member 5 (ACSL5), a pivotal gene within 7-hub gene signature panel, was validated through in vitro assays. Our study identified a 7-hub gene signature associated with fatty acid biosynthesis-related genes (FRGs), providing a robust tool for prognosis prediction. The high-FRGs score group displayed a poorer prognosis, decreased immune cell infiltration, and a higher tumor mutation burden. Interestingly, this group exhibited enhanced responsiveness to various compounds according to the Genomics of Drug Sensitivity in Cancer (GDSC) database. Notably, ACSL5 was upregulated in PDAC and essential for tumor progression. In conclusion, our research defined two novel fatty acid biosynthesis-based subtypes in PDAC, characterized by distinct transcriptional profiles. These subtypes not only served as prognostic indicator, but also offered valuable insights into their metastatic propensity and therapeutic potential.

Keratin 17 modulates the immune topography of pancreatic cancer

BackgroundThe immune microenvironment impacts tumor growth, invasion, metastasis, and patient survival and may provide opportunities for therapeutic intervention in pancreatic ductal adenocarcinoma (PDAC). Although never studied as a potential modulator of the immune response in most cancers, Keratin 17 (K17), a biomarker of the most aggressive (basal) molecular subtype of PDAC, is intimately involved in the histogenesis of the immune response in psoriasis, basal cell carcinoma, and cervical squamous cell carcinoma. Thus, we hypothesized that K17 expression could also impact the immune cell response in PDAC, and that uncovering this relationship could provide insight to guide the development of immunotherapeutic opportunities to extend patient survival.MethodsMultiplex immunohistochemistry (mIHC) and automated image analysis based on novel computational imaging technology were used to decipher the abundance and spatial distribution of T cells, macrophages, and tumor cells, relative to K17 expression in 235 PDACs.ResultsK17 expression had profound effects on the exclusion of intratumoral CD8+ T cells and was also associated with decreased numbers of peritumoral CD8+ T cells, CD16+ macrophages, and CD163+ macrophages (p < 0.0001). The differences in the intratumor and peritumoral CD8+ T cell abundance were not impacted by neoadjuvant therapy, tumor stage, grade, lymph node status, histologic subtype, nor KRAS, p53, SMAD4, or CDKN2A mutations.ConclusionsThus, K17 expression correlates with major differences in the immune microenvironment that are independent of any tested clinicopathologic or tumor intrinsic variables, suggesting that targeting K17-mediated immune effects on the immune system could restore the innate immunologic response to PDAC and might provide novel opportunities to restore immunotherapeutic approaches for this most deadly form of cancer.

A mucus production programme promotes classical pancreatic ductal adenocarcinoma

ObjectiveThe optimal therapeutic response in cancer patients is highly dependent upon the differentiation state of their tumours. Pancreatic ductal adenocarcinoma (PDA) is a lethal cancer that harbours distinct phenotypic subtypes...

Genomic Profiling of Rare Undifferentiated Sarcomatoid Subtypes of Pancreatic Carcinomas: In Search of Therapeutic Targets

PURPOSE The highly aggressive undifferentiated sarcomatoid carcinoma (USC) subtype of pancreatic ductal adenocarcinoma (PDAC) remains poorly characterized because of its rarity. Previous case reports suggest that immune checkpoint inhibitors could be a promising treatment strategy, but the prevalence of established predictive biomarkers of response is largely unknown. The objective of this study was to leverage comprehensive genomic profiling of USC PDAC tumors to determine the prevalence of biomarkers associated with potential response to targeted therapies. METHODS USC tumors (n = 20) underwent central pathology review by a board-certified gastrointestinal pathologist to confirm the diagnosis. These samples were compared with non-USC PDAC tumors (N = 5,562). Retrospective analysis of DNA and RNA next-generation sequencing data was performed. RESULTS USC PDACs were more frequently PD-L1+ by immunohistochemistry than non-USC PDAC (63% v 16%, respectively, P &lt; .001). Furthermore, USC PDAC had an increase in neutrophils (8.99% v 5.55%, P = .005) and dendritic cells (1.08% v 0.00%, q = 0.022) and an increased expression of PDCD1LG2 (4.6% v 1.3%, q = 0.001), PDCD1 (2.0% v 0.8%, q = 0.060), and HAVCR2 (45.9% v 21.7%, q = 0.107) than non-USC PDAC. Similar to non-USC PDAC, KRAS was the most commonly mutated gene (86% v 90%, respectively, P = 1). CONCLUSION To our knowledge, this work represents the largest molecular analysis of USC tumors to date and showed an increased expression of immune checkpoint genes in USC tumors. These findings provide evidence for further investigation into immune checkpoint inhibitors in USC tumors.

Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction.

Recently, two molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) have been proposed: the "Classical" and "Basal-like" subtypes, with the former showing better clinical outcomes than the latter. However, the "molecular" classification has not been applied in real-world clinical practice. This study aimed to establish patient-derived organoids (PDOs) for PDAC and evaluate their application in subtype classification and clinical outcome prediction. We utilized tumor samples acquired through endoscopic ultrasound-guided fine-needle biopsy and established a PDO library for subsequent use in morphological assessments, RNA-seq analyses, and in vitro drug response assays. We also conducted a prospective clinical study to evaluate whether analysis using PDOs can predict treatment response and prognosis. PDOs of PDAC were established at a high efficiency (> 70%) with at least 100,000 live cells. Morphologically, PDOs were classified as gland-like structures (GL type) and densely proliferating inside (DP type) less than 2weeks after tissue sampling. RNA-seq analysis revealed that the "morphological" subtype (GL vs. DP) corresponded to the "molecular" subtype ("Classical" vs. "Basal-like"). The "morphological" classification predicted the clinical treatment response and prognosis; the median overall survival of patients with GL type was significantly longer than that with DP type (P < 0.005). The GL type showed a better response to gemcitabine than the DP type in vitro, whereas the drug response of the DP type was improved by the combination of ERK inhibitor and chloroquine. PDAC PDOs help in subtype determination and clinical outcome prediction, thereby facilitating the bench-to-bedside precision medicine for PDAC.

Expression of Selected miRNAs in Undifferentiated Carcinoma with Osteoclast-like Giant Cells (UCOGC) of the Pancreas: Comparison with Poorly Differentiated Pancreatic Ductal Adenocarcinoma.

Undifferentiated carcinoma with osteoclast-like giant cells (UCOGC) of the pancreas represents a rare subtype of pancreatic ductal adenocarcinoma (PDAC). Despite a distinct morphology and specific clinical behavior, UCOGCs exhibit unexpected similarities in regard to DNA mutational profiles with conventional PDAC. Treating pancreatic ductal adenocarcinoma is particularly challenging, with limited prospects for cure. As with many other malignant neoplasms, the exploration of microRNAs (miRNAs, miRs) in regulating the biological characteristics of pancreatic cancer is undergoing extensive investigation to enhance tumor diagnostics and unveil the therapeutic possibilities. Herein, we evaluated the expression of miR-21, -96, -148a, -155, -196a, -210, and -217 in UCOGCs and poorly differentiated (grade 3, G3) PDACs. The expression of miR-21, miR-155, and miR-210 in both UCOGCs and G3 PDACs was significantly upregulated compared to the levels in normal tissue, while the levels of miR-148a and miR-217 were downregulated. We did not find any significant differences between cancerous and normal tissues for the expression of miR-96 and miR-196a in G3 PDACs, whereas miR-196a was slightly, but significantly, downregulated in UCOGCs. On the other hand, we have not observed significant differences in the expression of the majority of miRNAs between UCOGC and G3 PDAC, with the exception of miR-155. UCOGC samples demonstrated lower mean levels of miR-155 in comparison with those in G3 PDACs.

Axon guidance cue SEMA3A promotes the aggressive phenotype of basal-like PDAC

ObjectiveThe dysregulation of the axon guidance pathway is common in pancreatic ductal adenocarcinoma (PDAC), yet our understanding of its biological relevance is limited. Here, we investigated the functional role of...

Keratin 17 is a prognostic and predictive biomarker in pancreatic ductal adenocarcinoma.

To determine the role of keratin 17 (K17) as a predictive biomarker for response to chemotherapy by defining thresholds of K17 expression based on immunohistochemical tests that could be used to optimize therapeutic intervention for patients with pancreatic ductal adenocarcinoma (PDAC). We profiled K17 expression, a hallmark of the basal molecular subtype of PDAC, by immunohistochemistry in 2 cohorts of formalin-fixed, paraffin-embedded PDACs (n = 305). We determined a K17 threshold of expression to optimize prognostic stratification according to the lowest Akaike information criterion and explored the potential relationship between K17 and chemoresistance by multivariate predictive analyses. Patients with advanced-stage, low K17 PDACs treated using 5-fluorouracil (5-FU)-based chemotherapeutic regimens had 3-fold longer survival than corresponding cases treated with gemcitabine-based chemotherapy. By contrast, PDACs with high K17 did not respond to either regimen. The predictive value of K17 was independent of tumor mutation status and other clinicopathologic variables. The detection of K17 in 10% or greater of PDAC cells identified patients with shortest survival. Among patients with low K17 PDACs, 5-FU-based treatment was more likely than gemcitabine-based therapies to extend survival.

HCST Expression Distinguishes Immune-hot and Immune-cold Subtypes in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is the most prevalent malignancy of the pancreas, and the incidence of this disease is approximately equivalent to the mortality rate. Immunotherapy has made a remarkable breakthrough in numerous cancers, while its efficacy in PDAC remains limited due to the immunosuppressive microenvironment. Immunotherapy efficacy is highly correlated with the abundance of immune cells, particularly cytotoxic T cells. Therefore, molecular classifier is needed to identify relatively hot tumors that may benefit from immunotherapy In this study, we carried out a transcriptome analysis of 145 pancreatic tumors to define the underlying immune regulatory mechanism driving the PDAC immunosuppressive microenvironment. The immune subtype was identified by consensus clustering, and the underlying PDAC immune activation mechanism was thoroughly examined using single sample gene set enrichment analysis (ssGSEA). Area under the curve (AUC) of the receiver operating characteristic (ROC) curve was used to assess the accuracy of the molecular classifier in differentiating immunological subgroups of PDAC.5 The protein level of molecular classifier was verified by immunohistochemistry in human PDAC tissue. Immune-hot tumors displayed higher levels of immune cell infiltration and immune checkpoint, in line with enriched immune escape pathways. Hematopoietic cell signal transducer (HCST), a molecular classifier used to differentiate immunological subtypes of PDAC, has shown a substantial link with the expression levels of cytotoxic markers, such as CD8A and CD8B. At the single cell level, we found that HCST was predominantly expressed in CD8T cells. By immunohistochemistry and survival analysis, we further demonstrated the prognostic value of HCST in PDAC. We identified HCST as a molecular classifier to distinguish PDAC immune subtypes, which may be useful for early diagnosis and targeted therapy of PDAC.

Abstract 1587: Multimodal spatial transcriptomics uncover distinct tumor microenvironment states and cell-cell communication networks in molecular pancreatic cancer subtypes

Abstract The tumor microenvironment (TME) presents a complex ecosystem comprising a diversity of immune and stromal cell populations that influence tumor progression, drug delivery and therapy outcome. High levels of inter- and intra-tumor heterogeneity in TME state are driven by molecular tumor phenotypes. Pancreatic ductal adenocarcinoma (PDAC), one of the most lethal cancer types, displays a high genetic heterogeneity along with an immunosuppressive TME. However, it remains largely elusive how distinct TME states are mechanistically influenced, and which molecular processes dictate the emergence of different modes of immunosuppression within the TME of molecular PDAC subtypes.Here, we performed a systematic analysis of functional associations between the major molecular PDAC subtypes, the classical and mesenchymal subtype, and their TME states. We describe the TME composition and complex cell-cell communication networks within PDAC subtypes using a multimodal integration of spatial transcriptomics (ST) with complementary approaches, such as scRNA-seq, MS-based Secretomics and multiplexed histocytometry. We generated ST data sets (Visium) of a tumor cohort derived from a Kras-driven PDAC mouse model. To analyze TME composition as well as spatial niches and cell type communities, we computationally enhanced the spot-resolution of ST datasets, followed by cell type deconvolution and cell-cell communication analysis to identify subtype-specific TME communities and communication networks.To this end, we generated a large resource of PDAC mouse models which represent molecular subtypes of the disease and mimic the heterogeneity of TME states found in human PDAC cohorts. This analysis revealed that a set of subtype-specific secreted factors shape the immunosuppressive PDAC TME via direct and indirect communication networks with immunosuppressive myeloid and T cells in molecular PDAC subtypes. Multimodal ST analysis delineated spatial subtype-specific TME communities as well as spatial communication patterns. We functionally investigate the tumor cell intrinsic regulation of the identified subtype-specific secreted factors, providing potential therapeutic vulnerabilities for more effective combinatorial subtype-specific therapies including immunotherapeutic approaches. Citation Format: Stefanie Baerthel, Chiara Falcomatà, Vanessa Goelling, Daniele Lucarelli, Rushin Gindra, Constantin Schmitt, Jonathan Swietlik, Felix Meissner, Marc Schmidt-Supprian, Dieter Saur. Multimodal spatial transcriptomics uncover distinct tumor microenvironment states and cell-cell communication networks in molecular pancreatic cancer subtypes [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 1587.

Abstract 3939: Ror2, a novel key regulator driving cell fate decisions throughout pancreatic tumor progression

Abstract Introduction: Reprogramming of pancreas cell fate drives development of pancreatic ductal adenocarcinoma (PDAC). Acinar cells, the most probable origin of pancreatic cancer, undergo a rapid cell identity switch towards a duct-like phenotype upon KrasG12D expression and when combined with pancreatitis or the loss of acinar differentiation factors. Metaplastic and dysplastic duct-like cells are heterogeneous with a proportion acquiring features reminiscent of gastric lineages. While some gastric signatures are maintained in the classical PDAC subtype, they are eroded in the more aggressive, basal-like PDAC. Since subtype identity has a major impact on prognosis and therapeutic targetability, druggable targets that regulate cellular reprogramming in pancreatic cancer can be exploited to increase sensitivity to therapy. Methods: To elucidate mechanisms responsible for early reprogramming, pancreatic tissue of mice with conditional KrasG12D expression and loss of Pdx1 was analyzed by single-nucleus ATAC-seq. Expression of identified target genes was studied in precancerous lesions and PDAC by using multiplex RNAscope and IHC staining. Computational analyses of publicly available sequencing data were used to establish correlation to PDAC subtype identity. Genes were functionally studied in PDAC cell lines. Results: By performing snATAC-seq and RNA-seq of early transformed pancreatic tissue, we discovered that acinar cells with the combined expression of KrasG12D and loss of Pdx1 activate expression of a gastric metaplastic gene signature accompanied by elevated levels of the receptor kinase Ror2. Ror2 is also highly expressed in distinct subpopulations of metaplastic and dysplastic cells, associated with a gastric neck cell phenotype and enhanced proliferative capacity. In contrast, Ror2Low lesions are characterized by a gastric pit cell-like and a senescent phenotype. Genetic ablation of Ror2 resulted in a shift in lesion identity, enriching those with a pit cell and senescent identity. In PDAC, we found that Ror2 anti-correlates with a similar gastric pit cell phenotype that is maintained in the classical subtype PDAC but is strongly associated with the more aggressive basal-like subtype. Overexpression of ROR2 in human PDAC cell lines with a classical differentiation induced loss of the classical gene signature as well as epithelial-to-mesenchymal transition. Moreover, ROR2 enforces a strong dependency on AKT signaling, causing increased vulnerability of ROR2-expressing cells to AKT inhibition, but increased resistance to the KRAS inhibitor MRTX1133. Conclusions: We discovered Ror2 as a critical determinant of precancerous lesion as well as PDAC subtype identity. Its role in driving an aggressive PDAC phenotype that is inherently resistant to Kras inhibition suggests that inhibiting this receptor tyrosine kinase will enhance sensitivity to the new generation of targeted therapies. Citation Format: Simone Benitz, Alexander Steep, Malak Nasser, Jonathan Preall, Ujjwal Mahajan, Ian Loveless, Holly McQuithey, Erick Davis, Hui-Ju Wen, Daniel Long, Thomas Metzler, Samuel Zwernik, Daniel Salas-Escabillas, Ling Huang, Nina Steele, Ivonne Regel, Filip Bednar, Howard Crawford. Ror2, a novel key regulator driving cell fate decisions throughout pancreatic tumor progression [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 3939.

Whole-genome bisulfite sequencing identifies stage- and subtype-specific DNA methylation signatures in pancreatic cancer

In pancreatic ductal adenocarcinoma (PDAC), no recurrent metastasis-specific mutation has been found, suggesting that epigenetic mechanisms, such as DNA methylation, are the major contributors of late-stage disease progression. Here, we performed the first whole-genome bisulfite sequencing (WGBS) on mouse and human PDAC organoid models to identify stage-specific and molecular subtype-specific DNA methylation signatures. With this approach, we identified thousands of differentially methylated regions (DMRs) that can distinguish between the stages and molecular subtypes of PDAC. Stage-specific DMRs are associated with genes related to nervous system development and cell-cell adhesions, and are enriched in promoters and bivalent enhancers. Subtype-specific DMRs showed hypermethylation of GATA6 foregut endoderm transcriptional networks in the squamous subtype and hypermethylation of EMT transcriptional networks in the progenitor subtype. These results indicate that aberrant DNA methylation contributes to both PDAC progression and subtype differentiation, resulting in significant and reoccurring DNA methylation patterns with diagnostic and prognostic potential.

Preoperative plasma fibrinogen and C-reactive protein/albumin ratio as prognostic biomarkers for pancreatic carcinoma.

Pancreatic carcinoma is characterised by high aggressiveness and a bleak prognosis; optimising related treatment decisions depends on the availability of reliable prognostic markers. This study was designed to compare various blood biomarkers, such as neutrophil/lymphocyte ratio (NLR), lymphocyte/monocyte ratio (LMR), platelet/lymphocyte ratio (PLR), C-reactive protein (CRP), albumin (Alb), plasma fibrinogen (PF), and CRP/Alb in patients with pancreatic carcinoma. Our study retrospectively reviewed 250 patients with pancreatic carcinoma diagnosed between July 2007 and December 2018. The Cutoff Finder application was used to calculate the optimal values of CRP/Alb and PF. The Chi-square test or Fisher's exact test was used to analyse the correlation of CRP/Alb and PF with other clinicopathological factors. Conducting univariate and multivariate analyses allowed further survival analysis of these prognostic factors. Multivariate analysis revealed that, in a cohort of 232 patients with pancreatic ductal adenocarcinoma (PDAC), the PF level exhibited statistical significance for overall survival (hazard ratio (HR) = 0.464; p = 0.023); however, this correlation was not found in the entire group of 250 patients with pancreatic carcinoma. Contrastingly, the CRP/Alb ratio was demonstrated statistical significance in both the entire pancreatic carcinoma cohort (HR = 0.471; p = 0.026) and the PDAC subgroup (HR = 0.484; p = 0.034). CRP/Alb and PF demonstrated a positive association (r=0.489, p<0.001) as indicated by Spearman's rank correlation analysis. Additionally, in 232 PDAC patients, the combination of the CRP/Alb ratio and PF had synergistic effects on prognosis when compared with either the CRP/Alb ratio or the PF concentration alone. PF concentration is a convenient, rapid, and noninvasive biomarker, and its combination with the CRP/Alb ratio could significantly enhance the accuracy of prognosis prediction in pancreatic carcinoma patients, especially those with the most common histological subtype of PDAC.

An alternative splicing signature defines the basal-like phenotype and predicts worse clinical outcome in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterized by extremely poor prognosis. PDAC presents with molecularly distinct subtypes, with the basal-like one being associated with enhanced chemoresistance. Splicing dysregulation contributes to PDAC; however, its involvement in subtype specification remains elusive. Herein, we uncover a subtype-specific splicing signature associated with prognosis in PDAC and the splicing factor Quaking (QKI) as a determinant of the basal-like signature. Single-cell sequencing analyses highlight QKI as a marker of the basal-like phenotype. QKI represses splicing events associated with the classical subtype while promoting basal-like events associated with shorter survival. QKI favors a plastic, quasi-mesenchymal phenotype that supports migration and chemoresistance in PDAC organoids and cell lines, and its expression is elevated in high-grade primary tumors and metastatic lesions. These studies identify a splicing signature that defines PDAC subtypes and indicate that QKI promotes an undifferentiated, plastic phenotype, which renders PDAC cells chemoresistant and adaptable to environmental changes.

Abstract C109: Nanostring-based subtyping of pancreatic ductal adenocarcinoma is strongly influenced by the stromal compartment

Abstract The prognostic significance of basal-like and classical subtypes of pancreatic ductal adenocarcinoma (PDAC) is well-established, and ongoing clinical trials are poised to validate the predictive utility of such subtypes in guiding first-line treatment decision-making. While the Purity-independent (PurIST)-based subtyping strategy provides a method for PDAC subtype determination based on the Nanostring gene expression quantification platform, the utility of this platform has not been tested in a real-world patient setting. Here, we leverage a retrospective dataset of patients with resectable PDAC (n=299) that received Nanostring sequencing in combination with comprehensive clinical metadata curation and histopathological analysis. All sequencing analyses were performed using formalin-fixed paraffin-embedded (FFPE) tumor whole sections. The proportion of basal-like cases (15%) was comparable with other resectable PDAC cohorts, and patients with basal-like tumors showed reduced overall survival (p=3.9e-4). Histopathological quantification of epithelial, stromal and normal components in each sample revealed significantly (p=0.007) reduced classical gene expression in stroma-high samples. Out of 29 patients with repeat sampling from different FFPE blocks derived from the same tumor and surgery, 31% of tumors received discordant subtypes calls and increases in the amount of stroma sequenced between two samples from the same tumor was negatively correlated with expression of classical subtype genes (p=0.02). Taken together, these data demonstrate the presence of intra-tumoral subtype heterogeneity, highlight the quantity of stroma sequenced as a major contributing factor in PurIST-based subtype determination and generate insight into the reproducibility of this subtyping strategy in a real-world clinical setting. Citation Format: James T. Topham, Steve E. Kalloger, Joanna M. Karasinska, Jenny E. Chu, Hassan Ali, Dongxia Gao, Christine Chow, Andrew Metcalfe, Jonathan M. Loree, David F. Schaeffer, Daniel J. Renouf. Nanostring-based subtyping of pancreatic ductal adenocarcinoma is strongly influenced by the stromal compartment [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 C109.

Abstract A072: Keratin 17-signature for stratification of chemotherapy in pancreatic adenocarcinoma

Abstract Introduction: Keratin 17 (K17) is a hallmark of the most aggressive molecular subtype of pancreatic ductal adenocarcinoma (PDAC). However, it is still unknown if K17 can predict the response to the two standard-of care treatments for PDAC: 1) 5-fluorouracil, irinotecan, leucovorin, and oxaliplatin (FFX) and 2) Gemcitabine/nab-paclitaxel (Gem/Nab). Thus, we hypothesized that K17 expression in patient tumors could be utilized as a biomarker to guide clinical decision-making in predicting the most effective standard-of-care treatment for patients with PDAC. Given that 85% of patients do not undergo resection, to circumvent this limitation we tested the predictive value of K17 using the tissue collected during endoscopic biopsies, which are routine in PDAC diagnosis. Methods: Our pilot study included 68 patients diagnosed with PDAC from Yale-New Haven Hospital treated with either FFX or Gem/Nab. Endoscopic biopsies were evaluated for tumor cellularity and then underwent an immunohistochemical (IHC)-based K17 test using the ABC detection method. Samples were scored by two independent pathologists using the PathSQ method. Results: Of the 68 patients included in the study, 20 (29.4%) were treated with Gem/Nab and 48 (70.6%) were treated with FFX. Based on Akaike’s Information Criterion, a K17 threshold of 45% and 60% were found to maximize stratification of patients by therapy response. At the 45% cutoff, 17 (25.0%) patients were found to have high K17 expression. At the 60% cutoff, 12 (17.6%) patients were found to have high K17 expression. Patients with low K17 expression were found to have similar overall survival (OS) despite treatment. However, patients with high K17 expression both at the 45% cutoff (p=0.031 and HR = 2.68 (CI 0.8, 8.99)) and 60% cutoff (p=0.006, HR = 6.79 (1.20, 38.32)) had decreased survival when treated with Gem/Nab compared to FFX. Conclusions: Patients with high K17 expression had lower overall survival than those with low K17 expression, validating our previous findings of K17 as a negative prognostic biomarker in PDAC. High K17 expression may be a promising predictive biomarker in PDAC, with an observed increase in OS in high K17-expressing patients treated with FFX compared to patients treated with Gem/Nab, indicating a potential biomarker to best determine response to standard-of-care treatments. Citation Format: Sumedha Chowdhury, Deanne Yugawa, Robert Tseng, Mauricio Mejia, Jill Lacy, Timil Patel, Luisa Escobar-Hoyos, Kenneth Shroyer, Guoping Cai, Marie Robert, Michael Cecchini, John Kunstman, James Farrell, Kimberly Johung. Keratin 17-signature for stratification of chemotherapy in pancreatic 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 A072.

Altered histone acetylation patterns in pancreatic cancer cell lines induce subtype‑specific transcriptomic and phenotypical changes.

Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at advanced tumor stages with chemotherapy as the only treatment option. Transcriptomic analysis has defined a classical and basal‑like PDAC subtype, which are regulated by epigenetic modification. The present study aimed to determine if drug‑induced epigenetic reprogramming of pancreatic cancer cells affects PDAC subtype identity and chemosensitivity. Classical and basal‑like PDAC cell lines PaTu‑S, Capan‑1, Capan‑2, Colo357, PaTu‑T, PANC‑1 and MIAPaCa‑2, were treated for a short (up to 96h) and long (up to 30weeks) period with histone acetyltransferase (HAT) and histone deacetylase (HDAC) inhibitors. The cells were analyzed using gene expression approaches, immunoblot analysis, and various cell assays to assess cell characteristics, such as proliferation, colony formation, cell migration and sensitivity to chemotherapeutic drugs. Classical and basal‑like PDAC cell lines showed pronounced epigenetic regulation of subtype‑specific genes through acetylation of lysine 27 on Histone H3 (H3K27ac). Moreover, classical cell lines revealed a significantly decreased expression of HDAC2 and increased total levels of H3K27ac in comparison with the basal‑like cell lines. Following HAT inhibitor treatment, classical cell lines exhibited a loss of epithelial marker gene expression, decreased chemotherapy response gene score and increased cell migration invitro, indicating a tumor‑promoting phenotype. HDAC inhibitor treatment, however, exerted minimal reprogramming effects in both subtypes. Epigenetic reprogramming of classical and basal‑like tumor cells did not have a major impact on gemcitabine response, although the gemcitabine transporter gene SLC29A1 (solute carrier family 29 member 1) was epigenetically regulated.

Abstract A035: Stromal composition, fibroblast heterogeneity and spatial organization in pancreatic adenocarcinoma

Abstract Background: The pancreatic ductal adenocarcinoma (PDAC) microenvironment is characterized by highly abundant stromal fibroblasts that are hypothesized to influence tumor behavior. While recent studies have identified multiple populations of stromal fibroblasts with divergent roles in PDAC biology, stromal composition remains incompletely characterized in human tumors, including the landscape of fibroblast subtypes and their spatial organization. Design: We designed multiplex immunofluorescence assays to quantify tumor cells (cytokeratin), immune cells (CD45), fibroblasts (αSMA, CD74, FAP, LaminA), other cells (CD31, CD56, CALD1, NG2), and collagen I in fixed tissue sections. Combinatorial fibroblast marker expression identified myofibroblasts (myCAF), inflammatory fibroblasts (iCAF), antigen-presenting fibroblasts (apCAF), and other hybrid fibroblast subtypes. We characterized fibroblast populations in up-front resected and neoadjuvant-treated cohorts of patients with localized PDAC and in patients with biopsies of metastatic lesions. Using digital imaging, supervised machine learning, and spatial proximity metrics, we quantified cell phenotypes, fibroblast subtype composition and spatial organization at the single-cell level and in the context of tumor clinicopathologic features and patient outcomes. Results: Across 301 up-front resected tumors, we cumulatively analyzed 1.7 million cells, including 611,000 fibroblasts. Stromal fibroblast density ranged from 632 to 4150 cells/mm2. Five main fibroblast subtypes constituted more than 85% of the fibroblast population in these tumors: αSMA+ (myCAF), FAP+αSMA+ (FAP+ myCAF), LaminA+ (iCAF), αSMA+ LaminA+ (myCAF/iCAF), and FAP+ αSMA+ LaminA+ (FAP+ myCAF/iCAF). Unexpectedly, 39% of fibroblasts showed co-expression of markers previously considered distinct for major fibroblast subtypes. By unsupervised clustering of fibroblast subtype proportions, we identified 3 fibroblast-defined tumor subgroups, including tumors rich in FAP+ fibroblasts, hybrid fibroblasts, and single positive fibroblasts (myCAFs, iCAFs, and apCAFs), which were associated with patient survival. Furthermore, fibroblast subtypes were spatially organized, with preferential localization of FAP+ myCAFs near tumor cells and iCAFs more distant from tumor cells yet closer to immune cells. FAP+ myCAFs were more abundant in basal-like tumors than in classical tumors, and FAP+ myCAFs were located closer to basal-like tumor cells than classical tumor cells within individual tumors. Compared to up-front resected primary tumors, neoadjuvant FOLFIRINOX treated tumors and metastatic lesions harbored distinct fibroblast profiles. Conclusion: Fibroblasts in the PDAC microenvironment are heterogeneous both in abundance and subtype composition, exhibit distinct spatial organization and are associated with patient outcomes. Treatment with FOLFIRINOX alters the composition of fibroblast subtypes in primary PDAC, and metastatic PDAC lesions have a different fibroblast composition compared to primary tumors. Citation Format: Dalia Elganainy, Andressa Dias Costa, Alexander Jordan, Suryun Kim, Sara A. Väyrynen, Hannah L. Williams, Chen Yuan, Douglas A. Rubinson, Kimberly Perez, Harshabad Singh, Richard F. Dunne, Thomas E. Clancy, David C. Linehan, Daniel T. Chang, Aram F. Hezel, Albert C. Koong, Andrew Aguirre, Brian M. Wolpin, Jonathan A. Nowak. Stromal composition, fibroblast heterogeneity and spatial organization in pancreatic 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 A035.

Abstract C067: Correlation of keratin17 expression with tumor cell proliferation and invasion in PDAC

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) shows variable degrees of differentiation, with both intratumoral, regional, and case to case heterogeneity, including glandular elements, sheet-like aggregates, cell clusters, and single diffusely infiltrative tumor cells. Prior research from our lab and others have established keratin 17 (K17) to be a defining hallmark of the basal molecular subtype of PDAC. In addition to its role as a component of the cytoskeleton, soluble forms of K17 undergo nuclear translocation to drive cell cycle progression and chemoresistance to first line chemotherapy. While K17 is heterogeneously expressed in the gland-forming elements of PDACs, it is most consistently expressed in tumor cells which are either in small groups or are single diffusely infiltrative. The aims of the current study are to define the correlation between K17 expression and tumor cell differentiation, with the focus on glandular versus single diffusely infiltrative components of PDAC, and to relate these findings to established biomarkers of cell proliferation and invasion. Methods: Archival human PDACs were provided by the Stony Brook Cancer Center Biobank and K17 immunohistochemistry was performed by indirect immunoperoxidase method, as previously described, to select cases with both glandular and diffusely infiltrative cell components and heterogeneous K17 expression. Multiplex immunofluorescence with a panel of antibodies to K17 (Cell Signaling Technology), pan-cytokeratin, Ki-67 and vimentin [KS1] (Miltenyi Biotec) was performed on 5-micron FFPE sections using the MACSima system (Miltenyi Biotec). Distribution patterns of K17 were evaluated in glandular and diffusely invasive components and were related to the Ki-67 status. Results: Cytoplasmic staining for K17 was found in the minority of tumor cells in glands and displayed intraglandular heterogeneity but was found in most diffusely infiltrative tumor cells. Also, nuclear K17 was rarely detected in the glandular components but was found in a high proportion of the diffusely infiltrative cells. Ki-67 was detected mainly in glandular cells, unrelated to K17 status, and rarely in single diffusely infiltrative cells, never co-localizing with nuclear K17. Of note, only a small fraction of tumor cells co-expressed K17 and vimentin, suggesting that majority of diffusely infiltrative tumor cells were not engaged in epithelial to mesenchymal transition. Conclusion: While cytoplasmic K17 is heterogeneously expressed in the glandular components of PDAC, strong staining for K17 in both the cytoplasm and the nucleus is a hallmark of diffusely infiltrative, Ki-67-negative tumor cells. These observations support the paradigm that tumor cells are committed to either cell division in the glandular components, or to diffuse single cell invasion, highlighted by increased cytoplasmic and nuclear K17 expression. Therefore, the results emphasize the importance of understanding the expression of PDAC biomarkers in both gland-forming elements and diffusely infiltrative tumor cells. Citation Format: Shayan Sarkar, Lyanne Oblein, Michael Horowitz, Luisa Escobar-Hoyos, Natalia Marchenko, Kenneth Shroyer. Correlation of keratin17 expression with tumor cell proliferation and invasion in PDAC [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 C067.