Basal-like Phenotype Research Articles

ASCL1 Drives the Development of Neuroendocrine Prostate Cancer.

Therapeutic resistance to androgen receptor (AR)-targeting agents remains a significant clinical problem during the treatment of prostate cancer, with the incidence rate of resistant disease increasing as more men are treated with next-generation AR-targeted therapies. Lineage plasticity and progression to neuroendocrine prostate cancer (NEPC) are mechanisms by which prostate tumors lose dependence on androgen signaling and escape treatment. Although many known genetic alterations can predispose tumors to acquiring the NEPC phenotype, it remains unclear what, if any, drivers are essential to this progression. In this issue of Cancer Research, Rodarte and colleagues identified ASCL1 as one such essential regulator. Through the use of genetically engineered mouse models, the authors demonstrated that whereas ASCL1 was dispensable for tumor formation and growth, ASCL1 loss nearly completely abrogated the development of NEPC and instead redirected lineage trajectories toward a basal-like phenotype. This study provides an important new model for the study of NEPC, reveals the ability of ASCL1+ NEPC cells to also assume a NEUROD1+ state, and demonstrates the changes to tumor cell phenotypes following ASCL1 loss. See related article by Rodarte et al., p. 3522.

Abstract A077: The role of RhoV in basal-like pancreatic cancer

Abstract Background Pancreatic ductal adenocarcinoma is a devastating disease lacking targeted therapy. Basal-like pancreatic cancer is a tumor subtype with a worse clinical outcome than other subtypes. These cancers are characterized by the expression of basal keratins and mesenchymal markers. However, the genes that drive the basal-like phenotype are poorly understood. Ras homolog family member V (RhoV) is one of the Rho GTPases, and it has been demonstrated to drive the progression of lung and breast cancers. The current study aims to reveal the role of RhoV in basal-like pancreatic cancer. Design RhoV, p63, and CK5/6 were stained in sequential sections by immunohistochemistry. Expression of RhoV in pancreatic cancer and cell lines was reanalyzed based on the data from ProteinAtlas and Broad Insitute DepMap Portal. Basal cell line, BxPC3, and non-basal cell line, Panc1 were selected for functional evaluation based on their differentiated RhoV expression. RhoV gene was overexpressed and knocked down using the CRISPR/gRNA-based Lentiviral system, followed by sphere formation, colony formation, migration, and invasion assays. Results RhoV, p63, and CK5/6 were expressed in the same histologic location of basal pancreatic cancer. The gene expression level of RhoV was co-expressed with p63 (a classic basal marker) in four pancreatic cancer cell lines (broadinstitute.org). Knockout of RhoV by three runs of gRNAs in BxPC3 cells all significantly attenuated tumor sphere formation with less colony formation as compared to mock knockout. Overexpression of RhoV in non-basal-like cells, Panc 1, significantly increased the size of sphere formation, numbers of colony formation, and p38 activation compared to EV control. Cell migration and invasion assays showed the same RhoV-dependent migration and invasion in corresponding cells. Panc1 cells with RhoV knockout significantly generated smaller tumor xenografts in immunodeficient mice and RhoV overexpression led to larger tumor sizes. Conclusion Finding the driver of the basal-like phenotype helps to reveal the pathophysiology of the basal-like subtype of pancreatic cancer and facilitates the identification of new targets for therapeutic purposes. Our preliminary results indicated that RhoV, a small G protein from the Rho family of GTPases, played essential roles in tumor proliferation and progression, by activating the p38 signaling pathway. Further study will be focused on revealing Rhov's downstream pathways and exploring the role of RhoV in apoptosis/cell cycle, cell metabolism, autophagy, etc. in basel-like pancreatic cancer. Citation Format: Shang Wu, Jia Feng, Selina Gao, Ting Wang, Zebang Li, Yifei Liu, Chiung-Kuei Huang, Shaolei Lu. The role of RhoV in basal-like pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A077.

Abstract C063: Inhibition of PRMT5 reduces aggressiveness in basal-like pancreatic ductal adenocarcinoma

Abstract The basal-like pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive type of mesenchymal PDAC that resists treatment and has a poor prognosis. Understanding the mechanisms driving basal-like PDAC biology is crucial for unraveling the intricacies of PDAC plasticity and developing effective treatment strategies for this aggressive tumor. Recent studies from our laboratory have shown that protein arginine methyl transferase 5 (PRMT5) significantly contributes to PDAC plasticity and progression towards the basal-like subtype. Specifically, our data show that patients with high levels of PRMT5 expression have a worse outcome, thus arguing that PRMT5 plays a role in PDAC aggressiveness and outcome. Moreover, our experiments indicate that inhibiting PRMT5, either genetically or chemically, in basal-like PDAC cells induces the expression of epithelial markers like GATA6 and E-CADHERIN, suggesting that PRMT5 promotes mesenchymal features in PDAC. Using wound healing and transwell assays, we have demonstrated that pharmacological inhibition of PRMT5 significantly suppresses cell migration and invasion. Additionally, colony formation and cell proliferation are markedly reduced upon PRMT5 inhibition in basal-like PDAC. Collectively, these findings suggest that inhibiting PRMT5 can effectively constrain the aggressive cellular features characteristic of basal-like PDAC, such as cell proliferation, clonogenicity, and migration. Recent research indicates that PRMT5 preferentially methylates splicing factors in various cell types, implying that RNA splicing regulation is crucial to PRMT5’s role in enhancing tumor plasticity and aggressiveness. We are currently investigating whether PRMT5-mediated RNA splicing alterations contribute to the maintenance of the basal-like PDAC phenotype. These studies provide key evidence that PRMT5 is essential for maintaining the aggressive characteristics of basal-like PDAC, highlighting its potential as a therapeutic target for this challenging cancer subtype. Citation Format: Christina Wang, Zamira Guerra Soares, Dakarai Esgdaille, Stephano Spano Mello. Inhibition of PRMT5 reduces aggressiveness in basal-like pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C063.

BUB1 as a novel marker for predicting the immunotherapy efficacy and prognosis of breast cancer.

Budding uninhibited by benzimidazole 1 (BUB1) is a highly conserved serine/threonine kinase, showing prominent importance for proper function during mitosis. However, little is known about BUB1 mRNA expression in breast cancer (BRCA) and its correlation with prognosis and immune infiltration. Hence, we aimed to unveil its potential as groundbreaking biomarkers for immunotherapy efficacy and the prognosis of BRCA. Database for Annotation, Visualization, and Integrated Discovery (DAVID) is a potent tool for identifying significant clusters of genes and pathways in the resulting dataset. In this study, gene set enrichment analysis of BUB1 was conducted using DAVID. The clinical characteristics of patients with or without altered BUB1 mRNA expression were compared using cBioPortal. Tumor Immune Estimation Resource (TIMER) is a known as database for comprehensive analysis of tumor-infiltrating immune cells in various cancers. In the present study, the relationship between BUB1 expression and the abundance of immune infiltrates was explored using TIMER in BRCA. Immunohistochemistry staining was performed to analyze the protein expression of BUB1 in tumor tissue specimens. We used PrognoScan and Kaplan-Meier Plotter to evaluate the prognosis of patients with different BUB1 expression levels. The expression of BUB1 in various tumor tissues was higher than that in adjacent normal tissues. BUB1 was mainly localized to the nucleoplasm and additionally localized to the cytosol. Functional enrichment analyses revealed that the cell cycle was the most significant pathway. Abnormal BUB1 mRNA expression was more frequently detected in invasive ductal carcinoma with higher histological grades and BRCAs with estrogen receptor (ER)-negative, human epidermal growth receptor 2 (HER2)-negative, and basal-like phenotypes. The BUB1 expression was correlated positively with tumor purity, B cells, CD8+ T cells, CD4+ T cells, neutrophils, and dendritic cells, while BUB1 had no significant correlation with macrophages. The results of immunohistochemical staining from clinical samples further confirmed that BUB1 was overexpressed in BRCA compared to benign tumor (fibroadenoma of breast) (P<0.01). BRCA patients with lower BUB1 expression had a better prognosis than those with higher BUB1 expression in overall survival (OS) curves, distant metastasis-free survival (DMFS) curves, and relapse-free survival (RFS) curves (P<0.05). Our results suggest that BUB1 is a potential molecular biomarker for evaluating the prognosis and predicting the effectiveness of immunotherapy for BRCA.

Clinical and molecular features of early onset pancreatic adenocarcinoma.

Pancreatic adenocarcinoma (PDAC) is a major health burden and may become the second cause of death by cancer in developed countries. The incidence of early-onset pancreatic cancer (EOPC, defined by an age at diagnosis <50 years old) is increasing. Here, we conducted a study of all PDAC patients followed at our institution. Patients were classified as EOPC or non-early onset (nEOPC, >50). Eight hundred and seventy eight patients were included, of which 113 EOPC, exhibiting a comparable performance status. EOPC were more often diagnosed at the metastatic stage (70.0% vs 58.3%) and liver metastases were more prevalent at diagnosis (60.2% vs. 43.9%). The median overall survival (OS) from diagnosis was 18.1 months, similar between EOPC and nEOPC. Among patients who underwent surgery, recurrence-free survival was similar between age groups. Among metastatic patients, first line progression free survival was similar but EOPC received more treatment lines (72.3% vs. 58.1% received ≥2 lines). Regarding molecular alterations, the mean tumor mutational burden (TMB) was lower in EOPC (1.42 vs. 2.95 mut/Mb). The prevalence of KRAS and BRCA1/2 mutations was similar, but EOPC displayed fewer alterations in CNKN2A/B. Fifty eight patients (18.6%) had actionable alterations (ESCAT I-III) and 31 of them received molecularly matched treatments. On the transcriptomic level, despite its clinical aggressiveness, EOPC was less likely to display a basal-like phenotype. To conclude, EOPC were diagnosed more frequently at the metastatic stage. OS and 1st line PFS were similar to nEOPC. EOPC displayed specific molecular features, such as a lower TMB and fewer alterations in CDKN2A/B.

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...

Genomic and tumor microenvironment dynamics of brain metastases in breast cancer.

1018 Background: Brain metastases (BM) in breast cancer (BC) have a poor prognosis, with median survival at 7.2-13 months. Interplay between genomic evolution of cancer cells and development of BM is obscure. We sought to identify genomic aberrations associated with BM. Methods: We included 14095 BC samples: 429 BM, 7858 extra-cerebral metastases (ECM) and 5808 primary tumors (PT) were analyzed by next generation sequencing of DNA (NextSeq, 592 genes and NovaSeq, WES) and RNA (NovaSeq, WTS) (Caris Life Sciences, AZ). Tumor mutational burden-high (TMB-H) was defined as ≥10 mt/MB. Cut-off for PD-L1 immunohistochemistry positivity was ≥2 intensity and &gt;5% staining (SP142). Global loss of heterozygosity (gLOH) used a cut-off of ≥ 16%. PAM50 was evaluable for a subset (n=9724, 69%) with WTS data. Statistical significance determined using chi-square and Mann-Whitney U test and adjusted for multiple comparisons (q&lt;0.05). Results: Median age was lower in BM than ECM and PT (55 vs 62 vs 59 years, q&lt;0.05). BM subtype was triple negative (TNBC, 40.1%), HR+/HER2- (30.5%), or HER2+ (29.4%) vs. ECM primarily HR+/HER2- (65.4%) and PT HER2+ (52.5%). BM were Basal-like (35.3%) or HER2-enriched (35.3%), whereas ECM were Luminal B (47.2%) and PT were Basal-like (34.4%) or Luminal B (34.6%). The Table summarizes molecular findings. In HR+/HER2- BC, BM were associated with TMB-H vs. ECM and PT (q&lt;0.05). BM had higher GATA3-mt and ESR1-mt compared to PT (q&lt;0.05). In HER2+ BC, BM had lower PD-L1+ (11.8% vs 39.3%) and higher ESR1-mt than PT. BM had higher ERBB2-amp (93.5% vs 75.2%) and RARA-amp (27.3% vs 6.7%) than PT (q&lt;0.05). TNBC BM had higher proportion of TMB-H tumors but lower PD-L1+ (20.8% vs 50.7%) than PT. BM had increased gLOH than ECM (59.2% vs 36.2%). PIK3CA was lower in BM vs. ECM. In all subtypes, BM, when compared to ECM and PT respectively, were associated with decreased AR+ (HR+/HER2-: 57.7% vs 80.8% vs 85.7%; HER2+: 54.4% vs 77.1% vs 81%; TNBC: 15.1% vs 27.7% vs 23.1%), increased dendritic cell infiltration (HR+/HER2-: 3.2% vs 2.6% vs 2.5%; HER2+: 3.85% vs 2.41% vs 2.36%; TNBC: 3.96% vs 2.89% vs 3.05%) but lower IFN score (HR+/HER2-: -0.56 vs -0.41 vs-0.35; HER2+: -0.53 vs -0.39 vs -0.30; TNBC: -0.55 vs -0.30 vs -0.28). Conclusions: BM in BC are more frequently associated with TNBC and Basal-like BC phenotypes than ECM or PTs. BM have a higher proportion of ESR1-mut than PTs, highlighting a possible association between endocrine resistance and development of BM. BM had lower IFN score and PDL-1 expression highlighting an immunosuppressed tumor microenvironment. [Table: see text]

Abstract A016: NRF2 activation promotes a fitness disadvantage in normal urothelium and drives a basal-like phenotype

Abstract Introduction: Nuclear factor erythroid 2-related factor 2 (NRF2) is a transcription factor that plays a key role in protecting cells from oxidative stress. NRF2 is negatively controlled by Kelch-like ECH-associated protein 1 (KEAP1), which facilitates NRF2 ubiquitination and proteosomal degradation under homeostatic conditions. NRF2 activating mutations occur at a frequency of 5.9% in muscle-invasive bladder cancer (MIBC). However, the role of NRF2 in MIBC has not been fully understood. The aim of this study is to clarify how NRF2 affect to the normal epithelial cells and the tumor cells in bladder. Methods: We used genetically engineered mice (GEM) with a Cre inducible Nrf2 activating mutation (LSL-Nrf2-E79Q). To evaluate how Nrf2 affects the tumorigenesis process in vivo, the N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN) was administered to Upk3a-CreERT2; LSL-Nrf2-E79Q/+ (UN) mice. We also established normal urothelial organoids and BBN tumor derived organoids from wild-type (WT) and Krt5-CreERT2; LSL-Nrf2-E79Q/+ (K5N) mice for ex vivo study. To induce overexpression of NRF2, we utilized KI696 (KEAP1-NRF2 inhibitor) as a pharmacological agent and performed NAD/NADH assay to quantify the reductive stress. Additionally, we performed single cell RNA sequencing (scRNA-seq) with WT, UN and K5N mice bladder to identify the effect of Nrf2E79Q on the normal epithelial cells. Results: In BBN induced tumor model in vivo, UN mice did not differ in time to tumor development from the control WT mice. Furthermore, UN tumors had lost the post-recombination allele of LSL-Nrf2-E79Q in genomic PCR, meaning cells expressing Nrf2E79Q are selected against during the process. In ex vivo study, KI696 induced reductive stress in both WT normal urothelial organoids and BBN tumor derived organoids, but inhibited cell proliferation only in normal urothelial organoids. In K5N organoids, Nrf2E79Q activation enhanced relative mRNA expression of a number of basal related genes. In addition to that, vehicle organoids in differentiation media showed phenotypic differentiation, whereas those treated with tamoxifen did not demonstrate phenotypic signs of differentiation suggesting Nrf2 activation promotes a basal-like phenotype. Furthermore, we annotated three clusters in mice bladder epithelial cells as luminal, intermediate and basal using scRNA-seq and looked at their proportion among WT, UN and K5N mice. We found that the percentage of luminal cells was decreased and intermediate and basal cells increased in both UN and K5N mice compared to WT mice. This indicated that Nrf2E79Q promotes disadvantage in luminal cells in UN mice, whereas it contributes to the increase in intermediate and basal cells in K5N mice. Conclusion: These results suggested that Nrf2E79Q promotes a fitness disadvantage in normal mice urothelium. Furthermore, Nrf2E79Q inhibits differentiation of K5N organoids and drives a basal-like phenotype in GEM models. Further investigation is needed to clarify the mechanism of NRF2 activating mutation contributing the tumorigenesis in bladder. Citation Format: Akihiro Hamada, Yuki Kita, Di Wu, Mi Zhou, Sean Clark-Garvey, Andrew Gdowski, Michael Sturdivant, Wolfgang Beckabir, Elliott Drew Toomer, Emily Kounlavong, Lucia Lim, Kathryn Gessner, Jeffrey Damrauer, William Kim. NRF2 activation promotes a fitness disadvantage in normal urothelium and drives a basal-like phenotype [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr A016.

An insight into immunohistochemical profile of triple negative breast carcinoma in a tertiary care center

Introduction: Triple Negative Breast Cancer (TNBC) is a type of breast cancer that fails to express Estrogen Receptor (ER), Progesterone Receptor (PR) and Human Epidermal Growth Factor Receptor 2 (HER2) in Immunohistochemical analysis. TNBC has a unique molecular profile, aggressive nature and lack of efficient targeted therapies. The aim of the study was to evaluate the expression of basal markers like Epidermal Growth Factor Receptor (EGFR) and Cytokeratin 5/6 (CK 5/6) and to correlate their expression with the clinico-pathological parameters, thus enabling the identification of the aggressive basal like phenotype of TNBC in resource-constrained settings. Methodology: The study was conducted at a South Indian tertiary care centre for 2 years. Data such as age of presentation, tumour measurements, margins and necrosis, numbers, levels and sizes of lymph nodes were collected. Data on histological type and grade, in situ component, lymphovascular and perineural invasion, stromal reaction and lymph node status were recorded. Primary Immunohistochemical studies were performed for the markers ER,PR and HER2.Patients with negative expression for all the three markers were identified. IHC studies for EGFR and Cytokeratin 5/6(CK5/6) were done on tissue blocks and the expression of these two markers were equated with the clinico-pathological parameters. Results: Among the 94 cases, 44 cases (46.8%) expressed CK5/6 and 46 (48.9%) expressed EGFR. A plausible association was noted between the expression of the two markers with age of the patient, tumour size, histological grade and tumour necrosis. Conclusion: Combination of the time honoured gross and histopathological examinations along with the application of basal markers like CK 5/6 and EGFR, helps in identifying the basal-like phenotype with dismal clinical outcome among the triple-negative breast cancers in resource-constrained settings. An insight into such an aggressive tumour, provided by these markers may be critical in designing personalized treatment strategies for such patients.

Abstract 6125: Differential expression of chemokine genes by race and Breast Cancer Consensus Subtypes in hormone receptor positive breast cancer

Abstract Hormone receptor positive (HR+) breast cancer is a heterogeneous subtype and African American women (AAW) are twice as likely to have HR+ tumors with lower levels of HR staining (1-10%) compared to European American women (EAW). These tumors are associated with substantially worse survival compared to strongly HR+ tumors. We further hypothesized that HR+ tumors from AAW would be more likely to have molecular features typically associated with HR-negative breast cancer and poor prognosis. To test this, we used the Breast Cancer Consensus Subtyping (BCCS) method and evaluated expression of chemokine receptors known to be differentially expressed by race, PAM50 subtypes, and survival. We downloaded The Cancer Genome Atlas (TCGA) expression data for 394 female EA and AA HR+/HER2- breast cancer patients using the cBio Cancer Genomics Portal. Breast Cancer Consensus Subtypes (BCCS) were determined using the R program BCCSclassifier. BCCS classification results in five subtypes: ER-negative non-basal-like (BCS1), ER-negative basal-like (BCS2), ER+ highly proliferative with poor prognosis (BCS3), ER+ stromal infiltration with good prognosis (BCS4), and ER+ hormone response genes highly expressed with good prognosis (BCS5). High and low expression of chemokines (ACKR1, ACKR4, CCR3, CCR6, CCRL2, CXCR1, CXCR2, CXCR4, CXCR6, CX3CR1) was dichotomized based on median expression of each gene within our study cohort. Distribution of BCCS by race was assessed with multinomial logistic regression. Associations between chemokine gene expression, BCC subtype and race were evaluated using logistic regression. An alpha value of 0.05 was set to determine statistical significance. From the TCGA cohort, AAW were more likely to have the BCS2 ER-negative basal-like phenotype (OR=7.17, p&amp;lt;0.001) as well as the poor prognosis highly proliferative ER+ BCS3 phenotype (OR=2.83, p=0.036) versus the high hormone expression BCS5 subtype. In multivariable models evaluating both race and BCCS subtype, AAW were 6.17 times more likely to have lower than median expression of CX3CR1 (p&amp;lt;0.001) and CXCR2 (OR=2.23, p=0.0096) compared to EAW. Notably, all chemokine receptors consistently showed significantly lower expression in BCS1-4 subtypes compared to BCS5. For CCRL2, the effect estimates for BCS4 vs. BCS5 significantly differed by race (p=0.039). In AAW, BCS4 was associated with higher than median expression (OR=1.99, p=0.49), although not statistically significant. In EAW, BCS4 was associated with lower than median expression (0.23, p&amp;lt;0.001). Our findings show that AAW with HR+ breast cancer have tumors with more inherently aggressive molecular subtypes associated with poor prognosis compared to EAW. These results also further support the premise that HR+/HER2- tumors are highly heterogeneous and strongly suggest that chemokine gene expression is associated with breast cancer subtype. Citation Format: Abigail M. Fielder, Manohar Ratnam, Gregory Dyson, Kristen Purrington. Differential expression of chemokine genes by race and Breast Cancer Consensus Subtypes in hormone receptor positive breast cancer [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 6125.

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 A108: Spatial transcriptomic analysis of venous invasion in human pancreatic adenocarcinoma reveals widespread attenuation in features associated with aggression and mortality

Abstract In pancreatic ductal adenocarcinoma (PDAC), venous invasion (VI) is a necessary precursor to hematogenous dissemination, but little is known about the molecular features of VI. To investigate these features, we performed spatial transcriptomic analysis of foci of VI, PDAC in stroma (PDAC-S), and normal pancreatic duct in surgically resected human PDAC tissue samples from eight treatment naïve patients. We performed GeoMx Digital Spatial Profiler analysis of 35 regions of VI, 39 regions of PDAC-S, and 14 regions of normal duct. Through unbiased hierarchical clustering, we observe that normal duct foci cluster more closely to VI than to PDAC-S. When comparing differentially expressed genes (DEGs) between VI and PDAC-S, we observe that VI shows high expression of genes which are highly expressed by normal duct relative to PDAC-S. These genes have well characterized roles in normal pancreatic exocrine function and development. Within the upregulated VI DEGs, we observe another group of genes which are elevated in VI relative to both PDAC-S and normal duct, which includes mucins, cell adhesion molecules such as CEACAM5 and TSPAN8, and transcription factors such as FOS and ZFPM1. Pathway analysis of the differentially expressed genes reveals enrichment for MYC signaling and oxidative phosphorylation. When compared to PDAC-S, VI demonstrates downregulation of many genes involved in epithelial-mesenchymal-transition (EMT), such as collagens, laminins, S100 proteins and other EMT-associated genes such as FN1, VIM, MMP11, TGFBI, TGM2, and POSTN. When compared to PDAC-S, VI shows increased expression of genes from the classical phenotype of the Moffitt classification, while PDAC-S has increased expression of the basal-like signature. We performed morphologic subtyping of the VI foci, with 11 samples classified as VI-Destructive (disruption of the venous lumen and associated fibrosis) and 22 samples classified as VI intraepithelial neoplasia-like or VI-IN-Like (complete circumferential replacement of the venous lumen). Compared to VI-IN-Like, VI-Destructive shows increased expression of EMT-associated genes, increased expression of the basal-like gene signature, and reduced expression of the classical signature. Compared to VI-IN-Like and PDAC-S, VI-Destructive showed intermediate expression of EMT-associated genes. Transfer learning of our data to publicly available RNA-Seq data sets reveals that metastatic pancreatic cancer bears greater similarity to PDAC-S than to VI, and circulating tumor cells express features of both VI and PDAC-S. Overall, our data suggest that VI regains transcriptional features of normal ductal epithelium, and demonstrates widespread downregulation of features associated with aggression and mortality, such as genes associated with EMT and the basal-like phenotype. We observe that this transcriptional shift is associated predominantly with the VI-IN-Like morphology, and that VI-Destructive is a transcriptional intermediate between VI-IN-Like and PDAC-S. Citation Format: Alexander T.F. Bell, Peter Chianchiano, Katsuya Hirose, Doreen Gisder, Alexander I. Damanakis, Luciane T. Kagohara, Elana J. Fertig, Laura D. Wood. Spatial transcriptomic analysis of venous invasion in human pancreatic adenocarcinoma reveals widespread attenuation in features associated with aggression and mortality [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 A108.

Abstract C021: Clinicopathological features and basal-like phenotype expression in triple negative breast cancer at Uyo, Niger-Delta region of Nigeria

Abstract (A) AN INTRODUCTORY SENTENCE INDICATING THE PURPOSES OF THE STUDY: Patients of African Ancestry (AA) experience higher rates of TNBC and mortality than European Ancestry (EA) patients, despite lower overall breast cancer (BC) incidence. BC is the most frequently diagnosed cancer in Nigeria and USA as well as being the second most common cause of cancer-related death in women, although there have been significant advances in treatment strategies over the past few decades. In addition to conventional therapies, in the molecular era, breast cancer patients often receive targeted treatments based on their unique cancer biology in both adjuvant and neoadjuvant settings. There is limited data on the prevalence of Basal-like breast carcinomas in Nigeria owing to the high cost of gene expression profiling which is the gold standard for molecular classification and immunohistochemistry (which can be used as a surrogate). This study aimed to analyze the clinico-pathological features and immunohistochemical expression of basal-like phenotype in TNBC at Uyo, as well as stratifying of invasive breast carcinomas into main molecular subtypes and correlating the Basal-like breast carcinoma subtype with the size of tumour, grade and age of patient. (B) A BRIEF DESCRIPTION OF PERTINENT EXPERIMENTAL PROCEDURES: One hundred and fifteen formalin fixed, paraffin embedded blocks of Invasive breast carcinomas were assembled, stained and analysed for ER, PR, HER-2, Ki67, CK5/6 and EGFR proteins using immunohistochemistry. Stratification of invasive breast carcinomas into four (4) main molecular groups (Luminal, HER-2, Basal-like and normal breast subtypes) was done. Patient’s record and immunohistochemical results were reviewed. The data was analyzed and their results were presented as tables, graphs and photomicrographs. (C) A SUMMARY OF THE NEW, UNPUBLISHED DATA: The mean age of the TNBC patients was 39.0 years (range: 25–74 years). Invasive carcinoma (no special type) was the predominant histologic subtype (90.4%). Out of the 115 cases, ER, PR and HER-2 were positive in 53.0 %, 33.0 % and 12.2 % of cases respectively. CK5/6 and EGFR were also positive in 16.5% and 11.3 % of cases respectively. Ki67 was high (&amp;gt;14 %) in 26.1 % of cases. Our study illustrated that majority of TNBC expressed basal-like markers (51.3 %) and occurred at the 35-44 years age group (33.3%) with a substantial proportion being grade 3 (poorly differentiated) carcinomas (48.7%). There was a significant association between basal-like breast carcinoma and tumour grade.(D) CONCLUSION: Our study illustrated that majority of TNBC expressed basal - like markers and occurred at 35-44 years age group with a substantial proportion being grade 3 (poorly differentiated) carcinomas. There was a positive correlation between basal-like breast carcinoma and tumour grade. It is hoped that research in unraveling biology of basal-like carcinomas among patients of African Ancestry (AA) and Caucasian Ancestry (CA) will be carried out in the future. Citation Format: Emmanuel Kunle Abudu, Obioha Kanu, Ikwo Jonathan Kudamnya, Emem Imo Akpanudo, Oluwasayo Omolara Abudu. Clinicopathological features and basal-like phenotype expression in triple negative breast cancer at Uyo, Niger-Delta region of Nigeria [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C021.

Association between SMAD4 Mutations and GATA6 Expression in Paired Pancreatic Ductal Adenocarcinoma Tumor Specimens: Data from Two Independent Molecularly-Characterized Cohorts.

Several molecular biomarkers have been identified to guide induction treatment selection for localized pancreatic ductal adenocarcinoma (PDAC). SMAD4 alterations and low GATA6 expression/modified "Moffitt" basal-like phenotype have each been associated with inferior survival uniquely for patients receiving 5-FU-based therapies. SMAD4 may directly regulate the expression of GATA6 in PDAC, pointing to a common predictive biomarker. To evaluate the relationship between SMAD4 mutations and GATA6 expression in human PDAC tumors, patients with paired SMAD4 mutation and GATA6 mRNA expression data in the TCGA and CPTAC were identified. In 321 patients (TCGA: n = 180; CPTAC: n = 141), the rate of SMAD4 alterations was 26.8%. The rate of SMAD4 alteration did not vary per tertile of normalized GATA6 expression (TCGA: p = 0.928; CPTAC: p = 0.828). In the TCGA, SMAD4 alterations and the basal-like phenotype were each associated with worse survival (log rank p = 0.077 and p = 0.080, respectively), but their combined presence did not identify a subset with uniquely inferior survival (p = 0.943). In the CPTAC, the basal-like phenotype was associated with significantly worse survival (p < 0.001), but the prognostic value was not influenced by the combined presence of SMAD4 alterations (p = 0.960). SMAD4 alterations were not associated with poor clinico-pathological features such as poor tumor grade, advanced tumor stage, positive lymphovascular invasion (LVI), or positive perineural invasion (PNI), compared with SMAD4-wildtype. Given that SMAD4 mutations were not associated with GATA6 expression or Moffitt subtype in two independent molecularly characterized PDAC cohorts, distinct biomarker-defined clinical trials are necessary.

FOXC1 and SOX10 in Estrogen Receptor-Low Positive/HER2-Negative Breast Cancer: Potential Biomarkers for the Basal-like Phenotype Prediction.

Breast cancer with low (1%-10%) estrogen receptor (ER) expression (ER-low positive) constitutes a small portion of invasive breast cancers, and the treatment strategy for these tumors remains debatable. To characterize the features and outcomes of ER-low positive patients, and clarify the clinical significance of FOXC1 and SOX10 expression in ER-low positive/HER2-negative tumors. Among 9082 patients diagnosed with primary invasive breast cancer, the clinicopathologic features of those with ER-low positive breast cancer were characterized. FOXC1 and SOX10 mRNA levels were analyzed in ER-low positive/HER2-negative cases from public data sets. The expression of FOXC1 and SOX10 in ER-low positive/HER2-negative tumors was evaluated by immunohistochemistry. The clinicopathologic study of ER-low positive tumors indicated more aggressive characteristics compared with those tumors with ER >10%, while they had more overlapping features with ER-negative tumors irrespective of the HER2 status. The intrinsic molecular subtype of ER-low positive cases with high FOXC1 and SOX10 mRNA expression was more likely to be nonluminal. Among the ER-low positive/HER2-negative tumors, 56.67% (51 of 90) and 36.67% (33 of 90) were positive for FOXC1 and SOX10, respectively, which was significantly positively correlated with CK5/6 expression. In addition, the survival analysis demonstrated no significant difference between patients who received and who did not receive endocrine therapy. ER-low positive breast cancers biologically overlap more with ER-negative tumors. ER-low positive/HER2-negative cases demonstrate a high rate of FOXC1 or SOX10 expression, and these cases might be better categorized as a basal-like phenotype/subtype. FOXC1 and SOX10 testing may be used for the intrinsic phenotype prediction for ER-low positive/HER2-negative patients.

Abstract P2-11-17: Prognostic value of Trop2 expression levels in non-metastatic triple-negative breast cancer and correlation with other biomarkers

Abstract Background: Since the development of anti Trop2 antibody-drug conjugates (ADC), Trop2 has been validated as a major therapeutic target for antibody-drug conjugates in metastatic triple-negative breast cancer (TNBC). However, very few data have been reported regarding the prognostic implication, or clinicopathological variables, associated with Trop2 expression levels in early TNBC. Our aim was to evaluate Trop2 expression and its prognostic value in a retrospective series of patients with non-metastatic TNBC and a long follow-up, characterized for Basal-like (BL) or molecular apocrine-like (MA) IHC profiles as well as TILs infiltrate, PDL1 expression and PIK3CA/PTEN mutations. Patients and methods: The analysis was performed in a series of 228 patients with non-metastatic TNBC treated in our center between 2002 and 2012 arrayed on 6 TMA. BL and MA profiles were defined as IHC CK5/6 and/or EGFR expression, and Androgen-receptor and FOXA1 IHC expression, respectively. Trop2 expression levels were tested for their association with baseline clinicopathological variables, and for Relapse-Free Survival (RFS) and Overall survival (OS). Trop2 IHC level of expression was evaluated using the ENZ-ABS380 mouse monoclonal antibody and the methodology described by Bardia et al. (Annals of Oncology, 2021) to quantify the membrane signal. First, we established a score grid, according to staining intensity (no labeling: 0; weak labeling: 1; moderate labeling: 2; strong labeling: 3). Then, for each sampled core, the percentage of labeled invasive tumor cells in each intensity was reported. The overall membrane expression was then calculated using the H-Score method (3 x % of cells with labeling intensity 3 + 2 x % of cells with intensity 2 + 1 x % of cells with intensity 1). The scores obtained ranged from 0 to 300. Results: Median age was 58.2 years (range 28.5-89.1). 43.9% of tumors were classified pT1 and 63.5% pN0. 83.8% of patients had ductal carcinomas. Histological grade 1-2 represented 22.7% of all tumors. A BL phenotype was observed in 68.1% of cases, and an MA profile in 39.4% of the cases. Adjuvant chemotherapy (ACT) was delivered in 74% of patients. We observed low Trop2 expression (H-Score &amp;lt; 100) in 12.3% of the cases (28/228 samples), moderate Trop2 expression (H-Score 100-200) in 28.9% of the cases (66/228 samples), and strong Trop2 expression (H-Score &amp;gt;200) in 58.8% of the cases (134/228 samples). We only identified 3 tumors without any Trop2 expression. Regarding baseline clinicopathological correlations, Trop2 levels were only found significantly associated with pT stage, pT1 tumors displaying more frequently high Trop2 scores compared to tumors &amp;gt;= pT2 (p=0.002). No significant correlation was found between Trop2 expression levels and HER2 levels (0 vs. 1+/2+), BL or MA status. With a median follow-up of 9.7 years, Trop2 levels were not associated with RFS nor OS in univariate analysis. In multivariate analysis, poor RFS was associated with classical variables in the early TNBC setting: tumors &amp;gt;=T2 stage (Hazard Ratio (HR) 2.13, p=0.02), N+ status (HR 3.51, p&amp;lt; 0.001), while high (&amp;gt;5%) TILs infiltration levels (HR 0.54, p=0.03) and adjuvant chemotherapy use (HR 0.49, p=0.007) were associated with improved RFS. Conclusions: Trop2 is expressed in nearly all early TNBC cases, and Trop2 levels of expression, while associated with T stage, did not impact survival in this population. These results are consistent with the ones reported in the metastatic setting in the ASCENT trial. Trop2 level of expression appearing homogeneous distributed in all the clinicopathological subtypes of TNBC, advocating for the evaluation of combined treatments with anti-Trop2 ADCs and dedicated targeted therapies in specific TNBC subgroups. Citation Format: William Jacot, Marie-Christine Chateau, Simon Thezenas, Séverine Guiu, Nelly Firmin, Florence Boissière-Michot. Prognostic value of Trop2 expression levels in non-metastatic triple-negative breast cancer and correlation with other biomarkers [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-11-17.

Abstract PD4-09: PD4-09 Single cell RNA-sequencing identifies intra-tumoral cellular heterogeneity and drug-induced subpopulation shifts in Triple Negative Breast Cancer mouse models

Abstract Introduction: Triple Negative Breast Cancer (TNBC) is an aggressive disease with a poor prognosis that accounts for 10-20% of breast cancer cases worldwide. Intra-tumoral heterogeneity and tumor cell plasticity are thought to contribute to drug resistance in TNBCs. Our work aims to: 1) precisely identify the intra-tumoral heterogeneity in cellular states present within TNBC, and 2) test whether drugs can block or initiate plasticity between subpopulations to improve drug sensitivity. We hypothesize that treatment(s) induce cellular plasticity, thus causing cells to shift into resistant states that persist until treatment is removed. We further hypothesize that these resistant subpopulations give rise to new tumor outgrowths once the treatment stops. Methods: To test this, we are treating TP53-/- Genetically Engineered Mouse Model (GEMM) syngeneic transplant tumors of the basal-like TNBC phenotype with the chemotherapeutic doublet of carboplatin/paclitaxel, and targeted agents implicated in plasticity including the MEK inhibitor trametinib, a chromatin remodeling inhibitor I-BET151, and the dihydroorotate dehydrogenase inhibitor brequinar. To identify cellular subpopulations and examine their response to treatment, we performed both in vivo and in vitro drug sensitivity testing, as well as gene expression profiling using single cell RNA-sequencing (scRNAseq). Results: We have identified clear intra-tumoral heterogeneity with at least 6 distinct cell states present, including basal, mesenchymal/claudin-low, and proliferative subpopulations in vivo in most TNBC GEMM models. We performed 18 individual scRNAseq experiments on the TP53-/- 2225L GEMM transplant line with the aforementioned treatments and untreated controls in triplicate and compared subpopulation frequencies in treated versus untreated tumors. Notably, treatment with trametinib and brequinar caused the rise of two rare subpopulations (i.e. 1% to 3-4% of total tumor cells) that express genes consistent with previously described drug-tolerant persisters (DTP), which we have called “Epithelial-DTP” (Tacstd2, Krt6a, and Cryab enriched) and “Mesenchymal-DTP” (Snai2 and Sca-1 enriched). A gene signature generated from the Epithelial-DTP subpopulation predicted poor patient outcomes in neoadjuvant chemotherapy treated TNBC patients. Further, in TNBC patient-derived xenografts (PDX), these two DTP subpopulations are also present and induced by treatment to an even greater frequency. Ongoing experiments include the use of fluorescence-activated cell sorting to isolate and functionally test the tumor-initiating capabilities of these two rare cell subpopulations. In addition, many experiments are underway to identify means to therapeutically target these DTP cells, with these results to be presented. Ultimately, identifying these rare drug resistant subpopulations, and identifying means to eradicate them, could vastly improve therapeutic regimens and outcomes for patients with TNBCs. Citation Format: Cherise R. Glodowski, Kevin R. Mott, Denis Okumu, Michael P. East, Timothy C. Elston, Gary L. Johnson, Charles M. Perou. PD4-09 Single cell RNA-sequencing identifies intra-tumoral cellular heterogeneity and drug-induced subpopulation shifts in Triple Negative Breast Cancer mouse models [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD4-09.

Correlation of the TIGIT-PVR immune checkpoint axis with clinicopathological features in triple-negative breast cancer.

T cell immunoreceptor with Ig and ITIM domains (TIGIT) interacts with poliovirus receptor (PVR) to contribute to cancer immune escape. Recently, TIGIT and PVR have been identified as promising immunotherapy targets. Their gene expression is upregulated in many solid tumors, but their protein expression level is not well documented, particularly in triple negative breast cancer (TNBC), the breast cancer subtype that most benefit from immunotherapy. TIGIT and PVR expression levels were assessed by immunohistochemistry in 243 surgically resected localized TNBC and then their relationship with clinical-pathological features and clinical outcome was analyzed. TIGIT expression was observed in immune cells from the tumor microenvironment, whereas PVR was mainly expressed by tumor cells. High TIGIT expression was significantly associated with age (p=0.010), histological grade (p=0.014), non-lobular histology (p=0.024), adjuvant chemotherapy (p=0.006), and various immune cell populations (tumor infiltrating lymphocytes (TILs), CD3+, CD8+, PD-1+ cells; all p<0.0001), PD-L1+ tumor cells (p<0.0001), and PD-L1+ stromal cells (p=0.003). Infiltration by TIGIT+ cells tended to be higher in non-molecular apocrine tumors (p=0.088). PVR was significantly associated with histological grade (p<0.0001), the basal-like (p=0.003) and non-molecular apocrine phenotypes (p=0.039), high TILs infiltration (p=0.011), CD3+ (p=0.002), CD8+ (p=0.024) T cells, and PD-L1 expression in tumor (p=0.003) and stromal cells (p=0.001). In univariate analysis, only known prognostic factors (age, tumor size, lymph node status, adjuvant chemotherapy, TILs and CD3+ T-cell infiltrate) were significantly associated with relapse-free survival (RFS) and overall survival. High TIGIT and PVR expression levels tended to be associated with longer RFS (p=0.079 and 0.045, respectively). The analysis that included only non-molecular apocrine TNBC revealed longer RFS for tumors that strongly expressed TIGIT or PVR (p=0.025 for TIGIT and 0.032 for PVR). These results indicated that in TNBC, TIGIT+ cells can easily interact with PVR to exert their inhibitory effects. Their wide expression in TNBC and their association with other immune checkpoint components suggest the therapeutic interest of the TIGIT-PVR axis.

Replication stress identifies novel molecular classification associated with treatment outcomes in pancreatic cancer

BackgroundReplication stress is a prominent hallmark of tumor cells, which is crucial for maintaining genomic integrity. However, it remains poorly understood whether replication stress can serve as a surrogate biomarker to indicate prognosis and treatment response of pancreatic cancer. MethodsTranscriptomic and clinical data were obtained from The Cancer Genome Atlas and literature. An integrated signature of 18 replication-stress associated genes (termed as REST18) was established using the cox proportional hazards regression analysis. Tumors were sorted into REST18-low and REST18-high groups. Survival analysis, gene set enrichment analysis and composition of immune cells were compared between these tumors. ResultsPatients with REST18-high tumors showed worse prognoses than those with REST18-low tumors in the TCGA database and the finding is validated in an independent cohort of pancreatic cancer. Comparison of REST18 model and other molecular classifications showed that REST18-high tumors are positively correlated to basal-like or squamous phenotypes, which have higher metastasis potential. DNA repair pathway is enriched in the REST18-high tumors. Analysis of tumor immune microenvironment found that REST18-high tumors are characterized with “immune-cold” features. Univariate and multivariate analysis show that REST18 is an independent risk factor for overall survival and predicts outcomes of chemotherapy in pancreatic cancer. ConclusionREST18 is a novel biomarker to indicate prognosis and treatment response of chemotherapy in pancreatic cancer.

Abstract A058: Meta-analysis of single-cell RNA expression in genetically engineered mouse models of pancreatic ductal adenocarcinoma reveals inter-model heterogeneity

Abstract Background: Genetically engineered mouse models (GEMMs) are widely used in the study of pancreatic ductal adenocarcinoma (PDAC) because of their immune-competent tumor microenvironment (TME); however, the extent to which particular GEMMs recapitulate the tumor and TME observed in the patient population has not been systematically evaluated. In this study, we integrate single-cell RNA sequencing (sc-RNA-seq) data from multiple studies and multiple GEMM backgrounds to identify differences in the cellular compositions of popular PDAC GEMMs. Methods: A total of 49,191 cells were used from three studies, including normal mouse pancreas (N=2) and five different GEMM backgrounds (N=16). Data curation, integration, and analysis were based on the Seurat pipeline in R. SingelCellNet was used to train a random forest model on manually labeled human sc-RNA-seq data from 20 patients. To enable cross-species use, the classifier was trained using only genes with both human and mouse homologues. Cells classified as neoplastic were further clustered to quantify the number of classical and basal-like cells based on signature gene expression levels. The ratio of these subtypes in each GEMM and the relationship between the modified genes in each model were examined. Results: Ad-hoc clustering and a human-cell-trained single-cell classifier showed 79% agreement in an integrated data set of PDAC GEMMs. Cells identified by both methods as tumor (8,303 cells, 17% of total) were assessed for PDAC tumor subtype via subsequent clustering analysis (basal-like or classical). When comparing the ratio of differently subtyped tumor cells, we identified stark differences between GEMM genetic backgrounds. Among five different models, KIC (KrasLSL−G12D/+Ink4a/Arffl/flPtf1aCre/+), KPPCN (KrasLSL−G12D/+Trp53fl/flPdx1Cre/+Nsdhlfl/fl), and pdx1-KPC (KrasLSL−G12D/+Trp53LSL-R172H/+Pdx1Cre/+) exhibited a higher proportion of basal-like PDAC cells compared to KPfC/KPPC (KrasLSL−G12D/+Trp53fl/flPdx1Cre/+) and ptf1a-KPC (KrasLSL−G12D/+Trp53LSL-R172H/+Ptf1aCre/+). Interestingly, in the KIC model, which was harvested at early and late time points (40 or 60 days), classical PDAC was overrepresented in early models, and basal-like PDAC was more prevalent in the older tumors. While sample sizes are limited in this study, in Pdx1 driven models, we observed a bias towards basal-like phenotype in GEMMs using the Trp53LSL-R172H/+ method compared to those with Trp53fl/fl. Conclusions: In a comparison of publicly available sc-RNA-seq, we highlight potential biases in the molecular subtypes that arise from specific PDAC GEMMs. Because of the known link between tumor subtype and therapeutic response, these results suggest translational work may benefit from GEMM selection that considers transcriptomic diversity. Citation Format: Yun Jae Yoo, Ki H Oh, Luke A. Torre-Healy, Richard A. Moffitt. Meta-analysis of single-cell RNA expression in genetically engineered mouse models of pancreatic ductal adenocarcinoma reveals inter-model heterogeneity [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 A058.