Epithelial-mesenchymal Transition Pathway Research Articles

Epithelial-mesenchymal transition induced by tumor cell-intrinsic PD-L1 signaling predicts a poor response to immune checkpoint inhibitors in PD-L1-high lung cancer.

We investigated the role of tumor cell-intrinsic PD-L1 signaling in the epithelial-mesenchymal transition (EMT) in non-small-cell lung cancer (NSCLC) and the role of EMT as a predictive biomarker for immune checkpoint inhibitor (ICI) therapy. PD-L1-overexpressing or PD-L1-knockdown NSCLC cells underwent RNA-seq and EMT phenotype assessment. Mouse lung cancer LLC cells were injected into nude mice. Two cohorts of patients with NSCLC undergoing ICI therapy were analyzed. RNA-seq showed that EMT pathways were enriched in PD-L1-high NSCLC cells. EMT was enhanced by PD-L1 in NSCLC cells, which was mediated by transforming growth factor-β (TGFβ). PD-L1 promoted the activation of p38-MAPK by binding to and inhibiting the protein phosphatase PPM1B, thereby increasing the TGFβ production. Tumor growth and metastasis increased in nude mice injected with PD-L1-overexpressing LLC cells. In the ICI cohort, EMT signature was higher in patients with progressive disease than in those with responses, and EMT was significantly associated with poor survival in PD-L1-high NSCLC. In PD-L1-high NSCLC, EMT was associated with increased M2-macrophage and regulatory T-cell infiltrations and decreased cytotoxic T-cell infiltration. Tumor cell-intrinsic PD-L1 function contributes to NSCLC progression by promoting EMT. EMT may predict an unfavorable outcome after ICI therapy in PD-L1-high NSCLC.

Epithelial-mesenchymal transition-related signaling pathways in gastric Cancer cells distinctively respond to long-term experimental ketosis.

The interrelationship between cellular metabolism and the epithelial-to-mesenchymal transition (EMT) process has made it an interesting topic to investigate the adjuvant effect of therapeutic diets in the treatment of cancers. However, the findings are controversial. In this study, the effects of glucose limitation along and with the addition of beta-hydroxybutyrate (bHB) were examined on the expression of specific genes and proteins of EMT, Wnt, Hedgehog, and Hippo signaling pathways, and also on cellular behavior of gastric cancer stem-like (MKN-45) and non-stem-like (KATO III) cells. The expression levels of chosen genes and proteins studied in cancer cells gradually adopted a low-glucose condition of one-fourth, along and with the addition of bHB, and compared to the unconditioned control cells. The long-term switching of the metabolic fuels successfully altered the expression profiles and behaviors of both gastric cancer cells. However, the results for some changes were the opposite. Glucose limitation along and with the addition of bHB reduced the CD44+ population in MKN-45 cells. In KATO III cells, glucose restriction increased the CD44+ population. Glucose deprivation alleviated EMT-related signaling pathways in MKN-45 cells but stimulated EMT in KATO III cells. Interestingly, bHB enrichment reduced the beneficial effect of glucose starvation in MKN-45 cells, but also alleviated the adverse effects of glucose restriction in KATO III cells. The findings of this research clearly showed that some controversial results in clinical trials for ketogenic diet in cancer patients stemmed from the different signaling responses of various cells to the metabolic changes in a heterogeneous cancer mass.

Single-Cell and Spatial Transcriptome Profiling Identifies the Transcription Factor BHLHE40 as a Driver of EMT in Metastatic Colorectal Cancer.

Colorectal cancer (CRC) is one of the most common malignant tumors in humans, with liver metastasis being the primary cause of mortality. The epithelial-mesenchymal transition (EMT) process endows cancer cells with enhanced metastatic potential. To elucidate the cellular mechanisms driving EMT in CRC, we analyzed single-cell RNA-sequencing (scRNA-seq) data from 11 non-metastatic primary tumors (TnM) and 11 metastatic primary tumors (TM) from CRC patients. Compared to TnM group, the TM samples showed elevated numbers of malignant epithelial cell and cancer-associated fibroblast (CAF) subsets that displayed enrichments of EMT, angiogenesis, and TGF-β signaling pathways. One specific TM-enriched subgroup of malignant epithelial cells underwent EMT to trans-differentiate into CXCL1+ CAFs that subsequently differentiated into SFRP2+ CAFs, which was validated by spatial transcriptomic and pseudotime trajectory analyses. Furthermore, cell-cell communication analysis identified BHLHE40 as a probable key transcription factor driving EMT that was associated with poor prognosis. Finally, in vitro and in vivo experiments functionally substantiated that BHLHE40 promoted the proliferation, invasion, migration, EMT, and liver metastasis of CRC cells. In summary, this study identified BHLHE40 as a key transcription factor regulating EMT that promotes liver metastasis in CRC.

Integrated analysis of single-cell RNA-seq and bulk RNA-seq reveals immune suppression subtypes and establishes a novel signature for determining the prognosis in lung adenocarcinoma.

Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer with lower survival rates. Recent advancements in targeted therapies and immunotherapies targeting immune checkpoints have achieved remarkable success, there is still a large percentage of LUAD that lacks available therapeutic options. Due to tumor heterogeneity, the diagnosis and treatment of LUAD are challenging. Exploring the biology of LUAD and identifying new biomarker and therapeutic targets options are essential. We performed single-cell RNA sequencing (scRNA-seq) of 6 paired primary and adjacent LUAD tissues, and integrative omics analysis of the scRNA-seq, bulk RNA-seq and whole-exome sequencing data revealed molecular subtype characteristics. Our experimental results confirm that CDC25C gene can serve as a potential marker for poor prognosis in LUAD. We investigated aberrant gene expression in diverse cell types in LUAD via the scRNA-seq data. Moreover, multi-omics clustering revealed four subgroups defined by transcriptional profile and molecular subtype 4 (MS4) with poor survival probability, and immune cell infiltration signatures revealed that MS4 tended to be the immunosuppressive subtype. Our study revealed that the CDC25C gene can be a distinct prognostic biomarker that indicates immune infiltration levels and response to immunotherapy in LUAD patients. Our experimental results concluded that CDC25C expression affects lung cancer cell invasion and migration, might play a key role in regulating Epithelial-Mesenchymal Transition (EMT) pathways. Our multi-omics result revealed a comprehensive set of molecular attributes associated with prognosis-related genes in LUAD at the cellular and tissue level. Identification of a subtype of immunosuppressive TME and prognostic signature for LUAD. We identified the cell cycle regulation gene CDC25C affects lung cancer cell invasion and migration, which can be used as a potential biomarker for LUAD.

Identification of a robust biomarker LAPTM4A for glioma based on comprehensive computational biology and experimental verification.

Glioma, a highly invasive and deadly form of human neoplasm, presents a pressing need for the exploration of potential therapeutic targets. While the lysosomal protein transmembrane 4A (LATPM4A) has been identified as a risk factor in pancreatic cancer patients, its role in glioma remains unexplored. The analysis of differentially expressed genes (DEG) was conducted from The Cancer Genome Atlas (TCGA) glioma dataset and the Genotype Tissue Expression (GTEx) dataset. Through weighted gene co-expression network analysis (WGCNA), the key glioma-related genes were identified. Among these, by using Kaplan-Meier (KM) analysis and univariate/multivariate COX methods, LAPTM4A emerged as the most influential gene. Moreover, the bioinformatics methods and experimental verification were employed to analyze its relationships with diagnosis, clinical parameters, epithelial-mesenchymal transition (EMT), metastasis, immune cell infiltration, immunotherapy, drug sensitivity, and ceRNA network. Our findings revealed that LAPTM4A was up-regulated in gliomas and was associated with clinicopathological features, leading to poor prognosis. Furthermore, functional enrichment analysis demonstrated that LATPM4A played a role in the immune system and cancer progression. In vitro experiments indicated that LAPTM4A may influence metastasis through the EMT pathway in glioma. Additionally, we found that LAPTM4A was associated with the tumor microenvironment (TME) and immunotherapy. Notably, drug sensitivity analysis revealed that patients with high LAPTM4A expression were sensitive to doxorubicin, which contributed to a reduction in LAPTM4A expression. Finally, we uncovered the FGD5-AS1-hsa-miR-103a-3p-LAPTM4A axis as a facilitator of glioma progression. In conclusion, our study identifies LATPM4A as a promising biomarker for prognosis and immune characteristics in glioma.

Zinc finger Protein207 orchestrates glioma migration through regulation of epithelial-mesenchymal transition.

Glioma represents the predominant primary malignant brain tumor. For several years, molecular profiling has been instrumental in the management and therapeutic stratification of glioma, providing a deeper understanding of its biological complexity. Accumulating evidence unveils the putative involvement of zinc finger proteins (ZNFs) in cancer. This study aimed to elucidate the role and significance of ZNF207 in glioma. Utilizing online data such as The Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), the Genotype-Tissue Expression (GTEx) project, the Clinical Proteomic Tumor Analysis Consortium (CPTAC), and the Human Protein Atlas (HPA) databases, in conjunction with bioinformatics methodologies including GO, KEGG, GSEA, CIBERSORT immune cell infiltration estimation, and protein-protein interaction (PPI) analysis, enabled a comprehensive exploration of ZNF207's involvement in gliomagenesis. Immunohistochemistry and RT-PCR techniques were employed to validate the expression level of ZNF207 in glioma samples. Subsequently, the biological effects of ZNF207 on glioma cells were explored through in vitro assays. Our results demonstrate elevated expression of ZNF207 in gliomas, correlating with unfavorable patient outcomes. Stratification analyses were used to delineate the prognostic efficacy of ZNF207 in glioma with different clinicopathological characteristics. Immunocorrelation analysis revealed a significant association between ZNF207 expression and the infiltration levels of T helper cells, macrophages, and natural killer (NK) cells. Utilizing ZNF207 expression and clinical features, we constructed an OS prediction model and displayed well discrimination with a C-index of 0.861. Moreover, the strategic silencing of ZNF207 attenuated glioma cell advancement, evidenced by diminished cellular proliferation, weakened cell tumorigenesis, augmented apoptotic activity, and curtailed migratory capacity alongside the inhibition of the epithelial-mesenchymal transition (EMT) pathway. ZNF207 may identify as a prospective biomarker and therapeutic candidate for glioma prevention, providing valuable insights into understanding glioma pathogenesis and treatment strategies.

Prognostic implications of MXRA8 expression in colorectal cancer and its role in tumor progression

Matrix Remodeling Associated 8 (MXRA8) is a type I transmembrane protein capable of modulating integrin signaling and regulating cell-cell interactions, and also functions as a receptor for multiple arthritogenic alphaviruses. Although limited numbers of studies have provided evidence indicating a potential role of MXRA8 in different types of cancer, the potential contrubition of MXRA8 in colorectal cancer (CRC) has not yet been fully elucidated. Therefore, our aim was to conduct a comprehensive analysis elucidating the prognostic value of MXRA8 in CRC. The results revealed that MXRA8 was highly expressed in CRC compared to normal tissue. Notably, there was a substantial correlation with the TNM stage, and elevated MXRA8 expression was indicative of a poorer prognosis in CRC cases. Furthermore, co-expression analysis indicated that MXRA8 is predominantly involved in hypoxia and epithelial-mesenchymal transition pathway. In conclusion, this study demonstrates the potential roles of MXRA8 in predicting CRC prognosis and contributes to the elucidation of how MXRA8 might be involved in the mechanisms underlying CRC carcinogenesis.

Identification of a cisplatin resistant-based prognostic immune related gene signature in MIBC

Cisplatin resistance plays a significant role in the dismal prognosis and progression of muscle-invasive bladder cancer (MIBC). However, the strategies to predict prognosis and cisplatin resistance are inefficient, and it remains unclear whether cisplatin resistance is associated with tumor immunity. In this study, we integrated the transcriptional data from cisplatin-resistant cell lines and a TCGA-MIBC cohort to establish cisplatin-resistance-related cluster classification and a cisplatin-resistance-related gene risk score (CRRGRS). Kaplan–Meier survival curves showed that compared with those in low CRRGRS group, MIBC patients belonging to high CRRGRS group had worse prognosis in TCGA-MIBC cohort and external GEO cohorts. Meanwhile, CRRGRS was able to help forecast chemotherapy and immunotherapy response of MIBC patients in the TGCA cohort and IMvigor210 cohort. Moreover, compared with the low CRRGRS group, the high CRRGS group possessed a relatively immunosuppressive “cold tumor” phenotype with a higher tumor immune dysfunction and exclusion (TIDE) score, ESTIMATE score, stromal score and immune score and a lower immunophenoscore (IPS) score. The upregulated expression levels of immune checkpoint genes, including PD-1, PD-L1 and CTLA4, in the high CRRGRS group also further indicated that a relative immunosuppressive tumor microenvironment may exist in MIBC patients belonging to high CRRGRS group. In addition, we integrated CRRGRS and clinical characteristics with prognostic value to develop a nomogram, which could help forecast overall survival of MIBC patients. Furthermore, DIAPH3 was identified as a regulator of proliferation and cisplatin resistance in MIBC. The expression of DIAPH3 was increased in cisplatin-resistant cell lines and chemotherapy-unsensitive people. Further mechanism exploration revealed that DIAPH3 facilitated tumor proliferation and cisplatin resistance by regulating the NF-kB and epithelial-mesenchymal transition (EMT) pathways. In conclusion, the comprehensive investigations of CRRGRS increased the understanding of cisplatin resistance and provided promising insights to restrain tumor growth and overcome chemoresistance by targeting DIAPH3.

Secreted frizzled-related protein 5 protects against renal fibrosis by inhibiting Wnt/β-catenin pathway.

Renal fibrosis (RF) is an important pathogenesis for renal function deterioration in chronic kidney disease. Secreted frizzled-related protein 5 (SFRP5) is an anti-fibrotic adipokine but its direct role on RF remains unknown. It was aimed to study the protective effect of SFRP5 against RF and interference with Wnt/β-catenin signaling pathway for the first time. First, the therapeutic efficacy of SFRP5 was evaluated by adenovirus overexpression in rats with unilateral ureteral obstruction (UUO) in vivo. Thirty-six rats were randomly divided into the sham, UUO, and SFRP5 (UUO + Ad-SFRP5) groups. Half rats in each group were selected at random for euthanasia at 7 days and the others until 14 days. Then, the transforming growth factor (TGF)-β1-induced epithelial-mesenchymal transition (EMT) was established in HK-2 cells in vitro. The cells were divided into four groups: the control group, the TGF-β1 group, the TGF-β1 + SFRP5 group, and the TGF-β1 + SFRP5 + anti-SFRP5 group. The makers of EMT and Wnt/β-catenin pathway proteins were investigated. In the UUO model, expression of SFRP5 showed compensatory upregulation, and adenoviral-mediated SFRP5 over-expression remarkably attenuated RF, as demonstrated by maintenance of E-cadherin and suppression of α-smooth muscle actin (SMA). In vitro, SFRP5 was shown to inhibit TGF-β1-mediated positive regulation of α-SMA, fibronectin, collagen I but negative regulation of E-cadherin. Furthermore, SFRP5 abrogated activation of Wnt/β-catenin, which was the essential pathway in EMT and RF pathogenesis. The changes after a neutralizing antibody to SFRP5 confirmed the specificity of SFRP5 for inhibition. These findings suggest that SFRP5 can directly ameliorate EMT and protect against RF by inhibiting Wnt/β-catenin pathway.

Poly (ADP-ribose) polymerase-1 (PARP-1) is a good prognostic marker for pancreatic/periampullary cancers.

Periampullary cancer (PAC) is highly aggressive with no effective adjuvant therapy or prognostic markers. Recently, poly (ADP-ribose) polymerases-1 (PARP-1) have emerged as a target in solid cancers, and its relationship with epithelial-mesenchymal transition (EMT) has been observed. However, the relationship between PARP-1 and EMT in PAC has not explored well. We assessed the prognostic significance of PARP1 in 190 PACs patients and correlated it with EMT markers, including FGF8, FGFR4, MMP2, MMP3, Snail, and ZEB1. Immunohistochemistry for PARP-1 and EMT markers was performed using a tissue microarray. PARP-1 and FGF8 expression were associated with better survival unlike other solid cancers (P = 0.006 and P = 0.003), and MMP3 and ZEB1 expression were associated with poor prognosis in multivariate and survival analyses (P = 0.009 and P < 0.001). In addition, PARP-1 is related negatively to Snail but not related with other EMT markers, implying an independent mechanism between PARP-1 and EMT in PACs. PARP-1 and FGF8 are independent good survival markers in PACs unlike other solid cancers. PARP-1 and FGF8 in PACs could not be related to the EMT pathway but must be rather understood in light of similar cancer-protective roles. Further studies are required on EMT-associated immune markers in PACs.

Identification of non-coding RNA signatures in idiopathic pulmonary fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a deadly, chronic, progressive, irreversible interstitial lung disease characterized by the formation of scar tissue resulting in permanent lung damage. The average survival time following diagnosis is only 3-5years, with a 5-year survival rate shorter than that of many cancers. Alveolar epithelial cell injury followed by irregular repair is the primary pathological process observed in patients with IPF. An evident characteristic of IPF is the development of fibroblastic foci representing active fibrotic areas. Most of the cells within these foci are believed to be myofibroblasts, which are thought to be the primary source of abnormal extracellular matrix production in IPF. The lung phenotype in IPF is characterized by significantly different processes from healthy lungs, including irregular apoptosis, oxidative stress, and epithelial-mesenchymal transition (EMT) pathways. The exact cause of IPF is not fully understood and remains mysterious. It is not suppressing that non-coding RNAs are involved in the development and progression of IPF. Accordingly, here we aimed to identify non-coding RNA molecules during TGFβ-induced myofibroblast activation. Differential expression and functional enrichment analysis were employed to reveal the impact of non-coding RNAs during TGFβ-associated lung fibrosis. Remarkably, LOC101448202, CZ1P-ASNS, LINC01503, IER3-AS1, MIR503HG, CLMAT3, LINC02593, ACTA2-AS1, LOC102723692, LOC107985728, and LOC105371064 were identified to be differentially altered during TGFβ-stimulated myofibroblast activation. These findings strongly suggest that the mechanism of lung fibrosis is heavily under control of non-coding RNAs, and RNA-based therapies could be a promising approach for future therapeutic interventions to lung fibrosis.

Abstract 1163: Increased spatial coupling of integrin and collagen IV in the immunoresistant clear cell renal cell carcinoma tumor microenvironment

Abstract Immunotherapy (IO) has improved the survival of patients with clear cell renal cell carcinoma (ccRCC); however, most patients will not have a durable complete response and will die from their disease. Our understanding of the development of IO resistance for ccRCC is very limited. We employed spatial transcriptomics (ST) with single cell resolution on patients with IO naïve tumors and IO exposed tumors to characterize spatial properties and differences between these two populations. Fourteen matched tumor and adjacent stromal fields of view (FOV) from surgically resected primary kidney specimens were analyzed using CosMx Spatial Molecular Imager (SMI). Non-tumor cell phenotyping was performed using the Kidney Cell Atlas. A generalized linear model was developed to identify malignant tumor cells in kidney tissues and validated by a pathologist. Differential cell abundance, clustering, and gene expression for each cell phenotype were compared between the two groups. Spatial gene set enrichment (GSEA) of modified hallmark gene sets were also compared. CD8+ T cells were more abundant in IO exposed vs IO naïve tumor FOVs. YES1 expression in the malignant tumor cells was significantly higher in IO exposed samples compared to IO naïve samples (false discovery rate [FDR] = 0.084). Spatial GSEA showed significant clustering of many gene sets (cells of high enrichment closer together than expected by chance), most notably epithelial-mesenchymal transition (EMT) pathway. Next, a post-hoc analysis of genes belonging to known ligand-receptor pairs in the EMT pathway was completed using bivariate Moran’s I to estimate spatial autocorrelation. We found significantly higher spatial autocorrelation of ITGAV-COL4A1 in the stroma of IO exposed FOVs than IO naïve FOVs (FDR = 0.008). Cell types with the highest expression of ITGAV and COL4A1 were found to be fibroblasts, endothelial, and tumor cells. Protein validation with multiplex immunofluorescence (mIF) confirmed cells positively stained for anti-integrin alpha-V were more abundance on stromal FOVs (p &amp;lt; 0.001) in IO exposed samples. Fibroblast (SMA+) cells in stromal FOVs were more likely to be positively stained for anti-integrin alpha-V (p &amp;lt; 0.001) in IO exposed than IO naïve FOVs. ITGAV protein is involved in migration from primary to metastatic disease in several cancers, and its inhibition increases T cell killing indicating ccRCC endothelial and tumor cells may be using this signaling for immune evasion and disease progression. Further, collagen and cancer associated fibroblasts (CAFs) play a role in tumor growth. To our knowledge, this is the first study to leverage single-cell resolution ST to identify potential ways by which ccRCC tumors become resistant to IO therapy. Citation Format: Alex C. Soupir, Mitchell T. Hayes, Taylor C. Peak, Oscar E. Ospina, Nicholas H. Chakiryan, Anders E. Berglund, Paul A. Stewart, Jonathan Nguyen, Carlos M. Moran-Segura, Natasha L. Francis, Paola M. Ramos-Echevarria, Jad Chahoud, Roger Li, Kenneth Y. Tsai, Jodi A. Balasi, Yamila Caraballo-Perez, Jasreman Dhillon, Lindsey A. Martinez, Warren E. Gloria, Nathan Schurman, Sean Kim, Mark Gregory, James J. Mule, Brooke L. Fridley, Brandon J. Manley. Increased spatial coupling of integrin and collagen IV in the immunoresistant clear cell renal cell carcinoma tumor microenvironment [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 1163.

Abstract 1726: Targeted epigenomic control of MYC as a strategy to treat EGFR inhibitor-resistant NSCLC

Abstract EGFR tyrosine kinase inhibitors (EGFRi) have improved outcomes for non-small cell lung cancer (NSCLC) patients harboring activating EGFR mutations. However, patients receiving EGFRi therapy frequently relapse with an EGFR T790M mutation. While osimertinib, a third generation EGFRi, blocks EGFR T790M activity, resistance eventually develops through various EGFR-dependent and EGFR-independent mechanisms, such as acquiring additional mutations in EGFR (e.g. C797S), activating bypass signaling pathways, or undergoing an epithelial to mesenchymal transition (EMT). MYC is a master transcription factor critical for mediating oncogenic signal transduction and has been implicated in EGFRi resistance, suggesting that MYC targeting may overcome multiple EGFRi resistance mechanisms. To evaluate this, we have developed a NSCLC-specific programmable epigenomic mRNA therapy, termed a MYC epigenomic controller (NSCLC MYC-EC), designed to selectively target regulatory elements in MYC’s insulated genomic domain and downregulate MYC expression. We have previously shown that NSCLC MYC-EC effectively decreases MYC expression pre-transcriptionally and have demonstrated that MYC-EC combination with osimertinib synergistically reduces viability of EGFR mutant NSCLC cells. Here, we demonstrate NSCLC MYC-EC activity in models that have developed EGFRi resistance through EGFR-dependent and -independent mechanisms. To test the effect of NSCLC MYC-EC in NSCLC cells with T790M mutant EGFR, we treated H1975 (L858R, T790M) and PC9-T790M cells (del19, engineered T790M) with MYC-EC alone or in combination with osimertinib. MYC-EC combination with osimertinib enhanced MYC protein downregulation and synergistically reduced cell viability in both models. To evaluate the effect of MYC-EC in osimertinib-resistant cells, we engineered H1975 and PC9-T790M cells with an EGFR C797S mutation. While osimertinib treatment did not impact cell viability in these models, MYC-EC maintained activity, downregulating MYC levels and reducing cell viability. To investigate MYC-EC activity in cells with alternative resistance mechanisms, we generated osimertinib-resistant H1975 cells by stepwise dose escalation. Protein analysis showed highly reduced phospho-EGFR levels, suggesting an EGFR-independent mechanism of survival. RNA-sequencing analysis revealed that EMT pathway was highly activated in these resistant cells. Importantly, this model retained sensitivity to NSCLC MYC-EC treatment, demonstrating that selectively targeting MYC can treat osimertinib-resistant NSCLC cells with a mesenchymal phenotype. Together, these data demonstrate that pre-transcriptional downregulation of MYC through NSCLC MYC-EC treatment effectively inhibits viability of EGFRi-resistant NSCLC through both EGFR-dependent and -independent mechanisms and supports the development of NSCLC MYC-EC in EGFRi-resistant NSCLC. Citation Format: Eugine Lee, Padraich Flahardy, Cameron Vergato, Stephen Siecinski, Justin Chen, Charles O’Donnell, Graeme Hodgson, Defne Yarar, Thomas McCauley. Targeted epigenomic control of MYC as a strategy to treat EGFR inhibitor-resistant NSCLC [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 1726.

Abstract 4294: The emerging role of deubiquitinase enzymes in lung cancer plasticity

Abstract Lung cancer is characterized by a high degree of genetic and molecular heterogeneity. Lineage plasticity has emerged as a source of intratumoral heterogeneity and drug resistance, resulting in poor prognosis and treatment failure. The molecular mechanisms driving lung cancer plasticity remain unclear. Ubiquitin-Specific Peptidase 13 (USP13), a deubiquitinating enzyme, is one of the most amplified genes in lung squamous cell carcinoma (LUSC). We developed a USP13 knock-in overexpressing mouse model in KrasLSL-G12D/+; Trp53fl/fl (KP) background (KPU mice). USP13 overexpression resulted in aggressive tumorigenesis and a shortened survival in Kras/Trp53-driven lung cancer. Notably, while KP mice developed lung adenocarcinoma (LUAD), KPU mice developed LUSC and LUAD. LUSC in KPU mice faithfully recapitulated the key pathohistological, molecular features, and cellular pathways of human LUSC. Bulk RNA-sequencing analysis showed that KPU tumors were heterogeneous and enriched in lineage reprogramming pathways including basal cell signaling, stem cell pluripotency, and epithelial-mesenchymal transition (EMT). Using cell-type-restricted adenoviral Cre to target cells expressing surfactant protein C (SPC) or club cell antigen 10 (CC10), we identified bronchiolar secretory club cells as the predominant cell origin of LUSC. USP13 altered the levels of lineage transcription factors such as TTF-1 and SOX2 in club cells during early tumorigenesis. Altered expression of these factors reinforced the fate of CC10+ club cells to squamous carcinoma development rather than adenocarcinoma. In addition, USP13 directly acted on the K48-linked ubiquitination of c-Myc and increased its protein stability, contributing to the elevation of squamous gene expression (SOX2, CK5, P40) in the primary mouse and advanced human lung cancer cells. These results suggest that USP13 promotes lineage plasticity in club cells during the early stage of cancer development and drives reprogramming into LUSC. We also found a potential functional association between USP13 and EMT pathway. Notably, irrespective of cell origin, USP13 overexpression enhanced EMT marker expression including N-cadherin, SNAI1, and ZEB1 in lung cancer cells, promoting cell migration and invasion. USP13 increased tumorigenic and metastatic abilities of lung cancer cells in 3D organoid culture and syngeneic mouse models. Collectively, our research highlights the pivotal significance of USP13 in unleashing lineage plasticity during lung cancer progression, suggesting the potential role of deubiquitinase enzymes in regulating lineage plasticity, which may lead to novel therapeutics for treating lung cancer. Citation Format: Juntae Kwon, Jinmin Zhang, Boram Mok, Samuel Allsup, Cecil Han. The emerging role of deubiquitinase enzymes in lung cancer plasticity [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 4294.

Abstract 4414: Genome-wide DNA methylation classifier diagnoses pancreatic ductal adenocarcinoma in CUP setting

Abstract Introduction: The metastasis of a pancreatic ductal adenocarcinoma (PAAD) is a diagnosis of exclusion and one of the most common causes of cancer of unknown primary (CUP). We have recently developed a genome-wide DNA methylation-based neural network classifier that can accurately differentiate between liver metastasis of a PAAD and intrahepatic cholangiocarcinoma (iCCA) (PAAD-iCCA-Classifier). Therefore, the aim of our study was to test whether our PAAD-iCCA-Classifier can be extended to be used to correctly diagnose PAAD metastases from other sites in CUP setting. Methods: For this purpose, we enhanced the anomaly detection layer of the classifier by incorporating ten mimicker carcinomas to be excluded by this layer. We used a validation set 1 (n=3786) including primary PAAD (n=242), PAAD liver metastases (n=20), iCCA (n=151) and 10 other mimicker carcinomas (n=3373) and a validation set 2 (n=26) including primary PAAD from a real-life clinical cohort from an independent institution to validate the classifier. Next, we tested the classifier on 16 PAAD initially considered CUP samples (test set) from different sites: peritoneum, lung, liver, and lymph node. The clinical history and diagnostic imaging of these samples were used to confirm PAAD as the most probable origin. We further performed differentially methylated probes (DMP) and copy number alterations (CNA) analysis of primary PAAD and metastatic PAAD from different locations. Results: The improved version of the PAAD-iCCA-Classifier achieved an accuracy of 98.43% on the validation set 1 and was able to exclude most of the mimicker carcinomas. On validation set 2, the classifier achieved an accuracy of 88.46%. Medical history, imaging and immunohistochemical analysis of the test set samples confirmed the diagnosis of PAAD. The DNA methylation classifier correctly labeled 15/16 PAAD metastatic samples as PAAD (93.75% accuracy). We observed that the classifier performance was negatively affected by a high CD3+ immune infiltrate and positively affected by high tumor purity and high proliferation rate. CNA revealed that PAAD liver metastases have a distinct CNA profile characterized by chromosome 6, 9 (CDKN2A/B) and 18q (SMAD4) deletions. DMP analysis showed that PAAD liver metastases have global hypomethylation of both promoter- and enhancer-associated CpGs compared to primary PAAD and PAAD peritoneal carcinomatosis. Finally, gene ontology analysis revealed that different epithelial-mesenchymal transition pathways are activated in PAAD liver metastases compared to PAAD peritoneal carcinomatosis. Conclusion: Our tool performs well in classifying metastatic PAAD samples and could be of great clinical use when a PAAD origin is suspected in the case of a CUP. DMP and CNA profiles show that PAAD liver metastases may have a distinct DNA methylation and copy number profile compared to primary and peritoneal carcinomatosis PAAD. Citation Format: Teodor G. Calina, Eilís Perez, Simon Schallenberg, Horst David, Erik Knutsen, David Capper, Mihnea P. Dragomir. Genome-wide DNA methylation classifier diagnoses pancreatic ductal adenocarcinoma in CUP setting [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 4414.

Abstract 3890: Comprehensive molecular and immunological characterization of early-onset esophagogastric cancer

Abstract Background: The incidence of early-onset esophagogastric cancer (EOEGC), defined as age of diagnosis &amp;lt;50, has increased in recent decades. Compared to average-onset esophagogastric cancer (AOEGC), EOEGC are more likely to be genomically stable, have diffuse histology, and present with more advanced disease. Here, we utilized a large real-world data cohort to characterize EOEGC with molecular and immune signatures. Methods: 5,175 esophagogastric cancer (EGC) samples (&amp;lt;50 yrs, n=530; ≥50 yrs, n=4645) were tested by next generation sequencing (NGS) (592, NextSeq; WES, NovaSeq) and whole transcriptome sequencing (WTS) (NovaSeq) (Caris Life Sciences, Phoenix, AZ). EGC patients with age &amp;lt;50 and ≥50 were classified as EOEGC and AOEGC, respectively. Deficient mismatch repair (dMMR)/microsatellite-instability (MSI) was tested by IHC and NGS. Tumor mutational burden (TMB) totaled somatic mutations per tumor (high&amp;gt;10 mt/MB). Pathway enrichment determined by Gene Set Enrichment Analysis (Broad Institute, Cambridge, MA). Immune cell fractions were calculated by deconvolution of WTS: Quantiseq. Statistical significance was determined using chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q &amp;lt; 0.05). Results: EOEGC had higher frequency of CDH1 (18.9% vs 6.5%) but lower frequency of TP53 (65.9% vs 74.4%) mutations compared to AOEGC (all q&amp;lt;0.05). EOEGC had higher frequency of CCNE1 (6.8% vs 4.4%), MYC (6.1% vs 4.1%) and FGFR2 (3.45% vs 1.87%) copy number alterations and ARHGAP26 (5.67% vs 2.2%) fusion. EOEGC had lower frequency of TMB high (3.8 vs 10.1%) and dMMR/MSI-H (1.3% vs 5.7%) (all p&amp;lt;0.05). EOEGC had pathway enrichment of epithelial mesenchymal transition (EMT) (NES: 1.8, FDR: 0.0) and angiogenesis (NES: 1.3, FDR: 0.24). EOEGC had lower median MAPK pathway activity score (MPAS) (-0.16 vs 0.13, p&amp;lt;0.05). Analysis of inferred immune cell infiltrates showed that EOEGC had increased infiltration of B cells (4.7% vs 3.9%) and M2 macrophages (3.6% vs 3%) but decreased infiltration of M1 macrophages (3.7% vs 4%) (all q&amp;lt;0.05). EOEGC had increased T cell inflamed signature (31.3% vs 26.1%, p&amp;lt;0.05) and increased expression of HAVCR2 (TIM3) but decreased expression of FOXP3 and CD274 (PD-L1) (FC: 0.84-1.09, all p&amp;lt;0.05). There was no difference in LAG3, CTLA4, and IDO1 gene expression. Conclusion: EOEGC has several unique molecular and tumor immune microenvironment features. In this real world cohort, EOEGC has increased frequency of CDH1 mutations, ARHGAP26 fusions, enrichment of EMT and angiogenesis pathways, decreased MAPK pathway activity, decreased frequency of TMB high and dMMR/MSI-H, and a unique immune cell infiltrate with decreased M1 macrophages and increased M2 macrophages. These unique differential characteristics present therapeutic opportunities but also demonstrate the limitations of currently approved therapies in this subset of patients. Citation Format: Lawrence W. Wu, Sachin K. Deshmukh, Sharon Wu, Joanne Xiu, Alex Farrell, Vincent Lam, Emil Lou, Sanjay Goel, Chadi Nabhan, Ryan H. Moy. Comprehensive molecular and immunological characterization of early-onset esophagogastric 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 3890.

Abstract 2079: Tumor-derived fibrinogen promotes pancreatic ductal adenocarcinoma progression

Abstract Background: Hypercoagulability is a common clinical manifestation in patients with cancers, especially in pancreatic ductal adenocarcinoma (PDAC). Over 20% of PDAC patients with advanced-stage and worse prognosis undergo a venous thromboembolism (VTE) incidence. Fibrinogen (FG) may contribute to VTE due to its high expression in advanced PDAC tumors. Here, we set to determine the biological roles of tumor-derived FG in PDAC. In addition, our previous study showed that Von Willebrand Factor (VWF) A2 domain can effectively bind to FG and reduce platelet clot formation. Therefore, the functional roles of A2 on FG in PDAC were also studied. Methods: The correlation between survival rate and FG expression in PDAC was analyzed using RNAseq profiles of 149 PDAC patient samples from the TCGA database. PDAC subtyping of Baylor College of Medicine (BCM) PDAC patient-derived xenograft (PDX) cohort was performed using RNAseq data according to Moffitt’s criteria. The FG (three chains FGA, FGB, FGG) overexpression (OE) and knock-out (KO) PDAC cell lines were established. The gene expression and biological functions of FG were performed in PDX and cell lines using IHC and immunoblot assays. The FG effect on PDAC progression in vivo was studied in mouse models. Results: TCGA analysis showed that elevated tumor-derived FG gene expression is significantly correlated with worse overall survival and disease-free survival rates in PDAC patients. PDX lines RNAseq analysis clearly separated BCM PDAC PDXs into two subtypes: basal-like and classical PDACs. Basal-like PDXs showed significantly stronger FG staining than that in classical ones. Compared to the classical subtype, the basal-like subtype showed significantly upregulated genes that are associated with the epithelial-mesenchymal transition (EMT), IL6/JAK/STAT3, and TNFα signaling pathways. Accordingly, basal-like subtype PDAC exposed to IL6 or TNFα significantly increased FG and FG receptor expression with activated STAT3 and AKT pathways and elevated EMT markers, whereas classical subtype cells have minimal changes. In addition, we found that the FG-OE cells exhibit enhanced cell proliferation and migration properties whereas FG-KO cells reduced the effects. Consistent with in vitro data, FG-OE PDAC showed significantly higher tumor burdens than that of control PDAC in both orthotopic and subcutaneous PDAC mouse models. Furthermore, A2 protein treatment can effectively block the FG function and dramatically inactivate the FG-induced EMT process and AKT signaling pathway. Conclusions: Tumor-derived fibrinogen is upregulated in a basal-like subtype of PDAC cells and may contribute to tumor growth and metastasis by activating aberrant signaling pathways and promoting EMT. Our findings imply that elevated fibrinogen in PDAC could contribute to tumor progression and the A2 protein which target to fibrinogen may be a promising therapy for basal-like subtype PDAC. Citation Format: Dongliang Liu, Lisa Brubaker, Yichi Niu, Emily LaPlante, George Van Buren, Aleksandar Milosavljevic, Changyi Chen, Chenghang Zong, Miguel Cruz, Qizhi Yao. Tumor-derived fibrinogen promotes pancreatic ductal adenocarcinoma 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 2079.

Abstract 2756: Single cell analysis reveals treatment response-associated plastic cell state and lineage switching in aggressive variant prostate cancer

Abstract Prostate cancer (PCa) is a common malignancy in men over 65, ranking as the second leading cause of cancer-related deaths among men in the United States. While most prostate cancers respond to androgen receptor (AR) targeting therapies, Aggressive Variant Prostate Cancers (AVPCs), characterized by RB1, Tp53, and/or PTEN alterations, do not. AVPCs exhibit lineage plasticity in preclinical models, enabling the expression of non-prostate epithelial lineage markers to adapt to therapeutic pressures. However, a measurable definition of lineage plasticity as a potential therapeutic target for clinical trials is currently lacking. To arrive at said definition, we perform single-nuclei RNA sequencing (snRNA-seq) on lymph node metastases from twelve AVPC patients with matched sample pairs of both pre- and post-treatment. Additionally, we include snRNA-seq data from eight non-AVPC patients as a baseline. Expanding upon our prior establishment of tumor-specific total mRNA expression (TmS) as an indicator of tumor cell lineage plasticity (Nature Biotechnology, PMID: 35697807), we employ unique molecular identifier (UMI) counts from individual cells to quantify this plasticity. We reveal a distinct cluster of tumor cells with notably high UMI counts in resistant samples, indicative of a less differentiated state and increased transcriptional diversity. This high-UMI cluster is marked by significant enrichment in pathways associated with epithelial-mesenchymal transition (EMT), stemness, one-carbon metabolism, and arginine metabolism pathways. Concurrently, there is a reduction in activity within the androgen receptor (AR) and DNA damage repair pathways. These characteristics suggest an enhanced capacity for lineage switching in AVPC tumor cells, potentially contributing to evasion from targeted therapies. Moreover, immune components within resistant samples consistently display lower UMI counts, indicating a diminished propensity for lineage plasticity. In conclusion, we present a better understanding of lineage switching in therapeutic resistance in AVPCs, paving the way for novel treatment strategies in PCa management. Citation Format: Shuai Guo, Elavarasan Subramani, Daniel E. Frigo, Patrick G. Pilié, Sangeeta Goswami, Rama Soundararajan, Ana Aparicio, Wenyi Wang. Single cell analysis reveals treatment response-associated plastic cell state and lineage switching in aggressive variant prostate 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 2756.

Abstract 6434: Microenvironment of adjacent non-neoplastic regions determines prognostic outcomes in locally advanced colorectal cancer after surgical resection: A multi-center &amp; multi-omics study

Abstract Background: There is an unmet need for additive predictive biomarkers for the recurrence of stage II/III colorectal cancer (CRC) after surgery. We hypothesized that the heterogeneities of tumors present a substantial impediment to finding agnostic biomarkers. To avoid this, we focused on the normal tissue from the margins of resected specimens. Methods: We divide the groups using RNA sequencing derived from 273 tumors and 273 paired normal tissues from 5 Korean cancer centers. Groups were defined as follows: tumor-like microenvironment in normal mucosa (tNME): high level of tumor signature in normal mucosa; healthy normal microenvironment (hNME): low tumor signature in normal tissue. The impact of this classification was further evaluated in TCGA cohort. For the mechanistic explanation, we conducted 16s rRNA metagenomics and single-cell RNA sequencing from 47 patients and validated by spatial transcriptomics. Results: There were no significant differences between subgroups in baseline characteristics, including age, sex, medical centers, sidedness, stage and the distance between tumor and paired normal tissue. With a median follow-up of 58.2 months, the tNME group showed poor 5-year recurrence-free survival (54.7 vs. 73.0%, HR=1.94, P=0.002) and 5-year overall survival (OS; 78.2 vs. 83.0%, HR=1.76, P=0.033). In addition, tNME showed a trend toward poorer 5-year OS (34.5% vs. 68.8%, HR=3.76, P=0.071) in TCGA. The pathway analysis exhibited tNME had decreased maintenance of membrane while increased expression of humoral reaction to bacteria. Only the tNME group showed similar microbiome diversity between tumor and normal tissues, consisting of more proportion of carcinogenic genera, including fusobacterium and bacteroides than hNME. scRNA-seq revealed a positive co-occurrence of Th17, GZMKhighCD8+T cells, and IL1Bhigh neutrophils in the tumor and normal tissues of tNME. A high proportion of EMP1high epithelial cells, were observed in the tNME group, with upregulated epithelial-mesenchymal transition (EMT), bacterial-cellular-invasion and leukocyte signaling pathways. The cell-cell interaction analysis suggest Th17 cells promote IL1Bhigh neutrophil retention, increasing crosstalk with CD8+ T cells, and inducing the production of high levels of GZMK, which in turn decreases E-cadherin in the intestinal epithelium. A weak intestinal barrier may provoke more bacteria-infected cancer cells, promoting cancer cell progression via EMT and recruiting IL1Bhigh neutrophils and GZMKhighCD8+T cells, resulting in a vicious cycle. Conclusions: The microenvironmental status of normal tissues offers a promising biomarker for stage II/III CRC. Microbiota dysbiosis-induced organized microniches with immune and epithelial cells was related to metachronous recurrence after surgical resection. Citation Format: Yeong Hak Bang, Ji Hye Choi, Kyunghee Park, Jinyeong Lim, Dae Hee Pyo, Yong Beom Cho, Tae-You Kim, Kyu Joo Park, Seung-Bum Ryoo, Sung-Bum Kang, Chang Sik Yu, Kil-yong Lee, Jaeim Lee, Jin-Young Lee, Young-Joon Kim, Woong-Yang Park. Microenvironment of adjacent non-neoplastic regions determines prognostic outcomes in locally advanced colorectal cancer after surgical resection: A multi-center &amp; multi-omics study [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 6434.

Abstract 5067: Exploring the genomic landscape of de novo neuroendocrine prostate cancer: Insights for innovative therapies from spatial gene expression analysis

Abstract Introduction &amp; Objectives Neuroendocrine prostate cancer (NEPC) accounts for less than 1% of all prostate cancers but has a worse prognosis than androgen receptor-positive prostate adenocarcinoma (ARPC). Rare cases exist where both de novo NEPC and ARPC are found in the same tissue sample. Our study examines one such unique case: a 78-year-old male treated at Ehime University Hospital who was diagnosed with both ARPC and adjacent de novo metastatic NEPC. This case provides an excellent opportunity for studying gene expression in these two types of prostate cancer. Materials &amp; Methods We used Visium CytAssist Spatial Gene Expression technology from 10x Genomics to analyze formalin-fixed, paraffin-embedded (FFPE) tissue samples from this unique patient. Results We observed elevated expression levels of specific neuroendocrine markers like PEG10, DLL3, NCAM1, SYP, and CHGA in de novo NEPC regions. In contrast, androgen receptor markers such as KLK3, ACPP, TMPRSS2, and NKX3.1 were more prevalent in ARPC areas. Furthermore, genes like Chek1, BRCA1/2, TOP2A, and FANCA were also elevated in NEPC, suggesting that PARP and TOP2 inhibitors could be effective. Expression levels of Rbfox3 and SFRTM2 were lower in NEPC areas, implying possible roles in epithelial-mesenchymal transition (EMT) and Wnt signaling pathways. Additionally, fibrotic markers like HGF, HMOX1, ELN, and GREM1 were upregulated, suggesting that de novo NEPC tumors might be 'immune cold,' thus requiring treatments to boost the effectiveness of immune checkpoint inhibitors. Conclusion The data from additional cases could open the door for new treatment options for NEPC and improve survival rates for castration-resistant prostate cancer patients. Our research serves as a pioneering application of Visium CytAssist on FFPE samples and is the first to examine gene expression in both ARPC and de novo NEPC. A subset of these findings was published in the International Journal of Molecular Science (IJMS) in May 2023. Citation Format: Ryuta Watanabe, Noriyoshi Miura, Mie Kurata, Riko Kitazawa, Tadahiko Kikugawa, Takashi Saika. Exploring the genomic landscape of de novo neuroendocrine prostate cancer: Insights for innovative therapies from spatial gene expression analysis [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 5067.