Primary Tissue Research Articles

Abstract 4555: c-Met/AXL crosstalk in mediating therapeutic resistance in renal cell carcinoma

Abstract Receptor Tyrosine Kinase (RTK), c-Met, is overexpressed in renal cancer and correlates with a decreased survival rate. Upon binding with its specific ligand, Hepatocyte Growth Factor (HGF), c-Met activates pro-tumorigenic signaling. c-Met/RTK inhibitors are used for the treatment of advanced renal cell carcinoma (RCC). However, acquired therapeutic resistance is a major clinical problem and the underlying mechanisms are largely unknown. Hence, novel therapeutic targets are needed to overcome the clinical hurdles; and the RTK, AXL, can be a potential target. AXL is overexpressed and a poor prognostic marker in RCC. AXL overexpression drives wide-ranging processes, including epithelial-to-mesenchymal transition (EMT), tumor angiogenesis, and resistance to chemotherapeutics. Cabozantinib (XL184/Cabo), is approved for advanced-stage RCC and can inhibit c-Met and VEGFR2 activation (including AXL and a few other RTKs); however, it is not a specific/potent inhibitor of AXL. Hence, inhibiting c-Met alone may not be sufficient when AXL remains active. Therefore, the pro-tumorigenic role of AXL and its cross-talk with c-Met in renal cancer need to be thoroughly investigated. We compared the expression of c-Met and AXL in TCGA and found significantly high expression of both c-Met and AXL in primary renal tumor tissues compared to normal tissues. Our data showed that AXL forms a complex with c-Met and may have a significant cross-talk which can be involved in therapeutic resistance. We have also found that prolonged treatment of c-Met inhibitor Cabo, (including Crizotinib and PF-4217903) induced c-Met and AXL overexpression in RCC cells. Interestingly, c-Met inhibitor(s)-induced overexpressed c-Met can also be increasingly phosphorylated (at low concentrations) in the presence of HGF, which may cause enhanced downstream tumor-promoting signaling. To understand the role of AXL in tumor-promoting pathways and therapeutic resistance, we have generated CRISPR/Cas9-mediated AXL knock-out cells (AXL-KO) and found that silencing AXL can prevent c-Met-inhibitor(s)-mediated c-Met overexpression. Furthermore, to identify the effect of AXL-KO on pro-tumorigenic signaling, transcriptional profiles of control clones and AXL-KO cells were compared. The gene set enrichment analysis (GSEA) showed that genes involved in ‘EMT’, ‘Hypoxia’, and ‘K-Ras’ signaling pathways were significantly downregulated. We have also utilized an AXL-specific small molecule inhibitor, TP-0903, in combination with Cabo and validated our data. We have also generated a Cabo-resistant cell line (Caki-1) and found high expression of c-Met and AXL in these cells. Furthermore, either silencing of AXL (using siRNA) or inhibiting AXL (using TP0903) induced significant apoptosis in these Cabo-resistant cells. Together, our data suggest that inhibition of AXL along with c-Met can be beneficial in preventing acquired therapeutic resistance in RCC. Citation Format: Akash Sabarwal, Laxminarayan Rawat, Johannes Wedel, Murugabaskar Balan, Gwo-Shu Mary Lee, Toni K. Choueiri, Soumitro Pal. c-Met/AXL crosstalk in mediating therapeutic resistance in renal cell carcinoma [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 4555.

Abstract 6900: Patient-derived xenografts from circulating cancer stem cells and their potential utility in personalized medicine of pancreatic cancer

Abstract Background: Pancreatic cancer carries a poor prognosis in the majority of patients, with an overall 5-year survival rate of less than 10%. Therefore, the development of new therapies and preclinical models is crucial and urgently needed. Circulating cancer stem cells (cCSCs) are a subset of circulating cancer cells that have stem cell-like properties and play a significant role in tumor progression, metastasis, and treatment resistance. Patient-derived xenografts (PDX) reflect the genotypic and phenotypic landscape of patients' cancers and are useful for drug screening, biomarker development, and preclinical evaluation of personalized medicine strategies. In this study, we describe a fast, simple, and cost effective method to generate PDX on Chorioallantoic Membrane (CAM) from circulating cancer stem cells. Methods: In this study, primary cultures from circulating cancer stem cells were established using sphere-forming assays from 30 patients with newly diagnosed pancreatic cancer. Subsequently, tumorspheres were transplanted onto the CAM membrane of fertilized chicken eggs to form patient- derived xenografts. Results: For the identification of cCSCs from peripheral blood of pancreatic cancer patients, an innovative in vitro sphere-forming assay was established. The number of tumorspheres was correlated with clinicopathological parameters like tumor size, lymph node involvement and grading status of the primary tumor. Implantation of tumorspheres onto the CAM was successful in ~90 % of the applied samples. The histological analysis suggests that the PDX tumors were morphologically and pathologically identical to primary tumor tissue. Conclusions: The number of tumorspheres was associated with clinicopathological parameters. Further follow-up is needed to evaluate the prognostic significance of tumorsphere detection in pancreatic cancer. Generation of PDX from cCSCs on CAM has a high success rate and may become an integral part of the drug development arena, including drug screening and biomarker development. Citation Format: Monika Pizon, Dorothea Schott, Andreas Ettner-Sittner, Benedikt J. Wagner, Katharina Pachmann, Thiha Aung, Christina Hackl, Silke Haerteis. Patient-derived xenografts from circulating cancer stem cells and their potential utility in personalized medicine of pancreatic 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 6900.

Abstract 1194: Understanding radiation and immunotherapy induced cell state shifts in the pancreatic tumor microenvironment

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with few effective treatment options. It is characterized by a highly desmoplastic tumor microenvironment and a paucity of dendritic cells, leading to low immune cell infiltration and poor outcomes with immunotherapy treatments that are highly effective in other cancers. In a recent pilot study, metastatic PDAC patients who had progressed on chemotherapy were treated with a combination of dual immune checkpoint blockade (ICB) therapy and radiation which resulted in an 18% overall response rate (ORR) and 29% disease control rate (DCR). This led to a phase 2 study in order to further test this combination with the goal of deep correlative analysis to understand the determinants of immunotherapy response and resistance. In this follow up there was a 3.6% ORR, 10.7% DCR, progression free survival (PFS) of 2.3 months, and a single patient with complete response. We collected 36 samples from 23 patients including primary pancreas tumor tissue and liver metastases, and 13 pairs of pre and on treatment biopsies. We performed single-nucleus and paired single-cell RNA and TCR sequencing on these samples to provide comprehensive insight into the cell types and biology present in this unique tumor microenvironment. Using supervised non-negative matrix factorization we have identified both previously established and novel gene programs that co-vary between cell types. Within the various tissue sites we have identified differing proportions of basal to classical tumor cell types and a distinct shift towards the classical state post-radiation. Of particular interest is a group of interferon related gene programs present within epithelial cell subtypes, C1QC+ and MHCII+ macrophages, and CD14+/CD16+ monocytes that indicate cell type specific responses to treatment. Focusing on the T cells, we found a distinct shift towards exhausted or proliferating states on treatment and using TCR sequencing data we have identified novel and expanding clones on treatment, largely consisting of those same cell subtypes. We also collected spatial transcriptomics data on a subset of patient samples, and analysis is ongoing to further confirm the cell type relationships identified in single-cell resolution data, along with spatial localization of basal to classical tumor states. This vast multimodal dataset allows us novel insight into the radiation and dual ICB induced cellular state shifts in the tumor microenvironment. Citation Format: Milan Parikh, Ryan Park, Aparna R. Parikh, Julie L. Koenig, Leon Pappas, Moshe Sade-Feldman, Lynn Bi, Nicole Carzo, Tarin M. Grillo, Islam Baiev, Olanike Asupoto, Irena Gushterova, Tom LaSalle, Anna Gonye, Emily Blaum, David P. Ryan, David T. Ting, Theodore S. Hong, Dana Pe'er, Nir Hacohen, Arnav Mehta. Understanding radiation and immunotherapy induced cell state shifts in the pancreatic 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 1194.

Abstract 5199: Protease-activated CDCP1 as a marker for aggressive primary prostate cancer and castration resistance

Abstract CUB domain-containing protein 1 (CDCP1) is a type 1 transmembrane protein overexpressed in many cancers, including prostate cancer. CDCP1 has been associated with tumor progression, metastasis, drug resistance and poor prognosis in prostate cancer, making it a potential prognostic biomarker and therapeutic target. It has been shown to be overexpressed in a subset of castration resistant prostate cancers (CRPC) and cooperate with the loss of tumor suppressor PTEN to promote metastatic dissemination. Extracellular serine proteases activate CDCP1 by cleaving it into an N-terminal and C-terminal fragments. Proteolytic cleavage has been associated with the tumor-promoting functions of CDCP1. We studied the expression of full-length and cleaved form of CDCP1 in grade group 2-4 primary prostate cancer tissues and CRPCs using immunohistochemistry. Total CDCP1 staining was observed in 60% of primary prostate cancer samples, while the staining of cleaved CDCP1 was somewhat less frequently observed (45%). The results will be further analyzed regarding the PTEN status and for association with survival of the patients. In conclusion, so far, our results have indicated that cleaved CDCP1, which likely represents activated CDCP1, is detectable in GG 2-4 prostate cancers. Citation Format: Ruusu-Maaria Merivirta, Timo-Pekka Lehto, Antti Rannikko, Tuomas Mirtti, Hannu Koistinen. Protease-activated CDCP1 as a marker for aggressive primary prostate cancer and castration resistance [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 5199.

Abstract 5488: AI-enhanced spatial proteomics reveals B-cells & FoxP3+ cells interactions in HPV(+) oropharyngeal squamous cell carcinoma Progression

Abstract Background: Analyzing interactions and the microanatomical distribution of the tumor immune microenvironment (TIME) is essential for a comprehensive understanding of tumor progression. Imaging Mass Cytometry (IMC) is a high-dimensional tissue imaging system that enables the deeper and multiparametric in situ exploration of tumor microenvironments at a single-cell level. This study describes a pipeline for analyzing 39-plex IMC images of human HPV(+) oropharyngeal squamous cell carcinoma (OPSCC) tumor sections, elucidating immune cells' nature, functions, and interactions with tumor cells. The IMC data analysis provides valuable information for clinical studies that could be used for the identification of prognostic biomarkers and mechanisms of resistance to current immunotherapies. Methods: A retrospective study was conducted on (N=20) patients (10 progressors and 10 non-progressors) with HPV(+) OPSCC. The dataset comprises paired hematoxylin and eosin (H&E) images with IMC data from multiple Regions of Interest (ROIs) (N=82), enabling the in-situ profiling of 39 proteins in primary tumor tissue. Cell segmentation was followed by employing original images and their segmentation masks for cell phenotype identification using a probabilistic neural network method to spatially profile cancer cells, macrophages, NK-M cells, B-cells, and distinct T-cell populations. We identified protein expression at single-cell resolution and investigated the impact of multicellular spatial organization on the disease progression. The spatial neighborhood interaction score of tumor cells with various other cells was computed for all the ROIs across the two groups. Results: The markers showed varying expression levels of intensity distribution, likely due to differences in tissue sample composition. Specifically, CD3, CD4, CD8, CD19, CD20, and CD68 showed significantly higher intensity in non-progressors. Interestingly, FoxP3 also had a significantly higher intensity level in non-progressors. Cell phenotyping emphasized that non-progressors generally have increased levels of NK-M cell markers. Spatial analysis revealed a significant increase in interaction between CD3 cells and tumor cells in non-progressors (p-value=0.07, Mann-Whitney U test). Furthermore, a significant rise in the interaction between B-cells and FoxP3+ cells was observed in non-progressors (p-value<0.05, Mann-Whitney U test) suggesting a coordinated suppression of tumor growth. Conclusion: We developed a deep learning-based pipeline to analyze spatial relationships in the TIME of IMC data, demonstrating its clinical relevance in predicting disease progression. Our findings emphasize the importance of spatial relationships in the TME for response and suggest that proximity between either CD3+ T-cells to cancer cells or B-cells to FoxP3+ cells are candidate biomarkers. Citation Format: Sumanth Reddy Nakkireddy, Routman David, Kathleen Bartemes, Daniel Ma, Tae Hyun Hwang, Kathryn Van Abel, Chadi Nimeh Abdel-Halim. AI-enhanced spatial proteomics reveals B-cells & FoxP3+ cells interactions in HPV(+) oropharyngeal squamous cell carcinoma 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 5488.

Abstract 4737: The combination of the BET inhibitor JQ1 and gemcitabine induces regressions in gemcitabine resistant patient-derived xenograft models of pancreatic cancer

Abstract Efforts to develop targeted therapies for drug resistant tumors have been relatively unsuccessful. The 5-year survival for patients with advanced pancreatic cancer is ~3%. Gemcitabine is usually combined with nab-paclitaxel as a standard of care for treatment of locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC). However, no chemotherapeutic regimens thus far evaluated have been curative. We developed the first PDAC patient-derived xenograft (PDX) models in which resistance against gemcitabine was acquired in vivo. We used RNA-seq and ingenuity pathway analysis to compare expression profiles of paired parent vs gemcitabine resistant PDX models. This comparison suggested a previously unreported mechanism for gemcitabine resistance, involving aberrations of cholesterol biosynthesis and lipid metabolism pathways. We also made the unexpected observation that gemcitabine-resistant PDAC models derived from primary tumors have high levels of 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), an enzyme essential to cholesterol biosynthesis and rate limiting in ketogenesis. Notably, the BET bromodomain inhibitor JQ1 decreases HMGCS2 levels; and BET inhibitors + gemcitabine exert synergistic cytotoxicity in gemcitabine-resistant PDAC cells. We determined that the BET bromodomain inhibitor JQ1 + gemcitabine induces regressions of two in vivo gemcitabine-resistant tumor models which we developed directly from primary human tumor tissue. These mechanism-based studies suggest that inhibiting HMGCS2 represents a novel approach to therapy for PDAC. We propose that combining gemcitabine with agents that decrease levels of HMGCS2 comprises effective treatment for patients with drug resistant PDAC. Citation Format: Aubrey L. Miller, Samuel C. Fehling, Eric Josh Brown, Eric O. Heard, Tracy L. Gamblin, Rebecca B. Vance, Karina J. Yoon. The combination of the BET inhibitor JQ1 and gemcitabine induces regressions in gemcitabine resistant patient-derived xenograft models of pancreatic 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 4737.

Abstract 4597: RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal cancer

Abstract The widespread presence of N1-methyladenosine (m1A) modifications controls RNA metabolism and is pivotal to fundamental biological processes. However, the understanding of RNA m1A involved in cancer is still minimal. Here we reported the oncogenic role and the therapeutic targeting of RNA m1A methyltransferase TRMT61A in colorectal cancer (CRC). We observed consistent elevation of TRMT61A expression and RNA m1A levels in primary CRC tissues, which was significantly associated with poor patient survival in two independent cohorts (both P<.001). CRISPR/Cas9 screenings revealed that TRMT61A is the most essential gene among m1A regulators. TRMT61A facilitates the growth and metastasis of CRC cells by increasing the stability of mRNA of crucial targets, such as ONECUT2, which leads to the activation of MAPK/ERK signaling in an m1A-dependent manner. Notably, depletion of ONECUT2 or inhibition of MAPK/ERK could abrogate the tumor-promoting role of TRMT61A, implying that TRMT61A induces ONECUT2-MAPK/ERK axis to facilitate CRC. Inhibiting TRMT61A with nanoparticle-encapsulated siTRMT61A or our recently identified small molecule compound PGG shows promising anti-CRC effects in vitro and in vivo. Together, our study reveals the promoting role of TRMT61A-induced m1A modification in MAPK/ERK signaling and highlights the potential of targeting TRMT61A as a promising therapeutic approach in CRC treatment. Citation Format: Xiaoting Zhang, Na Qin, Fenfen Ji, Hao Su, Hongyan Chen, Haiyun Shang, Huarong Chen. RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal 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 4597.

Abstract 5894: Novel splicing-derived neoantigen in triple negative breast cancer uncovered by SpliceIO™ a robust platform for the discovery and validation of disease-specific immunotherapies

Abstract Splicing dysregulation is a major hallmark of cancer, affecting tumor progression, metastasis, and therapy resistance. Aberrant alternative splicing (AS) plays a critical role in generating tumor-specific neoantigens targetable through an arsenal of immunotherapeutic modalities. Such neoantigens cannot be discovered using conventional DNA-based tools; they require specialized software for AS analysis using RNA-seq data. SpliceIO is Envisagenics’ AI platform for AS-derived neoantigen discovery. SpliceIO uses a “predictive ensemble” approach to uncover neoantigens that are both stably expressed and located on the extracellular membrane of cancer cells. Using SpliceIO, we have analyzed more than 10,000 RNA-seq samples from 5 patient cohorts covering 5 breast cancer subtypes as well as 2,647 normal RNA-seq samples from GTEx. Our analysis has identified tumor-specific neoantigens present in AS transmembrane proteins specific for Triple Negative Breast Cancer. SpliceIO target candidates were validated experimentally using our well-established pipeline in which isoform specific transcripts are tested in cancer cell lines by PCR and primary tumor tissues by qPCR to confirm RNA expression. Tumor heterogeneity and prevalence is confirmed by RNA in-situ hybridization in Tissue Microarrays. Extracellular localization of the novel epitope is confirmed by clone generation with GFP and c-Myc tagging followed by microscopy, Western blotting, and proteomic analysis. Our top validated target presents high TNBC tumor specificity and heterogeneous distribution, and contains a novel extracellular N-terminal domain. These results strongly support the role of aberrant AS as a major source of tumor-specific neoantigens. Our combined computational and experimental approach promotes novel target discovery, enabling the development of novel immunotherapeutic for TNBC patients who are in critical need of better treatment options. Citation Format: Nicole Williams, Miguel A. Manzanares, Kendall Anderson, Hasan Zunrut, Sakshi Gera, Nayab Habib, Shaleigh Stanton, Taylor Floyd, Sanjana Shah, Devon Trahan, Martin Akerman, Gayatri Arun. Novel splicing-derived neoantigen in triple negative breast cancer uncovered by SpliceIO™ a robust platform for the discovery and validation of disease-specific immunotherapies [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 5894.

Abstract 6835: Profiling of new prostate cancer vulnerabilities through single-nucleus RNAseq implicates the CAF-specific TGF-β pathway in tumor progression

Abstract Background: Transcriptomic profiles of primary high grade prostate cancer (hgPCa) have been extensively studied and prognostic gene expression signatures to classify patients for risk have been identified. However, such studies have employed bulk genomic techniques that blur the contributions of the different cell types. Indeed, tumor microenvironment (TME) cells can significantly contribute to these transcriptomic signatures thereby confounding the lineage of potential therapeutic targets. These challenges underscore the potential of single-nucleus (sn)RNAseq to elucidate new PCa vulnerabilities. We set out to assess whether the TME, particularly cancer-associated fibroblasts (CAFs) drive poor outcome in PCa. Methods: We obtained 15 treatment-naïve frozen primary high risk PCa tissue samples, mostly Gleason >=8. A PCa nuclei dissociation protocol was adapted for single nucleus snRNAseq (10X Genomics). Sample profiling included all cell populations in the tissue including tumor and TME. Output was analyzed using Seurat (v.4.1.1), corrected for ambient RNA expression with CellBender (v.0.3.1) and detected and removed doublets with Scds (v.3.9). Tumor cells were distinguished from normal epithelium cells by a combination of inferCNV (v.1.12.0) and supervised learning with random forests classification. Results: Through snRNAseq, we show that CAFs, and not tumor cells, entirely drive the expression of previously validated poor prognostic signatures (Mortensen, 2015). Our analysis revealed that the TGFβ pathway expression, TGF-β1 in particular, is upregulated in CAFs rather than PCa cells. This pathway, along with poor prognosis signatures are selectively elevated in CAFs from patients with Gleason high compared to low, implicating the TGFb axis as a PCa vulnerability. We also derived a snRNAseq CAF signature that differentiates non-responders to immune checkpoint therapy in mCRPC (Nivolumab+Ipilimumab). Furthermore, cluster profiling of tumor nuclei revealed that hgPCa harbors high heterogeneity with distinct niches of hgPC, mCRPC or neuroendocrine phenotypes for each patient. Conclusions: Through snRNAseq we show that CAFs are the main contributors to prior bulk RNAseq classifiers of poor response, resulting in a refined CAF signature that allows for direct investigation of the contribution of CAFs in other patient segments (mCRPC). Our findings point to a hgPCa patient segment with high CAF representation that may benefit from the addition of a CAF targeting agent (ie.TGFbi) to androgen deprivation therapy. This data has the potential to help refine our prognostic classifiers for patient selection and clinical applicability. Further study of the reported tumor heterogeneity will inform rational combination therapies to tackle resistance mechanisms. Citation Format: Alexandre P. Alloy, Sharmila Chamling Rai, Brendan O'Brien, Anna Lyubetskaya, Arnaud Amzallag, Benjamin Chen, Ana Lako. Profiling of new prostate cancer vulnerabilities through single-nucleus RNAseq implicates the CAF-specific TGF-β pathway in tumor progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6835.

Abstract 1498: TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in CMS4 colorectal cancer

Abstract Background: Colorectal cancer (CRC) is characterized by a metastatic pattern that shows tropism towards the liver which is the major cause of CRC-related deaths. The current CRC classification, Consensus Molecular Subtypes (CMS), suggests an association between transforming growth factor (TGF)-β signaling, cancer-associated fibroblasts (CAFs), and the risk of liver metastasis. However, the key downstream effectors of TGFβ signaling in CAFs and their role in hepatic metastases remain poorly understood. Methods: The aim of this study was to investigate the TGF-β/CAF dependent cross talk with the hepatocytes in pre-metastatic niche formation. CAFs from 18 primary CRC tissues and 7 liver-metastasized CRC were stimulated with TGFβ1 and qPCR arrays/ELISAs were performed to identify differentially expressed genes. Results were cross-referenced with RNAseq expression data of CMS-classified CRC and in fresh samples from CRC patients. To investigate CAF-liver crosstalk hepatocytes were stimulated with the TGFβ primed CAF-derived cytokines and the effect on pro-inflammatory gene expression and neutrophil migration was determined. Subsequently, blockade of these pathways via chemical inhibition and CRISPR/Cas9 genetic ablation was performed to study the molecular mechanism involved in the induction of this hepatic pro-inflammatory program. Results: TGFβ signaling in primary CRC-derived CAFs leads to increased expression of different IL-6 cytokine family members, which was also reflected in human CRC samples. CAF-derived IL6 family members induce upregulation of myeloid chemoattractants, including SAA1, in hepatocytes and increased neutrophil-to-hepatocyte migration in vitro. Chemical blockade and genetic ablation of the IL-6 family cytokine signaling pathway showed the critical role of the gp130 co-receptor in the regulation of this inflammatory response in hepatocytes and the potential formation of a premetastatic niche. Conclusion: TGFβ signaling in CAFs actively contributes to the formation of a neutrophil-dependent, pre-metastatic hepatic niche, and this mechanism might play a role in CMS4 subtype CRC. Citation Format: Subinuer Abudukelimu, Tom J. Harryvan, Stef G. Janson, Imke Stouten, Els M. Verdegaal, Lukas JAC Hawinkels. TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in CMS4 colorectal 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 1498.

Abstract 1054: Reciprocal circRNA-miRNA expression axes indicative of early tumor initiation in breast

Abstract Cancer prevention and early detection are the most effective tools for cancer control. In this study, we adopt a novel approach of identifying a network of proteins/mRNA-circRNA-miRNA axes. We hypothesize that mutation of oncogenes or tumor suppressor genes during pre-oncogenic stage result in aligned change in levels of circular RNAs-derived genes, as well as, reciprocally, in corresponding sponged miRNAs. These epigenetic risk predictive proteins/mRNA-circRNA-miRNA axes serve as potential tool for early detection of changes leading to breast cancer (BC) and can be further used as non-invasive screening biomarkers of patients’ blood in populations susceptible to cancer. BC patients in GDC Data Portal, TCGA-BRCA project are selected based on several criteria such as their age at diagnosis (20-50 years old), early clinical stage of cancer (stage I) and disease type (ductal and lobular neoplasms). Differentially expressed genes are acquired from mRNA sequencing data by comparing Stage I Breast cancer versus normal primary tissues using R Studio. Then, mRNAs whose expression is aligned with the differentially expressed circRNAs and their host genes acquired from Gene Expression Omnibus (GEO) (GSE182471, Triple Negative Breast cancer tissues versus normal tissues) are selected. Differentially expressed miRNAs, in reciprocal expression with circRNAs, are defined using miRNA sequencing data of the same previously chosen TCGA BRCA patients. Selected miRNAs are hypothesized to be sponged with high confidence by selected circRNAs based on a context percentile binding score in CircInteractome. Using KM Plotter, the survival analysis of corresponding miRNAs in grade I BC patients is examined. The predicted miRNA expression was correlated with lower survival rates among stage I BC patients in KM Plotter. MiRNA-enrichment analysis is used to further validate the involvement of selected miRNAs in early tumorigenic events through exploring in which molecular pathways their downstream genes are enriched. We have constructed more than 20 potential proteins/mRNA-circRNA-miRNA axes for non-invasive screening of patients’ body fluid (i.e. Blood) in populations susceptible to BC using RNA and miRNA sequencing data available in online databases and further validate the proposed axes using in-silico tools. The described axes, once validated in clinical samples could provide a potential tool for early-stage BC prediction and prevention. Citation Format: Nour Abbas Maatouk, Sarah Hussein Marei, Abdallah Bilal Kurdi, Nadim Shady Hamade, Rihab Raif Nasr, Rabih Shakib Talhouk. Reciprocal circRNA-miRNA expression axes indicative of early tumor initiation in breast [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 1054.

Abstract 6454: Genomic characterization of vulvar squamous cell carcinoma

Abstract Introduction: Understanding the molecular underpinnings of vulvar squamous cell carcinoma (vSCC) has strong potential for clinical impact, given the unmet need for this rare cancer. vSCCs have two main etiologies, including human papillomavirus (HPV) infection or skin conditions such as lichen sclerosis. Clinically, few treatment options with limited efficacy are available for recurrent vSCCs and large whole transcriptome disease subtyping studies are limited due to the rarity of this cancer type. Here, we present a whole transcriptome subtyping study of 244 vSCC clinical samples with DNA genomic profiling. Furthermore, we compared vSCCs to other SCC disease subtypes (pan-SCC), including lung, esophageal, skin, urothelial, anal, and head and neck (HN). Our goal was to gain novel insights into the molecular landscape of vSCCs to inform new routes of therapy. Methods: Deidentified records of SCC patients were selected from the Tempus clinico-genomic database. The vSCC cohort was predominantly composed of, but not exclusively, naive or pre-treatment primary tissue. The pan-SCC cohort was limited to randomly sampled primary pre-treatment female samples with paired RNA and DNA sequencing. To perform vSCC subtyping, we used bulk RNA-seq and clustered the samples using FastPG-CC, an internally developed consensus-clustering extension of FastPG, a graph-based parallelized clustering tool. We next performed differential expression, pathway analysis, and cell type abundance estimation. Results: Unbiased gene expression clustering analysis identified three vSCCs clusters; an HPV+ cluster (HPV+, 32% of vSCC samples), HPV- cluster (HPV-, 33%), and an intermediate cluster which contained both HPV+ and HPV- samples (Mix, 35%). The HPV- cluster was enriched for TP53 and TERT promoter mutations, EMT and tumor microenvironment gene expression-derived pathways, and was most similar to HPV- oral HN tumors. The HPV+ cluster was enriched with PIK3CA mutations, cell cycle gene expression and was most similar to other HPV+ SCC samples, including cervical, anal, and HN. The Mix cluster was enriched for neutrophils, fatty acid metabolism and was most similar to skin SCC. Conclusions: We performed a multi-modal molecular subtyping analysis on a large cohort of vSCCs and identified three molecular subtypes, which enabled us to identify heterogeneity within vSCC, and observe that a subset of vSCCs share features with SCC tumor types for which there are emerging therapy options. Thus, this approach identifies a subset vSCCs that may be responsive to existing SCC therapeutics. Citation Format: Sara R. Selitsky, Tasha Thong, Kimberley Roche, Justin Guinney, Praveen Sethupathy, Catherine Igartua. Genomic characterization of vulvar squamous cell carcinoma [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 6454.

Prognostic Signature in Osteosarcoma Based on Amino Acid Metabolism-Associated Genes.

Background: Osteosarcoma (OS) is undeniably a formidable bone malignancy characterized by a scarcity of effective treatment options. Reprogramming of amino acid (AA) metabolism has been associated with OS development. The present study was designed to identify metabolism-associated genes (MAGs) that are differentially expressed in OS and to construct a MAG-based prognostic risk signature for this disease. Methods: Expression profiles and clinicopathological data were downloaded from Gene Expression Omnibus (GEO) and UCSC Xena databases. A set of AA MAGs was obtained from the MSigDB database. Differentially expressed genes (DEGs) in GEO dataset were identified using "limma." Prognostic MAGs from UCSC Xena database were determined through univariate Cox regression and used in the prognostic signature development. This signature was validated using another dataset from GEO database. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, single sample gene set enrichment analysis, and GDSC2 analyses were performed to explore the biological functions of the MAGs. A MAG-based nomogram was established to predict 1-, 3-, and 5-year survival. Real-time quantitative polymerase chain reaction, Western blot, and immunohistochemical staining confirmed the expression of MAGs in primary OS and paired adjacent normal tissues. Results: A total of 790 DEGs and 62 prognostic MAGs were identified. A MAG-based signature was constructed based on four MAGs: PIPOX, PSMC2, SMOX, and PSAT1. The prognostic value of this signature was successfully validated, with areas under the receiver operating characteristic curves for 1-, 3-, and 5-year survival of 0.714, 0.719, and 0.715, respectively. This MAG-based signature was correlated with the infiltration of CD56dim natural killer cells and resistance to several antiangiogenic agents. The nomogram was accurate in predictions, with a C-index of 0.77. The expression of MAGs verified by experiment was consistent with the trends observed in GEO database. Conclusion: Four AA MAGs were prognostic of survival in OS patients. This MAG-based signature has the potential to offer valuable insights into the development of treatments for OS.

Unveiling spatial complexity in solid tumor immune microenvironments through multiplexed imaging.

Deciphering cellular components and the spatial interaction network of the tumor immune microenvironment (TIME) of solid tumors is pivotal for understanding biologically relevant cross-talks and, ultimately, advancing therapies. Multiplexed tissue imaging provides a powerful tool to elucidate spatial complexity in a holistic manner. We established and cross-validated a comprehensive immunophenotyping panel comprising over 121 markers for multiplexed tissue imaging using MACSima™ imaging cyclic staining (MICS) alongside an end-to-end analysis workflow. Applying this panel and workflow to primary cancer tissues, we characterized tumor heterogeneity, investigated potential therapeutical targets, conducted in-depth profiling of cell types and states, sub-phenotyped T cells within the TIME, and scrutinized cellular neighborhoods of diverse Tcell subsets. Our findings highlight the advantage of spatial profiling, revealing immunosuppressive molecular signatures of tumor-associated myeloid cells interacting with neighboring exhausted, PD1high T cells in the TIME of hepatocellular carcinoma (HCC). This study establishes a robust framework for spatial exploration of TIMEs in solid tumors and underscores the potency of multiplexed tissue imaging and ultra-deep cell phenotyping in unraveling clinically relevant tumor components.

The 40-gene Expression Profile (40-GEP) Test Identifies Cutaneous Squamous Cell Carcinoma (cSCC) Patients at High Risk of Metastasis within Lower-Staged Tumors to Better Guide Treatment Decisions

Introduction- The development of metastases has a profound impact on cSCC patient survival. Lower-stage tumors are those that lack factors that portend higher risk for disease progression and therefore not typically considered for increased surveillance or treatment. However, up to one-third of all metastatic events have been reported for patients originally staged as T1. The 40-GEP test is validated to accurately classify risk for regional and/or distant metastasis in patients with primary cSCC with at least one high-risk factor.  The current study investigated whether the 40-GEP test could independently improve identification of lower-staged tumors at increased risk of metastasis. 
 Methods- In an IRB-approved, retrospective, multi-center study, primary tumor tissue and associated clinical data from patients with cSCC and one or more clinicopathologic risk factors (n=897) were collected. Within this overall cohort, lower Brigham and Women’s Hospital (BWH) T-staged samples (n=444 T1 and n=335 T2a) were evaluated by Kaplan-Meier survival analysis to determine metastasis-free survival (MFS) according to 40-GEP risk class (Class 1-low metastatic risk; Class 2A-higher risk; Class 2B-highest risk).
 Results- There was a total of 118 metastatic events in the overall cohort, of which 25% (29/118) and 38% (45/118) occurred in BWH T1 and T2a, respectively. BWH T1 tumors had an overall event rate of 6.5% (29/444), with T1/Class 2B tumors having a 5.1-fold increased event rate of 33.3%. BWH T2a tumors had an overall event rate of 13.4% (45/335), with T2a/Class 2B tumors having a 2.7-fold increased event rate of 36.4%. Stratification by the 40-GEP test resulted in significantly different metastasis rates across all three 40-GEP classes within both the T1 and T2a subsets (log-rank tests, p<0.0001 each subset). 
 Conclusion- Within a cohort of cSCC patients considered lower risk by current staging alone, the 40-GEP identified patients with a substantial increase in metastatic risk.  The observed rates of metastasis over 10% and 20% are clinically actionable for nodal staging or postoperative adjuvant radiation, respectively. Combining clinicopathologic risk assessment with individual biologic risk, as provided by the 40-GEP test, improves the accuracy of risk assessment used clinically as the basis of treatment decisions.

BTN1A1 is a novel immune checkpoint mutually exclusive to PD-L1

BackgroundWhile Programmed cell death protein 1 (PD-1)/programmed cell death-ligand 1 (PD-L1) blockade is a potent antitumor treatment strategy, it is effective in only limited subsets of patients with cancer, emphasizing...

Establishment and characterization of NCC-ASPS2-C1: a novel patient-derived cell line of alveolar soft part sarcoma.

Alveolar soft part sarcoma (ASPS) is a rare mesenchymal tumor characterized by rearrangement of the ASPSCR1 and TFE3 genes and a histologically distinctive pseudoalveolar pattern. ASPS progresses slowly, but is prone to late metastasis. As ASPS is refractory to conventional chemotherapy, the only curative treatment is complete surgical resection. The prognosis of advanced and metastatic cases is poor, highlighting the need for preclinical research to develop appropriate treatment options. However, ASPS is extremely rare, accounting for < 1% of all soft tissue sarcomas, and only one patient-derived ASPS cell line is available from public cell banks worldwide for research. This study reports the establishment of a novel ASPS cell line derived from the primary tumor tissue of an ASPS patient, named NCC-ASPS2-C1. This cell line retains the ASPSCR1-TFE3 fusion gene, which is characteristic of ASPS. The characterization of this cell line revealed stable growth, spheroid formation, and invasive properties. By screening a drug library using NCC-ASPS2-C1, we identified several drugs that inhibited the proliferation of ASPS cells. In conclusion, the establishment of NCC-ASPS2-C1 provides a valuable resource for advancing ASPS research and developing novel treatments for this challenging disease.

Genetic alterations in CDKN2A interacting network and their putative association with head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a complex, polygenic disorder involving the host, microbial, and environmental factors. The present study investigated the CDKN2A (cyclin-dependent kinase inhibitor 2 A) gene interacting network. This gene is a key player in the cell cycle pathway, and any abnormalities in this gene have been linked to abnormal cell cycle processes. The present study followed an observational study design wherein computational tools were used to demonstrate the genetic alterations, expression profile, and survival status of head and neck cancer patients. The head and neck squamous cell carcinoma and oral squamous cell carcinoma datasets (The Cancer Gene Atlas (TCGA), Firehose Legacy) were analyzed. The cBioportal and UALCAN [University of ALabama at Birmingham CANcer data analysis Portal] were used to demonstrate the genetic alterations and gene expression profile alongside the survival of patients. The oncoprint data analysis of the CDKN2A gene network showed 72% and 48% of aberrations in the TP53 gene among HNSCC and OSCC (Oral Squamous Cell Carcinoma) cases, respectively. The gene expression profile demonstrated over-expression of CDKN2A in primary tissues. The survival analysis showed a statistically significant difference between the low/medium and high expression groups. The deep deletion was the common alteration observed among head and neck cancer patients of the CDKN2A gene. The gene expression profile showed significant upregulation of CDKN2A in primary tissues [p = 〈10−12]. The genetic alterations observed in the CDKN2A gene were found to correlate well with the survival status of head and neck cancer patients. The functional validation of the mutations and alterations observed in this gene would aid us in understanding the vital role of this gene network in the process of oral carcinogenesis.

MiR-29a-3p mediates phosphatase and tensin homolog and inhibits osteoarthritis progression.

Despite substantial progress in clinical trials of osteoarthritis (OA) gene therapy, the prevalence of OA is still on the rise. MiRNAs have a potential biomarker and therapeutic target for OA. OA cartilage and chondrosarcoma cells were studied to determine the role of miR-29a-3p and PTEN. OA cartilage and human chondrosarcoma cells (SW1353) were obtained. miR-29a-3p and PTEN signature expression was determined by RT-qPCR. The binding relationship between miR-29a-3p and PTEN was investigated by dual-luciferase reporter gene and western blot assay. TUNEL, immunohistochemistry, CCK-8, and flow cytometry were utilized to determine the proliferation and apoptosis of SW1353 cells. This study indicated downregulation of miR-29a-3p expression and upregulation of PTEN expression in human OA primary chondrocytes or OA tissue samples, compared with the normal cartilage cells or tissues. PTEN expression was negatively correlated with miR-29a-3p expression, and miR-29a-3p targeted PTEN mechanistically. miR-29a-3p reduced SW1353 cell activity and proliferation and promoted cell apoptosis. However, the aforementioned effects could be reversed by downregulating PTEN. miR-29a-3p can stimulate chondrocyte proliferation and inhibit apoptosis by inhibiting PTEN expression.

Establishment and characterization of two novel patient-derived cell lines from giant cell tumor of bone: NCC-GCTB8-C1 and NCC-GCTB9-C1.

Giant cell tumor of bone (GCTB) is a rare osteolytic bone tumor consisting of mononuclear stromal cells, macrophages, and osteoclast-like giant cells. Although GCTB predominantly exhibits benign behavior, the tumor carries a significant risk of high local recurrence. Furthermore, GCTB can occasionally undergo malignant transformation and distal metastasis, making it potentially fatal. The standard treatment is complete surgical resection; nonetheless, an optimal treatment strategy for advanced GCTB remains unestablished, necessitating expanded preclinical research to identify appropriate therapeutic options. However, only one GCTB cell line is publicly available from a cell bank for research use worldwide. The present study reports the establishment of two novel cell lines, NCC-GCTB8-C1 and NCC-GCTB9-C1, derived from the primary tumor tissues of two patients with GCTB. Both cell lines maintained the hallmark mutation in the H3-3A gene, which is associated with tumor formation and development in GCTB. Characterization of these cell lines revealed their steady growth, spheroid-formation capability, and invasive traits. Potential therapeutic agents were identified via extensive drug screening of the two cell lines and seven previously established GCTB cell lines. Among the 214 antitumor agents tested, romidepsin, a histone deacetylase inhibitor, and mitoxantrone, a topoisomerase inhibitor, were identified as potential therapeutic agents against GCTB. Conclusively, the establishment of NCC-GCTB8-C1 and NCC-GCTB9-C1 provides novel and crucial resources that are expected to advance GCTB research and potentially revolutionize treatment strategies.