1167P Transcriptomic tumor microenvironment subtypes in cervical cancer reveal prognostic and therapeutic opportunities

Technical differences between sequencing and microarray platforms impact transcriptomic subtyping of colorectal cancer.

Introduction. Translocation Renal Cell Carcinoma (tRCC) is a distinct and aggressive molecular subtype of kidney cancer unusually prevalent in children and adolescents. tRCC has a poor prognosis with no specific therapies and is incurable in the metastatic setting. tRCC is characterized by chromosomal translocations involving three out of the four Microphthalmia (MiT) family transcription factors, TFE3, TFE3, and MITF. The most commonly involved gene is TFE3, which most often fuses with ASPSCR1. However, the molecular mechanisms by which ASPSCR1-TFE3 (and more broadly MiT/TFE fusion proteins) dictates tRCC tumorigenesis remain unclear and advances are hampered by the paucity of animal models. Herein, we sought to model tRCC and performed integrative genomic analyses to dissect molecular mechanisms underpinning tRCC tumorigenesis with the goal of translating this knowledge into therapeutic opportunities. Methods. We conditionally expressed a human ASPSCR1-TFE3 fusion in the Pax8 and Sglt2 lineages and performed phenotypic analyses as well as WES and RNAseq of emerging tRCC tumors. Similar genomic analyses of a human tRCC cohort were performed. The mutational landscape, cooperating pathways, and potential therapeutic targets were identified through comparative genomic and transcriptomic analyses. Emerging hypotheses were tested through in vitro and in vivo assays. Results. We show that human ASPSCR1-TFE3 driven by Pax8-Cre, a credentialled RCC driver, disrupted nephron development causing neonatal death, whilst Sglt2-Cre resulted in tRCC with complete penetrance and short latency. In both models, ASPSCR1-TFE3 induced characteristic morphological changes, loss of epithelial markers, and an EMT program, but only in the Sglt2-Cre model was proliferation observed. Given that Pax8-Cre, but not Sglt2-Cre¸ induce clear cell RCC (ccRCC), these data show that tRCC and ccRCC originate from different cell types. Comparative murine/human genomic analyses show that tumorigenesis by MiT/TFE fusion proteins is broadly cooperative (i.e. p53, ATM/ATR, Fanconi anemia, SWI/SNF, Hippo, and Wnt). Gene expression and functional studies implicate EPHA5 as well as Met/Ret in tRCC tumorigenesis. Antitumor/antiproliferative activity was observed with the therapeutic targeting of these pathways. Conclusion. This study provides insight into the tRCC mutational landscape, the cell of origin, and MiT/TFE-driven transcriptional programs offering several avenues for therapeutic development. Citation Format: Gopinath Prakasam, Akhilesh Mishra, Alana Christie, Jeffrey Miyata, Vanina T. Tcheuyap, Hui Ye, Quyen N. Do, Kevin B. Jones, Mai-Carmen Requena-Komuro, Ivan Pedrosa, Dinesh Rakheja, Payal Kapur, James Brugarolas. Comparative genomic analysis of novel translocation renal cell carcinoma model reveals molecular mechanisms of disease progression and therapeutic opportunities [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR004.

Pancreatic ductal adenocarcinoma (PDAC) remains a devastating malignancy characterized by profound lethality, aggressive local invasion, dismal prognosis, and significant resistance to existing therapies. Two critical biological features underpin the challenges in treating PDAC: extensive perineural invasion (PNI), the process by which cancer cells infiltrate and migrate along nerves, and a profoundly immunosuppressive, or “cold,” tumor microenvironment (TME). PNI is not only a primary route for local tumor dissemination and recurrence but also a major contributor to the severe pain often experienced by patients. Concurrently, the PDAC TME is typified by a dense desmoplastic stroma, hypoxia, and an abundance of immunosuppressive cells—including cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs), myeloid-derived suppressor cells (MDSCs), and regulatory T cells (Tregs)—while lacking sufficient infiltration of effector T cells, rendering it largely unresponsive to immunotherapies like checkpoint inhibitors. Although historically studied as separate entities, accumulating evidence reveals a deep-seated and complex bidirectional crosstalk between the neural components involved in PNI and the immune and stromal cells constituting the TME. Key cellular mediators, such as CAFs and TAMs, and shared signaling pathways, including the CXCL12/CXCR4 axis, TGF-β signaling, and neurotrophin pathways (e.g., NGF/TrkA), appear to act as critical nodes, coordinating the progression of PNI while simultaneously shaping and maintaining the immunosuppressive TME. This review synthesizes the current understanding of these intricate neuro-immune interactions in PDAC. We delineate the molecular and cellular mechanisms governing this crosstalk and explore how targeting these shared regulatory networks presents novel therapeutic opportunities, potentially disrupting PNI while concurrently “heating” the cold TME to overcome immunotherapy resistance. Elucidating this interplay is crucial not only for a deeper comprehension of PDAC’s invasive and metastatic mechanisms but also for uncovering new therapeutic vulnerabilities to improve patient outcomes.

Background: Current surveillance strategies after treatment of endometrial cancer remain largely based on clinical stage and histological grade, reflecting a pre-molecular understanding of disease behavior. However, molecular classification has revealed profound biological heterogeneity across endometrial cancer subtypes, including differences in recurrence patterns, prognosis, and treatment responsiveness. Despite this progress, surveillance strategies have not yet been systematically adapted to molecular risk stratification. Objective: To propose a biology-driven surveillance framework for endometrial cancer that integrates molecular subtype, clinicopathological risk factors, and recurrence phenotype. Methods: This narrative review and conceptual framework synthesizes evidence from cohort studies, molecular classification analyses, international guidelines, and literature addressing recurrence patterns and treatment responsiveness across molecular subtypes of endometrial cancer. Results: We propose a three-tier surveillance model stratifying patients into low-, intermediate-, and high-risk groups. The framework integrates molecular subtype with clinicopathological modifiers and expected recurrence phenotype. Within the no specific molecular profile (NSMP) subtype, CTNNB1 mutation status is incorporated as a primary modifier, assigning CTNNB1-mutated tumors to the intermediate-risk group regardless of estrogen receptor (ER) status. In CTNNB1 wild-type NSMP tumors, ER expression functions as a secondary modifier, allowing identification of a biologically low-risk subgroup. L1CAM expression is considered a high-risk modifier within NSMP. The framework also accounts for differences in therapeutic modifiability of recurrence, including the role of immunotherapy in mismatch repair-deficient tumors. Conclusions: Uniform post-treatment surveillance does not reflect the biological diversity of endometrial cancer. The proposed framework provides a biologically grounded approach to surveillance that aligns follow-up intensity with recurrence phenotype and therapeutic opportunities. This model may serve as a conceptual basis for prospective studies evaluating personalized surveillance strategies in endometrial cancer.

<div>Abstract<p>The identification of early breast cancer patients who may benefit from adjuvant chemotherapy has evolved to include assessment of clinicopathologic features such as tumor size and nodal status, as well as several gene-expression profiles for ER-positive, HER2-negative cancers. However, these tools do not reliably identify patients at the greatest risk of recurrence. The mutation and copy-number landscape of triple-negative breast cancer (TNBC) subtypes defined by gene expression is also largely unknown, and elucidation of this landscape may shed light on novel therapeutic opportunities. The USO01062 phase III clinical trial of standard chemotherapy (with or without capecitabine) enrolled a cohort of putatively high-risk patients based on clinical features, yet only observed a 5-year disease-free survival event rate of 11.6%. In order to uncover genomic aberrations associated with recurrence, a targeted next-generation sequencing panel was used to compare tumor specimens from patients who had a recurrence event with a matched set who did not. The somatic mutation and copy-number alteration landscapes of high-risk early breast cancer patients were characterized and alterations associated with relapse were identified. Tumor mutational burden was evaluated but was not prognostic in this study, nor did it correlate with PDL1 or CD8 gene expression. However, TNBC subtypes had substantial genomic heterogeneity with a distinct pattern of genomic alterations and putative underlying driver mutations.</p>Implications:<p>The present study uncovers a compendium of genomic alterations with utility to more precisely identify high-risk patients for adjuvant trials of novel therapeutic agents.</p></div>

Despite the success of approved systemic therapies for estrogen receptor α (ER)-positive breast cancer, drug resistance remains common. We hypothesized that secreted factors from the human tumor microenvironment could modulate drug resistance. We previously screened a library of 297 recombinant-secreted microenvironmental proteins for the ability to confer resistance to the anti-estrogen fulvestrant in 2 ER+ breast cancer cell lines. Herein, we considered whether factors that enhanced drug sensitivity could be repurposed as therapeutics and provide leads for drug development. Screening data revealed bone morphogenic protein (BMP)4 as a factor that inhibited cell growth and synergized with approved anti-estrogens and cyclin-dependent kinase 4/6 inhibitors (CDK4/6i). BMP4-mediated growth inhibition was dependent on type I receptor activin receptor-like kinase (ALK)3-dependent phosphorylation (P) of mothers against decapentaplegic homolog (SMAD/P-SMAD)1 and 5, which could be reversed by BMP receptor inhibitors and ALK3 knockdown. The primary effect of BMP4 on cell fate was cell-cycle arrest, in which RNA sequencing, immunoblot analysis, and RNA interference revealed to be dependent on p21WAF1/Cip1 upregulation. BMP4 also enhanced sensitivity to approved inhibitors of mammalian target of rapamycin complex 1 and CDK4/6 via ALK3-mediated P-SMAD1/5 and p21 upregulation in anti-estrogen-resistant cells. Patients bearing primary ER+ breast tumors, exhibiting a transcriptomic signature of BMP4 signaling, had improved disease outcome following adjuvant treatment with anti-estrogen therapy, independently of age, tumor grade, and tumor stage. Furthermore, a transcriptomic signature of BMP4 signaling was predictive of an improved biologic response to the CDK4/6i palbociclib, in combination with an aromatase inhibitor in primary tumors. These findings highlight BMP4 and its downstream pathway activation as a therapeutic opportunity in ER+ breast cancer.-Shee, K., Jiang, A., Varn, F. S., Liu, S., Traphagen, N. A., Owens, P., Ma, C. X., Hoog, J., Cheng, C., Golub, T. R., Straussman, R., Miller, T. W. Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER+ breast cancer.

Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related deaths, with a five-year survival rate around 12%. In PDAC, cancer-associated fibroblasts (CAFs) play a vital role in promoting the desmoplastic and immunosuppressive tumor microenvironment (TME), and have emerged as relevant cancer targets. CAFs produce intratumoral hyaluronic acid (HA) whose accumulation induces high interstitial fluid-pressure (IFP) which can interfere with drug delivery. Moreover, HA has been linked with tumor escape from immune surveillance. Systemic administration of Hyaluronidase, via the PEGPH20 formulation, has reduced stromal HA, normalized IFP, and consequently improved the efficiency of the cytotoxic compound, gemcitabine, leading to increased survival in mice. In this study we have decided to eliminate HA by a different approach involving its synthesis rather than inducing its degradation. To this end, we have genetically targeted the three genes encoding HA synthases (Has1, 2, 3). Has1 and Has3 null alleles were generated by CRISPR technology in mouse embryos since they are nor essential for embryonic development. To eliminate Has2, we used existing conditional Has2lox alleles (Matsumoto et al. 2019, PMID XXXX) along an inducible allele, Rosa26-CreERT2, encoding an inducible Cre-ERT2 recombinase to allow the systemic ablation of the conditional Has2lox alleles in adult mice upon exposure to a Tamoxifen-containing (TAM) diet. These alleles were added to the standard KPF strain (KRas +/FSFG12V;P53F/F;Pdx1-FlpO) to determine the effect of HA elimination in tumor-bearing mice. Exposure of these adult animals to the TMA diet induced significant levels of HA depletion leading to reprogramming of tumoral, stromal and immune cells leading to significantly reduced tumor progression. Tumor cells were more differentiated as illustrated by higher expression of cytokeratin19 and additional epithelial cell adhesion molecules. Furthermore, these tumor cells displayed reduced proliferative capacity, mor limited EMT, migration and invasive capacity. Interestingly, they also exhibited upregulated Kras expression. At the stroma level, we observed less fibrotic tissue, decreased collagen deposition, reduced CAFs activation,and changes in the CAF populations, with high content of iCAFs (Inflammatory CAFs) and very low content in myCAFs (Myofibroblast CAFs). More importantly, we also observed infiltration of CD8+ T cells. Notably, HA depletion enhanced the efficacy of gemcitabine, the anti-CTLA-4 and the panras inhibitor darasonrasib, either alone or in combination of anti-CTLA-4. In summary, HA depletion in PDAC produced multiple changes at different levels that opens up new opportunities for therapeutic interventions. Citation Format: Pian Sun, Ángeles Durán, Federico Virga, María Diaz-Meco, Jorge Moscat, Carmen Guerra, Mariano Barbacid. Targeting hyaluronic acid in pancreatic ductal adenocarcinoma uncovers novel therapeutic opportunities [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_3):Abstract nr B031.

Four gene expression subtypes of high-grade serous ovarian cancer (HGSC) have been previously described. In these early studies, a fraction of samples that did not fit well into the four subtype classifications were excluded. Therefore, we sought to systematically determine the concordance of transcriptomic HGSC subtypes across populations without removing any samples. We created a bioinformatics pipeline to independently cluster the five largest mRNA expression datasets using k-means and nonnegative matrix factorization (NMF). We summarized differential expression patterns to compare clusters across studies. While previous studies reported four subtypes, our cross-population comparison does not support four. Because these results contrast with previous reports, we attempted to reproduce analyses performed in those studies. Our results suggest that early results favoring four subtypes may have been driven by the inclusion of serous borderline tumors. In summary, our analysis suggests that either two or three, but not four, gene expression subtypes are most consistent across datasets.

Purpose of the study: YAP1 is the most frequently amplified oncogene in cervical cancer. The Cancer Genome Atlas Research Network study showed that the YAP1 (11q22) oncogene is amplified in 11% of cervical cancer cases. Our lab recently identified that YAP1 oncogene amplification is associated with a 12-year earlier age of diagnosis, poorer survival, and defies a novel aggressive cervical cancer subtype that is more frequent in minority populations. The present study aims to characterize 19 YAP1 amplified cervical cancers from Guatemala and Venezuela via Oxford Nanopore technology (ONT) whole genome long-read sequencing. Methods: In this study, 380 cervical cancer patients were assessed for YAP1 amplification using a TaqMan assay, with 45 samples identified as positive for YAP1 amplification. These 45 samples were then subjected to whole genome sequencing with 5x coverage using Oxford Nanopore Technologies (ONT) to confirm the amplification status. A subset of 19 YAP1-amplified samples underwent deeper sequencing via ONT-LSK114 library preparation. The HPV integration status in these samples was determined by uploading the sequencing data (fastq_pass files) to the Cancer Genomics Cloud, where breakpoints were manually examined using the Integrated Genome Viewer (IGV). HPV and human DNA segments were further analyzed and identified using bioinformatics tools such as BLAT and BLAST. Results: In our study, we confirmed YAP1 amplification in 24 out of 45 tumor samples using barcode sequencing, and due to limited DNA availability (1 µg), only 19 of these samples underwent deep sequencing with 25-30x coverage. Notably, we observed a higher frequency of HPV integration (11/19) in YAP1-amplified tumors compared to those with episomal HPV status, suggesting a potential link between HPV integration and YAP1 amplification. We noticed that YAP1 amplification is driven by Breakage-Fusion-Bridge (BFB) events, which also lead to the co-amplification of the nearby BIRC2/3 genes, contributing to genomic instability and immune escape. This mechanism was further supported by a similar pattern observed in the TCGA whole genome sequence data, where 27 out of 31 YAP1-amplified cervical tumors also exhibited BFB events. Finally, treatment with the PIK3CA inhibitor Alpelisib resulted in a decrease in YAP1 protein levels in CaSki cells, a cervical cancer cell line with mutated PIK3CA and amplified YAP1 expression. Conclusions: These findings highlight a possible interplay between HPV integration and BFB-driven amplification of YAP1 and its neighboring genes, offering insights into potential therapeutic targets for this novel aggressive subtype of cervical cancer. Citation Format: Sonam Tulsyan, Hong Lou, Yi Xie, Emma Robinson, Danielle Kayembe, Eduardo Gharzouzi, Roberto Orozco, Enrique Alvirez, Michael Dean. Identifying a novel aggressive subtype of cervical cancer predominantly affecting minority populations through long-read whole genome sequencing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Functional and Genomic Precision Medicine in Cancer: Different Perspectives, Common Goals; 2025 Mar 11-13; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(5 Suppl):Abstract nr B018.

Targeting lipid metabolism in CAFs: A therapeutic opportunity in solid tumors.

Until recently, barriers to immunotherapy clinical successes for pancreatic cancer have been due to a lack of understanding of the immune pathways within the pancreatic tumor microenvironment that hinder successful immune responses. Recent advances have identified new targets for developing cancer specific vaccines and new targets for modulating the tumor microenvironment to allow more potent activation and improved access of vaccine induced immune responses. We are just learning that non-neoplastic cells, including cancer-associated myofibroblasts, regulatory T cells, dendritic cells, myeloid-derived suppressor cells, and tumor-associated macrophages, are hijacked by pre-invasive and invasive cancer cells to create a tolerogenic tumor microenvironment. Current research is focused on elucidating the mechanisms of this tolerogenic polarization within the tumor microenvironment with the goal of tipping the balance in favor of an anticancer immune response. With the recent advances in molecular technologies and the development of relevant pancreatic cancer mouse models, it is now within our reach to dissect the inhibitory pathways within the pancreatic tumor microenvironment. This will in turn, lead to new therapeutic opportunities that will eliminate these barriers and convert this deadly cancer into a treatable disease.

Pre-transcriptional regulation through alternative promoter usage is a critical yet underexplored mechanism influencing gene expression in Triple-Negative Breast Cancer (TNBC), a highly aggressive and heterogeneous breast cancer subtype. While short-read RNA sequencing data are widely available, they offer limited resolution in accurately capturing transcript-level diversity. To overcome this, we focused on promoter-level quantification to infer active promoter usage and investigate transcriptional regulation dynamics in TNBC. Using RNA-seq data from 360 TNBC tumors and 88 adjacent normal tissues, we identified TNBC-specific and subtype-enriched Active Alternative Promoters (AAPs). Integration with H3K4me3 and H3K27ac ChIP-seq data confirmed a key promoter switching event in the HDAC9 gene: the promoter pr1077 was downregulated while another promoter pr1079 was specifically activated in TNBCs. This switch was epigenetically supported by differential enrichment of histone marks, implicating HDAC9 promoter switching as a tumor-specific regulatory mechanism. Further, we identified subtype-specific alternative promoters in TNBC, including basal subtype–enriched activity of SEC31A and reduced promoter usage of AKAP9, which were not reflected at the gene expression level but were evident through promoter-level analysis. Next, we identified alternative promoters of HUWE1 and FTX as independent predictors of relapse-free survival (RFS) in TNBC. Their prognostic value remained significant after adjusting for copy number alterations and transcriptomic subtypes. A 4-feature model integrating these two promoter activities with two clinical variables (Tumor size, Ki67 index) achieved an AUROC of 0.73 and improved patient risk stratification, with a Net Reclassification Improvement (NRI) of 0.40-0.48 over the clinical-only model, underscoring the potential of promoter activity as a biomarker in TNBC.

The mechanical properties of the tumor microenvironment (TME) undergo significant changes during tumor growth, primarily driven by alterations in extracellular (ECM) stiffness and tumor viscoelasticity. These mechanical changes not only promote tumor progression but also hinder therapeutic efficacy by impairing drug delivery and activating mechanotransduction pathways that regulate crucial cellular processes such as migration, proliferation, and resistance to therapy. In this review, we examine the mechanisms through which tumor cells sense and transmit mechanical signals to maintain homeostasis in the biomechanically altered TME. We explore current computational modelling strategies for mechanotransduction pathways, highlighting the need for developing models that incorporate additional components of the mechanosignaling machinery. Furthermore, we review available methods for measuring the mechanical properties of tumors in clinical settings and strategies aiming at restoring the TME and blocking deregulated mechanotransduction pathways. Finally, we propose that proper characterization and a deeper understanding of the mechanical landscape of the TME, both at the tissue and cellular levels, are essential for developing therapeutic strategies that account for the influence of mechanical forces on treatment efficacy.

Natural killer (NK) cells are key effector cells involved in tumor immune surveillance, yet their function within the tumor microenvironment (TME) exhibits considerable complexity and plasticity that cannot be adequately explained by the classical CD56/CD16 dichotomy. This functional diversity arises from the phenotypic adaptability and dynamic differentiation of distinct NK cell subsets shaped by the TME. In this review, we systematically examine the defining characteristics and functional roles of recently identified NK cell subsets in the TME; elucidate the molecular mechanisms governing their regulation; and highlight the functional transitions and cooperative interactions among these subsets. Moreover, building on current evidence, we summarize emerging immunotherapeutic approaches targeting specific NK cell subsets. Together, these perspectives offer new insights and strategic directions for deciphering the multifaceted roles of NK cells in antitumor immunity and advancing the development of subset-targeted therapies.

Background: Colorectal cancer (CRC) is the third most common malignancy, with over 1.85 million new cases and 850, 000 deaths annually. Significant intratumoral heterogeneity in CRC contributes to recurrence, chemotherapy resistance, and poor prognosis. This study aimed to explore the spatial distribution of subtype clones and the diversity of the tumor microenvironment (TME), which are not captured by the traditional gene expression-based CMS classification. Additionally, it sought to investigate cancer trajectories and their contributions to metastatic phenotypes using spatial transcriptomics (ST). Methods: Spatial analysis was performed using public 10X Genomics Visium data from 4 CRC and 4 CRC-liver metastasis (CRC-LM) patients (GSE226997, GSE217414). Cell-type deconvolution utilized single-cell RNA-seq datasets (GSE178318, GSE132465). Copy number alterations (CNA) were inferred, and subclone development trajectories were modeled using inferCNV, DPT, and PAGA analyses. Pathway and functional enrichment analyses, expression score calculations, and correlation analyses were conducted using ClusterProfiler, AddModuleScore, and statistical methods. A Wilcoxon test with an adjusted p-value < 0.05 was used to determine statistical significance. Results: Distinct CRC and CRC-LM subclones were identified through CNA inference, revealing spatially segregated CNA clusters. These included malignant subclones and boundary-associated clusters, characterized by varying proportions of differentiation and mesenchymal traits. Immune-related signaling pathways demonstrated differential activation, with increased MAPK, JAK-STAT, and TNFα-NFκB in specific regions and elevated WNT, VEGF signaling, MYC, and E2F4 in others. Certain subclones also showed enrichment of SPP1+ macrophages and myofibroblasts, indicating diverse invasive characteristics. Evolutionary trajectories of subclones, inferred through hierarchical trees, revealed CSC features and a common ancestral clone. Progression toward malignancy was associated with enhanced pathway activity linked to critical biological processes. In CRC-LM, subclones were categorized by TAM subtypes, with one subtype displaying significantly elevated SPP1 expression compared to primary CRC. Immune-related features were reduced in metastatic tissues, reflecting a less immunogenic TME. Conclusion: Intratumoral heterogeneity in CRC evolves from a single common ancestral clone into distinct progression states, resulting in spatially unique TMEs. Understanding the interactions between clones across different progression states offers valuable insights into disease dynamics and therapeutic opportunities. Citation Format: YeonJu Lee, Woong-Yang Park. Mapping intratumoral heterogeneity in colorectal cancer: Spatially resolved subclones and tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2666.