Abstract B039: Genomic and epigenomic complexity underlies barrett’s esophagus progression to adenocarcinoma

Abstract A017: FAP-Activated Prodrugs Target Cancer Stem Cells in Esophageal Adenocarcinoma

Esophageal adenocarcinoma (EAC) is a rare and lethal malignancy that evolves through a stepwise mucosal progression — from an intestinal metaplasia known as “Barrett's esophagus (BE)” to low-grade dysplasia (LGD), high-grade dysplasia (HGD), and finally invasive carcinoma — each stage harboring rare clonogenic stem cells (approximately 1:1,000 cells) that drive disease evolution, therapeutic resistance, and recurrence. These lesion-specific cancer stem cells (CSCs) display intralesional genomic heterogeneity and enormous proliferative potential, yet remain inadequately targeted by current systemic regimens, underscoring the unmet need in this rare malignancy. We previously established that TP101 — a synthetic lethal combination of the bivalent squaramide-linked IAP antagonist 7532N and ponatinib — selectively eradicates BE, LGD, HGD, and EAC stem cells at low-nanomolar potency while sparing normal esophageal stem cells. Mechanistically, 7532N drives rapid degradation of cIAP1/2 and, together with ponatinib, triggers selective caspase-3 activation in malignant cells; in vivo, this combination produced near-complete regression of EAC xenografts and depletion of FAP-positive cancer-associated fibroblasts (CAFs) (Xian et al., 2025). However, ponatinib's dose-limiting vascular, cardiac, and hepatic toxicities constrain its systemic use in solid tumors. To address this, we engineered FAP-activated prodrugs of ponatinib that exploit the selective, high-level expression of fibroblast activation protein alpha (FAP) in EAC stromal CAFs to focus drug activation to the tumor microenvironment. FAP-dependent cleavage of prodrugs was confirmed in biochemical and cell-based assays, with minimal activation under FAP-negative conditions. In KCL-22 (ABL-activated CML line) xenograft models, the ponatinib prodrugs achieved antitumor efficacy comparable to parental ponatinib, while prodrug-treated animals exhibited minimal body-weight change versus marked weight loss (greater than 10%) observed with ponatinib at equivalent efficacious doses — indicating a meaningfully improved systemic tolerability profile. Bystander killing of adjacent malignant tissue including CSCs, pericytes, and endothelial cells was confirmed as the mechanistic basis for tumor eradication beyond the FAP-expressing stromal compartment. Broad anti-tumor activity of the synthetic lethal was further demonstrated across FAP-high solid tumor models including stomach, lung, and pancreatic cancers. These data demonstrate that FAP-activated ponatinib prodrugs achieve selective, TME-compartmentalized delivery with substantially reduced systemic exposure and, when combined with the IAP antagonist 7532N as the TP101 regimen, provide a precision, stem cell-selective synthetic lethal strategy for this rare and aggressive malignancy. Frank McKeon, Wa Xian, Ruiwen Zhang, Jaffer Ajani, Christopher Crum, Souneek Chakraborty, Yen-hsiang Huang, Guanglin Zhang, Guangyan Zhou, Longyue Liu, Melina Khorrami, Huiqin Wang, Thomas Benton. FAP-Activated Prodrugs Target Cancer Stem Cells in Esophageal Adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Breaking Barriers in the Fight against Rare Cancers; 2026 Jul 18-20; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(14_Suppl):Abstract nr A017.

Transcriptomic Changes and Biomarkers in Barrett’s Metaplasia, Dysplasia and Cancer

Mapping Functional Tumor Suppressor Networks in Esophageal Adenocarcinoma Using In Vivo CRISPR Screening and Perturb-sequencing

Esophageal adenocarcinoma (EAC) is a genetically heterogeneous malignancy with few recurrent drivers, limiting effective targeted therapies. Although EAC arises from Barrett’s esophagus (BE), mechanisms driving progression from this premalignant state to invasive cancer remain unclear. We combined pooled CRISPR-Cas9 loss-of-function screening, in vivo tumorigenicity assays, and Perturb-seq profiling to define functional drivers of BE transformation. We identified 37 tumor suppressors whose loss promotes progression to EAC, defining a functional landscape of tumor initiation. Despite genetic diversity, these losses converged on four transcriptional programs involving metabolic reprogramming, cell cycle progression, RNA processing, and cellular motility. Furthermore, we identify loss of NIPBL, TGFBR2, and RPL22 as key mediators of resistance to platinum- and taxane-based chemotherapy. Collectively, these findings provide a unifying framework for genomic heterogeneity in EAC, uncover underappreciated tumor suppressor pathways, and establish a resource to guide mechanistic and translational studies aimed at improving treatment strategies in this aggressive cancer.

Abstract A027: Leveraging genomic copy-number complexity in uveal melanoma to drive novel therapeutic development

Uveal Melanoma (UM) is a rare tumor characterized by activating mutations in GNAQ or GNA11, followed by a secondary mutation in BAP1, SF3B1 or EIF1AX. Notably, chromosome 3 copy-number loss, enriched among BAP1-mutant patients, is associated with an increased likelihood of metastasis. While chromosome 3 loss remains a dominant prognostic marker, patient tumor genomic analyses reveal a substantially more complex landscape, including recurrent arm level alterations across multiple chromosomes such as 1p loss, 8q amplification and 16q loss, that collectively define increasingly aggressive disease states ranging from low risk to ultra-high-risk disease. The purpose of this study is to elucidate how coordinated CN evolution drives transcriptional states, functional dependencies, and exploitable therapeutic vulnerabilities in UM. We integrated genomic data from patient tumors and UM cell line models selected to match patient-defined CN states, enabling inference of transcriptional and functional consequences associated with disease progression. Cytoband-anchored RNA profiling was performed across genomically aligned models to link regional CN evolution with transcriptional output. Functional interrogation included genome-wide and custom library CRISPR loss-of-function screens and drug sensitivity profiling. Cytoband-resolved transcriptional profiling of genomically matched UM models revealed coordinated activation of programs associated with invasion and metastatic fitness that tracked with cumulative CN burden rather than chromosome 3 loss alone. These transcriptional states emerged progressively as CN complexity increased, supporting a genomic evolution continuum underlying UM progression. Integration of CRISPR screening within this framework identified a heightened dependency on CBP and p300 in models corresponding to advanced patient CN states, implicating chromatin-dependent transcriptional control as a core driver of high-risk disease. To address the commonly faced issues of toxicity induced by traditional CBP/p300 inhibitors, we engineered a B7-H3 anchored degrader antibody conjugate (DAC) designed to selectively eliminate the transcriptional coactivators CBP and p300 in B7-H3 expressing cells. Our B7-H3 anchored DAC demonstrated potent, selective activity in vitro, highlighting significant response in both low and high-risk UM models. These findings demonstrate that UM progression reflects an integrated CN-transcriptional ecosystem extending beyond chromosome 3 loss, with cytoband-level genomic evolution shaping malignant fitness and therapeutic response. Anchoring therapeutic strategies within this complex genomic context enables rational targeting of advanced UM. Johnathon Rose, Sanjana Srinivasan, Amy Cooper, Jieqing Chen, Pijus Mandal, Guolin Ma, Chiu Yi Liu, Parth Shah, Rosalba Minelli, Joseph Daniele, Michael Peoples, Jason Gay, Khalida Wani, Anastasia Lopez, Ningping Feng, Christopher Vellano, Joseph Marszalek, Giulio Draetta, Alessandro Carugo, Scott Woodman, Alexander Lazar, Andrew Futreal, Giannicola Genovese, Chunhua Shi, Michael Soth, Faika Mseeh, Timothy Heffernan, Piergiorgio Pettazzoni, Virginia Giuliani. Leveraging genomic copy-number complexity in uveal melanoma to drive novel therapeutic development [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Breaking Barriers in the Fight against Rare Cancers; 2026 Jul 18-20; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(14_Suppl):Abstract nr A027.

P1.108. Molecular Determinants of Tumor Morphology in Esophageal Adenocarcinoma

The first validated morpho-molecular classification of Esophageal adenocarcinoma is reported, with the transitional and signet ring signatures associated with worse prognosis compared to tumors with a glandular signature.

Understanding the Epigenetic Landscape of Barrett's Esophagus and Esophageal Cancer: A Review of Current Findings, Caveats and Future Directions

ABSTRACT Esophageal cancer (OC) is currently the eighth most common form of cancer worldwide with a 5‐year survival rate of 10%–20%, with the primary risk factor of esophageal adenocarcinoma (OAC) being the development of Barrett's Esophagus (BO). Despite its clinical significance, the molecular pathogenesis underlying both BO and OC is not well understood. In recent years, epigenetic dysregulation, particularly aberrant DNA methylation, has emerged as a critical area of investigation, given its potential utility in the identification of diagnostic, prognostic, and therapeutic biomarkers. This review examines the evolving epigenetic landscape of esophageal cancer, including a focus on its origins in BO with a particular emphasis on DNA methylation, the most extensively researched epigenetic mechanism. Key DNA methylation‐associated alterations involved in OAC and OSCC initiation and progression are discussed, alongside their potential clinical application as biomarkers for early detection, prognosis, and risk stratification in BO populations. Furthermore, the role of these epigenetically regulated genes in the disruption of Wnt signaling and cell cycle control pathways implicated in esophageal carcinogenesis is explored. The review concludes by outlining future research directions, current challenges, and the promise of epigenetic studies in advancing our understanding of OC pathogenesis and improving patient outcomes.