tbuckley/cabot-search huggingface dataset:
Abstract PL04-01: The various layers of intratumor heterogeneity and their impact on tumor immunity
Authors: Yardena Samuels
Journal: Cancer Research (2025)

Abstract The current understanding in the immunotherapy field suggests that tumors with higher mutational loads present more neoantigens, thereby enhancing their immunogenicity. However, tumors with similar mutational burdens exhibit variable immune responses, and some cancers with low mutational loads can still respond to immunotherapy, challenging this association. Additionally, intra-tumor heterogeneity is recognized as a significant factor influencing immune surveillance. This talk will delve into the complex layers of intra-tumor heterogeneity, exploring how genomic, epigenetic, and neoantigen diversity impact immune response. Using novel comparative mouse models, we will examine the genomic effects of mutational load and intra-tumor heterogeneity on immune response. Furthermore, we will investigate how the canonical and non-canonical neopeptide landscape contributes to intra-tumor heterogeneity and its impact on tumor immunity. Our research also explores the untapped potential of cancer neopeptides, including those derived from intracellular microbial antigens and aberrant protein synthesis. As a proof of concept, we will discuss our recent study, which investigated how defective translation machinery components in cancer cells generate aberrant peptides, enhancing tumor immunogenicity and sensitivity to checkpoint blockade immunotherapy. Our findings suggest that inhibiting translation fidelity regulators could be a potent novel immunotherapy strategy, potentially leading to long-lasting anti-tumor control. By understanding and leveraging these mechanisms, we aim to redefine intra-tumor heterogeneity as both a barrier and a therapeutic opportunity, paving the way for more effective treatments. Citation Format: Yardena Samuels. The various layers of intratumor heterogeneity and their impact on tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr PL04-01.
Abstract LB450: Dissecting the role of condensation in signaling from RTK fusion oncoproteins
Authors: Lukasz Bugaj, David Gonzalez-Martinez, Thomas Mumford
Journal: Cancer Research (2025)

Abstract Receptor tyrosine kinase (RTK) fusions are a diverse class of oncoproteins that have been identified in ∼5% of cancers. RTK fusions are chimeric proteins where the intracellular domain of an RTK is fused to an oligomeric domain from an unrelated protein. Such fusions can drive oncogenic signaling from the RTK fragment despite their cytoplasmic localization, away from the plasma membrane where normal transmembrane RTK signaling occurs, thus posing fundamental mechanistic questions of how RTK fusions transmit oncogenic signals. Recent studies have suggested that signaling might result from the formation of large cytoplasmic granules or condensates, which allow organization of important signaling machinery. In our study we tested this hypothesis using live cell fluorescent imaging, quantitative analysis of condensation, single-cell analysis, and synthetic biology, focusing on condensation of EML4-ALK, a granule-forming RTK fusion that is found in ∼5% of non-small cell lung cancer. Surprisingly, we found weak correspondence between condensate formation and downstream signaling. Although signaling (Erk activation) was a direct function of oncogene expression, condensation was maximal only at intermediate expression levels, resulting in high-expressing cells that had the strongest signaling but no condensation as assessed under high magnification confocal microscopy. Furthermore, increasing the magnitude of condensation through multiple methods did not result in increase in downstream signaling. We then constructed synthetic fusions to test the lower limit of multimerization that could trigger signaling. While monomers of the ALK domain did not signal, dimers triggered signaling to approximately the same magnitudes as EML4-ALK but did not form condensates. Finally, a survey of 9 distinct oncogenic RTK fusions found marked heterogeneity in the propensity of condensate formation. Nevertheless, all fusions could strongly activate signaling, independent of whether or not they formed condensates. Our work thus suggests that condensation is not essential for RTK fusion signaling and that strong signaling can result from fusions that appear diffuse under fluorescence microscopy, from both synthetic and natural fusions. These results suggest a more nuanced role of condensation in RTK fusion signaling and call for further mechanistic studies to understand how cytoplasmic fusions can productively trigger oncogenic signals. Citation Format: Lukasz Bugaj, David Gonzalez-Martinez, Thomas Mumford. Dissecting the role of condensation in signaling from RTK fusion oncoproteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB450.
Abstract SY04-01: Mapping the functional microproteome in cancer
Authors: John R. Prensner
Journal: Cancer Research (2025)

Abstract In the 20 years since the completion of the Human Genome Project, cancer biology remains rooted in the belief that the human genome encodes ∼20,000 protein-coding genes. This assumption has been fundamentally challenged by the discovery of microproteins, which are encoded across the genome by thousands of non-canonical open reading frames (ORF). Whether these microproteins reflect a previously untapped source of cancer genes may therefore have a profound impact on our understanding of cancer biology. To address this question, we have interrogated the prevalence and impact of non-canonical ORF translation across multiple cancer types. Using ribosome profiling, ORF cDNA libraries, expression profiling and CRISPR/Cas9 screens, we find that thousands of non-canonical ORFs are translated in cancer cells; nearly half (46%) of tested non-canonical ORFs may make a detectable microprotein; nearly 30% induced gene expression changes in cancer cell lines; and 10% induced a cancer cell viability defect when knocked-out. High-resolution CRISPR saturation mutagenesis identified a subset of non-canonical ORFs with exquisite genetic selectivity in about one-third of cases, providing high-confidence genetic evidence for a causal role of the non-canonical ORF in cancer cell viability. To position specific candidates in the context of cancer biology, we have characterized two cancer-associated microproteins encoded by non-canonical ORFs. In breast cancer, we described G029442 - renamed glycine-rich extracellular protein-1 (GREP1) - as a secreted protein that is a preferential genetic dependency in this disease through its regulation of the oncogenic cytokine, GDF15. Moreover, GREP1 expression is prognostic for poor patient outcomes. In childhood medulloblastoma, we found that MYC-driven medulloblastoma cells preferentially upregulated an upstream open reading frame in the ASNSD1 5’ untranslated region, termed ASNSD1-uORF. ASNSD1 uORF was a top genetic vulnerability in multiple models of medulloblastoma and it functions as a component of the prefoldin-like complex, which post-translationally regulates nascent proteins. Together, ASNSD1-uORF and the prefoldin-like complex impacted cancer cell cycle through the proteomic regulation of proteins involved in mitosis and chromosome spindle complexes. In summary, our work supports a generalizable principle that ncORFs commonly encode biologically-active microproteins in diverse malignancies. Ongoing investigation of ncORFs therefore represents a new frontier in cancer research with the potential to define the next generation of therapeutic target genes. Citation Format: John R. Prensner. Mapping the functional microproteome in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr SY04-01.
Abstract LB382: synDNA vaccines against TCR and EL4 derived neoantigens induce tumor control in a murine T cell lymphoma model
Authors: Pratik Sanjivkumar Bhojnagarwala, Joshua Jose, David B. Weiner
Journal: Cancer Research (2025)

Abstract T cell lymphomas constitute approximately 10% of all non-Hodgkin lymphomas and are associated with poor prognosis. Patients experiencing early relapse exhibit a 5-year overall survival rate of only 11%, underscoring the urgent need for novel therapeutic strategies. T cell cancers are predominantly clonal, making the T cell receptor (TCR) an appealing target for immunotherapy. Additionally, neoantigens, derived from somatic mutations within tumor cells, present another promising target for anti-cancer vaccine development. In this study, we developed and evaluated two synDNA vaccines: one targeting the TCR⍺, β, and γ chains (TCRfull), and another targeting 15 neoantigens identified through whole exome sequencing and RNA sequencing of the EL4 murine T cell lymphoma model (EL4neo). Immunogenicity studies revealed robust immune responses against all three TCR chains, with identification of immunodominant peptides for each chain. Notably, no significant differences in the number of live T cells were observed between TCRfull-vaccinated mice and control groups, indicating the vaccine's ability to selectively break tolerance against the vaccinated TCR without broadly depleting T cells. The EL4neo vaccine elicited strong immune responses against 5/15 encoded neoantigens. In a minimal residual disease model, both vaccines independently delayed EL4 tumor progression and improved survival of tumor bearing mice. Analysis of tumors from TCRfull treated mice revealed downregulation of TCR expression. This suggests that under immune pressure, tumors can downregulate TCR expression highlighting a potential immune escape mechanism. Co-administration of the TCRfull and EL4neo vaccines achieved superior tumor control compared to either vaccine alone, and further improved animal survival, demonstrating that neoantigen targeting can partially mitigate TCR antigen loss. These findings highlight the potential of combining TCR-targeted and neoantigen-based immunotherapies for the treatment of T cell lymphomas. Further investigation of this dual-vaccine approach is warranted to optimize its therapeutic efficacy and provide a novel therapeutic approach for this difficult to treat cancer. Citation Format: Pratik Sanjivkumar Bhojnagarwala, Joshua Jose, David B. Weiner. synDNA vaccines against TCR and EL4 derived neoantigens induce tumor control in a murine T cell lymphoma model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB382.
Abstract LB320: Broad and synergistic anti-tumor effects of small-molecule dual HIF-1/2 inhibitors in combination with immune checkpoint inhibitors
Authors: Shaima Salman, Tina Y. Huang, Yousang Hwang, Anmol Kumar, Alexander D. MacKerell, Gregg L. Semenza
Journal: Cancer Research (2025)

Abstract Motivation: Hypoxia inducible factors (HIFs) are critical transcriptional regulators that play fundamental roles in adaptive responses to low oxygen, both in normal and disease conditions. Dysregulated activation of HIFs has been implicated in a variety of cancers due to their role in mediating a broad range of key processes including angiogenesis, glycolysis, immune evasion, cancer stem cell specification, and metastasis. Methods: In this study, we utilized virtual and cell-based screening approaches to identify compounds that directly bind to HIF-1α and HIF-2α to HIF-1β, leading to their degradation and suppression of HIF target gene expression. Results: In syngeneic mouse models of melanoma, breast, colorectal, and prostate cancer, we observed significant tumor regression when dual HIF-1/2 inhibitors were combined with anti-CTLA4 immunotherapy. The combined treatment enhanced the infiltration of T cells and natural killer (NK) cells into the tumor microenvironment. An orally-administered dual HIF-1/2 inhibitor showed superior anti-tumor efficacy to the HIF-2-selective inhibitor PT2385 in a colorectal cancer model. Conclusion: This study demonstrates the anti-tumor effects of dual HIF-1/2 inhibitors and their ability to modulate the tumor immune cell microenvironment, resulting in sustained tumor regression when added to immunotherapy. The promising outcomes of this study warrant further exploration of these inhibitors as potential cancer treatment modalities. Citation Format: Shaima Salman, Tina Y. Huang, Yousang Hwang, Anmol Kumar, Alexander D. MacKerell Jr., Gregg L. Semenza. Broad and synergistic anti-tumor effects of small-molecule dual HIF-1/2 inhibitors in combination with immune checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB320.
Abstract LB405: BTN1A1 and YAP1 expression as biomarkers in colon cancer: Phase 1b trial results of hSTC810
Authors: Bong-Ki Hong, Seung-Hoon Lee, Chunai Wu, Young-Seung Kim, Andrew H. Park, Stephen S. Yoo
Journal: Cancer Research (2025)

Abstract Background: Butyrophilin 1A1 (BTN1A1) is a novel immune checkpoint protein expressed onvarious human tumors and immune cells. BTN1A1 has been shown to interact with Yes-associated protein 1 (YAP1), a key regulator of the Hippo pathway, which is involved in tumor growth, immune evasion, and chemoresistance. High BTN1A1 and nuclear YAP1 expression levels have been observed in colon cancer, highlighting their potential as therapeutic targets. This Phase 1b clinical trial investigates the safety, pharmacokinetics, and efficacy of the anti-BTN1A1 antibody (hSTC810) in patients with advanced colon cancer. Recently, a Phase 1clinical trial of Nelmastobart, a BTN1A1-targeting antibody, was successfully completed. The subsequent Phase 1b/2 trial investigating BTN1A1 inhibition in combination with chemotherapy is currently ongoing. Methods: Colon cancer patients were enrolled in the study and treated with hSTC810 in combination with capecitabine to evaluate the efficacy and safety of the combination therapy. A3+3 dose-escalation design was used to determine dose-limiting toxicities (DLT) and themaximum tolerated dose (MTD)/recommended Phase II dose (RP2D). Pretreatment tissue specimens were collected and analyzed for YAP1 expression to stratify patients based on YAP1 localization and intensity. The primary endpoints included safety, tolerability, and immune response markers, while the secondary endpoints included progression-free survival (PFS) and overall response rate (ORR). Tumor biopsies were also analyzed for BTN1A1 and nuclear YAP1 expression prior to treatment. Results: Among the enrolled patients, 28.57% exhibited high nuclear YAP1 expression in baseline tissue specimens, which correlated with BTN1A1 positivity. Treatment with hSTC810 demonstrated a favorable safety profile, with the most common adverse events being low-grade fatigue and infusion-related reactions. Early signs of efficacy included tumor size reductions in 42.86% (data pending analysis) of evaluable patients. Notably, patients with high YAP1expression demonstrated better PFS compared to those with low YAP1 expression. Conclusions: Findings from this Phase 1b trial suggest that targeting BTN1A1 with hSTC810 is a safe and promising therapeutic strategy for colon cancer, particularly in patients with highYAP1 expression. These results support further investigation in larger, randomized trials to confirm the efficacy and biomarker-driven utility of hSTC810 in colon cancer therapy. Citation Format: Bong-Ki Hong, Seung-Hoon Lee, Chunai Wu, Young-Seung Kim, Andrew H. Park, Stephen S. Yoo. BTN1A1 and YAP1 expression as biomarkers in colon cancer: Phase 1b trial results of hSTC810 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB405.
Abstract LB306: 3D epigenomic analysis reveals non-coding DNA regions that can reverse prostate cancer phenotypes
Authors: Huan Cao, Zexun Wu, Baixi Ji, Seolyn Yang, Leonardo Gonzalez-Smith, Suhn K. Rhie
Journal: Cancer Research (2025)

Abstract New evidence shows that non-coding DNA regions are recognized as cancer drivers. However, there are currently challenges to systematically identifying oncogenic non-coding DNA regions. To address these challenges, we have taken advantage of functional genomics which can identify non-coding DNA regions involved in transcriptional regulation, termed regulatory elements. By analyzing hundreds of Chromatin Immunoprecipitation coupled with sequencing (ChIP-seq) datasets generated from normal prostate and prostate tumor tissues and cells, we identified prostate cancer-specific regulatory elements that have the potential to drive carcinogenesis. Among these regulatory elements, we noted that enhancers are bound by prostate cancer-specific transcription factors such as FOXA1 and HOXB13, which have previously been identified as drivers of prostate cancer. Using genome-wide chromatin conformation capture techniques such as Hi-C and Micro-C, and integrating them with RNA-seq, we identified chromatin interaction hubs in prostate cancer that are anchored in exclusively activated enhancers and co-localized with oncogenes exhibiting elevated expression. To dissect the mechanisms of carcinogenesis, we screened the identified prostate cancer-specific enhancers using the CRISPR/Cas9 system and followed up with multi-omics analyses, including ChIP-seq, ATAC-seq, RNA-seq, and Region Capture Micro-C (RCMC) in prostate cancer cells. We found that deletion of the selected enhancers led to reduced activities of other enhancers specifically activated in prostate cancer within the hub. Moreover, we observed that enhancer deletion led to changes in FOXA1 binding and chromatin accessibility, suggesting an important pioneer role for FOXA1 in prostate cancer-specific chromatin hub formation. Furthermore, we noted that targeting these enhancers can reverse cancer phenotypes, such as cell proliferation and colony formation. We are currently interrogating changes in chromatin interactions, enhancer activities, and chromatin accessibility associated with prostate cancer-specific chromatin hub formation by altering the activity of transcription factors. Overall, our study not only provides mechanistic insights into the spatial regulation of enhancer-promoter hubs but also identifies new non-coding drivers in prostate tumorigenesis. Citation Format: Huan Cao, Zexun Wu, Baixi Ji, Seolyn Yang, Leonardo Gonzalez-Smith, Suhn K. Rhie. 3D epigenomic analysis reveals non-coding DNA regions that can reverse prostate cancer phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB306.
Abstract LB381: Preclinical toxicology and efficacy of NG34C: A novel oncolytic HSV-1 expressing truncated GADD34 gene for the treatment of glioblastoma
Authors: Min J. Kim, Silja Schule, Tran Nguyen, Kazue Kasai, Michal O. Nowicki, Alexander L. Ling, William F. Goins, Hiroshi Nakashima, E. Antonio Chiocca
Journal: Cancer Research (2025)

Abstract Glioblastoma (GBM) remains a formidable medical challenge with limited therapeutic progress. Oncolytic viruses (OVs) offer promise by triggering immunogenic cell death that potentially activates anti-tumor immunity. We recently completed a Phase I clinical trial of rQNestin34.5v2 (CAN-3110), an oncolytic virus encoding the viral neurovirulence gene ICP34.5 under the nestin promoter, demonstrating safety at doses up to 1 x 1010 PFU (Ling et al., Nature, 2023). The human GADD34 gene, a stress-response protein homologous to the C-terminal region of ICP34.5, has been used to replace ICP34.5 in oHSV (NG34). This modified virus showed comparable efficacy to rQNestin34.5 with reduced toxicity (Nakashima et al., Clinical Cancer Research, 2018). However, GADD34 is inherently unstable due to rapid proteasomal degradation. To enhance GADD34 stability, we deleted its N-terminal region responsible for proteasomal degradation, generating NG34C. This modified oncolytic virus maintained stable GADD34 expression in gliomas, sustained eIF2α dephosphorylation, and improved replication under hypoxia by mitigating elevated eIF2α phosphorylation. NG34C produced viral yields comparable to rQNestin34.5 and NG34 under normoxia while outperforming them in hypoxia. Toxicology and efficacy studies in mice demonstrated NG34C’s safety, with no neurotoxicity at doses up to 3 × 107 PFU and minimal toxicity at 108 PFU. Unlike wild-type HSV-1 (F strain), which caused significant lethality, NG34C did not persist in normal brain tissue, as viral DNA and RNA levels were comparable to PBS by day 3. In a 1694 GBM model (human EGFR overexpression with Cdkn2a and Pten loss), NG34C significantly improved survival at 3 × 105 and 3 × 107 PFU doses (P &amp;lt; 0.0001 vs. PBS). These results establish NG34C as a safe, hypoxia-adapted, and effective oncolytic virus for GBM. NG34C is now being produced under GMP for an upcoming INS-clinical study. Citation Format: Min J. Kim, Silja Schule, Tran Nguyen, Kazue Kasai, Michal O. Nowicki, Alexander L. Ling, William F. Goins, Hiroshi Nakashima, E. Antonio Chiocca. Preclinical toxicology and efficacy of NG34C: A novel oncolytic HSV-1 expressing truncated GADD34 gene for the treatment of glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB381.