tbuckley/cabot-search huggingface dataset:
Abstract 2718: Investigating the interaction of NF1 with the Polycomb Repressive Complex 2
Authors: Asra Noor, Peng Zhang, Pinpin Sui, Feng-Chun Yang
Journal: Cancer Research (2025)

Abstract Neurofibromin 1 (NF1) is a tumor suppressor gene frequently mutated in myeloid leukemias. The encoded neurofibromin protein negatively regulates the RAS pathway in the cytosol. Inactivating mutations in NF1 lead to hyperactive RAS signaling, phenocopying activating mutations in RAS itself. This aberrant signaling drives downstream activation of pathways such as MAPK and PI3K/Akt/mTOR. Despite the prevalence of NF1-mutated leukemia, effective therapies remain elusive, highlighting the need for a deeper understanding of NF1-mediated leukemogenesis. To identify key dysregulated genes in NF1-driven leukemogenesis, we performed bulk RNA sequencing on hematopoietic stem cells from Nf1 knockout mice exhibiting myelodysplastic syndrome. Gene set enrichment analysis revealed significant dysregulation of pathways involved in histone methylation and RNA modification. Etv4, Id2, and Bcl6 were among the top upregulated genes, although their dysregulation is likely secondary to RAS activation. To uncover novel, non-canonical targets of NF1, we identified Phf19 as a dysregulated gene not directly regulated by RAS. PHD finger protein 19 (PHF19) is a component of the Polycomb Repressive Complex 2 (PRC2), a complex that mediates histone H3 lysine 27 trimethylation (H3K27me3) through the catalytic activity of EZH2. This finding is particularly intriguing as previous studies have suggested nuclear localization of neurofibromin, but its function in the nucleus has remained unclear. To explore the potential nuclear role of neurofibromin, we employed TurboID proximity labeling to identify its interaction partners in both the nucleus and cytoplasm. We found that neurofibromin interacts with the core PRC2 components EZH2 and SUZ12 in the nucleus, a finding confirmed by co-immunoprecipitation. Ongoing studies aim to elucidate the functional consequences of Phf19 upregulation and the impact of the neurofibromin-PRC2 interaction on apoptosis, cell cycle progression, and proliferation in Nf1 knockout mouse model. Citation Format: Asra Noor, Peng Zhang, Pinpin Sui, Feng-Chun Yang. Investigating the interaction of NF1 with the Polycomb Repressive Complex 2 [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 2718.
Abstract 1480: Unlocking DNA repair mechanisms with dynamic single-molecule analysis
Authors: Paul Pease, Jack O'Sullivan, Trey Simpson, Josephine Yeh, Andrea Candelli
Journal: Cancer Research (2025)

Abstract The maintenance of genomic information through processes such as DNA replication, recombination, and repair is critical to cellular function. Errors in these underlying mechanisms play a major role in diseases such as cancer. As a result, insights into the molecular details are needed to advance our understanding, improve biological models, and develop novel therapeutics. Dynamic single-molecule technologies offer an exciting opportunity to meet these challenges and to study protein function and activity in real time. Here, we present our efforts for enabling discoveries in the field of DNA repair using the combination of fluorescence microscopy with optical tweezers. This technology has been used to study CMG helicase dynamics, the role of BRCA2 in RAD51 nucleation, and the mechanism of the DNA repair complex FANCD2-FANCI. It is also suitable for many applications involving mismatch repair (MMR), base excision repair (BER), and nucleotide excision repair (NER), among other lesions. We present several examples in which our technologies and biochemistry enhanced the understanding of these systems. Importantly, we show that advances in dynamic single-molecule methods can be turned into an easy-to-use and stable instrument that is unlocking new avenues for studying DNA-binding proteins in the field of DNA repair. Citation Format: Paul Pease, Jack O'Sullivan, Trey Simpson, Josephine Yeh, Andrea Candelli. Unlocking DNA repair mechanisms with dynamic single-molecule analysis [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 1480.
Abstract 1885: Identification of the novel immune synapse-localized proteome for immuno-oncology using Microscoop®-induced targeted photo-biotinylation
Authors: Chantal Hoi Yin Cheung, Weng Man Chong, Chun-Kai Huang, Hsiao-Jen Chang, Chia-Wen Chung, Jung-Chi Liao, Joseph Breier
Journal: Cancer Research (2025)

Abstract Although numerous immune synapse (IS) protein species have been identified, many IS-localized protein species remain unknown. Understanding the proteome of the IS between a target cell and a lymphocyte is crucial for advancing immuno-oncology. However, the low abundance of ISs and the absence of a definitive enrichment marker have hindered efficient proteomic profiling. In this study, we utilized Microscoop®, an innovative system that integrates microscopy, machine learning, and photochemical labeling to enable precise and spatially specific enrichment of IS proteins, thereby facilitating proteomic discovery for the IS. We employed Raji B cells as antigen-presenting cells (APCs) and induced IS formation with Jurkat T cells. The system first employed immunofluorescence imaging of CD3, a common IS marker in Jurkat T cells, and utilized a convolutional neural network-based deep learning algorithm to recognize IS formation from CMTPX-stained Raji B cells. Our automated system successfully achieved spatially targeted biotin-tagging of proteins at ISs through multiple rounds of imaging, deep learning-driven pattern generation, and photochemical labeling. Subsequent streptavidin pull-down and mass spectrometry analysis enabled the identification of IS-specific proteins. Remarkably, our spatial proteomic approach led to the isolation and identification of hundreds of different species at the IS interface, including proteins associated with key components of T-cell receptor (TCR) signaling pathways such as the TCR/CD3 complex, Src and Tec family tyrosine kinases, and pivotal NF-kB signaling proteins. Additionally, we identified a significant enrichment of proteins not previously associated with the IS. Our study not only illuminates previously unknown aspects of immune regulation at the IS interface but also has significant implications for cancer research, particularly in understanding and manipulating immune responses for therapeutic purposes. Citation Format: Chantal Hoi Yin Cheung, Weng Man Chong, Chun-Kai Huang, Hsiao-Jen Chang, Chia-Wen Chung, Jung-Chi Liao, Joseph Breier. Identification of the novel immune synapse-localized proteome for immuno-oncology using Microscoop®-induced targeted photo-biotinylation [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 1885.
Abstract 532: Single-cell analysis reveals neuroblastoma heterogeneity and therapeutic opportunities
Authors: Michele Tomanelli, Jennifer Hoti, Matteo Saettone, Daniele Reverberi, Adriana Bajetto, Tullio Florio, Aldo Pagano
Journal: Cancer Research (2025)

Abstract Neuroblastoma is the most common extracranial tumor found in neonatal patients, arising from neural crest cells. By utilizing specific Neuroblastoma cell lines, we have developed clones that express the non-coding RNA NDM29. These investigations have enabled the assessment of NDM29's role in tumor differentiation, identifying new therapeutic targets for controlling tumor malignancy. Further studies highlighted the presence of different cell subpopulations in this model by performing a single-cell sequencing analysis. These subpopulations were isolated with FACS analysis. The cellular heterogeneity characterizing this model reflects what is observed in patients. The gene expression of potential therapeutic targets identified in the heterogeneous model was evaluated in individual subpopulations. The individual subpopulations were pharmacologically treated by inhibiting some of these targets. These treatments revealed subpopulations that were either more sensitive or more resistant to specific inhibitors. By performing gene ontology analyses using sequencing data, we identified potential new pharmacological targets to enhance the mortality of even the resistant cells. Citation Format: Michele Tomanelli, Jennifer Hoti, Matteo Saettone, Daniele Reverberi, Adriana Bajetto, Tullio Florio, Aldo Pagano. Single-cell analysis reveals neuroblastoma heterogeneity and therapeutic opportunities [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 532.
Abstract 3102: Spliceosome perturbation enhances immunotherapy in SCLC by triggering ZBP1-driven necroptosis in cancer-associated fibroblasts
Authors: Xinpei Jiang, Xueying Ma, Yunyun Zhou, Siddharth Balachandran, Israel Cañadas
Journal: Cancer Research (2025)

Abstract Small cell lung cancer (SCLC) is the most lethal form of lung cancer with a 5-year overall survival of 5%. Despite advancements in immunotherapy, SCLC is characterized by an immunologically ‘cold’ tumor microenvironment (TME) and the majority of SCLC patients remain unresponsive to these treatment strategies. This combination of poor survival outcomes and limited therapeutic options underscores the critical urgency of identifying innovative strategies to treat SCLC. A potential approach to activate an innate immune response within tumors is by promoting the accumulation of endogenous "virus-like" nucleic acids in cancer cells, thereby initiating an antiviral response, concept known as ‘viral mimicry’. Here, we demonstrated that targeting the spliceosome component SF3B1 is an effective strategy to induce viral mimicry not only in cancer cells but also in cells from the TME, including cancer associated fibroblasts (CAFs). SF3B1 inhibition induced the formation of Z-form RNAs (Z-RNAs), which are unique, left-handed dsRNA species and necroptosis-activating ligands for Z-DNA binding protein 1 (ZBP1). Notably, we found that SF3B1 inhibition triggered ZBP1-dependent necroptosis, a highly immunogenic cell-death, through the RIPK3- ZBP1-MLKL axis in necroptosis-competent cancer cells and patient-derived CAFs. In vivo, SF3B1 inhibition promoted a decreased tumorigenicity and increased immunogenicity, as well as ZBP1-driven necroptosis in CAFs, enhancing response to immune checkpoint blockade (ICB). These findings have significant implications for inducing viral mimicry in immunologically "cold" tumors. Since SF3B1 inhibition can trigger necroptosis by targeting any necroptosis-competent cell, including CAFs within the TME, our results suggest that this approach could create a more immunogenic TME in all SCLC patients, regardless of whether their tumor cells have impaired necroptosis signaling. Thus, SF3B1 inhibitors and potentially other spliceosome-targeted therapies represent a promising strategy with exceptional translational potential for inducing necroptosis and enhancing ICB responsiveness in aggressive “cold” tumors, such as SCLC. Citation Format: Xinpei Jiang, Xueying Ma, Yunyun Zhou, Siddharth Balachandran, Israel Cañadas. Spliceosome perturbation enhances immunotherapy in SCLC by triggering ZBP1-driven necroptosis in cancer-associated fibroblasts [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 3102.
Abstract 2800: Unraveling long non-coding RNA dynamics in uveal melanoma: Insights into pathogenesis, biomarkers, and targeted therapies
Authors: Vasileios Alevizos, Nikitas Gerolimos, Sabrina Edralin, Clark Xu, Akebu Simasiku, Georgios Priniotakis, George A. Papakostas, Zongliang Yue
Journal: Cancer Research (2025)

Abstract Uveal melanoma (UM), a rare yet aggressive intraocular cancer with an estimated 5 cases per million people annually, presents a high metastatic risk and poor prognosis, highlighting an immeasurable need for novel diagnostic and therapeutic strategies. Not only is UM characterized by complex genetic and epigenetic aberrations, but it is also prone to deregulation of non-coding RNAs that could be used as therapeutic targets of diagnostic markers. In this study, we analyzed whole exome sequencing data from tumor and control samples of patients diagnosed with both uveal and cutaneous melanoma, focusing on a patient with a germline mutation in MBD4. Our framework, made up to work with long non-coding RNAs (lncRNAs), aims to flesh out these molecules' novel roles in disease etiology and progression. We identified several lncRNAs significantly associated with UM progression and computationally validated them in conjunction with microenvironmental factors in existing literature. LncRNAs are instructive in maintaining cellular homeostasis and, when deregulated, contribute to oncogenesis. Our results implied that the interaction between lncRNAs and other non-coding RNAs might be one of the most relevant mechanisms influencing UM pathogenesis. More interestingly, microenvironmental factors and lncRNA interplay are crucial in disease progression. The clinical relevance of our findings was tested using radiation treatment to evaluate potential therapeutic implications. Over and above that, we assessed the potential of lncRNAs as biomarkers and therapeutic targets in personalized medicine for UM patients to address ineffective treatments. The new lncRNA panels could serve as a new avenue for targeted therapy. With an in-depth understanding of the descent of molecular alterations and how lncRNAs interact within the tumor microenvironment, we can better size up potential strategies to cast off the challenges UM poses. Our work provides instructive insights into lncRNAs underpinnings of UM, emphasizing the significance of lncRNAs in tumor biology and their interactions within the microenvironment. We believe our findings will lay the groundwork for future therapeutic strategies and underscore the necessity for continued research to unravel the complex mechanisms in UM pathogenesis. Citation Format: Vasileios Alevizos, Nikitas Gerolimos, Sabrina Edralin, Clark Xu, Akebu Simasiku, Georgios Priniotakis, George A. Papakostas, Zongliang Yue. Unraveling long non-coding RNA dynamics in uveal melanoma: Insights into pathogenesis, biomarkers, and targeted therapies [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 2800.
Abstract 2723: Unveiling epigenetic mechanisms driving RasGRP3 upregulation via oncogenic Gαq signaling in uveal melanoma
Authors: Zaizhou Liu, Boris Bastian, Xu Chen
Journal: Cancer Research (2025)

Abstract Uveal melanoma (UM) is a rare but aggressive cancer originating from melanocytes within the eye. It is distinct from cutaneous melanoma (CM) and genetically defined by somatic mutations activating the Gαq signaling pathway, most commonly affecting the Gαq subunits GNAQ or GNA11. UM remains a highly lethal melanoma subtype that cannot be effectively treated by current treatment regimens, including immune checkpoint blockade and targeted therapies. RasGRP3 (RAS Guanyl Releasing Protein 3), a guanine nucleotide exchange factor (GEF) for Ras, is markedly (&amp;gt;100-fold mRNA levels compared to CM) and selectively upregulated in UM and serves as a critical signaling hub connecting Gαq signaling to the MAPK pathway. Elucidating the mechanisms underlying the RasGRP3 upregulation unique for UM promises to unveil alternative therapeutic targets. We compared the epigenetic landscape of the RasGRP3 locus in UM and CM cells using ChIP-seq for H3K27ac (marking active enhancer/promoters), H3K4me1 (active enhancers), and H3K4me3 (active promoter). In UM but not CM cells, the RasGRP3 locus was highly enriched for H3K27ac and H3K4me1 modifications, and two of its three transcription start sites were marked with elevated H3K4me3 levels, indicating the expression of two major isoforms in UM. Treatment of UM cells with the Gαq inhibitor YM-254890 (YM) or the PKC inhibitor LXS-196 (LXS) for 24 hours significantly reduced all three histone modifications (H3K4me3, H3K27ac, H3K4me1) at the RasGRP3 locus. No changes were observed in CM cells. Our findings indicate an active super-enhancer that regulates RasGRP3 expression in UM, which is under control of the Gαq pathway through epigenetic modifications at its promoter and enhancer regions. These findings explain the selective upregulation RasGRP3 characteristics of UM. Ongoing investigations aim to delineate the precise mechanisms by which Gαq signaling drives these epigenetic changes. Our results highlight the potential of targeting specific histone modifiers as a novel therapeutic strategy for UM treatment. Citation Format: Zaizhou Liu, Boris Bastian, Xu Chen. Unveiling epigenetic mechanisms driving RasGRP3 upregulation via oncogenic Gαq signaling in uveal melanoma [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 2723.
Abstract 1680: Therapeutically targeting genes and pathways activated by high-fat diet in high-risk neuroblastoma
Authors: Md Jahidul Hasan, Ritu Mittra, Marie Joseph, Mukesh Raipuria, Nisitha Jayatilleke, Daniel R Carter, Margaret J Morris, Belamy B Cheung, Glenn M Marshall
Journal: Cancer Research (2025)

Abstract MYCN-amplified neuroblastoma (NB) is one of the most aggressive and treatment refractory cancers in children. NB has a prenatal origin, and therefore environmental factors in utero may play a critical role in driving NB tumorigenesis. A recent epidemiological study showed that children born to mothers who gained weight more than 30 kg during pregnancy had a 2-fold higher risk of developing NB. Using the Th-MYCN NB transgenic mouse model, we found that high-fat diet (HFD)-induced maternal obesity resulted in accelerated NB tumorigenesis in the Th-MYCN homozygous offspring. Transcriptomic patterns in tumour tissues from Th-MYCN homozygous offspring of HFD-fed mothers showed upregulation of fatty acid (FA) metabolism and mitochondrial oxidative phosphorylation (OXPHOS) pathways. We then used human NB cell lines exposed to excess FA to study mechanisms and therapeutics. In vitro studies showed that excess FA increased growth, proliferation, and colony formation in human NB cell lines, which was reversed by Fatostatin, a FA metabolism inhibitor, with an effect which was partially MYCN-dependent. Fatostatin showed significant synergy in combination with doxorubicin and vincristine in reversing FA-accelerated growth, proliferation, and colony formation in human NB cell lines, with a wide therapeutic window. ATP5G1 and ATP5G2 (genes encoding human mitochondrial ATP synthase membrane c-subunit) were identified as candidate genes in the HFD-activated OXPHOS pathways. siRNA knockdown of both genes significantly reversed FA-accelerated growth and proliferation in human NB cell lines. Chromatin immunoprecipitation (ChIP)-PCR showed that ATP5G1 and ATP5G2 are transcriptional targets of MYCN, and their transcription is significantly increased in the presence of FA. Further, the overall ATP production was significantly increased in the presence of FA in human NB cell lines, but not in human normal fibroblasts. siRNA knockdown of ATP5G1 and ATP5G2 significantly decreased this effect. Together, our data strongly support a role for OXPHOS and FA metabolism pathways in HFD-accelerated NB tumorigenesis and highlight a key role of the mitochondrial ATP synthase membrane c-subunit genes, ATP5G1 and ATP5G2 in HFD-accelerated NB tumorigenesis. Citation Format: Md Jahidul Hasan, Ritu Mittra, Marie Joseph, Mukesh Raipuria, 1 Nisitha Jayatilleke, Daniel R Carter, Margaret J Morris, Belamy B Cheung, Glenn M Marshall. Therapeutically targeting genes and pathways activated by high-fat diet in high-risk neuroblastoma [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 1680.
Abstract 3508: Breaking down solid tumor barriers with a bispecific T cell engager against a novel pHLA target
Authors: Marvin H. Gee, Joshua Goldsmith, Ryan Stafford, Christine Cheng, Bindu Hegde, Tina Giese, Tamson Moore, Lisa Kirkemo, Tanmayee Khadilkar, Lena Flood, Jake Kleiner, Florian Schustek, Aurelien Sarde, Joanna Dreux, Alaina K. Cagalingan, Ricardo Herrada, Gabriel Michaels, Kyle Pelot, Azita Tabrizi, Stefan Scherer
Journal: Cancer Research (2025)

Abstract Recent clinical results show the ability to target intracellular proteins through peptides presented by human leukocyte antigen (pHLA), opening up a unique avenue to targets inaccessible to conventional biologics. Bispecific T cell engagers are an effective therapeutic modality to redirect T cell immune responses towards tumors. However, there is still significant unmet need in a number of solid tumor indications with limited treatment options and few pHLA targets. Using a high-throughput discovery platform utilizing experimental screening and machine learning approaches to map patient T cell immune responses to their respective pHLA targets, a novel wildtype tumor-associated pHLA target with sufficient tumor versus normal expression has been identified. This target contributes directly to tumor stability and growth and is widely expressed in colorectal cancer, triple-negative breast cancer, and squamous non-small cell lung cancer among other indications. 3T-403, a CD3 bispecific T cell engager utilizing a T cell receptor mimic (TCRm) antibody has been developed to this novel target. The pHLA binding arm of 3T-403 has undergone specificity analysis using classical alanine scan as well as analysis via a novel high-throughput combinatorial library to de-risk potential pHLA off-targets. Potency assays conducted with 3T-403 show lysis against a panel of tumor cell lines, while minimal cytotoxicity was observed on primary healthy tissues, which provides a therapeutic window. Investigational new drug (IND) application completion is expected early 2026. Such a bispecific T cell engager against a novel target shows significant promise to address multiple solid tumor indications. Citation Format: Marvin H. Gee, Joshua Goldsmith, Ryan Stafford, Christine Cheng, Bindu Hegde, Tina Giese, Tamson Moore, Lisa Kirkemo, Tanmayee Khadilkar, Lena Flood, Jake Kleiner, Florian Schustek, Aurelien Sarde, Joanna Dreux, Alaina K. Cagalingan, Ricardo Herrada, Gabriel Michaels, Kyle Pelot, Azita Tabrizi, Stefan Scherer. Breaking down solid tumor barriers with a bispecific T cell engager against a novel pHLA target [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 3508.