tbuckley/cabot-search huggingface dataset:
Abstract 6792: Investigating differential expression of Palladin isoform 3 in 2D and 3D pancreatic cancer cell cultures
Authors: Sonali Biswas, Jason A. Bush
Journal: Cancer Research (2024)

Abstract Palladin (PALLD) is an actin-binding protein widely expressed in mammalian tissues that modulates cytoskeletal dynamics. Palladin is linked to the progression of breast, pancreatic, and renal cancers. There are at least 9 known isoforms of PALLD but isoforms 3 (iso3) and 4 (iso4) appear most significant in cancer cells and associated fibroblasts. Our goal is to understand iso3 in pancreatic cancer (PC) cell lines grown in various culture environments to shed light on the intricate interplay between culture conditions and gene regulation. Cell models were developed as 3D spheroids from hanging drops after optimizing culture conditions by utilizing a combination of inexpensive methylcellulose (MC) and rat tail collagen viscosity ranges across cell seeding densities. The quality of the developed spheroids was assessed using multiple parameters, like diameter, integrity, and circularity to determine ideal spheroid characteristics. Spheroids that formed at a lower MC viscosity range (350-550 mPa·s) led to peripheral loose cells and a higher viscosity range (7,000-10,000 mPa·s) resulted in elongated shapes. Moderate viscosity ranges (1,000-1,800 mPa·s and 3,500-5,600 mPa·s) consistently produced circular and compact spheroids. Optimal incubation times varied from 72 to 96 hr depending on the cell line. Invasion dynamics within collagen-MC gels revealed that PANC-1 had significantly higher invasion potential compared to BxPC-3 and a control cell line C2C12. RT-qPCR results show that PALLD iso3 was particularly overexpressed in the 3D culture environment of PANC-1, suggesting that elevated PALLD isoform 3 expression may be a characteristic of 3D culture, particularly in invasive PC types. Taken together, the study validates the importance of extracellular viscosity for influencing spheroid characteristics toward generating reproducible 3D spheroids. The investigation also highlights PALLD iso3 as a potentially valuable biomarker for aggressive forms of pancreatic cancer. Citation Format: Sonali Biswas, Jason A. Bush. Investigating differential expression of Palladin isoform 3 in 2D and 3D pancreatic cancer cell cultures [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 6792.
Abstract 6600: Investigating molecular regulators of a dual identity state in lung adenocarcinoma
Authors: Gabriela Fort, Soledad Camolotto, Rushmeen Tariq, Pengshu Fang, Katherine L. Gillis, Chris Stubben, Eric L. Snyder
Journal: Cancer Research (2024)

Abstract Lung adenocarcinoma (LUAD) is the largest subtype of lung cancer and is the most common cause of cancer related death. LUAD progression is driven by both genetic alterations and epigenetic changes that confer increased lineage plasticity and heterogeneity, but underlying mechanisms dictating cell identity in LUAD remain incompletely understood. The lineage defining transcription factors, NKX2-1 and FoxA1/2, coordinately maintain a pulmonary identity in LUAD. Recent work suggests that NKX2-1-positive (NKX2-1+) LUAD evolves from an alveolar-like state and adopts various disparate cell fates that drive progression, including “dual-identity” states, characterized by acquisition of gastrointestinal (GI) and pulmonary-like states in the same cell. Using sophisticated genetically engineered mouse models and 3D organoid cultures, we demonstrated that the gastrointestinal transcription factor HNF4α, which robustly marks the dual-identity state, is critical for growth in NKX2-1+ LUAD. We performed bulk RNA-seq and single cell RNA-seq in vitro and in vivo, and we found that loss of HNF4α alters the differentiation state of NKX2-1+ LUAD, causing cells to shed elements of their gastric identity in favor of alternate differentiation states. Using paired chromatin immunoprecipitation sequencing and RNA-seq in dual-identity organoids, we found that HNF4α can access and activate many of its canonical gastrointestinal target genes despite being aberrantly expressed in the lung, where it is typically epigenetically silenced early in development. Surprisingly, HNF4α also colocalizes with NKX2-1 and FoxA1/2 and binds at novel sites, suggesting that HNF4α acquires expanded activity in this state beyond its canonical roles. Together, our work unveils key insights into the mechanisms by which lineage defining transcription factors regulate cellular identity and growth in LUAD. Citation Format: Gabriela Fort, Soledad Camolotto, Rushmeen Tariq, Pengshu Fang, Katherine L. Gillis, Chris Stubben, Eric L. Snyder. Investigating molecular regulators of a dual identity state in lung adenocarcinoma [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 6600.
Abstract 5503: Ultrahigh-plex spatial phenotyping of head and neck cancer tissue uncovers multiomic signatures of immunotherapy response
Authors: Aditya Pratapa, Lydia Hernandez, Bassem Ben Cheikh, Niyati Jhaveri, Arutha Kulasinghe
Journal: Cancer Research (2024)

Abstract Background Targeted immune checkpoint inhibitors (ICI) with anti-PD-1/PD-L1 therapy offer durable treatment of mucosal head and neck squamous cell cancer (HNSCC), in both human papillomavirus-positive (HPV+) and negative (HPV-) patients. However, currently available biomarker signatures for targeted ICI therapies have limited predictive value. Our recent ultrahigh-plex profiling of HNSCC tissue with 100+ cancer hallmarks of tumor and immunobiology uncovered distinct spatial domains that serve as defining factors for clinical response and resistance. Methods Our unbiased analysis of whole-slide metastatic HNSCC tumors is from a clinical cohort of patients treated with Pembrolizumab/Nivolumab. The cohort consisted of patients with a range of outcomes from complete vs partial vs progressive disease responses to ICI therapy. We first characterized the tumor microenvironment using our ultrahigh-plex protein panel with 100+ antibodies on the PhenoCycler®-Fusion platform. To expand upon our biomarker discovery, we included multiomic cancer hallmarks with a multimodal protein/RNA detection panel. Targeted spatial RNA detection was performed to complement and augment the microenvironment characterization achieved by our protein panel. To further consolidate the multiomic data, we leveraged MaxFuse, a state-of-the art computational framework that integrates multimodal spatial and single-cell expression data. Results Our multiomic spatial phenotyping uncovered diverse tumor regions, each with distinct biomarker expression that is reflected across modalities including protein, RNA, and metabolic activity, indicating regions likely associated with resistance to immunotherapy. Our multiomic data integration also revealed spatial signatures associated with different tissue compartments, such as the tumor and non-tumor associated tertiary lymphoid structures. Conclusions We demonstrate a multi-pronged approach that incorporated both novel experimental and computational techniques for elucidating tumor microenvironment in HNSCC tissue prior to ICI-based immunotherapy. Our multiomic approach provides deeper characterization of the HNSCC at the transcriptomic and proteomic level incorporating depth across the entire transcriptome and single-cell spatial resolution of key protein determinants for predicting and furthering our understanding of immunotherapy response to ICI therapy. Citation Format: Aditya Pratapa, Lydia Hernandez, Bassem Ben Cheikh, Niyati Jhaveri, Arutha Kulasinghe. Ultrahigh-plex spatial phenotyping of head and neck cancer tissue uncovers multiomic signatures of immunotherapy response [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 5503.
Abstract 409: Deciphering chromosomal instability in consensus molecular subtypes (CMS) in CRC: Insights from an integrative multi-omics approach
Authors: Julia Bischof, Jonathan Woodsmith, David Church
Journal: Cancer Research (2024)

Abstract CRC is a heterogeneous disease with different molecular subtypes, which can have a profound impact on treatment response and patient outcomes. CMS classification based on gene expression profiles has been shown to differentiate patients into clinically relevant sub-groups. However, deep multi-omics characterization of the CMS classes based on high quality patient data is lacking. Through the integration of multi-omics data, we aim to enhance our understanding of CRC’s molecular heterogeneity and thereby facilitate the development of personalized therapeutic strategies. We performed a multi-omics analysis of CRC patients to identify potential new features of CMS groups. 890 fresh-frozen, surgically resected CRC tumor and adjacent normal samples were used to analyze whole genome and RNA sequencing data. DNA and RNA was prepared using Qiagen AllPrep Universal and KAPA Hyper Prep kit (DNA), as well as TruSeq Stranded Total mRNA kits and sequenced on a NovaSeq6000 system. We identified CMS subtypes based on RNA-Seq data and performed all statistical analyses using R. Our analysis revealed distinct molecular characteristics across the four CMS subtypes, including unique driver mutations, signaling cascades, and immune cell infiltration profiles. The poor prognosis associated with CMS4 patients was corroborated by our clinical data. Notably, we observed high global chromosomal instability (CIN) profiles for both CMS2 and CMS4 and identified recurrent global aneuploidy patterns within these subtypes that link alterations of known cancer genes to these large-scale structural events. We found higher levels of CIN in CMS2 compared to CMS4, which appears to be predominantly driven by numerical, rather than structural CIN. Specifically, in CMS2, SMAD2/4 is commonly impacted by deletion on chromosome arm 18q, while PLCG1 is more influenced by amplifications on 20q respectively, suggesting potential values as CRC CMS biomarkers. In conclusion, our integrative multi-omics analysis offers a comprehensive understanding of CRC molecular subtypes, which can inform personalized treatment strategies. Our findings underscore the importance of considering not only specific driver mutations but also large-scale structural rearrangements in the context of CMS subtypes. Citation Format: Julia Bischof, Jonathan Woodsmith, David Church. Deciphering chromosomal instability in consensus molecular subtypes (CMS) in CRC: Insights from an integrative multi-omics approach [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 409.
Abstract 6611: Unbiased functional genetic screens reveal essential RNA modifications in human cancer and drug resistance
Authors: Cornelius Pauli, Michael Kienhöfer, Carsten Müller-Tidow, Michaela Frye
Journal: Cancer Research (2024)

Abstract RNA modification pathways are mis-regulated in multiple types of human cancer. To comprehensively identify cancer-relevant RNA modifications and their regulators, we screened all 150 annotated human RNA modifying proteins across 18 different normal and cancer cell lines using a CRISPR-based genetic knockout system. Fifty RNA modifying proteins were essential for survival of at least one cell type. A third of these essential genes were amplified in 38 different human primary cancer types and potentially drive cancer growth. Unexpectedly, the number of essential genes per cell line varied considerably, and this variation was not due to tissue of origin. Instead, we found that cancer cell-specific mitochondrial metabolic plasticity was responsible for the unique requirement of certain RNA modifications. For example, leukemia cells with high intrinsic drug tolerance required mitochondrial flexibility to survive treatment with the anti-leukemic drugs cytarabine and venetoclax. Synthetic lethality screens revealed that drug-resistance is abolished by deleting the mitochondrial methyltransferase TRMT5, which is responsible for the formation of N1-methylguanosine (m1G) in the tRNA anticodon loop. In summary, our study identifies cancer-relevant RNA modifying enzymes, and reveals a novel promising drug target for therapy-resistant acute myeloid leukemia. Citation Format: Cornelius Pauli, Michael Kienhöfer, Carsten Müller-Tidow, Michaela Frye. Unbiased functional genetic screens reveal essential RNA modifications in human cancer and drug 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 6611.
Abstract 1110: Estrogen receptor β signaling induced radio-resistance in bladder cancer
Authors: Hiroki Ide, Tetsushi Murakami, Eiji Kashiwagi, Sotaro Kitaoka, Akari Komatsuda, Chugo Nishimura, Shinsuke Funakoshi, Mototsugu Oya, Hiroshi Miyamoto
Journal: Cancer Research (2024)

Abstract Introduction and Objective: Although radiotherapy (RT) combined with chemotherapy shows comparable outcomes to surgery, women tend to have higher mortality from bladder cancer (BC) compared to men. Emerging evidence indicated the involvement of estrogen receptorβ (ERβ) signaling in BC progression and the association of ER signaling with DNA repair pathways which are involved in radio-resistance. Therefore, we evaluated the association between ERβ signaling and the sensitivity to BC cells. Methods: We compared the inhibitory effect of RT on BC cell viability between ERβ positive [5637 and T24 expressing control short-heparin RNA (shRNA)] and ERβ negative (5637 and T24 expressing ERβ-shRNA) cells. Moreover, we compared DNA double-strand breaks (DSB) via γ-H2AX foci formation, as well as the expression levels of DNA repair genes, in these cells after RT. Finally, in a mouse xenograft model, we evaluated it on the growth of ERβ positive tumor treated with radiation combined with mock or tamoxifen treatment. Results: In vitro experiment showed that ionizing radiation reduced the numbers of viable cells in ERβ negative cells more significantly than those in ERβ positive cells. Moreover, tamoxifen treatment reduced the numbers of viable cells more than mock treatment in ERβ positive cells, while tamoxifen didn’t show significant effects in ERβ negative cells. The down-regulation of ERβ resulted in a delay in DSB repair 4-24 hours after RT. We then established radio-resistant cells and confirmed considerable elevation of the expression of ERβ as well as DNA repair genes including RAD51 and RAD54. Estradiol treatment induced the expression of these genes and tamoxifen abolished these effects. Finally, in vivo experiment showed that tamoxifen enhanced the cytotoxic effects of RT in xenograft bearing mice. Conclusions: These results indicated that ERβ signaling inversely correlated with sensitivity to RT in BC. Thus, ERβ inhibition have a potential of enhancing the cytotoxic effects of radiation, especially in ERβ positive BC cells. Citation Format: Hiroki Ide, Tetsushi Murakami, Eiji Kashiwagi, Sotaro Kitaoka, Akari Komatsuda, Chugo Nishimura, Shinsuke Funakoshi, Mototsugu Oya, Hiroshi Miyamoto. Estrogen receptor β signaling induced radio-resistance in bladder 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 1110.
Abstract 4162: Peptide-targeted probe identifies pancreatic cancer using optoacoustic imaging
Authors: Emma Sanderson, Tereza Husarova, Lacey McNally
Journal: Cancer Research (2024)

Abstract Introduction: Advanced pancreatic ductal adenocarcinoma (PDAC) suffers from inadequate early detection, inoperability, and poor outcomes. While tumor identication in an intraoperative setting largely utilize ultrasound, ultrasound suffers from insufficient resolution and lacks the ability to identify molecular features to differentiate tumor from non-tumor. To overcome these limitations, we utilized optoacoustic imaging combined with a pH-sensitive peptide-based probe, V3, to identify pancreatic cancer in orthotopic mouse models. Methods: The V3 peptide was synthesized using microwave chemistry which resulted in a peptide of &amp;gt;90% purity. The V3 peptide was conjugated to a fluorescent dye and dialyzed to make the V3-750 probe. S2VP10 cancer cell line was plated in a 6-well plate and acclimated to 7.4, 6.8, and 6.6 pH media to mimic a healthy microenvironment and the acidic tumor microenvironment found in pancreas cancer. Cells were treated with 1 micromolar of V3-750 probe for 1 hour, then imaged on the near-infrared fluorescence imager. Treated cells were loaded into tissue mimicking phantoms and imaged using multispectral optoacoustic tomography. Athymic mice were orthotopically implanted with S2VP10 cells and tumor grew to 3 mm. V3-750 was intraveneously injected and mice were imaged 3h after injection with MSOT. Results: Signal values for the samples displayed a trend that the V3-750 probe has higher signal values in the 6.8 and 6.6 pH as compared to the 7.4 pH. MSOT data supported this trend, with the signal values from the 6.8 and 6.6 pH being greater than the 7.4 pH by 10-fold (p&amp;lt;0.05). Biodistribution demonstrates peak tumor-specific uptake at 3h post injection (3.1 a.u., 0.003 a.u. liver, 0.002 a.u. kidney). Conclusion: The heightened signal values for the acidic pH’s from the fluorescence imaging and the MSOT suggest that the V3-750 probe can contrast acidic cancer cells from healthy cells because it targets the acidic cancer microenvironment. Citation Format: Emma Sanderson, Tereza Husarova, Lacey McNally. Peptide-targeted probe identifies pancreatic cancer using optoacoustic imaging [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 4162.
Abstract 3731: Spliceosome: A gatekeeper for necroptosis
Authors: Xinpei Jiang, Xueying Ma, Siddharth Balachandran, Israel Cañadas
Journal: Cancer Research (2024)

Abstract Small cell lung cancer (SCLC) is the most aggressive type of lung cancer with a 5-year overall survival of approximately 5%. SCLC has high prevalence of somatic mutations, yet express low to zero neoantigen. Despite promising advances in immunotherapy, highly metastatic SCLC remains a devastating disease and only a small fraction of SCLC patients respond to immunotherapy. These poor survival and lack of therapy options stresses the unmet need to identify novel and effective targeted therapies for metastatic SCLC. Here, we demonstrate that targeting the splicing core component, SF3B1, in SCLC, is a molecular trigger for tumor killing and viral mimicry.SF3B1 inhibition through the small molecule Pladienolide B (PlaB) induces the accumulation of immunogenic double-stranded RNAs (dsRNAs), including right-handed dsRNA conformation (A-RNA), provoking a tumor-intrinsic innate immune response and tumor cell death in SCLC preclinical models. Strikingly, we discovered that PlaB treatment also induces the formation of Z-form nucleic acids (Z-NAs), which are unique, left-handed nucleic acids and necroptosis-activating ligands for the host sensor ZBP1.These endogenous A-RNAs and Z-NAs initiate tumor-intrinsic antiviral interferon (IFN) signaling in SCLC cells leading to tumor-intrinsic immunogenicity and apoptosis. Notably, we also found that Z-NAs derived from spliceosome inhibition trigger the activation of ZBP1, inducing RIPK3-mediated MLKL activation and eventual necroptosis, a highly immunogenic cell-death pathway, in ‘necroptosis competent’ cells, including mouse embryonic fibroblasts (MEFs). This opens unexplored strategies for spliceosome inhibitors to activate anti-tumor immune pathways not only in tumor cells themselves, but also in cells of the Tumor Microenvironment (TME), which too can break tolerance and enhance anti-tumor T cell responses which is crucial to enhance cancer immunotherapy responses. These findings demonstrate a unique and novel spliceosome-targeted mechanism to remodel the immunosuppressive TME of SCLCs. Also, our study suggests that SF3B1 inhibitors and potentially other spliceosome inhibitors might be used not only to selectively kill tumor cells, but also as compounds to generate Z-NAs in tumor cells and cells of the TME and trigger on-demand necroptosis without need for an active virus infection. Citation Format: Xinpei Jiang, Xueying Ma, Siddharth Balachandran, Israel Cañadas. Spliceosome: A gatekeeper for necroptosis [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 3731.
Abstract 5471: Ribosome heterogeneity and RNA polI inhibition in osteosarcoma heterogeneity
Authors: Marc Baud'huin, Elvina Colleville, Rose Anne Thepault, Emilien Orgebin, Francois Lamoureux, Benjamin Ory
Journal: Cancer Research (2024)

Abstract Osteosarcoma is the most common primary bone tumour in adolescents and young adults, with an incidence rate of 3.8 per million. These tumors affect the long bones of the body such as femur. Current standard therapy includes tumour resection associated with multi-drug chemotherapy. The 5-year survival rate can reach 65% but is significantly reduced to 30% when pulmonary metastases are detected at the time of diagnosis. As this rate has not improved in the last 50 years, it is necessary to identify new therapeutic strategies. Inhibition of ribosomal biogenesis is one of the strategies developed in many cancer studies. This can be obtained by inhibition of RNA pol I, and in particular by BMH-21. The objective of this study was to analyze the complexity and heterogeneity of osteosarcomas through the ribosomal spectrum. The effect of BMH-1 on survival was also studied in osteosarcoma cell lines. The data obtained showed that there was no difference in ribosome protein composition in the “core” ribosome in different osteosarcoma cell lines. In addition, BMH-21 decreased cell viability in all osteosarcoma and chemoresistant cell lines. However, any activation of the apoptotic pathway by caspases was detected, nor any impact on the formation of new colonies after treatment with BMH-21. These results suggest a rather cytostatic mechanism. Moreover, a G0/G1 arrest in cell cycle was shown for U2OS cells. Finally, BMH-21 does not appear to have any impact on migration in HOS and U2OS cells. The different molecular mechanisms involved in the regulation of proliferation need to be further investigated. Citation Format: Marc Baud'huin, Elvina Colleville, Rose Anne Thepault, Emilien Orgebin, Francois Lamoureux, Benjamin Ory. Ribosome heterogeneity and RNA polI inhibition in osteosarcoma heterogeneity [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 5471.