tbuckley/cabot-search huggingface dataset:
Abstract 4417: Development of biochemical screening assays to facilitate drug discovery in RNA m6A modification regulators
Authors: Safnas F. AbdulSalam, Sung Won Oh, Brenna P. Lee, Joseph J. Ferry, John R. Ries, Kurumi Y. Horiuchi
Journal: Cancer Research (2024)

Abstract Over the recent years, knowledge of RNA modifications and their regulation has expanded extensively, providing novel insights and strategies to explore potential therapeutics for pathogenesis of various diseases, including cancer. Several chemical modifications in RNA have been identified so far, among these N6-methyladenosine (m6A) modification is the most abundant and well-studied epitranscriptomic marker found in mRNA and long noncoding RNA. Abnormal m6A expression is proven to be associated with tumorigenesis, cancer stemness and drug resistance of cancers. Methylation in 6-Adenosin of RNA is a dynamic and reversible process tightly regulated by its writer, m6A methyltransferase complex and erasers, FTO and ALKBH5. m6A methyltransferase complex contains METTL3-METTL14-WTAP as core components. METTL3 is the catalytic component, which is activated by heterodimer formation with METTL14. High METTL3 expression is found in several cancers such as breast, lung, liver, gastric, colorectal, AML and a METTL3 catalytic inhibitor is found to delay AML progression in mouse models. Protein that binds RNA m6A modification to execute it signaling are known as m6A readers. Readers are categorized into three main classes, YTH domain proteins, IGF2 mRNA-binding proteins and heterogeneous nuclear ribonucleoproteins. YTH family readers are found to have oncogenic roles in several cancers including AML, breast, lung, CRC and glioblastoma. Recent studies suggest inhibition of m6A binding of individual YTH family proteins is a promising therapeutic strategy however, potent inhibitors are yet to be identified. This poster summarizes current assays we have developed to facilitate cancer therapeutic discovery in m6A related protein targets. We present development and validation of an assay suitable identify in METTL3 catalytic inhibitors using our proprietary hotspot technology. We also show development of HTRF based biochemical assays for all five YTH family protein YTHDF1-3 and YTHDC1-2, to screen for molecules that disrupt protein-m6A interaction. We further study the selectivity of an FDA approved drug Tegaserod, a reported YTHDF1 inhibitor by a structure based virtual screening, between YTH family proteins. Citation Format: Safnas F. AbdulSalam, Sung Won Oh, Brenna P. Lee, Joseph J. Ferry, John R. Ries, Kurumi Y. Horiuchi. Development of biochemical screening assays to facilitate drug discovery in RNA m6A modification regulators [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 4417.
Abstract 6278: Effect of tumor size and BRAF mutational status in Middle Eastern differentiated thyroid cancer
Authors: Rong Bu, Abdul K. Siraj, Sandeep K. Parvathareddy, Kaleem Iqbal, Saud Azam, Zeeshan Qadri, Maha Al-Rasheed, Wael Haqawi, Allianah D. Benito, Khawla S. Al-Kuraya
Journal: Cancer Research (2024)

Abstract Background: Risk stratified treatment strategies have become a focus in the treatment of Differentiated Thyroid Cancer (DTC). Tumor size at diagnosis has been widely used as a major mortality risk factor in risk stratification of DTC, but whether this is generally applicable, particularly in patient with different BRAF genetic backgrounds, is unclear. The current study was designed to analyze whether tumor size at diagnosis is a major prognostic factor in Middle Eastern DTC. Methods: We conducted a comparative study of the relationship between tumor size at diagnosis and event free survival with respect to BRAF status in 1709 consecutive patients treated surgically for Middle Eastern DTC. Patients were divided into four groups according to the size of tumor (≤4 cm vs. &amp;gt;4 cm) and BRAF mutation status: Group 1 (≤4 cm without BRAF mutation, n = 587), Group 2 (≤4 cm with BRAF mutation, n = 765), Group 3 (&amp;gt;4 cm without BRAF mutation, n = 198) and Group 4 (&amp;gt;4 cm with BRAF mutation, n = 159). Predictors of event-free survival (EFS) were compared using the Log-rank test and Cox proportional hazards models. Results: Following multivariate analysis, patients with tumors &amp;gt;4cm did worse than patients with tumors &amp;lt;4cm with respect to EFS (Group 3 vs Group1 HRadjusted=1.38, 95% CI=1.02-1.86, p = 0.0359; Group 4 vs Group 2 HRadjusted=1.61, 95% CI=1.20-2.16, p = 0.0017). However, patients did not differ according to EFS, regardless of the presence of BRAF mutation within each size category (Group 2 vs Group 1 HRadjusted=0.98 CI=.78-1.23, p=0.8415 ; Group 4 vs Group 3 HRadjusted=1.17, 95% CI=0.84-1.62, p=0.3523] Conclusion: Tumor size is an independent predictor of EFS in Middle Eastern DTC patients, regardless of BRAF mutational status. Citation Format: Rong Bu, Abdul K. Siraj, Sandeep K. Parvathareddy, Kaleem Iqbal, Saud Azam, Zeeshan Qadri, Maha Al-Rasheed, Wael Haqawi, Allianah D. Benito, Khawla S. Al-Kuraya. Effect of tumor size and BRAF mutational status in Middle Eastern differentiated thyroid 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 6278.
Abstract 2759: Transcriptional intra-tumoral heterogeneity of putative therapeutic targets in colorectal cancer peritoneal metastases
Authors: Joseph J. Zhao, Johnny CA Ong, Daryl Kai Ann Chia, Melissa Ching Ching Teo, Qiu Xuan Tan, Gillian Ng, Joey Wee-Shan Tan, Haoran Ma, Xuewen Ong, Su Ting Tay, Patrick Tan, Raghav Sundar
Journal: Cancer Research (2024)

Abstract Background: The poor prognosis of peritoneal metastasis (PM) in colorectal cancer (CRC) is typically attributed to, and characterized by, resistance to systemic chemotherapy and immunotherapy. The evolutionarily conserved plasma-peritoneal barrier as well as reduced tumor tissue vascularity contributes to poorer responses to systemically administered antineoplastic therapy. Beyond these, we sought to understand transcriptomic variations of important therapeutic targets implicated in peritoneal organotropism and by extension, resistance to systemic regimens in CRC PM. Methodology: FFPE tissue samples from CRC patients were collected during oncological surgical resection of the synchronous PM (cytoreductive surgery [CRS] with or without hyperthermic intra-peritoneal chemotherapy [HIPEC]), or exploratory laparotomy for palliative surgery, with the majority of patients receiving systemic therapy prior to surgery. Samples were sequenced with whole transcriptomic sequencing. Paired and unpaired T-tests between PT and PM samples were undertaken with log2(fragments per kilobase of exon per million mapped [FPKM]) gene expression values. Results: Fifty-six (22 primary tumor [PT], 34 peritoneal metastases [PM]) samples from 35 patients, comprising 21 paired PT-PM samples, were included in this analysis. TEAD1 (unpaired T-test, p=0.087; paired T-test, p=0.041), FGFR1 (unpaired T-test, p=0.003; paired T-test, p&amp;lt;0.001), PIK3CA (unpaired T-test, p=0.034; paired T-test, p=0.003), SMAD4 (unpaired T-test, p=0.095; paired T-test, p=0.010), and HAVCR2 (unpaired T-test, p=0.009; paired T-test, p=0.007) were found to be upregulated in the PM. Conversely, MET was found to be downregulated in PM samples (unpaired T-test, p=0.004; paired T-test, p=0.002). There were no significant differences in gene expression profiles of BRAF, RHOA, CD274, CTLA4, PDCD1 and TIGIT between PT-PM (all p&amp;gt;0.05). Conclusion: Through CRC PT-PM comparisons, we identify potential therapeutic targets implicated in transcoelomic metastasis and provide rationale for development of immunotherapeutic biology and drug discovery for CRC PM. These findings underscore an exigent need to develop intra-peritoneal therapeutic strategies to overcome resistance to systemic regimens. Citation Format: Joseph J. Zhao, Johnny CA Ong, Daryl Kai Ann Chia, Melissa Ching Ching Teo, Qiu Xuan Tan, Gillian Ng, Joey Wee-Shan Tan, Haoran Ma, Xuewen Ong, Su Ting Tay, Patrick Tan, Raghav Sundar. Transcriptional intra-tumoral heterogeneity of putative therapeutic targets in colorectal cancer peritoneal metastases [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 2759.
Abstract 4457: Skeletal muscle-infiltrating CD8 T cells exacerbate muscle atrophy in a syngeneic lung cancer cachexia mouse model
Authors: Se-Young Park, Bomi Kim, Myunggyo Lee, Haeseung Lee, Na-Young Song
Journal: Cancer Research (2024)

Abstract Cancer-associated cachexia (CAC) is a devastating syndrome of irreversible body weight loss and muscle wasting. CAC has been reported to often lead to poor outcomes of immune checkpoint inhibitors (ICIs), emerging as a standard treatment for various types of cancer. Previously, we have demonstrated that KRAS-mutant lung tumor tissues display an immunosuppressive microenvironment with decreased CD8 T cells and increased regulatory T cells (Tregs). In this orthotopic lung cancer mouse model, treatment with an anti-PD-L1 antibody, a representative ICI, reduced tumor burden, whereas accelerated loss of body weight and skeletal muscle mass. We thus assumed that CD8 T cells could facilitate skeletal muscle wasting in lung tumor-bearing mice, a key feature of CAC. First, we established a syngeneic CAC mouse model through orthotopic transplantation of murine lung cancer cells. At 7 weeks post-injection, these mice developed CAC, displaying over 20 % body weight loss, almost total loss of epididymal fats, and profound skeletal muscle wasting. In line with our assumption, CAC mice showed an increased number of CD8 T cells but a reduced number of Tregs in skeletal muscles, compared to tumor-free control mice. We then investigated whether skeletal muscle-infiltrating CD8 T cells directly induce muscle atrophy indeed. In CAC mice, CD8 neutralization led to restoration of muscle mass and downregulation of muscle atrophy markers, but was not able to significantly affect lung tumor burden. Moreover, direct co-culture with splenic CD8 T cells exacerbated C2C12 myotube atrophy in a conditioned medium from lung cancer cells, further supporting the involvement of CD8 T cells in CAC. To elucidate its underlying mechanism, RNA sequencing analysis was conducted in both skeletal muscles and lung tumors of CAC mice. Based on the differently expressed gene analysis, Cxcl13 was upregulated in skeletal muscles of CAC mice, while downregulated in lung tumors. It is well documented that CXCL13 can mediate recruitment of CD8 T cells. In this regard, CXCL13 might be a plausible regulator in CD8 T cell-induced skeletal muscle atrophy, which requires further investigation to fully understand the molecular mechanism. Citation Format: Se-Young Park, Bomi Kim, Myunggyo Lee, Haeseung Lee, Na-Young Song. Skeletal muscle-infiltrating CD8 T cells exacerbate muscle atrophy in a syngeneic lung cancer cachexia mouse model [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 4457.
Abstract 3277: PAI-1 mediates resistance to MET-targeted therapy in non-small cell lung cancer
Authors: Tomoaki Higashihara, Yin Min Thu, Ken Suzawa, Keiichi Date, Atsushi Matsuoka, Daisuke Mizuno, Ryo Yoshichika, Naohiro Hayashi, Fumiaki Mukohara, Mao Yoshikawa, Kazuhiko Shien, Hiromasa Yamamoto, Shinichi Toyooka
Journal: Cancer Research (2024)

Abstract [Purpose] The mesenchymal epithelial transition factor receptor (MET) is a potential therapeutic target in various cancers, including non-small cell lung cancer (NSCLC). In NSCLC, the activation of MET pathway is thought to occur through diverse mechanisms that influence properties affecting cancer cell survival, growth, and invasiveness. These tumors show oncogene addiction to MET and exhibit remarkable responses to MET-Tyrosine Kinase Inhibitors (TKIs). However, the long-term effectiveness of MET-TKIs is usually limited due to acquired drug resistance. The mechanisms underlying primary and acquired resistance to MET-TKIs in the management of NSCLC remain unclear. In this study, we investigated the mechanisms acquired for crizotinib in MET-amplified lung carcinoma cell lines. [Experimental Designs] Two MET-amplified lung cancer cell lines, EBC-1 and H1993, were established for acquired resistance to MET-TKI crizotinib and were functionally elucidated. The factors contributing to the resistance mechanism were assessed by genomic and transcriptomic data, and the alterations hypothesized to confer resistance were validated. [Results] Multiple mechanisms underlay acquired resistance to crizotinib in MET-amplified lung cancer cell lines. In EBC-1-derived resistant cells, the drug resistance mechanism was mediated by the overexpression of SERPINE1, the gene encoding plasminogen activator inhibitor-1 (PAI-1). Crizotinib resistance was overcome by combination therapy with PAI-1 inhibitor and PAI-1 knockdown. Another mechanism of resistance in different subline cells of EBC-1 was evaluated as epithelial to mesenchymal transition (EMT) with the upregulation of antiapoptotic proteins. In the H1993-derived resistant cells, the phosphorylated forms of MEK and ERK were observed to be upregulated and MEK inhibitors could be a potential therapeutic strategy for overcoming the resistance. [Conclusions] In this study, we revealed the different mechanisms of drug resistance to MET-TKI treatment and presented some possible strategies to overcome the resistance. Citation Format: Tomoaki Higashihara, Yin Min Thu, Ken Suzawa, Keiichi Date, Atsushi Matsuoka, Daisuke Mizuno, Ryo Yoshichika, Naohiro Hayashi, Fumiaki Mukohara, Mao Yoshikawa, Kazuhiko Shien, Hiromasa Yamamoto, Shinichi Toyooka. PAI-1 mediates resistance to MET-targeted therapy in non-small cell lung 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 3277.
Abstract 1387: SETD2 loss promotes macrophage infiltration and metastasis in RCC
Authors: Emily N. Arner, Melissa M. Wolf, Logan Vlach, Jeffrey C. Rathmell, W. Kimryn Rathmell
Journal: Cancer Research (2024)

Abstract Across human cancer, tumors that are high grade, poorly differentiated, and have undergone epithelial-to-mesenchymal transition (EMT) carry a worse prognosis with a high likelihood of metastasizing to distant organs. Despite significant research efforts, metastatic cancers and relapse remain the primary cause of cancer related deaths. In renal cell carcinoma (RCC), metastasis is present in one-third of patients at the time of diagnosis, and one-third of patients who initially present with locally advanced disease eventually develop local or distant recurrence following resection of the primary tumor, highlighting the need for new RCC therapies and further insight into the metastatic process. Using RCC patient biopsies, we found that patients with more epithelial tumors have a significantly lower risk of recurrence. Additionally, tumors that had a mesenchymal protein signature had significantly increased macrophage infiltration, which was significantly associated with a higher stage at diagnosis and worse overall survival, suggesting that macrophages may play an important role in EMT and metastasis in ccRCC. Whole exome sequencing of these patient samples revealed that mutational loss of SETD2, a histone methyltransferase that is lost in about 20% of RCC patients, correlated strongly with increased macrophage infiltration within the primary tumor and was necessary for the correlation between macrophages and EMT. SETD2 loss in syngeneic kidney cancer mouse models confirmed that SETD2 loss within tumor cells resulted in increased EMT, macrophages within the primary tumor microenvironment (TME), and spontaneous metastasis, further supporting the role of macrophages in promoting metastasis in the absence of SETD2. Further characterization of the gene signatures and immune cell infiltrate in RCC will lead to a better understanding of metastasis in an oncogene- and tissue-specific manner and thus lead to more efficacious therapies for metastatic patients. Citation Format: Emily N. Arner, Melissa M. Wolf, Logan Vlach, Jeffrey C. Rathmell, W. Kimryn Rathmell. SETD2 loss promotes macrophage infiltration and metastasis in RCC [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 1387.
Abstract 1725: Role of PRMT5 in neuroendocrine prostate cancer development
Authors: Hye Seung Nam, Xuehong Deng, Chang-Deng Hu
Journal: Cancer Research (2024)

Abstract Background: Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer responsible for an estimated 20-30% of castration resistant prostate cancer (CRPC) deaths. While NEPC can arise de novo, the majority of these cases emerge as treatment-induced NEPC (tNEPC). Our data establish PRMT5:MEP50 as a key epigenetic regulator in NEPC and provide a potential predictive biomarker for tNEPC. Methods: Here we generated an in vitro cell culture model and mouse model to mimic the clinical conditions in androgen signaling inhibitor (ASI) or androgen deprivation treatment (ADT) We developed an in vitro cell culture and in vivo model to mimic the clinical conditions in enzalutamide-resistant prostate cancer. Regulation and role of protein arginine methyltransferase 5 (PRMT5) and its cofactor methylosome protein 50 (MEP50) were determined by treating cells and mice tumors with doxycycline inducible-shRNAs and catalytic inhibitors followed by analysis of cell viability, neurite growth, and effects on neuroendocrine related gene transcription. Pro-NEPC development effects were analyzed by immunofluorescence, immunohistochemical analysis, and western blot. PRMT5:MEP50-dependent methyltransferase activity was further validated by observing histone deposition levels via western blot and ChIP-qPCR. For clinical correlation, PRMT5 and MEP50 expression levels were comprehensively analyzed in both CRPC and NEPC patient prostate tissue samples. Results: Our clinical and computational analyses have identified increased expression of PRMT5:MEP50 in NEPC. Overexpression of PRMT5 and MEP50 in prostate cancer cells is sufficient to induce neuroendocrine differentiation (NED) in prostate cancer cells. Gene depletion of PRMT5 and MEP50 prevented the NE phenotype induced by androgen receptor inhibition and resensitized the prostate cancer cells to ASI/ADT. PRMT5 and MEP50 facilitate chromatin modulation through the dimethylation of H4R3, which is highly correlated with the NED phenotype. Moreover, overexpression of PRMT5 and MEP50 in mouse prostate induces NEPC development, and gene downregulation can prevent NED in a xenograft mouse model. Elevated PRMT5 and MEP50 correlated with increased recurrence in prostate cancer patients receiving ADT and their recurrence probability after the treatment. Conclusion: Our data establish PRMT5:MEP50 as a key epigenetic regulator in NEPC and provide a potential predictive biomarker for tNEPC. Citation Format: Hye Seung Nam, Xuehong Deng, Chang-Deng Hu. Role of PRMT5 in neuroendocrine prostate cancer development [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 1725.
Abstract 6538: Modulation of human macrophage differentiation, phenotype and function <i>in vitro</i> as a strategy to characterize novel tumor microenvironment modulators
Authors: Carla N. Castro, Tamara Sahner, Cynthia Obodozie, Philipp Metzger, Holger Weber
Journal: Cancer Research (2024)

Abstract Macrophage infiltration of the tumor microenvironment is a key process that can determine the success or failure of anti-tumor therapies. Thus, many immunooncology therapies are being developed to modulate the macrophage differentiation program towards the anti-tumor M1 subset, while hindering the M2 subset associated with tumor progression. Monocyte-derived macrophages comprise a crucial in vitro cellular tool to evaluate the plasticity potential between the different polarization states. Several hurdles like their in vitro adherence, low cell number yield and the donor-to-donor variability pose technical challenges when using in vitro differentiated macrophages for compound screening and titration or functional assays. At Reaction Biology we have established human macrophage assay pipelines to evaluate the novel macrophage polarization compounds in vitro. By isolating monocytes from frozen PBMC stocks it is possible to have access to the same donor or group of donors PBMC for repetitive analysis. We have developed a differentiation protocol that allows us to use different plate format from 6-well to 48 well plates, and thus increase and modulate the throughput according to the required readout. The effect of therapeutic compounds can be analyzed by flow cytometry. Our data shows that human primary monocytes grown under M1 polarizing conditions express high levels of CD86 and CD80 in contrast to those cultivated under M2 polarizing conditions, with high expression of CD163, CD206, and CD209. Cell culture supernatant can be used to determine cytokine secretion. The functionality of the different macrophage subtypes can be further investigated using a pH-sensitive phagocytosis tracker, like pHRodo-Zymosan or pHRodo-Ecoli, which shows differential uptake according to differentiation profile. Moreover, treated macrophages can be used in coculture with T cells to investigate their capability to foster or inhibit an immune response. Our data shows the value of monocyte-derived macrophage assays in the evaluation and efficacy assessment of TME modulators. Citation Format: Carla N. Castro, Tamara Sahner, Cynthia Obodozie, Philipp Metzger, Holger Weber. Modulation of human macrophage differentiation, phenotype and function in vitro as a strategy to characterize novel tumor microenvironment modulators [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 6538.