tbuckley/cabot-search huggingface dataset:
Abstract 5644: The impact of ATF3, JDP2, FOXR2, NAA10, FOXL2, DDX20, and p14ARF on the transactivation of p53
Authors: William H. Yang, Wei-Hsiung Yang
Journal: Cancer Research (2024)

Abstract Cancer stands as a formidable health challenge in the 21st century, evoking widespread fear. Presently, the mortality rate associated with cancer in humans ranges from approximately 11% to 25%. Numerous nuclear and cytoplasmic proteins have demonstrated interactions with p53, influencing both its activity and abundance. In our prior, unpublished findings, we established that JDP2 interacts with p53, modulating its activity. Consequently, in the present investigation, we broaden our exploration to identify novel proteins capable of regulating p53 transactivation. First, we found a synergistic effect of ATF3 and JDP2 on p53 transactivation. Moreover, deSUMOylation of ATF3 and dephosphorylation of JDP2 further enhance p53 transactivation. Secondly, FOXR2 (an epigenetically regulated pan-cancer oncogene) and NAA10 (an acetyltransferase) also remarkably increase p53 transactivation in H1299 (p53 null) cells. Thirdly, in addition to MDM2 and MDM4 (MDMX) as p53 negative regulators, we further found that FOXL2 (a transcription factor in steroidogenesis regulation), DDX20 (a transcription factor for embryonic development and ovarian function), and p14ARF (for cell cycle regulation) significantly down-regulate p53 transactivation. Taken together, our preliminary results demonstrate that several transcription factors regulate p53 transactivation and possible p53 stability and/or degradation. This data is presented to substantiate the idea that numerous newly discovered proteins may engage with p53 and control its transactivation. Citation Format: William H. Yang, Wei-Hsiung Yang. The impact of ATF3, JDP2, FOXR2, NAA10, FOXL2, DDX20, and p14ARF on the transactivation of p53 [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 5644.
Abstract 3110: An enhanced and cost-efficient method for neoantigen immunogenicity screening method: Double Barcode Neoepitope ScanTM
Authors: Seong Gwang Kim, Min-Ho Jung, Hyun-Ji Hwang, Sejin Oh, Seong-Eui Hong, Soonmyung Paik, Hae-Suk Kim
Journal: Cancer Research (2024)

Abstract Neoantigens, HLA bound peptides generated by tumor-specific mutations, have emerged as promising targets for cancer immunotherapeutic. However, the significant challenge in neoantigen-based therapies is that the neoantigens are rare and difficult to predict. Therefore, in addition to prediction algorithms, the optimization of validation methods is essential for the reliable selection of highly immunogenic neoepitopes. In this study, we have developed a cost-effective screening method to validate large scale of neoantigen candidates. The DNA library-based methods have been employed for antigen selection and T cell receptor identification. We improved the DNA library-based neoantigen screening method by adding two barcodes to each minigene transcribing multiple neoantigen candidates and pooled synthesis of minigenes. We initially designed the barcodes to allow analysis in a 10 by 10 format for screening of hundreds of neoantigens so that PCR with each barcode result in amplification of ten candidates. The second barcode allowed the deconvolution of immunogenicity results without the need for synthesis of individual peptides. In this method B cell was used as antigen-presenting cell, which were co-transfected with mRNA for a minigene pool, 41BBL, and OX40L after expansion with CD40L/IL4/IL21. The resulting B cells were co-cultured with T cells and T cell responses were evaluated using ELISpot. To validate the method the TESLA consortium reported tetramer positive neoantigens were included in minigene. In results, the neoantigens including each barcode were amplified to form a pool of ten neoantigens as a minigene and confirmed that the neoantigens were equally amplified by nested PCR. The neoantigen pools synthesized as mRNA were transfected for presentation in B cells. The result of the targeting a neoantigen pool containing tetramer-positive neoantigens of the TESLA consortium showed a positive for ELISpot. In conclusion, our optimized screening method, employing the double barcode system, offers a time- and cost-efficient approach for the selection of immunogenic neoantigens without the need for individual peptides. This method will facilitate large-scale screening to identify actual neoantigens with immunogenic potential, contributing to the development of neoantigen-targeted vaccines. Citation Format: Seong Gwang Kim, Min-Ho Jung, Hyun-Ji Hwang, Sejin Oh, Seong-Eui Hong, Soonmyung Paik, Hae-Suk Kim. An enhanced and cost-efficient method for neoantigen immunogenicity screening method: Double Barcode Neoepitope ScanTM [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 3110.
Abstract 5639: TIP60-independent mechanism of BRD8 is involved in colorectal tumorigenesis
Authors: Kiyoshi Yamaguchi, Saya Nakagawa, Rui Yamaguchi, Paul Sheridan, Kiyoko Takane, Tsuneo Ikenoue, Satoru Nagatoishi, Hiroko Kozuka-Hata, Masaaki Oyama, Susumu Aikou, Yuka Ahiko, Dai Shida, Kouhei Tsumoto, Satoru Miyano, Seiya Imoto, Yoichi Furukawa
Journal: Cancer Research (2024)

Abstract Modifications of histone tails control chromatin structure, and the acetylation is generally associated with euchromatin and transcriptional activation. Acetylated lysine residues are recognized by bromodomains, which serve as acetyl-lysine binding modules and participate in transcriptional regulation. Bromodomain-containing protein 8 (BRD8) is a subunit of the NuA4/TIP60-histone acetyltransferase complex. Although BRD8 has been considered to act as a co-activator of the complex, its biological role remains to be unclear. In this study, we revealed that BRD8 accumulates in colorectal cancer cells through the inhibition of ubiquitin-dependent protein degradation by the interaction with MRG domain binding protein (MRGBP). RNA-seq analysis coupled with genome-wide mapping of BRD8-binding sites disclosed that BRD8 transactivates a set of genes independently of TIP60, a catalytic subunit of NuA4 complex, and that BRD8 regulates the expression of multiple subunits of the pre-replicative complex (pre-RC) in concert with the activator protein-1 (AP-1) transcription factor. Depletion of BRD8 induced cell-cycle arrest at the G1 phase and suppressed proliferation of colorectal cancer cells. We have also shown that the bromodomain of BRD8 is indispensable for not only the interaction with histone H4 or transcriptional regulation but also its own protein stability. These findings provide a new insight into the roles played by BRD8 in human colorectal carcinogenesis and will contribute to the development of new chemotherapeutic agents targeting the bromodomain of BRD8. Citation Format: Kiyoshi Yamaguchi, Saya Nakagawa, Rui Yamaguchi, Paul Sheridan, Kiyoko Takane, Tsuneo Ikenoue, Satoru Nagatoishi, Hiroko Kozuka-Hata, Masaaki Oyama, Susumu Aikou, Yuka Ahiko, Dai Shida, Kouhei Tsumoto, Satoru Miyano, Seiya Imoto, Yoichi Furukawa. TIP60-independent mechanism of BRD8 is involved in colorectal tumorigenesis [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 5639.
Abstract 3106: Integrated <i>in vitro</i> and machine learning approaches for targeted drug screening in gliomas with concurrent NF1 and ATRX loss
Authors: Swati Dubey, Somesh Mohapatra, Ming Yuan, Charles G. Eberhart, Fausto J. Rodriguez
Journal: Cancer Research (2024)

Abstract Neurofibromatosis type 1 (NF1) frequently precipitates the development of brain and nerve tumors, with subsets of associated solid tumors demonstrating an aggressive phenotype often characterized by alpha thalassaemia mental retardation X-linked (ATRX) loss. In response, we executed an in vitro high-throughput drug screening utilizing a 10,000-compound library in an NF1-associated ATRX mutant glioblastoma cell line (JHH-NF1-GBM1) and in U251 cells with ATRX knockout, mimicking the concurrent loss of ATRX and NF1. The screening protocol aimed to pinpoint compounds selectively targeting vulnerabilities arising from the co-occurrence of ATRX and NF1 loss. To enhance the precision of our results, we employed an unsupervised-supervised machine learning approach. Unsupervised models identified distinctive chemical groups associated with heightened sensitivity in ATRX/NF1-deficient cells. Subsequently, supervised models were trained, and their uncertainty estimates were utilized to further narrow down the selection of hit compounds. We also utilized pre-trained models to predict ADME and toxicity properties, facilitating a further filtration. This multi-step in vitro screening, coupled with in silico analyses, successfully identified promising compounds, subsequently validated through biophysical characterization. The integration of machine learning in our screening pipeline enhances the identification of potential targeted therapies for aggressive tumors (gliomas) characterized by ATRX/NF1 loss, offering a comprehensive and efficient approach to drug discovery in the pursuit of more effective treatments. Citation Format: Swati Dubey, Somesh Mohapatra, Ming Yuan, Charles G. Eberhart, Fausto J. Rodriguez. Integrated in vitro and machine learning approaches for targeted drug screening in gliomas with concurrent NF1 and ATRX loss [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 3106.
Abstract 3112: Colorectum metabolome map revealed etiological and survival heterogeneity in cancers of different subsites: Challenging the proximal versus distal classification
Authors: Abhishek Jain, Caroline Johnson, Domenica Berardi, Sajid Khan, Montana Morris
Journal: Cancer Research (2024)

Abstract Objective: Colorectal cancer (CRC) is usually classified as proximal, distal and rectal cancer. clinicopathological, molecular features and risk factors do not change abruptly and variations exist even among the refined subsites, which may contribute to the failure of mechanism-targeted therapies for CRC and poor accuracy of potential CRC biomarkers. We generated a CRC metabolome map describing etiological and survival heterogeneity in cancers of different subsites of the colorectum. Design: Utilizing 372 tumor tissues with matched normal mucosa liquid chromatography-mass spectrometry was applied to examine metabolomics profiles along 7 subsites of the colorectum: cecum (n=63), ascending colon (n=44), transverse colon (n=32), descending colon (n=28), sigmoid colon (n=75), rectosigmoid colon (n=38) and rectum (n=92). Linear regression showed distribution of metabolites along the subsites. Survival heterogeneity along subsites were statistically tested by cox regression analysis. Metabolome profiles were obtained from invitro cultures of 310 human microbial species. Results: 40 and 76 significantly altered metabolites (including bile acids, lysoPCs and LysPEs) among tumors and normal mucosa showed metabolic heterogeneity existed among CRC subsites. Gradual changes in metabolites abundance with significantly linear trend from cecum to rectum: 23 metabolites in tumor, 30 metabolites in normal mucosa and 15 metabolites in both tumor and normal mucosa, revealed concentration gradient depends on the disease status. Exclusively significant alteration of metabolites only in one subsite showed the differences in cancers among the 7 subsites of colorectum. We identified the metabolites associated with survival were different and unique to each subsite. Integration of microbial metabolome with CRC metabolome revealed microbial metabolites contributed to etiological and survival heterogeneity among CRC subsites. Conclusions: Gradual changes of metabolites from cecum to rectum and the association of different metabolites with CRC risk and survival in each subsite of colorectum, revealed the differences in cancers along the colorectum and challenge the simple classification of CRC in LCC, RCC and rectum. Human microbial metabolites contributed to etiological and survival heterogeneity among CRC subsites. Citation Format: Abhishek Jain, Caroline Johnson, Domenica Berardi, Sajid Khan, Montana Morris. Colorectum metabolome map revealed etiological and survival heterogeneity in cancers of different subsites: Challenging the proximal versus distal classification [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 3112.
Abstract 3113: Development of HTS enzymatic assays for WRN helicase and exonuclease functions
Authors: Ha Pham, Mahbbat Ali, Anibal Ramos Martinez, Robert Lowery
Journal: Cancer Research (2024)

Abstract WRN, a double strand break repair enzyme with ATP-dependent DNA-helicase and 3’- &amp;gt;5’ exonuclease activities, is under intense focus as a therapeutic target because of its synthetic lethality in tumors with microsatellite instability. To accelerate discovery of WRN inhibitors, we developed and validated homogenous, fluorescence-based high throughput assays for WRN helicase and exonuclease enzymatic activities using the Transcreener HTS Assay platform, which relies on highly selective antibodies to detect nucleotides in a homogenous (mix-and-read) format with far red fluorescent readouts. We produced the WRN helicase domain (aa 500-946, N-terminal 6xHis) in BaV-infected insect cells and optimized detection of its dsDNA-dependent ATPase activity using the Transcreener ADP2 Assay in FP, TR-FRET, and FI detection modes. Optimal reaction conditions included 50 μM ATP (approximate Km) and saturating concentration (100 nM) of a 3’ flapped duplex DNA oligomer; these conditions yielded a good signal with 250 pM WRN, a kcat of 300 min−1, and a Z’ of 0.85. An IC50 of 35 nM was determined for the probe inhibitor NSC-617145, and a 1,280 compound pilot screen (Tocris 2.0 Micro) identified multiple hits that were confirmed in dose response experiments. We produced the WRN 3’-5’ exonuclease domain (aa 1-133-6xHis) in E. coli and used the Transcreener dAMP Exonuclease Assay to allow direct, FP-based detection of dAMP monomers released from a 52 bp dsDNA oligomer with a 5’ overhang. With saturating DNA present (1 μM), the assay produced a good signal with 1 nM enzyme; the Z’ value was 0.89. There are no published inhibitors for the WRN exonuclease, but suramin inhibited with an IC50 of approximately 100 nM. These assays allow sensitive, robust, quantitative detection of WRN ATPase and exonuclease activities using an extensively validated HTS platform; they should be valuable tools for screening and optimizing small molecules targeting specific WRN functions. Citation Format: Ha Pham, Mahbbat Ali, Anibal Ramos Martinez, Robert Lowery. Development of HTS enzymatic assays for WRN helicase and exonuclease functions [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 3113.
Abstract 5645: HuR regulates aerobic glycolysis in triple negative breast cancer (TNBC)
Authors: Arundhathi Dev J R, Ajay Gogia, Sandeep R. Mathur, S.V.S. Deo, Chandra Prakash Prasad
Journal: Cancer Research (2024)

Abstract Introduction: The RNA-binding protein Human Antigen R (HuR/ELAVL1) is ubiquitously expressed and exerts post-transcriptional regulation on mRNAs characterized by U/AU-rich sequences in their 3' UTR. Elevated cytoplasmic expression of HuR has been associated with various malignancies, influencing key cellular processes such as proliferation, apoptosis, angiogenesis, and metastasis. The involvement of HuR influences prognostic outcomes and hence is a potential biomarker and therapeutic target in cancer research. The present study investigates the oncogenic role of HuR in TNBCs, an aggressive subtype of breast cancer. Methods: Immunohistochemistry was performed on TNBC patient tumor tissue (n=40) to asses the expressions of HuR and MMP9. Human TNBC cell lines MDA-MB-231 and MDA-MB-468 were used for in vitro studies after confirming cytoplasmic HuR accumulation in these cells via Immunofluorescence. The RNA binding activity of HuR was disrupted using CMLD2, a specific inhibitor of HuR, and subsequent physiological changes were assessed through functional assays. An exploratory investigation of HuR-moderated metabolic changes was performed employing NANOSTRING nCounter XT gene expression assay using metabolic pathways panel. Investigation and/or validation of molecular changes were done via immunoblotting. Results: Meta-analysis using Liu-2014 TNBC dataset correlated high HuR protein expression with reduced patient survival (p=0.028). HuR (77%) and MMP9(55%) were found to be overexpressed in TNBC tissues. Inhibiting HuR with CMLD2 resulted in the downregulation of the protein and its downstream targets CDK2, MMP9, and β catenin. HuR inhibition compromised proliferation, migration, Matrigel invasion and EMT (downregulated E-Cadherin, N-Cadherin, and Vimentin) in TNBC cell lines. Further, HuR inhibition resulted in decreased clonogenicity in 2D and 3D TNBC cultures. Transcriptomics studies showed that HuR inhibition in MDA-MB-231 altered the profile of glycolytic genes in addition to other pathways such as cell cycle and DNA damage repair. In accordance, the expression of glycolytic proteins was reduced upon CMLD2 treatment. Similar results were obtained on HuR knockdown by siRNA suggesting that HuR-mediated effects on TNBC progression might be in part through its modulation of aerobic glycolysis. Conclusion: Overall, our results demonstrate HuR as a positive regulator of aerobic glycolysis in TNBCs and the ability of CMLD2 to inhibit HuR provides a rationale to consider it as a potential anticancer agent for TNBCs. Citation Format: Arundhathi Dev J R, Ajay Gogia, Sandeep R. Mathur, S.V.S. Deo, Chandra Prakash Prasad. HuR regulates aerobic glycolysis in triple negative breast cancer (TNBC) [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 5645.
Abstract 3105: Computational integration with phage library to optimize clones of DEFB4A antibodies for cancer diagnostics and therapeutics
Authors: Yichen Guo, Jina Yom, Andy (Xi) Han, Zhaoying Guo, Eden Zewdu, Rachel Gonzalez, Tianli Qu, Bailey Gilmore, Xuan Liu, Wei Fu, Xiaomin Hu
Journal: Cancer Research (2024)

Abstract DEFB4A, a human beta-defensin, functions as a potential cancer biomarker, with elevated expression observed in various cancers, making it a candidate for diagnostic and prognostic applications. Additionally, its role in immune modulation suggests that DEFB4A may hold promise as a target for novel cancer treatments, particularly in the context of immunotherapy. This study aimed to develop a stable and high-affinity DEFB4A antibody for clinical and pre-clinical use. To achieve this, a combination of high-diversity phage libraries and computation-assisted analysis was employed to generate single-chain variable fragments (ScFv) clones specifically targeting DEFB4A. This research presents a robust approach for the generation of DEFB4A-targeting single-chain variable fragments (ScFv) from a phage library characterized by a high diversity of 109 unique clones and high titer of 1013 cfu/mL. Computational optimization was then applied to enhance the affinity, stability, and expression of these candidates through rational design and virtual mutagenesis programs. The binding activity of the optimized mutants was validated using biophysical methods such as surface plasmon resonance (SPR) and thermal stability assays. The process showed a remarkable 100-fold increase in affinity and stability. Additionally, the selected ScFv clone was further employed in immunohistochemistry (IHC) to detect DEFB4A in breast, prostate, and gastric cancers, showing higher expression levels compared to initial clones. This study highlights the synergy of high-diversity phage libraries and computational methods in crafting DEFB4A antibodies with enhanced affinity, stability, and expression. The findings advance the field of antibody engineering, emphasizing the crucial integration of experimental and computational approaches. This work lays the groundwork for the development of high-performance biologics with diagnostic and prognostic applications across diverse cancer types. Furthermore, it demonstrates the possibility of integrating computational approaches in antibody development, offering the promise of expediting the process in the future. Citation Format: Yichen Guo, Jina Yom, Andy (Xi) Han, Zhaoying Guo, Eden Zewdu, Rachel Gonzalez, Tianli Qu, Bailey Gilmore, Xuan Liu, Wei Fu, Xiaomin Hu. Computational integration with phage library to optimize clones of DEFB4A antibodies for cancer diagnostics and therapeutics [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 3105.