tbuckley/cabot-search huggingface dataset:
Abstract 3138: Discovery of AT65474, a highly selective anti-CLDN6 ADC with a proprietary payload
Authors: Chen Zhong, You Xue Wu, Xi Yun Zhang, Yin Wen Cheng, Qian Wang, Ping Du, Shao Jun Liu, Bin Zou
Journal: Cancer Research (2024)

Abstract CLDN6 is a membrane-bound oncofetal protein and a promising target for cancers such as ovarian and testicular cancer. CLDN6 shares high sequence homology with other CLDN family members which are expressed in normal tissues, making a high degree of selectivity required for CLDN6-targeting therapies. In particular, CLDN6 is closest to CLDN9 in sequence with a difference of only three residues in the extracellular loops, making it challenging to generate a highly selective antibody. We report the development of a humanized anti-CLDN6 antibody with high affinity and high selectivity for targeted cells which displays &amp;gt; 800-fold higher binding affinity for CLDN6 over CLDN9. The antibody was refined for use as an ADC and incorporates AxcynCYSTM technology for site-specific conjugation which can reproducibly achieve high DAR4 ratios of greater than 97% by HIC analysis. AT65474 is an ADC candidate that incorporates a proprietary payload derived from an FDA approved drug that was optimized in-house for increased potency and improved PK properties to limit systemic exposure. In vitro, the payload displays broad sub-nanomolar activity across a wide range of cancer cell lines including those resistant to paclitaxel, DM1, MMAE and DXd. The payload is conjugated via an enzyme-cleavable linker optimized for solubility, stability, and high drug to antibody ratios. We provide evidence characterizing AT65474 as a highly potent ADC with high DAR4 homogeneity and strong in vivo activity at low doses. Compared with a benchmark ADC in clinical development, AT65474 shows stronger binding, higher internalization, superior in vitro cytotoxicity, and stronger bystander killing effect. When evaluated in PA-1 and OV90 xenograft models of ovarian cancer, AT65474 displays significantly higher efficacy over the benchmark ADC. Furthermore, we show that AT65474 displays an ADCC effect that contributes to tumor suppression in the OV90 model. AT65474 was shown to be well tolerated in all xenograft mouse models and a pre-tox study in non-human primates. The combined data support further development of AT65474.​ Citation Format: Chen Zhong, You Xue Wu, Xi Yun Zhang, Yin Wen Cheng, Qian Wang, Ping Du, Shao Jun Liu, Bin Zou. Discovery of AT65474, a highly selective anti-CLDN6 ADC with a proprietary payload [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 3138.
Abstract 6646: Investigating the combination of radiation and subsequent immune checkpoint inhibitor treatment in head and neck squamous cell carcinoma models
Authors: Hanne Lind, Alexander Strait, Spencer Hall, Jack B. Goon, John D. Aleman, Samantha Chen, Philip Owens, Jing H. Wang, Christian Young, Xiao-Jing Wang
Journal: Cancer Research (2024)

Abstract Purpose: Head and neck squamous cell carcinoma (HNSCC) is often marked by an immunosuppressive tumor microenvironment, which contributes to the dismal 10-20% response rate to immune checkpoint inhibitor (ICI) therapy in HNSCC patients. Radiotherapy (RT) is a currently standard of care and frontline therapy for HNSCC, yet resistance is common. We sought to examine the combination therapy of RT followed by ICI therapy to test if RT induces an in situ vaccination which enhances the efficacy of subsequent ICI. Methods: We utilized SCC cell lines derived from K15.KrasG12D/Smad4−/− SCCs, which mimic the progression of HPV-unrelated HNSCC, and transplanted SCC cells into immune-competent C57BL/6J mouse recipients. Mice were subjected to RT followed by anti-PD-L1/anti-TGFb therapy. CD8+ splenic T cells of responder or non-responder mice were examined by paired single-cell VDJ sequencing and single cell RNA sequencing (TCR/sc-RNAseq) to look for adaptations of the cytotoxic T cell compartment following combination therapy. Responder and non-responder tumor lines or tumors were treated with RT alone in vitro and in vivo, respectively, to examine major histocompatibility complex I (MHC-I) levels on tumor cells. Results: Responders to this combination therapy exhibited complete tumor eradication while non-responders displayed rapid tumor progression. When re-challenged with same HNSCCs cells, responders rejected implanted tumor cells while naïve recipients rapidly developed HNSCCs. Single-cell TCR sequencing of splenic CD8+ T cells revealed that responders, but not naïve recipients exhibited multiclonal CD8+ T cell expansion specifically of memory cell populations. Responder tumor cells exhibited greater levels of MHC-I protein level presentation than non-responders when stimulated with RT. Conclusions: Our data suggest that 1) elevated MHC-I by SCC tumor cells presentation driven by RT and ICI combination therapy facilitate a systemic expansion of memory CD8+ T cell clonotypes which drive anti-tumor immunity and 2) MHC-I expression at baseline or when induced by RT may serve as a predictive marker for therapeutic response to RT and ICI combination therapy in HNSCCs. Citation Format: Hanne Lind, Alexander Strait, Spencer Hall, Jack B. Goon, John D. Aleman, Samantha Chen, Philip Owens, Jing H. Wang, Christian Young, Xiao-Jing Wang. Investigating the combination of radiation and subsequent immune checkpoint inhibitor treatment in head and neck squamous cell carcinoma models [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 6646.
Abstract 5772: Structural insights and rational design, optimization of highly potent and selective novel GRK5/6 inhibitors for cancer therapy
Authors: Yueyi Chen, Amol D. Sonawane, Rajesh Manda, Ranjith K. Gadi, Arun K. Ghosh, John J. Tesmer
Journal: Cancer Research (2024)

Abstract G protein-coupled receptor kinases (GRKs) regulate cell signaling by triggering receptor desensitization via phosphorylation on G protein-coupled receptors (GPCRs). There are seven human GRKs (GRK1−GRK7) where GRK5 and GRK6 are structurally similar. GRK5 is ubiquitous and required for cancer progression in various cancer types. Knock-down of GRK5 has been shown to suppress prostate cancer and non-small-cell lung cancer growth. GRK6 is highly abundant in immune cells and is overexpressed in multiple myeloma (MM). Knocking down GRK6 has been shown to cause apoptosis of MM cells. Therefore, targeting GRK5 or 6 is a potential chemotherapeutic strategy. Currently, we are developing a series of inhibitors for GRK5/6 based on a lead compound derived from sunitinib and utilizing Cys474 residue unique in GRK5/6 to enhance selectivity by covalent capture. We tested a series of novel inhibitor warheads to improve potency and selectivity without potentially toxic functional groups. So far, we have identified several inhibitors with low nanomolar IC50 for GRK5 and more than 100,000-fold selectivity over GRK2, another closely related member expressed in the heart. I have developed a pipeline of X-ray crystallography of GRK5 available for soaking various ligands and have solved several structures of novel inhibitor-bound GRK5. The structure elucidated the binding mode of this new class of GRK5 inhibitors, where the core interacts with the adenine site, a fluorophenyl group stabilizes the P loop and density suggests in some cases covalent bond forming between the reversible covalent warhead and Cys474. Our ongoing studies focus on further compound optimizations based on SAR. Overall, the discovery of the inhibitors can significantly facilitate understanding and treatment and cancers. Citation Format: Yueyi Chen, Amol D. Sonawane, Rajesh Manda, Ranjith K. Gadi, Arun K. Ghosh, John J. Tesmer. Structural insights and rational design, optimization of highly potent and selective novel GRK5/6 inhibitors for cancer therapy [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 5772.
Abstract 2432: Improved liquid biopsy assay performance using sequencing by binding (SBB)
Authors: Dan Nasko, Phillip Pham, Stuti Joshi, Kristi Kim, Nairi Pezeshkian, Young Kim, Alexandra Sockell, Jonas Korlach
Journal: Cancer Research (2024)

Abstract Liquid biopsy is revolutionizing the field of early cancer detection research through non-invasive detection of tumor DNA in the blood. However, existing liquid biopsy assays are limited in their sensitivity for ctDNA detection at low variant allele frequencies (VAFs), with most relying on extreme sequencing depth and computational error correction to separate the true ctDNA signal from background errors. This limitation is particularly problematic in the area of early cancer detection, in which expected ctDNA allele frequencies are extremely low. Novel strategies are therefore needed to help improve liquid biopsy assay sensitivity and reduce per-sample sequencing requirements. Here we describe PacBio’s application of the Onso short-read sequencing system to enable detection of ctDNA at low VAFs using the SeraCare Complete ctDNA Mutation Mix reference standard. The Onso system makes use of a novel sequencing by binding (SBB) method to achieve up to 15x greater quality scores, with ≥90% of reads at Q40 or above. We performed targeted capture and sequencing of libraries prepared from the SeraCare reference mix diluted into WT human DNA at the following VAFs: 0.00% (WT), 0.05%, 0.10%, 0.25%, and 0.50%, and compared the sensitivity at each VAF for SBB compared to a competitor method using sequencing by synthesis (SBS) at varying sequencing depths. We observed superior sensitivity for ctDNA detection at low VAFs (0.05%, 0.1%) using SBB at half the sequencing depth compared to SBS, in part due to reduced false positive calling in the WT sample for SBB. Furthermore, SBB was able to achieve comparable sensitivity results to SBS using four-fold less sequencing, and without the use of computational error correction. Finally, combining SBB with computational error-correction methods boosted sensitivity even further, suggesting an additive value for these technologies. Taken together, our results demonstrate the potential of SBB to improve upon existing methods of liquid biopsy and better enable research on early cancer detection. Citation Format: Dan Nasko, Phillip Pham, Stuti Joshi, Kristi Kim, Nairi Pezeshkian, Young Kim, Alexandra Sockell, Jonas Korlach. Improved liquid biopsy assay performance using sequencing by binding (SBB) [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 2432.
Abstract 7401: High-level multiplexed virtual immunofluorescence staining using holotomography and deep learning
Authors: Juyeon Park, Su-Jin Shin, Geon Kim, Kwang Suk Lee, Ji Eun Heo, YongKeun Park
Journal: Cancer Research (2024)

Abstract Multiplexed immunofluorescence (IF) staining plays a crucial role in cancer research, allowing simultaneous visualization of multiple biomarkers to elucidate complex cellular interactions within the tumor microenvironment. However, the conventional multiplexed IF approach has inherent limitations, characterized by labor-intensiveness and a constrained capacity for high-level multiplexing. These challenges hinder its scalability and comprehensive analysis of intricate molecular landscapes.To overcome the limitations of conventional multiplexed IF, we propose a novel approach that integrates holotomography (HT) and deep learning. HT is a label-free imaging technique that quantitatively measures the refractive index distribution of the specimen without any staining. To provide subcellular specificity to the label-free HT images, HT is integrated with virtual staining. Virtual staining is a deep learning-based framework that converts label-free images to the desired stained images, in this case, from HT images to multiplexed IF images. This synergistic combination of HT and deep learning may address the current limitations of multiplexed IF protocols.Our proposed methodology aims at high-level multiplexed virtual IF staining from label-free cancer tissue slides using HT and deep learning. This approach not only eliminates the need for chemical staining but also enhances the level of multiplexing through computational staining. Specifically, we acquire HT and fluorescence images of stained tissue slides for training. Utilizing this paired dataset, we then employ supervised learning to create a neural network that can map between label-free HT images and corresponding fluorescence images. Subsequently, the trained neural network is applied to label-free tissue slides, inferring fluorescence images without the need for chemical staining.We believe the proposed virtual staining framework will contribute to a more efficient and scalable paradigm for cancer research, facilitating a deeper understanding of tumor biology, and advancing the field of precision medicine. Citation Format: Juyeon Park, Su-Jin Shin, Geon Kim, Kwang Suk Lee, Ji Eun Heo, YongKeun Park. High-level multiplexed virtual immunofluorescence staining using holotomography and deep learning [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 7401.
Abstract 5838: Un-methylation of NUDT21 promotes the development of enzalutamide resistance in prostate cancer by regulation of 3’UTR usage switch
Authors: Shin-Chih (Kenny) Lin, Shih-Chieh Lin
Journal: Cancer Research (2024)

Abstract Enzalutamide, a second-generation anti-androgen drug, is a new treatment option for castration resistant prostate cancer (CRPC) patient. However, almost all CRPC patients develop drug resistance for enzalutamide after six to twelve months of treatment. According to our current findings, 3'UTR usage switches of RNA transcripts were observed in the prostate cancer specimen after acquiring enzalutamide resistance and nudix hydrolase 21 (NUDT21), an alternative polyadenylation (APA) regulator, was overexpressed in the enzalutamide resistant (EnzaR) cells, suggesting its potential role involved in regulation of 3'UTR usage switch. However, the underlying mechanism of how NUDT21 regulates 3'UTR usage switch during the development of enzalutamide resistance is still unclear. Interestingly, a potential mono-methylation (MME) is identified in NUDT21 protein by us, and it has never been examined before. Thus, we hypothesize that MME of NUDT21 may regulate the specificity of 3'UTR usage switch and involve in the development of EnzaR. To test the idea, a monoclonal antibody recognized NUDT21 MME was generated by us. Moreover, protein arginine methyltransferase 7 (PRMT7) was identified to be responsible for adding MME to NUDT21. In addition, androgen treatment increased both expression levels of NUDT21 MME and PRMT7 while decreased the expression level of NUDT21 total form in LNCaP cells via androgen receptor (AR) dependent manner. Next, co-treatment of enzalutamide and PRMT7 inhibitor leaded to increase of un-MME form of NUDT21 and it greatly enhanced the enzalutamide resistance in LNCaP cells. Importantly, binding profile of NUDT21 total form indeed had 3'UTR usage switch from distal to proximal APA site in COUP-TFII transcript after acquiring enzalutamide resistance, while its MME form attenuated this phenomenon. In addition, expression levels of NUDT21 MME and its total form were shown to conversely express in prostate cancer specimens. Finally, un-MME form of NUDT21 promoted the cancer growth in vitro and in vivo while its MME form did not. Taken together, our results suggest that down-regulation of PRMT7 by enzalutamide may lead to decrease of NUDT21 MME level and contribute to develop enzalutamide resistance by causing the 3'UTR usage switch of NUDT21 downstream transcript. Citation Format: Shin-Chih (Kenny) Lin, Shih-Chieh Lin. Un-methylation of NUDT21 promotes the development of enzalutamide resistance in prostate cancer by regulation of 3’UTR usage switch [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 5838.
Abstract 7381: Mathematical modeling and validation of mechanistic target of rapamycin and N-myristoyltransferase signaling pathways in breast cancer
Authors: Abinash Meher, Shailly Varma Shrivastav, Anouska Agarwal, Sheen Dube, Stephanie Portet, Anuraag Shrivastav
Journal: Cancer Research (2024)

Abstract Hormone receptor-positive (HR+) breast cancer (BC) makes up approximately 65% of all breast cancers diagnosed. The prognosis for early-stage disease is excellent with mainstay endocrine therapy (ET). Despite the effectiveness of standard ET, as many as 41% of HR+ early-stage BC diagnosed women will experience distant recurrence. The resistance to endocrine therapy and recurrence is partly attributed to the activation of the insulin pathway and the independence of HR+ BC cells on the ER pathway for their growth. Earlier, we demonstrated the crosstalk between insulin/mTOR and ER pathways. N-myristoyltransferase (NMT) exists in humans in two paralogues (NMT1 and NMT2) that catalyze myristoylation reaction. Recent studies from our laboratory demonstrated that NMTs are downstream targets of insulin and ER pathways. In this study, we have designed mathematical models using differential equations to study the activation of the insulin pathway and its effect on NMT. The mathematical modeling incorporated the partition of cellular organelles and the sequential flow of information with cascades of equations representing signaling reactions. The activated mathematical model was designed by activating the insulin receptor (IR) or insulin-like growth factor receptor (IGF1R) and compared with the control model. The mathematical models were validated by wet lab experiments. The HR+ BC cells (MCF7) were treated with insulin or IGF1 for short term and long term. The expression patterns of NMT1, NMT2, and mTOR were determined by cell fractionation and western blot analysis. The results revealed the correlation between the differential expression patterns of NMTs and the proliferation of MCF7 cells when the insulin pathway was activated by insulin or IGF. The mathematical modeling was validated by simulations and data fittings. The results demonstrated that differential equation-based mathematical modeling could predict the NMT-related oncogenic changes in HR+ BC cells. Citation Format: Abinash Meher, Shailly Varma Shrivastav, Anouska Agarwal, Sheen Dube, Stephanie Portet, Anuraag Shrivastav. Mathematical modeling and validation of mechanistic target of rapamycin and N-myristoyltransferase signaling pathways in breast 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 7381.
Abstract 1768: Investigating oncogene amplifications in brain metastasis of esophageal adenocarcinoma samples
Authors: Nora Lawson, Lingqun Ye, Bo Zhao, Andy Futreal, Kadir Akdemir
Journal: Cancer Research (2024)

Abstract Esophageal Adenocarcinoma (EAC) exhibits a rising incidence and dismal survival rate in the US, primarily attributed to frequent distant metastases. Brain metastasis, though uncommon is an aggressive tumor type, remains poorly understood in EAC. To address this knowledge gap, we conducted a comprehensive analysis of 9 brain metastasis samples, profiling their whole-genome with matched normal and comparing them to the primary EAC tumors, other EAC metastasis types and other brain metastasis types, including the Hartwig Institute and PCAWG. Overall, our sample size comprised over 4,500 tumor whole-genome data and we utilized a uniform data analysis pipeline for robust comparisons between cohorts. Our analysis revealed that brain metastasis samples have significantly higher single-nucleotide variants, however, the structural variant burden in brain metastases closely resembled those observed in the primary tumor. Notably, the incidence of whole genome doubling is significantly higher in brain metastasis compared to other primary cancer types and metastases. This significant difference stems from the higher WGD incidence in primary EACs compared to other tumor types. Mutational signature analysis revealed no significant changes compared to the primary tumor, and we observed an enrichment of SBS 17a/b, previously associated with tumor progression in primary esophageal adenocarcinoma, along with a prevalent presence of the APOBEC mutagenesis signature in most samples. Notably, ERBB2 and TP53 emerged as prominent driver genes present in most brain metastasis samples. We also observed an upregulation of ERBB2 expression in brain metastasis samples. Interestingly, ERBB2 appeared to play a more significant role in brain metastasis progression compared to the primary tumor and other metastasis types, suggesting its potential as a therapeutic target. These findings advance our comprehension of brain metastasis in EAC, providing crucial insights into genomic alterations and mutational processes that could inform future therapeutic strategies and clinical management for this previously understudied metastatic type. Citation Format: Nora Lawson, Lingqun Ye, Bo Zhao, Andy Futreal, Kadir Akdemir. Investigating oncogene amplifications in brain metastasis of esophageal adenocarcinoma samples [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 1768.