tbuckley/cabot-search huggingface dataset:
Abstract 2102: Understanding the mechanism of action of rigosertib in recessive dystrophic epidermolysis bullosa-associated squamous cell carcinoma through single cellanalysis
Authors: Andrew P. South, Suhao Han, Paolo Fortina
Journal: Cancer Research (2024)

Abstract The allosteric inhibitor rigosertib (an experimental therapeutic) was previously identified as an effective inducer of G2M arrest and apoptosis in squamous cell carcinoma (SCC) keratinocytes isolated from patients with the rare genetic disease recessive dystrophic epidermolysis bullosa (RDEB), both in vitro and in vivo. Early clinical trial data treating RDEB-associated SCC with rigosertib has shown remarkable efficacy in a sub-set of patients and understanding the mechanism of action of rigosertib in this lethal cancer would provide rationale for patient stratification. Multiple mechanisms of action were previously attributed to rigosertib, including polo-like kinase-1 (PLK1), PI3-kinase, activated RAS and microtubule polymerization inhibition. Our published data comparing PLK1 siRNA with PI3-Kinase inhibitors, MAPK inhibitors and microtubule disruption favored PLK1 as a mechanism of action without definitive conclusion. We therefore sought to determine the mechanism of action using transcriptomic profiling. Flow cytometry experiments identified three main categories of time to increase G2M in nine separate RDEB SCC keratinocyte populations in culture ranging from 1 to 6 hours after exposure to 1uM rigosertib. Bulk-RNA sequencing of representative populations from time to G2M groupings failed to identify consistent transcriptional change after exposure to rigosertib. However, single cell sequencing was able to identify increases in sub-populations of cells associated with G2M as well as transient emergence of unique populations that were specific to individual patient populations after exposure to rigosertib in culture. Of note a transient population of RDEB SCC keratinocytes only present after 1 hour of exposure to rigosertib was characterized by increased expression of the potassium regulator KCNRG which has previously been associated with apoptosis in chronic lymphocytic leukemia. Ongoing work is determining the role this gene may play in the mechanism of apoptosis induction in RDEB SCC keratinocytes after exposure to rigosertib. Citation Format: Andrew P. South, Suhao Han, Paolo Fortina. Understanding the mechanism of action of rigosertib in recessive dystrophic epidermolysis bullosa-associated squamous cell carcinoma through single cellanalysis [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 2102.
Abstract 5034: Analytic validation of an ultra-sensitive tumor-informed circulating tumor DNA assay based on whole genome sequencing
Authors: Josette Northcott, Gabor Bartha, Jason Harris, Shuyuan Ma, Manqing Hong, Qi Zhang, Richard Chen, John Lyle
Journal: Cancer Research (2024)

Abstract Monitoring of circulating tumor DNA (ctDNA) levels has demonstrated utility in the detection of residual and recurrent disease after tumor resection, and as a prognostic indicator of patient outcome following initial therapy, in a wide range of cancers. Here we describe the analytic validation of the NeXT Personal® assay, an ultra-sensitive, quantitative, tumor-informed ctDNA assay for use in patients diagnosed with solid tumors. NeXT Personal utilizes whole genome sequencing (WGS) of tumor and normal samples and advanced noise suppression to accurately identify somatic variants and generate a patient-specific diagnostic panel based on up to ~1,800 single nucleotide variants. This personalized panel is used to test for the presence of ctDNA in the patient’s blood samples. The NeXT Personal validation was performed using 123 matched tumor, normal and plasma clinical sample sets representing 9 cancer types. The assay achieved 100% specificity on donor normal plasma samples with an in silico approach giving us a confidence interval of 99.87% to 100%. The analytical range measurements were performed using two paired tumor and normal cell lines, one of which is a commercially available MRD control. The detection threshold for the analytical range measurement was 1.68 parts per million (PPM) with a limit of detection at 95% (LOD95) of 3.52 PPM. Furthermore, NeXT Personal showed linearity over a range of 0.8 PPM to 300,000 PPM (Pearson correlation coefficient= 0.9998) with a limit of quant (LOQ) of 10 PPM. The assay also demonstrated strong performance across varying cfDNA input amounts from 2 ng to 30 ng. These studies demonstrate that NeXT Personal is an ultra-sensitive, highly specific, quantitative and robust assay, giving it the potential to detect residual disease and recurrence earlier than less sensitive assays. Citation Format: Josette Northcott, Gabor Bartha, Jason Harris, Shuyuan Ma, Manqing Hong, Qi Zhang, Richard Chen, John Lyle. Analytic validation of an ultra-sensitive tumor-informed circulating tumor DNA assay based on whole genome sequencing [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 5034.
Abstract 773: Overexpression of phosphoserine phosphatase (PSPH) in prostate cancer and in tumor microenvironment promotes tumor cell proliferation
Authors: Liankun Song, Noriko Yokoyama, Jun Xie, Yunjie Hu, Zhenyu (Arthur) Jia, Beverly Wang, Dan Mercola, Edward Uchio, Thomas Ahlering, Michael Lilly, Xiaolin Zi
Journal: Cancer Research (2024)

Abstract Reprogrammed cellular metabolism is one of the key features of cancer and tumor microenvironment. L-3-phosphoserine phosphatase (PSPH) is one of the five rate-limiting enzymes in the biosynthesis of serine from glucose that supports cell proliferation. Here, we aim to study the role of PSPH in prostate cancer (PCa) and its tumor microenvironment. We find that PSPH not only is overexpressed in prostate cancer cell lines compared to normal prostate epithelial cells (PrEC) and benign prostate epithelial cells (BPH-1), but also exhibits a higher level in patient-derived carcinoma-associated fibroblasts (CAFs) compared to the matched benign associated fibroblasts (BAFs), which are derived from fresh radical prostatectomy specimens of African American (AA) and European American (EA) men. Notably, MDAPCa2b cells derived from an AA prostate cancer patient and AA CAFs have even higher expression of PSPH protein. The mRNA levels of PSPH are also significantly elevated in prostate cancer tissues in AA men compared to EA men and predict poor survival in PCa patients. Knock-down of PSPH expression significantly inhibits the proliferation and colony formation of prostate cancer cells. Growth of xenograft tumors derived from PSPH knockdown MDAPCa2b cells has also been suppressed markedly. Gene expression profiling revealed that suppression of PSPH expression by shRNAs in LNCaP and MDAPCa2b cells is associated with the regulation of gene expression related to metabolism, immunity, extracellular matrix remodeling, and Ion channels. Similarly, analysis of publicly available PCa RNA seq databases also demonstrates that PSPH amplification or over-expression is associated with alterations of gene expression related to metabolism and immunity. Our results suggest that PSPH is upregulated in prostate cancer cells and their surrounding fibroblasts to support tumor growth via reprogramming metabolic pathways and transcriptomes. Citation Format: Liankun Song, Noriko Yokoyama, Jun Xie, Yunjie Hu, Zhenyu (Arthur) Jia, Beverly Wang, Dan Mercola, Edward Uchio, Thomas Ahlering, Michael Lilly, Xiaolin Zi. Overexpression of phosphoserine phosphatase (PSPH) in prostate cancer and in tumor microenvironment promotes tumor cell proliferation [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 773.
Abstract 6052: Systematic identification of novel targeted protein degradation mechanisms using SITESEEKER® technology
Authors: Christian Dillon
Journal: Cancer Research (2024)

Abstract The rise of Targeted Protein Degradation (TPD) is rapidly changing perceptions about therapeutic target druggability and is rewriting many preconceived notions on drug design. However, the majority of monovalent molecular glue and heterobifunctional degraders in clinical and preclinical development rely predominantly on the recruitment of a single E3 ligase, Cereblon. Arising resistance, toxicities and restricted Protein-of-Interest scope may limit clinical potential, highlighting the need to uncover novel TPD mechanisms. To expand the potential of this modality, we have developed SITESEEKER®, a screening technology operating at substantially greater magnitude of complexity than extant target discovery platforms. SITESEEKER® utilizes computationally-derived encoded mini-protein fragments with huge shape diversity to systematically identify novel degrader mechanisms and define functionally-active binding sites on targets. SITSEEKER® allows for the discovery of targets that may be missed through traditional gene editing or knockdown approaches and can additionally provide valuable mechanistic insights that help to inform, unlock and truncate the path from target ID to drug discovery. We describe the identification of a cache of degrader motifs which showcase the breadth of proteome space yet to be explored within TPD. Moreover, we identify peptide motifs capable of driving degradation in a selective manner with potential to be translated into tissue- or cancer-selective degraders. The functional dependencies of prioritized degraders have been mapped to their cognate E3 ligase using combinatorial screening, giving rise to a number of E3 ligases with potential to be hijacked for TPD. PhoreMost is progressing a pipeline of monovalent and heterobifunctional oncology degrader programs arising from its platform. We demonstrate the effective hijacking of selected E3 ligases, identified by SITESEEKER®, through the discovery of high affinity small molecule binders and subsequent discovery of efficient heterobifunctional degraders against selected Proteins-of-Interest. Citation Format: Christian Dillon. Systematic identification of novel targeted protein degradation mechanisms using SITESEEKER® technology [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 6052.
Abstract 4651: A macrocyclic kinase inhibitor overcomes the compound mutations that cause the resistance to all approved EGFR inhibitors in EGFR-positive lung cancer
Authors: Ryohei Katayama, Ken Uchibori, Makoto Nishio, Naoya Fujita
Journal: Cancer Research (2024)

Abstract EGFR mutant cancers account for 20-30 % of non-small cell lung cancers and show marked sensitivity to EGFR tyrosine kinase inhibitors (TKIs). However, the tumor almost inevitably relapses due to acquired resistance. To date, several EGFR-TKIs have been approved, and the third-generation EGFR-TKI, osimertinib, has been widely used both as first-line therapy and for patients with the EGFR-T790M mutation after 1st or 2nd generation EGFR-TKI therapy. However, the EGFR-T790M+C797S compound mutation confers resistance to all approved EGFR-TKIs. In our previous study, we experimentally demonstrated that brigatinib with anti-EGFR antibody was effective against osimertinib-resistant EGFR-C797S and EGFR-T790M+C797S mutants, and is currently undergoing clinical studies. However, the tumor would relapse because of the acquisition of additional resistance mutations. Here, we first demonstrated the binding mode of brigatinib to the EGFR-T790M/C797S mutant by crystal structure analysis and predicted brigatinib-resistant mutations through a cell-based assay, including N-ethyl-N-nitrosourea (ENU) mutagenesis. We found that clinically reported L718 and G796 compound mutations appeared, consistent with their proximity to the binding site of brigatinib, and brigatinib-resistant quadruple mutants, such as EGFR-activating mutation/T790M/C797S/L718M, were resistant to all clinically available EGFR-TKIs. BI-4020, a fourth-generation macrocyclic EGFR inhibitor plus anti-EGFR antibody, overcomes the quadruple and major EGFR-activating mutants in vitro and in vivo, but not the minor mutants such as L747P. Microsecond molecular dynamics simulations revealed the binding mode and affinity between BI-4020 and the EGFR mutants. This study identified potential therapeutic strategies using new-generation macrocyclic EGFR inhibitor to overcome the emerging resistance mutants. Citation Format: Ryohei Katayama, Ken Uchibori, Makoto Nishio, Naoya Fujita. A macrocyclic kinase inhibitor overcomes the compound mutations that cause the resistance to all approved EGFR inhibitors in EGFR-positive 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 4651.
Abstract 4971: Integrating artificial intelligence and functional precision oncology for individualized cancer therapies
Authors: Fernando Eguiarte-Solomon, Rowan Prendergast, Bianca Carapia, Javier Rodriguez, Kristen Buck, Derrick Gorospe, Elizabeth Valencia, Jose Lopez-Ramos, Itzel Gutierrez, Rafaella Pippa, Yuan-Hung Chien, Warren Andrews, Long Do, Jantzen Sperry, Jonathan K. Nakashima
Journal: Cancer Research (2024)

Abstract Precision oncology seeks to tailor cancer treatments to individual patients. Patient-derived xenografts (PDXs) have emerged as a promising platform for selecting efficacious, personalized therapies and developing new oncology drugs. Here, we present a workflow for selecting and validating treatments for patients with colorectal cancer (CRC) that integrates orthotopic PDX (O-PDX) models, molecular profiling, machine learning, and in vivo pharmacological validation. Of the nine tumor biopsies collected, seven were successfully developed into O-PDX models (78%) with a median time to establishment of 119 days. Models were molecularly profiled for gene expression and were serially passaged to perform orthotopic pharmacology studies to validate test agents selected by oncologists as well those suggested by CertisAITM, a novel ensemble of machine learning models for the prediction of drug response in human cancers. The correlation between CertisAI's predicted therapy responses and the actual observed tumor growth inhibition (TGI) was r = 0.7, encompassing 37 distinct treatments across studies from six patients. This research collectively illustrates that the integration of artificial intelligence with functional in vivo assays offers a powerful platform for precision oncology, enabling the identification and validation of tailored treatments for individual cancer patients. Citation Format: Fernando Eguiarte-Solomon, Rowan Prendergast, Bianca Carapia, Javier Rodriguez, Kristen Buck, Derrick Gorospe, Elizabeth Valencia, Jose Lopez-Ramos, Itzel Gutierrez, Rafaella Pippa, Yuan-Hung Chien, Warren Andrews, Long Do, Jantzen Sperry, Jonathan K. Nakashima. Integrating artificial intelligence and functional precision oncology for individualized cancer therapies [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 4971.
Abstract 6461: Prevalence and implications of potentially pathogenic germline variants among adult patients in the Philippines with solid malignancies who underwent tumor genomic profiling: A multi-institutional, cross-sectional study
Authors: Paula Isabel Gimena Franco, Frances Victoria Que, Jose Jasper Andal, Daphne Ang
Journal: Cancer Research (2024)

Abstract Background: In high income countries, 2-10% of tumor genomic profiling reports reveal incidental pathogenic germline variants. A third of these patients would not qualify for genetic testing based on current guidelines. In South East Asia, despite increased use of outsourced genomic profiling platforms, there are no published studies exploring the prevalence of these potentially pathogenic germline variants (PPGV). Our study determined the prevalence of PPGVs among adult patients with solid malignancies who underwent liquid or tissue-based tumor genomic profiling in the Philippines. Methods: Annotated reports of patients with solid cancers who underwent tumor genomic profiling using FoundationOne or FoundationOne Hemebetween January 2021 to July 2023 were reviewed (Ethical Board ID: SL-23143). PPGVs were identified according to recommendations from American Board of Medical Genetics and Genomics and expert review. PPGV criteria include having a variant allele frequency of &amp;gt;30% and were categorized as: 1) high penetrance gene (HP), founder variant (FV), or variant associated with clinical presentation (VA). Cross-checking the pathogenicity through ClinVar database was also done. Results: Out of 446 patients, 13 PPGV variants were found in 50 (11.2%) patients at a median age of 60.5 years. Of these, 28 (54%) had high penetrance (BRCA1, BRCA2, MSH2, MSH6, MLH1, RAD51C, RAD51D), 24 (46%) patients had VA (APC, SMAD4, CDH1, CDKN2A,PTEN) and two patients with lung cancer had a founder variant (EGFR p.Thr790Met). PPGVs were primarily found in colorectal (42% of 50 patients with PPGVs), breast (16%), ovarian (6%) and lung (6%) cancer patients (p&amp;lt;0.001). HP genes were mostly found in females (71.4%, p = 0.03), driven by BRCA1/2 variants (15 females and 2 males). Conclusions: The presence of PPGVs warrants formal genetic counselling and germline testing. Given the similar prevalence of PPGVs in this study compared with data from other countries, and the diagnostic and therapeutic implications of detecting incidental PPGVs, we underscore the need for cancer genetics to be incorporated into standard oncologic care in the Philippines. Citation Format: Paula Isabel Gimena Franco, Frances Victoria Que, Jose Jasper Andal, Daphne Ang. Prevalence and implications of potentially pathogenic germline variants among adult patients in the Philippines with solid malignancies who underwent tumor genomic profiling: A multi-institutional, cross-sectional study [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 6461.
Abstract 4275: Targeting tumor extracellular matrix to improve response to therapy
Authors: Oliver Matthew Pearce
Journal: Cancer Research (2024)

Abstract Introduction. Building on our previous findings that tumor extracellular matrix (ECM) composition associates with immune cell phenotype (Pearce et al, Cancer Disco, 2018), and ECM can directly educate tumor-associated immune phenotypes (Puttock et al, Nat Commun, 2023), we present here the identification of specific ECM components that associate with tumor immune phenotype, and discuss our approach to target these components as a way to improve anti-tumor immunity and immunotherapy response. Methods. We use a combination of transcriptomics, proteomics, glycomics, and spatial tissue analysis to identify correlations between ECM composition and the immune landscape in breast and ovarian cancers. Correlations are tested within a decellularized tumor model made from patient samples which allow immune cell movement, interaction with ECM, and tumor killing to be measured in real-time. Results. Through our analysis pipeline we have identified a specific ECM molecule that appears to regulate the spatial location of tumor infiltrating CD8 T-cell populations via post-translational modifications that are present on the molecule. Deletion of this molecule in injectable orthotopic murine models dramatically alters the immune landscape within the tumor. Within an in vitro decellularized tumor tissue model the in situ deletion of the ECM molecule drives tumors into an inflamed phenotype which is more responsive to cell-based cancer therapy. Conclusions. Tumor ECM can direct immunity in two ways. These are educating or stimulating immune cells to develop specific phenotypes that tend to be immunosuppressive, and secondly directing the movement of cells within the tissue. These immunosupressive effects can be overcome through small modifications to ECM structure, indicating therapeutics that make subtle changes to ECM composition may be used in combination with current cell-based therapies to improve tumor response. Citation Format: Oliver Matthew Pearce. Targeting tumor extracellular matrix to improve response to 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 4275.
Abstract 4325: CX-4945 (Silmitasertib) induces cell death through impairment of lysosomal utilization in <i>KRAS</i> mutant cholangiocarcinoma cell lines
Authors: Chorong Kim, Da Sol Lee, Minwoo Han, Seonmin Lee, Kyu-pyo Kim, Changhoon Yoo
Journal: Cancer Research (2024)

Abstract Purpose: Macropinocytosis is a non-selective endocytosis that uptakes extracellular substances such as nutrients and macromolecules into the cells. In KRAS-driven cancer such as pancreatic ductal adenocarcinoma, the macropinocytosis and following lysosomal utilization are enhanced to overcome metabolic stress. In this study, we investigated the role of CK2 in micropinocytosis and the following metabolic process in the KRAS mutant CCA cell line. Materials and Methods: The BSA uptake indicating micropinocytosis was performed by flow cytometry using the HuCCT1, cholangiocarcinoma cell line harboring KRAS mutation. To validate macropinosome, the Rab7 and LAMP2 were labeled and analyzed via immunocytochemistry and Western blot. The CX-4945, CK2 inhibitor, was used to investigate the role of CK2 in micropinocytosis and following lysosomal metabolism. Results: The HuCCT1, a KRAS mutant CCA cell line, showed micropinocytosis. Although CX-4945, a CK2 inhibitor, induced morphological changes accompanied by accumulation of intracellular vacuoles and cell death rate, the level of micropinocytosis was not changed. The vacuoles accumulated in the cell were identified as late macropinosomes representing Rab7 before fusion with lysosomes. In addition, the CX-4945 suppressed LAMP2 expression following inhibition of the Akt-mTOR signaling pathway which interrupts mature macropinosome and lysosomal metabolic utilization. Conclusion: These results support the utilization of micropinocytosis as an energy source even in CCA cell line harboring KRAS mutation. The inhibition of CK2, the regulator of macropinosome maturation, by CX-4945, alters lysosome dependent metabolism and leads to cell death in KRAS mutant CCA cell lines. Citation Format: Chorong Kim, Da Sol Lee, Minwoo Han, Seonmin Lee, Kyu-pyo Kim, Changhoon Yoo. CX-4945 (Silmitasertib) induces cell death through impairment of lysosomal utilization in KRAS mutant cholangiocarcinoma cell lines [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 4325.