tbuckley/cabot-search huggingface dataset:
Decoding the glycoproteome: a new frontier for biomarker discovery in cancer
Authors: Kai He, Maryam Baniasad, Hyunwoo Kwon, Tomislav Caval, Gege Xu, Carlito Lebrilla, Daniel W. Hommes, Carolyn Bertozzi
Journal: Journal of Hematology & Oncology (2024)

Abstract Cancer early detection and treatment response prediction continue to pose significant challenges. Cancer liquid biopsies focusing on detecting circulating tumor cells (CTCs) and DNA (ctDNA) have shown enormous potential due to their non-invasive nature and the implications in precision cancer management. Recently, liquid biopsy has been further expanded to profile glycoproteins, which are the products of post-translational modifications of proteins and play key roles in both normal and pathological processes, including cancers. The advancements in chemical and mass spectrometry-based technologies and artificial intelligence-based platforms have enabled extensive studies of cancer and organ-specific changes in glycans and glycoproteins through glycomics and glycoproteomics. Glycoproteomic analysis has emerged as a promising tool for biomarker discovery and development in early detection of cancers and prediction of treatment efficacy including response to immunotherapies. These biomarkers could play a crucial role in aiding in early intervention and personalized therapy decisions. In this review, we summarize the significant advance in cancer glycoproteomic biomarker studies and the promise and challenges in integration into clinical practice to improve cancer patient care.
Abstract 7383: G2PT: Mechanistic genotype-phenotype translation using hierarchical transformers
Authors: Ingoo Lee, Sungjoon Park, Hojung Nam, Trey Ideker
Journal: Cancer Research (2024)

Abstract Motivation: Many machine learning models have been proposed that use genotypes to predict various phenotypes. Recently, these models have focused not only on an accurate prediction but mechanistic interpretation, in that they attempt to describe the hierarchy of biological systems underlying the predicted phenotype. Such models still face major challenges, however, including how to robustly quantify the importance of systems mediating phenotypic outcomes and how to represent the bidirectional flow of information among genes, systems, phenotypes, and cell environment. Results: To address these challenges we introduce G2PT, a general Genotype-to-Phenotype Transformer, which we apply here to the classic G2P problem of modeling tumor cell sensitivity to drugs. We show that the framework of hierarchical transformers can represent biological systems spanning a wide range of physical scales and provide a quantitative assessment of the interplay between biological components important for phenotype prediction. When used to analyze a high-throughput cell screen of 436 drugs exposed to 1,097 cell types, we show that the model achieves good performance in predicting cell sensitivity for 83% of drugs (⍴ &amp;gt; 0.5 in cross-validation). G2PT provides a robust and interpretable model with potential application to many challenges in genotype-phenotype translation. Citation Format: Ingoo Lee, Sungjoon Park, Hojung Nam, Trey Ideker. G2PT: Mechanistic genotype-phenotype translation using hierarchical transformers [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 7383.
Abstract 1371: SLAMF9 promotes tumor progression and immunotherapy resistance by reshaping the tumor microenvironment
Authors: Tao Fan, Chu Xiao, Ziqin Deng, Wenpeng Cai, He Tian, Liyu Wang, Chunxiang Li, Jie He
Journal: Cancer Research (2024)

Abstract Tumor prognosis and immunotherapy efficacy coincides with the infiltration ratio and functional status of immune cells in the tumor microenvironment (TME). Signaling lymphocytes activating molecule factors (SLAMFs) has been reported to play a key role in regulating tumor immunity. Herein, using multi cohorts, in vitro and in vivo experiments, we showed that SLAMF9 worsens tumor and suppresses immune therapy responses by remodeling TME. A pan-cancer analysis showed that SLAMF9 had relatively high transcriptional levels within tumor tissues compared with normal tissues across most cancer types. High SLAMF9 expression is associated with poor prognosis and anti-PD-L1 therapy resistance in advanced clear cell renal cell carcinoma cohorts and metastatic urothelial cancer cohorts. SLAMF9 expression was markedly upregulated in anti-CTLA-4-resistant murine B16 melanoma compared with parental tumors. In particular, SLAMF9 expression was generally negatively correlated with CD8+T cell infiltration score in 12159 patients of 40 cancer types even using different immune cell infiltrating algorithms. Although in vitro experiments have shown that SLAMF9 knockdown has almost no effect on the malignant phenotype of tumor cells, subcutaneous melanoma and lung adenocarcinoma with SLAMF9 deficiency grew slowly, which featured with increased infiltration of CD8+T and PD-1+cells. More importantly, SLAMF9-knockdown significantly increases the sensitivity of subcutaneous melanoma to anti-CTLA-4 inhibitor or anti-PD-L1 antibodies and improved the survival benefits of tumor-bearing mice. This work highlights SLAMF9 as a new target in reshaping the tumor immune microenvironment by controlling the functional status of CD+8 T cells and to improve the efficacy of immunotherapy. Citation Format: Tao Fan, Chu Xiao, Ziqin Deng, Wenpeng Cai, He Tian, Liyu Wang, Chunxiang Li, Jie He. SLAMF9 promotes tumor progression and immunotherapy resistance by reshaping the tumor microenvironment [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 1371.
Abstract 4653: Unraveling the vulnerabilities of targeted therapy-tolerant persister cells in NSCLC
Authors: Donghwa Kim, Dmitry Kuchenov, Aubhishek Zaman, Neal Bennett, Emilio Ramos, Ken Nakamura, Arun P. Wiita, Sourav Bandyopadhyay, Trever Bivona
Journal: Cancer Research (2024)

Abstract Genetic profiling and the development of targeted therapy has improved survival of many cancer patients, but resistance to targeted therapy remains a major barrier to long-term patient survival. To develop more pro-active strategies to improve clinical outcomes, our research focuses on drug-tolerant persister cells that constitute a reservoir of cancer cells that survive and adapt during the initial stage of therapy. These cells typically display therapy resistance in a reversible manner and set the stage for the subsequent emergence of cells with full acquired resistance. We utilized quantitative proteomics to characterize persister cells generated from EGFRmut, KRASmut, and ALKmut non-small cell lung cancer (NSCLC) cell lines after treatment with osimertinib, sotorasib, and lorlatinib, respectively. Integrating proteomics data with network analysis revealed a decrease in the signaling network associated with cell cycle regulation and DNA replication. Meanwhile, persister cells exhibited an enrichment in proteins linked to lysosomes, amino acids, and fatty acid metabolism. The data revealed a consistent metabolic shift in persister cells, with an increased dependence on oxidative phosphorylation (OXPHOS) for ATP generation. Small-scale drug screening was performed based on findings from proteomics and confirmed that persister cells are vulnerable to inhibitors of OXPHOS mitochondrial complexes. Combination treatment of OXPHOS inhibitors and each targeted therapy delayed the emergence of resistance. One complex V inhibitor, Gboxin, selectively inhibited the growth of persister cells. The therapeutic potential of complex V was further validated by CRISPR-based genetic knockdown studies. The metabolic transition in drug tolerant persister cells may serve as a critical adaptive resistance mechanism to provide a survival advantage under targeted therapy-induced stress. Understanding this metabolic shift may lead to new treatments that aim to prevent or delay the onset of acquired resistance in NSCLC. Citation Format: Donghwa Kim, Dmitry Kuchenov, Aubhishek Zaman, Neal Bennett, Emilio Ramos, Ken Nakamura, Arun P. Wiita, Sourav Bandyopadhyay, Trever Bivona. Unraveling the vulnerabilities of targeted therapy-tolerant persister cells in NSCLC [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 4653.
Abstract 6227: A systems biology approach for identifying targetable vulnerabilities in Ewing sarcoma
Authors: Filemon S. Dela Cruz, Prabhjot S. Mundi, Armaan Siddiquee, Kristina Guillan, Daoqi You, Glorymar Ibanez Sanchez, Andoyo Ndengu, Andrea Califano, Andrew L. Kung
Journal: Cancer Research (2024)

Abstract Background: Targeting fusion oncoproteins like the canonical EWS/ETS fusions in Ewing sarcoma remain an elusive challenge. To circumvent these challenges, we have utilized transcriptome-based systems biology approaches that identify targetable Master Regulator proteins (MRs) critical to maintaining the cancer cell state. OncoTarget analysis generates a rank order list of targetable MRs while OncoTreat analysis uses cognate cell lines matched to patient tumors to identify drugs that invert the MR signature. We used OncoTarget and OncoTreat analyses to identify existing drugs which could be repurposed to target MRs active in Ewing sarcoma. Methods: A gene regulatory interactome was developed from 122 pediatric sarcoma samples to enable identification of MR targets using OncoTarget. To enable OncoTreat analysis, 2 cognate cell lines were subjected to high-throughput drug perturbational screens. Cells were treated with sub-lethal concentrations of 335 compounds (FDA approved or investigational drugs). Ex vivo drug screens using PDX-derived cells were performed as a complementary assay to validate predictions. In vivo validation was performed in Ewing sarcoma PDXs. Results: The MR architecture of 3 Ewing sarcoma PDX models was evaluated using OncoTarget. OncoTreat analysis identified 43 drugs predicted to be active in at least 1 Ewing sarcoma PDX while OncoTarget analysis identified 20 MR targets predicted in at least 1 Ewing sarcoma PDX. DOT1L and AURKB were predicted targets across multiple Ewing sarcoma PDXs. Ex vivo screening of dissociated cells from 2 Ewing sarcoma PDXs was performed to select the most potent agents for in vivo validation. Three OncoTreat (clarithromycin, tivozanib and obataclax) and two OncoTarget (DOT1L targeted with EPZ-5676 and AURKB targeted with baracertib) predicted drugs were evaluated in a STAG2 mutant Ewing sarcoma PDX and all demonstrated significant abrogation of tumor growth including complete regression in baracertib-treated animals (p&amp;lt;0.01). Conclusion: These systems biology approaches can identify non-oncogene encoded vulnerabilities in Ewing sarcoma and hold the potential for expanding the number of therapeutic options for tumors driven by untargetable oncoproteins. Citation Format: Filemon S. Dela Cruz, Prabhjot S. Mundi, Armaan Siddiquee, Kristina Guillan, Daoqi You, Glorymar Ibanez Sanchez, Andoyo Ndengu, Andrea Califano, Andrew L. Kung. A systems biology approach for identifying targetable vulnerabilities in Ewing sarcoma [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 6227.
Abstract 4439: Decoding the metabolic symphony TP53 mutation-driven rewiring of cellular metabolism in non-small cell lung carcinoma
Authors: Jiyauddin Khan, Asad Ur Rehman, Ankit Mathur, Naveen Kumar Bhatrajuc, Anannya Tulid, Divya Rajput, Mohammad Askandar Iqbal, Daman Saluja
Journal: Cancer Research (2024)

Abstract TP53 is a critical regulator of major metabolic pathways. Metabolic reprogramming is one of the "hallmarks of cancer" and drives tumorigenesis. Frequent p53mutations not only eradicate tumour suppressor capacities but also confer various activities that impact the alteration of metabolic pathways now regarded as central for tumour development and progression. We selected three hotspot mutants (R175H, R273H and R249S) and wtp53 to evaluate the effects in the human non-small cell lung carcinoma cell line (NCI-H1299). Differential expressions of p53 mutants were observed in normal and glucose/glutamine starvation. However, WTp53 expression was not found to be affected. Under both the glucose and glutamine starvation, inhibition of the cell growth and migratory potential of mutant cells was observed which was more prominent in glutamine starvation. Basal respiration and ATP production in p53-/- R273H and R249S significantly increased under glucose starvation. However, Non-mitochondrial oxygen consumption and maximal respiration were found to be decreased in all the cell lines. Importantly, the cells harbouring mutation R175H increase the glycolysis and TCA cycle. The metabolic intermediates of the urea cycle were found to be increased by nearly fourfold in R273H cells. Indicating increased utilization of the urea cycle instead of the TCA cycle, which has been known to be fueled by glutamine for anaplerosis. This study demonstrates that mutp53 influences several metabolic processes and has an influence on cancer cell aggression under starvation of main carbon sources (Glucose and Glutamine). In starved conditions, cells with p53 mutations enhance mitochondrial activity and use alternative pathways in non-small cell lung cancer cells. This might provide a foundation for the development of more effective targeted therapeutics/pharmacological approaches toward variants of mutant p53. Citation Format: Jiyauddin Khan, Asad Ur Rehman, Ankit Mathur, Naveen Kumar Bhatrajuc, Anannya Tulid, Divya Rajput, Mohammad Askandar Iqbal, Daman Saluja. Decoding the metabolic symphony TP53 mutation-driven rewiring of cellular metabolism in non-small cell lung carcinoma [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 4439.
Abstract 1720: 53BP1 regulates heterochromatin through liquid-liquid phase separation (LLPS)
Authors: Xinran Geng, Youwei Zhang
Journal: Cancer Research (2024)

Abstract As compacted DNA, heterochromatin represses abnormal gene expression by inhibiting DNA transcription and maintains genome integrity by protecting aberrant chromosome segregation. Therefore, abnormalities in heterochromatin function are commonly found in cancer. However, how exactly heterochromatin preserves the genome integrity remains poorly understood due largely to the complex structure of heterochromatin. Recently, increasing evidence suggests that heterochromatin factors, including HP1α, KAP1, and SUV39H1/2, could drive the soluble heterochromatin into phase-separated droplets/condensates to promote gene silencing, which is referred to as liquid-liquid phase separation (LLPS). TP53-binding protein 1 (53BP1) has traditionally been a critical factor in DNA double-strand break (DSB) repair. We recently reported an unexpected finding that under normal growth conditions, 53BP1 regulates heterochromatin function through LLPS, which is independent of its DSB repair function. Our studies reveal a new paradigm in studying 53BP1, heterochromatin, and genome stability. However, an important question remains unanswered: how 53BP1 is recruited to heterochromatin to undergo LLPS and the associated broad biological impact. To address this question, we performed a special crosslinking coupled mass spectrometry to uncover potential factors in the 53BP1 condensates assembled on heterochromatin. We identified many factors associated with DNA methylation and histone modification, which are the two main steps in restoring heterochromatin epigenetic modification. Their interactions with 53BP1 at heterochromatin were confirmed by different approaches. We further focused on one of the key factors, PCNA, and carried out a detailed analysis of the interaction between PCNA and 53BP1 and the role of such interaction in 53BP1 LLPS, DSB repair, and heterochromatin function. These findings reveal the previously uncharacterized function of 53BP1 at heterochromatin during normal DNA replication. Citation Format: Xinran Geng, Youwei Zhang. 53BP1 regulates heterochromatin through liquid-liquid phase separation (LLPS) [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 1720.
Abstract 1911: Dato-DXd mediates anti-tumor activity in preclinical TROP2-expressing intracranial tumor model
Authors: Kristen Jones Jones, Montira Suksomboon, SaraAnn rosenthal, Jacob Gordon, Corinne Reimer, Matthew Sung, Chetan Rane
Journal: Cancer Research (2024)

Abstract Datopotamab deruxtecan (Dato-DXd) is an antibody-drug conjugate (ADC) consisting of a humanized anti-TROP2 monoclonal antibody linked to a potent DNA topoisomerase I (TOP1) inhibitor payload via a plasma-stable, tumor-selective, tetrapeptide-based cleavable linker. Dato-DXd is currently under clinical investigation for the treatment of patients with solid tumors including non-small cell lung cancer (NSCLC), hormone receptor positive (HR+ BC) and triple negative breast cancer (TNBC). Pharmacotherapy of brain tumors can be limiting due to restricted drug delivery across blood brain and blood tumor barrier. Enhertu®, that uses the same DXd ADC technology, has reported clinical activity in patients with brain metastases from HER2+ breast cancer, but very little information is available on what drives ADC biodistribution and activity in CNS-involved cancers. Here, we investigated whether systemically administered ADCs can penetrate the brain microenvironment and mediate anti-tumor activity in a preclinical model. Luciferase-tagged H1373 (TROP2-expressing NSCLC) tumor cells were intracranially implanted into NSG mice. Tumor-bearing mice were dosed with Dato-DXd or matched isotype Control IgG-ADC (DAR4) at 10mpk 7 days or 14 days post intracranial tumor implant. Dato-DXd inhibited intracranial tumor growth better than Control ADC (Day 7: 105% TGI vs 38% TGI; Day 14: 65% TGI vs &amp;lt;10% TGI, respectively, compared to Vehicle). Immunohistochemistry analysis of brain tissue validated localization of Dato-DXd in the tumor, suggesting Dato-DXd can distribute into the local tumor microenvironment in this preclinical tumor model. Additionally, treatment with Dato-DXd provided a significant survival benefit over Control ADC (Median survival of 63 days vs 43 days, P=0.0002). This preclinical study supports the inclusion of Dato-DXd in treatment of patients with CNS-involved tumors. Understanding the pharmacological determinants of Dato-DXd activity in the CNS will help outline strategies to implement Dato-DXd-based treatment of patients with CNS-involved tumors. Citation Format: Kristen Jones Jones, Montira Suksomboon, SaraAnn rosenthal, Jacob Gordon, Corinne Reimer, Matthew Sung, Chetan Rane. Dato-DXd mediates anti-tumor activity in preclinical TROP2-expressing intracranial tumor 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 1911.
Abstract 1436: Cancer associated fibroblast dependency in a model of bladder cancer
Authors: Henkel Valentine, Uttam Satyal, Laura Bukavina, Hassan Uddin, Yousttena Beyamin, Rhea Arya, Philip Abbosh
Journal: Cancer Research (2024)

Abstract Introduction: The relationship between genotype and phenotype in targeted therapy has proven to be crucial for most kinase inhibitors. In bladder cancer, the PI3K/AKT/mTOR pathway is widely activated by mutation but untargeted. Our study focuses on developing an immunocompetent, CRISPR-edited bladder cancer mouse model that mirrors common PI3K/AKT/mTOR mutations. We aim to establish genotype-effective kinase inhibitor pairings using in vitro CRISPR-edited organoids and Cancer Associated Fibroblasts (CAFs) to create a pro-tumorigenic environment in vivo. Methods and Results: Urothelial cells were isolated from the bladder of Rosa26 Lox-Stop-Lox-Cas9/GFP transgenic mice to develop organoids. These organoids were co-edited for Trp53 and Rb1 KO, and further editing of the Pten gene resulted in a nine-fold increase in sensitivity to the kinase inhibitor ipatasertib. Despite successful engraftment into mouse bladder, these edited cells regressed before tumor formation, and intradermal injection did not yield subcutaneous tumors. An alternate model featuring a 9p21 deletion with Trp53 KO also displayed similar regression post-engraftment into bladder or skin. However, co-injection with skin-cancer-derived CAFs subcutaneously yielded palpable subcutaneous tumors that grew for 12 weeks. Enhancing orthotopic model fidelity, we established a BBN bladder-tumor-derived CAF line, leading to the formation of tumors with squamous differentiation upon intramural co-injection with edited organoids. These models displayed immune-excluded architecture and a predominance of M2 over M1 macrophages. Following our accomplishments in establishing bladder tumors, we aimed to enhance our model's adaptability by introducing common PI3K/AKT/mTOR mutations, specifically TSC1/TSC2 KO and Pik3ca hotspots, into our 9p21/Trp53 KO model. While TSC1/TSC2 KO lines exhibited elevated P-S6K signaling, they displayed resistance to Torin 1, Voxtalisib, and Everolimus—kinase inhibitors targeting mTORC1/2. In parallel, we employed CRISPR-mediated HDR to successfully introduce a Pik3ca H1047R hotspot into our 9p21/Trp53 KO model, as evidenced by increased Phosphorylation of AKT compared to wild-type 9p21/Trp53 KO cell lines. Conclusions: Our research establishes the crucial role of CAFs in bladder tumor formation. Our now established customizable model of bladder cancer is suitable for direct targeting by kinase inhibitors while providing a platform for understanding the genotype-phenotype relationship in bladder cancer. Citation Format: Henkel Valentine, Uttam Satyal, Laura Bukavina, Hassan Uddin, Yousttena Beyamin, Rhea Arya, Philip Abbosh. Cancer associated fibroblast dependency in a model of 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 1436.