tbuckley/cabot-search huggingface dataset:
Abstract 1080: Using genome-wide CRISPR screening to develop novel combination therapies for high-risk Ewing’s sarcoma
Authors: Daenikka Ravindrarajah, Sukriti Krishan, Kayleen Simpson, Twishi Gulati, Belamy B. Cheung, Glenn M. Marshall
Journal: Cancer Research (2024)

Abstract Ewing’s sarcoma (EWS) is an aggressive bone and soft-tissue cancer, characterized by a hallmark fusion oncoprotein comprising the amino terminus of a FET gene and the carboxy terminus of an ETS gene, most commonly (85%), the EWSR1-FLI1 t (11,22) fusion.TK-216 is a first-in-class EWSR1-FLI1 inhibitor currently in phase II clinical trials for EWS. Although TK-216 was designed to target the fusion protein interaction directly, it has demonstrated limited efficacy as a monotherapy. Thus, more effective TK-216 combination therapies are needed. We have used genome wide Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Knockout screening in EWS cells treated with TK-216 to identify novel synthetic lethality. We have identified 97 genes whose deletion potentially enhances the action of TK-216 in EWS cells. We have also identified several druggable targets, such as USP9X and the oxidative phosphorylation (OXPHOS) pathway as synthetic lethal interactions for TK-216. USP9X is known to deubiquitinate and stabilize the EWS-FLI1 fusion protein. USP9X and EWS-FLI1 protein expression levels were found to be positively correlated in EWS clinical specimens. USP9X siRNA-mediated gene silencing reduced EWS cell viability. Most importantly, USP9X siRNA-mediated gene silencing sensitized EWS cells to TK-216 treatment. In addition, inhibition of USP9X with a small-molecule inhibitor WP1130, led to significant cell death in EWS alone and in combination with TK-216 with wide therapeutic indices. The molecular mechanism of synergy and in vivo efficacy of the novel TK-216 combination will be determined in our study for future clinical translation. Citation Format: Daenikka Ravindrarajah, Sukriti Krishan, Kayleen Simpson, Twishi Gulati, Belamy B. Cheung, Glenn M. Marshall. Using genome-wide CRISPR screening to develop novel combination therapies for high-risk Ewing’s 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 1080.
Abstract 102: LMP1-mediated recruitment of ALIX directs exosomal PD-L1 sorting and contributes to immunosuppression in EBV+ nasopharyngeal carcinoma
Authors: Fajian He, Yan Gong, Yajuan Zhou, Conghua Xie
Journal: Cancer Research (2024)

Abstract Epstein-Barr virus (EBV) is known to cause multiple cancers and plays a pivotal role in tumor immune evasion. Latent membrane protein 1 (LMP1) is a key viral oncoprotein expressed in most EBV-associated cancers and contributes to tumor microenvironment remodeling. However, the exact role of LMP1 in modulating tumor immunity remains unclear. In this study, we elucidate how LMP1 interacts with PD-L1 and ALIX to form a trimolecular complex, facilitating the selective sorting of PD-L1 into exosomes and consequently impairing CD8+ T cell function in nasopharyngeal carcinoma (NPC). Specifically, the transmembrane domain of LMP1 interacts with and stabilizes PD-L1, while the intracellular domain of LMP1 binds to ALIX, thus enabling access to the exosomal secretory pathway. This interaction leads to the formation of a trimolecular complex comprising LMP1, PD-L1, and ALIX, which is indispensable for the exosomal trafficking of PD-L1. Importantly, disrupting ALIX significantly diminishes LMP1-induced exosomal PD-L1 secretion, thereby restoring CD8+ T cell functionality. Furthermore, we found that elevated levels of LMP1/ALIX expression are positively associated with immunosuppressive characteristics and poorer outcomes in human NPC. Our findings highlight the crucial role of the LMP1/ALIX axis in exosomal PD-L1 sorting and EBV-mediated immune evasion, presenting a novel and promising target for cancer immunotherapy. Citation Format: Fajian He, Yan Gong, Yajuan Zhou, Conghua Xie. LMP1-mediated recruitment of ALIX directs exosomal PD-L1 sorting and contributes to immunosuppression in EBV+ nasopharyngeal 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 102.
Abstract 4178: Non-invasive shortwave infrared imaging of cytotoxic T lymphocyte infiltration for monitoring responses to combination immunotherapy and chemotherapy
Authors: Jay V. Shah, Jake N. Siebert, Xinyu Zhao, Shuqing He, Richard E. Riman, Mei Chee Tan, Mark C. Pierce, Edmund C. Lattime, Vidya Ganapathy, Prabhas V. Moghe
Journal: Cancer Research (2024)

Abstract Although triple-negative breast cancer (TNBC) can be treated with anti-PD-1 checkpoint immunotherapy in combination with chemotherapy, there remains a challenge in effectively monitoring therapeutic responses. Current non-invasive clinical imaging tools to evaluate response to treatment are reliant upon measurements of tumor volume and may fail to distinguish true progression from increased immune cell infiltration. Invasive biopsy sampling and immunohistochemistry (IHC) can elucidate changes in the immune landscape of treated tumors, but these methods are not conducive to providing real-time information. This study presents shortwave infrared (SWIR) imaging as a potential tool to detect treatment-induced cytotoxic T lymphocyte (CTL) infiltration non-invasively and in real time using rare earth metal-doped nanoparticles encapsulated in human serum albumin nanocomposites (ReANCs). ReANCs were chemically conjugated with anti-CD8α antibodies as targeting ligands to facilitate binding of the nanoprobes to CTLs with high specificity in a syngeneic mouse model of breast cancer. After treating the mice with combination anti-PD-1 and doxorubicin, volumetric analysis of the mammary fat pad tumors did not show any significant impact of treatment compared to single treatment and untreated control mice. However, increased CTL infiltration in the tumors of mice that received combination treatment was detected by in vivo SWIR imaging. CTL infiltration was validated with ex vivo IHC staining, and a monotonic relationship was observed between SWIR fluorescence and CD8 positivity. IHC staining of other immune markers, including CD45, CD3, CD4, and PD-L1, showed that combination treatment may influence in the expression of these markers, presenting additional targets that could be imaged with ReANCs in the future. In conclusion, the increase in SWIR signal from CD8-targeted ReANCs in tumors treated with combination immunotherapy and chemotherapy and the relationship with IHC staining highlight the ability to use SWIR imaging for non-invasive assessment of changes in immune dynamics following treatment. Citation Format: Jay V. Shah, Jake N. Siebert, Xinyu Zhao, Shuqing He, Richard E. Riman, Mei Chee Tan, Mark C. Pierce, Edmund C. Lattime, Vidya Ganapathy, Prabhas V. Moghe. Non-invasive shortwave infrared imaging of cytotoxic T lymphocyte infiltration for monitoring responses to combination immunotherapy and chemotherapy [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 4178.
Abstract 4141: Quantitative measurement of 3D tumor spheroid invasion using live cell time-lapse imaging
Authors: Grace Yang, Tian Wang, Peifang Ye, Xiaoyu Zhang
Journal: Cancer Research (2024)

Abstract 90% of the death of cancer individuals is related to cancer metastasis1. The invasion and migration of cancer cells into surrounding tissues and chambers is the first step of metastasis2. To have a better and more in-depth understanding of the pathophysiological activities involved in metastatic cancer, accurate and reliable methods for evaluating cell invasion are urgently needed. Compared to the 2D cell model, the 3D system mimics the natural physiological properties and conditions, such as structure, physiology, biological signals of living tissues, cell-matrix interactions4. In this study, we followed the commonly used protocol for 3D tumor invasion assay3 to generate spheroids in Ultra-Low-attachment (ULA) round bottom 96-well plate and subsequently embedded them in Matrigel® (5 mg/mL). After polymerization, the Matrigel that contains tumor spheroid was submerged in 100 μL cell culture media. The invasion of the 3D spheroid in the presence or absence of drug treatment was monitored and quantified using the brightfield and fluorescence live cell time-lapse image acquisition and image analysis functions of the Agilent xCELLigence RTCA eSight. The progress of spheroid invasion and the drug-inhibitory effects on tumor invasion were quantified by tracking and calculating the area of invasive protrusion from the spheroid. Our data show that 1) different types of cancer cells had different metastatic potentials demonstrated by the level of invadopodium extending into the Matrigel at desired time points; 2) the invasion of 3D HT1080 spheroid was inhibited by cytochalasin D (Cyto D), an inhibitor of actin polymerization, and GM6001, a potent broad-spectrum inhibitor of matrix metalloproteinases (MMP), in a dose-dependent manner; 3) Cyto D exhibited higher efficacy of inhibiting tumor invasion than GM6001. In summary, our approach by combining the 3D tumor spheroid invasion model with the RTCA eSight’s capability of live cell imaging and automatic quantification of the area of invasive protrusion can facilitate and enhance the development of new treatments at the preclinical stage in the future. Citation Format: Grace Yang, Tian Wang, Peifang Ye, Xiaoyu Zhang. Quantitative measurement of 3D tumor spheroid invasion using live cell time-lapse imaging [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 4141.
Abstract 6569: KLIPP: Precision targeting of cancer with CRISPR
Authors: Mats Ljungman, Huibin Yang, Radhika Suhas Hulbatte, Natalie Gratsch, Alan Kelher, John Raupp, Yin Wang, Kristen Hong Dorsey, Troy Halseth, Anna Schwendeman, Philip Palmbos
Journal: Cancer Research (2024)

Abstract Current cancer therapeutic treatments are typically associated with significant collateral damage to normal tissues and the emergence of treatment resistance. Thus, there is an unmet need to develop therapies that are uniquely cancer specific and unhindered by the emergence of resistance. We have developed an RNA therapy approach based on CRISPR technology, known as “KLIPP”, that targets cancer-specific structural variant junctions (SVJs), a so far untapped cancer “Achilles heel”, that are highly abundant across cancer types. KLIPP uses a “split enzyme” system consisting of dCas9 conjugated to an endonuclease, Fok1, that requires dimerization for its activity. By designing sgRNAs that bind to sequences flanking the cancer-specific SVJs, Fok1-dCas9 dimers are formed, leading to the induction of DNA double strand breaks (DSBs) specifically at SVJs in cancer cells. We verify induction of DSBs by γH2AX foci staining in the nucleus of KLIPP-treated cells and resulting loss of clonogenic survival and induction of apoptosis, while cells lacking the targeted SVJs are unaffected. Importantly, we show elimination of orthotopic bladder cancer tumors in vivo after turning on expression of the KLIPP reagents by doxycycline in the drinking water. Finally, we show successful lipid nanoparticle delivery of KLIPP reagents to orthotopic bladder tumors in vivo using catheter-mediated delivery, leading to specific targeting of bladder cancer cells. Independently of the cancer-driving mutations, the omnipresence of cancer-specific SVJs is exploited by KLIPP to force cancer cells into apoptosis while leaving normal cells unperturbed. We believe that the successful implementation of precision KLIPP therapy could be transformative for the treatment of cancer patients. Citation Format: Mats Ljungman, Huibin Yang, Radhika Suhas Hulbatte, Natalie Gratsch, Alan Kelher, John Raupp, Yin Wang, Kristen Hong Dorsey, Troy Halseth, Anna Schwendeman, Philip Palmbos. KLIPP: Precision targeting of cancer with CRISPR [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 6569.
Abstract 309: AHNAK nucleoprotein 2 tune oxidative stress and resistance to chemotherapy in triple negative breast cancer
Authors: Na Hao
Journal: Cancer Research (2024)

Abstract Background: Resistance to chemotherapy is a major reason for the poorerprognosis in patients with triple negative breast cancer (TNBC). Growing evidence suggests that oxidative stress induced by reactive oxygen species (ROS) is an important factor in both tumourprogression and responses to chemotherapies, however, many signalling pathways and key molecular underlying the regulation of cancer cells to the ROS metabolism remains unclear. Aim: (i) To investigate the mechanistic role of AHNAK nucleoprotein 2 (AHNAK2) in TNBC and its links with breast cancer mortality, particularly caused by chemotherapeutic resistance; and (ii) to test a hypothesis that AHNAK2 facilitates the abnormal activation of ROSscavenging system, result in the resistance to chemotherapy in TNBC. Methods: The expression level of AHNAK2 was determined by immunohistochemical staining and analysed the mRNA expression profiles from The Cancer Genome Atlas of triple negative breast tumors. Roles of AHNAK2 in cancer cell growth, metastasis, chemotherapeutic resistanceand activation of oxygen scavenging systemwere determined by molecular and cell biology methods. A jetPEI nanocarrier was used as the vehicle for anti-AHNAK2 siRNAs in mouse models of cancer therapeutics. Results: AHNAK2 is a novel triple negative breast cancer target, which is overexpressed in TNBC tissues and significantly associated with clinical pathology of chemotherapeutic resistance and poor prognosis of tumour patients. Mechanistically, AHNAK2 antagonizes the ROS accumulation induced by epirubicinvia activating JAK-STAT signaling pathway and transportingphosphorylated STAT1 &amp; STAT4 to the nucleus to promote the expression of SOD2, a key gene in ROS metabolism.And epirubicin enhanced AHNAK2 expression by induced the accumulation of ROS,which hence the Sp1-driven transcription of AHNAK2,result inde novo resistance. Furthermore, AHNAK2-specific siRNAs encapsulated by jetPEI nanocarriers prominently inhibit tumor growth and epirubicin-induced resistance in vivo. Conclusions: AHNAK2 plays a key role in resistance to chemotherapyby regulating the oxidative stressand ROS metabolism,representing a future biomarker and therapeutic target of TNBC. Citation Format: Na Hao. AHNAK nucleoprotein 2 tune oxidative stress and resistance to chemotherapy in triple negative 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 309.
Abstract 3094: Biophysics in kinase drug discovery programs: Spectral shift technology from fragment screening to mechanism of action
Authors: Celine Legros, Vanessa Porkolab, Maud Sigoillot, Olivier Mirguet
Journal: Cancer Research (2024)

Abstract Using Eurofins Discovery’s state-of-the art Hit-Finding platform, our experts designed an optimized screening cascade combining cutting-edge High-throughput Screening (HTS) technologies with the latest Biophysics techniques. With advanced technologies, such as the Echo® MS and RapidFire MS for HTS, and SPR, MST, TSA, nanoDSF and ITC for Biophysics, the cascade is effective for primary screening, orthogonal assays and evaluating Mechanism of Action (MoA). There are many biophysical approaches which bring value to drug discovery programs, and it is the target properties which drive the selection of the most suitable technology. In this presentation, we will highlight the novel Spectral Shift technology, one of the techniques employed by the Dianthus (well-known for the MST-TRIC). The goal was to rapidly implement an assay that monitors the ability of PIM3 to bind to ATP, as well as to compounds and fragments in solution. Using the Echo MS’ acoustic-droplet ejection, nanoliter dispensing in 394-well plates, robust data by Spectral Shift were quickly generated for the fragment-based screening campaign. Hits were confirmed in Dose-response with µM-range affinity values (KD), and TSA was used as an orthogonal assay for the identification of stabilizers among the selected PIM3 binders. For a defined set of 826 proprietary fragments, a single dose screening at 600µM using Spectral Shift was run, leading to the identification of 11% of potential binders. The 100 fragments were then confirmed in dose-response titration and 80 binders were confirmed. The top 30 binders were selected for orthogonal characterization using TSA. This led to the selection of the top 6 confirmed fragments, on which a MoA study in MST-TRIC was performed. Following this evaluation, 3 allosteric binders were identified, with KD from 355 to 550µM (affinity of orthosteric binders from 55 to 333µM). Biophysics plays an important role in drug discovery by qualifying valuable assets and increasing the success rates of future Hit-finding programs. The fragment hits selected in this PIM3 Kinase project, which show ADP-Glo™ activities, are now ready for crystallography studies (NMR &amp; X-ray co-crystallization). Citation Format: Celine Legros, Vanessa Porkolab, Maud Sigoillot, Olivier Mirguet. Biophysics in kinase drug discovery programs: Spectral shift technology from fragment screening to mechanism of action [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 3094.
Abstract 3084: Aldob regulates fructose metabolism to confer ferroptosis and immune response in colorectal cancer harboring microsatellite instability
Authors: Yu-Chan Chang, Chi-Long Chen
Journal: Cancer Research (2024)

Abstract Microsatellite instability (MSI) is a genetic alteration that occurs during cancer progression, specifically in colorectal cancer. Objective evidence demonstrates that colorectal cancer patients with MSI have better survival rates than those without MSI. Moreover, patients with both dMMR and MSI respond equally well to immunotherapy. We evaluated the MSI status of colorectal cancer specimens and identified an activation of aldolase B (ALDOB), the primary regulator of fructose metabolism, in the MSI group. Our analysis of the cancer cell panel revealed that the expression level of ALDOB in MSI+ cells (HCT116 and LoVo) was significantly higher than that in the microsatellite stable (MSS) group (SW480 and HT29). We also discovered a significant negative correlation between ALDOB and numerous dMMR-related genes, such as MLH1 and MSH2. We investigated how fructose concentration and pathway activation affected MSI occurrence. Our results demonstrated that abnormal fructose metabolism leaded to SLC7A11-mediated ferroptosis. SLC7A11 functioned as the active subunit and generated glutathione, GPX4, and lipid epoxides in response to transported cystine. This may explain the better clinical outcomes observed in colorectal patients with MSI. On the other hand, we also observed that ALDOB could increase certain immune ratios, such as CD4+ T cells and B cells. This aligns with the implementation of immunotherapy in the MSI community, which has been proven to yield positive effects. Consistent results were still being shown. Our study revealed significant increases in various chemokines and cytokines in media conditioned with fructose. It was interesting to note that fructose resulted in more significant changes than glucose. Based on the gathered evidence, it could be posited that ALDOB plays a crucial role as a promoter of fructose metabolism, leading to the induction of ferroptosis and immune responses in MSI colorectal cancer. The findings shed new light on known consequences and provide new avenues of information. Citation Format: Yu-Chan Chang, Chi-Long Chen. Aldob regulates fructose metabolism to confer ferroptosis and immune response in colorectal cancer harboring microsatellite instability [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 3084.
Abstract 4756: Targeting DNA topoisomerase II to manage acquired resistance to third generation EGFR tyrosine kinase inhibitors in the treatment of EGFR mutant NSCLC
Authors: Zhen Chen, Karin A. Vallega, Dongsheng Wang, Zihan Quan, Songqing Fan, Qiming Wang, Ticiana A. Leal, Suresh S. Ramalingam, Shi-Yong Sun
Journal: Cancer Research (2024)

Abstract Development of effective strategies to manage the inevitable acquired resistance to osimertinib, a 3rd generation EGFR inhibitor with proven clinical efficacy in prolonging survival of patients with EGFR mutant (EGFRm) non-small cell lung cancer (NSCLC), is an urgent and critical area of unmet need in the clinic. Effort toward this direction led us to find that the DNA topoisomerase II (Topo II) inhibitors, doxorubicin and etoposide (VP-16), but not other chemotherapeutic agents, synergistically decreased the survival of osimertinib-resistant cell lines when combined with osimertinib. The combination of osimertinib with either doxorubcin or VP-16 effectively induced DNA damage and apoptosis in osimertinib-resistant cells, suppressed the growth of osimertinib-resistant tumors, and delayed the emergence of acquired resistance to osimertinib. Mechanistic studies found that osimertinib as well other EGFR-TKIs effectively decreased Topo IIα levels in EGFRm NSCLC cells by facilitating its proteasomal degradation and induced DNA damage; these effects were lost in cell lines with osimertinib acquired resistance that possessed elevated basal levels of Topo IIα. In the majority of EGFRm NSCLC tissues relapsed from EGFR-TKI treatment, Topo IIα levels were substantially increased. Enforced expression of ectopic TOP2A genes in sensitive EGFRm NSCLC cells conferred resistance to osimertinib in inducing DNA damage and apoptosis, whereas knockdown of TOP2A in osimertinib-resistant cell lines restored their responses to undergo osimertinib-induced DNA damage and apoptosis. Together, these results reveal a previously undiscovered essential role of Topo IIα modulation in regulating the responses of EGFRm NSCLC cells to osimertinib, providing scientific rationale for targeting Topo II to manage acquired resistance to osimertinib and possibly other third generation EGFR-TKIs, thus warranting clinical validation of this strategy. (This study was supported by NIH/NCI R01 CA223220 and UG1 CA233259 and Emory Winship Cancer Institute lung cancer research pilot funds). Citation Format: Zhen Chen, Karin A. Vallega, Dongsheng Wang, Zihan Quan, Songqing Fan, Qiming Wang, Ticiana A. Leal, Suresh S. Ramalingam, Shi-Yong Sun. Targeting DNA topoisomerase II to manage acquired resistance to third generation EGFR tyrosine kinase inhibitors in the treatment of EGFR mutant 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 4756.