tbuckley/cabot-search huggingface dataset:
Abstract 2060: Automation of 3D cancer spheroid assay for compound screening
Authors: Oksana Sirenko, Angeline Lim, Astrid Michlmayr, Zhisong Tong, Emilie Keidel, Felix Spira
Journal: Cancer Research (2024)

Abstract Finding efficient drug combinations to treat cancer patients is critical for therapy success. Accordingly, there is a critical need to develop methods for efficient testing drug efficacy to discover new therapeutic targets. 3D cancer models are highly valuable tools for cancer research and drug development. However, the complexity of performing 3D assays remains a hurdle for adopting these methods for compound screening. To alleviate the bottlenecks that come with labor-intensive manual protocols we developed cell culture automation methods using CellXpress.ai instrument. The instrument enables automation of 2D or 3D culture for prolonged complex workflows. The CellXpress.ai provides automated plating, passaging, media exchanges, monitoring organoids, alone with compound treatment and the end point assays with high content image analysis. In the present study we describe full automation of imaging, analysis, and cell culture process which enables scaling up complex 3D cell-based assays and compound screening. As an example of 3D protocol, we automated culture and imaging of colorectal cancer 3D spheroids formed from HCT116 cell line in U-shape low attachment plates. HCT116 cells were expanded in 2D, then spheroids were formed after automated dispensing of cell suspension into U-shape 96 or 384 plates. After 48h spheroids were treated with 12 anti-cancer compounds, at multiple concentrations for 3-5 days, then stained and imaged. Cell plating, compound additions, media exchange, and staining were performed automatically by CellXpressAI instrument. During the culture spheroids were monitored using transmitted light, with immediate analysis of phenotypic changes, including inhibition of growth or spheroid disintegration. For endpoint assay spheroids were stained with combination of Hoechst nuclear stain and viability dyes Calcein AM and EtHD, then imaged, and analyzed for multiple read-outs including spheroid size, marker intensities, and live-dead cell scoring. We observed concentration-dependent inhibition of spheroid growth and cell death in response to anti-cancer compounds and evaluated effective compound concentrations for cytotoxic or cytostatic effects. Cell culture process automation for 3D assays, powered by imaging and image analysis has a potential to bring 3D biology into another level, allowing to increase throughput and reproducibility, and enabling variety of high throughput drug discovery and precision medicine applications. Citation Format: Oksana Sirenko, Angeline Lim, Astrid Michlmayr, Zhisong Tong, Emilie Keidel, Felix Spira. Automation of 3D cancer spheroid assay for compound screening [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 2060.
Abstract 5947: Discovery of ACE-47228211, a highly potent and selective SOS1 inhibitor
Authors: Junmei Wang, Wenqian Li, Sanjeev Kumar, Weitao Pan, Zhiming Wen, Tinggui Yin, Genshi Zhao, Kuo-Long Yu
Journal: Cancer Research (2024)

Abstract Dysregulation of receptor tyrosine kinase (RTKs) and KRAS signaling is the most frequent causes of cancer development and progression. SOS1 is one of the major guanine nucleotide exchange factors (GEFs) that facilitates the conversion of the inactive GDP-bound KRAS “off” state to the activated GTP-bound KRAS “on” state. SOS1 is therefore required for dysregulated RTKs, and wildtype and mutant KRAS proteins to drive cancer cells. In addition, SOS1 plays a crucial role in modulating the reactivation of the RAS/MAPK signaling upon the treatment of RAS/MEK/ERK inhibitors. Thus, blocking SOS1 and KRAS protein-protein interactions could be an effective strategy for targeting KRAS-MAPK driven cancers. Here, we report the discovery of a highly potent and orally bioavailable small molecule SOS1 inhibitor, ACE-47228211. This molecule has a unique novel scaffold. It exhibits an IC50 of 8.5 nM in the SOS1-KrasG12D (GDP) exchange assay and 5.0 nM in cellular ERK phosphorylation assay in H1957 cells. ACE-47228211 at 3 mg/kg (BID) demonstrated significant tumor growth inhibition in MiaPaca-2 KRAS G12C tumor model than MRTX0920 at 50 mg/kg (BID). When combined with Sotorasib (5 mg/kg QD), a Kras G12C inhibitor, ACE-47228211 at 3 mg/kg exhibited synergistic effect similar to MRTX0920 at 50 mg/kg. Further, ACE-47228211 demonstrated synergistic effects with EGFR and FGFR2 inhibitors in RTK mutant tumor models. ACE-47228211 has excellent ADME and physical properties with low risks of hERG, CYP inhibition and drug-drug interactions. The evaluation of ACE-47228211 in a safety panel of 87 targets and a kinase panel of &amp;gt;500 targets shows that this molecule has favorable selectivity and safety profiles. The molecule is currently in IND enabling stage of development. Citation Format: Junmei Wang, Wenqian Li, Sanjeev Kumar, Weitao Pan, Zhiming Wen, Tinggui Yin, Genshi Zhao, Kuo-Long Yu. Discovery of ACE-47228211, a highly potent and selective SOS1 inhibitor [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 5947.
Abstract 2066: Measuring the activity of SMUG1 DNA glycosylase with a novel sSTRIDE-SMUG1 assay
Authors: Karolina Stepien, Franek Sierpowski, Zsombor Prucsi, Szymon Koman, Monika Jarosz, Agnieszka Waligorska, Magdalena Kordon-Kiszala, Kamil Solarczyk
Journal: Cancer Research (2024)

Abstract On average, spontaneous deamination of cytosine to aberrant base uracil happens 70-200 times per human genome per day. These mutagenic U/G mispairs are, however, corrected by error-free base repair (BER) initiated by uracil-DNA glycosylases. SMUG1 (single-strand selective monofunctional uracil DNA glycosylase), as one of the major glycosylases, removes uracil and oxidized pyrimidines from DNA. In spite of the name, SMUG1 removes uracil also from double-stranded DNA. Unrepaired by SMUG1 U/G mispairs are mutagenic, and alterations in SMUG1 expression levels have been linked to cancer development. Low SMUG1 transcripts are associated with poor prognosis in breast cancer and SMUG1 loss has been shown to cause PARPi resistance in HR-deficient background. Hence, tools describing SMUG1 activities in DNA damage response may provide new approaches for cancer cell treatment. We report here the development, optimization and validation of an assay measuring the activity of SMUG1. The new assay is based on the STRIDE platform technology, which enables direct and sensitive detection of single- or double-strand DNA breaks in situ, in fixed cells. sSTRIDE-SMUG1 assay detects DNA nicks localized in close proximity to the SMUG1 protein and can thus be utilized as a direct reporter of its activity. The experiments were performed in HAP1 cells. First, in untreated cells we have shown that the sSTRIDE-SMUG1 signals constitute ca. 1-2% of total single-strand DNA breaks foci detected by the classic sSTRIDE assay variant, while the negative controls have shown that the number of false-positive foci does not exceed 15% of the total number of signals. As expected, treatment of cells with a cytotoxic nucleotide hydroxymethyl-deoxyuridine (hmdU) resulted in an increase in the number of detected sSTRIDE-SMUG1 signals. To verify the specificity of the assay, SMUG1 was knocked-down in HAP1 wild-type cells using siRNA and then the level of sSTRIDE-SMUG1 signals was measured in both untreated and hmdU-treated cells. In all tested conditions, SMUG1 expression silencing has resulted in a decrease in sSTRIDE-SMUG1 foci. We believe that the sSTRIDE-SMUG1 assay can prove to be a very useful solution to study DNA repair mechanisms involving aberrant base excision. Additionally, sSTRIDE-SMUG1 measurements may be of the utmost importance in characterization of agents inducing synthetic lethality or trapping BER intermediates. Citation Format: Karolina Stepien, Franek Sierpowski, Zsombor Prucsi, Szymon Koman, Monika Jarosz, Agnieszka Waligorska, Magdalena Kordon-Kiszala, Kamil Solarczyk. Measuring the activity of SMUG1 DNA glycosylase with a novel sSTRIDE-SMUG1 assay [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 2066.
Abstract 3313: Discovery of a potent, selective, and orally available small molecule for disruption of the SOS1-RAS interaction
Authors: Dong Hyuk Ki, Hana Yu, Donggeon Kim, Yeejin Jeon, Seongin Jo, Joonwoo Nam, Eun-Jung Kim, Sungeun Kim, Hunmi Choi, Jieun Kim, Jihyun Yu, Sungpil Choi, Wooseok Han
Journal: Cancer Research (2024)

Abstract KRAS mutations represent one of the most common genetic alterations in many cancers including non-small cell lung cancer (NSCLC), pancreatic ductal adenocarcinoma (PDAC), and colorectal cancer (CRC). While Sotorasib and Adagrasib, KRAS G12C inhibitors, have received approval, they exhibit limited responsiveness in clinical trials and are not applicable to various other KRAS mutation types. SOS1 (Son of Sevenless 1) functions as a guanine nucleotide exchange factor (GEF) on RAS, facilitating the transition of inactive GDP-bound RAS to its active GTP-bound state. In addition, SOS1 plays a pivotal role in negative feedback by actively contributing to the reactivation of ERK during treatment with inhibitors targeting the RTK/RAS/MAPK pathway. Inhibiting SOS1, which impedes the reactivation of ERK, has the potential to enhance the effectiveness of inhibitors targeting the RTK/RAS/MAPK signaling cascade and prevent the emergence of resistance mechanisms via H-RAS and N-RAS bypass pathways. Therefore, combining the inhibition of SOS1 with inhibitors targeting the RTK/RAS/MAPK pathway may enhance outcomes and mitigate relapse associated with observed resistances. Here, we present the discovery of a potent, selective, and orally bioavailable small molecule SOS1 inhibitor that effectively disrupts the interaction between SOS1 and RAS. It has demonstrated remarkable synergy effects with RTK/RAS/MAPK pathway inhibitors, significantly impeding the growth of tumors carrying KRAS or EGFR mutations in vivo. Overall, our development candidate has demonstrated significant therapeutic potential in combination with inhibitors targeting the RTK/RAS/MAPK pathway for cancers bearing activating mutations in this pathway. Citation Format: Dong Hyuk Ki, Hana Yu, Donggeon Kim, Yeejin Jeon, Seongin Jo, Joonwoo Nam, Eun-Jung Kim, Sungeun Kim, Hunmi Choi, Jieun Kim, Jihyun Yu, Sungpil Choi, Wooseok Han. Discovery of a potent, selective, and orally available small molecule for disruption of the SOS1-RAS interaction [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 3313.
Abstract 3316: LY3962673, an oral, highly potent, mutant-selective, and non-covalent KRAS G12D inhibitor demonstrates robust anti-tumor activity in KRAS G12D models
Authors: Xueqian Gong, Hong Gao, Mark H. Bender, Wenyu Ming, Youyan Zhang, Trent R. Stewart, Chun Ping Yu, Wei Guo Xu, Aurthur Xintian You, Wen Ting Bian, Binghui Li, Tao Wang, Huimin Bian, Manuj Tandon, Andrew Capen, Rachel N. Cavitt, Bryan D. Anderson, Wayne Bocchinfuso, Anke Klippel, Chandrasekar Iyer
Journal: Cancer Research (2024)

Abstract KRAS G12D mutations are activating oncogenic events that occur in approximately 35%, 13%, and 4% of pancreatic, colorectal, and non-small cell lung cancers, respectively, and less commonly in other cancers. We previously demonstrated that LY3962673 is a highly potent inhibitor of KRAS G12D and is selective against wild-type (WT) KRAS in mutant -cell lines and -in vivo models. Here, we describe the mechanism by which LY3962673 inhibits KRAS G12D and report a more comprehensive evaluation of LY3962673 activity across a panel of genetically and histologically diverse cancer cell lines, as well as in multiple patient-derived xenograft (PDX) models. LY3962673 is a non-covalent KRAS G12D inhibitor with high affinity binding to KRAS G12D-GDP (Kd 0.071 nM) compared to KRAS G12D-GTPγS (Kd 26.7 nM). In a panel of cancer cell lines with KRAS G12D mutations, non-G12D mutations or KRAS WT, LY3962673 selectively suppressed MAPK signaling and inhibited the growth of KRAS G12D mutant cancer cells while sparing KRAS WT and non-G12D mutant cells. Sensitivity to LY3962673 varied among the KRAS G12D-mutant cells tested, suggesting that not all cell lines share the same dependence on KRAS G12D for their growth and survival. Furthermore, in multiple KRAS G12D-mutant PDX models representing diverse tumor types, LY3962673 demonstrated anti-tumor activities, ranging from tumor growth inhibition to robust tumor regression. LY3962673 also showed enhanced efficacy when combined with other anti-cancer agents. Taken together, the findings underscore the potential of LY3962673 as a monotherapy or in combination with other anti-cancer agents, as a promising oral therapeutic option for a range of cancer types with KRAS G12D mutations. Citation Format: Xueqian Gong, Hong Gao, Mark H. Bender, Wenyu Ming, Youyan Zhang, Trent R. Stewart, Chun Ping Yu, Wei Guo Xu, Aurthur Xintian You, Wen Ting Bian, Binghui Li, Tao Wang, Huimin Bian, Manuj Tandon, Andrew Capen, Rachel N. Cavitt, Bryan D. Anderson, Wayne Bocchinfuso, Anke Klippel, Chandrasekar Iyer. LY3962673, an oral, highly potent, mutant-selective, and non-covalent KRAS G12D inhibitor demonstrates robust anti-tumor activity in KRAS G12D 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 3316.
Abstract 2684: Pan-cancer neutrophil profiling illuminates anti-tumor antigen-presenting potency
Authors: Ying Cheng Wu, Jiaqiang Ma, Qiang Gao
Journal: Cancer Research (2024)

Abstract Neutrophils, the most abundant and efficient defenders against pathogens, exert opposing functions across cancer types. However, given their short half-life and fragile proliferation, it remains challenging to explore how neutrophils adapt to specific fates in cancer. Here we generated and integrated single-cell neutrophil transcriptomes from 17 cancer types (225 samples, 143 patients). Neutrophils exhibited extraordinary complexity, with 10 distinct cell states along differentiation paths including inflammation, angiogenesis, and antigen presentation. Notably, the antigen-presenting program was associated with favorable survival in most cancers and could be evoked by leucine metabolism and subsequent histone H3K27ac modification. These neutrophils could further invoke both (neo)antigen-specific and antigen-independent T-cell responses. Neutrophil delivery or leucine diet fine-tuned the immune balance to boost anti-PD-1 therapy in various murine cancers. In summary, these data not only unravel the neutrophil divergence across cancers, but also offer therapeutic opportunities such as antigen-presenting neutrophil delivery. Citation Format: Ying Cheng Wu, Jiaqiang Ma, Qiang Gao. Pan-cancer neutrophil profiling illuminates anti-tumor antigen-presenting potency [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 2684.
Abstract 1742: A universal spike-in normalization strategy for CUT&amp;RUN, CUT&amp;Tag and ATAC-seq
Authors: Sarah Traynor, Bradley Townsley, Julianna Weber, Mary Anne Jelinek, Brian Egan, Benjamin Delatte
Journal: Cancer Research (2024)

Abstract The development of simple and efficient genome-wide approaches has recently democratized the study of epigenetics. For instance, CUT&amp;RUN and CUT&amp;Tag were developed as fast and affordable alternatives to ChIP-seq, whereas ATAC-seq readily identifies regions of open chromatin. These methods are ideal to look for genome-wide alterations in chromatin structures but are only semi-quantitative and can miss global changes when performed without normalization spike-ins. In fact, many standard computational pipelines fail to detect a reportedly substantial global H3K27me3 decrease in the presence of GSK126, a therapeutic target for lymphoma and potent inhibitor of the EZH2 methyltransferase. To overcome this challenge, we developed a spike-in approach using Drosophila melanogaster nuclei for normalization of ATAC, CUT&amp;RUN and CUT&amp;Tag experiments using human cells. The addition of the spiked-in nuclei allowed for the detection of the expected global changes in open regions of chromatin (ATAC-seq), H3K27me3 (CUT&amp;Tag), R-loops (CUT&amp;Tag), EED and p53 binding (CUT&amp;RUN) upon treatment of K562 cells with GSK126. By contrast, these same changes were all missed when omitting the spike-in nuclei. This streamlined spike-in normalization strategy can be easily applied to any number of cells and on a large variety of conditions. Citation Format: Sarah Traynor, Bradley Townsley, Julianna Weber, Mary Anne Jelinek, Brian Egan, Benjamin Delatte. A universal spike-in normalization strategy for CUT&amp;RUN, CUT&amp;Tag and ATAC-seq [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 1742.
Abstract 1876: Development of therapeutic antibodies targeting the GLUT-1 transporter to restrict cancer cell growth
Authors: Siret Tahk, Kai Virumae, Korneelia Anton, Paule Hermet, Robin Pau, Mario Plaas, Maiken Abel, Denis Belitškin, Luciano Galdieri, Steven Garner, Jillian Krings, Kaleb Collver, Emily Schultz, Kaitlyne Powers, Alastair King, Francisca Neethling, Anu Planken, Mart Ustav, Joan Terya, Andres Mannik, Mart Ustav
Journal: Cancer Research (2024)

Abstract Background: Upregulated glucose metabolism is one of the strategies cancer cells use to fuel their abnormal cell growth and division. Targeting the cancer-specific glucose transporter GLUT-1 is a promising approach to restrict glucose uptake and challenge the metabolic needs of tumor cells. Antibodies, as opposed to small molecule inhibitors, are an attractive modality to therapeutically target complex muti-pass membrane transporters. Here we report the development of antibodies that very specifically block the function of only GLUT-1. Methods: Monoclonal antibodies against GLUT-1 were generated using virus-like particles. For immunization, chickens were used as they are evolutionarily distant from mammals and can produce antibodies with prolonged CDR3-s in VH, which could facilitate their binding to the limited extracellular region of GLUT-1. Antibody discovery was performed with HybriFree B cell cloning technology followed by functional screens with 2-deoxyglucose uptake interference or cell proliferation measurements. Results: The discovered antibodies specifically bind to GLUT-1 with low nanomolar EC50 values and do not target other glucose transporters. The lead candidate, ICO-33, inhibits glucose uptake and rewires the metabolism of GLUT-1-dependent cancer cells to rely on oxidative phosphorylation. This results in a significantly synergistic cancer proliferation inhibition with ICO-33 and OXPHOS inhibitor combinations in doses that do not inhibit proliferation as single agents. ICO-33 and OXPHOS inhibitor treatment is well-tolerated and demonstrates a drastic tumor growth inhibition in in vivo colorectal and pancreatic cancer models. Conclusions: We describe the discovery of highly specific monoclonal antibodies targeting GLUT-1. We further demonstrate that the restriction of the much-needed glucose uptake by ICO-33 makes cancer cells highly susceptible to OXPHOS inhibitor co-therapy both in vitro and in vivo, validating the antibody as a promising candidate for clinical development. Citation Format: Siret Tahk, Kai Virumae, Korneelia Anton, Paule Hermet, Robin Pau, Mario Plaas, Maiken Abel, Denis Belitškin, Luciano Galdieri, Steven Garner, Jillian Krings, Kaleb Collver, Emily Schultz, Kaitlyne Powers, Alastair King, Francisca Neethling, Anu Planken, Mart Ustav, Joan Terya, Andres Mannik, Mart Ustav. Development of therapeutic antibodies targeting the GLUT-1 transporter to restrict cancer cell growth [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 1876.
Abstract 3329: Development of HM-001 as a therapeutic drug for non-muscle invasive bladder cancer
Authors: Shinji Mima, Monta Sakaki, Noriaki Kiya, Atsunari Kawashima, Norio Nonomura, Chihaya Kakinuma
Journal: Cancer Research (2024)

Abstract HM-001 is a drug containing sodium chlorite as the active ingredient that is being developed as a drug for non-muscle invasive bladder cancer (NMIBC), and is currently undergoing physician-led clinical trials. It has been discovered that sodium chlorite generates radicals in an acidic environment, and phosphatidylserine on the surface of tumor cells acts as a Lewis acid to generate radicals. HM-001, like other anticancer drugs and BCG, is intended to be injected into the bladder, retained, and then excreted. GLP studies using the same administration method has been completed, and no toxic changes have been observed in human trial doses. The efficacy of HM-001 against NMIBC was evaluated using an orthotopic transplantation model of UM-UC-3, a bladder cancer cell line. In the model, cells were transplanted into the bladder of SCID mouse after epithelial removal with trypsin, 600, 800, 1,600, and 3,200 ppm of HM-001 were administered once a week, and the weight of the excised bladder was calculated. After 4 weeks, the tumor weight was calculated and the tumor weight suppression rate in the control group was evaluated. As a result, the medicinal efficacy was confirmed at concentrations of 800ppm or higher. On the other hand, the UM-UC-3 model is a commonly used model, but it mimics CIS (carcinoma in situ) and can only partially mimic NMIBC. That is, other models are needed to evaluate efficacy for low- and high-grade NMIBC other than CIS. Therefore, we established high-grade and low-grade PDX and evaluated the effectiveness of HM-001 against low- and high-grade PDX through ex vivo testing. First, patient-derived tissue was transplanted into SCID mice, allowed to grow, and then removed. After extraction, they were cut into 2 mm3 pieces, exposed to HM-001 at 800, 1600, and 3200 ppm for 2 hours, and then transplanted into SCID mice. As a result of comparing the tumor size after transplantation with the control group, a dose-dependent tumor regression effect was confirmed in high-grade and low-grade PDX. NMIBC is divided into low-, medium-, and high-risk categories, with different treatment methods and drugs used for each. In particular, low-grade forms are restricted to low- and intermediate-risk groups. The results of this study show that HM-001 is effective not only for high-risk (including CIS) NMIBC but also for low- and intermediate-risk (low-grade) NMIBC. Citation Format: Shinji Mima, Monta Sakaki, Noriaki Kiya, Atsunari Kawashima, Norio Nonomura, Chihaya Kakinuma. Development of HM-001 as a therapeutic drug for non-muscle invasive 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 3329.