bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 631: Functional genetics of APR-246 rescuable TP53 mutants
Authors: Saunders Anais , Tong Caili , Karnezis Anthony N. , Leiserowitz Gary S. , Chein Jeremy R. 
Published: March 2024

Abstract
TP53, often referred to as the guardian of the genome, encodes for the p53 tumor suppressor protein, and is one of the most frequently mutated genes in human cancers. Some cancer sub-types, such as non-small cell lung carcinoma (NSCLC) and high grade serous carcinoma (HGSC), have high TP53 mutation rates reaching up to 56% and 96%, respectively. Given its multi-faceted role in human cancers, there have been several emerging therapeutic approaches targeting mutant p53. APR-246 is a small molecule drug currently in clinical trials for the functional rescue of p53 missense mutants, the most common type of p53 mutant protein, across various cancer types. APR-246 is proposed to bind mutant p53 and promote thermodynamic stabilization of the protein allowing it to regain wild-type-like conformation and consequentially regain WT-like functionality. However, there has yet to be a functional genomic screening of p53 mutants to systematically catalog which mutants are rescuable by APR-246. To address this critical gap, we have performed functional genetic screenings using a TP53 mutagenesis library. This pooled lentiviral library contains ~8,000 amino acid variants, spanning the entirety of the TP53 gene. Following stable transduction of this library into p53-null NSCLC and HGSOC cell lines, we performed functional screenings against sublethal doses of APR-246. Next-generation sequencing of the untreated and treated cell population allows for comparison of variant representation and determination of APR-246-sensitivity of p53 mutants. Preliminary statistical analysis of our screens has identified a pool of 117 “hit” mutants which are significantly depleted following treatment, indicative of APR-246-sensitivity. Two of these mutants, C242F and G266V, are non-functional, damaging mutations which occur in patients. Identifying p53 mutants that can be rescued by APR-246 will help identify which patients may benefit most from treatment with the drug.
Citation Format: Anais Saunders, Caili Tong, Anthony N. Karnezis, Gary S. Leiserowitz, Jeremy R. Chein. Functional genetics of APR-246 rescuable TP53 mutants [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 631.
Abstract 6321: Developing a lenalidomide-inducible safety switch for CAR T cell therapy
Authors: Sarkar Ditsa , Lin William , Kim Joanna Y. , Knudsen Nelson H. , Lane Isabel C. , Kienka Tamina , Kann Michael C. , Bouffard Amanda A. , Cheng Andy , Maus Marcela V. , Manguso Robert T. , Jan Max 
Published: March 2024

Abstract
While CAR T cell therapy is a medical breakthrough against various hematological malignancies, yet treatment failures often occur at least in part due to excessive engineered T cell activity leading to severe toxicities. To combat this, strategies pairing CAR T cells with safety systems, for example, suicide switches engineered to induce cell death are being actively pursued. However, existing designs have limited performance characteristics and generally use unapproved small molecule controllers or non-human sequences. To overcome these issues, we have developed a novel suicide switch leveraging the well-tolerated, FDA-approved anti-cancer drug lenalidomide, as a controller of the stability of fusion proteins tagged with a “degron” sequence. Specifically, we engineered a stoichiometric pair of transgenes using the apoptotic DNase pair, caspase activating DNase (CAD) and its degron tagged inhibitor (ICAD-degron). We hypothesized that the overexpressed ICAD-degron could restrain CAD, until lenalidomide treatment degrades ICAD to unleash CAD for apoptosis. We found that our system was stably overexpressed and rapidly induced cell death even at sub-nanomolar concentrations of lenalidomide. A comparison of our design with the frontline safety switch, inducible Caspase 9 in primary human T cells revealed that the lenalidomide-induced suicide switch enabled more complete depletion of engineered cells. We tested the effects of our suicide switch on CAR T cell function and found comparable proliferation and tumor cell cytolysis with fast depletion upon lenalidomide addition. In vivo, lenalidomide suicide switch CAR T cells exhibited similar anti-tumor function as control CAR T cells and were rapidly depleted after drug treatment. In summary, utilizing all human sequences and a clinically approved drug controller, we developed a suicide switch that is well tolerated and can rapidly induce cell death even at sub-therapeutic concentrations of lenalidomide. More broadly, chemogenetic regulation of stoichiometric protein pairs is a generalizable strategy for post-translational control of highly active transgenic elements.
Citation Format: Ditsa Sarkar, William Lin, Joanna Y. Kim, Nelson H. Knudsen, Isabel C. Lane, Tamina Kienka, Michael C. Kann, Amanda A. Bouffard, Andy Cheng, Marcela V. Maus, Robert T. Manguso, Max Jan. Developing a lenalidomide-inducible safety switch for CAR T cell 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 6321.
Abstract 6351: MUC1*-ADCs are effective against heterogeneous solid tumor cancers
Authors: Bamdad Cynthia Carol , Smagghe Benoit S. , Moe Scott T. , Carter Mark G. , Grant Trevor J. , Yi Kevin R. , Nash Michael J. , Marquez Jacy P. , Miller Natalie K. , Nash Jac-Leen S. , Miller Dan S. , Walkley Danica M. , Stewart Andrew K. 
Published: March 2024

Abstract
Purpose: To develop a MUC1*-ADC for the treatment of over 75% of solid tumor cancers.
Methods: MUC1* (muk 1 star) is a growth factor receptor created after cleavage and release of the N-terminal portion of MUC1. The targeting antibody, huMNC2, has already demonstrated safety and cancer selectivity in a 1st-in-human CAR-T clinical trial for treatment of metastatic breast cancers. MNC2 is an IgG1 antibody that only recognizes the conformational epitope created when MUC1 is cleaved by specific tumor-associated enzymes. Confocal microscopy and pHlourin2 were employed to measure antibody internalization as a function of time. We conjugated MNC2 to MMAE, MMAF, Dxd and exatecan via several different linkers. MUC1*-ADCs with DARs ranging from 4-8 were tested in vitro and in vivo for efficacy against a panel of solid tumor cancers. Heterogenous MUC1* tumors were made by mixing different ratios of mCherry wild-type cancer cells with GFP MUC1* overexpressed cancer cells. Resulting H scores ranged from 10-280 (max 300).
Results: Cancer cells internalized the MUC1* MNC2 antibody within 2 hours. In vitro, MUC1*-ADC IC50s ranged from 1.3nM to 20.0nM, depending on the linker-payload and cancer subtype, wherein the majority had an IC50 of about 10nM. In general, efficacy in animals was seen across multiple cancer sub-types treated with multiple MUC1*-ADCs. Efficacy in animals xenografted with heterogeneous MUC1* tumors showed a dependence on antigen density. Greatest efficacy was observed for breast cancer xenografts with an H Score &gt;10 treated with MNC2-Deruxtecan. However, only pancreatic tumors with higher H Scores were completely eliminated by MNC2-MMAE, MNC2-Deruxtecan and MNC2-exatecan. MNC2-ADC and MNC2-CAR share the same antibody. No off-tumor toxicity was observed in animals treated with MNC2-ADC, which mimicked lack of off-target toxicities for MNC2-CAR T cells in humans.
Conclusions: These data, combined with MNC2-CAR T data from our 1st-in-human trial for metastatic breast cancer, supports a conclusion that the MUC1* antibody MNC2 is safe and could have high therapeutic value as a MUC1*-ADC for multiple solid tumors with both high and low antigen density.
Citation Format: Cynthia Carol Bamdad, Benoit S. Smagghe, Scott T. Moe, Mark G. Carter, Trevor J. Grant, Kevin R. Yi, Michael J. Nash, Jacy P. Marquez, Natalie K. Miller, Jac-Leen S. Nash, Dan S. Miller, Danica M. Walkley, Andrew K. Stewart. MUC1*-ADCs are effective against heterogeneous solid tumor cancers [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 6351.
Abstract 6424: A patient centric full spectrum flow cytometry assay for comprehensive phenotyping of CAR T cells in clinical trials
Authors: Vaughan Keegan , Muthusamy Selvam , Zhao Coral , Carbajal Austin , Fu Charlie , Dakappagari Naveen , Alfonso Zeni 
Published: March 2024

Abstract
Purpose While there is a strong desire to fully understand next generation CAR-T product characteristics in clinical trials, limited amounts of blood specimens are available as the enrolled patients are very sick and lymphodepleted. To address this high unmet need, we developed a single tube 20-color full spectrum flow cytometry assay for an in-depth characterization of CAR-T cells that support fulfilment of five key clinical trial endpoints, namely, manufacturing success (fitness and memory state), pharmacokinetics, response or resistance (ICIs), efficacy (gross tumor burden) and safety (B cell regeneration) for use across a broad range of CAR-T therapies and clinical indications.
Study Design: The single tube 20-parameter full spectrum flow cytometry (FC) assay was designed to include CD45, HLA-DR, CD3, CD4, CD8, CD56 as backbone markers, CD45RA, CCR7, CD95, CD25 and CD127 antibodies allowed for the identification of all major subsets of CD4 and CD8 T cells. CXCR3, CD38, PD1, LAG3, and TIM3 were used for identification of activation/exhaustion phenotypes, while CD20 and HLA-DR were useful for identification of B cells and monocytes respectively. Additionally, we left two parameters (PE and AF647) open for customized CAR-T detection reagents or other customized markers. This assay was developed using Cytek® Northern Lights™ and frozen PBMCs.
Results This robust 20-color full spectrum FC assay allowed a thorough analysis of the major T cell populations cells. FMO (Fluorescence-Minus-One) control studies confirmed the specificity of the antibodies and of the panel in identifying Naïve, EMRA, CM, EM, Th17, T stem cell memory and regulatory T cells with minimum background on all parameters. This method showed to be highly reproducible and can be adapted for use with many CAR-T detection reagents.
Conclusion In summary, we developed a robust 20-parameter multiparameter full spectrum flow cytometry assay focused on different populations of T cells in a single tube. The inclusion of drop ins for prospective CAR-T cell detection reagents allows for easy integration of future advances in CAR-T cell research. This universal panel shows great potential for usage across CAR-T clinical trials, as it serves as a valuable tool understand product fitness, PK, biomarker monitoring and disease burden simultaneously.
Citation Format: Keegan Vaughan, Selvam Muthusamy, Coral Zhao, Austin Carbajal, Charlie Fu, Naveen Dakappagari, Zeni Alfonso. A patient centric full spectrum flow cytometry assay for comprehensive phenotyping of CAR T cells in clinical trials [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 6424.
Abstract 6564: SOS1 inhibitor treatment improves response to Venetoclax in acute myeloid leukemia
Authors: Kostyrko Kaja , Hinkel Melanie , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Gerlach Daniel , Waizenegger Irene 
Published: March 2024

Abstract
Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. First-line treatment of AML patients consists primarily of chemotherapy, sometimes combined with a targeted therapy. However, elderly patients unfit for chemotherapy receive venetoclax, a BCL2 inhibitor, combined with azacitadine or decitabine. While responses in these patients are high (50-70%, with median OS of 10-17 months), around 30-50% of them do not respond and most relapse within 1-10 years. Increased MAPK pathway activity or low frequency RAS pathway mutations have been identified as key mediators of resistance to standard-of-care targeted therapies for AML, including venetoclax. Here, we found that in DepMap whole-genome CRISPR screens, leukemia cell lines, including AML, show a particular dependency on SOS1. A subsequent PRISM screen with a selective inhibitor of SOS1 confirmed these results. To validate these results in vitro, we treated 7 AML cell lines showing strongest dependency on SOS1 based on DepMap and PRISM screens, with SOS1i or a SHP2 inhibitor. We found that in 4 of 7 cell lines treatment with SOS1i or SHP2i strongly impaired proliferation. In 3 of 4 responding cell lines, the anti-proliferative effect with either SOS1i or SHP2i was stronger than azacytidine single agent treatment. We next treated 29 primary ex vivo cultures of AML with SOS1i and found that the treatment induced strong or intermediate anti-proliferative effect in 21 of 29 models (72%). In two AML PDX models, treatment with SOS1i as a single agent resulted in approximately 25% reduction of human CD45+ AML blast cells in both models. Venetoclax treatment led to approximately 75% decrease in AML blasts, while the combined venetoclax and SOS1i treatment resulted in near complete eradication of the disease. Annexin V staining of AML monoblasts demonstrated that this decrease was due to an increase in apoptosis in the combination groups. In summary, we demonstrate that SOS1 inhibitor treatment may be used to improve responses to venetoclax in AML patients.
Citation Format: Kaja Kostyrko, Melanie Hinkel, Matthew G. Rees, Melissa M. Ronan, Jennifer A. Roth, Daniel Gerlach, Irene Waizenegger. SOS1 inhibitor treatment improves response to Venetoclax in acute myeloid leukemia [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 6564.
Abstract 6569: KLIPP: Precision targeting of cancer with CRISPR
Authors: Ljungman Mats , Yang Huibin , Hulbatte Radhika Suhas , Gratsch Natalie , Kelher Alan , Raupp John , Wang Yin , Dorsey Kristen Hong , Halseth Troy , Schwendeman Anna , Palmbos Philip 
Published: March 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 657: Discovery of a novel brain penetrant SHP2 allosteric inhibitor with anti-tumor effects
Authors: Kim Miyeon , Kim Dongsu , Jeon Yeejin , Yoon Kyeong Jin , Jang Anna , Lee Mijung , Jeon Dahye , Jang Soyeon , Kim Jinhwan , Kim Eunji , Park Jihoon , Hong Victor , Jung Hayoun , Choi Sungpil 
Published: March 2024

Abstract
KRAS is the most frequently dysregulated oncogene with high prevalence in non-small cell lung cancer (NSCLC), colorectal cancer (CRC), and pancreatic ductal adenocarcinoma (PDAC). Currently, FDA-approved sotorasib and adagrasib provide ground breaking through therapies for cancer patients harboring KRAS G12C mutation. However, there is still high unmet medical needs for inhibitors targeting broader KRAS-driven tumor, especially a substantial unmet medical need for agents that can penetrate BBB to control the brain metastases. SHP2, a key activator of KRAS located in the upstream of RAS pathway, facilitates the conversion of GDP-bound KRAS (off) state to GTP-bound KRAS (on) state serving as a key mechanism of KRAS activation. Therefore, SHP2 could be a promising therapeutic target to shut down the oncogenic RAS pathway as a broad combination partner with RAS/RAF/MEK/ERK pathway inhibitors. Here we report a highly potent and selective brain penetrant SHP2 inhibitor that is designed to target solid tumors metastazied to brain. KT-01766 showed excellent potency against SHP2 protein in various biochemical and cellular assays and showed the robust synergistic effect with RAS pathway inhibitors. KT-01766 as a mono therapy and in combination with KRAS G12C inhibitors demonstrated great anti-tumor efficacy with no apparent toxicity in mouse xenograft models harboring KRAS mutations. Furthermore, robust anti-tumor acitivty was confirmed in intracranial brain tumor model, supporting its potential to control brain-metastasized tumors. The present data suggest that KT-01766 is a potential candidate for combination therapy with agents targeting RAS pathway, as it is able to effectively suppress tumor growth both systemically and within the brain in KRAS mutated cancers.
Citation Format: Miyeon Kim, Dongsu Kim, Yeejin Jeon, Kyeong Jin Yoon, Anna Jang, Mijung Lee, Dahye Jeon, Soyeon Jang, Jinhwan Kim, Eunji Kim, Jihoon Park, Victor Hong, Hayoun Jung, Sungpil Choi. Discovery of a novel brain penetrant SHP2 allosteric inhibitor with anti-tumor effects [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 657.
Abstract 6600: Investigating molecular regulators of a dual identity state in lung adenocarcinoma
Authors: Fort Gabriela , Camolotto Soledad , Tariq Rushmeen , Fang Pengshu , Gillis Katherine L. , Stubben Chris , Snyder Eric L. 
Published: March 2024

Abstract
Lung adenocarcinoma (LUAD) is the largest subtype of lung cancer and is the most common cause of cancer related death. LUAD progression is driven by both genetic alterations and epigenetic changes that confer increased lineage plasticity and heterogeneity, but underlying mechanisms dictating cell identity in LUAD remain incompletely understood. The lineage defining transcription factors, NKX2-1 and FoxA1/2, coordinately maintain a pulmonary identity in LUAD. Recent work suggests that NKX2-1-positive (NKX2-1+) LUAD evolves from an alveolar-like state and adopts various disparate cell fates that drive progression, including “dual-identity” states, characterized by acquisition of gastrointestinal (GI) and pulmonary-like states in the same cell. Using sophisticated genetically engineered mouse models and 3D organoid cultures, we demonstrated that the gastrointestinal transcription factor HNF4α, which robustly marks the dual-identity state, is critical for growth in NKX2-1+ LUAD. We performed bulk RNA-seq and single cell RNA-seq in vitro and in vivo, and we found that loss of HNF4α alters the differentiation state of NKX2-1+ LUAD, causing cells to shed elements of their gastric identity in favor of alternate differentiation states. Using paired chromatin immunoprecipitation sequencing and RNA-seq in dual-identity organoids, we found that HNF4α can access and activate many of its canonical gastrointestinal target genes despite being aberrantly expressed in the lung, where it is typically epigenetically silenced early in development. Surprisingly, HNF4α also colocalizes with NKX2-1 and FoxA1/2 and binds at novel sites, suggesting that HNF4α acquires expanded activity in this state beyond its canonical roles. Together, our work unveils key insights into the mechanisms by which lineage defining transcription factors regulate cellular identity and growth in LUAD.
Citation Format: Gabriela Fort, Soledad Camolotto, Rushmeen Tariq, Pengshu Fang, Katherine L. Gillis, Chris Stubben, Eric L. Snyder. Investigating molecular regulators of a dual identity state in lung adenocarcinoma [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 6600.