bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4322: Inhibition of ULK and KRASG12C control tumor growth in preclinical models of lung cancer
Authors: Ghazi Phaedra , O'Toole Kayla , Boggaram Sanjana , Scherzer Michael , Bogdan Madhumita , Smith Bryan , Flynn Dan , Kinsey Conan , McMahon Martin 
Published: March 2024

Abstract
Approximately 30% of lung cancers are driven by mutationally activated KRAS. The recent FDA approval of sotorasib, a direct pharmacological inhibitor of KRASG12C, marks a critical milestone in the treatment of this important subset of lung cancer. However, a major obstacle in treating lung cancer is resistance to current therapeutic treatments. In response to cellular stresses such as RAS pathway-targeted therapeutics, RAS-mutated cancer cells have been demonstrated to increase autophagy, an intracellular recycling pathway. However, the mechanism(s) underlying treatment-induced autophagy is not well understood. Here, we demonstrate that KRASG12C-driven lung cancer cells increase autophagy in response to treatment with sotorasib. Currently, the only therapeutics in clinical use to inhibit autophagy are lysosomal inhibitors (hydroxy)chloroquine. High concentrations of these compounds are needed to achieve modest inhibition of autophagy, suggesting that the potency of these compounds may limit clinical responses. ULK kinases are serine/threonine kinases that are necessary for the initiation of autophagy. DCC-3116 is a potent inhibitor of the ULK1/2 protein kinases, master regulators of autophagy. Treatment with sotorasib and DCC-3116 led to superior anti-tumor effects in preclinical models of lung cancer. Additionally, about 30% of lung cancer patients with KRAS mutations also have deletions or inactivating mutations in LKB1, a protein involved in the regulation of nutrient sensing and autophagy. In other KRAS-driven cancers, the LKB1-AMPK-ULK1 signaling axis is a proposed mechanism as to how autophagic flux increases following KRAS pathway inhibition. However, our preliminary data demonstrates that LKB1 is dispensable for sotorasib-induced autophagy, suggesting the mechanism(s) of autophagy induction in KRASG12C-driven lung cancer may be different from those detected in other KRAS mutated cancers. Consequently, we have generated genetically engineered mouse models (GEMMs) of KRASG12C-driven lung cancer in which LKB1 is silenced to further investigate the role of LKB1 in the autophagy response of KRASG12C-driven lung cancers to pathway-targeted blockade of oncogenic KRAS signaling. We have treated KRASG12C-driven GEMMs with sotorasib and/or DCC-3116 to test the sensitivity of lung tumors to these treatment options.
Citation Format: Phaedra Ghazi, Kayla O'Toole, Sanjana Boggaram, Michael Scherzer, Madhumita Bogdan, Bryan Smith, Dan Flynn, Conan Kinsey, Martin McMahon. Inhibition of ULK and KRASG12C control tumor growth in preclinical models of lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4322.
Abstract 4325: CX-4945 (Silmitasertib) induces cell death through impairment of lysosomal utilization in KRAS mutant cholangiocarcinoma cell lines
Authors: Kim Chorong , Lee Da Sol , Han Minwoo , Lee Seonmin , Kim Kyu-pyo , Yoo Changhoon 
Published: March 2024

Abstract
Purpose: Macropinocytosis is a non-selective endocytosis that uptakes extracellular substances such as nutrients and macromolecules into the cells. In KRAS-driven cancer such as pancreatic ductal adenocarcinoma, the macropinocytosis and following lysosomal utilization are enhanced to overcome metabolic stress. In this study, we investigated the role of CK2 in micropinocytosis and the following metabolic process in the KRAS mutant CCA cell line.
Materials and Methods: The BSA uptake indicating micropinocytosis was performed by flow cytometry using the HuCCT1, cholangiocarcinoma cell line harboring KRAS mutation. To validate macropinosome, the Rab7 and LAMP2 were labeled and analyzed via immunocytochemistry and Western blot. The CX-4945, CK2 inhibitor, was used to investigate the role of CK2 in micropinocytosis and following lysosomal metabolism.
Results: The HuCCT1, a KRAS mutant CCA cell line, showed micropinocytosis. Although CX-4945, a CK2 inhibitor, induced morphological changes accompanied by accumulation of intracellular vacuoles and cell death rate, the level of micropinocytosis was not changed. The vacuoles accumulated in the cell were identified as late macropinosomes representing Rab7 before fusion with lysosomes. In addition, the CX-4945 suppressed LAMP2 expression following inhibition of the Akt-mTOR signaling pathway which interrupts mature macropinosome and lysosomal metabolic utilization.
Conclusion: These results support the utilization of micropinocytosis as an energy source even in CCA cell line harboring KRAS mutation. The inhibition of CK2, the regulator of macropinosome maturation, by CX-4945, alters lysosome dependent metabolism and leads to cell death in KRAS mutant CCA cell lines.
Citation Format: Chorong Kim, Da Sol Lee, Minwoo Han, Seonmin Lee, Kyu-pyo Kim, Changhoon Yoo. CX-4945 (Silmitasertib) induces cell death through impairment of lysosomal utilization in KRAS mutant cholangiocarcinoma cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4325.
Abstract 4350: Characterization of PUF60 splicing activity that is essential for the survival of triple negative breast cancer
Authors: Tankka Alexandra , Gomberg Trent , Zhou Cathy , Pham Vivian , Yeo Gene 
Published: March 2024

Abstract
Alternative splicing driven by RNA-binding proteins (RBPs) plays a significant role in TNBC, however, pharmacological modulators of core spliceosomal proteins can disrupt early stages of spliceosome assembly and lead to toxic effects in normal tissues, limiting their utility as safe therapeutics. Here, we used in vivo CRISPR-Cas9 screening to evaluate RBP dependencies in TNBC and identified 17 splicing regulatory candidates that are essential in TNBC but dispensable for normal cell growth and survival. Within this cohort, the alternative splicing factor, PUF60, was the most significantly upregulated candidate in patient TNBC tumors. We found that depletion of PUF60 induced apoptosis in human TNBC cell lines and impeded xenografted tumor growth in vivo while upregulation of PUF60 expression increased TNBC cellular proliferation. Although PUF60 has been shown to also bind DNA and influence transcription, TNBC cells constructed with a previously characterized mutation (L140P) required for 3’ splice site recognition displayed significantly decreased cellular proliferation compared to cells containing wild type PUF60. Integrated eCLIP and KD RNA-sequencing revealed that PUF60 selectively regulates the splicing of mRNAs in TNBC that contribute to essential processes including DNA repair, replication and cell cycle progression. RNA-seq following L140P-mediated inhibition of 3’ ss recognition revealed a cohort of splicing events within genes enriched for similar processes following knockdown of endogenous PUF60 including cell cycle and histone modification. Altogether, our study highlights a critical role for PUF60-mediated splicing in the maintenance of genomic integrity in TNBC as well as the therapeutic potential of identifying and targeting splicing effector RBPs only responsible for TNBC survival.
Citation Format: Alexandra Tankka, Trent Gomberg, Cathy Zhou, Vivian Pham, Gene Yeo. Characterization of PUF60 splicing activity that is essential for the survival of 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 4350.
Abstract 4351: Differential dependency mapping of chimeric RNAs across cancer reveals a new landscape of functional fusion transcripts
Authors: Lalani Samir , Gadh Sehajroop , Elfman Justin , Singh Sandeep , Li Hui 
Published: March 2024

Abstract
Chimeric RNAs are RNA transcripts containing sequences originating from multiple distinct genetic loci and can form through a variety of mechanisms such as DNA rearrangement, cis-splicing of adjacent genes, or RNA trans-splicing. Chimeras have long been known to be a hallmark of cancer and due to their unique properties are promising targets for precision medicine. Appropriately, fusion proteins transcribed from chimeras such as BCR-ABL1 and TPM3-NTRK1 have been shown to be effective targets. Due to these past successes, there exists an opportunity to identify new chimeras as therapeutic targets. While modern chimera prediction software allows for the fast and accurate identification of chimeric RNAs from RNA sequencing data, investigations separating therapeutically relevant transcripts from “transcriptional noise” remain lacking. In this study we performed an in-silico functional screen of chimeras across cell lines representing a wide variety of cancers. We used state-of-the-art chimeric RNA prediction software to create a database of chimeric RNAs across 1017 cell lines from The Cancer Cell Line Encyclopedia. For each chimera we assessed factors such as frequency, recurrence, breakpoint coordinates, frame, and coding potential. To identify specific functional transcripts, we integrated publicly available shRNA knockdown data with our predictions and developed an in-silico functional analysis pipeline comparing differential knockdown effects between chimera and corresponding parental transcripts. For each transcript we assessed the average fold change of chimera-mapping probes, a function score defined as the difference between the fold change of chimera-mapping and parent-specific probes, and a p-value assessing the confidence of our functional score. From our initial screen of 127,819 transcripts, we identified 1088 high-confidence functional chimeras. We successfully identified nearly all known functional chimeras screened including PAX3-FOXO1, EWSR1-FLI1, and TCF3-PBX1. We also identified previously unknown chimeras that that we predict have a function in cell growth and proliferation. Overall, the results of our study reveal a new landscape of functionally relevant chimeric transcripts in cancer. Follow-up studies can further investigate these transcripts to determine their potential as therapeutic targets.
Citation Format: Samir Lalani, Sehajroop Gadh, Justin Elfman, Sandeep Singh, Hui Li. Differential dependency mapping of chimeric RNAs across cancer reveals a new landscape of functional fusion transcripts [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 4351.
Abstract 4365: Mechanistic effects of N361 glycosylation in epidermal growth factor receptor protein
Authors: Lam Dennis , Liberchuk Ariel N. , Arroyo Brandon , Wolfe Andrew L. 
Published: March 2024

Abstract
Glycosylation is a tightly regulated post-translational modification where structured sugar groups are added to protein amino acid backbones, most commonly on asparagine for N-glycosylation. The glycosylation-regulating metabolic enzyme uridine diphosphate-glucose pyrophosphorylase 2 (UGP2) is required in oncogene-transformed cancer cells, but not in normal cells. UGP2 heavily regulates glycosylation of epidermal growth factor receptor (EGFR) at asparagine 361 (N361), a key site near the ligand binding domain. EGFR is a transmembrane tyrosine kinase receptor that promotes cell proliferation via growth cascades. Mutations and amplifications in EGFR account for a significant fraction of non-small cell lung carcinomas and breast adenocarcinoma, with L858R being the most common oncogenic hotspot. Other glycosylation sites on EGFR have been implicated in ligand binding, dimerization, and phosphorylation of downstream targets. Molecular dynamic simulations suggested that N361 may be important for dimerization or ligand binding. However, the functional relevance of how glycosylation of EGFR at N361 impacts EGFR protein and cellular behaviors remains unclear. To determine the functional relevance of glycosylation at N361, we created glycosylation-defective EGFR N361A mutant, with or without an additional oncogenic EGFR L858R mutant. We expressed these constructs in MCF10A and 293T cells, which do not have pre-existing activation of this pathway. Immunofluorescence and flow cytometry showed that the mutants were each well expressed at the cell membrane. Proximity ligation assays measuring dimerization of EGFR in cells showed that EGFR N361A greatly increased dimerization relative to wildtype controls. Loss of glycosylation of EGFR N361 impacted cell viability when grown in dose courses of its high affinity ligand EGF or lower affinity ligand amphiregulin. Furthermore, EGFR N361A desensitized cells expressing the oncogenic EGFR L858R to inhibitors targeting the extracellular domain, possibly because the mutation alters the antibody binding interface. N361A sensitized EGFR L858R to inhibitors targeting the cytoplasmic domain of EGFR. These findings help us understand the intricate relationship between EGFR and N-glycosylation, reinforcing the critical functional relevance of post-translational modifications on oncogenes.
Citation Format: Dennis Lam, Ariel N. Liberchuk, Brandon Arroyo, Andrew L. Wolfe. Mechanistic effects of N361 glycosylation in epidermal growth factor receptor protein [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 4365.
Abstract 4378: Identification of novel TXNIP-dependent antitumor pathways in breast cancer
Authors: Singh Jasvinder , Sah Bindeshwar , Clarke Robert , Liu Liang 
Published: March 2024

Abstract
Thioredoxin-interacting protein (TXNIP) plays a critical role in glucose metabolism and redox signaling. TXNIP has recently emerged as a potent tumor suppressor in various cancer models. In previous studies, we found TXNIP was activated by UNC0642, an inhibitor of histone methyltransferase, in MDA-MB-231 breast cancer cells. TXNIP activation was coupled with significant suppression of cell proliferation and tumor growth. In contrast, TXNIP knockdown increased MDA-MB-231 cell proliferation and in tumor growth and metastasis in vivo. TXNIP-reconstitution in TXNIP-deficient HCC1954 cells reduced cell proliferation and migration coupled with increased reactive oxygen species production. TXNIP-reconstitution also significantly decreased mitochondrial respiration, mitochondrial membrane potential and glycolysis in HCC1954 cells. To understand the mechanisms underlying TXNIP’s antitumor activity, we performed co-immunoprecipitation and proteomic analyses to uncover TXNIP-interacting proteins. We identified calpastatin (CAST) as a novel TXNIP-interacting protein in breast cancer cells. CAST is an endogenous inhibitor of calpains, a family of calcium-activated cysteine proteases. Intriguingly, CAST association with TXNIP was readily detectable in TXNIP-low, but not in TXNIP-high breast cancer cells. The disassociation of CAST from TXNIP in TXNIP-high cells might allow CAST to inhibit calpain activity to augment TXNIP’s antitumor function. Through RNAseq analysis, we identified a positive correlation between TXNIP expression and IL-24 activation in various breast cancer cells, which were also confirmed by western blotting. IL-24 has emerged as an important cancer therapy target because of its role in promoting cancer-specific apoptosis. Our data also demonstrated that TXNIP upregulated the level of IL-24 and downregulated STAT-3. Moreover, TXNIP exerts multifaceted effects on BC development through the IL24-STAT3 signaling axis, deepening our understanding of its complex role in the disease. Taken together, these studies identified novel TNXIP-dependent pathways and their potential new mechanisms in breast cancer pathogenesis with significant clinical implications.
Citation Format: Jasvinder Singh, Bindeshwar Sah, Robert Clarke, Liang Liu. Identification of novel TXNIP-dependent antitumor pathways in 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 4378.
Abstract 4388: Tumor-associated RhoA mutants interact with effectors in both GDP- and GTP-bound states
Authors: Lin Yuan , Ramelot Theresa A. , Senyuz Simge , Gursoy Attila , Jang Hyunbum , Nussinov Ruth , Keskin Ozlem , Zheng Yi 
Published: March 2024

Abstract
RhoA is the founding member of the Ras-homology (Rho) small GTPase family and is a master regulator for multiple cell functions. Recurrent RhoA mutations have been identified in several human cancers, particularly in leukemia/lymphoma and gastric cancer. Intriguingly, both gain-of-function and loss-of-function mutations of RhoA are present, suggesting that RhoA GTPase may have a more sophisticated role in cancer and requires more rigorous investigations. Here, we have focused on two of the gain-of-function RhoA mutations identified in Adult T cell Leukemia/lymphoma (ATLL) at residue A161 (A161P and A161V) and aim to reveal the underlying mechanistic basis for their function by biochemical and structural analyses. We found that in contrast to conventional gain-of-function RhoA mutants such as RhoAG14V and RhoAQ63L which affect the GTP-hydrolysis activity, RhoAA161P and RhoAA161Vare both fast-cycling with drastically increased nucleotide dissociation and association rates, but only slightly reduced GTP-hydrolysis activity. We solved the crystal structures of GDP-bound RhoAA161P and RhoAA161V and saw that while RhoAA161P displays impaired solvent-mediated interactions to the bound nucleotide, RhoAA161V has a more exposed nucleotide binding pocket compared to RhoAWT and RhoAA161P. Interestingly, RhoAA161P and RhoAA161Vcan interact with effector targets in the GDP-bound states. Further 1H-15N HSQC NMR study provides evidence of the active population in GDP-bound RhoAA161V. Molecule dynamics (MD) simulations show that the dynamic properties of RhoA switch regions are affected differently by the two mutations. Thus, RhoAA161V and RhoAA161P are fast-cycling mutants with distinct mechanisms, and both likely endow their GDP-bound state towards an active conformation. These findings provide a better understanding of the oncogenic role of RhoA mutations in cancer and shine light on how changes in RhoA protein dynamic properties caused by mutations may affect its function.
Citation Format: Yuan Lin, Theresa A. Ramelot, Simge Senyuz, Attila Gursoy, Hyunbum Jang, Ruth Nussinov, Ozlem Keskin, Yi Zheng. Tumor-associated RhoA mutants interact with effectors in both GDP- and GTP-bound states [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 4388.
Abstract 4390: IGFBP-6 is induced by progesterone to regulate progesterone receptor expression in breast cancer cells
Authors: Lariz Francisco Javier , Botero Pacha , Houston Kevin 
Published: March 2024

Abstract
Insulin-like growth factor binding protein-6 (IGFBP-6) is induced by progesterone (P4) in T-47D breast cancer cells. IGFBP-6 regulates insulin-like growth factor 2 (IGF2) by sequestering it to inhibit receptor binding and extend its extracellular half-life. IGF2 binds to insulin-like growth factor 1 receptor or insulin receptor A to promote breast cancer cell proliferation and survival. Progesterone is an ovarian steroid hormone which has complex roles in breast cancer through the actions of progesterone receptor A and B (PR-A and B). Progesterone antagonizes the actions of estradiol (E2), another steroid hormone which promotes proliferation and survival in breast cancer. T-47D cells treated with both P4 and E2 exhibit significantly reduced proliferation compared to treatment with E2 alone. To better understand the role of IGFBP-6 in progesterone signaling, T-47D cells which over-express IGFBP-6 were treated with P4, E2, or both. Overexpressing cells exhibited stronger antagonism compared to controls when co-treated with P4 and E2. RNA-interference was performed to knockdown IGFBP-6 induction in the presence of P4 and E2. Knockdown of IGFBP-6 in the presence of P4 and E2 decreases the antagonistic effects of P4. Expression of both PR-A and PR-B decreases by about 50% when IGFBP-6 is knocked down. These results indicate that IGFBP-6 increases PR expression in response to P4 stimulation.
Citation Format: Francisco Javier Lariz, Pacha Botero, Kevin Houston. IGFBP-6 is induced by progesterone to regulate progesterone receptor expression in breast cancer cells [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 4390.
Abstract 4400: Transcriptional dysregulation of chromosomes localized into the micronucleus
Authors: Norkunaite Danguole , Al-Rawi Duaa , Bakhoum Samuel 
Published: March 2024

Abstract
Chromosomal Instability (CIN) is a characteristic of the most aggressive and drug-resistant cancers. Chromosomally unstable cells form micronuclei (MN), a structure with an unstable nuclear membrane that spontaneously surrounds missegregating chromosomes upon mitotic exit. Several studies have demonstrated that CIN drives drug resistance and metastasis through the karyotypic diversity caused by copy number alterations. Beyond facilitating karyotypic diversity, CIN has recently been demonstrated to cause durable epigenetic alterations including reduction of the activating histone H3K27ac mark in chromosomes localized to micronuclei. This reduction in histone H3K27 acetylation persists after the relocalization of the missegregated chromosome to the primary nucleus (PN). Given the loss of transcription-associated epigenetic modifications, we hypothesized that MN would exhibit transcriptional impairment. Indeed, by using nascent RNA assays and immunofluorescence, we found that chromosomes localized into the MN are less transcriptionally active and exhibit lower levels of active RNA polymerase II (RNAP2). Transcriptional inhibitors targeting RNAP2 largely abrogate MN transcription. Conversely, class-specific histone deacetylase inhibitors (HDACi) cause increased hyperacetylation of the MN relative to the PN, which persists beyond MN reincorporation into the PN. We also hypothesized that transcription in MN depends on the manner of MN biogenesis. Preliminary data shows that MN formed from breakage-fusion-bridge (BFB) events may cause less transcriptionally active MN than ones generated from treatment with the MPS1 inhibitor, reversine. To better understand the mechanisms that regulate transcription in the MN, our ongoing work is focused on an unbiased investigation of the micronuclear transcriptome.
Citation Format: Danguole Norkunaite, Duaa Al-Rawi, Samuel Bakhoum. Transcriptional dysregulation of chromosomes localized into the micronucleus [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 4400.