bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5608: The BRCA1-associated role of CDK9 in response to DNA damage is independent of its canonical role in transcription
Authors: Nepomuceno Thales C. , Carvalho Marcelo A. , Monteiro Alvaro N. 
Published: March 2024

Abstract
The understanding of the biological role of BRCA1 in maintaining genomic integrity through homologous recombination (HR) repair has driven the development of targeted treatments with PARP inhibitors (PARPi) in BRCA1-linked tumors with promising results. Recently, cyclin-dependent kinase 9 (CDK9) inhibitors have emerged as therapeutic options to treat cancer. We have previously implicated CDK9 in genome integrity maintenance through HR repair by modulating BRCA1 recruitment to double-stranded break sites. CDK9 is a component of the positive transcription elongation (PTEF-b) complex and more recently was proposed by the hereditary breast case-control (BEACCON) study as a putative breast cancer (BC) predisposition gene in non-BRCA families. Differently from BRCA1-linked BCs, loss-of-function mutations in CDK9 were significantly correlated with ER-positive and Lobular BCs. CDK9 expression is also elevated in metastatic and recurrent ovarian cancer (OC) tissue and correlates with poor prognosis in OC patients. Here we characterize the BRCA1/BARD1/CDK9 complex using protein-protein interaction assays. Our data indicate that the CDK9/BARD1 interaction occurs indirectly through BRCA1. We also generated a separation-of-function mutation in CDK9 (mutCDK9) that disrupts its interaction with BRCA1 but retains its kinase activity and preserves its role in transcription. We rescued the mutCDK9/BRCA1 interaction using a complementary mutation in BRCA1 (cmutBRCA1), that retains BRCA1 role in cell viability. Further, we employed CRISPR-based genome editing to generate genetically defined haploid HAP1 cell lines that express mutCDK9 in various TP53BP1 and BRCA1 backgrounds. The mutCDK9 cells preserve global RNA transcription and the phosphorylation status of the RNA polymerase II. We observed that mutCDK9 cells are more sensitive to the PARPi, rucaparib when compared to wild-type cells in proficient and deficient TP53BP1 backgrounds. However, mutCDK9 expression did not affect the sensitivity of HAP1 cells expressing cmutBRCA1. Collectively, our data suggest that CDK9 acts in genome integrity maintenance by HR through its interaction with BRCA1 independently of its canonical role in transcription.
Citation Format: Thales C. Nepomuceno, Marcelo A. Carvalho, Alvaro N. Monteiro. The BRCA1-associated role of CDK9 in response to DNA damage is independent of its canonical role in transcription [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 5608.
Abstract 5615: Functional analysis of variants of uncertain significance in the MSH6 mismatch repair gene
Authors: Szabo Elizabeth , Blackburn Emily , Radecki Alexander , Rath Abhijit , Heinen Christopher 
Published: March 2024

Abstract
Lynch syndrome (LS) is a hereditary condition that increases patients’ lifetime risk of cancer, primarily colorectal cancer. LS is caused by germline mutations in mismatch repair (MMR) genes, MLH1, MSH2, MSH6, and PMS2. Identification and classification of these mutations is important in LS diagnosis for guiding treatment plans and preventative care for patients’ and their families. However, the consequences of some variants in these genes are not immediately obvious, granting them classification as variants of uncertain significance (VUS). Laboratory functional analysis to determine whether these variants disrupt MMR function in human cells can provide important evidence for understanding the pathogenicity of VUS and reclassifying them. Half of known variants in the MMR gene MSH6 are VUS and, thus, the goal of my project is to provide evidence for a subset of these variants to help provide evidence for reclassification for these variants. We are calibrating and validating functional assays for MSH6 variants, using known MSH6 pathogenic and benign controls. We will then test MSH6 VUS identified in patients as reported in the InSiGHT database, ClinVar database, and current literature. We are using CRISPR gene editing to recreate these variants in the endogenous MSH6 loci in human embryonic stem cells (hESC). Using these edited hESC lines we are examining the impact of the variants on RNA and protein stability, repair of DNA microsatellites, which is a hallmark of normal MMR function, and induction of the MMR-dependent DNA damage response. With this compilation of data, we will convert the results into a quantitative Odds of Pathogenicity value. This Odds of Pathogenicity score can be used by expert variant interpretation committees to help readily reclassify these variants and provide a clearer diagnosis for these suspected Lynch syndrome patients.
Citation Format: Elizabeth Szabo, Emily Blackburn, Alexander Radecki, Abhijit Rath, Christopher Heinen. Functional analysis of variants of uncertain significance in the MSH6 mismatch repair gene [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 5615.
Abstract 5622: Uncovering the transcriptional regulation of TPPP3
Authors: Lord James W. , Leshchiner Dmitry , Horibata Sachi 
Published: March 2024

Abstract
Tubulin Polymerization Promoting Protein 3 (TPPP3) is a protein coding gene primarily associated with microtubule bundling. However more recent research is beginning to reveal more diverse roles it may play in the cell, including B-catenin signaling and endothelial injury. TPPP3 has also been associated with increased cancer growth and proliferation as well epithelial to mesenchymal transition. However, it is unknown how TPPP3 is regulated. We used high grade serous ovarian cancer (HGSOC) as a model to uncover the regulation of TPPP3 as it is highly expressed in many HGSOC cases. To start, we downloaded ~500 HGSOC RNA-seq datasets from The Cancer Genome Atlas (TCGA) and, using python, created a co-expression network to identify a subset of genes exhibiting expression patterns correlated with TPPP3 across all datasets, resulting in the identification of 222 genes. Dynein arm assembly, cilia movement and assembly, and microtubule movement and structure were among the top GO-terms after gene ontology analysis. The genes associated with these processes are typically upregulated in the fallopian tube tissue which aligns with the fact that a majority of HGSOCs originate in the fallopian tube. Fork-head box J1 (FOXJ1) is a transcription factor associated with ciliogenesis and was among the top 222 genes from the co-expression network. It has not been confirmed to transcriptionally regulate TPPP3, but their expression patterns line up across many tissue types. In addition, the TPPP3 promoter contains an RFX2 binding site. RFX2 is DNA binding protein that FOXJ1 uses as a scaffold to bind to proximal promoters due to it binding at to DNA at a distal location. As a result of this evidence, we hypothesize that FOXJ1 transcriptionally regulates TPPP3 via RFX2. To test this hypothesis, we inhibited FOXJ1 and identified TPPP3 downregulation. We are further investigating the regulatory function of how TPPP3 is regulated.
Citation Format: James W. Lord, Dmitry Leshchiner, Sachi Horibata. Uncovering the transcriptional regulation of TPPP3 [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 5622.
Abstract 570: The role of CD5L in chronic liver disease
Authors: Hong Handan , Tu Taojian , He Lina , Razaviyayn Meisam , Suan Sze-Chuan , Yuan Liyun , Stiles Bangyan L. 
Published: March 2024

Abstract
Macrophage migration inhibitory factor (MIF) is a CD5 molecule like glycoprotein synthesized and secreted by macrophages, also termed CD5L. In liver cancer, serum levels of CD5L has been reported to be higher in steatohepatitis and hepatocellular carcinoma (HCC) patients and proposed to be a serum marker for these conditions. In the liver, steatosis and steatohepatitis is a major comorbid factor for HCC development and associated with poor response to therapy, particularly immune-checkpoint therapy. Here, we assessed the levels of CD5L in plasma samples from 50 advanced HCC patients obtained at baseline prior to initiation of systemic immunotherapy and compared them with that of healthy controls. The data demonstrated a 50% higher plasma CD5L levels in HCC patients vs. healthy donors. Furthermore, CD5L concentrations are higher in patients with higher Child Pugh score. In patients treated with immune checkpoint single or combination therapy, serum CD5L was found to correlate with clinical benefit. To address the role of CD5L and CD5L secreting macrophage in HCC development, we performed in-silico analysis of single cell RNA-seq data and identified Cd5l as a unique gene expressed on liver resident macrophages, the Kupffer cells (KCs). This finding was validated with additional datasets and using two steatosis mouse models representing ALD and NAFLD. Furthermore, our immunofluorescent staining and flow cytometry further confirmed the main source of Cd5l is KCs. In HFD fed mice, we showed that the expression and serum levels of CD5L became more significant with the severity of liver injury, particularly steatotic liver injury. We hypothesize that CD5L may be involved in establish the tumor microenvironment established by steatohepatitis, we performed a free fatty acid (FFA) uptake assay and found that CD5L increased the uptake of FFA in hepatic stellate cells. This ability of CD5L may have contributed to therapy resistance observed in the CD5L high patients who showed reduced clinical benefit.
Citation Format: Handan Hong, Taojian Tu, Lina He, Meisam Razaviyayn, Sze-Chuan Suan, Liyun Yuan, Bangyan L. Stiles. The role of CD5L in chronic liver disease [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 570.
Abstract 5721: Dual targeting of CDK4/6 and CDK7 pathways augments tumor response in breast cancer
Authors: Son Eugene , Kim Sungsoo , Park Haram , Kim Minah , Yang Hee Won 
Published: March 2024

Abstract
CDK7 plays a pivotal role in cell proliferation, serving as both a cell-cycle CDK regulator and a transcription machinery component. Clinical trials are currently exploring CDK7 inhibitors (CDK7i) as a second-line treatment for hormone receptor-positive (HR+) breast cancer post-CDK4/6 inhibitor (CDK4/6i) therapy progression and as a first-line treatment in triple-negative breast cancer (TNBC). This study evaluates the impact of CDK7i on transcription and CDKs activities and the synergistic potential of CDK7i in combination with CDK4/6i. Kinetic analyses indicate that CDK7i preferentially target global transcription over CDKs activities. Furthermore, a combination of CDK7i and CDK4/6i effectively suppresses cell proliferation in drug-naïve cells, albeit without the same efficacy in CDK4/6i-resistant cells. Our findings provide valuable insights into the evolving field of CDK inhibition strategies and provide critical guidance on the potential therapeutic application of CDK7i in breast cancer treatment.
Citation Format: Eugene Son, Sungsoo Kim, Haram Park, Minah Kim, Hee Won Yang. Dual targeting of CDK4/6 and CDK7 pathways augments tumor response 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 5721.
Abstract 5784: Structure-based drug design against caPCNA for selective cancer chemotherapy development
Authors: Jossart Jennifer , Haratipour Pouya , Gu Long , li Carone M. , Lingeman Robert , Liu Yilun , Hickey Robert J. , Malkas Linda H. , Perry Jeff J. 
Published: March 2024

Abstract
Proliferating cell nuclear antigen (PCNA) is critical to DNA replication and repair processes, and it is also a proliferation biomarker in a variety of human tumors. A unique cancer-associated isoform of the protein, caPCNA, has been previously identified, allowing for rational-based drug discovery studies to develop leads with the potential for selective therapeutic targeting of cancer cells. Several strategies have been employed to develop agents targeting caPCNA, including peptide and small molecule-based inhibitors, but the success in developing therapeutically tractable compounds has been limited so far. Here, we present the crystal structures and corresponding biochemical characterizations of our novel small molecule-based caPCNA inhibitors, which bind into the PIP-box binding pocket of PCNA. One of our lead compounds is now an investigational new drug that we observed selectively kills cancer cells, and it appears to induce replication stress, apoptosis and increase cancer cell sensitivity to genotoxic agents, while these effects are not observed in non-malignant cell controls. This caPCNA inhibitor is orally administrable, metabolic stable and it suppresses tumor growth as a monotherapy or as a combination treatment, and it has entered clinical trials in the United States. PCNA plays a critical role in temporarily dislodging RNA polymerase II from transcription replication conflict sites, to enable the replication fork to proceed. Thus, structure-based drug discovery approaches to target transcription replication conflict resolution machinery, such as PCNA protein, may open a novel therapeutic avenue for exploiting this cancer-selective vulnerability.
Citation Format: Jennifer Jossart, Pouya Haratipour, Long Gu, Carone M. li, Robert Lingeman, Yilun Liu, Robert J. Hickey, Linda H. Malkas, Jeff J. Perry. Structure-based drug design against caPCNA for selective cancer chemotherapy development [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 5784.
Abstract 5804: Preclinical evaluation of LCB84, a novel next-generation TROP2 directed ADC utilizing a cancer selective linker and an MMAE payload
Authors: Slocum Stephen , Kim Hyejung , Chung Chul-Woong , Park Changsik 
Published: March 2024

Abstract
LCB84 is an antibody-drug conjugate (ADC) that consists of an antibody targeting human trophoblast cell-surface antigen-2 (TROP2) linked to monomethyl auristatin E (MMAE) via a beta-glucuronidase cleavable linker with a drug-to-antibody ratio (DAR) of 4. LCB84 demonstrates tumor selective killing by multiple mechanisms, increasing both safety and efficacy in parallel. Firstly, the over-expression of TROP2 in many solid tumors allows for targeted delivery of MMAE by LCB84 to Trop2-positive tumor tissues. Secondly, the overexpression of beta-glucuronidase in the lysosome of most tumors facilitates the selective release of active payload within tumor cells compared to normal healthy tissues. Thirdly, the intrinsic selectivity of tubulin inhibitor payloads, such as MMAE, for proliferating cells provides additional protection for non-proliferating normal cells. MMAE is also cell-permeable in its free drug form and can lead to increased efficacy of LCB84 via a bystander effect, enabling activity in heterogenous tumors. LCB84 demonstrates superior efficacy in mouse tumor xenograft studies when compared to benchmark TROP2-targeting ADCs, including sacituzumab govitecan and datopotamab deruxtecan. LCB84 also shows an improved safety profile compared to these clinical benchmarks, as well as compared to traditional MMAE-bearing ADCs, in both in vitro and in vivo toxicity assessments. Additionally, LCB84 shows a stable preclinical pharmacokinetic profile with minimal loss of payload over time. The utilization of an ADC for target-mediated delivery, in combination with a stable beta-glucuronide trigger for selective payload release in tumors, allows for a superior preclinical therapeutic index which is expected to translate to a best-in-class ADC in the clinic.
Citation Format: Stephen Slocum, Hyejung Kim, Chul-Woong Chung, Changsik Park. Preclinical evaluation of LCB84, a novel next-generation TROP2 directed ADC utilizing a cancer selective linker and an MMAE payload [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 5804.
Abstract 5846: Inhibiting elements of the proteasome recovery pathway sensitizes glioblastoma to proteasome inhibitors
Authors: Anand Alisha , Shaikh Muhammad Vaseem , Chokshi Chirayu , Brakel Benjamin , Maich William , Grewal Shan , Venugopal Chitra , Singh Sheila 
Published: March 2024

Abstract
Bacground: Glioblastoma (GBM) is the most common primary brain tumor, accounting for 15% of all central nervous system related tumors. Despite the aggressive standard of care treatment including chemotherapy, radiotherapy, and maximally safe surgical resection, patient outcomes are abysmal: with 95% of patients relapsing and a median overall survival of 15 months. Thus, this necessitates the rapid query for personalized therapeutics and agents that can potentiate the clinical effects of currently approved treatments. One such pathway that demonstrates aberrant functioning in cancer and is a targetable mechanism is the ubiquitin-proteosome pathway (UPP). Studies have shown that UPP related proteolysis remains constitutively active in cancer cells leading to the rapid degradation of proteins that regulate tumor suppressor genes and oncogenes. Despite robust preclinical evaluations for the usage of proteosome inhibitors against GBM, most tested proteosome inhibitors failed in phase II and III trials, indicating resistance.
Methods: We conducted an unbiased genome wide CRISPR-Cas9 screen in human HAP1 cells treated with the proteosome inhibitor, Bortezomib (BTZ), to identify genes that may lead to a BTZ-resistant phenotype. We identified several genes that when perturbed, sensitized cells to BTZ including N-glycanase-1 (NGLY-1), Nuclear factor Erythroid 2-Like-1 (NFE2L1), and DNA damage inducible 1 homolog 2 (DDI2). Herein we sought to evaluate the effects of perturbing components of the proteosome rescue pathway in our Singh lab patient derived GBM cell lines by utilizing CRISPR/Cas9 knockout technology in vitro and in vivo.
Results: The generation of NGLY-1, DDI2, and NFE2L1 KO cell lines demonstrated functional sensitivity to the proteosome inhibitor Marizomib (MZB) as observed through a significant reduction of the IC50 in the KO cell lines compared to a control. Functional evaluation also revealed a reduction in proliferation capacity as well as sphere formation in these genetically modified GBM lines. Ongoing in vivo work will aim to evaluate the mitigation of this resistant pathway in our NSG mouse models orthotopically transplanted with these patient derived KO cell lines. In an ongoing collaborative effort, we are working to identify and functionally assess a novel small molecule NGLY-1 inhibitor to evaluate preclinical sensitivity to MZB in our in vitro and in vivo models.
Citation Format: Alisha Anand, Muhammad Vaseem Shaikh, Chirayu Chokshi, Benjamin Brakel, William Maich, Shan Grewal, Chitra Venugopal, Sheila Singh. Inhibiting elements of the proteasome recovery pathway sensitizes glioblastoma to proteasome inhibitors [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 5846.
Abstract 5859: PLK1 predicts aggressive behavior in CRC patients and its inhibition reverse chemoresistance in CRC cells
Authors: Padmaja Divya , Al-Rasheed Maha , Poyil Pratheesh Kumar , Siraj Abdul K. , Parvathareddy Sandeep Kumar , Haqawi Wael , Al-Dayel Fouad , Al-Kuraya Khawla S. 
Published: March 2024

Abstract
Polo-like kinase 1 (PLK1) is a serine/threonine-protein kinase, that is involved in multiple stages of cell cycle progression in mammals. Dysregulation of PLK1 has been found in a variety of human cancers and was associated with poor prognoses in various cancers. However, its role in the pathogenesis of CRC from Middle Eastern ethnicity has not yet been explored. Therefore, we examined the expression of PLK1 protein in a large cohort of over 1000 Middle Eastern CRC cases by immunohistochemistry. Correlation with clinico-pathological parameters were performed. PLK1 overexpression was noted in 60.3% (693/1149) CRC cases and was significantly associated with larger tumor size (T3/T4 tumors), lymphnode metastasis, Stage III tumors, MSI-H status and p-ERK1/2 over-expression. Interestingly, on multivariate logistic regression analysis, we found that PLK1 was an independent predictor of lymphnode metastasis. However, no association was noted between PLK1 expression and clinical outcomes (DFS, RFS, OS, CSS). Our in vitro experimentation revealed that CRC cells expressing high levels of PLK1 exhibited resistance to 5-Fu treatment, whereas cells with low PLK1 expression demonstrated sensitivity to the treatment. To explore the role of PLK1 on chemoresistance, we inhibited PLK1 using specific inhibitor, volasertib and we showed that volasertib effectively reversed 5-Fu resistance in these cells. Furthermore, knockdown of PLK1 reduced the progression of epithelial-to-mesenchymal transition (EMT) and the stem cell-like properties in 5-Fu resistant cells, showing the role of PLK1 on inducing EMT and stemness in CRC. Interestingly, the forced expression of PLK1 triggered the activation of the CRAF-MEK-ERK-ZEB1 signaling cascade, whereas its inhibition led to the suppression of this cascade. In addition, we showed that silencing of ERK1/2 reversed the chemoresistance, EMT and stemness of PLK1 expressing CRC cell lines. Our findings underscore the significant role of PLK1 in conferring chemoresistance, and targeting PLK1 could represent a viable therapeutic approach for the treatment of patients with an aggressive subtype of CRC.
Citation Format: Divya Padmaja, Maha Al-Rasheed, Pratheesh Kumar Poyil, Abdul K. Siraj, Sandeep Kumar Parvathareddy, Wael Haqawi, Fouad Al-Dayel, Khawla S. Al-Kuraya. PLK1 predicts aggressive behavior in CRC patients and its inhibition reverse chemoresistance in CRC 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 5859.