bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 458: Targeting p27Kip1 to inhibit CDK4/6/2 as a novel therapeutic strategy to treat pancreatic ductal adenocarcinoma
Authors: Guido Carolina , Gottesman Susan RS , Blain Stacy W. 
Published: April 2023

Abstract
CDK4/6 inhibitors are powerful tools used clinically to treat metastatic, HR+ BC patients. While combined CDK4/6i treatment in combination with Estrogen modulation significantly extends Progression Free Survival (PFS) in metastatic HR+ breast cancer patients, those treated invariably develop aquired resistance, which results in only marginal improvement in Overall Survival (OS). The drug resistance seen in the presence of CDK4/6i, such as palbociclib, has been shown to be attributed to activation and compensation by CDK2. Pancreatic ductal adenocarcinoma (PDAC) is characterized by aberrant activation of the CyclinD-CDK4/6 signaling pathway and inactivation of the CDKN2A locus encoding the CDK4/6 inhibitor, p16INK4A, and was initially thought to be a good candidate for CDK4/6i use. Surprisingly, CDK4/6i do not show response in most PDAC lines and have not been used clinically in this tumor type. We hypothesized that PDAC may be intrinsically resistant to CDK4/6 inhibition due to activation of CDK2 and as such inhibition of both CDK4/6 and CDK2 may be required. We have developed a novel strategy to kill drug-resistant tumor cells using a therapeutic liposomal:peptide formulation, IpY.1, to inhibit the tyrosine phosphorylation of p27Kip1(CDKN1B), which in turn inhibits both CDK4/6 and CDK2. IpY.1 is specific for p27, and this reduces toxicity relative to that seen with the small molecule ATP-competitive CDK4/6i or CDK2i. IpY.1 blocks DNA replication in HR+ breast cancer (BC) cells and mouse models, but unlike CDK4/6i or CDK2i treatment, it induces ROS-dependent necroptosis to kill the tumor cells.
Palbociclib did not have a significative effect on ATP levels or proliferation of PDAC cell lines. In contrast, we found that IpY.1 was able to block proliferation and reduce viability in palbociclib-resistant PDAC lines, suggesting that dual CDK4/6 and CDK2 inhibition via p27 targeting was required. Some PDAC lines were “super sensitive” and responded with IC50 values ~10X less than seen with the ER+ BC lines, and we are currently screening for biomarkers of response. CDK2 activity was reduced in IpY.1 treated lines and markers of necroptosis were detected. Immunoblot analysis showed decreased pY88 phosphorylation of p27 (the target of IpY) demonstrating target engagement. We have demonstrated that unlike palbociclib, IpY.1 blocks proliferation and viability in all PDAC lines tested, suggesting that targeting p27 may be a viable approach to treat PDAC.
Citation Format: Carolina Guido, Susan RS Gottesman, Stacy W. Blain. Targeting p27Kip1 to inhibit CDK4/6/2 as a novel therapeutic strategy to treat pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 458.
Abstract 4605: Chronic VEGF-C signaling exacerbates the progression of non-alcoholic steatohepatitis and hepatocarcinoma through endothelial VEGFR2 and VEGFR3
Authors: Youn Seock-Won , Eng Jason W.-L. , Swaminathan Bhairavi , Teneqexhi Pamela , Vadakath Rahul , Kitajewski Jan K. 
Published: April 2023

Abstract
Obesity, aging, and metabolic diseases contribute to non-alcoholic fatty liver disease (NAFLD) that can progress to non-alcoholic steatohepatitis (NASH) due to ongoing inflammation and pathological angiogenesis. At present, NASH is a leading cause of cirrhosis, hepatocarcinoma cancer (HCC) and liver transplant within the United States. Pathological angiogenesis of liver sinusoidal endothelial cells (LSECs) is one of the hallmarks of liver injury that disrupt normal LSEC physiology. Therefore, strategies which target factors involved in LSEC dysregulation may improve the progression of hepatic diseases. Examination of a human tissue microarray identified increased levels of vascular endothelial growth factor-C (VEGF-C) in NASH livers compared with healthy individuals. Additionally, single nuclei RNA sequencing and immunofluorescent staining revealed that the receptors for VEGF-C, VEGFR2 and VEGFR3, are primarily expressed by the LSECs. Using murine models of NASH, we further investigated the role of VEGF-C during disease progression. Chronic over expression of VEGF-C by adeno-associated viral (AAV) infection in mice fed a western diet with carbon tetrachloride injections increased NASH progression compared with control AAV infected NASH mice. Interestingly, overexpression of VEGF-C C156S, a variant of VEGF-C which exclusively binds to VEGFR3, resulted in significantly increased hepatic steatosis, but only minimal fibrosis. To determine whether blockade of VEGF-C signaling would delay disease progression, we administered lenvatinib, a tyrosine kinase inhibitor which primarily blocks VEGFR2 and VEGFR3 at low doses, to NASH mice. We discovered that low dose lenvatinib resulted in significantly decreased amount of fibrosis, steatosis, and tumor formation. Analysis of vehicle treated and lenvatinib treated livers by single nuclei RNA sequencing uncovered significant changes in endothelial cell genes associated with extracellular interactions and inflammation, as well as hepatocyte genes involved in lipid synthesis and metabolism. Taken together, these findings indicate that chronic VEGF-C production in NASH plays a role in promoting liver fibrosis and steatosis as well as HCC development, and that blockade of the downstream receptors for VEGF-C, VEGFR2 and VEGFR3, may be a promising therapeutic strategy to mitigate disease severity.
Citation Format: Seock-Won Youn, Jason W.-L. Eng, Bhairavi Swaminathan, Pamela Teneqexhi, Rahul Vadakath, Jan K. Kitajewski. Chronic VEGF-C signaling exacerbates the progression of non-alcoholic steatohepatitis and hepatocarcinoma through endothelial VEGFR2 and VEGFR3. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4605.
Abstract 4612: Microphysiological vascularized solid liver tumor model for drug and cell therapy
Authors: Vasudevan Jyothsna , Vijayakumar Ragavi , Reales-Calderon Jose Antonio , Lam Maxine Sin , Ow Jin Rong , Aw Joey , Tan Damien , Adriani Giulia , Pavesi Andrea 
Published: April 2023

Abstract
Development of efficacious therapeutic strategies against solid tumors is limited by the lack of pre-clinical models that can reliably predict treatment outcomes in patients. This is primarily because models often do not accurately reflect the complexity of the tumor microenvironment (TME). The TME consists of vasculature, stromal cells and immune cells that can promote tumor resistance or prevent targeted drug and cell therapy. Here, we developed an in vitro vascularized liver tumor model in a microfluidic device to evaluate drug delivery and immunotherapy approaches. The model consists of a tumor spheroid surrounded by a perfusable self-organized vasculature bed with physiologically relevant permeability. Sorafenib (Nexavar) efficacy was evaluated by assessing tumor spheroid viability, quantified by the loss of fluorescence signal. The presence of vasculature showed enhanced cytotoxicity, highlighting the importance of tumor-vascular interactions for testing therapeutic efficacy. Engineered immune cells (chimeric antigen receptor (CAR) T-cell and transiently expressing T-cell receptors (TCR)) were introduced into the model to demonstrate immunotherapy validation. Our results showed that the engineered immune cells were more effective at infiltrating the tumor spheroid without a vasculature but were more cytotoxic in the presence of the vasculature. By removing the cultured microtissue from the device and performing digital spatial transcriptomics on standard paraffin-embedded sections, we identified known and novel genes involved in creating a pro-tumorigenic microenvironment. This platform can be utilized to model critical features of the in vivo TME, providing better predictability of drug responses, with potential applications towards personalized medicine.
Citation Format: Jyothsna Vasudevan, Ragavi Vijayakumar, Jose Antonio Reales-Calderon, Maxine Sin Lam, Jin Rong Ow, Joey Aw, Damien Tan, Giulia Adriani, Andrea Pavesi. Microphysiological vascularized solid liver tumor model for drug and cell therapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4612.
Abstract 4649: Design and validation of ultrahigh-plex discovery panels for immuno-oncology and oncology
Authors: He Yan , Berry Shannon , Shang Olive , McLane Michael , Ihley Nicholas , Zheng Yi 
Published: April 2023

Abstract
Introduction Ultrahigh-plex single-cell spatial phenotyping is revolutionizing cancer research through deeper interrogation of cellular and protein-level co-expression, localization, and arrangements within cancer tissues. To enable in-depth characterization of the tumor microenvironment (TME), we have developed and validated pre-optimized antibody panels on cancer tissues to reveal key cell types and cellular architecture using the PhenoCycler™-Fusion system. Here, we present our methodology for the development and validation of multiplex spatial phenotyping panels for oncology and immuno-oncology.
Methods We designed panel modules such that each module answers specific biological questions about the TME and can be multiplexed together for a more comprehensive view of the structure and function of the tumor and TME. The resulting PhenoCode™ Discovery panel modules include markers that identify key immune cell types, immune activations and checkpoints, mediators of proliferation, and other hallmarks of cancer. Each antibody in the panel module was conjugated to an oligo barcode and stained on human formalin-fixed paraffin-embedded (FFPE) tissue. The slide was imaged on a PhenoCycler™-Fusion platform, where dye-labeled oligo reporters (complementary to the barcodes) are hybridized to the barcode to visualize the antibody. The results were compared serial sections run with a 3,3’-Diaminobenzidine (DAB) chromogenic immunohistochemistry assay to ensure specificity of the antibody was retained. Antibody concentration, exposure time, and corresponding dye were further optimized, verified, and validated as a whole module using tonsil and cancer tissues based on image analysis and intensity analysis, to achieve an ultrahigh-plex detection.
Results and Conclusions In this study, we showcased the rigorous process used for development and validation of PhenoCode™ Discovery panel modules and demonstrated how they can seamlessly work together to collect more data out of one tissue sample. The introduction of these pre-optimized antibody panel modules mark a pivotal point in the evolution of ultrahigh-plex spatial phenotyping. They not only simplify experimental design and assay set up, with panels that make it easier for researchers to answer important questions with this technology, but also save precious time and resources, while reducing overall costs.
Citation Format: Yan He, Shannon Berry, Olive Shang, Michael McLane, Nicholas Ihley, Yi Zheng. Design and validation of ultrahigh-plex discovery panels for immuno-oncology and oncology. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4649.
Abstract 4652: A cellular and transcriptomic dissection of the human breast for studying mechanisms of cell and tissue function
Authors: Toro Katelyn Del , Sayaman Rosalyn W. , Thi Kate , Licon-Munoz Yamhilette , Hines William C. 
Published: April 2023

Abstract
A fundamental question in biology, central to our understanding of cancer and other pathologies, is determining how different cell types coordinate to form and maintain tissues. Recognizing the distinct features and capabilities of the cells that compose these tissues is critical. Unfortunately, the complexity of tissues often hinders our ability to distinguish between neighboring cell types and, in turn, scrutinize their transcriptomes and generate reliable and tractable cell models for studying their inherently different biologies. A lack of comprehensive methods to identify, isolate, and culture each cell type from many tissues have impeded progress. Here, we will describe such a method for the breadth of cell types composing the human breast. Furthermore, we have sequenced mRNAs from each purified population and investigated transcriptional patterns that reveal their distinguishing features. These analyses have exposed differentially expressed genes and enriched biological pathways that capture the essence of each cell type, along with transcripts that display intriguing expression patterns. These data, analytic tools, and transcriptional analyses form a rich resource whose exploration provides remarkable insights into the inner workings of the cell types composing the breast, thus furthering our understanding of the rules governing normal cell and tissue function.
Citation Format: Katelyn Del Toro, Rosalyn W. Sayaman, Kate Thi, Yamhilette Licon-Munoz, William C. Hines. A cellular and transcriptomic dissection of the human breast for studying mechanisms of cell and tissue function. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4652.
Abstract 4738: Dysregulated miR-371b-5p/CSDE1/RAC1 axis is involved in pathogenesis of triple-negative breast cancer
Authors: Kim Yesol , Ko Je Yeong , Lee Soo-Been , Jun Jaehee , Ahn Yejin , Min Jinui , Oh Chaewon , Park Jong Hoon 
Published: April 2023

Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer; however, pathogenesis of TNBC has not yet been fully understood. Here, we identified dysregulated microRNAs (miRNAs) by analyzing miRNA microarray of TNBC patients. MiR-371b-5p expression was reduced, and ectopic expression of miR-371b-5p significantly inhibited TNBC progression in vitro and in vivo. In addition, we found that expression of cold shock domain-containing protein E1 (CSDE1), a direct target gene of miR-371b-5p, was upregulated in TNBC cells, and inhibition of CSDE1 alleviated TNBC cell growth by decreasing RAC1 known as pro-metastatic gene. Mechanistically, CSDE1, phosphorylated C-terminal domain (p-CTD) of RNA polymerase II (RNAPII), and CDK7 form a complex, and downregulation of CSDE1 results in weak interaction between RNAPII p-CTD and CDK7, which leads to a decrease in RNAPII p-CTD expression to reduce RAC1 transcript levels in CSDE1-deficient TNBC cells. Our data revealed the oncogenic function of miR-371b/CSDE1 involved in Rac1 transcription regulation, thus providing a basis for the pathological mechanism of TNBC along with potential biomarkers for TNBC.
Citation Format: Yesol Kim, Je Yeong Ko, Soo-Been Lee, Jaehee Jun, Yejin Ahn, Jinui Min, Chaewon Oh, Jong Hoon Park. Dysregulated miR-371b-5p/CSDE1/RAC1 axis is involved in pathogenesis of triple-negative breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4738.
Abstract 4746: Amelioration of hemoglobinopathies by targeted deletion of zinc finger domain within BCL11A gene using CRISPR-Cas9 technology
Authors: Hussain Irfan , Mumtaz Kainaat , Hassan Hammad , Mian Afsar Ali 
Published: April 2023

Abstract
Background: In humans, the β-like globin genes are encoded from a single locus comprising five globin genes (ε-, Gγ-, Aγ-, δ-, and β-globin in sequence) and their expression is under developmental control. The γ-globin genes (Gγ- and Aγ-) are expressed during fetal life and replaced by adult β-globin after birth. Mutations in the β-globin gene cause β-hemoglobinopathies such as sickle cell disease (SCD) and β-thalassemia. The clinical severity of SCD and β-thalassemia can be mitigated by elevated fetal hemoglobin (HbF) levels, which have been found in individuals with the benign hereditary persistence of fetal hemoglobin (HPFH) syndrome. Thus, reactivating the expression of γ-globin genes is an attractive treatment strategy for β-hemoglobinopathies. Reactivation of γ-globin expression by disrupting the binding of the BCL11A transcriptional repressor complex to the γ-globin gene promoter, provides a novel approach for inducing fetal hemoglobin.
Methodology: The BCL11A binds a 5′-TGACCA-3′ element (spanning nucleotides −118 to −113) of globin genes using its three C-terminal Zinc fingers (Znf). The binding efficiency of Znf4, Znf5, and Znf6 was predicted by using in silico tools (SIFT, SNAP, PolyPhen-2, PANTHER, I-Mutant, PROVEAN, SNPs&GO, mCSM, and PhD-SNP), molecular dynamic simulation and homology modelling. K562 cells were electroporated with CRISPR-Cas9 targeting the BCL11A Znf4.
Results: The binding energy scores illustrate that deleting Znf5 and Znf6 decreased the binding affinity by ~3.7-fold, whereas deleting Znf4 decreased the affinity by &gt; 70-fold. Using CRISPR-Cas9 genome-editing strategy, we deleted Znf4 (260bp genomic region) within the BCL11A in K562 cell lines. Znf4 deletion resulted in a readily detectable γ-globin increase with a preferential increase in G-gamma.
Conclusion: Altogether, our findings highlight the valuable insights for improving gene editing therapy strategies by either deleting Znf4 of BCL11A or the TTGACCA motif to disrupt the interaction between BCL11A and other interacting partners and the γ-globin gene promoter. Complete failure in the protein-protein interactions with functional partners and to the γ-globin gene promoter revealed that Znf4 is a suitable target for disrupting BCL11A-mediated hemoglobin switching.
Citation Format: Irfan Hussain, Kainaat Mumtaz, Hammad Hassan, Afsar Ali Mian. Amelioration of hemoglobinopathies by targeted deletion of zinc finger domain within BCL11A gene using CRISPR-Cas9 technology. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4746.
Abstract 4750: TWIST2 mediated chromatin remodeling promotes fusion-negative rhabdomyosarcoma
Authors: Shah Akansha M. , Guo Lei , Morales Maria Gabriella , Jaichander Priscilla , Chen Kenian , Huang Huocong , Hernandez Karla Cano , Xu Lin , Bassel-Duby Rhonda , Olson Eric N. , Liu Ning 
Published: April 2023

Abstract
Rhabdomyosarcoma (RMS) is a common soft tissue sarcoma in children that resembles the developing skeletal muscle. Unlike normal muscle cells, RMS cells fail to differentiate despite expression of the myogenic determination protein MYOD. The TWIST2 transcription factor is frequently overexpressed in fusion-negative RMS (FN-RMS). TWIST2 blocks differentiation by inhibiting MYOD activity in myoblasts, but its role in FN-RMS pathogenesis is incompletely understood. Here, we show that knockdown of TWIST2 enables FN-RMS cells to exit the cell cycle and undergo terminal myogenesis. TWIST2 knockdown also substantially reduces tumor growth in a xenograft model of FN-RMS. Mechanistically, TWIST2 controls H3K27 acetylation at distal enhancers by interacting with the chromatin remodelers SMARCA4 and CHD3 to activate growth-related and repress myogenesis-related target genes, respectively. These findings provide novel insights into the role of TWIST2 in maintaining an undifferentiated and tumorigenic state of FN-RMS and highlight the potential of suppressing TWIST2-regulated pathways to treat FN-RMS.
Citation Format: Akansha M. Shah, Lei Guo, Maria Gabriella Morales, Priscilla Jaichander, Kenian Chen, Huocong Huang, Karla Cano Hernandez, Lin Xu, Rhonda Bassel-Duby, Eric N. Olson, Ning Liu. TWIST2 mediated chromatin remodeling promotes fusion-negative rhabdomyosarcoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4750.
Abstract 4755: Screening non-small cell lung cancer organoids with epigenetic probes
Authors: Jafarova Khadija , Prinos Panagiotis , Radulovich Nikolina , Koga Takamasa , Arrowsmith Cheryl , Liu Geoffrey , Tsao Ming Sound 
Published: April 2023

Abstract
Introduction: NSCLC is associated with high cancer-related mortality worldwide. Epigenetic modifications at the chromatin level have widely been linked to carcinogenesis. Epigenetic regulation not only contributes to the development of cancer, but it may also confer resistance to therapies by promoting the survival of clones that can overcome treatment-induced stress or give rise to complex tumor heterogeneity in response to cancer therapy. Investigating susceptibility resulting from epigenetic aberrations in tumor cells may reveal novel markers of therapies that target epigenetic aberrations. In this study, we treated NSCLC organoid models with a library of 41 epigenetic probes to identify epigenetic targets that affect tumor cell survival.
Methods: Epigenetic screen. NSCLC organoid models were established from resected patient tumors or patient-derived xenografts. Organoids were dissociated into single cells and plated in matrigel-coated 384-well plate. Each model was treated with a library of epigenetic probes (1uM) and a DMSO control over a period of 8 days. Library was provided by Structural Genomics Consortium (www.thesgc.org) and contained compounds targeting a variety of protein domains some of which had activity on acetylation, methylation, histone de-methylation etc. CellTiter-Glo assay was performed to measure cell survival.
Results: Among the epigenetic probe compounds tested on 26 models, LLY 283 (PRMT5 inhibitor) showed the most significant effect on inhibition of cell growth in 69% of organoid models
(18/26) with suppression of &gt;=40% as compared to the DMSO control. To assess differential responses to treatment with LLY 283, four organoid models were treated with 21 different concentrations of PRMT5 inhibitor. Growth curves of a sensitive (XDO181) and a less sensitive (XDO4056) models were compared. For XDO181 and XDO4056, IC50 values were calculated to be 4.7 nM and 31.8 nM respectively, indicating that a less sensitive model is associated with a 7-fold increase in IC50 value compared to the sensitive model.
Conclusion: A screen using epigenetic compounds on NSCLC patient-derived organoids revealed sensitivity to PRMT5 inhibitor in 69% of the organoid models tested. Further investigation will explore the mechanisms that are associated with sensitivity to PRMT5 inhibition.
Citation Format: Khadija Jafarova, Panagiotis Prinos, Nikolina Radulovich, Takamasa Koga, Cheryl Arrowsmith, Geoffrey Liu, Ming Sound Tsao. Screening non-small cell lung cancer organoids with epigenetic probes. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4755.