bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4412: Defining chromatin alterations in liver cancer at single cell resolution
Authors: Ramirez Miguel , Stephan Tabea , Schaeffer Daivd , Hoodless Pamela 
Published: March 2024

Abstract
Hepatocellular carcinoma (HCC) is the most common liver cancer and arises from the malignant transformation of hepatocytes. HCC tumors often express genes critical for hepatocyte development but the regulatory mechanisms driving aberrant expression remain unclear. Recent evidence indicates that epigenetic alterations contribute to HCC progression with nearly 50% of cases associated with mutations in chromatin modifiers. Thus, it is imperative to understand how chromatin is altered in HCC and identify the DNA regulatory sequences associated with HCC tumorigenesis. Our study aims to map the chromatin landscape and transcriptome in HCC tumors using a multiomic approach at single cell resolution. Single-cell ATAC- and RNA-seq will be conducted in HCC tumors, matched controls and normal livers to identify regulatory sequences and their target genes critical for HCC tumor progression. We will characterize these regulatory sequences in the context of liver development using genetic manipulation and epigenomic datasets generated from human pluripotent stem cells differentiated to hepatic lineages. Our goal is to elucidate how epigenetic alterations in HCC drive cancer progression and how they relate to a dedifferentiated state.
Citation Format: Miguel Ramirez, Tabea Stephan, Daivd Schaeffer, Pamela Hoodless. Defining chromatin alterations in liver cancer at single cell resolution [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 4412.
Abstract 4413: Identifying genome-wide histone profiles in patient derived models of AML for predictive biomarker development
Authors: Simmons Alysha , Oswald Eva , Kuales Georg , Keogh Michael , Kumary Vishnu U. , Brill Eva , Cowles Martis W. , Venters Bryan , Schueler Julia B. 
Published: March 2024

Abstract
Acute myeloid leukemia (AML) is a complex disease with highly individualized treatment plans for patients. Mostly these are based on genetic and phenotypic markers of the disease, but the patient’s overall condition is playing a significant role as well. To develop innovative drugs for a broad patient cohort, it is essential to understand the biological implications of these differences and to model them preclinically. In this study, we are assessing the utility of EpiCypher’s CUT&Tag-FFPE platform to characterize the epigenome of AML PDX samples. CUT&Tag-FFPE is an epigenome profiling assay that is compatible with Formalin-Fixed Paraffin-Embedded (FFPE) samples, enabling robust genome-wide profiling of histone modifications from limited clinical samples. We derived PDX model LEXFAM 2799 (NPM1 wt; FLT3 wt, t(8;21)) and LEXFAM 2966 (NPM1 mut; FLT3 wt) from treatment naïve patients and established in immunocompromised NSG mice. LEXFAM 2799 is a fast-growing model with passaging times of 33 days, whereas LEXFAM 2966 displays a passaging time of 140 days. We next treated with Standard of Care (SoC) agents Decitabine, Cytarabine and all-trans-retinoic acid (ATRA): LEXF 2966 was highly sensitive towards Decitabine leading to complete remission. Cytarabine induced a partial remission and ATRA had only minor effect on tumor growth. In contrast LEXFAM 2799 was resistant towards treatment with ATRA and showed only partial remission under treatment with Cytarabine or Decitabine. Using the CUT&Tag-FFPE platform we are analyzing FFPE slides from the above mentioned two AML PDX models to investigate differences in the genome-wide histone profile that relate to the different growth behavior as well as sensitivity towards SoC treatment. The goal of these studies is to identify tumor model specific profiles that correlated specifically with the sensitivity towards the hypomethylating agent Decitabine. In addition, we plan to analyze additional untreated as well as treated AML PD models to validate the identified signatures confirming them as predictive biomarkers for sensitivity towards current standard of care and prospectively as well innovative compounds.
Citation Format: Alysha Simmons, Eva Oswald, Georg Kuales, Michael Keogh, Vishnu U. Kumary, Eva Brill, Martis W. Cowles, Bryan Venters, Julia B. Schueler. Identifying genome-wide histone profiles in patient derived models of AML for predictive biomarker 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 4413.
Abstract 4468: Elucidating the phosphoinositide-modulatory function of INPP5B in regulating cancer stemness and tumorigenesis in liver cancer
Authors: Liu Linglin , Wang Yifei , Xie Yunong , Tong Man 
Published: March 2024

Abstract
Hepatocellular carcinoma (HCC) represents a major global health challenge, characterized by its heterogeneity and aggressive nature. Solid evidence has now suggested that tumor growth is driven by subpopulations of tumor cells with less differentiated cell states, called cancer stem cells (CSCs), which govern therapeutic resistance and tumor recurrence. Therefore, characterization of CSCs and their associated oncogenic signaling pathways is crucial to the development of more specific and sensitive HCC prognostic markers and to the design of novel targeted therapies against CSCs for HCC treatment. In search of the altered genes and pathways that are tightly associated with cancer stemness trait in HCC, we exploited the stemness and oncogenic dedifferentiation signature to mine the HCC dataset of the Cancer Genome Atlas. Phosphoinositide signaling was identified to be enriched and downregulated in the transcriptomes of HCC patients with strong stemness and dedifferentiated signature. Subsequent clinical correlation analysis found inositol polyphosphate-5-phosphatase B (INPP5B) to be the top downregulated gene in phosphoinositide signaling with its expression correlated with poor survival in HCC patients. Functional studies showed that INPP5B overexpression reversed the oncogenic and stemness properties while INPP5B knockout promoted tumor growth in immunocompetent mice. Subsequent RNA sequencing and molecular assays revealed INPP5B deregulation to be associated with lipid metabolism remodeling. Collectively, our results suggest an intricate relationship between phosphoinositide signaling and lipid metabolism through the regulation of INPP5B in HCC. The findings may open new avenue for future research aimed at devising targeted therapies to interfere with liver CSCs and enhance the prognosis of HCC patients.
Citation Format: Linglin Liu, Yifei Wang, Yunong Xie, Man Tong. Elucidating the phosphoinositide-modulatory function of INPP5B in regulating cancer stemness and tumorigenesis in liver 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 4468.
Abstract 4477: The development of a small molecule dual inhibitor of CXCR4 and Mcl-1 to target bortezomib resistant and stem-like cells in multiple myeloma
Authors: Elbezanti Weam Othman , Al-Odat Omar S. , Jonnalagadda Subash C. , Budak-Alpdogan Tulin , Pandey Manoj K. 
Published: March 2024

Abstract
Multiple myeloma (MM) is a malignant plasma-cell illness defined by clonal growth of malignant plasma cells within the bone marrow (BM) microenvironment. Despite the availability of many therapeutic alternatives, MM remains consistently lethal, demanding the development of novel techniques. The intimate relationship between myeloma cells and the BM microenvironment is a distinguishing hallmark of MM. The chemokine stromal cell-derived factor-1 (SDF-1) and its receptor CXCR4 enhance the homing of MM cells to the BM, which has important functional implications. The BM microenvironment secretes a variety of hormones and cytokines that activate several signaling pathways, resulting in enhanced production of the anti-apoptotic Mcl-1 protein, boosting the proliferation, survival, and migration of MM cells and conferring resistance to standard chemotherapy. As a result, we created GA-A, a hybrid molecule in which we coupled an aralkyl carboxylic acid moiety, known to preferentially inhibit Mcl-1, to gambogic acid, which has previously been demonstrated to inhibit CXCR4 in MM. Our western blot has shown that this unique hybrid compound successfully suppressed CXCR4 and Mcl-1. Interestingly, using qPCR we found that CXCR4 was observed to be higher expressed in CD138- versus CD138+ cells, while GA-A inhibited CXCR4 in both subpopulations. In addition, using annexin-V flow cytometry staining we found that GA-A increased the apoptotic effect of bortezomib in MM stem-like cells while inhibiting the viability of bortezomib resistant cells. Using human cytokine array we found that GA-A activates some of proinflammatory cytokines that can activate the immune system such as GM-CSF, IFN gamma, IL-2 and IL-12. In summary, our findings indicate the successful creation of a novel dual CXCR4-Mcl1 inhibitor that demonstrates efficacy against the stem cell-like population and bortezomib resistant cells and enhances the effectiveness of bortezomib.
Citation Format: Weam Othman Elbezanti, Omar S. Al-Odat, Subash C. Jonnalagadda, Tulin Budak-Alpdogan, Manoj K. Pandey. The development of a small molecule dual inhibitor of CXCR4 and Mcl-1 to target bortezomib resistant and stem-like cells in multiple myeloma [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 4477.
Abstract 4479: Design, synthesis, and evaluation of amino acid conjugated niclosamide prodrugs as a PepT1 substrate
Authors: McDonough Alaina C. , Cheng Jeffery Y. , Mohammed Shabber , Li Pui-Kai , Bhutia Yangzom 
Published: March 2024

Abstract
The anthelmintic drug, Niclosamide, has a multitude of promising anticancer properties including inhibition of key signaling pathways involved in tumorigenesis, disruption of mitochondrial function, degradation of the overexpressed androgen receptor, and more. However, a key limitation of the clinical use of Niclosamide in cancer treatment is its low solubility and cellular uptake, which result in poor pharmacokinetic properties and dose-limiting GI toxicities at concentrations lower than the therapeutic threshold of the drug. To overcome this, we hypothesized that we could use amino acid conjugated niclosamide prodrugs to improve cellular uptake by creating a substrate of the PepT1 transport protein. The overexpression of the PepT1 transport protein that is involved in many hormonal cancers is being used to our advantage. Our study involved first synthesizing a group of niclosamide and niclosamide analogs conjugated with polar or nonpolar amino acids. Next, we conducted a Glycine-Sarcosine assay measuring changes in the uptake of the dipeptide glycyl-sarcosine (Gly-Sar). Our initial step was to examine if our conjugates could disrupt the absorption of Gly-Sar. The active conjugate will be tested whether they are substrates or inhibitors of the transporter. For the future, we have plans to determine the half-maximal inhibitory concentration (IC50) of niclosamide conjugates in various cancer cell lines and to quantify cleavage of the prodrugs intracellularly.
Citation Format: Alaina C. McDonough, Jeffery Y. Cheng, Shabber Mohammed, Pui-Kai Li, Yangzom Bhutia. Design, synthesis, and evaluation of amino acid conjugated niclosamide prodrugs as a PepT1 substrate [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 4479.
Abstract 4500: A high-throughput approach to discover and characterize glueable ligase-target pairs
Authors: Sen Arpita , Burke Phil , Bansal Ruchi , Krayushkina Dasha , Noble David , McGowan Kerry , Murakowska Natasha Seelam , Reed Paxton , Barrett Juliana , Lopez Randolph 
Published: March 2024

Abstract
Targeted protein degradation can be induced with monovalent small molecules, termed molecular glues, that modify the substrate-binding interface of E3 ligases and reroute them to novel targets. Despite there being over 600 E3 ligases encoded in the human genome, most glues have focused on only a few. Expanding to additional ligases and targets is challenging due to the low probability of successful 'glueing.' Many have suggested that a weak basal interaction between a ligase and neo-substrate is an important prerequisite for the function of a molecular glue, but such weak interactions are challenging to discover. To address this need, we have harnessed AlphaSeq, a synthetic biology platform that measures protein-protein interactions at scale and with high sensitivity, to identify and characterize novel E3-target pairs. Our approach is twofold. First, we test for novel weak interactions (~100nM to 10uM) between a panel of E3 ligases and a library of disease relevant target proteins. Second, starting from a weakly interacting protein pair, we build mutational libraries of both proteins and measure their binding strengths. Mutations that strengthen binding serve to validate the weak interaction, provide structural insights into the nature of binding, and help to inform subsequent small molecule discovery. Here, we present our approach to discover and evaluate glueable ligase-target pairs using AlphaSeq, validation through proof-of-concept experiments involving a known interaction agonized by small molecules, and examples of novel glueable ligase-target pairs that we have recently discovered.
Citation Format: Arpita Sen, Phil Burke, Ruchi Bansal, Dasha Krayushkina, David Noble, Kerry McGowan, Natasha Seelam Murakowska, Paxton Reed, Juliana Barrett, Randolph Lopez. A high-throughput approach to discover and characterize glueable ligase-target pairs [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 4500.
Abstract 4508: Defining PIM kinase protein regulation and PROTAC for pre-clinical testing
Authors: Liou Hope , Brognard John , Swenson Rolf , Torres-Ayuso Pedro , Warfel Noel 
Published: March 2024

Abstract
The PIM kinase family are serine/threonine kinases known to be overexpressed in castration-resistant prostate cancer (CRPC). PIM1, an isoform of PIM, is known to regulate cell survival, migration, and proliferation. Uniquely, PIM kinases are constitutively active due to the lack of a regulatory domain. Therefore, PIM protein levels are reflected in PIM activity and are regulated by protein degradation and synthesis. PIM inhibitors have been developed, targeting the PIM kinase activity and inhibiting phosphorylation of downstream targets, but have had limited efficacy. Our lab and others demonstrate that PIM inhibitor treatment increases total PIM protein levels, suggesting that PIM kinases control protein stability via autophosphorylation. To elucidate the mechanism of autophosphorylation dependent regulation of PIM1, we used phospho-proteomics to identify potential autophosphorylation sites on PIM1. We have identified overexpression of deubiquitinase USP28 inhibiting degradation of PIM1, leading to the investigation of the role of F-box protein Fbw7 in regulating PIM1. Dominant-negative expression of Fbw7 results in increased PIM1 total protein. Additionally, coimmunoprecipitation of Fbw7 knockdown cells resulted in decreased PM1 ubiquitination compared to control. Therefore, we have identified Fbw7 as a putative E3 ligase responsible for PIM1 degradation. To address the limited efficacy of PIM inhibitors, we have developed the first PIM-PROTAC (PIMTAC) with our collaborators. Proteolysis targeting chimera (PROTAC) is a promising approach to eliminating the pro-tumorigenic effects of PIM. The PIMTAC selectively targets PIM kinases for degradation and we have demonstrated in vitro efficacy. PIMTAC successfully maintains degradation of all isoforms of PIM for over 72 hours. In vitro assessment of anti-tumor efficacy demonstrated increased apoptotic death with PIMTAC alone compared to PIM inhibitor or docetaxel. Furthermore, dual treatment of PIMTAC and docetaxel had more apoptotic death compared to PIM inhibitor with docetaxel. We aim to develop the PIMTAC for pre-clinical testing.
Citation Format: Hope Liou, John Brognard, Rolf Swenson, Pedro Torres-Ayuso, Noel Warfel. Defining PIM kinase protein regulation and PROTAC for pre-clinical testing [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 4508.
Abstract 4510: Potent and orally efficacious PROTAC degraders of estrogen receptor α (ERα)
Authors: Rej Rohan K. , Chen Zhixiang , Acharyya Ranjan K. , Wu Dimin , Hu Biao , Xu Guozhang , Nagilla Rakesh , Metwally Hoda , Wang Yu , Wen Bo , Sun Duxin , Bai Longchuan , Wang Shaomeng 
Published: March 2024

Abstract
The estrogen receptor α (ERα) plays a crucial role in hormonally driven breast cancer, making it a clinically validated oncology target. Over the past 30 years, SERMs, SERDs, and AIs have been the mainstay of endocrine therapy for ER+ breast cancer, but relapse and resistance remains a significant challenge for metastatic breast cancer, leading to cancer recurrences, metastasis, and mortality. We report the discovery and extensive evaluations of potent and orally efficacious ERα degraders using the PROTAC technology through extensive optimization of the cereblon ligands, the linker and ER ligands. Our lead compounds (UM-ERD-3111 and UM-ERD-4001) achieved sub-nanomlar DC50 values in ER degradation and demonstrate excellent oral bioavailability. Oral administration of these ER degraders effectively reduces the ER wild-type and ER mutated proteins in tumor tissues in mice. Both ERD-3111 and UM-ERD-4001 are capable of inducing tumor regression in vivo and are more efficacious than ARV-471, a PROTAC ER degrader currently in phase 3 clinical development. UM-ERD-3111 and UM-ERD-4001 are highly promising compounds for extensive evaluations as potential new therapies for the treatment of ER+ human breast cancer.
Citation Format: Rohan K. Rej, Zhixiang Chen, Ranjan K. Acharyya, Dimin Wu, Biao Hu, Guozhang Xu, Rakesh Nagilla, Hoda Metwally, Yu Wang, Bo Wen, Duxin Sun, Longchuan Bai, Shaomeng Wang. Potent and orally efficacious PROTAC degraders of estrogen receptor α (ERα) [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 4510.
Abstract 4511: Discovery of the first-in-class G9a/GLP PROTAC degrader
Authors: Velez Julia , Han Yulin , Park Kwang-Su , Kabir Md , Yang Peiyi , Xiong Yan , Kaniskan H. Umit , Jin Jian 
Published: March 2024

Abstract
G9a and GLP are lysine methyltransferases that catalyze dimethylation of histone H3 lysine 9 (H3K9me2), a transcriptionally repressive mark. Aberrantly expressed G9a/GLP has been implicated in numerous cancers, including prostate, lung, and leukemia. The oncogenic activity of G9a/GLP is attributed to both its catalytic and non-catalytic functions, such as forming co-activator complexes with p300, CARM1, GRIP1, and Mediator to positively regulate gene transcription. As such, current G9a/GLP enzymatic inhibitors display limited anti-cancer activity. As an alternative therapeutic strategy, PROTAC degraders harness the ubiquitin-proteasome system (UPS) to effectively eliminate oncoproteins and abrogate all catalytic and non-catalytic functions. Here, we present the first-in-class G9a/GLP PROTAC degrader, MS8709, which potently degrades G9a and GLP in a time-, concentration-, and UPS-dependent manner. Moreover, MS8709 induces superior cell growth inhibition compared to its parent inhibitor in prostate, lung, and leukemia cell lines. Overall, MS8709 is a useful chemical tool to investigate G9a/GLP biology and offers a novel approach for the treatment of G9a/GLP-dependent cancers.
Citation Format: Julia Velez, Yulin Han, Kwang-Su Park, Md Kabir, Peiyi Yang, Yan Xiong, H. Umit Kaniskan, Jian Jin. Discovery of the first-in-class G9a/GLP PROTAC degrader [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 4511.
Abstract 4519: Discovery of highly potent, selective and efficacious STAT3 PROTAC degraders capable of achieving complete tumor regression
Authors: Zhou Haibin , Wu Dimin , Bai Longchuan , Acharyya Ranjan K. , Metwally Hoda , McEachern Donna , Wen Bo , Sun Duxin , Wang Shaomeng 
Published: March 2024

Abstract
STAT3 (signal transducer and activator of transcription 3) is a transcription factor and a promising therapeutic targets for cancer and other human diseases. We have previously reported the discovery of SD-36 and SD-91 as potent, selective and highly efficacious STAT3 degraders. In the present study, we report the discovery and extensive evaluation of highly potent, selective and efficacious new STAT3 degraders designed using novel cereblon ligands and novel STAT3 ligands. Our most potent STAT3 degraders are &gt;10-times more potent than SD-36 in inducing STAT3 degradation in cells and demonstrates &gt;100-fold degradation selectivity over other STAT members. They achieve nanomolar IC50 values in leukemia and lymphoma cancer cell lines with activated STAT3. A single intravenous dose of these STAT3 degraders reduces the STAT3 protein for &gt;48 hrs in xenograft tumor and native tissues, without reducing another other STAT members. Weekly administration of these STAT3 degraders is capable of achieving complete tumor regression in xenograft tumor models without any signs of toxicity. Taken together, these STAT3 degraders are promising lead compounds for extensive evaluation for the treatment of the treatment of human cancers and other human diseases in which STAT3 plays a key role.
Citation Format: Haibin Zhou, Dimin Wu, Longchuan Bai, Ranjan K. Acharyya, Hoda Metwally, Donna McEachern, Bo Wen, Duxin Sun, Shaomeng Wang. Discovery of highly potent, selective and efficacious STAT3 PROTAC degraders capable of achieving complete tumor regression [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 4519.