bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5165: Novel approach to colorectal cancer drug target discovery in human FFPE tissue using the Adaptive Dynamic Artificial Polyligand Targeting System
Authors: Williams Stephanie , Sima Chao , Hornung Tassilo , Rosenow Matthew , Tinder Teresa , Maher Varun , Kassner Michelle , Ortiz Gerri , Mok Perrin , Helle Nicholas , Logie Stephen , ONeill Heather , Miglarese Mark , Spetzler David 
Published: September 2020

Abstract
Identification of novel biomarkers and drug targets for colorectal cancer remains a critically unmet medical need. Target identification has historically been driven by preclinical models which poorly recapitulate the complex biology of human cancers. We describe a unique approach to drug target identification and comprehensive profiling directly in clinical specimens. Using the Adaptive Dynamic Artificial Polyligand Targeting (ADAPT) system, we aimed to identify such disease specific drug targets using a highly complex library of single-stranded oligodeoxynucleotides (ODNs). To generate the library, the ODNs were enriched using FFPE tissue specimens from pathologically determined colorectal cancer (CRC) and counter-selected against normal adjacent tissue (NAT) regions. Once the specificity of the library was verified via differential binding on independent CRC cases, it was used to affinity purify cognate biding partners from 393 CRC FFPE lysates with appropriate representation of cases with either KRAS, NRAS or BRAF mutations. Greater than 700 proteins were identified by mass spectrometry exclusively in the CRC FFPE tissue lysates and not in the NAT FFPE tissue lysates for all 393 CRC cases. Classification of these proteins into the druggable protein classes revealed G-protein coupled receptors, transporters, voltage-gated ion channels, proteases, and protein kinases. In addition, subsequent verification studies confirmed novel candidate cell surface protein targets appropriate for targeting by antibody-drug conjugates (ADC) or other biologic modalities. mRNA expression corresponding to the 700 potential targets was analyzed in over 1600 CRC FFPE tumor samples and &gt;9000 other cancer types as well as in a broad panel of normal tissues by Whole Transcriptome Sequencing (WTS) and immunohistochemistry (IHC). We conclude that the unbiased ADAPT platform provides a robust and novel approach to drug target discovery with highly selective expression profiles directly from FFPE clinical specimens.
Citation Format: Stephanie Williams, Chao Sima, Tassilo Hornung, Matthew Rosenow, Teresa Tinder, Varun Maher, Michelle Kassner, Gerri Ortiz, Perrin Mok, Nicholas Helle, Stephen Logie, Heather ONeill, Mark Miglarese, David Spetzler. Novel approach to colorectal cancer drug target discovery in human FFPE tissue using the Adaptive Dynamic Artificial Polyligand Targeting System [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5165.
Abstract 5196: CSFR-1R a potential therapeutic target in 4T1 xenograft breast cancer model
Authors: Elia Jeanne , Zhang Hong , Wen Chiaokai , Yang Xifeng 
Published: September 2020

Abstract
The 4T1 cell line is a mouse mammary carcinoma which can mimic stage IV breast cancer in humans. When these cells are xenografted into a BALB/c mouse there is an infiltration of macrophages into the spleen, bone marrow and blood which was observed 11 days after engraftment. Increased cell proliferation was also detected in the spleen and blood. We found that 4T1 cells produced high levels of M-CSF in culture. In this study we attempt to neutralize the secreted cytokine from the tumor cells with anti-M-CSF (clone, A10603L) or to block the receptor with anti-M-CFR (CSF-1R) (clone, AFS98). Mice were xenografted with 4T1 cells then given one dose of 100 ug of neutralizing antibodies to either anti-M-CSF or anti-CSF-1R two days post tumor engraftment. Animals were sacrificed at multiple time points between 1-3 weeks. Treatment with one dose of anti-M-CSF showed minimal to no difference compared to the 4T1 xenograft group. Treatment with anti-CSF-1R showed reduced macrophage infiltration in the bone marrow, spleen and blood at day 11. BrdU incorporation levels dropped in the spleen and blood of these animals. Spleen size and total cell numbers were also reduced by 40% compared to the 4T1 xenograft group.
Citation Format: Jeanne Elia, Hong Zhang, Chiaokai Wen, Xifeng Yang. CSFR-1R a potential therapeutic target in 4T1 xenograft breast cancer model [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5196.
Abstract 521: CD45 targeted engineered toxin bodies deplete hematopoietic and malignant cells
Authors: Iberg Aimee , Robinson Garrett L. , LeMar Sara , Dekker Joseph D. , Zhao Jay , Ramos Hilario J. , Singh Melissa M. , Willert Erin K. 
Published: September 2020

Abstract
CD45 is highly expressed on the cell surface of all nucleated hematopoietic cells, including malignant cells of B, T and myeloid lineage. CD45, a receptor tyrosine phosphatase that has important roles in antigen receptor signaling, has multiple isoforms that are differentially expressed on immune cell subsets. Targeting of CD45 with antibody-based therapies, tested in conjunction with reduced dose chemotherapy and radiation regimens, has shown promise in preclinical models and clinical trials as a conditioning therapy for bone marrow transplant (BMT), although these approaches are associated with safety limitations. A single agent, targeted conditioning method could increase patient safety and eliminate genotoxic effects associated with the conditioning regimens. Conditioning therapy by depletion of CD45 positive cells specifically has potential applications in oncology as well as non-oncologic, hematopoietic disease settings where engraftment of donor or modified stem cells could provide benefit. Engineered toxin bodies (ETBs) are comprised of a proprietarily engineered form of Shiga-like Toxin A subunit (SLT-A) genetically fused to antibody-like binding domains. ETBs work through novel mechanisms of action and are capable of forcing internalization, self-routing through intracellular compartments to the cytosol, and inducing potent cell-kill via the enzymatic and permanent inactivation of ribosomes. Targeted ETBs are being developed to specifically target and destroy CD45 expressing cells. ETBs targeting CD45 specifically bind to, internalize into and then trigger cell death of the target cells in vitro. ETBs have been designed using antibody fragments that recognize all isoforms of CD45. The CD45 targeted ETB has shown high potency in immortalized blood cancer cell lines of T cell, B-cell and eosinophil origin, including leukemia and lymphoma cell lines. Additionally, the ability of the CD45 targeted ETBs to deplete primary cells from healthy donors has been demonstrated. The direct cell kill activity of the CD45 targeted ETBs have the potential to deplete immune cells in the periphery and the bone marrow, as well as to deplete malignant hematological cells expressing CD45. In vivo depletion of human immune cells in murine models by CD45 targeted ETBs will be evaluated.
Citation Format: Aimee Iberg, Garrett L. Robinson, Sara LeMar, Joseph D. Dekker, Jay Zhao, Hilario J. Ramos, Melissa M. Singh, Erin K. Willert. CD45 targeted engineered toxin bodies deplete hematopoietic and malignant cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 521.
Abstract 5212: The benefits of Didox in triple negative breast cancer treatment targeting mutant p53
Authors: Sultana Nahid , Wilson Elizabeth A. , Shah Khyati N. , Elford Howard L. , Faridi Jesika S. 
Published: September 2020

Abstract
Triple-negative breast cancer (TNBC) is an aggressive histological subtype of malignancy with limited treatment options. Frequently, doxorubicin (DOXO)- based chemotherapy is utilized in this patient population due to the lack of molecular targets available. While DOXO is an effective chemotherapeutic agent, its efficacy is limited due to acquired drug resistance and cardiotoxicity. Therefore the identification of other treatment options for TNBC is needed. TNBC is a heterogeneous malignancy, with 70% of cases classified as a basal subtype, which further complicates the search for an effective molecular target. However, it has been identified that 80% of TNBC samples carry TP53 (tumor protein p53) mutations, which leads to a mutant p53 protein no longer able to act as a tumor suppressor and thus failing to halt cell growth. Mutant p53, when present in malignant cells, is far less susceptible to degradation than its wild-type counterpart, and thus accumulates within the cell. As such, the TP53 is an attractive therapeutic target for TNBC. We have previously identified that ribonucleotide reductase M2 (RRM2) is upregulated in TNBC cells and is a key contributor to acquired drug resistance. The ribonucleotide reductase inhibitor Didox has been shown to be a powerful free radical scavenger and iron chelator. Through these mechanisms, Didox alleviates the non-selective cytotoxic effects of DOXO on non-cancerous tissue, including cardiotoxicity and potentiates DOXO's efficacy against malignant cells. We have previously reported that Didox in combination with DOXO effectively treats TNBC by enhancing tumor inhibition and minimizing DOXO-induced heart damage. Our current study shows that Didox alone or in combination with DOXO downregulates mutant p53 protein levels in the mutant p53 TNBC cell lines MDA-MB 468, MDA-MB 231 and BT-20. This effect is notably absent in breast cancer cell lines with wild-type p53, including MCF7, A3B5 and ZR751, where p53 successfully acts as a tumor suppressor allowing for cell cycle arrest or apoptosis after DNA damage. We hypothesize that mutant p53 is a valid therapeutic target in TNBC. As shown here, the addition of Didox downregulates mutant p53 levels and thus enhances tumor inhibition while alleviating DOXO-associated cardiotoxicity.
Citation Format: Nahid Sultana, Elizabeth A. Wilson, Khyati N. Shah, Howard L. Elford, Jesika S. Faridi. The benefits of Didox in triple negative breast cancer treatment targeting mutant p53 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5212.
Abstract 5230: Real-time monitoring of PROTAC and molecular glue targeted degradation in living cells
Authors: Cosby Neal C. , Riching Kristin M. , Mahan Sarah , Caine Elizabeth A. , Daniels Danette L. , Urh Marjeta 
Published: September 2020

Abstract
The emergence of targeted protein degradation as a broad, new therapeutic modality has greatly expanded the opportunities for treatments of many diseases. Currently, small molecule degrader compounds fall under two major categories; molecular glues and heterobifunctional PROTACs. The two types of compounds both facilitate and induce a ternary complex consisting of an E3 ligase-degrader-target protein, bringing into proximity the machinery proteins required to ubiquitinate and ultimately degrade the target protein. Significant challenges exist in characterization and rank-ordering of degradation compounds in live cells given the differences in dynamics of protein loss and recovery among compounds. Currently, the availability of technologies to interrogate real-time protein degradation is severely lacking. Here, we present a live-cell, luminescence-based technology platform with these capabilities. We employ CRISPR/Cas9 endogenous tagging of target proteins with the small peptide, HiBiT, which has high affinity for and can complement with the LgBiT protein to produce NanoBiT luminescence. This allows for sensitive detection of endogenous protein levels in living cells, and can also serve as a BRET energy donor to study protein:protein or protein:small molecule interactions. We demonstrate the power of this technology in continuous 24-hour monitoring of endogenous target protein levels, and the ability to quantify key degradation parameters for compound ranking including rate, Dmax, and DMax50. We further show the ability to measure the mechanistic steps important for the degradation including kinetics of PROTAC- or molecular glue-induced ternary complex formation and target ubiquitination. These studies facilitate discernment of individual parameters required for successful degradation, ultimately enabling chemical design strategies for optimization and rank ordering of therapeutic degradation compounds.
Citation Format: Neal C. Cosby, Kristin M. Riching, Sarah Mahan, Elizabeth A. Caine, Danette L. Daniels, Marjeta Urh. Real-time monitoring of PROTAC and molecular glue targeted degradation in living cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5230.
Abstract 5235: In vitro validation of drug-target interactions revealed in silico by Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning (CROssBAR) in HCC
Authors: Nalbat Esra , Rifaioglu Ahmet Sureyya , Dogan Tunca , Martin Maria Jesus , Cetin-Atalay Rengul , Atalay Volkan 
Published: September 2020

Abstract
Computational methods are more commonly employed for our understanding of cellular signaling mechanisms with the aim to develop cures for diseases including cancer. Identification of disease specific targeted drugs requires systems level analysis of cellular networks. Our research group developed a comprehensive resource, called CROssBAR, which connects various biological data sources in order to provide a well-connected resource with a focus on drug discovery and precision medicine. CROssBAR aims to predict and reveal novel drug-target interactions using deep learning algorithms. CROssBAR predictions were validated on hepatocellular carcinoma cells which is the 5th most prevalent and 3th deadliest cancer worldwide. We have selected 2 new small molecule kinase inhibitors Lenvatinib, Sunitinib along with Sorafenib and Regorafenib which are currently used in clinics. CROssBAR identifies novel and known gene targets for Lenvatinib, Sunitinib in comparison with Sorafenib and Regorafenib. Genes from SAPK/JNK and PI3K/Akt pathway that were not previously associated with hepatocellular carcinoma therapeutics were determined. All selected small molecules were bioactive on Huh7 and Mahlavu cells by SRB assay. Cell death was characterized by Annexin V which was due to G1/S cell cycle arrest. Further analysis of proteins involved in the SAPK/JNK, PI3K/Akt pathways and apoptotic markers such as PARP and Caspases were examined with immunoblotting upon treatment. As a result, cellular stress mechanisms activated PI3K/Akt and SAPK/JNK pathways which caused programmed cell death in HCC. With our deep learning approach, we were able to demonstrate a correlation between Lenvatinib and Sunitinib and their novel targets in HCC. Our validation results have illustrated that the comprehensive CROssBAR tool developed by our research group achieved in vitro significant predictions of new drugs and their targets against HCC that were not previously reported. Hence with this study we were able to demonstrate the use and validity of the CROssBAR tool along with new targets for primary liver cancer therapeutics.
Citation Format: Esra Nalbat, Ahmet Sureyya Rifaioglu, Tunca Dogan, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay. In vitro validation of drug-target interactions revealed in silico by Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning (CROssBAR) in HCC [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5235.
Abstract 5259: HSPA6 may be a new target by thyraquinone inhibiting migration and invasion of breast cancer cells
Authors: Shen Shiyi , Xiao Ting , Zhou Ju , Wei Chunli , Fu Junjiang 
Published: September 2020

Abstract
Background and Objective: Breast cancer is the malignant tumor with the highest incidence and the second highest mortality among women, and the incidence of breast cancer in China is increasing year by year. The treatment of breast cancer includes radiotherapy, chemotherapy, endocrine therapy, biological targeted therapy and traditional Chinese medicine adjuvant therapy; but the efficacy still needs to be further improved to benefit the patients. Thymoquinone (TQ) is a key component of black grass seed oil and has anti-cancer properties in a variety of tumors. Preliminary studies in our laboratory demonstrated that TQ has a significant inhibitory effect on the migration and invasion of triple negative breast cancer cells.
Methods: To find the new target genes for the inhibition of migration and invasion of breast cancer cells by TQ, RNA-sequencing (RNA-seq) was conducted with and without TQ in human breast cancer cell line BT-549 with high invasion and migration characteristics. Quantitative and semi-quantitative RT-PCR was used to further verify the genes regulated by TQ, and then Western Blotting was used to compare the changes of the genes regulated by TQ at the protein level. Finally, the molecular mechanism of TQ inhibiting migration and invasion of human breast cancer cells was investigated by increasing or decreasing the expression of these genes.
Results: Eighteen differentially expressed genes, which were closely related to the carcinomas in the experimental group and the control group, were obtained by RNA-seq. HSPA6 gene changed significantly, and showed an up-regulation after adding TQ, which was consistent with the results of RNA-seq. By RT-PCR and Western Blotting from different cell lines (BT549, MCF-7, ZR-75-30, SiHa, Caski), we found that the expression of HSPA6 in the experimental group was higher than that in the control group. The subsequent TQ treatment after knockdown / over-expression will be completed for HSPA6 protein functional effects by TQ.
Conclusion: HSPA6 may be a new target gene for TQ to inhibit the migration and invasion of breast cancer cells. The success of this study will provide a new candidate target for clinical treatment of breast cancer. Funding support: National Natural Science Foundation of China (Grant No. 81672887, 81172049)
Citation Format: Shiyi Shen, Ting Xiao, Ju Zhou, Chunli Wei, Junjiang Fu. HSPA6 may be a new target by thyraquinone inhibiting migration and invasion of breast cancer cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5259.
Abstract 5267: Utilizing stimulated Raman scattering microscopy to study intracellular distribution of label-free ponatinib in live cells
Authors: Sepp Kristel , Lee Martin , Bluntzer Marie T. , Helgason G. Vignir , Hulme Alison N. , Brunton Valerie G. 
Published: September 2020

Abstract
Ponatinib is a clinically approved tyrosine kinase inhibitor used to treat chronic myeloid leukemia (CML). Drug resistance is a widespread problem in CML treatment, where ponatinib resistant patients have very limited treatment options. In this study stimulated Raman scattering (SRS) microscopy was used to allow label-free imaging of intracellular ponatinib with high sensitivity and specificity in live human CML cell lines, in the context of ponatinib resistance.
Ponatinib has an alkyne moiety in its structure that makes it inherently Raman active in the cellular silent region of the Raman spectrum. SRS microscopy represents a powerful imaging tool for visualizing label-free drug molecules within cells with high resolution, without the need for additional labels, or nanoparticle sensors as used in many other optical imaging technologies. It provides Raman imaging with minimal spectral distortion and a quantitative output, allowing the intracellular concentrations of drug molecules to be accurately determined.
Intracellular visualization of ponatinib was achieved at biologically relevant, nanomolar concentrations for the first time using SRS. It was determined that ponatinib is sequestered into the lysosomes, with a higher lysosomal concentration found in drug resistant cells. This was associated with increased lysosome biogenesis. Target engagement studies showed that treatment with chloroquine reduced ponatinib accumulation in lysosomes, but did not re-sensitise cells to ponatinib, confirming BCR-ABL independent resistance mechanism in this CML cell model.
In summary, we have visualized intracellular ponatinib localization for the first time using SRS, demonstrating that acquired drug resistance can influence drug uptake and localisation in CML, which in turn has an effect on target engagement.
Citation Format: Kristel Sepp, Martin Lee, Marie T. Bluntzer, G. Vignir Helgason, Alison N. Hulme, Valerie G. Brunton. Utilizing stimulated Raman scattering microscopy to study intracellular distribution of label-free ponatinib in live cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5267.
Abstract 527: Isolation of large and diverse monoclonal antibody panels against the multipass membrane protein targets Kv1.3, P2X7, and Claudin 18.2
Authors: Stafford Lewis J. , Willis Sharon , Rucker Joseph , Doranz Benjamin , Chambers Ross 
Published: September 2020

Abstract
Monoclonal antibodies (MAbs) are a well-established treatment approach in oncology and other diseases. Nevertheless, multipass membrane proteins are largely inaccessible as MAb targets due to their poor expression, membrane-dependent structure, small extracellular regions, and high sequence conservation between humans and rodents. Integral Molecular's MPS Antibody Discovery platform specifically addresses each of these challenges. Using this platform, we have isolated large and diverse panels of functional (agonist/antagonist) MAbs against targets including Claudin 18.2 and the ion channels P2X7 and Kv1.3. A key feature that enables the success of the platform is the use of divergent species for immunization. Chickens are immunized with a combination of DNA and Lipoparticles (high-concentration membrane proteins) to obtain high-titer immune responses against the native membrane protein. Our optimized phage-display protocols allow the isolation of large panels of MAbs against diverse epitopes. The MPS Antibody Discovery platform offers the potential for discovering MAbs against difficult targets in cancer with a success rate over 95%.
Citation Format: Lewis J. Stafford, Sharon Willis, Joseph Rucker, Benjamin Doranz, Ross Chambers. Isolation of large and diverse monoclonal antibody panels against the multipass membrane protein targets Kv1.3, P2X7, and Claudin 18.2 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 527.