bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1723: Spatial analysis of tumor-infiltrated immune cells with highly specific RNAscope™ RNA-protein Co-detection assays
Authors: Dikshit Anushka , Basak Sayantani , Doolittle Emerald , Kovalenko Ilya , Bunting Michaeline 
Published: June 2022

Abstract
Interrogating complex tumor microenvironment requires a multi-omics approach that can provide high level of sensitivity and specificity. Identifying immune cell subsets within the tumor can be vital for predicting response and determining therapeutic efficacy. Detecting target immune cell markers using immunohistochemistry/Immunofluorescence (IHC/IF) and visualizing cytokine expression with in situ hybridization (ISH) can provide comprehensive information about the activation states of immune cells. Here, we demonstrate a newly developed integrated ISH and IHC/IF workflow compatible with manual and automated platforms that can substantially improve RNA-protein co-detection. We demonstrate the use of our RNA-Protein Co-detection assay in combination with the automated RNAscope Multiplex Fluorescent v2 assay, automated RNAscope Chromogenic Duplex assay and manual RNAscope Multiplex Fluorescent v2 assay to detect T cell markers, macrophage markers and checkpoint markers in the tumor microenvironment by using a microarray with different tumor samples. We identified CD4+ helper T cells and CD8+ cytotoxic T lymphocytes. Additionally, we determine the activation states of CD8+ T cells by visualizing IFNG, GZMB and IL-2 expression. We were also able to identify macrophages detected by CD68 protein expression and the M1 and M2 subsets were differentiated by using the M2-specific marker, CD163. We could also delineate tumor-stroma border in the samples by using the Pan-CK probe which distinctly marks the tumor cells and visualize the expression of immunoregulatory receptors PD-L1 and CTLA4 in the tumor cells. This assay is enabled for multiplexing by combining with our fluorescent assay platforms. Similarly, for researchers interested in detecting target expression while retaining morphological context, the codetection assay should be combined with our chromogenic assays. Overall, the new RNAscope-ISH-IHC co-detection workflow and reagents enable optimized simultaneous visualization of RNA and protein targets by enhancing the compatibility of antibodies with minimal optimization.
Citation Format: Anushka Dikshit, Sayantani Basak, Emerald Doolittle, Ilya Kovalenko, Michaeline Bunting. Spatial analysis of tumor-infiltrated immune cells with highly specific RNAscope™ RNA-protein Co-detection assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1723.
Abstract 1780: Functional inhibition of RNA-binding protein HuR reverses chemotherapeutic resistance in triple-negative breast cancer
Authors: Wei Lanjing , Zhang Qi , Zhong Cuncong , Aubé Jeffrey , Welch Danny R. , Wu Xiaoqing , Xu Liang 
Published: June 2022

Abstract
The 5-year relative survival rate of patients with triple-negative breast cancer (TNBC) is lower than the overall patients with breast cancer. The primary systemic treatment for TNBC remains to be chemotherapy. But chemoresistance frequently develops with the conventional usage of chemotherapy drugs, which results in poorer prognosis and higher recurrence of TNBC than other subtypes of breast cancer. Therefore, to improve the treatment for TNBC, overcoming chemoresistance is a critical challenge to conquer. The RNA-binding protein Hu antigen R (HuR) is a posttranscriptional regulator. It can stabilize target mRNAs through binding to U- or AU- rich elements mainly in 3’ untranslated region (UTR) of mRNA and upregulate their translation level in most cases. The encoded proteins of HuR target mRNAs are implicated in multiple cancer hallmarks, including chemotherapeutic sensitivity. The cytoplasmic accumulation of HuR is reported to contribute to chemoresistance in multiple cancer cells, and HuR inhibition sensitizes cancer cells to chemodrugs. We hypothesize that inhibition of HuR function by disrupting its interaction with mRNA can accelerate the decay of target mRNAs and thus reduce the translation level of proteins responsible for chemoresistance. Recently, our lab identified a small molecule HuR inhibitor, KH-3, which potently inhibits HuR function by disrupting HuR-mRNA interactions. In this study, KH-3 is used as a tool compound to investigate the roles HuR plays in chemoresistance development and evaluate whether HuR inhibition can enhance the efficacy of chemotherapy for TNBC cells. Two MDA-MB-231 cell sublines resistant to docetaxel (231-TR) or doxorubicin (231-DR) were generated in our lab. Compared to the parental cell line, two sub-lines exhibit similar sensitivity to KH-3, and KH-3 re-sensitizes chemoresistant cells to docetaxel or doxorubicin in the MTT-based cytotoxicity assay and the colony formation assay, indicating that HuR inhibition can overcome the acquired chemoresistance. The in vivo efficacy studies in orthotopic xenograft mouse models of human TNBC confirm that KH-3 synergizes docetaxel treatment. Regarding to mechanisms of action, several HuR direct target mRNAs implicated in chemoresistance were found upregulated in the resistant cells, which were reversed by KH-3 treatment. Detailed molecular mechanisms are now under investigation. This study suggests that HuR inhibition is a promising strategy to overcome the challenge of chemoresistance of TNBC.
Citation Format: Lanjing Wei, Qi Zhang, Cuncong Zhong, Jeffrey Aubé, Danny R. Welch, Xiaoqing Wu, Liang Xu. Functional inhibition of RNA-binding protein HuR reverses chemotherapeutic resistance in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1780.
Abstract 1788: Engineered destabilized AU rich elements on the 3UTR of HER2 degrades HER2, inhibits proliferation, and induces apoptosis in HER2 positive trastuzumab resistant breast cancer cells
Authors: Awah Chidiebere U. , Dong Fu , Levine Fayola , Ash Leonard , Glemaud Yana , Ogunwobi Olorunseun 
Published: June 2022

Abstract
Resistance to molecular targeted therapy is a major challenge facing breast cancer patients and unfavorably impacts clinical outcomes, leading to hundreds of thousands of deaths yearly. Resistance to cancer therapies arises from many factors. One of the key factors driving resistance is oncogenes which initiate pro-growth, pro-survival and metastatic programs that enable cancers escape various therapies. In HER2+ breast cancer, the oncogene HER2 is the master driver of this tumor. Trastuzumab effectively targets HER2. While this is generally successful, some patients who have HER2+ breast cancer develop resistance to trastuzumab and there are limited treatment options for them. Moreover, for low HER2+ expressing breast cancer, there are limited treatment options for them. And in African American women who have HER2+ breast cancer, there is disparity in their treatment outcomes. We have discovered that 3’UTR of HER2 is enriched with poly U stabilizing AU rich elements (ARE). We have developed a novel technology wherein we engineered the stabilizing HER2 3’UTR ARE motifs to destabilizing motif in HER2+ and HER2+ trastuzumab resistant breast cancer cells to control HER2 transcript. We achieved complete degradation of HER2 within 4-8 days in HER2+ wildtype breast cancer cells and 9-11 days in HER2+ trastuzumab resistant breast cancer cells. We had loss of cancer cell viability by more than 90%. We also show that control of HER2 transcript downregulated HER2-dependent kinases, transcription factors, and HER2 interactome. Mechanistically, the control of HER2 transcript was achieved by destabilized ARE sequence specificity which triggered the proteins PARN, XRN1 and CNOT1 to degrade HER2 transcript and this led to induction of active caspase 3/7, reduction of cell size, and severe distortion and disruption of the cancer cell membrane leading to cell death. Taken together, we have a developed a novel approach to control HER2 transcript expression both on spatial and temporal scale. This novel approach offers applications for targeting HER2+ trastuzumab resistant breast cancer as well as other cancers resistant to HER2 targeted therapy and driven by pervasive oncogenic signals.
Citation Format: Chidiebere U. Awah, Fu Dong, Fayola Levine, Leonard Ash, Yana Glemaud, Olorunseun Ogunwobi. Engineered destabilized AU rich elements on the 3UTR of HER2 degrades HER2, inhibits proliferation, and induces apoptosis in HER2 positive trastuzumab resistant breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1788.
Abstract 1792: FGFR3 mediated PARP1 tyrosine 158 phosphorylation promotes PARP inhibitor resistance
Authors: Chen MeiKuang , Gao Yuan , Xia Weiya , Wang Yu-Han , Litton Jennifer K. , Chu Yu-Yi , Meric-Bernstam Funda , Piwnica-Worms Helen , Arun Banu , Ahnert Jordi Rodon , Wei Yongkun , Chang Wei-Chao , Wang Hung-Ling , Tapia Coya , Albarracin Constance T. , Wang Shao-Chun , Wang Ying-Nai , Hortobagyi Gabriel N. , Lin Chunru , Yang Liuqing , Yu Dihua , Hung Mien-Chie 
Published: June 2022

Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi), which induce DNA damage by inhibiting PARP1 enzymatic activity and trapping PARP on the damaged DNA, are used to eliminate BRCA1/2-mutated (BRCAm) cancer. However, clinical observations suggest that BRCAm tumors develop PARPi resistance. Current strategies to overcome PARPi resistance include impeding multiple DNA repair pathways to induce excessive DNA damage. Here, we propose a novel strategy targeting oncogenic receptor tyrosine kinases to enhance PARP trapping. By developing triple-negative breast cancer (TNBC) cells with acquired talazoparib resistance, we observed a high prevalence of activated fibroblast growth factor receptor 3 (FGFR3) kinase in these cells through kinase antibody array analysis. Mass spectrometry analysis and in vitro kinase assay suggested that FGFR3 phosphorylated PARP1 at tyrosine residues 158 and 176. Biochemistry studies suggested that only PARP1 tyrosine 158 phosphorylation contributes to PARPi resistance in the cells we developed. We then developed a monoclonal antibody against tyrosine 158 phosphorylated PARP1, and found that high-level PARP1 tyrosine 158 phosphorylation positively correlated with PARPi resistance in breast cancer patient-derived xenograft models. We further demonstrated that the combination of FGFR inhibitor and PARPi delayed DNA repair with prolonged PARP trapping. Moreover, synergy between PARPi and FGFR inhibition was observed in multiple TNBC cell lines with PARPi resistance in vitro. The combination of PARPi and FGFR inhibitor also showed synergism in vivo, and treatment with the combination of PARPi and FGFR inhibitor was tolerated in mouse models. These findings reveal that PARP1 tyrosine 158 phosphorylation facilitates resolving of the PARPi-induced PARP-trapping, and that the tyrosine 158 phosphorylated PARP1 may be an effective biomarker to indicate FGFR3 mediated PARPi resistance.
Citation Format: MeiKuang Chen, Yuan Gao, Weiya Xia, Yu-Han Wang, Jennifer K. Litton, Yu-Yi Chu, Funda Meric-Bernstam, Helen Piwnica-Worms, Banu Arun, Jordi Rodon Ahnert, Yongkun Wei, Wei-Chao Chang, Hung-Ling Wang, Coya Tapia, Constance T. Albarracin, Shao-Chun Wang, Ying-Nai Wang, Gabriel N. Hortobagyi, Chunru Lin, Liuqing Yang, Dihua Yu, Mien-Chie Hung. FGFR3 mediated PARP1 tyrosine 158 phosphorylation promotes PARP inhibitor resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1792.
Abstract 1813: DIACC2010, a selective inhibitor of KIF20A
Authors: COLLETTE Yves , CASTELLANO Rémy , AURRAND-LIONS Michel , SICARD Hélène , VEY Norbert , BOUGERET Cécile 
Published: June 2022

Abstract
Mitotic kinesins are essential regulators of cancer cell replication and migration. The microtubule associated motor protein KIF20A (also called MKlp2), a member of the kinesin-6 family, plays an essential role during cytokinesis and is also involved in the fission of RAB6-positive vesicles from Golgi membrane, therefore contributing to intracellular vesicular trafficking (1). KIF20A plays a critical role in the development and progression of many cancers, and its high expression is associated with disease progression and poor survival outcome (2). More specifically, immature hematopoietic cells, exhibit high KIF20A expression, whereas mature peripheral blood cells do not (3). Herein we describe the preclinical anti-leukemic efficacy of DIACC2010, sole-in-class selective KIF20A inhibitor. DIACC2010 demonstrated potent and consistent cytotoxic activity in-vitro against a panel of 9 human AML cell lines, with median IC50 of 40 nM (range 10-77 nM). In the same experimental conditions, cytarabine (CYTA) had median IC50 of 207 nM (range 4-1580 nM). In parallel, no in-vitro toxicity of DIACC2010 was observed on human normal cells such as peripheral blood mononuclear cells (PBMC) and primary hepatocytes (IC50 &gt;50 µM). DIACC2010 was subsequently evaluated in-vivo in xenograft models of CYTA-sensitive and CYTA-resistant AML cell lines: DIACC2010 significantly improved overall survival as compared to CYTA in all models, with dose-dependent efficacy. On a mechanistic standpoint, DIACC2010-exposed AML cells displayed characteristic Golgi scattering leading to cell death, as hallmarks of DIACC2010 mode of action and target engagement. Altogether, these results confirm the relevance of KIF20A-directed therapeutic approaches and support the development of DIACC2010 for the treatment of AML. (1) Coupling fission and exit of RAB6 vesicles at Golgi hotspots though kinesin-myosin interactions, S. Miserey-Lenkei et al, Nature com, 2017, 104:300 (2) Prognostic significance of KIF2A and KIF20A expression in human cancer. X. Li et al, Medicine, 2019, 98:46 (3) KIF20A, highly expressed in immature hematopoietic cells, supports the growth of HL60 cell line, H. Morita et al, Int J Immunol, 2018,108:607
Citation Format: Yves COLLETTE, Rémy CASTELLANO, Michel AURRAND-LIONS, Hélène SICARD, Norbert VEY, Cécile BOUGERET. DIACC2010, a selective inhibitor of KIF20A [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1813.
Abstract 1837: Low dose actinomycin D preferentially activates p53-p21 pathway in aerodigestive tract cancers: Implication for cyclotherapy
Authors: Adeluola Adeoluwa A. , Amin A. R. M Ruhul 
Published: June 2022

Abstract
Actinomycin D (ActD) was the first anti-cancer antibiotic approved for the management of human cancers. However, the notorious toxicity profile limits its widespread application in cancers including cancers of the aerodigestive tract. Recent studies show that combining low-dose ActD with existing chemotherapies could potentially reduce the toxicity of chemotherapy drugs through p53 mediated cyclotherapy (protection of normal cells while eliminating cancer cells), a recently coined concept. An understanding of ActD’s effect on p53 signaling is critical for meaningful application of ActD in cyclotherapy-based combinations. This study evaluated the antitumor efficacy and mechanism of action of ActD in aerodigestive tract cancers. We found that ActD strongly inhibited the growth of a panel of aerodigestive tract cancer cell lines and induced efficient apoptosis although the sensitivity varies among cell lines. The IC50 values of ActD spanned between 0.021-2.96nM. Mechanistic studies revealed that ActD time- and dose-dependently increased the expression of total and phosphorylated p53 (ser15). Furthermore, ActD-induced apoptosis is dependent on p53 in cells expressing wild-type p53. Further studies demonstrated that ActD induced context-dependent differential expression of downstream targets p21 and PUMA without significant effects on p27. Interestingly, our study revealed that p53-p21 is the predominant pathway activated by low-dose ActD in cells with wild type p53. Therefore, our findings further rationalize the premise for future studies to explore the application of low-dose ActD as a chemoprotectant for cyclotherapy combinations in aerodigestive tract cancers. (Supported by NIH Grant P20GM103434 to the West Virginia IDeA Network for Biomedical Research Excellence)
Citation Format: Adeoluwa A. Adeluola, A. R. M Ruhul Amin. Low dose actinomycin D preferentially activates p53-p21 pathway in aerodigestive tract cancers: Implication for cyclotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1837.
Abstract 1868: Targeting adenosine deaminase enhances anticancer effects of 3'-deoxyadenosine in uveal melanoma
Authors: Lee Su-Chan , Alaali Lujain , Kwon HyukJean , Rigi Mohammed , Eberhart Charles G. 
Published: June 2022

Abstract
Uveal melanoma, which arises from melanocytes located in the uveal tract, is one of the most common primary intraocular cancers. GNAQ and GNA11 mutations, which are detected most of primary uveal melanoma, activate MAPK signaling pathway, increasing cancer cell proliferation, tumor progression and growth. BAP1 mutation is highly associated with liver metastasis and death. However, there are no good therapeutic compounds for uveal melanoma treatment in clinic. 3’-deoxyadenosine (cordycepin) is an adenosine analog which inhibits growth of several types of cancer. However, its anticancer effects have been showed in limited cancer cell lines. In addition, action mechanism of 3’deoxyadenosin is poorly understood. In this study, we found different adenosine deaminase (ADA) expression or activity affects different anticancer results in uveal melanoma. Inhibition of ADA using either siRNA or pharmacologic approaches sensitized tumors to 3’-deoxyadenosine in vitro and in vivo, resulting in increased apoptosis, reduced clonogenic capacity and slower migration of uveal melanoma cells in vitro. These potent ADA-dependent anti-tumor effects were also seen in various cancer cell lines. Therefore, we suggest the potential of adenosine deaminase (ADA) as both a biomarker predicting response to 3’-deoxyadenosine, and a target for combination therapy.
Citation Format: Su-Chan Lee, Lujain Alaali, HyukJean Kwon, Mohammed Rigi, Charles G. Eberhart. Targeting adenosine deaminase enhances anticancer effects of 3'-deoxyadenosine in uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1868.
Abstract 1883: Large scale viability screening with PRISM underscores non-inhibitory properties of small molecules
Authors: de Waal Lucian , Larpenteur Kevin , Wang Li , Zhu Cong , Bryan Jordan , Kocak Mustafa , Aghia Corrie , Bittker Joshua , Jones Victor , Vrcic Anita , McBride Edward , Bender Samantha , Gore Kalea , Li Frank , Chen Zhenghao , Tsherniak Aviad , Subramanian Aravind , Koller Daphne , Settleman Jeffery , Mader Chris C. , Stokoe David , Firestone Ari , Roth Jennifer A. , Golub Todd R. 
Published: June 2022

Abstract
Oncology drug discovery has been dependent on phenotypic screening that lead to discovery of many drugs that remain essential cancer treatments to this day. Historically, logistical and technological limitations have hampered the scale of phenotypic small molecule screening across genomic diverse models. Until recently, large scale phenotypic screening across many cell lines, reflecting the somatic diversity in cancer, has not been possible. The PRISM technology does allow for a high-throughput approach to phenotypic viability screening by pooling cell lines and deconvoluting their response to small molecules using unique integrated DNA-barcodes. Here, we report on the results of a large phenotypic screening effort to identify novel small molecules and targets that can expand our knowledge on cancer vulnerabilities and can spur development of phenotypic drug discovery. A library of 18.000 compounds was assembled based on structural diversity and ability to induce gene-expression changes. Of these 18.000 compounds, around 3.500 were found to reduce cell viability of at least 5 cell lines in the PRISM assay. Of the cytotoxic compounds, we did not identify many small molecules that correlated strongly with CRISPR KO dependency data from project Achilles, and instead found that gene-expression correlations hold much more predictive value. By using additional approaches, we were able to identify the target of select novel cytotoxic small molecules and their respective mechanism-of-action. To our surprise, we have identified few compounds that act as canonical inhibitors of cancer drivers, and instead found compounds that act as molecular glues, prodrugs or inhibitors of more general cellular processes. These findings make a strong case for large scale phenotypic viability screening across genomically diverse models as a complementary approach to target identification next to target based drug discovery.
Citation Format: Lucian de Waal, Kevin Larpenteur, Li Wang, Cong Zhu, Jordan Bryan, Mustafa Kocak, Corrie Aghia, Joshua Bittker, Victor Jones, Anita Vrcic, Edward McBride, Samantha Bender, Kalea Gore, Frank Li, Zhenghao Chen, Aviad Tsherniak, Aravind Subramanian, Daphne Koller, Jeffery Settleman, Chris C. Mader, David Stokoe, Ari Firestone, Jennifer A. Roth, Todd R. Golub. Large scale viability screening with PRISM underscores non-inhibitory properties of small molecules [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1883.