bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract P064: Novel engineering of therapeutic Fusobacterium nucleatum phage for colorectal cancer treatment
Authors: Ninio-Many Lihi , Zigelman Yael , Buchshtab Nufar , Elharar Yifat , Eylon Gal , Gidron Eliya , Berko-Ashur Dikla , Nicenboim Julian , Zelcbuch Lior , Gartman Einav Safyon , Kredo-Russo Sharon , Kowalsman Noga , Slutskin Ilya Vainberg , Weiner Iddo , Gahali-Sass Inbar , Zak Naomi , Puttagunta Sailaja , Bassan Merav 
Published: December 2021

Abstract
Fusobacterium nucleatum (FN) is enriched in human colorectal tumors [1] and its presence is correlated with poor prognosis [2]. Bacteriophages ("phages") are naturally occurring, self-amplifying viruses that are highly specific for particular bacterial species and strains and are recognized to have a high intrinsic safety. They offer a promising treatment strategy to both target FN associated with colorectal cancer (CRC) and, by phage engineering, to deliver an anti-tumoral immune-stimulating payload that may enhance the effectivity of other anti-cancer therapies such as checkpoint inhibitors in unresponsive colorectal cancer patients. The major challenge in engineering phages that target FN is the optimization of the eukaryotic payloads for high expression in this bacterial host. Since no data is available about codon usage and non-coding genetic sequences in the genome of FN bacteria, two computational approaches were used to optimize the codon usage for elevated payload expression of the first selected payload, murine IL-15. These approaches involved identifying ribosome binding sites and elongation speeds to optimize codon usage. Following design of an IL-15 expression vector, expression of this eukaryotic payload in FN bacteria was tested in vitro. For phage engineering, a plasmid containing the designed payload sequence was used to introduce the selected IL-15 encoding sequences into the phage genome. FN phage was successfully engineered to deliver a payload encoding the sequence of murine cytokine IL-15. Targeting of FN with engineered phage resulted in IL-15 protein expression in phage-infected bacteria in vitro. Given the specificity of FN for CRC tumors and the ability to locally express a eukaryotic protein by using FN targeting phage to deliver a payload, phage therapy may offer novel treatment approaches for patients with CRC.
Citation Format: Lihi Ninio-Many, Yael Zigelman, Nufar Buchshtab, Yifat Elharar, Gal Eylon, Eliya Gidron, Dikla Berko-Ashur, Julian Nicenboim, Lior Zelcbuch, Einav Safyon Gartman, Sharon Kredo-Russo, Noga Kowalsman, Ilya Vainberg Slutskin, Iddo Weiner, Inbar Gahali-Sass, Naomi Zak, Sailaja Puttagunta, Merav Bassan. Novel engineering of therapeutic Fusobacterium nucleatum phage for colorectal cancer treatment [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P064.
Abstract P080: Analysis of clinical BRCA1/2 reversions identifies hotspot mutations and predicted neoantigens associated with therapy resistance
Authors: Pettitt Stephen J. , Frankum Jessica , Punta Marco , Lise Stefano , Alexander John , Chen Yi , Haider Syed , Tutt Andre N. J. , Lord Christopher J. 
Published: December 2021

Abstract
Although PARP inhibitors and platinum salts form part of the standard-of-care for cancers with homologous recombination (HR) defects, drug resistance does emerge and is often caused by reversion mutations in BRCA1 or BRCA2. Reversion mutations are secondary mutations that restore functional protein or compensate for frameshift mutations. To better understand the nature and aetiology of these mutations, we collated, codified and analysed over 200 reversion mutations from 24 published studies. Most reversions have been reported as case reports or small clinical series – we have collected all published reports into a single freely-accessible database to which further cases can be submitted. The majority of reported reversion mutations are from BRCA1/2 mutant serous ovarian cancer, reflecting the longer use of platinum and PARP inhibitors in this disease. Our analysis identified reversion “hotspots” and “deserts” in the N- and C-terminal coding regions (respectively) of BRCA2, suggesting that pathogenic mutations in these domains may be at higher or lower chance of reversion, an effect not seen for BRCA1. Missense and splice-site pathogenic mutations in BRCA1/2 also appeared less likely to revert than frameshift-causing mutations. Unexpectedly, whilst most reversions were &lt;100 bp “second site” deletions, microhomology use was not universal, especially in BRCA1-mutant cancers, suggesting that multiple DNA repair processes cause reversion and these vary in BRCA1 vs. BRCA2 mutant tumours. Reversions in BRCA1 mutant tumours were less likely to be mediated by deletions. Many reversions contain novel protein sequence not found in the wild type protein, for example where a stretch of out-of-frame protein sequence is retained between the pathogenic and reversion mutations. We modelled MHC binding affinities for these sequences and found that many reversions were predicted to encode potentially immunogenic neopeptides, suggesting a route to the treatment of reverted disease. These observations have implications for how drug resistance might be managed in BRCA-mutant cancers.
Citation Format: Stephen J. Pettitt, Jessica Frankum, Marco Punta, Stefano Lise, John Alexander, Yi Chen, Syed Haider, Andre N. J. Tutt, Christopher J. Lord. Analysis of clinical BRCA1/2 reversions identifies hotspot mutations and predicted neoantigens associated with therapy resistance [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P080.
Abstract P095: Isogenic CRISPR anchor screens identified actionable nodes to CHK1/2 inhibitor prexasertib in TP53 mutant cancer
Authors: Teng Teng , Paik Stephen , Zhao Shan-chuan , Choi Ashley , Lombardo Steven A. , Liu Shangtao , Meier Samuel R. , Yu Yi , Anderson Jannik N. , Huang Alan , Li Fang , Pan Xuewen 
Published: December 2021

Abstract
TP53 is the most mutated tumor suppressor gene in human cancers and is a master regulator of a wide array of cellular processes including but not limited to cell cycle progression and DNA damage response. Due to its diverse functions, therapies specifically exploit the vulnerabilities created by TP53 loss remained elusive. We established a panel of TP53 isogenic pair cell line models by knocking out TP53 from WT cell lines and observed that CHK1/2 inhibitor prexasertib showed preferential selectivity toward TP53 KO cell lines. To thoroughly examine additional nodes which could further exploit this selective sensitivity, we carried out genome-wide prexasertib anchor screen in A549 isogenic lines employing CRISPRn, CRISPRi and CRISPRa platforms. From these functional genomics screens, we identified that targeting the anti-folate pathway genes (TYMS, DHFR) showed selective synergy with prexasertib specifically in TP53 KO cells. Secondly, a panel of iron metabolism genes was identified across different CRISPR platforms as candidate TP53 context specific synthetic lethal hits synergize with prexasertib. And lastly, additional sub-context was identified which may inform patient selection strategy for prexasertib as single agent.
Citation Format: Teng Teng, Stephen Paik, Shan-chuan Zhao, Ashley Choi, Steven A. Lombardo, Shangtao Liu, Samuel R. Meier, Yi Yu, Jannik N. Anderson, Alan Huang, Fang Li, Xuewen Pan. Isogenic CRISPR anchor screens identified actionable nodes to CHK1/2 inhibitor prexasertib in TP53 mutant cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P095.
Abstract P096: Using CRISPR-Cas9 screens to identify microRNA involved in aggressive prostate cancer phenotypes
Authors: Chow Jonathan Tak-Sum , Lee Daniel K. C. , Gabra Martino Marco , Fu Norman , Chen Keyue , Salmena Leonardo 
Published: December 2021

Abstract
Background: Prostate cancer (PCa) is the most common cancer diagnosis in Canadian men. For many, the tumour can remain “dormant” negating a need for treatment, but if the tumour progresses and becomes metastatic, prognosis is poor. Despite the introduction of new treatments, metastatic PCa remains a lethal and incurable disease. This is invariably due to the onset of castration-resistance in advanced cases producing a more aggressive tumour with increased metastatic potential. We hypothesize that microRNA can promote these aggressive PCa phenotypes due to their ability to regulate diverse gene networks simultaneously. Methods: We have generated miRKOv2, the second version of our microRNA CRISPR Knockout library using the latest on- and off-target scoring algorithms and other microRNA-specific features for CRISPR-Cas9 guide RNA (gRNA) design. miRKOv2 will be used in three separate screens to identify microRNA that are essential for PCa growth, microRNA that are involved in PCa metastasis, and microRNA that can confer castration-resistance, respectively. Results: Next generation sequencing of the plasmid miRKOv2 library showed a median gRNA coverage of ~1100X. In silico comparisons to other microRNA libraries demonstrate that miRKOv2 is a superior sgRNA library. DU145 cells stably expressing Cas9 are highly active and proof of principle growth assays demonstrate that essential gene knockout and subsequent decrease in cell viability is detectable. Generation of a Cas9+ PCa cell line panel and screens are ongoing. Conclusion: miRKOv2 is an improved microRNA-focused CRISPR library with high gRNA coverage. Proof of principle assays demonstrate that knockout of essential genes results in a reduction in cell viability, indicating that a CRISPR dropout screen is appropriate for our in vitro model. This project aims to identify microRNA dependencies in metastatic and castration-resistant PCa that can be leveraged into new biomarkers and therapies.
Citation Format: Jonathan Tak-Sum Chow, Daniel K. C. Lee, Martino Marco Gabra, Norman Fu, Keyue Chen, Leonardo Salmena. Using CRISPR-Cas9 screens to identify microRNA involved in aggressive prostate cancer phenotypes [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P096.
Abstract P108: In vivo CRISPR screens identify E3 ligase COP1 as a modulator of macrophage infiltration and cancer immunotherapy target
Authors: Wang Xiaoqing , Tokheim Collin , Gu Shengqing S. , Wang Binbin , Tang Qin , Li Yihao , Traugh Nicole , Zeng Zexian , Zhang Yi , Zhang Boning , Fu Jingxin , Xiao Tengfei , Li Wei , Meyer Clifford , Jiang Peng , Cejas Paloma , Lim Klothilda , Long Henry , Brown Myles , Liu X. Shirley 
Published: December 2021

Abstract
Despite remarkable clinical efficacies of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits in triple-negative breast cancer (TNBC) remain limited. Through pooled in vivo CRISPR knockout (KO) screens in syngeneic TNBC mouse models, we found that inhibition of the E3 ubiquitin ligase COP1 in cancer cells decreases the secretion of macrophage-associated chemokines, reduces tumor macrophage infiltration, enhances tumor immunity and ICB response. Transcriptomics, epigenomics, and proteomics analyses revealed COP1 functions through proteasomal degradation of the C/ebpδ protein. COP1 substrate TRIB2 functions as a scaffold linking COP1 and C/ebpδ, which leads to polyubiquitination of C/ebpδ. COP1 inhibition stabilizes C/ebpδ to suppress the expression of macrophage chemoattractant genes. Our integrated approach implicates COP1 as a target for improving cancer immunotherapy efficacy by regulating chemokine secretion and macrophage infiltration in the TNBC tumor microenvironment.
Citation Format: Xiaoqing Wang, Collin Tokheim, Shengqing S. Gu, Binbin Wang, Qin Tang, Yihao Li, Nicole Traugh, Zexian Zeng, Yi Zhang, Boning Zhang, Jingxin Fu, Tengfei Xiao, Wei Li, Clifford Meyer, Peng Jiang, Paloma Cejas, Klothilda Lim, Henry Long, Myles Brown, X. Shirley Liu. In vivo CRISPR screens identify E3 ligase COP1 as a modulator of macrophage infiltration and cancer immunotherapy target [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P108.
Abstract P117: Oncogenic Kit induces replication stress and induces Chk1/ATR inhibitor sensitivity in melanoma
Authors: Njauw Ching-Ni , Ji Zhenyu , Tsao Hensin , Simoneau Antoine , Kumar Raj , Flaherty Keith T. , Zou Lee , Pham Duc Minh 
Published: December 2021

Abstract
Contrary to cutaneous melanoma (CM), Acral and mucosal melanomas (AMM’s) lack effective therapy and exact a higher mortality. Since amplifications and point mutations of KIT are common in AMM, we created a multi-stage murine cellular model of human KIT melanomas (i.e. mKitK641E lines) based on the most common KIT mutation in human melanoma (p.K642E). Compared to its vector-controlled cells (mVec), mKitK641E cells exhibit greater chromosomal aberrations, and sustain 3D spheroid forming capability and aggressive tumor growth in C57BL/6J mice. In addition, DNA replication/RNA processing and ribosomal biogenesis pathways associated with KitK641E transformation. Surprisingly, an unbiased comparative drug screen uncovered a selective vulnerability to Chk1 inhibition in the KitK641E activated cells. mKitK641E cells displayed &gt;6-fold greater sensitivity compared to mVec cells (GI50=1.5 µM vs 10 µM) for Chk1 inhibitor PF477736 treatment. Furthermore, we proved that KitK641E induces profound DNA replication stress as evidenced by increased levels of γ-H2AX and p-RPA32Ser33 in replicating cells and defective replication fork progression. Thus, mKitK641E represents a novel model to study the biology of KIT-driven melanoma and therapy development.
Citation Format: Ching-Ni Njauw, Zhenyu Ji, Hensin Tsao, Antoine Simoneau, Raj Kumar, Keith T. Flaherty, Lee Zou, Duc Minh Pham. Oncogenic Kit induces replication stress and induces Chk1/ATR inhibitor sensitivity in melanoma [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P117.
Abstract P130: P-cadherin activates metabolic coupling in the tumor-mesothelial niche: From glycolysis through lactate to lipogenesis
Authors: Wang Kun , Ma Jing , Wong Carmen C. L. , Chan Chi Bun , Wong Alice S. T. 
Published: December 2021

Abstract
Peritoneal metastasis affects &gt;70% ovarian cancer patients, and its effective management is an unmet medical goal. Successful adhesion to the peritoneal mesothelium is a key rate-limiting step for metastasis formation, but it is unclear the selective advantage of why ovarian cancer cells colonize specifically to the unique mesothelial environment. Metabolic reprogramming is a hallmark of cancers. Still their role in peritoneal metastasis remains to be fully understood. To overcome the limitations of a lack of tightly controlled experimental model to pinpoint key molecules causing metastasis, we have established an isogenic model of spontaneous human ovarian cancer metastasis. Metabolism is characterized using RNA-seq, RT-PCR, real-time cell metabolic assay, targeted lipidomic analysis and neutral lipid staining. Using coculture, we showed that HM but not NM specifically activated peritoneal mesothelium in a P-cadherin-dependent manner compared to other cadherins, suggesting that there is a unique role for P-cadherin. RNA-seq revealed distinct regulation of lipogenic pathway in non-specific or P-cadherin siRNA treated HM. For these, we have confirmed that P-cadherin could promote the expression of lipogenic genes ACLY, FASN and ACAT2 in HM. Concomitantly, P-cadherin activated glycolysis (HK2, Gpi and PGK1) in the mesothelial cells. Targeted lipidomic analysis further showed that lactate acid that was enriched in the mesothelium was shuttled from the mesothelium to the HM to fuel de novo lipid synthesis in HM, revealing a feed-forward positive loop. Suppressing lactate uptake by using a monocarboxylate transporter 1 inhibitor could abolish the metabolic crosstalk and subsequent metastatic outgrowth. Together, these findings reveal the metabolic differences between metastatic versus non-metastatic tumor cells in understanding ovarian cancer metastasis to the mesothelium, and suggest targeting P-cadherin could be a promising therapeutic approach (RGC17105919).
Citation Format: Kun Wang, Jing Ma, Carmen C. L. Wong, Chi Bun Chan, Alice S. T. Wong. P-cadherin activates metabolic coupling in the tumor-mesothelial niche: From glycolysis through lactate to lipogenesis [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P130.
Abstract P131: The role of UDP-6 glucose dehydrogenase (UGDH) in estrogen-mediated phenotypes in both estrogen receptor positive and estrogen receptor negative breast cancer
Authors: Price Meghan , Lavau Catherine , Baeta Cesar , Byemerwa Jovita , Wardell Suzanne , Brueckner Olivia , Mukherjee Debarati , Haynes Corinne , Nguyen Annee , Chang Chingyi , McDonnell Donald , Goodwin C. Rory 
Published: December 2021

Abstract
A better understanding of pathologic mechanisms underlying breast cancer progression and metastasis is critical to improve current treatment modalities. UDP-6- glucose dehydrogenase (UGDH) is an enzyme that has become a recent oncologic target of interest across various cancer subtypes for its role in increasing the aggressiveness and migratory capacity of tumor cells both in vitro and in vivo. UGDH is ubiquitously expressed and plays a critical role in forming the extracellular matrix (ECM), producing nucleotide sugars, and processing hormones through glucuronidation. For these reasons, investigating the effect of UGDH on breast cancer in the setting of hormonal stimulation is important. We found that knocking down UGDH in estrogen receptor positive (ER+) breast cancer cell lines (MCF7 marco and T47D) and an estrogen receptor negative (ER-) breast cancer cell line (MDA-MB-231) could abrogate estrogen induced migration-specific phenotypes in vitro. Furthermore, we found that knocking down UGDH mitigated estrogen stimulated primary tumor growth in vivo for both MCF7 macro and MDA-MB-231 mammary fat pad tumor models in mice. Thus, we found that UGDH regulates estrogen stimulated migratory phenotypes in both ER+ and ER- breast cancers in vitro and primary tumor growth in vivo. For this reason, UGDH and its associated pathways are promising targets for future drug development and small molecular targets in the treatment of both metastatic ER positive and ER negative breast cancers.
Citation Format: Meghan Price, Catherine Lavau, Cesar Baeta, Jovita Byemerwa, Suzanne Wardell, Olivia Brueckner, Debarati Mukherjee, Corinne Haynes, Annee Nguyen, Chingyi Chang, Donald McDonnell, C. Rory Goodwin. The role of UDP-6 glucose dehydrogenase (UGDH) in estrogen-mediated phenotypes in both estrogen receptor positive and estrogen receptor negative breast cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P131.
Abstract P166: The rs35112940 CD33 polymorphism reduces CD33 internalization and efficacy of CD33-directed gemtuzumab ozogamicin
Authors: Gbadamosi Mohammed O. , Shastri Vivek M. , Meshinchi Soheil , Lamba Jatinder K. 
Published: December 2021

Abstract
CD33 is a myeloid-specific cell surface protein widely expressed on acute myeloid leukemia (AML) cells making it an excellent immunotherapeutic target. Current CD33-directed immunotherapeutic treatment strategies include gemtuzumab ozogamicin (GO), an antibody-drug conjugate (ADC) approved in 2017 for treatment AML and other ADCs are various stages of development. Previously, studies from our group have identified germline variations in CD33 that are associated with CD33 cell surface expression levels and clinical outcomes in response to GO. Among these germline variations is rs35112940 (G&gt;A; Arg304Gly), a missense polymorphism located in exon five of CD33 which is associated with lower CD33 expression and reduced benefit from treatment using GO. Herein, we functionally validated the effect of the rs35112940 variant by treating CD33KO-HL60 engineered to overexpress wildtype CD33 (HL60-CD33FL) or CD33 encoding the rs35112940 variant (HL60-CD33FL-rs35112940) with GO. After 48-hour treatment with 250 ng/mL of GO, we observed that HL60-CD33FL-rs35112940 cells were more resistant to GO than HL60-CD33FL cells (46.5% vs 66.4% cell viability, P = 0.02). Of note, all engineered cells expressed CD33 with less than 1-log fold difference in MFI (HL60-CD33FL median fluorescence intensity (MFI) vs HL60-CD33FL-rs35112940 MFI: 22536 vs 24882). One critical aspect of the mechanism of action of GO is the internalization of the GO-CD33 complex which allows free calicheamicin to induce DNA damage leading to cellular apoptosis. Given the proximity of the rs35112940 loci to the cytoplasmic immunoreceptor tyrosine-based inhibitory motif (ITIM) domain of CD33, which is critical for CD33 internalization, we hypothesized that the rs35112940 variation may impact CD33 internalization as well. To assess this, we performed a flow cytometry-based internalization assay to capture the remaining amounts of CD33 present on the cell surface after 4 hours allowing us to determine the internalization of CD33 over time. Over a 4-hour window, we observed that that HL60-CD33FL-rs35112940 cells had an approximate 10% reduction in CD33 internalization in comparison to HL60-CD33FL cells. Taken together these results provide insight into the effect of the rs35112940 variant on GO efficacy and CD33 biology, corroborating our previous findings, and support the use of CD33 polymorphisms to guide patient selection for treatment with GO.
Citation Format: Mohammed O. Gbadamosi, Vivek M. Shastri, Soheil Meshinchi, Jatinder K. Lamba. The rs35112940 CD33 polymorphism reduces CD33 internalization and efficacy of CD33-directed gemtuzumab ozogamicin [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P166.