bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5989: Brain metastasis mouse models for the evaluation of multikine inhibitors on ROS1-fusion-positive lung cancer
Authors: Qi Hui , Xiong Xia , Liu Huanhuan , Yang Yuying , Dai Chunlei , Zhao Haoxia , Han Bingrui , Tang Xuzhen , Ji Qunsheng 
Published: June 2022

Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Nearly 80% of lung cancers are non-small cell lung cancer (NSCLC) and 60% of them are diagnosed at the metastatic stage. Brain metastases affect more than 20% of NSCLC patients with poor prognosis and disabling symptoms. However, few therapies have been approved for the treatment of lung cancer brain metastases. A panel of rapid, predictive and clinically-relevant animal models are urgently needed to study the biology of brain metastases and to identify effective therapeutic approaches.Considering both progression and treatment of lung cancer brain metastases will be limited by the blood-brain barrier (BBB), here we describe methods for efficient establishment of brain metastases mouse models via different injection route (intracranial, intracardiac or intracarotid), to identify a model that permits tumor cell growth in the unique brain microenvironment without compromising BBB. Meanwhile, we established a novel ROS1 positive patient-derived xenograft (PDX) model together with its PDC sub-line, in which the exon 2 of SDC4 was fused to the exon 32 of ROS1 (SDC4ex2-ROS1ex32). The cell has been transduced with firefly luciferase expression vector for in vivo imaging detection. Three ROS1 inhibitors were tested on these brain metastasis and subcutaneous models to compare their efficacies. In summary, we established brain metastases lung cancer PDX models as reliable platforms for interrogation of targets and kinetics related mechanism and for drug screening. The use of such techniques will increase our knowledge of the metastatic process and help identify new targets of cancer metastasis.
Citation Format: Hui Qi, Xia Xiong, Huanhuan Liu, Yuying Yang, Chunlei Dai, Haoxia Zhao, Bingrui Han, Xuzhen Tang, Qunsheng Ji. Brain metastasis mouse models for the evaluation of multikine inhibitors on ROS1-fusion-positive lung 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 5989.
Abstract 5996: Single tube PCR-based NGS assay for detection of multiple gene fusions from cell free total nucleic acid
Authors: Modak Tejashree , Li Jilong , Polvino Sean , Ke Yue , Wang Zhaohui , Kotlar Alex V. 
Published: June 2022

Abstract
Introduction: Recently, liquid biopsy has begun to be adopted for treatment selection and drug-resistance assessment for cancers. However, currently liquid biopsy is mostly focused on analyzing cell-free DNA (cfDNA). Though analyzing RNA provides more accurate analysis for functional gene fusions, little is known about the stability and availability of cfRNA (cell free RNA). Here we report our one-tube robust cfTNA (cell free total nucleic acids) assay to analyze ctDNA and ctRNA simultaneously.
Methods: We assessed Pillar’s cell free TNA panel performance on 2 confirmed fusion positive and 5 fusion negative samples that were serially diluted to obtain a total of 88 samples including replicates. An input of 10ng cfTNA was used for fusion positive samples with fusion frequency ranging from 0.2% to 20%. A range of 5 to 30ng input was used for fusion negative samples. The amount of input cfRNA was estimated as equal to the cfDNA input. Total nucleic acids were extracted and cfRNA was reverse transcribed. Amplicons targeted the specific breakpoints of 36 known fusion transcripts. Fusion positive samples were diluted for library prep to achieve fusion frequency of 0.5%, 1%, 4%, 5% and 20%. Novaseq was used for sequencing with an average depth of 200,000X and downsampled by 25%. Pillar Variant Analysis Toolkit (PiVAT®) was used to map and call fusions.
Results: Among dilutions of &gt;=4%, PiVAT achieved &gt;=99% sensitivity and &gt;=99.9% specificity in calling RNA fusions from 10ng input. Even at extremely low dilutions of &lt;=1%, PiVAT achieved &gt;= 50% sensitivity.
Conclusion: Pillar’s cell free TNA panel offers a simple, rapid, and reliable workflow that enables detection of a broad range of clinically relevant gene fusions. Detection of fusion events in cell-free samples from noninvasive liquid biopsies represents an important step forward in cancer diagnosis and monitoring.
Citation Format: Tejashree Modak, Jilong Li, Sean Polvino, Yue Ke, Zhaohui Wang, Alex V. Kotlar. Single tube PCR-based NGS assay for detection of multiple gene fusions from cell free total nucleic acid [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 5996.
Abstract 5997: The role of neutrophil extracellular trap-CCDC25-integrin linked kinase complex in pancreatic cancer progression and metastasis
Authors: McDonald Paul C. , Brown Wells S. , Gerbec Zack , Awrey Shannon , Karasinska Joanna , Schaeffer David , Renouf Daniel , Stanger Ben , Dedhar Shoukat 
Published: June 2022

Abstract
Neutrophils and neutrophil extracellular traps (NETs) contribute to the hypoxic, immunosuppressive pancreatic ductal adenocarcinoma (PDAC) tumour microenvironment (TME) which promotes treatment resistance, increased invasion and metastasis. While recent studies have demonstrated a critical role of tumour cell CCDC25-ILK complex in promoting NET-DNA-induced tumour metastasis in breast cancer, here we have investigated the presence and function of NETosis-induced CCDC25-ILK signaling in the context of pancreatic cancer. We demonstrate that CCDC25 and ILK are expressed in human PDAC cell lines, patient-derived xenograft (PDX) cell lines and in cell lines derived from the KPCY genetic model of PDAC. Importantly, co-immunoprecipitation analyses showed that endogenous CCDC25 and ILK interact in PDAC cells, and the addition of neutrophil-derived NET-DNA resulted in a greater amount of ILK associated with CCDC25 and in increased wound-induced migration. Time-lapse imaging demonstrated a dramatic effect of inhibition of ILK activity on NET-DNA-induced migration by tumour cells in vitro. In vivo, co-localization of CCDC25 and ILK was observed in tumours and liver metastases from both the KPCY GEMM and the MIA PaCa-2 human PDAC xenograft models that were stained by multispectral immunofluorescence for these markers and analyzed by confocal microscopy. Similarly, both tumours and liver metastases showed the presence of infiltrating neutrophils and NETs as indicated by staining for myeloperoxidase and citrullinated histone H3. Collectively, these data identify the neutrophil extracellular trap-induced CCDC25-ILK interaction as an important contributor to PDAC progression and suggest the potential for targeting this axis to prevent NET-induced PDAC progression and metastasis.
Citation Format: Paul C. McDonald, Wells S. Brown, Zack Gerbec, Shannon Awrey, Joanna Karasinska, David Schaeffer, Daniel Renouf, Ben Stanger, Shoukat Dedhar. The role of neutrophil extracellular trap-CCDC25-integrin linked kinase complex in pancreatic cancer progression and metastasis [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 5997.
Abstract 6063: FOXK2 promotes stemness in ovarian cancer by regulating unfolded protein response signaling
Authors: Zhang Yaqi , Wang Yinu , Zhao Guangyuan , Tanner Edward J. , Adli Mazhar , Matei Daniela E. 
Published: June 2022

Abstract
Introduction: Cancer stem cells (CSCs), a rare cell population within tumors that possesses self-renewal and tumor initiation capacity, have been implicated in cancer relapse and resistance to chemotherapy. In ovarian cancer (OC), CSCs are characterized by a high expression of aldehyde dehydrogenase (ALDH). Understanding the regulatory programs promoting stemness could identify new treatments. We identified FOXK2 as a key transcription factor (TF) that promotes stemness in OC.
Methods: We generated FOXK2 knockdown OC models by stable transduction of shRNA targeting this TF and measured the population of ALDH+ CSCs, expression of stemness-associated genes, and in vivo tumor initiation capacities. Transcriptomic and ChIP-seq analyses were used to identify key FOXK2 targets. CRISPR-dCas9 genome editing was used to verify the regulatory function of FOXK2. Rescue experiments validated the roles of a newly discovered target gene of FOXK2.
Results: Through gene expression analyses in CSCs vs. non-CSCs, we identified FOXK2 as a highly expressed stemness-specific TF in OC. Genetic depletion of FOXK2 diminished stemness features and reduced in vivo tumor initiation capacity. Through ChIP-sequencing we discovered that FOXK2 directly regulates IRE1α (ERN1 gene) expression, a key sensor for the unfolded protein response (UPR). ChIP-sequencing analysis further revealed that FOXK2 binds to an intronic regulatory element of ERN1. Blocking FOXK2 from binding to this enhancer by using a CRISPR/dCas9 diminished IRE1α transcription. At the molecular level, FOXK2-driven upregulation of IRE1α led to alternative XBP1 mRNA splicing and activation of stemness pathways, while genetic or pharmacological blockade of IRE1α inhibited CSCs in OC models.
Conclusion: Our data establish a new function for FOXK2 as a key transcriptional regulator of CSCs and a mediator of the UPR, providing insight into potentially targetable new pathways in ovarian CSCs.
Citation Format: Yaqi Zhang, Yinu Wang, Guangyuan Zhao, Edward J. Tanner, Mazhar Adli, Daniela E. Matei. FOXK2 promotes stemness in ovarian cancer by regulating unfolded protein response signaling [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 6063.
Abstract 6069: HOXA9 overexpression contributes to stem cell overpopulation that drives development and growth of colorectal cancer
Authors: Osmond Brian T. , Facey Caroline O. , Opdenaker Lynn M. , Boman Bruce M. 
Published: June 2022

Abstract
HOX genes encode master regulatory transcription factors that regulate stem cells (SCs), but their role in carcinogenesis is not fully understood. SC overpopulation drives colorectal cancer (CRC) development, which is also linked with the aberrant expression of specific HOX genes. One such gene is HOXA9. Our goal is to find out how HOXA9-regulatory mechanisms play a role in the SC origin of CRC. Previous research in our lab reported that HOXA9 as well as other HOX proteins (e.g. HOXA4 & HOXD10) are selectively expressed in human colonic cancer SCs (CSCs). The SC marker aldehyde dehydrogenase (ALDH) and other retinoic acid (RA) pathway components are also selectively expressed in CSCs. Moreover, HOXA9 expression is positively correlated with expression of ALDH genes such as ALDH1A1. These findings suggest that RA signaling regulates HOXA9 gene expression in colonic ALDH+ SCs.
Hypothesis: Dysregulated HOXA9 expression leads to ALDH+ SC overpopulation, which contributes to CRC growth and development. We used immunofluorescent (IF) mapping to determine the histologic location of HOXA9+ cells in relation to colonic SCs and other differentiated colonic cell types in normal and neoplastic human colonic tissues. We also measured the effects of all-trans retinoic acid (ATRA) and the ALDH enzyme inhibitor diethylamino benzaldehyde (DEAB) on HOXA9 expression, cell proliferation and differentiation using CRC cell lines. Immunofluorescence mapping indicated that not only is HOXA9 selectively expressed in ALDH-positive SCs, but that HOXA9 expression is increased in colon carcinoma tissue compared to normal colon epithelium. Our results also showed that both ATRA and DEAB treatment decreased the proliferation of HT29 and SW480 CRC cell lines. Western blot analysis showed that HOXA9 has reduced expression in ATRA-treated HT29 CRC cells. Additionally, our independent bioinformatics analyses show that HOXA9 is predominantly expressed in both stem cells and neuroendocrine cells (NECs) in normal human colonic epithelium. Taken together, these findings indicate that regulation of HOXA9 gene expression by RA signaling controls differentiation of ALDH+ SCs along the NEC lineage in human colon tissue. Thus, our results show that HOXA9 is regulated by RA signaling and when dysregulated, contributes to CRC development and growth. These findings provide a mechanism that may be targeted in the design of novel treatments against SC overpopulation in CRC.
Citation Format: Brian T. Osmond, Caroline O. Facey, Lynn M. Opdenaker, Bruce M. Boman. HOXA9 overexpression contributes to stem cell overpopulation that drives development and growth of colorectal 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 6069.
Abstract 6071: Activation of NOTCH signaling via DLL1 is mediated by APE1-redox-dependent NF-κB activation in esophageal adenocarcinoma
Authors: Chen Lei , Lu Heng , Peng Dunfa , Cao Longlong , Chen Zheng , Bhat Ajaz , Zaika Alexander , Zhang Shutian , El-Rifai Wael 
Published: June 2022

Abstract
Esophageal adenocarcinoma (EAC) is one of the most lethal of all human malignancies. EAC arises in the setting of Barrett’s esophagus, which is an intestinal metaplastic precursor lesion that develops from chronic reflux of gastrointestinal contents (especially acidic bile salts). Here we report that NOTCH signaling is activated in the esophagus through a unique pathway during exposure to acidic bile salts and progression to EAC. Using a combination of public databases, EAC cell line models, transgenic mice, and patient tissue samples, we detected significant upregulation of several NOTCH signaling components in EAC. Activated NOTCH signaling was confirmed by nuclear accumulation of NOTCH1 cleaved fragment (NICD) with corresponding up-regulation of NOTCH targets in EAC cells in response to acidic bile salts. Moreover, we identified DLL1 as the predominant ligand contributing NOTCH1 activation. Remarkably, DLL1 was regulated by direct cross talk between redox and inflammatory pathways that are activated during both reflux and malignant transformation. Mechanistically, the APE1 redox function transcriptionally up-regulated NF-κB in response to bile salts. This licensed NF-κB to transcriptionally up-regulate DLL1 to activate and stimulate downstream NOTCH1 signaling, thereby defining a novel APE1-NF-kB-NOTCH pro-tumorigenic pathway. This pathway was important for maintaining tumor initiating (cancer “stem cell-like”) properties in vitro, recurrently detected in genetically engineered mouse models of EAC and in EAC patient samples in vivo, and portended an overall poor prognosis. Collectively, these findings indicate that progression from chronic injury to malignancy in the esophagus is driven by a unique mechanism that links redox balance, inflammation, embryonic development (NOTCH) together into a common pro-tumorigenic pathway that is intrinsic to EAC cells.
Citation Format: Lei Chen, Heng Lu, Dunfa Peng, Longlong Cao, Zheng Chen, Ajaz Bhat, Alexander Zaika, Shutian Zhang, Wael El-Rifai. Activation of NOTCH signaling via DLL1 is mediated by APE1-redox-dependent NF-κB activation in esophageal adenocarcinoma [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 6071.
Abstract 6075: ROS-Nrf2-ABCB1 axis accompanied with pFyn nuclear accumulation plays pivotal roles in vinorelbine resistance in non-small cell lung cancer
Authors: Tamari Shigeyuki , Menju Toshi , Toyazaki Toshiya , Miyamoto Hideaki , Chiba Naohisa , Noguchi Misa , Date Hiroshi 
Published: June 2022

Abstract
Introduction: Adjuvant cisplatin-vinorelbine is standard therapy for stage II/III lung cancer. Poor survival in lung cancer can be attributed to vinorelbine resistance arising from ABC sub-family B member 1 (ABCB1) and phosphorylated Fyn (pFyn) overexpression. However, the underlying mechanism remains unclear. Nrf2 regulates the cell-protective ABC family and activates nuclear transport of Fyn. Here, we aimed to evaluate the ROS-Nrf2-ABCB1 axis in both vinorelbine-resistant (VR) cells and clinical samples.
Methods: We established VR cells by exposing H1299 cells to vinorelbine, and determined intracellular reactive oxygen species (ROS) level of H1299 cells induced by vinorelbine using DCFH-DA. We evaluated the total and subcellular expression of Nrf2, ABCB1, and pFyn in VR cells and performed immunofluorescence of VR cells to confirm the precise subcellular localization of pFyn. Cell viability assay was used to examine whether the sensitivity of VR cells to vinorelbine depends on Nrf2 activity. For immunohistochemistry, we used 104 tissue samples from lung cancer patients who underwent surgery followed by cisplatin-vinorelbine treatment between December 2006 and June 2018.
Results: Persistent exposure to vinorelbine induced intracellular ROS formation of H1299 cells. Both ABCB1 and Nrf2 were overexpressed in VR cells, and ABCB1 expression was dependent on Nrf2 downstream activation. Subcellular fractionation and immunofluorescence revealed nuclear accumulation of pFyn in VR cells. Decreased expression of Nrf2 restored the sensitivity of VR cells to vinorelbine. In the 104 surgical samples, Nrf2 and ABCB1 were significantly associated with disease-free survival (p = 0.029 and 0.035, respectively), and pFyn was associated with overall survival (p = 0.040).
Conclusions: ROS-Nrf2 upregulates ABCB1 and accompanied by nuclear accumulation of pFyn, induces vinorelbine resistance. Our findings may facilitate drug resistance prevention strategies or new drug target development against non-small cell lung cancer.
Citation Format: Shigeyuki Tamari, Toshi Menju, Toshiya Toyazaki, Hideaki Miyamoto, Naohisa Chiba, Misa Noguchi, Hiroshi Date. ROS-Nrf2-ABCB1 axis accompanied with pFyn nuclear accumulation plays pivotal roles in vinorelbine resistance in non-small cell lung 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 6075.
Abstract 6081: The transcription factor SPDEF promotes the survival of mucinous pancreatic ductal adenocarcinoma of the classical subtype
Authors: Tonelli Claudia , Yordanov Georgi N. , Hao Yuan , Deschênes Astrid , Brosnan Erin , Doshi Abishek , Park Youngkyu , Preall Jonathan , Tuveson David A. 
Published: June 2022

Abstract
Pancreatic ductal adenocarcinoma (PDA) is characterized by intra-tumoral heterogeneity. Using single-cell RNA sequencing, we reveal multiple tumor subpopulations distinguished by their differentiation state and associated with different stages of tumor progression. We identify SPDEF as a factor required for tumorigenesis in pancreatic cancer cells of epithelial and mucinous nature. SPDEF levels correlate with glandular differentiation and high secretory activity, which are characteristic features of human PDA of the classical subtype. SPDEF can drive mucus production in pancreatic cancer cells and is essential for the growth of mucus-secreting tumors by regulating endoplasmic reticulum (ER) activity. These findings offer insights into the factors controlling differentiation in PDA and may inform new therapeutic strategies with improved efficacy.
Citation Format: Claudia Tonelli, Georgi N. Yordanov, Yuan Hao, Astrid Deschênes, Erin Brosnan, Abishek Doshi, Youngkyu Park, Jonathan Preall, David A. Tuveson. The transcription factor SPDEF promotes the survival of mucinous pancreatic ductal adenocarcinoma of the classical subtype [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 6081.
Abstract 6094: SRC inhibitor saracatinib enhances efficacy of PD-1/PD-L1 immune checkpoint blockade in non-small cell lung cancer
Authors: Lu Fei-Teng , Luo Fan , Qiu Miao-Zhen , Cao Jia-Xin , Luo Qiu-Yun , Yang Da-Jun , Zhao Hong-Yun 
Published: June 2022

Abstract
Background: Although immune checkpoint inhibitors (ICI) included PD-1/PD-L1 have demonstrated durable therapeutic responses in some cases, a significant portion of patients with cancer remain nonresponsive (e.g. only ~20% with anti-PD-1 in lung cancer). Substantial limitations in the rate of response underscore the need for suitable combination therapies. SRC family kinases is overexpressed or activated in multiple human malignancies, as a candidate target in regulating antitumor immunity. Saracatinib, an orally bioavailable multi-kinase inhibitor, has demonstrated clinical efficacy in CML. Here, we proved saracatinib as SRC inhibitor that were capable of increasing the antitumor immunity in non-small lung cancer.
Method: Cytotoxicity assays were used to determined antitumor activities of saracatinib in non-small lung cancer cell lines. The expression of PD-L1 expression in saracatinib 1 treated cell lines was investigated by western blots, quantitative PCR and flow cytometry. The effect of saracatinib in antitumor immunity alone or in combination with immunotherapy was also determined in vitro and in vivo. RNAi, overexpression, and gene expression analyses were used to define underlying mechanisms.
Result: We found that SRC inhibitor saracatinib robustly decreased expression of PD-L1 in non-small lung cancer cells and animal models. The observed inhibitory effect was time- and concentration-dependent. Furthermore, our results showed that saracatinib and anti-PD-L1 combined to improve T-cell-mediated killing of tumor cells in vitro and in vivo, which were associated with activation of CD8+ T cytotoxic cell included expression of IFN-γ and granzyme-B. Prolonged survival was also observed in mice treated with saracatinib in combination with PD-L1 blockade.
Conclusion: Our in vivo and in vitro data demonstrated that SRC inhibitor saracatinib enhance T-cell-mediated anti-tumor immune responses in non-small lung cancer. We also provide evidence that support the combination of saracatinib and anti-PD-1/PD-L1 as a potential combination therapeutic approach to increase the efficacy of immunotherapy in non-small lung cancer.
Citation Format: Fei-Teng Lu, Fan Luo, Miao-Zhen Qiu, Jia-Xin Cao, Qiu-Yun Luo, Da-Jun Yang, Hong-Yun Zhao. SRC inhibitor saracatinib enhances efficacy of PD-1/PD-L1 immune checkpoint blockade in non-small cell lung 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 6094.