bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3378: Systematic pharmacogenomic analysis of large patient derived xenografts data
Authors: Mer Arvind Singh , Ba-alawi Wail , Smirnov Petr , Wang Yi Xiao , Brew Ben , Tsao Ming-Sound , Cescon David , Goldenberg Anna , Haibe-Kains Benjamin
Published: August 2019

One of the key challenges in cancer precision medicine is finding robust biomarkers of drug response. Patient-derived tumor xenografts (PDXs) have emerged as reliable preclinical models since they better recapitulate tumor response to chemo- and targeted therapies. However, the lack of standard tools poses a challenge in the analysis of PDXs with molecular and pharmacological profiles. Efficient storage, access and analysis is key to the realization of the full potential of PDX pharmacogenomic data. To address this, we have developed Xeva (XEnograft Visualization & Analysis), an open-source software package for processing, visualization and integrative analysis of a compendium of in vivo pharmacogenomic datasets. The Xeva package follows the PDX minimum information (PDX-MI) standards and can handle both replicate-based and 1x1x1 experimental designs. We used Xeva to characterize the variability of gene expression and pathway activity across passages. We found that only a few genes and pathways have passage specific alterations (median intraclass correlation of 0.53 for genes and positive enrichment score for 92.5% pathways). For example, activity of the mRNA 3'-end processing and elongation arrest and recovery pathways were strongly affected by model passaging (gene set enrichment analysis false discovery rate [FDR] <5%). We then leveraged our platform to link the drug response and the pathways whose activity is consistent across passages by mining the Novartis PDX Encyclopedia (PDXE) data containing 1,075 PDXs spanning 5 tissue types and 62 anticancer drugs. We identified 87 pathways significantly associated with response to 51 drugs (FDR < 5%), including associations such as erlotinib response and signaling by EGFR in cancer pathways and MAP kinase activation in TLR cascade and binimetinib response. Among the significant pathway-drug associations, we found novel biomarkers based on gene expressions, Copy Number Aberrations (CNAs) and mutations predictive of drug response (concordance index > 0.60; FDR < 0.05). Xeva provides a flexible platform for integrative analysis of preclinical in vivo pharmacogenomics data to identify biomarkers predictive of drug response, a major step toward precision oncology.

Citation Format: Arvind Singh Mer, Wail Ba-alawi, Petr Smirnov, Yi Xiao Wang, Ben Brew, Ming-Sound Tsao, David Cescon, Anna Goldenberg, Benjamin Haibe-Kains. Systematic pharmacogenomic analysis of large patient derived xenografts data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3378.
Abstract 3394: Diagnosis of intrahepatic metastasis (IM) and multi-entric (MC) carcinogenesis by novel mutational signature in patients with multiple and recurrent hepatocellular carcinomas
Authors: Yang Pinghua , Bai Shilei , Zhang Yanpeng , Xie Zhihao , Cheng Zhangjun , Yang Jie , Li Jun , Wang Jiaqian , Lei Zhengqing , Xia Yong , Wang Kui , Li Zheng , Zhang Baohua , Wan Xuying , Wu Mengchao , Shen Feng
Published: August 2019

Hepatocellular carcinoma is a common solid tumor worldwide and represents the third leading cause of cancer death. Patients with hepatocellular carcinoma (HCC) have poor prognosis because of frequent multi-centric (MC) and intrahepatic metastasis (IM). The discrimination between MC and IM is profoundly important for interpreting tumorigenesis and treatment decision making. However, it is difficult to correctly estimate by histological. Previous studies suggest that HBV integration sites, mitochondrial D-loop mutations, microsatellite loss of heterozygosity (MSI LOH) may provide more accurate information. Paired two tumor lesions and adjacent non-tumor tissues from 10 HBV-position patients were collected for whole genome sequencing. The proportion of shared somatic SNV among the tumor lesions was used to separate MC and IM groups. 4 of 10 patients with shared mutation rate higher than 10% (15.89-49.48%) were identified as IMs. 6 patients with shared mutation rate lower than 10% (0.33-1.97%) were identified as MCs. We also used shared HBV integration rate, mitochondrial D-loop, MSI LOH, diameter ratio to identify IM and MC. The coincidence rates between shared mutation rate and shared HBV integration rate, mitochondrial D-loop, MSI LOH, diameter ratio is 88.89%, 77.78%, 88.89%, and 90%, respectively. It suggests that the diameter ratio of multiple HCCs provide a no-invasion method in clonality analysis. Finally, we developed a panel covering 1M regions to replace whole-genome sequencing to identify IM and MC. We validated the shared mutation rate of target panel region in another 19 whole-genome sequencing HCC patients with multiple tumor lesions from ICGC. A

consistent rate of 94.74% in shared mutation rate between target panel region and whole genome region, indicated that for patients with resectable multiple HCCs, sequencing-based molecular diagnosis using somatic single nucleotide variation information showed higher sensitivity compared to previous techniques. And a smaller size of target panel contains adequate information is more cost-effective approach for clinical decision making.

Citation Format: Pinghua Yang, Shilei Bai, Yanpeng Zhang, Zhihao Xie, Zhangjun Cheng, Jie Yang, Jun Li, Jiaqian Wang, Zhengqing Lei, Yong Xia, Kui Wang, Zheng Li, Baohua Zhang, Xuying Wan, Mengchao Wu, Feng Shen. Diagnosis of intrahepatic metastasis (IM) and multi-entric (MC) carcinogenesis by novel mutational signature in patients with multiple and recurrent hepatocellular carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3394.
Abstract 3415: Tumor fitness and immune exhaustion: Checkpoint vs endogenous settings
Authors: Bubie Adrian , Akers Nicholas , Villanueva Augusto , Losic Bojan
Published: August 2019

Recently proposed tumor fitness measures based on neoepitope profiling and viral epitope similarity have led to treatment efficacy and immune response prediction models in the checkpoint setting for melanoma (SKCM) and small-cell lung cancer (NSCLC). In this work we test if these checkpoint based fitness measures are associated with either tumor-infiltrating T-cell activity or abundance, and also overall patient survival, in the endogenous setting for the SKCM (n=337) and NSCLC (n = 307) TCGA cohorts. We also investigated if epitopes arising from tumor viral co-factors in Hepatitis B liver cancer (HBV+ HCC) drove T cell activity or response compared to neo-epitope burden.

We find no statistically significant correlation between immune activity and response (as measured by tumor RNA-seq profiling) and the proposed neo-epitope checkpoint-based fitness measures, and similarly no significant survival effect. Further, we found firm evidence that tumor neoepitopes dominate HBV viral epitopes in putative immunogenicity and drive immune response in TCGA HCC (n = 178), and confirmed this trend in multi-regional data (12 patients, 72 samples). These results suggest that tumor-immune response and recruitment in SKCM and NSCLC, and their interplay with viral-cofactor HBV in HCC, are fundamentally driven by different factors in the endogenous setting.

Finally, we propose that tumor fitness may be partially encoded by a simple T-cell exhaustion expression signature, which we demonstrate is a significant predictor of patient survival for SKCM and NSCLC and may translate more widely into other tumor types in the endogenous setting.

Citation Format: Adrian Bubie, Nicholas Akers, Augusto Villanueva, Bojan Losic. Tumor fitness and immune exhaustion: Checkpoint vs endogenous settings [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3415.
Abstract 3435: Targeting AKT activity inhibits MYCN and sensitizes neuroblastoma to chemotherapeutic agents
Authors: Grand Marion Le , Kimpton Kathleen , Gana Christine , Valli Emanuele , Mayoh Chelsea , Kavallaris Maria
Published: August 2019

MYCN-amplified neuroblastoma is one of the deadliest forms of childhood cancer and remains a significant clinical problem. Direct pharmacological inhibition of MYCN protein is challenging and one possible strategy to treat MYCN-amplified neuroblastoma patients is antagonizing proteins involved in its regulation. The AKT/GSK3β pathway directly regulates stabilization of MYCN, providing a therapeutic rational in MYCN-amplified neuroblastoma. In this study, we addressed the question of how AKT can play a pivotal role in MYCN-amplified neuroblastoma and whether small molecule AKT inhibitors can be promising anti-cancer compounds in children diagnosed from this cancer.

Bioinformatics analysis revealed that high gene expression of AKT1 and AKT2, but not AKT3 was correlated with MYCN amplification and was significantly associated with poor outcome in neuroblastoma patients. Using RNAi-mediated depletion of AKT isoforms or pharmacological inhibition, we then demonstrated that the total AKT activity inhibition rather than the expression of particular isoforms was necessary to cause a significant decrease in neuroblastoma cell proliferation. Our results showed that AKT activity inhibition led to a significant downregulation of MYCN expression through GSK3β regulation. These results demonstrated the potential of targeting AKT activity in MYCN-amplified neuroblastoma patients. Our in vitro and in vivo data revealed promising efficacy for the pan-AKT inhibitor perifosine combined with conventional cytotoxic drugs in MYCN-amplified neuroblastoma cell. Importantly, by genetically modulating MYCN expression (siRNA or plasmid vector), our results demonstrated that MYCN expression is required for perifosine chemosensitisation. This effect was linked to the combined actions of apoptosis activation and the downregulation of ABC transporter expressions.

Collectively, our data strongly support that combining the pan-AKT inhibitor perifosine, which is currently in clinical trial, with clinically-approved drugs for neuroblastoma patients could be a novel therapeutic strategy to indirectly target MYCN in neuroblastoma.

Citation Format: Marion Le Grand, Kathleen Kimpton, Christine Gana, Emanuele Valli, Chelsea Mayoh, Maria Kavallaris. Targeting AKT activity inhibits MYCN and sensitizes neuroblastoma to chemotherapeutic agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3435.
Abstract 3455: TNFAIP8 increases drug resistance and steatosis in liver cancer by inducing autophagy
Authors: Niture Suresh , Gyamfi Maxwell A. , Kumar Deepak
Published: August 2019

Tumor necrosis factor-α-inducible protein 8 (TNFAIP8) is a TNF-α inducible anti-apoptotic protein which facilitates tumor growth and progression in several cancers. The molecular mechanisms how TNFAIP8 modulates the progression of liver cancer remain elusive. The present study investigated the role of TNFAIP8 in the liver cancer cell growth, drug resistance/survival and cell steatosis. Tissue microarray data from patients demonstrated an increased expression of TNFAIP8 protein during development of different stages of liver cancer compared with normal liver tissues. To test the correlation between TNFAIP8 expression and liver cancer progression, we transiently/stably expressed TNFAIP8 protein in liver cancer cell lines. Expression of TNFAIP8 in liver cancer cells HepG2 and SK-Hep1 increased both cell growth/survival and drug resistance against anti-liver cancer drugs sorafenib and regorafenib by inhibition of apoptosis. In addition, TNFAIP8 knockdown sensitized tumor cell lines to sorafenib and regorafenib. Expression of TNFAIP8 modulates AKT/mTOR pathway and induced autophagy and thus increased drug resistance. Moreover, TNFAIP8 induced liver cancer cell steatosis by increasing the expression of L-FABP1, SCD1, ACC, and PPARγ proteins which involved in lipid synthesis. We also demonstrate that chronic EtOH induced steatosis in mice liver was associated with increased TNFAIP8 expression and autophagy suggesting that TNFAIP8 mediate EtOH induced steatosis. In addition, increased expression of TNFAIP8 and hepatic steatosis was observed in patients with a history of alcohol use compared with no history of alcohol use. Taken together our data suggested that TNFAIP8 increases drug resistance/survival, EtOH-induced cell steatosis and early liver cancer development by the induction of autophagy.

Citation Format: Suresh Niture, Maxwell A. Gyamfi, Deepak Kumar. TNFAIP8 increases drug resistance and steatosis in liver cancer by inducing autophagy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3455.
Abstract 3456: Distinct control of PERIOD2 degradation and circadian rhythms by the oncoprotein MDM2
Authors: Zou Xianlin , Liu Jingjing , Gotoh Tetsuya , Brown Anne M. , Jiang Liang , Wisdom Esther L. , Kim Jae Kyoung , Finkielstein Carla V.
Published: August 2019

The circadian clock relies on post-translational modifications to set the timing for degradation of core regulatory components and, thus, sets clock progression. Ubiquitin-modifying enzymes targeting clock components for degradation are known to mostly recognize phosphorylated substrates. A case in point is the circadian factor PERIOD 2 (PER2) whose phospho-specific turnover involves its recognition by β-transducin repeat containing proteins (β-TrCPs). Yet, the existence of this unique mode of regulation of PER2’s stability falls short of explaining persistent oscillatory phenotypes reported in biological systems lacking functional elements of the phospho-dependent PER2 degradation machinery.

In this study, we challenge the phosphorylation-centric view that PER2 degradation enhances circadian rhythm robustness by i) identifying the PER2:MDM2 endogenous complex, ii) establishing PER2 as a previously uncharacterized substrate for MDM2, iii) revealing an alternative phosphorylation-independent mechanism for PER2 ubiquitin-mediated degradation, iv) pinpointing residues for ubiquitin modification, and v) establishing the importance of MDM2-mediated PER2 turnover for defining the circadian period length. Our results not only expand MDM2’s suite of specific substrates beyond the cell cycle to include circadian components but also uncover novel regulatory players that likely impact our view of how other mechanisms crosstalk and modulate the clock itself.

Citation Format: Xianlin Zou, Jingjing Liu, Tetsuya Gotoh, Anne M. Brown, Liang Jiang, Esther L. Wisdom, Jae Kyoung Kim, Carla V. Finkielstein. Distinct control of PERIOD2 degradation and circadian rhythms by the oncoprotein MDM2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3456.
Abstract 346: E2F8 induces proliferation and invasion through the epithelial-mesenchymal transition and notch signaling pathways in ovarian cancer
Authors: Eoh Kyung Jin , Lee Jong Woo , Kim Young Tae , Koo Peter Jaseok
Published: August 2019

Purpose: Recent research has investigated the role of E2F8 in cancer progression. However, whether the progression of ovarian cancer involves E2F8 remains to be elucidated. In this study, the bio-functional consequences of E2F8 knockdown in vitro and in vivo were explored. Experimental

Design: E2F8 expression was compared between ovarian cancer and non-cancer tissues, and the association between E2F8 expression and progression-free survival in ovarian cancer patients was analyzed. To demonstrate the function of E2F8 in cell proliferation, migration, and invasion, RNA interference was employed to suppress E2F8 expression in ovarian cancer cell lines. Finally, the effect of E2F8-knockdown was investigated in an ovarian cancer xenograft mouse model.

Results: Ovarian cancer tissue exhibited significantly higher E2F8 expression than normal ovarian tissue. Clinical data confirmed that E2F8 was a significant predictor of progression-free survival, and ovarian cancer patients with high E2F8 expression exhibited poorer prognosis than patients with low E2F8 expression. In vitro experiments using E2F8-knockdown ovarian cancer cell lines showed that E2F8 knockdown inhibited cell proliferation, migration, and tumor invasion. Additionally, E2F8 was a potent inducer and modulator of the expression of epithelial-mesenchymal transition (EMT) and Notch signaling pathway-related markers. We confirmed the function of E2F8 in vivo, demonstrating that E2F8-knockdown was significantly correlated with reduced tumor size and weight.

Conclusions: In conclusion, our study suggests that E2F8 is highly correlated with ovarian cancer progression; hence, E2F8 may be a prognostic marker and therapeutic target for ovarian malignancy.

Note: This abstract was not presented at the meeting.

Citation Format: Kyung Jin Eoh, Jong Woo Lee, Young Tae Kim, Peter Jaseok Koo. E2F8 induces proliferation and invasion through the epithelial-mesenchymal transition and notch signaling pathways in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 346.
Abstract 3465: FANCD2 depletion suppresses tumor growth in esophageal squamous cell carcinoma
Authors: Lei Chan , Yu Zhuoyou , Ning Lvwen , Ko Mun-Yee , Wang Lidong , Lung Maria Li
Published: August 2019

Introduction: Esophageal squamous cell carcinoma (ESCC) has a remarkably high incidence in Northern China. Our next-generation sequencing analysis on familial ESCC samples suggests that members of the Fanconi Anemia (FA) pathway play important roles in ESCC development. Fanconi anemia complementation group D2 (FANCD2) as a key player of FA pathway has multiple cellular functions. It is well-known for its role in DNA damage repair through the FA pathway. Patients with germline FANCD2 mutations are prone to tumor formation. Identifying roles of FANCD2 in ESCC development may enhance our foundation for future development of specific treatment regimens for this deadly disease.

Methods and Results: To study the function of FANCD2 in ESCC, we applied the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technique to inhibit FANCD2 protein expression by functional knock-out (fKO). As expected, we observed increased DNA damage in FANCD2 fKO cells as shown by Comet assay, consistent with the classic role of FANCD2 in genome integrity. We also observed that the DNA damage by irradiation takes longer to be repaired in FANCD2 fKO cells, indicating that FANCD2 enhances irradiation-induced DNA damage repair but is not necessary. Similarly, cells with FANCD2 fKO are more sensitive to irradiation, as indicated by cell cycle arrest at S/G2 phase.

Surprisingly, without inducing any DNA damage, FANCD2 fKO cells also show cell cycle arrest at S/G2 phase. The MTT cell proliferation assay also show that FANCD2 fKO reduces proliferation and colony-forming ability. Consistent with the in vitro data, FANCD2 fKO cells also form smaller tumors in vivo by the nude mouse tumorigenicity assay.

Conclusion: These results indicate that FANCD2 plays important roles in ESCC development and suggest a pro-oncogenic feature of wildtype FANCD2 in ESCC. Further investigation is ongoing to examine the functional role and molecular mechanisms of the oncogenic FANCD2, ultimately aiming at improving ESCC disease management.

Acknowledgement: We acknowledge the grant support from the Hong Kong Research Grants Council Collaborative Research Fund (C7031.15G) and the Asian Fund for Cancer Research to M.L.L.

Citation Format: Chan Lei, Zhuoyou Yu, Lvwen Ning, Mun-Yee Ko, Lidong Wang, Maria Li Lung. FANCD2 depletion suppresses tumor growth in esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3465.
Abstract 3497: SAMHD1 is a Novel Biomarker and Therapeutic Target for Radiation Therapy and PARP Inhibition in Breast Cancer
Authors: Thompson Elizabeth
Published: August 2019

SAMHD1 is a Novel Biomarker and Therapeutic Target for Radiation Therapy and PARP Inhibition in Breast Cancer

Ashley Schlafstein, Waaqo Daddacha, David S. Yu

Background/Introduction:

Patients with breast cancer are often treated by ionizing radiation (IR) and PARP inhibitors; however, the effectiveness of these treatments is often limited by lack of response and/or resistance. Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a deoxyribonucleotide triphosphate (dNTP) triphosphohydrolase with a well-established role in HIV-1 restriction by depleting dNTPs required for reverse transcription and replication. SAMHD1 is also dysregulated in breast and other cancers and in autoimmune disease. In addition to its well-established dNTPase activity, our lab has defined a novel role for SAMHD1 in DNA end resection to facilitate DNA double strand break (DSB) repair by homologous recombination (HR). Because of its role in DNA DSB repair and its link to breast cancer, we hypothesized that SAMHD1 could be used as a novel biomarker and target for breast cancer therapy.

Methods:

We queried the TCGA database for patients with breast cancer who were treated with or without IR to determine if there was an association of SAMHD1 expression level with clinical outcome. We also determined if targeting SAMHD1 for proteasomal degradation with novel virus like particles (VLPs) containing Vpx, a viral accessory protein, can sensitize breast cancer cells and tumors to DNA damaging agents.

Results:

In patients with breast cancer treated with IR, low SAMHD1 expression was associated with a statistically significant improvement in overall survival, while for those not treated with IR, no significant difference in association of SAMHD1 expression with outcome was observed. Breast cancer cells and tumors treated with VLPs containing Vpx were hypersensitive to IR and PARP inhibitor.

Conclusion:

Our results identify SAMHD1 as a novel biomarker for stratifying breast cancer patients for treatment with IR. In addition, targeting SAMHD1 with VLPs containing Vpx may be a novel therapeutic strategy for sensitizing breast cancer to IR, PARP inhibitors, and other agents that induce DNA DSBs.

Citation Format: Elizabeth Thompson. SAMHD1 is a Novel Biomarker and Therapeutic Target for Radiation Therapy and PARP Inhibition in Breast Cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3497.
Abstract 3500: Highly potent and selective ATM kinase inhibitor M4076: A clinical candidate drug with strong anti-tumor activity in combination therapies
Authors: Fuchss Thomas , Graedler Ulrich , Schiemann Kai , Kuhn Daniel , Kubas Holger , Dahmen Heike , Zimmermann Astrid , Zenke Frank , Blaukat Andree
Published: August 2019

M4076 is an ATP-competitive inhibitor of the Ataxia telangiectasia mutated (ATM) kinase (IC50 < 1 nM), which targets tumor cell survival and growth by inhibiting double-strand break (DSB) repair as well as checkpoint control. DSB repair is crucial for survival of malignant tumor cells, especially under treatment with DNA damaging chemo- and radiotherapy. As such, the rationale of pharmacological inhibition of ATM is to increase and maintain the extent of unrepaired DNA damage generated by radio-, chemotherapy, and targeted therapies to drive tumor cells into cell death. We have developed an orally administered, sub-nanomolar potent & selective kinase inhibitor of ATM, M4076, for cancer therapy in combination with DNA damaging modalities. Here, we present its structure-activity relationship, its chemical structure (first-time disclosure) & physicochemical profile as well as its preclinical characterization using biochemical, cellular & human tumor xenograft models. M4076 sensitizes tumor cell lines to radiation therapy in vitro and strongly enhances the anti-tumor activity of ionizing radiation in vivo. These effects are due to the inhibition of ATM kinase activity as demonstrated by the inhibition of radiotherapy induced ATM autophosphorylation and CHK2 phosphorylation in xenograft lysates.

Citation Format: Thomas Fuchss, Ulrich Graedler, Kai Schiemann, Daniel Kuhn, Holger Kubas, Heike Dahmen, Astrid Zimmermann, Frank Zenke, Andree Blaukat. Highly potent and selective ATM kinase inhibitor M4076: A clinical candidate drug with strong anti-tumor activity in combination therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3500.
Abstract 351: A targeted nanocomplex of the IKBKE siRNA inhibits invasiveness and growth of triple negative breast cancer cells
Authors: Zhao Zhen , Li Yuanke , Cheng Kun
Published: August 2019

IκB kinase ϵ (IKBKE, or known as IKKϵ), an important mediator in the activation of NF-κB pathway, was recently identified as an oncogene in breast cancer and overexpressed in approximately 30% of breast carcinomas. It is also highly expressed in TNBC cells, which is correlated with angiogenesis process, high metastasis in NF-κB pathway of TNBC. We found that silencing IKBKE in TNBC cells using siRNA significantly inhibits the proliferation, migration and invasion of TNBC cells by specific silenced 71% of IKBKE in vitro. In vivo study indicated that IKBKE siRNA can inhibit TNBC tumor growth after peritumoral injection at a IKBKE siRNA dose of 0.3 mg/kg. We next developed a CD44-targeting, cholesterol-peptide based nanocomplex to co-deliver the IKBKE siRNA and cabazitaxel to TNBC cells. The nanocomplex showed the synergistic effect of the IKBKE siRNA and cabazitaxel on inhibiting the growth of TNBC tumors in vivo. Modification of the nanocomplex with CD44 further improved tumor uptake and anti-tumor efficacy of the nanocomplex. Our results suggest that IKBKE siRNA is a promising anti-tumor agent for TNBC therapy, and co-delivery of IKBKE siRNA and cabazitaxel using a CD44-targeting nanocomplex is a potential strategy for TNBC treatment. Moreover, this multifunctional delivery system provides a platform for other combination therapy including an siRNA and a chemotherapy drug.

Citation Format: Zhen Zhao, Yuanke Li, Kun Cheng. A targeted nanocomplex of the IKBKE siRNA inhibits invasiveness and growth of triple negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 351.
Abstract 3518: SPARC related signaling genes in non-small cell lung cancer by RNA-sequencing transcriptome analysis
Authors: Lakka Sajani S. , Ahir Bhavesh K.
Published: August 2019

Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, accounting for about 80 % cases of lung cancer and is the leading cause of cancer-related death in the United States and worldwide. SPARC (secreted protein acidic and rich in cysteine), a multicellular non-structural glycoprotein is known to be involved in the regulation of cell adhesion, cell proliferation as well as in tumorigenesis and metastasis in various cancers including NSCLC. SPARC contributes to matrix remodeling and turnover and is involved in modulating the tumor microenvironment. Previous studies have suggested that SPARC can be used as a prognostic factor for NSCLC and represents a highly promising therapeutic modality. In this study we used high-throughput RNA-sequencing transcriptome profiling analysis to delineate pathways involved in SPARC signaling. We assessed differentially expressed genes, novel genes, biological processes and biological signaling pathways in SPARC expressed NSCLC cell line. We identified a total of 3,280 upregulated and 1,608 downregulated differentially expressed genes with known functions in SPARC expressed NSCLC cells. KEGG enrichment analysis indicated that the differentially expressed genes were involved in cellular metabolic processes, regulation of biological processes or biological signaling pathways like cell cycle, spliceosome, apoptosis and WNT signaling pathway. The RNA-seq analysis further revealed that genes involved in apoptosis were significantly altered after SPARC modulation to NSCLC cells. Co-transfection experiments using SPARC shRNA indicated that SPARC modulation induced apoptosis via regulating PI3K/AKT signaling pathway. In summary, this study uncovers SPARC dependent regulatory mechanisms in NSCLC.

Note: This abstract was not presented at the meeting.

Citation Format: Sajani S. Lakka, Bhavesh K. Ahir. SPARC related signaling genes in non-small cell lung cancer by RNA-sequencing transcriptome analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3518.
Abstract 355: A novel anti-HER2 antibody that displays superior synergetic effects in Trastuzumab mediated HER2-overexpressing tumor arrest
Authors: Huang Haomin , zhang xuesai , Chen jianhe , Zhao Le , Li qingrou , zhu zhenping
Published: August 2019

The majority of patients with metastatic breast cancer on Trastuzumab, an anti-HER2 monoclonal antibody, generally develop resistance to the drug within a year after initiation of the treatment. Therefore, there is an unmet need for a novel agent to treat HER2 overexpressing breast cancers. Here we described a novel anti-HER2 humanized monoclonal antibody, 19H6-hu, which binds to HER2 ECD with high affinity and could inhibit the proliferation of multiple HER2-overexpressing cancer cell lines as a single agent, though, to a lesser degree when compared to Trastuzumab alone. Interestingly, when in combination with Trastuzumab, 19H6-hu exhibited much stronger potency in inhibition of BT474, N87 and SKBR3 cell growth relative to that of Perjeta in combination with Trastuzumab as well as in suppression of tumor growth in vivo when compared to Trastuzumab alone. Alanine scanning demonstrated that the antibody binds to an alpha-helix located within the domain III and in proximity to the domain IV of HER2 ECD, which is different from the known binding sites of Trastuzumab and Perjeta. Western blotting further confirmed that 19H6-hu in combination with Trastuzumab is more efficacious in blocking phosphorylation of ERK and phosphorylation of HER2 at Y1248 when compared to Trastuzumab in combination with Perjeta or applied alone. Thereby, our results highlight the functional variability of HER2 domains and provide a new insight into the design of HER2-targeting agents.

Citation Format: Haomin Huang, xuesai zhang, jianhe Chen, Le Zhao, qingrou Li, zhenping zhu. A novel anti-HER2 antibody that displays superior synergetic effects in Trastuzumab mediated HER2-overexpressing tumor arrest [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 355.
Abstract 3551: Dysregulation in microprocessor processing of a primary miRNA, mir-21, leads to downregulation of a tumor suppressor, GHR, progressing hepatocellular carcinoma
Authors: Park Seokju , Yang Hee Doo , Seo Jwawon , Nam Seokwoo , Nam Jin-Wu
Published: August 2019

Improper miRNA biogenesis produces the 5’ variants of miRNA with a shifted seed region (also called isomiRs). Although the presence of stably abundant isomiRs were repeatedly reported, it is still unclear whether the generation of isomiRs results either from the mistake of microprocessor or from the regulation by other intrinsic or extrinsic factors, and whether the isomiRs participate in critical cellular processes, particularly in cancer progress. Here, we performed both high-throughput RNA sequencing (RNA-seq) and small RNA sequencing (sRNA-seq) from 75 hepatocellular carcinoma (HCC) and normal samples (fresh frozen) of Korean HCC cohort. Combined analysis with other publicly available sequencing data, showed that although the expression signatures of isomiRs largely follow those of canonical ones, the relative abundance of some isomiRs are dynamically changed over cancer progression, forming new isomiR-target interactions. Particularly, the biogenesis of highly abundant miR-21 is dysregulated by interaction with HNRNPC to primary mir-21 during cancer progress, producing relatively more isomiR-21-5p in HCC. Introducing isomiR-21-5p mimic or antagomir against isomiR-21-5p, and the dysregulation of HNRNPC expression perturbed the relative abundance of isomiR-21-5p, leading to dysregulation of miRNA targeting on a tumor suppressor gene, GHR, and affecting cancer progress. Our study not only describes that isomiR-21-5p is an independent prognostic marker and a potential therapeutic target of HCC but also presents that the production of isomiRs is tightly regulated by other extrinsic factors in cells.

Citation Format: Seokju Park, Hee Doo Yang, Jwawon Seo, Seokwoo Nam, Jin-Wu Nam. Dysregulation in microprocessor processing of a primary miRNA, mir-21, leads to downregulation of a tumor suppressor, GHR, progressing hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3551.
Abstract 3565: Role of novel microRNA 4287 at a frequently deleted chromosome 8p region in prostate cancer
Authors: Bhagirath Divya , Yang Thao , Tabatabai Laura , Majid Shahana , Yamamura Soichiro , Dahiya Rajvir , Tanaka Yuichiro , Saini Sharanjot
Published: August 2019

Deletion of chromosome (chr)8p21-22 region that has been traditionally associated with the loss of homeodomain protein, NKX3.1 and with tumor initiation, is frequently observed in prostate cancer (PCa). More significantly, loss of this region is associated with aggressiveness and poor prognosis of PCa, thereby emphasizing a key role of this region in advanced prostate cancer. In a paradigm shifting hypothesis, we proposed that this frequently deleted locus is associated with a cluster of miRNA genes - miR-3622a/b and miR-383- that are lost in PCa and play an important mechanistic role in PCa progression and metastasis by regulating Epithelial-mesenchymal-transition (EMT) and stemness. Extending our hypothesis, in this study we evaluated the role of miR-4287, a miRNA gene located within this region in PCa. We profiled the expression of miR-4287 in laser capture microdissected (LCM) PCa tissues and matched adjacent normal regions by real time PCR. miR-4287 expression was down regulated in ~79% of tissue samples. High miR-4287 expression was observed in 20% of cases. Analyses of miR-4287 expression in prostate cell lines showed that its expression is specifically attenuated in PCa cell lines compared to normal or immortalized prostate epithelial cells. Further, we evaluated the functional role of miR-4287 in prostate cancer by overexpressing miR-4287 precursor in PCa cell lines PC3 and LNCaP. miR-4287 overexpression in PCa cell lines led to decreased cellular viabilities as compared to control cells. Moreover, PCa cell lines overexpressing miR-4287 showed an increase in apoptosis and G0/G1 arrest. Further, we found that miR-4287 inhibits epithelial to mesenchymal transition (EMT) in PCa as its overexpression in PCa cell lines led to increased E-cadherin and decreased vimentin expression concomitant with morphological changes consistent with mesenchymal to epithelial transition (MET). We identified SRC, SFPR4 and CD44 as potential miR-4287 targets. Taken together, our data suggests that miR-4287 plays a significant role as tumor suppressor in PCa pathogenesis.

Citation Format: Divya Bhagirath, Thao Yang, Laura Tabatabai, Shahana Majid, Soichiro Yamamura, Rajvir Dahiya, Yuichiro Tanaka, Sharanjot Saini. Role of novel microRNA 4287 at a frequently deleted chromosome 8p region in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3565.
Abstract 3567: A novel E2F1-regulated lncRNA, XLOC_000190, is required for S phase progression and cell proliferation
Authors: Ginsberg Doron , Nizri-Megnaji Tali , Baruch Esther
Published: August 2019

Long non-coding RNAs (lncRNAs) are major regulators of many cellular processes including cell cycle progression and cell proliferation. The pivotal transcription factor E2F1 induces both proliferation and cell death and is a critical downstream target of the tumor suppressor RB. The RB/E2F pathway is often inactivated in human tumors resulting in deregulated E2F activity. Here, we report that the human lncRNA XLOC_000190 is an E2F1- regulated lncRNA that plays a role in S phase progression. XLOC_000190 levels are elevated upon activation of E2F1. Furthermore, knockdown of E2F1 and E2F3 reduce XLOC_000190 levels and endogenous E2F1 binds the XLOC_000190 promoter. Moreover, expression of XLOC_000190 is cell cycle regulated and peaks near G1/S transition and in early S. Inhibition of XLOC_000190 expression increases percentage of S phase cells, suggesting that XLOC_000190 plays a role in S phase progression. Also, silencing of XLOC_000190 in cells that are synchronized at the G1/S delays progression of cells through S phase. In agreement with its suggested role in S phase, prolonged silencing of XLOC_000190 inhibits proliferation of human cancer cells in culture. XLOC_000190 is a nuclear lncRNA and its gene is localized downstream to the protein-coding gene CDKN2C that encodes the p18ink4c CDK inhibitor. In search for XLOC_000190 mode of action we do not detect any changes in the expression of this neighbor upon XLOC_000190 silencing. However, XLOC_000190 silencing leads to a significant decrease in the level of Ribonucleotide Reductase Regulatory Subunit M2 (RRM2), which is a critical player in S phase progression. Additional data indicate that RRM2 mediates, at least in part, the effect of XLOC_000190 on S phase progression. Importantly, low levels of XLOC_000190 are associated with increased survival of kidney cancer patients.

In conclusions, our data identify XLOC_000190 as a novel E2F-regulated lncRNA that has a potential role in human cancer and regulates cell-cycle progression and cell proliferation, at least in part, via regulation of RRM2.

Citation Format: Doron Ginsberg, Tali Nizri-Megnaji, Esther Baruch. A novel E2F1-regulated lncRNA, XLOC_000190, is required for S phase progression and cell proliferation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3567.
Abstract 3568: Metastasis-promoting role of H19 long non-coding RNA in pancreatic cancer cells
Authors: Sasaki Norihiko , Toyoda Masashi , Yoshimura Hisashi , Matsuda Yoko , Arai Tomio , Itakura Yoko , Gomi Fujiya , Aida Junko , Ishiwata Toshiyuki
Published: August 2019

The H19 long non-coding RNA is highly expressed and carries out various functions in different types of cancers. Recently, we reported that H19 contributes to the metastasis of pancreatic ductal adenocarcinoma (PDAC) cells and its inhibition reduces metastasis in vivo. However, the molecular mechanisms underlying the metastasis-promoting role of H19 in PDAC cells remain unclear. With a focus on cancer stem cells (CSCs), we elucidated the mechanisms by which H19 regulates PDAC metastasis through the overexpression and knockdown of H19 in PDAC cells. To determine whether H19 is expressed heterogeneously or homogeneously in human PDAC cells, we examined its expression in PANC-1 cells using a highly sensitive in situ hybridization technique. Under 2D-culture conditions, PANC-1 cells showed heterogeneous H19 expression and the presence of small populations of H19-expressing cells. In contrast, numerous H19-expressing PANC-1 cells were detected in 3D-cultured spheres. These results suggest that H19 is expressed in CSC-like cells among PANC-1 cells. To investigate the involvement of H19 in the development of CSC characteristics, we examined self-renewal ability, anti-cancer drug resistance, and CSC-marker expression. Sphere formation of PDAC cells depended on H19expression. However, other CSC characteristics of the cells, including CSC-marker expression and anticancer-drug resistance were unaffected by H19 levels. In addition to its role in the development of CSC characteristics, we investigated the involvement of H19 in stromal invasion, which is a key step in the metastatic cascade. Although the invasion ability of PDAC cells was dependent on H19 expression, metalloproteinase activity, a key mediator of invasion, was independent of H19 expression. During the process of invasion, a critical event is the adhesion of cancer cells to the extracellular matrix. Therefore, we investigated whether H19 contributes to this cell-to-matrix adhesion step. We found that H19 promoted cell adhesion by regulating the expression of integrins and CD24. Notably, the increased adhesion of H19-overexpressing cells was blocked by an anti-β1-integrin antibody, which resulted in the inhibition of sphere formation and invasion. Taken together, H19 plays critical roles in CSC self-renewal and cell adhesion of PDAC cells that lead to invasion and metastasis. Our findings suggest that H19 represents a novel therapeutic target for the metastasis of pancreatic cancer.

Citation Format: Norihiko Sasaki, Masashi Toyoda, Hisashi Yoshimura, Yoko Matsuda, Tomio Arai, Yoko Itakura, Fujiya Gomi, Junko Aida, Toshiyuki Ishiwata. Metastasis-promoting role of H19 long non-coding RNA in pancreatic cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3568.
Abstract 3579: Long non-coding RNA ADAMTS9-AS2 inhibits ovarian tumor growth via Annexin A1
Authors: Rodriguez-Aguayo Cristian , Bayraktar Emine , Mangala Lingegowda S. , Ivan Cristina , Lopez-Berestein Gabriel , Sood Anil K.
Published: August 2019

Non-coding RNAs (ncRNA), which account for more than 75% genome transcripts, have unique functions in regulating cancer pathogenesis. Long non-coding RNAs (lncRNAs) are key regulators of gene expression and are involved in cancer progression and metastasis. However, the role of long non-coding RNAs (lncRNAs) in high-grade serous ovarian cancer (HGSC) is not well understood. We used the NCode™ non-coding RNA array to screen downregulated lncRNAs in HGSCs. After analyzing the array data of lncRNAs in HGSCs (n=29) and normal ovarian (n=11) samples, the probes mapping to the top 25 most down-regulated non-coding RNAs were analyzed. Two lncRNAs (ADAMTS9-AS1 and ADAMTS9-AS2) were identified as the antisense of gene ADAMTS9, and we validate by in vitro translation assay, q-RT-PCR, in-situ hybridization and the biological functions of ADAMTS9-AS2 in ovarian cancer cells. Moreover, using A2780-CP20 orthotopic mouse models of ovarian cancer, we further demonstrated restoring ADAMTS9-AS2 resulted in profound reduction of tumor growth and metastasis. Here, we demonstrate that ADAMTS9-AS2 is highly down-regulated (5.01x10-13 and 1.6x10-19) in ovarian cancers. Overexpression of ADAMTS9-AS2 leads to significantly increased apoptosis (7.5% control and 19.5% AS2OE) and decreased proliferation (49.5% control and 37.0% AS2OE) compared with controls. Consistently, increased expression of ADAMTS9-AS2 led to significantly reduced tumor burden in A2780-CP20 orthotopic ovarian cancer mouse models. We identified the promoter region of Annexin A1 as the major target of ADAMTS9-AS2. The binding of lncRNA ADAMTS9-AS2 to the promoter region can facilitate the expression of tumor suppressor Annexin A1 thereby decrease the proliferation and increase apoptosis of cancer cells. Collectively, our data point to an important role for ADAMTS9-AS2 as a tumor suppressor in ovarian cancer.

Note: This abstract was not presented at the meeting.

Citation Format: Cristian Rodriguez-Aguayo, Emine Bayraktar, Lingegowda S. Mangala, Cristina Ivan, Gabriel Lopez-Berestein, Anil K. Sood. Long non-coding RNA ADAMTS9-AS2 inhibits ovarian tumor growth via Annexin A1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3579.
Abstract 358: Inhibition of AKT phosphorylation in acute myeloid leukemia by ISC 4
Authors: Thakur Shreya , Annageldiyev Charyguly , Ramisetti Srinivasa , Patel Trupti , Iyer Saumya , Dhanyamraju Pavan , Amiin Shantu , Sharma Arun , Claxton David , Sharma Arati
Published: August 2019

Acute myeloid leukemia (AML) is a heterogeneous disease with percent remission of 35-40% for younger patients and 5-15% for older patients and a survival of 5-10 months if left untreated. This emphasizes the urgent unmet need for new therapeutics in AML. The activation of PI3K/AKT signaling pathway plays an important role in cellular survival, proliferation and regulation of apoptosis in cancer cells including leukemia. Recent studies showed that activation of AKT may correlate with poor prognosis in AML. Furthermore, mutations such as FLT3-ITD in the PI3K-AKT pathway causing constitutive activation of AKT, are very common in AML, therefore, it remains as an important target for AML treatment. Phenylbutyl isoselenocyanate (ISC-4), a small drug-like molecule that is developed by our group through optimization of naturally occurring isothiocyanates, targets the P13K-AKT pathway in melanoma and other gastrointestinal malignancies. In this study, we demonstrated potent activity of ISC-4 against AML. We tested the cytotoxicity of ISC-4 in various human AML cell lines (n=6) and in samples collected from AML patients (n=8). AML cell lines exhibited dose-dependent sensitivity to ISC-4 in the low micromolar range (IC50: 2-5 uM) as did most primary AML cases. Western blotting showed a dose dependent decrease in AKT phosphorylation in MV-4-11 and AML-OCI3 cell lines, and lead to an increase in cleaved PARP levels, indicating the induction of apoptosis. Furthermore, ISC-4 treatment reduced the clonogenicity of primary AML cells at relatively low concentrations. Future studies will aim to further develop ISC-4 as a single agent and in combination with anti-leukemic agents and demonstrate the preclinical efficacy in AML animal models including AML patient derived xenografts (PDXs). Together, these data demonstrates the therapeutic potential of ISC-4 that can be a promising drug candidate for further development as a novel therapy for AML.

Citation Format: Shreya Thakur, Charyguly Annageldiyev, Srinivasa Ramisetti, Trupti Patel, Saumya Iyer, Pavan Dhanyamraju, Shantu Amiin, Arun Sharma, David Claxton, Arati Sharma. Inhibition of AKT phosphorylation in acute myeloid leukemia by ISC 4 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 358.