bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4495: DNA demethylation promotes ERV expression and activation of immune signaling in renal cell cancer cells
Authors: de Cubas Aguirre A. , Dunker William , Hongo Rachel , Bhatia Anuj , Zaninovich Andrew , Panda Anshuman , Beckermann Kathryn E. , Bhanot Gyan , Ganesan Shridar , Karijolich John , Rathmell W K.
Published: September 2020

Recently, we reported that expression of endogenous retroviruses (ERVs), a class of transposable element, is associated with response to immune checkpoint blockade (ICB) in renal cell carcinoma (RCC). Aberrant expression of ERVs can activate host antiviral responses, as well as produce neoantigens. ERV expression is repressed by DNA methylation and can be activated by DNA hypomethylating agents. Here, we investigate whether Decitabine, a DNA hypomethylating agent, can activate ERV expression and host antiviral defenses in RCC to potentially enhance response to ICB. Decitabine induced expression of ERV3-2 and ERV4700 in RCC cells lines, which was accompanied by activation of host antiviral defense genes and increased secretion of inflammatory cytokines. We validated this effect in primary human RCC cell lines. Knockout of RIG-I and MDA5 dsRNA sensors attenuated activation of antiviral responses associated with Decitabine treatment, and RIG-I and MDA5 immunoprecipitations showed increased ERV binding in RCC cells treated with Decitabine. Bioinformatic analysis of RNAseq data showed the Decitabine-induced gene signature could be associated with increased CD8 infiltration and response to ICB. Conditioned media from Decitabine treated RCC cells was capable of inducing host anti-viral defense in naïve RCC cells and could modestly improve activation of T-cells from healthy donors. Further, conditioned media from RCC cells treated with Decitabine significantly enhanced T-cell migration. In a small retrospective cohort of metastatic RCC patients treated with single-agent PD-1/PD-L1 blockade, activation of some host antiviral defense genes was significantly higher in responders compared with nonresponders. Thus, modulation of ERV expression by Decitabine to activate host antiviral defenses could represent a novel therapeutic strategy to enhance RCC patient response to immune checkpoint blockade.

Citation Format: Aguirre A. de Cubas, William Dunker, Rachel Hongo, Anuj Bhatia, Andrew Zaninovich, Anshuman Panda, Kathryn E. Beckermann, Gyan Bhanot, Shridar Ganesan, John Karijolich, W K. Rathmell. DNA demethylation promotes ERV expression and activation of immune signaling in renal cell cancer cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4495.
Abstract 4497: A single-cell multiomics approach to study tumor-driven perturbations during hematopoiesis in mice
Authors: Kara Nihan , Shi Xiaoshan , Samusik Nikolay , Widmann Stephanie , Tyznik Aaron J.
Published: September 2020

Cancer is associated with concomitant myeloid cell responses that are characterized by an expansion of tumor associated myeloid cells including, myeloid derived suppressor cells (MDSCs), tumor associated macrophages (TAMs) and neutrophils (TANs). These myeloid derived cells are known to modulate immune responses that enhance cancer cell stemness, angiogenesis, metastasis, invasion and immune escape. The prevailing paradigm is that cancer interferes with hematopoiesis and skews the host system to generate cells of myeloid origin with tumor-promoting functions. Intriguingly, tumor derived factors can perturbate normal bone marrow hematopoiesis and promote extramedullary hematopoiesis in organs such as the spleen. Advances in single cell multiomic technologies now enable the analysis of high dimensional protein and mRNA expression from thousands of cells simultaneously. Using the power of the BD Rhapsody™ Single-Cell Analysis system, we have carefully investigated melanoma associated extramedullary hematopoiesis in mice. To do this, we isolated four hematopoietic stem and progenitor cell populations simultaneously, including Lin- Sca-1+ c-Kit+ (LSK), common myeloid progenitor (CMP), granulocyte-macrophage progenitor (GMP) and megakaryocyte-erythrocyte progenitor (MEP) cells from the spleen and bone marrow of melanoma-bearing mice using the BD FACSMelody™ cell sorter in combination with a multiplex BD® AbSeq Oligos panel for surface protein expression and a single-cell whole transcriptome analysis. Using advanced analysis plugins in SeqGeq™ software, we were able to delineate the developmental trajectories of these hematopoietic stem and progenitor cells in this systemic immuno-suppressive myeloid environment. These advanced technologies are critical to uncover tumor mediated abnormalities in hematopoiesis.

Disclaimers: For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 Laser Product. BD, the BD Logo, FACSMelody and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Citation Format: Nihan Kara, Xiaoshan Shi, Nikolay Samusik, Stephanie Widmann, Aaron J. Tyznik. A single-cell multiomics approach to study tumor-driven perturbations during hematopoiesis in mice [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4497.
Abstract 4524: Non-genetic generation of IgG-like immune cell-redirecting antibodies lacking effector function
Authors: van Delft Floris L. , van Geel Remon
Published: September 2020

Since the early approval of catumaxomab and blinatumomab, T cell-redirecting antibodies have emerged as a promising biologics in cancer treatment. New technologies are overcoming the limitations of the 1st generation T-cell redirecting bispecifics, especially extending half-life to allow intermittent dosing, reducing immunogenicity and improving the safety profile. Today, T cell-engagers are generated as a wide variety of molecular architectures, typically IgG-type. However, nearly without exception, these bispecifics are generated by genetic fusion of a cancer-binding and an anti-CD3 antibody, which inevitably requires genetic reengineering of an existing targeting antibody and/or extensive optimization of antibody format.

We have shown earlier that the native glycan of a monoclonal antibody provides a privileged site for controlled attachment of small-molecule cytotoxic drugs.1 The resulting antibody-drug conjugates (ADCs) were found to display significantly improved therapeutic index versus conventional technologies, while improving manufacturability. This proprietary technology, known as GlycoConnect™, has been adapted by various ADC developers, and entered clinical phase early 2019.

Here we present the adaption of GlycoConnect™ technology for the generation of immune cell-redirecting antibodies, without requiring prior protein reengineering. Instead, a two-stage chemoenzymatic process is applied that allows the conversion of any IgG isotype into a T cell-engager by selective attachment of anti-CD3 scFv to the antibody glycan. Studies are presented to precisely control conjugation stoichiometry, providing molecular architectures with defined 2:1 or 2:2 ratio (target-binding:CD3-binding), as well as functional studies to corroborate the biological activity of these GlycoConnect™ bispecifics. Finally, early results will be presented regarding extension of the concept to bispecifics designed to redirect natural killer (NK) cells, or to engage T-cells by activation of costimulatory molecules, such as CD137 (4-1BB).

1 van Geel et al. Chemoenzymatic Conjugation of Toxic Payloads to the Globally Conserved NGlycan of Native mAbs Provides Homogeneous and Highly Efficacious Antibody−Drug Conjugates. Bioconj. Chem. 2015, 26, 2233-2242.

Citation Format: Floris L. van Delft, Remon van Geel. Non-genetic generation of IgG-like immune cell-redirecting antibodies lacking effector function [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4524.
Abstract 4563: Immunoprevention of triple negative breast cancer by a multi-antigen, multi-peptide vaccine
Authors: Wang Yian
Published: September 2020

Triple negative breast cancer (TNBC) is the most aggressive sub-type of breast cancer, comprising approximately 20% of all breast cancers, and has a poor prognosis due to its aggressive behavior and lack of effective targeted therapies. In the present study, we employed transcriptome and protein analyses to select genes that are uniquely overexpressed in human triple-negative breast cancer. Overexpression of selected genes, Cyclin A2, CDK1, Cyclin E2, PRC1, Kif15, TPX2, Ki67, Top2A, were confirmed on human breast cancer tissue microarrays and in TNBC derived cell lines from C3(1)/TAg mice. Antigen-specific MHC class II epitopes with promiscuous high-binding affinity were identified using the “combined scoring system”, based on their potential to elicit a selective Th1 immunity. Furthermore, all peptides were selected to have over 85% amino acid sequence homology between human and mice for potential clinical translation. Strong immunogenic peptides from five antigens were selected by immunogenicity testing in tumor naïve mice based on high IFN-γ and low IL-10 ELISpot response data. The selected peptides, Cyclin A2 (#335), CDK1 (#113), Cyclin E2 (#93, 298, 334), KIF15 (#129), and Top2A (#236, 410, 606), were combined to form a multi-antigen, multi-peptide vaccine (MAMPV). The tumor preventive efficacy of the MAMPV was evaluated in syngraft study using a TNBC model: C3(1)/TAg-REAR mice and a TNBC cell line derived from C3(1)/TAg (M6). MAMPV-vaccinated animals demonstrated a significant reduction in tumor volume, and significantly higher tumor infiltration of CD4+ T cells compared to the control animals. Pathological examination of major organs did not reveal any toxicity associated with the vaccine. Similar tumor preventive efficacy was demonstrated in genetically engineered mouse model (GEMM) using C3(1)/TAg mice. Taken together, our data indicate that formulation of the multi-antigen multi-peptide vaccine is highly immunogenic and has the potential to be safe and efficacious in the immunoprevention of TNBC.

Citation Format: Yian Wang. Immunoprevention of triple negative breast cancer by a multi-antigen, multi-peptide vaccine [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4563.
Abstract 4571: Development of glycoconjugate based anticancer immunotherapy
Authors: Huang Xuefei
Published: September 2020

Tumor associated carbohydrate antigens (TACAs) are attractive targets for the development of anticancer immunotherapy. Mucin-1 (MUC1) is a representative member of the TACA family. Naturally existing MUC1 can contain multiple types of O-linked glycans, including the Thomsen-Friedenreich (Tf) antigen and the Sialyl Thomsen-nouveau (STn) antigen. In order to target these antigens as potential anti-cancer vaccines, MUC1 glycopeptides SAPDT*RPAP (T* is the glycosylation site) bearing the Tf and the STn antigen respectively have been synthesized. Bacteriophage Qβ carrier is a powerful carrier for antigen delivery. The conjugates of MUC1-Tf and -STn glycopeptides with Qβ were utilized to immunize the immune-tolerant human MUC1 transgenic (MUC1.Tg) mice, which elicited superior levels of anti-MUC1 IgG antibodies with titers reaching over 2 million units. The IgG antibodies recognized a wide range of MUC1 glycopeptides bearing diverse glycans. Antibodies induced by Qβ-MUC1-Tf showed strongest binding with MUC1 expressing melanoma B16-MUC1 cells and effectively killed these cells in vitro. Vaccination with Qβ-MUC1-Tf first followed by tumor challenge in a lung metastasis model showed significant reductions of the number of tumor foci in the lungs of immunized mice as compared to those in control mice. This was the first time that MUC1-Tf based vaccine has shown in vivo efficacy in a tumor model. As such, Qβ-MUC1 glycopeptide conjugates have great potentials as anti-cancer vaccines.

Citation Format: Xuefei Huang. Development of glycoconjugate based anticancer immunotherapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4571.
Abstract 4621: Polymorphisms in JAK/STAT signaling pathway genes and risk of breast cancer
Authors: Gago-Dominguez Manuela , Martinez Maria E. , Milne Roger , Matabuena Marcos , Redondo Carmen , Castelao José Esteban , Jamieson Catriona
Published: September 2020

Background. Impaired function of JAnus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) signaling pathway genes leads to immunodeficiency; genetic variation in this pathway could affect breast cancer risk.

Methods. We evaluated associations between genetic polymorphisms (SNPs) in 14 genes in the JAK/STAT pathway (JAK3, STAT1, STAT2, STAT3, STAT4, STAT5a, STAT5b, STAT6, SCOS1, SCOS2, SCOS3, SCOS4, APOBEC and ADAR) and breast cancer risk using data from the OncoArray. As the JAK/STAT pathway interacts with ER and PR, we also examined these associations by breast cancer subtype. We examined a total of 203 genetic variants in 60,106 cases (38,531 ER positive, and 9,363 ER negative) and 46,300 controls.

Results. SNP rs738308 in APOBEC was associated with risk of overall breast cancer (P value <0.001), and ER+ breast cancer (P value < 0.002). SNPs in ADAR1/STAT were associated with risk of ER+ breast cancer (P value < 0.01). The associations were more pronounced for advanced-stage disease. Other SNPs, exhibited potential, weaker associations.

Conclusion. We found increased breast cancer risk associated with rs738308 in APOBEC, and SNPs in ADAR1, both involved in RNA editing processes. APOBEC has been linked with cancer development and cholesterol control. Increased ADAR expression has been found in 50% of triple negative breast cancers (TNBC), which has been associated with increased recurrence and worse survival. RNA seq analysis showed that ADAR1 is among the top 5% of upregulated genes in relapsed lobular breast cancer. Activation of the JAK2/STAT3 pathway has been associated with TNBC poor prognosis. Our next step is to analyze these genetic variants using the iCOGs dataset which includes 116,587 additional patients and controls.

Citation Format: Manuela Gago-Dominguez, Maria E. Martinez, Roger Milne, Marcos Matabuena, Carmen Redondo, José Esteban Castelao, Catriona Jamieson. Polymorphisms in JAK/STAT signaling pathway genes and risk of breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4621.
Abstract 4634: Breastfeeding and prognosis of breast cancer among Chinese women
Authors: Ren Zefang , Wang Xiang , Tang Luying
Published: September 2020

Breastfeeding that linked to breast cancer risk may also influence the prognosis. A few previous studies on this topic have yielded inconsistent results. This study aimed to explore the dose-effect relationship between breastfeeding duration and breast cancer survival among Chinese women. We collected breastfeeding status, first breastfeeding duration (FBD), total breastfeeding duration (TBD) and average breastfeeding duration per child (ABD) from 3110 primary breast cancer patients recruited between October 2008 and June 2016 in Guangzhou, China and followed up until June 30, 2018. Restricted cubic splines and Cox proportional regression models were conducted to estimate the hazard ratios (HRs) and 95% confidence intervals (95% CI) for overall survival (OS) and progression-free survival (PFS) in association with breastfeeding. Long FBD (≥13 months) (HR=1.56 [1.13-2.17]), ABD (≥13 months) (HR=1.43 [1.04-1.96]) and TBD (≥37 months) (HR=1.73 [1.07-2.80]) were found to be associated with an increased risk of progression compared to moderate durations (FBD/ABD of 7-12 months, TBD of 19-36 months). Similar associations were observed for all-cause death. When stratified by ER status, the above effects of long FBD and ABD occurred only among patients with ER-positive tumor and the interactions were significant (FBD: Pinteraction=0.04 and 0.06, ABD: Pinteraction=0.07 and 0.04 for OS and PFS, respectively). Additionally, short FBD (≤6 months) increased the risk of a poor prognosis among young patients (≤45 years) (HR=1.86 [1.04-3.32] and 1.58 [1.06-2.34] for OS and PFS, respectively) but not old women (Pinteraction=0.02 for both OS and PFS). These findings would help clinical counseling and gaining insight into the mechanisms of breast cancer development.

Citation Format: Zefang Ren, Xiang Wang, Luying Tang. Breastfeeding and prognosis of breast cancer among Chinese women [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4634.
Abstract 4648: Insulinemic and inflammatory dietary patterns and risk of prostate cancer
Authors: Fu Benjamin C. , Tabung Fred K. , Pernar Claire H. , Wang Weike , Gonzalez-Feliciano Amparo G. , Chowdhury-Paulino Ilkania M. , Clinton Steven K. , Folefac Edmund , Song Mingyang , Kibel Adam S. , Giovannucci Edward L. , Mucci Lorelei A.
Published: September 2020

Background: Studies of diet and prostate cancer have primarily focused on individual dietary factors, often with null or mixed findings. Assessment of dietary patterns is an alternative approach and has been increasingly used in nutritional epidemiology, providing the advantage of better accounting for added effects and interactions of dietary components. Hyperinsulinemia and inflammation are interrelated biological pathways that link diet with risk of several cancers, and studies have suggested that these may also increase prostate cancer risk. Whether dietary patterns based on these pathways contribute to the development and progression of prostate cancer is unclear.

Methods: We followed 39,776 men in the Health Professionals Follow-up Study (1986-2014) to examine associations between two empirical hypothesis-oriented dietary patterns with risk of total, local, advanced, and fatal prostate cancer. The two dietary patterns - empirical dietary index for hyperinsulinemia (EDIH) and empirical dietary inflammatory pattern (EDIP) - were constructed using the weighted sum of food groups that predicted plasma C-peptide (EDIH) and inflammatory biomarkers (EDIP). Dietary scores were calculated from food frequency questionnaires at baseline and updated every 4 years. Multivariable-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards regression.

Results: We documented 5,682 incident cases of total prostate cancer and 658 cases of fatal prostate cancer over 868,552 person-years of follow-up. In multivariable-adjusted models, men in the highest EDIH quintile had an 18% higher risk of advanced prostate cancer (HR: 1.18, 95% CI: 0.96-1.45; P=0.04 for trend) and a 24% higher risk of fatal prostate cancer (HR: 1.24, 95% CI: 0.96-1.59; P=0.03 for trend) compared to men in the lowest quintile. There were no significant associations for EDIP and prostate cancer risk. BMI did not modify the association for either dietary pattern.

Conclusion: Hyperinsulinemia may be a potential mechanism linking dietary patterns and risk of aggressive prostate cancer. Additional studies to define mechanisms of action and interventions to reduce prostate cancer risk are warranted.

Citation Format: Benjamin C. Fu, Fred K. Tabung, Claire H. Pernar, Weike Wang, Amparo G. Gonzalez-Feliciano, Ilkania M. Chowdhury-Paulino, Steven K. Clinton, Edmund Folefac, Mingyang Song, Adam S. Kibel, Edward L. Giovannucci, Lorelei A. Mucci. Insulinemic and inflammatory dietary patterns and risk of prostate cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4648.
Abstract 4666: Cigarette smoking and opium use in relation to the oral microbiome in Iran
Authors: Wu Zeni
Published: September 2020

Background: Cigarette smoking and opium use are associated with periodontal disease, which is linked to the changes in oral microbiome. We aimed to study the association between cigarette and/or opium use with the oral microbiome.

Methods: A total of 558 subjects included in the present analysis were from a case-control study of pancreatic cancer in Tehran, Iran conducted from 2011 to 2015. A questionnaire ascertained demographic, cigarette and opium use history, and lifestyle characteristics, and participants provided saliva samples. DNA was extracted using the DSP DNA Virus Pathogen kit and 16S rRNA gene sequencing was performed on the MiSeq. Sequences were clustered into amplicon sequence variants (ASVs) using QIIME2 and taxonomy was assigned against the Human Oral Microbiome Database. Logistic regression, MiRKAT and zero-inflated β regression models were calculated with adjustment for age, sex, body mass index, and case status.

Results: The average number of observed ASVs for users of cigarette only (82.13 ± 38.55), opium only (76.19 ± 40.71), or both cigarette and opium users (77.80 ± 42.83) were significantly lower than never cigarette/opium users (95.10 ± 44.03). Similar trends were observed for the Shannon index. The microbial communities appeared to differ by cigarette and opium use as indicated by the MiRKAT models from the three beta diversity matrices. Four phylum level relative abundances were associated with cigarette and opium use, while the presence/absence of nine genera was associated with users of both cigarette and opium in the zero-inflated β regression models. The phylum Firmicutes and class Bacilla (Firmicutes) were significantly associated with opium only use, which showed marginally significant adjusted P values in users of both cigarettes and opium. No taxa were specifically associated with cigarette use only.

Conclusion: Cigarette and/or opium use were related to overall oral microbiome community composition and the presence/absence as well as relative abundance of multiple taxa. Further studies are needed to investigate the impact of the changes to the oral microbiome through cigarette and/or opium use on human health and disease status.

Citation Format: Zeni Wu. Cigarette smoking and opium use in relation to the oral microbiome in Iran [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4666.
Abstract 47: Mutation in homologous recombination as a prognostic factor independent of TCGA molecular subtypes in endometrial cancer
Authors: Zhao Luyang , Dai Yibo , Hu Yuanjing , Wang Zhiqi , Li Chengcheng , Wang Guoqiang , Wang Jianliu
Published: September 2020

Background: Endometrial cancers have been categorized into four genomic classes by The Cancer Genome Atlas Research Network (TCGA) with comprehensive genomic analysis. However, TCGA molecular subtypes are hard to utilize in clinic as the expensive cost and a simply version of POLE, TP53 genes cannot fully differentiate the four subtypes. Therefore, more convenient and reliable biomarkers need to be identified for clinical practice.

Methods: Whole-exome sequencing and RNA sequencing data for 529 patients with endometrial carcinomas were downloaded from TCGA. Mutations in 62 genes of homologous recombination repair (HR) signaling were defined as HR mutation. Associations between HR mutation and survival and RNA expression were analyzed.

Results: HR mutation was associated with a prolonged disease specific survival (DSS) (HR, 0.47; 95% CI, 0.28-0.79; P <0.05), progression-free survival (PFS) (HR, 0.50; 95% CI, 0.35-0.72; P <0.05) and overall survival (OS) (HR, 0.48; 95% CI, 0.31-0.73; P <0.05) in endometrial cancers. HR mutation was related with clinical characteristics including FIGO stage (P<0.05), tumor grade (P<0.05) and histological types (P<0.05). HR mutation was enriched in MSI (hypermutated) group (49%) and copy-number low group (19.6%). In the multivariable cox proportional hazards regression model including FIGO 2008, histology types, tumor grade and TCGA subtypes, the association between HR mutation and PFS was still significant (HR, 0.22; 95% CI, 0.05-0.88; P = 0.03), which indicating the HR mutation is an independent prognostic factor for PFS. Gene set enrichment analysis suggested that HR mutation was involved with the increase of genes related to activated T cells, immune cytolytic activity, and IFN-γ release.

Conclusion: HR mutation was related with a favorable prognosis through increasing T cells signature. Identification of HR mutation by genomic profiling provides a potentially novel and convenient approach for endometrial cancer patients to predict the prognosis independent of TCGA four subtype classifications

Citation Format: Luyang Zhao, Yibo Dai, Yuanjing Hu, Zhiqi Wang, Chengcheng Li, Guoqiang Wang, Jianliu Wang. Mutation in homologous recombination as a prognostic factor independent of TCGA molecular subtypes in endometrial cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 47.
Abstract 4708: Comprehensive analysis of 71 VHL germline deletions and rearrangements
Authors: Vocke Cathy D. , Ricketts Christopher J. , Schmidt Laura S. , Ball Mark W. , Peterson James , Middelton Lindsay A. , Linehan W Marston
Published: September 2020

An estimated 35% of von Hippel-Lindau (VHL) disease patients possess a gross germline deletion of one, two, or all three exons of VHL. In this study, 71 germline deletions have been extensively characterized, including 59 partial deletions (PD) and 12 complete VHL deletions (CD). VHL patients possessing germline VHL deletions were enrolled on an IRB-approved protocol. An Agilent custom high-definition comparative genomic hybridization array (aCGH) including 21 probes within the VHL gene at an average probe density of 2 probes per kb was used to map most VHL deletions; 4 patients were evaluated using CLIA-approved VHL deletion/duplication analysis. Primers were designed adjacent to the estimated deletion boundaries, and the breakpoints were mapped by Sanger bidirectional sequencing. Fifty eight deletions (55 PD and 3 CD) have been mapped to the exact breakpoint. Nearly all (55 of 58) deletions involve Alu repeats at both breakpoints. Several novel observations have been made in this cohort, including two cases that have complex rearrangements involving both deletion and inversion, two cases that have inserted extra Alu-like sequences, three cases that involve breakpoints in Alu repeats situated in opposite orientations, and a “hotspot” PD of exon 3 involving the same pair of Alu repeats that is observed in 12 families. In conclusion, this is the largest study to date of germline deletions in VHL patients. Deletions almost always involve Alu repeats, which are enriched in and near the VHL gene. In two cases, both a deletion and an inversion are observed, implying that it may be possible for an inversion to occur in the absence of deletion.

Citation Format: Cathy D. Vocke, Christopher J. Ricketts, Laura S. Schmidt, Mark W. Ball, James Peterson, Lindsay A. Middelton, W Marston Linehan. Comprehensive analysis of 71 VHL germline deletions and rearrangements [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4708.
Abstract 4759: Nanoscale Huangjing extract from Mount Tai displays enzyme and biofuel enhancing activity: Potential in precision anti-cancer therapy
Authors: Kabulova Aigerim , Razbekova Madina , Xie Yingqiu , Dautov Adilet , Wang Qian , Fan Haiyan
Published: September 2020

Chinese herb Huangjing has been well-known for its anti-cancer characters in xenograft models of cancers and traditional Chinese herbal classical books. However, the mechanisms are largely unknown. The processed Huangjing has the pharmacological function but fresh forms may have toxicity. Mount Tai is famous for its traditional culture and Chinese medicine resources with special environmental and nutritional potential for enrichment of herbal chemical competent. Our study aimed to test phosphatase activity of nanoparticles produced in the process of herb and to identify whether its anti-cancer properties is related to the phosphatase activity. Phosphatase has been known for its function in dephosphorylating of many drug targets therein to inhibit cancer cell growth. We recently reported engineered nanoparticles were proved to exhibit phosphatase activity and here we further demonstrated that nanoscale Huangjing herb from Mount Tai showed positive results on a few phosphatase substrates. The corresponding substrate specificity and kinetics of the reaction including the substrate concentration, pH, and temperature dependence were studied in detail. In addition, using a Biorad Biofeul kit, Huangjing was observed to catalyze p-nitrophenyl glucopyranoside to p-nitrophenol reaction. Our data suggest that Huangjing may cleave the covalent bond between beta glucose and nitrophenol suggesting the biofuel-like activity. We then performed experiments to test the effectiveness of Huangjing at nanoscale for inhibiting growth of cancer cells wherein, the growth of MDA-MB-231 and PC3 cells was greatly inhibited while normal cells are planning for comparison and investigation in mechanisms. The study has a significance in developing potential novel nanoscale drugs with phosphatase-like activity for treatment of certain cancers with combination of targeted kinase inhibitors based therapy or as a drug delivery machinery. Our preliminary results suggest a kinase synergistic based signaling. Thus, our data provided the potential concept of the combination of traditional Chinese medicine with modern chemotherapy.

Citation Format: Aigerim Kabulova, Madina Razbekova, Yingqiu Xie, Adilet Dautov, Qian Wang, Haiyan Fan. Nanoscale Huangjing extract from Mount Tai displays enzyme and biofuel enhancing activity: Potential in precision anti-cancer therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4759.
Abstract 4762: Metabolome in 5-FU resistant gastric cancer organoids
Authors: Sakamoto Naoya , Naka Kazuhito , Ukai Shoichi , Honma Ririno , Taniyama Daiki , Takashima Tsuyoshi , Maruyama Ryota , Tanabe Kazuaki , Ohdan Hideki , Yasui Wataru
Published: September 2020

Recent advances in metabolomics have deepened our understandings of the roles that specific modes of metabolism play in the maintenance of stem cells. Several pieces of evidence have demonstrated that cancer stem cells (CSCs) play a key role in the acquisition of drug resistance. Organoid is a novel 3D cell culture system through using the specific niche factors in a dish and is believed to harbor abundant stem cells; cancer organoid could possibly be useful for scrutinizing CSC biology. In this study, we successfully established 5-FU resistant gastric cancer organoids (GCOs) from patient-derived specimens, which were further confirmed by significant changes in the expression of molecules related to 5-FU metabolism. We then performed metabolome analysis using 3 pairs of 5-FU resistant/ parental GCOs and 10 pairs of non-neoplastic gastric organoid/ GCOs generated from the same patients. PCA plotting revealed that 5-FU resistant GCOs showed a distinct signature compared to those of their parental GCOs and 10 pairs of non-neoplastic gastric organoid/ GCOs. Among various significant changes in the metabolic pathways, we focused on the excessive reliance on the energy from TAC cycle in 5-FU resistant GCO because the difference was specifically seen in the comparison between 5-FU resistant and parental GCOs: not found in the comparison between 10 pairs of non-neoplastic gastric organoid and GCOs. We examined IC50 value for Tigecyclin and VLX600, both of which have an inhibitory effect on TCA cycle, by MTT assay using 5-FU resistant GCO and 2 gastric cancer cell lines (MKN-45 and MKN-74). Although there was almost no difference in IC50 values for Tigecyclin and VLX600 between 2 gastric cell lines and their 5-FU resistant cells, IC50 for both of TCA cycle inhibitors in 5-FU resistant GCO was significantly lower compared to that in parental GCO. Further studies are ongoing in order to verify the significance of dependency on TCA cycle, which could potentially lead to the development of new therapy for 5-FU resistant gastric cancer.

Citation Format: Naoya Sakamoto, Kazuhito Naka, Shoichi Ukai, Ririno Honma, Daiki Taniyama, Tsuyoshi Takashima, Ryota Maruyama, Kazuaki Tanabe, Hideki Ohdan, Wataru Yasui. Metabolome in 5-FU resistant gastric cancer organoids [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4762.
Abstract 4800: Pyruvate dehydrogenase inhibition leads to decreased glycolysis and increased reliance on asparagine in acute myeloid leukemia
Authors: Anderson Rebecca , Pladna Kristin M. , Pardee Timothy S.
Published: September 2020

Acute myeloid leukemia (AML) is an aggressive disease characterized by poor outcomes and chemotherapy resistance. Devimistat (CPI-613 ®) is a novel agent that inhibits two key tricarboxylic acid (TCA) cycle enzymes, pyruvate dehydrogenase (PDH) and α-ketoglutarate dehydrogenase complexes (KGDH). Our lab has shown that genetic and pharmacologic inhibition of PDH sensitizes cells to chemotherapy and recent clinical trials of chemotherapy plus devimistat have been promising. However, the means by which AML cells adapt to PDH loss during devimistat treatment is unknown. AML cells with PDH deleted by CRISPR-Cas9 (PDH KO) show decreased mitochondrial oxygen consumption, membrane potential and altered mitochondrial morphology. Surprisingly, PDH KO cells also showed decreased glycolytic rates. In order to explore this mechanism we assessed glucose uptake and found PDH KO cells had significantly less glucose uptake. We next assessed expression of hexokinase II, a key enzyme that commits glucose retention in the cell, in PDH KO and devimistat treated cells. Strikingly, we found that hexokinase II expression was decreased in PDH KO cells, which was rescued with proteasomal inhibition. Consistent with disruption of the protective interaction between mitochondrial membrane channel VDAC1 and HKII. However, PDH KO and devimistat treated cells are more sensitive to the glycolytic inhibitor 2-deoxy-D-glucose. This indicates that even though TCA cycle inhibition decreases glycolysis through loss of HKII, the cells are still reliant on the activity that remains. Cells can supplement TCA cycle intermediates through amino acid metabolism. Two key amino acids, asparagine and glutamate, were reintroduced to devimistat treated, amino acid starved, AML cells and asparagine significantly rescued the cells. Asparaginase, which converts asparagine into aspartic acid and ammonia, significantly increased sensitivity to genetic and pharmacological inhibition of PDH in AML cells. This indicates that glycolysis inhibition and amino acid deprivation in combination with devimistat-mediated PDH inhibition should be further explored in clinical trials.

Citation Format: Rebecca Anderson, Kristin M. Pladna, Timothy S. Pardee. Pyruvate dehydrogenase inhibition leads to decreased glycolysis and increased reliance on asparagine in acute myeloid leukemia [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4800.
Abstract 4809: Monoethanolamine stimulates calcium-induced metabolic stress leading to autophagic cell death in prostate cancer
Authors: Garlapati Chakravarthy
Published: September 2020

Mitochondrial activity and metabolism are crucial to meet the energy demands of cancer cells. We have recently shown the efficacy of monoethanolamine (Etn), an orally deliverable lipid formulation, in reducing tumor growth in various xenograft models including prostate cancer (PCa). Etn increased the metabolic stress of PCa cells by depleting cellular glucose and glutamine levels. However, the precise mechanism of Etn-mediated metabolic stress in cancer cells remains elusive. Herein, we examined how Etn alters the activity and structure of the mitochondria to induce cell death. Etn treatment modulated phosphatidylethanolamine (PE) lipid and glycerophosphoethanolamine (GPE) levels in PCa cells. Altered PE lipids correlated with disruption of mitochondrial cristae and led to a concomitant accumulation of autophagosomes. Deregulated functional activity of mitochondria, as evidenced by reduced oxygen consumption rate (OCR), extracellular acidification rate (ECAR), were associated with structural distortions of the mitochondria and a transient increase in the intracellular calcium concentration. Etn treatment reduced the amount of cytosolic lipid droplets (LD) and caused a reduction in PE/GPE ratio. Further, we observed an increase in lipolysis and death-inducing autophagy activation in Etn-treated PCa cells. These data suggest that Etn is a promising anticancer agent for PCa and further studies to determine its efficacy in other cancer types are warranted.

Citation Format: Chakravarthy Garlapati. Monoethanolamine stimulates calcium-induced metabolic stress leading to autophagic cell death in prostate cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4809.
Abstract 4820: Novel protein AX-295aa encoded by circAX promotes gastric carcinogenesis by activating Wnt pathway
Authors: Peng Yin , Zhang Xiaojing , Deng Shiqi , He Jieqiong , Chen Wangchun , Zhu Xiaohui , Yuan Yuan , Feng Xianling , Fan Xinmin , Jin Zhe
Published: September 2020

Recently, traditionally non-encoding circRNA has been shown to encode a new protein to play an important role in oncogenesis. Based on the sequencing data and bioinformatics analysis, circAX was screened as an oncogenic circRNA encoding AX-295aa in gastric cancer. CircAX is highly expressed in gastric cancer and associated with lymph node metastasis. We found that circAX promotes GC cell proliferation and migration and it encodes a novel protein AX-295aa. AX-295aa interacts with APC and competitively inhibits AXIN1 binding to APC. It enhances β-catenin nuclear translocation and activates Wnt signaling pathway to promote the carcinogenesis and development of gastric cancer. The study reveals a new regulatory mechanism of circAX and clarify the mechanism by which circAX promotes gastric carcinogenesis. It will ultimately provide novel circRNA molecular markers for early diagnosis and targets for more effective treatment of gastric cancer.

Citation Format: Yin Peng, Xiaojing Zhang, Shiqi Deng, Jieqiong He, Wangchun Chen, Xiaohui Zhu, Yuan Yuan, Xianling Feng, Xinmin Fan, Zhe Jin. Novel protein AX-295aa encoded by circAX promotes gastric carcinogenesis by activating Wnt pathway [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4820.
Abstract 4836: Diagnostic and prognostic significance of microRNA modulation in oral cancer
Authors: Falzone Luca , Vivarelli Silvia , Crimi Salvatore , Bianchi Alberto , Candido Saverio , Libra Massimo
Published: September 2020

Oral cancer is one of the leading causes of cancer death worldwide. Despite the availability of screening programs, oral cancer is often not correctly diagnosed resulting in a significant fraction of late diagnosis.Currently, there are not effective biomarkers for the early diagnosis of oral cancer and for the definition of patients' prognosis. Therefore, the identification of new effective diagnostic and prognostic biomarkers is one of the main challenges for the management of this tumor. Our preliminary analyses of GEO DataSets and TCGA miRNA profiling datasets identified a set of microRNAs (miRNAs) significantly de-regulated in oral cancer. In addition, through the use of different bioinformatics tools (miRCancerdb, GO PANTHER, STRING and DIANA-mirPath), the diagnostic and prognostic significance of selected miRNAs, as well as the modulated molecular pathways and genes were predicted.Starting from these preliminary bioinformatics results, the aim of the present study was to validate the sensitivity and specificity of selected miRNAs in oral cancer patients and healthy controls. For this purpose, the expression levels of selected miRNAs were determined in plasma and matched saliva samples from a subset of oral cancer patients and healthy controls by using specific miRNA TaqMan probes and droplet digital PCR (ddPCR).The ddPCR results showed that the selected miRNAs can be easily detected in both plasma and saliva samples with concordant expression levels and that the expression levels of miRNAs were significantly different in oral cancer patients compared to healthy controls as predicted in the bioinformatics analyses. Furthermore, the comparison of the molecular data with the clinical-pathological features of patients allowed us to establish the prognostic significance of selected miRNAs.

Citation Format: Luca Falzone, Silvia Vivarelli, Salvatore Crimi, Alberto Bianchi, Saverio Candido, Massimo Libra. Diagnostic and prognostic significance of microRNA modulation in oral cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4836.
Abstract 4873: Molecular mechanism of neddylation-dependent suppression of cancer cell migration
Authors: Chun Yang-Sook , Seo Jieun , Park Jun Bum
Published: September 2020

Neddylation is a process by which NEDD8 is covalently conjugated to target proteins by sequential enzymatic reaction. Its role in cancer cell migration has only been recently acknowledged. Previously in cancer cell migration, the epithelial to mesenchymal transition (EMT) process has been well-known to play an important role in both invasion and metastasis by promoting mesenchymal phenotype in epithelial cells. However, the role of neddylation in the EMT process and its mechanistic details are yet to be elucidated. We recently reported that neddylation plays a crucial role in cancer cell migration through the PI3K-Akt pathway. Here, we report that inhibiting neddylation activates the hypoxia-inducible factor-1α through the PI3K-Akt pathway, which eventually regulates the EMT-activator zinc finger E-box binding homeobox 1 in various cancer cell lines. As induction of hypoxia-inducible factor-1α is known to deteriorate the state of cancer and EMT process is one of the hallmarks of metastasis in cancer, our findings uncover the novel association of hypoxia-inducible factor-1α and zinc finger E-box binding homeobox 1 through the process of neddylation.

Citation Format: Yang-Sook Chun, Jieun Seo, Jun Bum Park. Molecular mechanism of neddylation-dependent suppression of cancer cell migration [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4873.
Abstract 4879: Identification of degron motifs and mutations by analyzing a deep neural network
Authors: Chen Cynthia , Tokheim Collin , Liu Shirley
Published: September 2020

Degrons, short amino acid sequences on protein substrates, play a critical role in the ubiquitin-proteasome system (UPS), which regulates over 80 percent of protein degradation in cells. When recognized by E3 ubiquitin ligases, degrons signal the destruction of its substrate protein, determining the regulatory specificity of the UPS. While a few degrons have been reported to be affected by mutations driving cancer growth, the effect of specific mutations on degrons remains largely unidentified. In this study, we analyze a deep neural network model that predicts the likelihood of an input protein sequence to contain a degron. To characterize the important C-terminal degron motifs learned by the model, we ran computational methods including sequence ranking and selection, enrichment analyses, and sequence logo visualization. This revealed the discovery of 101 significant degron motifs across lengths 2, 3, and 4. While previous studies suggested that di-amino acid motifs might be the primary source of c-end degron, the new motifs suggest that additional complexity might exist with a longer extended degron. Using these putative motifs as targets for mutations, we performed in silico mutagenesis to identify high-impact amino acid mutations that cause degron loss or gain. Our discovery of degron motif-mutation pairs could inform the development of targeted small-molecule drugs for cancer treatments and identification mutational biomarkers used for early detection of cancers.

Citation Format: Cynthia Chen, Collin Tokheim, Shirley Liu. Identification of degron motifs and mutations by analyzing a deep neural network [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4879.