Database Of Gene Expression Profiles Research Articles

Effect of Jagged1 on the expression of genes in regulation of osteoblast differentiation and bone mineralization ontology in human dental pulp and periodontal ligament cells

ObjectiveTo define the effect of Jagged1 on the gene expression in osteoblast differentiation, regulation of osteoblast differentiation and regulation of bone mineralization ontology. MethodsHuman dental pulp and periodontal ligament cells were isolated using explant method. Cells were seeded on Jagged1 immobilized surface. The mRNA expression was determined using real-time polymerase chain reaction. Mineral deposition was evaluated using alizarin red s staining. Publicly available database of gene expression profiles (GSE126249 and GSE94989) were downloaded and performed bioinformatic analysis to identify gene expression in osteoblast differentiation and regulation of osteoblast differentiation and mineralization ontology. ResultsBoth human dental pulp cells and human periodontal ligament cells expressed higher Notch target gene (HES1 and HEY1) when cells were seeded on Jagged1 immobilization surface. Jagged1 significantly increased an in vitro mineral deposition in both cell types after maintaining in osteogenic induction medium for 14 days. Correspondingly, the significant increase of ALPL mRNA expression was observed, while there was no significant change in ANKH and ENPP1 mRNA expression in Jagged1 treated condition. From bioinformatic analysis of genes in osteoblast differentiation ontology, IARS, COL1A1, ALPL, COL6A1, CREB3L1, and SNAI2 mRNA levels were upregulated while GJA1 mRNA levels were decreased upon Jagged1 exposure. In the regulation of bone mineralization ontology, evidences supported that TFGB1 and TGFB3 were upregulated in Jagged1 treated condition. ConclusionJagged1 promote the mRNA expression of several genes in osteoblast differentiation related gene ontology. This could be further employed to identify the mechanism by which Jagged1 promoted osteogenic differentiation in human dental pulp and periodontal ligament cells.

Towards the early detection of ductal carcinoma (a common type of breast cancer) using biomarkers linked to the PPAR(γ) signaling pathway

Breast cancer is a leading cause of morbidity and mortality among women comprising about 12% females worldwide. The underlying alteration in the gene expression, molecular mechanism and metabolic pathways responsible for incidence and progression of breast tumorigenesis are yet not completely understood. In the present study, potential biomarker genes involved in the early progression for early diagnosis of breast cancer has been detailed. Regulation and Gene profiling of Ductal Carcinoma In-situ (DCIS), Invasive Ductal Carcinoma (IDC) and healthy samples have been analyzed to follow their expression pattern employing normalization, statistical calculation, DEGs annotation and Protein-Protein Interaction (PPI) network. We have performed a comparative study on differentially expressed genes among Healthy vs DCIS, Healthy vsIDC and DCIS vs IDC. We found MCM102 and SLC12A8as consistently over-expressed and LEP, SORBS1, SFRP1, PLIN1, FABP4, RBP4, CD300LG, ID4, CRYAB, ECRG4, G0S2, FMO2, ADAMTS5, CAV1, CAV2, ABCA8, MAMDC2, IGFBP6, CLDN11, TGFBR3as under-expressed genes in all the 3 conditions categorized for pre-invasive and invasive ductal breast carcinoma. These genes were further studied for the active pathways where PPAR(γ) signaling pathway was found to be significantly involved. The gene expression profile database can be a potential tool in the early diagnosis of breast cancer.

Preclinical Validation of Ubiquitin Receptor PSMD4 As Therapeutic Target in Multiple Myeloma

Background and Rationale Our preclinical studies have focused on Identification and validation of components within the ubiquitin proteasome system which can be targeted with novel therapies to overcome proteasome-inhibitor (PI)-resistance in multiple myeloma (MM). Our siRNA screening studies identified ubiquitin Receptor (UbR) PSMD4/Rpn10 as a mediator of MM cell growth and survival. Rpn10 is localized on the 19S regulatory lid of the proteasome, and plays a key role in chaperoning ubiquitinated substrate proteins for downstream 20S proteasomal degradation. Here, we show that inhibition of Rpn10 triggers potent anti-MM activity using both in in vitro and in vivo models of MM, including against PI-resistant MM cells. Materials and Methods Rpn10 knockout 293 cell line was generated using CRISPR/Cas9. Rpn10-inducible knockdown (KD) MM.1S cell line was generated using shRNA. Drug sensitivity, cell viability, and apoptosis assays were performed using WST/CellTiter-Glo assay, and Annexin V staining, respectively. Cell signaling and caspase activity were determined by western blotting. Proteasome activity was measured as previously described (Chauhan et al., Cancer Cell 2012, 22:345-358). A xenograft human MM model was used to characterize the role of Rpn10 on tumor progression. Statistical significance was assessed with Student's t test. Results 1) Analysis of MM patient gene expression profiling database showed that Rpn10 expression inversely correlates with overall survival (n=175; p= 0.00064). 2)Real-time PCR, immunoblotting, and immunohistochemistry of MM patient bone marrow showed higher Rpn10 levels in patient MM cells and MM cell lines versus normal cells. 3)Transient transfection of MM cells with Rpn10-siRNA decreased their viability; conversely, transfection with Rpn10-WT specifically rescued cells from growth-inhibitory activity of Rpn10-siRNA. Immunoblot analysis confirmed significant knockdown of Rpn10 by Rpn10-siRNA versus scrambled (scr)-siRNA, and restoration of Rpn10 levels in cells transfected with Rpn10-WT versus Rpn10-siRNA. 4)Genetic blockade of Rpn10 decreased viability in bortezomib-resistant MM cells. 5)CRISPR/Cas9-mediated knockout (KO) of Rpn10 decreased cell growth. 5)Both Rpn10-KO and inducible Rpn10-KD cells showed elevated levels of polyubiquitylated proteins. 6)Inhibition of Rpn10 induced apoptosis, cell-cycle arrest, activation of caspases, and endoplasmic reticulum stress response signaling. 7)Reduced tumor growth was noted in mice xenografted with Rpn10-KD MM.1S cells versus mice engrafted with WT-MM.1S cells. Conclusion Our data demonstrate the therapeutic potential of targeting ubiquitin receptor Rpn10/PSMD4, and provide the preclinical basis for development of Rpn10 inhibitors to overcome PI-resistance in MM. Disclosures Chauhan: C4 Therapeutics.: Equity Ownership; Stemline Therapeutics: Consultancy. Anderson:Sanofi-Aventis: Other: Advisory Board; Takeda: Consultancy, Speakers Bureau; Celgene: Consultancy, Speakers Bureau; Bristol-Myers Squibb: Other: Scientific Founder; Oncopep: Other: Scientific Founder; Amgen: Consultancy, Speakers Bureau; Janssen: Consultancy, Speakers Bureau.

KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors.

Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining target genes of TFs and exploring TF functions. Human gene expression profile datasets with TF knockdown and knockout are accumulating rapidly. Based on the urgent need to comprehensively and effectively collect and process these data, we developed KnockTF (http://www.licpathway.net/KnockTF/index.html), a comprehensive human gene expression profile database of TF knockdown and knockout. KnockTF provides a number of resources for human gene expression profile datasets associated with TF knockdown and knockout and annotates TFs and their target genes in a tissue/cell type-specific manner. The current version of KnockTF has 570 manually curated RNA-seq and microarray datasets associated with 308 TFs disrupted by different knockdown and knockout techniques and across multiple tissue/cell types. KnockTF collects upstream pathway information of TFs and functional annotation results of downstream target genes. It provides details about TFs binding to promoters, super-enhancers and typical enhancers of target genes. KnockTF constructs a TF-differentially expressed gene network and performs network analyses for genes of interest. KnockTF will help elucidate TF-related functions and potential biological effects.

Molecular and clinicopathological characterization of URST1 as a new biomarker and therapeutic target for breast cancer

Abstract Background Breast cancer is one of the most common causes of cancer death for women worldwide. Therefore, identification and evaluation of new prognostic biomarkers and therapeutic agents are required to overcome breast cancer. Methods 1) Selection of the candidate genes by gene expression profile database.2) Confirmation of high expression of candidate gene and its protein in breast cancer by qPCR andWestern-blotting. 3) Verification of clinicopathological significance of their protein expression by tissue microarray, 4) Evaluation of the cellular growth activity of gene products by siRNA experiments.During this process,we identify the biomarkers and therapeutic targets for breast cancer. Results We identified URST1 (Up-regulated Solid Tumor 1) as a candidate. Immunohistochemical analysis showed that URST1 was expressed in 195 of 257 (75%) breast cancers (69% in luminal type, 89% in HER2-positive cancer, and92% in TNBC) that had undergone curative surgery, whereas no staining was observed in adjacent normal breast tissues. URST1 expression was significantly related to poor clinical outcomes for breast cancer patients (P = 0.0126, Log-rank test) and multivariate analysis revealed that it was an independent prognostic factor. Knockdown of endogenous URST1 expression by siRNAs against URST1 or treatment with URST1 inhibitor significantly inhibited the breast cancer cell growth through cell cycle arrest at M phase and mitotic cell death as detected by flow cytometric analysis andcellular dynamicsanalysis of breast cancer cells using time-lapse microscopy. Conclusion URST1 appears to play an important role at the central spindle in mitosis of cancer cells. URST1 is a prognostic biomarker and therapeutic target for breast cancers.

66P - Dual inhibition of TGF-β and AXL as a novel treatment for colorectal cancer

BackgroundAXL and transforming growth factor β (TGF-β) signalling pathways play a key role in modulating tumour microenvironment by promoting epithelial to mesenchymal transition (EMT), stromal activation and regulating immune response in colorectal cancer (CRC). Here we have evaluated the effect of double blockade of TGF-β and AXL receptors, as an innovative therapeutic strategy for CRC. MethodsWe assessed the correlation of TGF-β and AXL by an in silico analysis of a human CRC gene expression profile database. Afterwards, an evaluation of AXL expression of in a panel of human CRC cell lines by Western Blot (WB) and Real time PCR was performed. The sensitivity of HCT116 and LOVO cells to treatment with galunisertib (LY21209761), a TGF-β R1 inhibitor, and R428, an AXL inhibitor, was assessed by MTT, cell migration, and colony forming assays. Furthermore we generated patient derived 3D spheroid cultures from primary CRC, and tested their susceptibility to galunisertib and R428 by MTT assay. Finally, in vivo experiments were done with HCT116 and LOVO tumour xenografts in immunodeficient mice. ResultsIn silico analysis showed an association between high expression levels of AXL and TGF-β R1 in CMS4 CRC. AXL was differently expressed on cell lines, and interestingly it resulted increased in HCT116 and LOVO after TGF-β inhibition, probably representing a mechanism of cancer cell escape. Dual blockade with galunisertib and R428 determined a reduction in cell migration of 50% in HCT116 and 37% in LOVO cells, respectively, and colony formation of approximately 90 % in both cell lines. Moreover, combined treatment displayed a strong synergistic activity in 3D cultures derived from five human CRC samples, resulting in the inhibition of proliferation ranging from 80 to 90%. The in vivo experiments of HCT116 and LOVO subcutaneous xenograft models are currently on going and results will be presented. ConclusionsCombined TGF-β and AXL inhibition showed a promising activity in preclinical models of CRC and could represent a novel potential therapeutic strategy for patients with CRC. Legal entity responsible for the studyUniversità degli studi della Campania "Luigi Vanvitelli". FundingICURE project, Università degli studi della Campania "Luigi Vanvitelli". DisclosureD. Melisi: Research grant/Funding (self): Lilly.

Abstract 391: Serine/threonine kinase LASK2 as a biomarker and therapeutic target for lung cancer

Abstract Since the number of lung cancer patients responding well to standard chemotherapies is still small, further development of new anti-cancer drugs with minimum risk of adverse effects and highly sensitive cancer biomarkers for precision medicine is eagerly required. We have been developing new molecular therapies targeting oncogenic proteins with their companion diagnostics by screening system as follows; i) To identify overexpressed genes in 120 lung cancers by our original gene expression profile database, ii) To confirm the candidate genes for their low expression in 23 normal tissues, iii) To validate the clinicopathological significance of their protein expression by tissue microarray covering hundreds of non-small cell lung cancers (NSCLCs), iv) To verify whether they are essential for the growth/invasion of cancer cells by siRNAs. During this process, we selected dozens of druggable oncoproteins with various enzymatic activities, and detected higher expression of serine/threonine kinase LASK2 (lung cancer-associated kinase 2) in the majority of various types of lung cancers, but scarce expression in normal tissues except testis. We further observed much higher expression patterns of LASK2 in brain metastasis as well as advanced primary lung tumors, compared to those in earlier-stage primary lung tumors. Immunohistochemical analysis using tissue microarray showed that strong LASK2 positivity was an independent prognostic factor for NSCLC (P<0.0001). Suppression of LASK2 expression with its siRNAs inhibited growth of lung cancer cells, whereas enhanced cellular proliferation by exogenous expression of LASK2 in mammalian cells also supported its oncogenic function in vitro and in mice model. Invasion of mammalian cells transfected with LASK2-expression vector through Matrigel was significantly enhanced, compared to the control cells transfected with mock or LASK2-kinase dead vector, suggesting that LASK2 could also contribute to the highly malignant phenotype of lung-cancer cells. Induction of LASK2 appeared to activate oncogenic signals for lung cancer such as phosphorylation of MAPK and PCNA. Our data indicate that LASK2 is a promising diagnostic biomarker and therapeutic target for developing precision medicine of lung cancer. Note: This abstract was not presented at the meeting. Citation Format: Yataro Daigo, Atsushi Takano, Yusuke Nakamura. Serine/threonine kinase LASK2 as a biomarker and therapeutic target for lung 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 391.

Abstract 4840: Characterization of URST1 as a biomarker and therapeutic target for precision medicine of lung cancer

Abstract This study aims to identify novel biomarkers and therapeutic targets for lung cancer. We initially screened genes that overexpressed in the majority of lung cancers by using our original gene expression profile database. During this process, we identified up-regulated in solid tumor 1 (URST1) as a candidate. Immunohistochemical staining showed that URST1 was expressed in 231 (64.5%) of 358 non-small cell lung cancer (NSCLC) that had undergone curative surgery. Strong URST1 expression was associated with poor prognosis for NSCLC patients (P = 0.0003 by log-rank test). In addition, multivariate analysis showed that strong URST1 expression was an independent prognostic factor for NSCLC patients. Reduction of URST1 expression by siRNA or treatment with selective URST1 inhibitor significantly suppressed cancer cell growth partly through cell cycle arrest at G2/M phase and mitotic cell death as detected by flow cytometric analysis and live cell imaging. Our findings suggest that URST1 could be a potential biomarker and therapeutic target for developing precision medicine of lung cancer. Note: This abstract was not presented at the meeting. Citation Format: Atsushi Takano, Yohei Miyagi, Yataro Daigo. Characterization of URST1 as a biomarker and therapeutic target for precision medicine of lung 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 4840.

Molecular Profiling of Cohorts of Tumor Samples to Guide Clinical Development of Pembrolizumab as Monotherapy.

Molecular profiling of large databases of human tumor gene expression profiles offers novel opportunities for informing decisions in clinical development programs. Gene expression profile of programmed death ligand 1 (PD-L1) was explored in a dataset of 16,000 samples, including approximately 4,000 metastatic tumors, across >25 tumor types prevalent in the United States, looking for new indications for the programmed death 1 (PD-1) inhibitor pembrolizumab. PD-L1 expression was highly concordant with several genomic signatures indicative of immune-inflamed tumor microenvironment. Prevalence of activated immune-inflamed tumors across all tumor types was explored and used to rank tumor types for potential response to pembrolizumab monotherapy. The analysis yielded 3 tiers of indications in which high levels of PD-L1 and immune-inflamed signatures were found in up to 40% to 60%, 20% to 40%, and 0% to 20% of tumors. Tier 1 contained novel indications known at the time of analysis to be responsive to PD-1 checkpoint blockade in the clinic (such as melanoma and non-small cell lung cancer), as well as indications not studied in the clinic previously, including microsatellite instability-high colorectal, head and neck, bladder, and triple-negative breast cancers. Complementary analysis of an Asian/Pacific cancer dataset (gastric cancer) revealed high prevalence of immune-inflamed tumors in gastric cancer. These data contributed to prioritization of these indications for clinical development of pembrolizumab as monotherapy. Data highlight the value of molecular profiling in identifying populations with high unmet needs with potentially favorable response characteristics and accelerating development of novel therapies for these patients.See related commentary by Mansfield and Jen, p. 1443.

VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases.

Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms. Despite the widespread availability of public resources, we lack databases that are capable of simultaneously providing gene expression profiles, variant annotations, functional prediction scores and pathogenic analyses. VariED is the first web-based querying system that integrates an annotation database and expression profiles for genetic variants. The database offers a user-friendly platform and locates gene/variant names in the literature by connecting to established online querying tools, biological annotation tools and records from free-text literature. VariED acts as a central hub for organized genome information consisting of gene annotation, variant allele frequency, functional prediction, clinical interpretation and gene expression profiles in three species: human, mouse and zebrafish. VariED also provides a novel scoring scheme to predict the functional impact of a DNA variant. With one single entry, all results regarding queried DNA variants can be downloaded. VariED can potentially serve as an efficient way to obtain comprehensive variant knowledge for clinicians and scientists around the world working on important drug discoveries and precision treatments.

Distinct expression and prognostic value of members of the epidermal growth factor receptor family in ovarian cancer.

BackgroundIncreased aberrant expression or activation of the epidermal growth factor receptor (EGFR) family members has been reported in a wide range of cancers, and the EGFR family of tyrosine kinases has emerged as an important therapeutic target in malignancies. However, the expression patterns and exact roles of each distinct EGFR family member, which contribute to tumorigenesis and progression of ovarian cancer (OC), are yet to be elucidated.Materials and methodsIn the current study, we report the distinct expression and prognostic value of EGFR family members in patients with OC by analyzing a series of databases including ONCOMINE, Gene Expression Profiling Interactive Analysis, Kaplan–Meier plotter, cBioPortal, and Database for Annotation, Visualization and Integrated Discovery .ResultsIt was found that in patients with OC, mRNA expression levels of ERBB2/3/4 were significantly upregulated, whereas the transcription levels of EGFR were downregulated. Aberrant EGFR expression and ERBB2/3/4 mRNA levels were associated with OC prognosis.ConclusionThese results suggest that EGFR and ERBB3/4 are distinct prognostic biomarkers and may be potential targets for OC. These results may be beneficial to better understand the molecular underpinning of OC and may be useful to develop tools for more accurate OC prognosis and for promoting the development of EGFR-targeted inhibitors for OC treatment.

Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans.

During haematopoiesis, haematopoietic stem cells differentiate into restricted potential progenitors before maturing into the many lineages required for oxygen transport, wound healing and immune response. We have updated Haemopedia, a database of gene-expression profiles from a broad spectrum of haematopoietic cells, to include RNA-seq gene-expression data from both mice and humans. The Haemopedia RNA-seq data set covers a wide range of lineages and progenitors, with 57 mouse blood cell types (flow sorted populations from healthy mice) and 12 human blood cell types. This data set has been made accessible for exploration and analysis, to researchers and clinicians with limited bioinformatics experience, on our online portal Haemosphere: https://www.haemosphere.org. Haemosphere also includes nine other publicly available high-quality data sets relevant to haematopoiesis. We have added the ability to compare gene expression across data sets and species by curating data sets with shared lineage designations or to view expression gene vs gene, with all plots available for download by the user.

Identification of potential whole blood MicroRNA biomarkers for the blood stage of adult imported falciparum malaria through integrated mRNA and miRNA expression profiling

Correlating aberrant miRNA levels with imported malaria during the blood stage is required to better understand the in vivo biological and molecular processes that are involved in the response to Plasmodium falciparum infection and to find new biomarkers and diagnosis tools. We used a parallel microarray-based approach to investigate an integrated view of how the host miRNA expression profile changes in response to P. falciparum infection in whole blood obtained from six subjects with adult imported falciparum malaria (AIFM) and six normal subjects. We first investigated the functions of 1007 significantly differentially expressed genes from microarrays and predicted 56 putative pathways participating in malaria pathogenesis, which reflected systemic changes in the host under falciparum infection. Then, we validated the in silico-predicted targets of 50 differentially modulated miRNAs (7 upregulated and 43 downregulated) by examining the actual mRNA expression of these particular genes in our gene expression profile database; putative target gene sets were grouped into functional categories to investigate the roles of differentially expressed miRNAs. We considered 36 intersecting putative pathways, most of which were involved in multiple immune response processes, such as cell defense response, immune response, TNF signaling pathway, and T cell receptor signaling pathway, which may actually be regulated by differentially expressed miRNAs. Additionally, we identified five enriched upregulated miRNA sets (miR-3135b, miR-6780b-5p, miR-1246, miR-6126, and miR-3613-5p) as potential blood biomarkers of immunopathological status and prediction of early host responses, disease prognosis, and severe outcomes in AIFM.

Abstract 2910: Identification of URST1 as a novel prognostic biomarker and therapeutic target for various subtypes of breast cancer

Abstract Breast cancer is one of the most common causes of cancer death for women worldwide. To identify diagnostic and therapeutic targets for breast cancer, we screened molecules that were highly expressed in the majority of breast cancers by our gene expression profile database. During this process, we identified URST1 (up-regulated in solid tumor 1) as a candidate. Immunohistochemical analysis showed that URST1 was expressed in 195 of 257 (75%) breast cancer cases (69% in luminal type, 88% in HER2-positive cancer, 86% in Triple-negative cancer) that had undergone curative surgery, whereas no staining was observed in adjacent normal breast tissues. URST1 expression was significantly related to poor clinical outcome for breast cancer patients (P = 0.01, Log-rank test) and multivariate analysis showed that it was an independent prognostic factor. Knockdown of endogenous URST1 expression by siRNAs against URST1 or treatment with URST1 inhibitor significantly inhibited the growth of breast cancer cells through cell cycle arrest at G2/M phase. Our data suggest that URST1 is likely to be a prognostic biomarker and therapeutic target for various subtypes of breast cancers. Citation Format: Masako Nakamura, Atsushi Takano, Phung Manh Thang, Yohei Miyagi, Yataro Daigo. Identification of URST1 as a novel prognostic biomarker and therapeutic target for various subtypes of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2910.

Abstract 1919: Characterization of URST1 as a prognostic biomarker and therapeutic target for oral cancer

Abstract Oral cancer shows a high mortality rate, and its incidence is increasing gradually worldwide. Current therapies for oral cancer include surgery, radiotherapy, and chemotherapy, however, local and regional recurrences account for up to 90% of treatment failures after surgery and radiotherapy. Therefore, next generation biomarkers and therapeutic strategies for oral cancer are eagerly awaited. To identify biomarkers and therapeutic targets for oral cancer, we screened genes that overexpressed in the majority of oral cancers by using our original gene expression profile database and identified up-regulated in solid tumor 1 (URST1) as a candidate. Immunohistochemical staining showed that URST1 expression was observed in the majority of oral cancer in 64 of 96 (67%) that had received curative surgery. URST1 expression was associated with poor prognosis for oral cancer patients (P = 0.032 by log-rank test). Reduction of URST1 expression by siRNAs against URST1 (si-URST1) significantly suppressed growth of oral cancer cells. Flow cytometric analysis revealed that si-URST1 increased the population of cancer cells at G2/M. In addition, exposure of cancer cells to selective URST1 inhibitor suppressed the growth of oral cancer cells. These data indicate that URST1 is a possible prognostic biomarker and therapeutic target for oral cancer. Citation Format: Atsushii Takano, Yohei Miyagi, Yataro Daigo. Characterization of URST1 as a prognostic biomarker and therapeutic target for oral cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1919.

ARNT/HIF‐1β links high‐risk 1q21 gain and microenvironmental hypoxia to drug resistance and poor prognosis in multiple myeloma

1q21 gain is a common cytogenetic abnormality featuring high‐risk multiple myeloma (HRMM). However, the molecular mechanism underlying the adverse prognostic effect of 1q21 gain remains largely unclear. Here, we report that ARNT/HIF‐1β, a 1q21 gene, is highly expressed in HRMM and induced by microenvironmental hypoxia, which confers drug resistance and correlates with inferior outcome. Analysis of the gene expression profile database revealed that ARNT expression was upregulated in MM and increased with disease progression or in HRMM subtypes (particularly 1q21 gain), while correlated to shorter overall survival. In a cohort of 40 MM patients, qPCR further validated that ARNT expression was higher in MM patients than normal donors. MM cells carrying 1q21 gain or acquired drug resistance displayed a robust increase in HIF‐1β protein level. Hypoxia induced HIF‐1β expression via a NF‐κB‐dependent process. Notably, HIF‐1β overexpression impaired bortezomib sensitivity, whereas shRNA knockdown of ARNT reversed hypoxia‐mediated drug resistance. Together, these findings suggest that ARNT/HIF‐1β might represent a novel biomarker for risk stratification and prognosis of HRMM patients, as well as a potential therapeutic target for overcoming 1q21 gain‐ or microenvironment‐mediated and acquired drug resistance in MM.

Development of transgenic male-sterile rice by using anther-specific promoters identified by comprehensive screening of the gene expression profile database 'RiceXPro'.

Because genomic selection is designed for the population breeding of allogamous species, a successive outcrossing system is required for efficient use of genomic selection in autogamous crops, such as Oryza sativa L. (rice). Transgenic and dominant male-sterility is a suitable tool for efficient outcrossing of autogamous crops. Though there have been some reports of dominant male-sterile rice developed using transgenic technology, the flowering habit was substandard. Here, to isolate promoters that, when linked to a lethal gene, induce dominant male-sterility while retaining a good flowering habit, we identified 38 candidate genes with anther-specific expression by using the ‘RiceXPro’ database. We then evaluated the abilities of the near-upstream regions of these genes to induce male-sterility when linked to the lethal gene barnase and introduced into the rice cultivar ‘Nipponbare’. Seven of the 38 promoters induced clear dominant male-sterility; promoters expressed in the later stage of anther development induced male-sterility while retaining better flowering habits when compared to ones expressed in the early stage. These seven promoters could potentially be used to facilitate development of an efficient outcross-based breeding system in rice.

Image-based drug screen identifies HDAC inhibitors as novel Golgi disruptors synergizing with JQ1.

The Golgi apparatus is increasingly recognized as a major hub for cellular signaling and is involved in numerous pathologies, including neurodegenerative diseases and cancer. The study of Golgi stress-induced signaling pathways relies on the selectivity of the available tool compounds of which currently only a few are known. To discover novel Golgi-fragmenting agents, transcriptomic profiles of cells treated with brefeldin A, golgicide A, or monensin were generated and compared with a database of gene expression profiles from cells treated with other bioactive small molecules. In parallel, a phenotypic screen was performed for compounds that alter normal Golgi structure. Histone deacetylase (HDAC) inhibitors and DNA-damaging agents were identified as novel Golgi disruptors. Further analysis identified HDAC1/HDAC9 as well as BRD8 and DNA-PK as important regulators of Golgi breakdown mediated by HDAC inhibition. We provide evidence that combinatorial HDACi/(+)-JQ1 treatment spurs synergistic Golgi dispersal in several cancer cell lines, pinpointing a possible link between drug-induced toxicity and Golgi morphology alterations.

Integration of the TGx-28.65 genomic biomarker with the flow cytometry micronucleus test to assess the genotoxicity of disperse orange and 1,2,4-benzenetriol in human TK6 cells

In vitro gene expression signatures to predict toxicological responses can provide mechanistic context for regulatory testing. We previously developed the TGx-28.65 genomic biomarker from a database of gene expression profiles derived from human TK6 cells exposed to 28 well-known compounds. The biomarker comprises 65 genes that can classify chemicals as DNA damaging or non-DNA damaging. In this study, we applied the TGx-28.65 genomic biomarker in parallel with the in vitro micronucleus (MN) assay to determine if two chemicals of regulatory interest at Health Canada, disperse orange (DO: the orange azo dye 3-[[4-[(4-Nitrophenyl)azo]phenyl] benzylamino]propanenitrile) and 1,2,4-benzenetriol (BT: a metabolite of benzene) are genotoxic or non-genotoxic. Both chemicals caused dose-dependent declines in relative survival and increases in apoptosis. A strong significant increase in MN induction was observed for all concentrations of BT; the top two concentrations of DO also caused a statistically significant increase in MN, but these increases were <2-fold above controls. TGx-28.65 analysis classified BT as genotoxic at all three concentrations and DO as genotoxic at the mid and high concentrations. Thus, although DO only caused a small increase in MN, this response was sufficient to induce a cellular DNA damage response. Benchmark dose modeling confirmed that BT is much more potent than DO. The results strongly suggest that follow-up work is required to assess whether DO and BT are also genotoxic in vivo. This is particularly important for DO, which may require metabolic activation by bacterial gut flora to fully induce its genotoxic potential. Our previously published data and this proof of concept study suggest that the TGx-28.65 genomic biomarker has the potential to add significant value to existing approaches used to assess genotoxicity.

Abstract 3573: VariED: an integrated database of variants and gene expression profiles for genetic diseases

Abstract It is now widely believed that low-frequency variants may play an important role in cancers. In addition, low-frequency variants are usually closely related to populations. To identify the disease-associated variants, several projects are now underway to build a reference of genetic variations from different populations. Furthermore, massive tools and databases are available to compare the dynamic gene expression among different organs and predict functional effects of genetic variants. These resources aid to identify genetic roots of cancers in populations easier. Despite the existence of population allele frequency information, gene expression databases and functional effects of protein mutations, a comprehensive platform providing an integrated annotation database in human genetic variants, is still lacking. In the study, we proposed a web-based database to determine potential variations in cancers with collected variant information from current common databases and integrated those data to provide comprehensive analyses. The web-site offers a function to upload a variant call format (VCF) files for variants annotation. Importantly, we integrated population allele frequency information from NHBI GO Exome Sequencing Project (ESP), 1000 Genomes Project and Tohoku Medical Megabank Project to help users figure out the correlation between disease and population. Additionally, we also collected gene expression profiles from The Human Protein Atlas, Expression Atlas and NCBI SRA in different organs of human, mouse, and zebrafish respectively to reflect the relationship between gene expression and genetic variations in a specific organ. Overall, the database aids to predict protein functions in mutations, analyze population allele frequency and gene expression information from provided variants of diseases. In the result, we use three EGFR mutations to display the proposed system. A recent study has reported that Asian patients with non-small cell lung cancer (NSCLC) carrying a higher rate of EGFR mutations than non-Asian patients. These mutations, such as chr7:55241708G&amp;gt;C (G719A), chr7:55249005G&amp;gt;T (S768I) and chr7:55259515T&amp;gt;G (L858R), are found approximately in 30% of Asian (Japanese) patients. In functional prediction results, these sites are exonic and nonsynonymous mutations. The REVEL scores of three EGFR mutations are 0.824, 0.765 and 0.961, and gerp++ scores are 5.5, 5.85 and 5.71, respectively. Both REVEL and gerp++ show high scores for severe damage of protein structure in the mutations. According to the results, researchers can infer that the three mutations are pathogenic variants implying the nucleotide positions with a higher constraint. Citation Format: Li Mei Chiang, Chien Yueh Lee, Liang Chuan Lai, Mong Hsun Tsai, Tzu Pin Lu, Eric Y. Chuang. VariED: an integrated database of variants and gene expression profiles for genetic diseases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3573. doi:10.1158/1538-7445.AM2017-3573