Set Of Target Genes Research Articles

Abstract 3436: Pan-cancer analysis of the HIF-transcriptional pathway and its association with genetic susceptibility to cancer

Abstract The purpose of this study was to determine whether specific components of the HIF-transcriptional pathway are under selective pressure during the development of cancer. Induction of HIF is a common feature of most cancers that frequently results from intra-tumour hypoxia but may also be activated as a result of oncogenic switching. Activation of such large transcriptional pathways commonly leads to heterogeneous effects on tumour biology that entrain multiple responses, which both promote and inhibit tumour formation. This generates a Darwinian pressure that selects for variants (either germline or somatic) that re-balance the numerous (often small) opposing effects of pathway activation to promote tumourigenesis. We have undertaken pangenomic analyses of the direct and indirect transcriptional targets of the HIF pathway in cell lines from six common cancer types (breast, prostate, lung, colon, kidney and liver) using combined ChIP-seq and RNA-seq assays. This identifies a small set of common HIF-target genes affecting discrete pathways as well as much larger sets of target genes that are cancer-type specific. Correlating these findings with RNA-seq analyses across 20 tumour types in the TCGA database confirms distinct patterns of expression and the importance of these genes to tumour biology. Furthermore, by relating our datasets to GWAS signals of cancer-susceptibility in each tumour type, we have identified a significant excess overlap between cancer-susceptibility loci and HIF-target genes. Notably, despite the importance of HIF in other tumour types, this overlap is specific to kidney cancer in which, by contrast, HIF activation, resulting from oncogenic switching, is inappropriate to the level of intra-tumour oxygenation. This analysis provides a comprehensive analysis of the HIF pathway across multiple cancer types and provides evidence that specific aspects of the HIF-pathway are under Darwinian selection in kidney cancer. Since these alter kidney cancer susceptibility, this analysis helps distinguish those components of the HIF transcriptional response that drive tumour formation from those that are simply co-activated as a consequence of large-pathway activation. Finally, this work supports a ‘pathway tuning' model of cancer and suggests that subtle re-balancing of inappropriately activated, cancer-specific pathways is important in oncogenesis. Citation Format: David R. Mole, Virginia Schmid, Olivia Lombardi, Silvia Halim, Veronique N. Lafleur, Ran Li, Rafik Salama, Leandro Colli, Stephen Chanock, Peter J. Ratcliffe. Pan-cancer analysis of the HIF-transcriptional pathway and its association with genetic susceptibility to 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 3436.

Abstract 6333: Genomic, transcriptomic, and epigenetic profiling of triple-negative breast cancer cells after Navitoclax treatment

Abstract Cancer cells possess various anti-apoptotic defense mechanisms that can protect them from drug induced cell death. We investigated the effects of treatment with the bcl-2/bcl-XL inhibitor Navitoclax on transcriptome, methylome, and genome of MDA-MB-231 cells. Two biological replicates were treated simultaneously and profiled using 10x Genomics single-cell RNA sequencing (scRNAseq; gene expression), bulk RNA sequencing (bRNAseq; gene expression), ATAC sequencing (ATAC; chromatin accessibility), bisulphite targeted sequencing (DNAm; DNA methylation) and shallow whole-genome sequencing (WGS; copy number variants) at baseline before treatment, after 3 days of 10µM navitoclax treatment, and after 10 days of cell recovery from treatment. Variance between biological replicates on transcriptome level was minimal before the treatment (R>0.99), but we noticed divergence in gene expression after recovery from the treatment (both on bulk and single-cell level), mostly driven by cell cycle genes. On other platforms, biological replicates were similar in all 3 phases. After treatment, we observed more genes with decreased expression (n=151) in comparison to baseline, but after 10 days of recovery there were more up-regulated genes (n=655) in comparison to samples after treatment. Chromatin accessibility for most genomic regions increased after treatment in comparison to baseline, suggesting an acute response to the stress caused by drug treatment, and then returned to baseline level after recovery period. DNA methylation patterns showed more regions with decreased methylation after treatment (n=529) in comparison to baseline which remained detectable even after the recovery period. In WGS data, we found 752 genes with deletions and amplifications only in baseline samples representing genomic background of drug sensitive cells, mostly enriched in epithelial mesenchymal transition pathway. On single-cell level, we identified a subset of cells that were resistant to treatment and discovered 2,324 genes significantly up-regulated in these cells, that could be potential markers of resistance. In gene set analysis, these markers were enriched in MYC and E2F target gene sets, and were involved in angiogenesis and JAK-STAT pathway. We measured the expression of 16 top up-regulated markers of resistance in 4 different TNBC cell lines using qPCR and found that 5 were significantly enriched after treatment in 3 cell lines, 5 in 2 cell lines and 5 in a single cell line. Summarizing, we thoroughly described molecular effects of Navitoclax treatment and showed that most cells return to the basal transcriptional state after the drug recovery period, but bulk genome and methylome are permanently changed. Finally, we provided a list of new markers of resistance that may be useful in the studies of combinational therapies with other drugs. This work was funded by Breast Cancer Research Foundation. Citation Format: Michal Marczyk, Vignesh Gunasekharan, Jun Zhao, Rihao Qu, Xiaotong Li, Gauri A. Patwardhan, Vikram B. Wali, Abhishek K. Gupta, Manoj M. Pillai, Yuval Kluger, Christos Hatzis, Lajos Pusztai. Genomic, transcriptomic, and epigenetic profiling of triple-negative breast cancer cells after Navitoclax treatment [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 6333.

Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas.

Gene expression is adjusted according to cellular needs through a combination of mechanisms acting at different layers of the flow of genetic information. At the posttranscriptional level, RNA-binding proteins are key factors controlling the fate of nascent and mature mRNAs. Among them, the members of the CsrA family are small dimeric proteins with heterogeneous distribution across the bacterial tree of life, that act as global regulators of gene expression because they recognize characteristic sequence/structural motifs (short hairpins with GGA triplets in the loop) present in hundreds of mRNAs. The regulatory output of CsrA binding to mRNAs is counteracted in most cases by molecular mimic, non-protein coding RNAs that titrate the CsrA dimers away from the target mRNAs. In γ-proteobacteria, the regulatory modules composed by CsrA homologs and the corresponding antagonistic sRNAs, are mastered by two-component systems of the GacS-GacA type, which control the transcription and the abundance of the sRNAs, thus constituting the rather linear cascade Gac-Rsm that responds to environmental or cellular signals to adjust and coordinate the expression of a set of target genes posttranscriptionally. Within the γ-proteobacteria, the genus Pseudomonas has been shown to contain species with different number of active CsrA (RsmA) homologs and of molecular mimic sRNAs. Here, with the help of the increasing availability of genomic data we provide a comprehensive state-of-the-art picture of the remarkable multiplicity of CsrA lineages, including novel yet uncharacterized paralogues, and discuss evolutionary aspects of the CsrA subfamilies of the genus Pseudomonas, and implications of the striking presence of csrA alleles in natural mobile genetic elements (phages and plasmids).

Conferring root-knot nematode resistance via host-delivered RNAi-mediated silencing of four Mi-msp genes in Arabidopsis

The root-knot nematode (RKN) Meloidogyne incognita is considered one of the most damaging pests among phytonematodes. The majority of nematode oesophageal gland effector genes are indispensable in facilitating M. incognita parasitization of host plants. We report the effect of host-delivered RNAi (HD-RNAi) silencing of four selected M. incognita effector genes, namely, Mi-msp3, Mi-msp5, Mi-msp18 and Mi-msp24, in Arabidopsis thaliana. Mi-msp5, Mi-msp18 and Mi-msp24, which are dorsal gland genes, were found to be maximally expressed in the adult female stage, whereas Mi-msp3, which is a sub-ventral gland gene, was maximally expressed in an earlier stage. In transgenic plants expressing dsRNA, the reduction in the number of galls on roots was 89 %, 78 %, 86 % and 89 % for the Mi-msp3, Mi-msp5, Mi-msp18 and Mi-msp24 RNAi events, respectively. Moreover, gene transcript abundance was significantly reduced in RKN females feeding on dsRNA-expressing lines by up to 60 %, 84 %, 31 % and 61 % for Mi-msp3, Mi-msp5, Mi-msp18 and Mi-msp24, respectively. Furthermore, the M. incognita reproduction factor was reduced up to 71-, 344-, 107- and 114-fold in Arabidopsis plants expressing Mi-msp3, Mi-msp5, Mi-msp18 and Mi-msp24 dsRNA constructs, respectively. This study provides a set of potential target genes to curb nematode infestation in economically important crops via the HD-RNAi approach.

Genome-Wide Analysis Identifies NURR1-Controlled Network of New Synapse Formation and Cell Cycle Arrest in Human Neural Stem Cells.

Nuclear receptor-related 1 (Nurr1) protein has been identified as an obligatory transcription factor in midbrain dopaminergic neurogenesis, but the global set of human NURR1 target genes remains unexplored. Here, we identified direct gene targets of NURR1 by analyzing genome-wide differential expression of NURR1 together with NURR1 consensus sites in three human neural stem cell (hNSC) lines. Microarray data were validated by quantitative PCR in hNSCs and mouse embryonic brains and through comparison to published human data, including genome-wide association study hits and the BioGPS gene expression atlas. Our analysis identified ~40 NURR1 direct target genes, many of them involved in essential protein modules such as synapse formation, neuronal cell migration during brain development, and cell cycle progression and DNA replication. Specifically, expression of genes related to synapse formation and neuronal cell migration correlated tightly with NURR1 expression, whereas cell cycle progression correlated negatively with it, precisely recapitulating midbrain dopaminergic development. Overall, this systematic examination of NURR1-controlled regulatory networks provides important insights into this protein’s biological functions in dopamine-based neurogenesis.

Abstract B035: Identification of a tumor cell adaptive stress response signaling pathway, which drives aggressive breast cancer phenotype and therapeutic resistance, in African American patients with locally advanced breast cancer subtypes

Abstract Introduction: The higher incidence of biologically aggressive and treatment-resistant breast cancer (BCa) subtypes, which includes triple negative (TN), basal, and inflammatory breast cancer (IBC), contributes to worse survival outcomes in African American/AA patients, 42% higher death rate compared to White BCa. Amongst locally advanced BCa, IBC is a model of aggressive, most lethal, frequently basal/TN, accounting for 10% AA BCa and disparity in outcomes exist after adjusting for socioeconomic and diagnosis factors. IBC exhibits a unique phenotype wherein malignant cells do not form solid masses and instead, present as hyperproliferative tumor cell clusters, termed tumor emboli, in the skin and lymphatics. Our key finding was the identification of a tumor cell adaptive stress response pathway linking the mitogen activated ser/thr kinase/MNK, X-linked inhibitor of anti-apoptotic protein, XIAP, and nuclear transcription factor, NFkB, mediated proliferative, invasive and immunosuppressive signaling. Our goal was to determine the role of the adaptive stress response pathway, which we have identified to contribute to aggressiveness of TNBC and IBC, in AA breast tumor biology. Methods: Expression of MNK, XIAP and NFkB target gene sets, a 40-gene oxidative stress response that correlates with response to cell death stimuli and a 79-gene IBC signature (identified from comparative analysis of IBC and non-IBC biospecimens) were evaluated in The Cancer Genome Atlas (TCGA) breast cancer datasets (1109 tumor; 113 normal) stratified according to race and molecular subtypes (luminal A, B, Her2, basal). The mean expression for each gene in these signatures were also assessed among different subtypes and race using R. Gene Ontology (GO) analysis was performed using GATHER online tool. XIAP immunohistochemistry (IHC) conducted in BCa samples (n=93) from Duke and MDACC biorepositories. Results: TCGA analysis of the IBC-related signatures identified genes differentially expressed (>2-fold change; Wilcoxon rank sum test, FDR<0.05) among BCa subtypes and between AA vs White within a subtype. Additionally, the oxidative stress response metagene was significantly upregulated in AA basal (p=0.037) whereas there were fewer differences in immune-related genes within AA subtypes suggesting attenuated immune response. IHC, to date, shows high XIAP in high grade, ER-negative and in majority of AA BCa and in IBC samples independent of molecular subtypes and grade. Conclusions: We report a heightened adaptive stress response gene signature and identify genes in the MNK:XIAP:NFkB pathway and IBC-related signatures in AA BCa, suggesting potential biomarkers and drug discovery targets. High XIAP expression in high grade BCa, frequent in AA patients, is of therapeutic relevance as XIAP, the most potent caspase inhibitor, is linked to chemo- and immunotherapy resistance and XIAP inhibitors are in clinical trials. Supported by DOD-Breakthrough-W81XWH-17-1-0297; Duke SOM bridge funds; NCI-1P20-CA202925-01A12. Citation Format: Gayathri R Devi, Muthana Al Abo, Larisa Gearhart-Serna, Joseph Geradts, Shannon J McCall, Savitri Krishnamurthy. Identification of a tumor cell adaptive stress response signaling pathway, which drives aggressive breast cancer phenotype and therapeutic resistance, in African American patients with locally advanced breast cancer subtypes [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr B035.

Soybean-derived miRNAs specifically inhibit proliferation and stimulate apoptosis of human colonic Caco-2 cancer cells but not normal mucosal cells in culture

MicroRNAs (miRNAs) are important regulators of gene expression in eukaryotes. Studies have shown that plant-derived miRNAs can be absorbed through diets and regulate gene expression in mammals. Although soybean-derived miRNAs have been reported, their biological functions are still unclear. In this study, we found that soybean-derived small RNAs (sRNAs) significantly inhibited the proliferation and stimulated the apoptosis of Caco-2 cells. Bioinformatics analysis indicated that the target gene set of soybean miRNAs was extensively enriched in cancer pathways. Besides, we obtained 8 target genes, including Transcription factor 7 (TCF7), associated with colon cancer through prediction. Further studies showed that gma-miR159a inhibited the proliferation of Caco-2 cells and played an important role in the inhibitory effect of sRNAs by inhibiting TCF7 protein, which are upregulated in colon cancer cells but not normal mucosal cells in culture. These findings provide a novel molecular mechanism of soybean-derived miRNAs for potential application in tumor prevention.

In-silico investigations of selective miRNA-gene targets and their validation studies in obstructive sleep apnea (OSA) patient cohorts

BackgroundObstructive sleep apnoea (OSA) is a prevalent form of sleep disordered breathing which results in sleep fragmentation and deprivation. Obesity and cardiovascular disorders are the major risk factors associated with OSA. Molecular analysis of the factors associated with OSA could demarcate the clinical analysis pattern in a population. ObjectiveThis study pertains to in-silico analyses of miRNA and their gene targets with validation for their potential role in OSA as putative biomarker candidates. MethodsmiRDB, TargetScan and miRanda databases were used to identify targets of miR-27 and let-7 that have documented role in OSA and co-related obesity and cardiovascular disorders. Quantitative PCR was used to analyze expression pattern of miR-27 and let-7 in obese and non-obese OSA patient cohorts with respective controls. In-silico analysis was done using PatchDoc to obtain atomic contact energy (ACE) scores that indicated the docked gene targets to the predicted miRNA structures. The docked structures were analysed using Maestro Suite 11 for the hydrogen and aromatic interactions. ResultsDownregulation of miR-27 and let-7 in OSA compared to controls was observed. In-silico data analysis was performed for gene targets (TGFBR1, TGFBR2, SMAD2, SMAD4, CRY2 and CNR1) of the selected miRNAs (miR-27 and let-7). Among all, CNR1 and CRY2 were found to be better targets for miR-27 and let-7 respectively as per ACE scores, ROC scores and expression fold change in OSA. ConclusionOur study gives insights to the expression profiling of miR-27 and let-7 and explore a set of potential target genes (CNR1 and CRY2) of these two miRNAs for a promising clinical relevance in OSA.

Single-cell RNA sequencing reveals a heterogeneous response to Glucocorticoids in breast cancer cells

Steroid hormone receptors such as the Glucocorticoid Receptor (GR) mediate transcriptional responses to hormones and are frequently targeted in the treatment of human diseases. Experiments using bulk populations of cells have provided a detailed picture of the global transcriptional hormone response but are unable to interrogate cell-to-cell transcriptional heterogeneity. To examine the glucocorticoid response in individual cells, we performed single cell RNA sequencing (scRNAseq) in a human breast cancer cell line. The transcriptional response to hormone was robustly detected in individual cells and scRNAseq provided additional statistical power to identify over 100 GR-regulated genes that were not detected in bulk RNAseq. scRNAseq revealed striking cell-to-cell variability in the hormone response. On average, individual hormone-treated cells showed a response at only 30% of the total set of GR target genes. Understanding the basis of this heterogeneity will be critical for the development of more precise models of steroid hormone signaling.

Tissue-Specific Metabolic Regulation of FOXO-Binding Protein: FOXO Does Not Act Alone.

The transcription factor forkhead box (FOXO) controls important biological responses, including proliferation, apoptosis, differentiation, metabolism, and oxidative stress resistance. The transcriptional activity of FOXO is tightly regulated in a variety of cellular processes. FOXO can convert the external stimuli of insulin, growth factors, nutrients, cytokines, and oxidative stress into cell-specific biological responses by regulating the transcriptional activity of target genes. However, how a single transcription factor regulates a large set of target genes in various tissues in response to a variety of external stimuli remains to be clarified. Evidence indicates that FOXO-binding proteins synergistically function to achieve tightly controlled processes. Here, we review the elaborate mechanism of FOXO-binding proteins, focusing on adipogenesis, glucose homeostasis, and other metabolic regulations in order to deepen our understanding and to identify a novel therapeutic target for the prevention and treatment of metabolic disorders.

Multi-kinase control of environmental stress responsive transcription.

Cells respond to changes in environmental conditions by activating signal transduction pathways and gene expression programs. Here we present a dataset to explore the relationship between environmental stresses, kinases, and global gene expression in yeast. We subjected 28 drug-sensitive kinase mutants to 10 environmental conditions in the presence of inhibitor and performed mRNA deep sequencing. With these data, we reconstructed canonical stress pathways and identified examples of crosstalk among pathways. The data also implicated numerous kinases in novel environment-specific roles. However, rather than regulating dedicated sets of target genes, individual kinases tuned the magnitude of induction of the environmental stress response (ESR)-a gene expression signature shared across the set of perturbations-in environment-specific ways. This suggests that the ESR integrates inputs from multiple sensory kinases to modulate gene expression and growth control. As an example, we provide experimental evidence that the high osmolarity glycerol pathway is an upstream negative regulator of protein kinase A, a known inhibitor of the ESR. These results elaborate the central axis of cellular stress response signaling.

The Integrated RNA Landscape of Renal Preconditioning against Ischemia-Reperfusion Injury.

Although AKI lacks effective therapeutic approaches, preventive strategies using preconditioning protocols, including caloric restriction and hypoxic preconditioning, have been shown to prevent injury in animal models. A better understanding of the molecular mechanisms that underlie the enhanced resistance to AKI conferred by such approaches is needed to facilitate clinical use. We hypothesized that these preconditioning strategies use similar pathways to augment cellular stress resistance. To identify genes and pathways shared by caloric restriction and hypoxic preconditioning, we used RNA-sequencing transcriptome profiling to compare the transcriptional response with both modes of preconditioning in mice before and after renal ischemia-reperfusion injury. The gene expression signatures induced by both preconditioning strategies involve distinct common genes and pathways that overlap significantly with the transcriptional changes observed after ischemia-reperfusion injury. These changes primarily affect oxidation-reduction processes and have a major effect on mitochondrial processes. We found that 16 of the genes differentially regulated by both modes of preconditioning were strongly correlated with clinical outcome; most of these genes had not previously been directly linked to AKI. This comparative analysis of the gene expression signatures in preconditioning strategies shows overlapping patterns in caloric restriction and hypoxic preconditioning, pointing toward common molecular mechanisms. Our analysis identified a limited set of target genes not previously known to be associated with AKI; further study of their potential to provide the basis for novel preventive strategies is warranted. To allow for optimal interactive usability of the data by the kidney research community, we provide an online interface for user-defined interrogation of the gene expression datasets (http://shiny.cecad.uni-koeln.de:3838/IRaP/).

Incorporating Clinical, Chemical and Biological Information for Predicting Small Molecule-microRNA Associations Based on Non-Negative Matrix Factorization.

Small molecule(SM) drugs can affect the expression of miRNAs, which plays crucial roles in many important biological processes. The chemical structure and clinical information of small molecule can simultaneously incorporate information such as anatomical distribution, therapeutic effects and structural characteristics. It is necessary to develop a novel model that incorporates small molecule chemical structure and clinical information to reveal the unknown small molecule-miRNA associations. In this study, we developed a new framework based on non-negative matrix factorization, called SMANMF, to discover the potential small molecules-miRNAs associations. First, the functional similarity of two miRNAs can be obtained by computing the overlap of the target gene sets in which the miRNAs interact together, and we integrated two types of small molecule similarities, including chemical similarity and clinical similarity. Then, we utilized a non-negative matrix factorization model to discover the unknown relationship between small molecules and miRNAs. The evaluation results indicate that our model can achieve superior prediction performance compared with previous approaches in 5-fold cross-validation. At the same time, the results of case studies also reveal that the SMANMF model has good predictive performance for predicting the potential association between small molecules and miRNAs.

P53-Related Transcription Targets of TAp73 in Cancer Cells-Bona Fide or Distorted Reality?

Identification of p73 as a structural homolog of p53 fueled early studies aimed at determining if it was capable of performing p53-like functions. This led to a conundrum as p73 was discovered to be hardly mutated in cancers, and yet, TAp73, the full-length form, was found capable of performing p53-like functions, including transactivation of many p53 target genes in cancer cell lines. Generation of mice lacking p73/TAp73 revealed a plethora of developmental defects, with very limited spontaneous tumors arising only at a later stage. Concurrently, novel TAp73 target genes involved in cellular growth promotion that are not regulated by p53 were identified, mooting the possibility that TAp73 may have diametrically opposite functions to p53 in tumorigenesis. We have therefore comprehensively evaluated the TAp73 target genes identified and validated in human cancer cell lines, to examine their contextual relevance. Data from focused studies aimed at appraising if p53 targets are also regulated by TAp73—often by TAp73 overexpression in cell lines with non-functional p53—were affirmative. However, genome-wide and phenotype-based studies led to the identification of TAp73-regulated genes involved in cellular survival and thus, tumor promotion. Our analyses therefore suggest that TAp73 may not necessarily be p53’s natural substitute in enforcing tumor suppression. It has likely evolved to perform unique functions in regulating developmental processes and promoting cellular growth through entirely different sets of target genes that are not common to, and cannot be substituted by p53. The p53-related targets initially reported to be regulated by TAp73 may therefore represent an experimental possibility rather than the reality.

Ethyl Acetate Fraction of Aqueous Extract of Lentinula edodes Inhibits Osteoclastogenesis by Suppressing NFATc1 Expression.

Bone tissue is continuously remodeled by the coordinated action of osteoclasts and osteoblasts. Nuclear factor-activated T cells c1 (NFATc1) is a well-known transcription factor for osteoclastogenesis and transcriptionally activated by the c-Fos and nuclear factor-kappa B (NF-κB) signaling pathways in response to receptor activation of NF-κB ligand (RANKL). Since excessive RANKL signaling causes an increase of osteoclast formation and bone resorption, inhibition of RANKL or its signaling pathway is an attractive therapeutic approach to the treatment of pathologic bone loss. In this study, we show that an ethyl acetate fraction (LEA) from the shiitake mushroom, Lentinula edodes, inhibited RANKL-induced osteoclast differentiation by blocking the NFATc1 signaling pathway. We found that the water extract and its subsequent ethyl acetate fraction of L. edodes significantly suppressed osteoclast formation. Comparative transcriptome analysis revealed that LEA specifically downregulated a set of RANKL target genes, including Nfatc1. Next, we found that LEA suppresses Nfatc1 expression mainly through the inhibition of the transactivity of p65 and NFATc1. Moreover, treatment of LEA rescued an osteoporotic phenotype in a zebrafish model of glucocorticoid-induced osteoporosis. Collectively, our findings define an undocumented role of the shiitake mushroom extract in regulating bone development.

Abstract P3-03-03: Inflammatory breast cancer exhibits amplification and transcriptional activation of MYC in conjunction with NOTCH and TGFβ signaling

Abstract Inflammatory breast cancer (IBC) is an aggressive and poorly characterized breast cancer subtype with few targets available for molecular therapy. Several attempts aimed at characterizing the disease at the genomic, transcriptomic and proteomic level. Together, these studies suggest that MYC is central to the biology of IBC. Here, we analyzed data sets from patient samples and preclinical models to corroborate this hypothesis. Genomic and transcriptomic profiles were obtained using next-generation sequencing and Affymetrix GeneChip analysis on a series of 101 and 137 samples from patients with IBC. In addition, non-IBC (nIBC) control samples were included from our own repositories (N=252) as well as from publicly available data sets (i.e. TCGA and METABRIC). Finally, RNA-sequencing and peptide phosphorylation data from preclinical IBC and nIBC models, both with and without TGFβ treatment, were explored. Apart from TP53 and ERBB2, MYC is the 3rd most frequently mutated gene with single nucleotide variants, indels and amplifications found in 22% of 101 patients. Furthermore, MYC mutations are mutually exclusive with alterations in the NOTCH genes (i.e. NOTCH1, -2, -3, and -4 and CREBBP). At the gene expression level, a MYC activation score is elevated in IBC as compare to nIBC and correlates with a NOTCH activation signature. Genes overexpressed in IBC are enriched for various sets of MYC target genes and are associated with MYC amplifications in TCGA and METABRIC samples. In preclinical models, MYC target genes are particularly responsive to TGFβ treatment in IBC cells but not in nIBC cells and analysis of peptide phosphorylation patterns suggest this interaction may be regulated via PTK2B. The present data suggest that MYC could be an important driver of IBC biology, which corroborates with the recent observation that MYC is an important hub in the signal transduction network of SUM149 and -190 cells. Furthermore, our data reveal that MYC activation is linked to NOCTH and TGFβ signaling. In earlier studies it was demonstrated that lymphovascular tumor emboli in the Mary-X mouse model of IBC exhibit NOTCH3 addition with downstream MYC overexpression, indicating that NOTCH/MYC signaling could be crucial for metastatic progression in IBC. In this context, it should be noted that an allele associated with metastatic risk in IBC patients resides at the 8q24 locus that harbors the MYC gene. Citation Format: Charlotte Rypens, François Bertucci, Patrice Viens, John WM Martens, Marcel Smid, Carolien Schröder, Naoto T Ueno, Massimo Cristofanilli, Piet Dirix, Peter Vermeulen, Luc Dirix, Steven Van Laere. Inflammatory breast cancer exhibits amplification and transcriptional activation of MYC in conjunction with NOTCH and TGFβ signaling [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-03-03.

Abstract WP127: Intravenous Administration of Microrna-122 Mimic for Treatment of Ischemic and Hemorrhagic Strokes in Rats

MicroRNAs(miRs)are very promising next generation drug targets due to their unique miR-target binding that is different from the traditional ligand-receptor. A single miR binds to complementary bases in the 3’ untranslated regions(3’UTR) of hundreds of target genes and down-regulates these genes. MiR therapeutics have been developed for treatment of various diseases, with several miR drugs(e.g., miR-122/miR-155 inhibitors, miR-16/29/34 mimics) being advanced into human trials in the last decade. Our previous studies showed that intravenous (i.v.) miR-122 mimic (2.4mg/kg, wrapped in PEG-liposomes) improves outcomes after suture middle cerebral artery occlusion(MCAO)-induced ischemic stroke (IS) with a 6 hour time window. In pilot whole genome miR expression studies, we demonstrated that microRNA-122 (miR-122) is the most significantly decreased miR in blood after intraventricularautologousfresh blood-induced intracerebral hemorrhage (ICH) in rats. As compared to sham controls, miR-122 decreased 28 fold at 3 hrs, 34 fold at 24 hrs, 31 fold at 7 days and 19 fold at 14 days in blood after ICH in rats. These miRNA expression data suggest that elevating miR-122 in blood has great potential to treat ICH in addition to IS. Therefore, we hypothesized that i.v. miR-122 mimic improves outcomes after ICH, in addition to IS. Our miR-122 targetome studies show that a set of miR-122 target genes (Pla2g2a, Vcam1, Nos2, Rhbdf1, Olig1, Nrep) are responsible for the therapeutic efficacy of miR-122 mimic on ischemic stroke, while another set of genes (Ywhaq, Klrk1, Tpst1, Vars2)account for efficacy in ICH. Using3’UTR luciferase reporter assays and anti-sense Morpholino Oligos (MOs), we show that miR-122 binds to 3’UTR of its target genes Pla2g2a and Vcam1, rather than Nos2. In addition, in vivo MO-miR-122-Pla2g2a blocks miR-122 mimic treatment-induced decrease of Pla2g2a in blood cells after ischemic stroke. In summary, our data suggest miR-122 mimic can treat IS and ICH. Therefore, the miR-122 mimic treatment for IS and ICH could likely be performed without brain imaging (e.g. in the ambulance, and/or emergency room) since it is broadly efficacious for both IS and ICH.

Identification of key molecular targets that correlate with breast cancer through bioinformatic methods.

The present study aimed to identify key molecular targets of breast cancer for targeted treatment and to improve the survival rate. Overlapped difference expression genes in three datasets were identified in a weighted gene co-expression network analysis (WGCNA) module and MetaDE.ES analysis. Combined with the prognosis information [time, death, status and relative survival (RS)] in GSE42568, single-factor Cox regression analysis was used to screen the genes that were significantly related to the prognosis in the target gene set. In total, 13 optimal gene combinations with a significantly correlated prognosis were obtained, including SSPN, NELL2, AGTR1, NRIP3, IKZF2, NAT1, CXCL12, NPY1R, PRAME, PPP1R1B, CRISP3, NMU and GSTP1. In addition, there was a significant correlation between the samples given by the prognostic prediction system and the validation dataset (GSE20685 and TCGA), with p values of 0.0299 in GSE20685 and 1.461 × 10-5 in TCGA, and an area under the receiver operating characteristic of 0.942 and 0.923, respectively. RS-related differentially expressed genes between high- and low-risk groups were significantly related to biological processes such as cell period and the hormone stimulation response, and were also significantly involved in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways such as cell period, the peroxisome proliferator-activated receptor signaling pathway and the cancer pathway. By predicting the survival risk of breast cancer patients based on the 13 optimal genes, high-risk patients would be detected early. Accordingly, this would help in the formulation of an appropriate treatment plan for patients.

LncRNA CSMD1-1 promotes the progression of Hepatocellular Carcinoma by activating MYC signaling.

Emerging evidence suggests that long non-coding RNAs (lncRNA) play critical roles in the development and progression of diverse cancers including hepatocellular carcinoma (HCC), but the underlying molecular mechanisms of lncRNAs that are involved in hepatocarcinogenesis have not been fully explored.Methods: In this study, we profiled lncRNA expression in 127 pairs of HCC and nontumor liver tissues (a Discovery Cohort) using a custom microarray. The expression and clinical significance of lncCSMD1-1 were then validated with qRT-PCR and COX regression analysis in a Validation Cohort (n=260) and two External Validation Cohorts (n=92 and n=124, respectively). In vitro and in vivo assays were performed to explore the biological effects of lncCSMD1-1 on HCC cells. The interaction of lncCSMD1-1 with MYC was identified by RNA pull-down and RNA immunoprecipitation. The role of LncCSMD1-1 in the degradation of MYC protein was also investigated.Results: With microarray, we identified a highly upregulated lncRNA, lncCSMD1-1, which was associated with tumor progression and poor prognosis in the Discovery Cohort, and validated in another 3 HCC cohorts. Consistently, ectopic expression of lncCSMD1-1 notably promotes cell proliferation, migration, invasion, tumor growth and metastasis of HCC cells in in vitro and in vivo experiments. Gene expression profiling on HCC cells and gene sets enrichment analysis indicated that the MYC target gene set was significantly enriched in HCC cells overexpressing lncCSMD1-1, and lncCSMD1-1 was found to directly bind to MYC protein in the nucleus of HCC cells, which resulted in the elevation of MYC protein. Mechanistically, lncCSMD1-1 interacted with MYC protein to block its ubiquitin-proteasome degradation pathway, leading to activation of its downstream target genes.Conclusion: lncCSMD1-1 is upregulated in HCC and promotes progression of HCC by activating the MYC signaling pathway. These results provide the evidence that lncCSMD1-1 may serve as a novel prognostic marker and potential therapeutic target for HCC.

Resolving noise-control conflict by gene duplication.

Gene duplication promotes adaptive evolution in two main ways: allowing one duplicate to evolve a new function and splitting ancestral functions between the duplicates. The second scenario may resolve adaptive conflicts that can rise when one gene performs different functions. In an apparent departure from both scenarios, low-expressing transcription factor (TF) duplicates commonly bind to the same DNA motifs and act in overlapping conditions. To examine for possible benefits of this apparent redundancy, we examined the Msn2 and Msn4 duplicates in budding yeast. We show that Msn2,4 function as one unit by inducing the same set of target genes in overlapping conditions. Yet, the two-factor composition allows this unit’s expression to be both environmentally responsive and with low noise, resolving an adaptive conflict that limits expression of single genes. We propose that duplication can provide adaptive benefit through cooperation rather than functional divergence, allowing two-factor dynamics with beneficial properties that cannot be achieved by a single gene.