The miR-96 and RAR gamma signaling axis governs androgen signaling and prostate cancer progression

Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RAR gamma) are commonly reduced in prostate cancer (PCa). Therefore, we sought to establish the cellular and gene regulatory consequences of reduced RAR gamma expression, and determine RAR gamma regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RAR gamma levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. ChIP-Seq defined the RAR gamma cistrome, which was significantly enriched at active enhancers associated with AR binding sites. Reflecting a significant genomic role for RAR gamma to regulate androgen signaling, RAR gamma knockdown in HPr1-AR cells significantly regulated the magnitude of the AR transcriptome. RAR gamma downregulation was explained by increased miR-96 in PCa cell and mouse models, and TCGA PCa cohorts. Biochemical approaches confirmed that miR-96 directly regulated RAR gamma expression and function. Capture of the miR-96 targetome by biotin-miR-96 identified that RAR gamma and a number of RAR gamma interacting co-factors including TACC1 were all targeted by miR-96, and expression of these genes were prominently altered, positively and negatively, in the TCGA-PRAD cohort. Differential gene expression analyses between tumors in the TCGA-PRAD cohort with lower quartile expression levels of RARG and TACC1 and upper quartile miR-96, compared to the reverse, identified a gene network including several RAR gamma target genes (e.g., SOX15) that significantly associated with worse disease-free survival (hazard ratio 2.23, 95% CI 1.58 to 2.88, p = 0.015). In summary, miR-96 targets a RAR gamma network to govern AR signaling, PCa progression and disease outcome.

Assessing the role of Hes1 and identification of target genes in human and murine T-ALL

Silvia Wirth

The Notch signalling pathway is an ancient cell signalling mechanism that enables short-range communications between cells and controls a broad spectrum of cell fates and developmental processes. In the haematopoietic system Notch signalling has been linked to physiological, but also to pathological phenotypes of T cell development. Identification of numerous activating mutations within the NOTCH1 receptor in human T cell acute lymphoblastic leukaemia (T-ALL) patient samples demonstrated that aberrant activation of this signalling pathway is a frequent event in T-ALL. Active Notch signalling leads to the expression of a plethora of genes that might be drivers or passengers in tumorigenesis including Hes1, which encodes a transcriptional repressor. We have therefore studied Hes1 in the context of T-ALL in mouse models that mimic human disease and in human T-ALL cell lines with the aim to evaluate whether Hes1 affects disease development and disease maintenance and to characterize its function on a molecular level. The first part of this study is dedicated to the functional characterisation of Hes1 in vivo in T-ALL mouse models and in vitro in human T-ALL cell lines. Using a retroviral bone marrow transplant model of T-ALL in which progenitor cells are transduced with a retrovirus expressing constitutive active Notch1 intracellular domain (NICD) we could show that Hes1 is not required in established, late stage T-ALL cells, but that it promotes tumour progression in the early stages of the disease. We have also investigated the function of HES1 in human T-ALL and can show that the overexpression of dominant negative versions of Hes1 in two patient derived cell lines (T-ALL1, CUTLL-1) does not affect proliferation or apoptosis, emphasising that HES1 does not affect cell viability once cells are fully transformed to the leukemic state. In the second part of the study we set out to systematically delineate the gene regulatory networks down-stream of Hes1 by combining RNA-seq and ChIP-seq analysis. Comparing the gene expression of murine premalignant, early stage NICD induced CD4+CD8+ DP cells in the presence and absence of Hes1 by RNA-seq, we unexpectedly found a predominant upregulation of genes in cells expressing Hes1 indicating that Hes1 might rather act as a positive regulator of transcription than as a transcriptional repressor of distinct target genes. Hes1 might influence transcription through secondary or indirect effects as combinatorial analysis of RNA-seq and ChIP-seq led to the identification of only a small number of potential direct target genes that are transcriptionally regulated by Hes1. In summary, the role of Hes1 in promoting the early stages of the disease appears to be highly complex and is likely to involve both direct and indirect control of gene regulatory networks.

EPFL2014

A conserved transcriptional enhancer that specifies Tyrp1 expression to melanocytes

Friedrich Beermann

Pigment cells of mammals originate from two different lineages: melanocytes arise from the neural crest, whereas cells of the retinal pigment epithelium (RPE) originate from the optic cup of the developing forebrain. Previous studies have suggested that pigmentation genes are controlled by different regulatory networks in melanocytes and RPE. The promoter of the tyrosinase-related family gene Tyrp1 has been shown to drive detectable transgene expression only to the RPE, even though the gene is also expressed in melanocytes as evident from Tyrp1-mutant mice. This indicates that the regulatory elements responsible for Tyrp1 gene expression in the RPE are not sufficient for expression in melanocytes. We thus searched for a putative melanocyte-specific regulatory sequence and demonstrate that a bacterial artificial chromosome (BAC) containing the Tyrp1 gene and surrounding sequences is able to target transgenic expression to melanocytes and to rescue the Tyrp1b (brown) phenotype. This BAC contains several highly conserved non-coding sequences that might represent novel regulatory elements. We further focused on a sequence located at -15 kb, which we identified as a melanocyte-specific enhancer as shown by cell culture and transgenic mice experiments. In addition, we show that the transcription factor Sox10 can activate this conserved enhancer. The presence of a distal Tyrp1 regulatory element, which specifies melanocyte-specific expression, supports the idea that separate regulatory sequences can mediate differential gene expression in melanocytes and RPE.

2006

Conversion of mouse neural stem cells into glioma cancer stem cells

Caroline Turk

Gliomas are the most common and lethal primary adult human brain cancers. The most lethal form of glioma is glioblastoma multiforme (GBM). Multiple apparently differentiated cell types are present within these tumours, including varying proportions of astrocytes and oligodendrocytes. The identification of new GBM subtypes, the role of the cell-of-origin and the role of commonly disrupted genes are active areas of investigation. Of particular interest to this laboratory is the recent realisation that GBMs may be driven by and initiated from tumorigenic stem cells. Our goal was to develop a mouse model of the disease based on genetic manipulation of in vitro neural stem (NS) cell lines. Importantly, this would enable us to define the contribution of each oncogenic pathway in altering the self-renewal of these cells. The original hypothesis was that the simultaneous activation of three critical pathways (RTK/PI3K, Rb and p53) would be required to confer a glioma-like phenotype. However, surprisingly we found that forced expression of the commonly amplified cyclin dependent kinase-4 (CDK4) was sufficient to elicit reduced dependency on growth factor signalling and a decreased sensitivity to the differentiation factor BMP4. Moreover, preliminary results indicate that the mRNA expression of the proto-oncogene Akt2 increases in CDK4 transfectants, suggestive of a feedback mechanism. We tested whether constitutive expression of Akt2 together with CDK4 increases the severity of the phenotype and initial results suggest this is the case. These findings provide encouragement that minimal genetic events will be required in order to transform NS cells in vitro. These cells can now be tested for in vivo tumorigenicity following transplantation. Finally, we have also generated CDK4 overexpressing cell lines in a specific NS cell variant which I identified as expressing an oligodendrocyte differentiation bias (MG1-7). We are therefore now in a position to assess whether differentiation behaviour is affected by the disruption of this pathway. Together these findings highlight the utility of mouse NS cells as a tool to study glioma