E Ahamed

Bio: E Ahamed is an academic researcher from Imperial College London. The author has contributed to research in topics: Estrogen receptor alpha & Cancer. The author has an hindex of 1, co-authored 2 publications receiving 92 citations.

The DEAD-box protein p72 regulates ERα-/oestrogen-dependent transcription and cell growth, and is associated with improved survival in ERα-positive breast cancer

Abstract: The DEAD-box RNA helicases p68 (DDX5) and p72 (DDX17) have been shown to act as transcriptional co-activators for a diverse range of transcription factors, including oestrogen receptor-alpha (ERalpha). Here, we show that, although both proteins interact with and co-activate ERalpha in reporter gene assays, small interfering RNA-mediated knockdown of p72, but not p68, results in a significant inhibition of oestrogen-dependent transcription of endogenous ERalpha-responsive genes and oestrogen-dependent growth of MCF-7 and ZR75-1 breast cancer cells. Furthermore, immunohistochemical staining of ERalpha-positive primary breast cancers for p68 and p72 indicate that p72 expression is associated with an increased period of relapse-free and overall survival (P=0.006 and 0.016, respectively), as well as being inversely associated with Her2 expression (P=0.008). Conversely, p68 shows no association with relapse-free period, or overall survival, but it is associated with an increased expression of Her2 (P=0.001), AIB-1 (P<0.001) and higher tumour grade (P=0.044). Our data thus highlight a crucial role for p72 in ERalpha co-activation and oestrogen-dependent cell growth and provide evidence in support of distinct but important roles for both p68 and p72 in regulating ERalpha activity in breast cancer.

Coactivation of estrogen receptor alpha by the DEAD-box RNA helicases p68 and p72 and its role in breast cancer

Abstract: We have previously demonstrated that the DEAD-box RNA helicase p68 is an important regulator of gene expression [1,2], whilst other groups have shown that p68 interacts with and coactivates estrogen receptor alpha (ERα) [3,4]. The main focus of our project is to investigate the molecular mechanism of ERα coactivation by p68 and to examine the potential consequences for breast cancer development. We have established that the interaction of p68 and ERα requires the DNA binding domain of ERα and the C terminus of p68. Importantly, this region of p68 lies outside the conserved helicase core and was previously shown by us to be essential for transcriptional regulation by p68. Additionally, coactivation of ERα by p68 requires the ligand binding/AF2 region of ERα and is consistent with the model that p68 is recruited to ERα-responsive promoters in response to estrogen [4]. We have also shown that p72, a helicase that is very highly related to p68 and that had previously been suggested to act in an analogous fashion to p68 [3], poorly coactivates ERα in standard transcriptional coactivation assays, using ER-responsive promoters. This is underscored by our finding that overexpression of p68, but not of p72, in cell lines results in stimulation of expression of physiological target genes of ERα. Interestingly, siRNA-mediated knockdown of endogenous p68 has little effect on the expression of ERα target genes. This observation is consistent with the idea that p68 has little effect on ERα function physiologically, but that the elevated p68 levels found in tumours may stimulate ERα-mediated gene expression in a pathological context. Strikingly, however, in contrast to p68, knockdown of endogenous p72 results in a marked inhibition of both baseline and estrogen stimulated-expression of these genes. These findings suggest, firstly, that p72 is important physiologically for ERα activity in the cell and, secondly, that p68 and p72 may be acting in an opposing rather than analogous fashion (as had been previously suggested [3]). Moreover, our preliminary data suggest that overexpression of p68 in cells may additionally coactivate ERα in an estrogen-independent manner, a finding that may have implications in the development of resistance to endocrine therapies. We are currently developing inducible p68/p72 overexpression and siRNA cell lines with a view to examining the effect of augmenting or suppressing p68/p72 expression in mouse xenograft models. Additionally we are screening a large panel of breast cancers to examine p68 and p72 expression/localisation in the context of ERα expression.

RBFOX1 regulates both splicing and transcriptional networks in human neuronal development

Abstract: RNA splicing plays a critical role in the programming of neuronal differentiation and, consequently, normal human neurodevelopment, and its disruption may underlie neurodevelopmental and neuropsychiatric disorders. The RNA-binding protein, fox-1 homolog (RBFOX1; also termed A2BP1 or FOX1), is a neuron-specific splicing factor predicted to regulate neuronal splicing networks clinically implicated in neurodevelopmental disease, including autism spectrum disorder (ASD), but only a few targets have been experimentally identified. We used RNA sequencing to identify the RBFOX1 splicing network at a genome-wide level in primary human neural stem cells during differentiation. We observe that RBFOX1 regulates a wide range of alternative splicing events implicated in neuronal development and maturation, including transcription factors, other splicing factors and synaptic proteins. Downstream alterations in gene expression define an additional transcriptional network regulated by RBFOX1 involved in neurodevelopmental pathways remarkably parallel to those affected by splicing. Several of these differentially expressed genes are further implicated in ASD and related neurodevelopmental diseases. Weighted gene co-expression network analysis demonstrates a high degree of connectivity among these disease-related genes, highlighting RBFOX1 as a key factor coordinating the regulation of both neurodevelopmentally important alternative splicing events and clinically relevant neuronal transcriptional programs in the development of human neurons.

DEAD box RNA helicase functions in cancer

Abstract: Members of the DEAD box family of RNA helicases are known to be involved in most cellular processes that require manipulation of RNA structure and, in many cases, exhibit other functions in addition to their established ATP-dependent RNA helicase activities. They thus play critical roles in cellular metabolism and in many cases have been implicated in cellular proliferation and/or neoplastic transformation. These proteins generally act as components of multi-protein complexes; therefore their precise role is likely to be influenced by their interacting partners and to be highly context-dependent. This may also provide an explanation for the sometimes conflicting reports suggesting that DEAD box proteins have both pro- and anti-proliferative roles in cancer.

Transcriptional regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNA.

Abstract: Nuclear receptors regulate gene expression in response to environmental cues, but the molecular events governing the cell type specificity of nuclear receptors remain poorly understood. Here we outline a role for a long noncoding RNA (lncRNA) in modulating the cell type-specific actions of liver X receptors (LXRs), sterol-activated nuclear receptors that regulate the expression of genes involved in cholesterol homeostasis and that have been causally linked to the pathogenesis of atherosclerosis. We identify the lncRNA MeXis as an amplifier of LXR-dependent transcription of the gene Abca1, which is critical for regulation of cholesterol efflux. Mice lacking the MeXis gene show reduced Abca1 expression in a tissue-selective manner. Furthermore, loss of MeXis in mouse bone marrow cells alters chromosome architecture at the Abca1 locus, impairs cellular responses to cholesterol overload, and accelerates the development of atherosclerosis. Mechanistic studies reveal that MeXis interacts with and guides promoter binding of the transcriptional coactivator DDX17. The identification of MeXis as a lncRNA modulator of LXR-dependent gene expression expands understanding of the mechanisms underlying cell type-selective actions of nuclear receptors in physiology and disease.

DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

Abstract: T helper 17 (TH17) lymphocytes protect mucosal barriers from infections, but also contribute to multiple chronic inflammatory diseases. Their differentiation is controlled by RORγt, a ligand-regulated nuclear receptor. Here we identify the RNA helicase DEAD-box protein 5 (DDX5) as a RORγt partner that coordinates transcription of selective TH17 genes, and is required for TH17-mediated inflammatory pathologies. Surprisingly, the ability of DDX5 to interact with RORγt and coactivate its targets depends on intrinsic RNA helicase activity and binding of a conserved nuclear long noncoding RNA (lncRNA), Rmrp, which is mutated in patients with cartilage-hair hypoplasia. A targeted Rmrp gene mutation in mice, corresponding to a gene mutation in cartilage-hair hypoplasia patients, altered lncRNA chromatin occupancy, and reduced the DDX5-RORγt interaction and RORγt target gene transcription. Elucidation of the link between Rmrp and the DDX5-RORγt complex reveals a role for RNA helicases and lncRNAs in tissue-specific transcriptional regulation, and provides new opportunities for therapeutic intervention in TH17-dependent diseases.