MicroRNAs (miRNAs) are endogenously expressed 20 -24 nucleotide RNAs thought to repress protein translation through binding to a target mRNA (1-3). Only a few of the more than 250 predicted human miRNAs have been assigned any biological function. In an effort to uncover miRNAs important during adipocyte differentiation, antisense oligonucleotides (ASOs) targeting 86 human miRNAs were transfected into cultured human pre-adipocytes, and their ability to modulate adipocyte differentiation was evaluated. Expression of 254 miRNAs in differentiating adipocytes was also examined on a miRNA microarray. Here we report that the combination of expression data and functional assay results identified a role for miR-143 in adipocyte differentiation. miR-143 levels increased in differentiating adipocytes, and inhibition of miR-143 effectively inhibited adipocyte differentiation. In addition, protein levels of the proposed miR-143 target ERK5 (4) were higher in ASO-treated adipocytes. These results demonstrate that miR-143 is involved in adipocyte differentiation and may act through target gene ERK5.The first miRNA 1 was identified in Caenorhabditis elegans as a gene important for timing of larval development (5). miRNAs have since been implicated in many processes in invertebrates, including cell proliferation and apoptosis (6, 7), fat metabolism (6), and neuronal patterning (8). As many miRNAs are conserved across species (9 -11), they are likely to be involved in developmental processes in all animals. Only a few mammalian miRNAs have been assigned any function, and at least two of these are involved in developmental processes: miR-181 promotes B cell development in mice (12) and miR196a regulates several Hox genes (13), which code for a family of transcription factors involved in various developmental programs in animals (14).We hypothesized that miRNAs may play a role in maturation of human adipocytes. Understanding the molecular events involved in adipocyte differentiation is of interest for development of therapeutics for metabolic diseases such as obesity and diabetes. In vitro cell culture systems, such as human primary subcutaneous pre-adipocytes, have been crucial in uncovering signaling pathways important for adipocyte differentiation (15). These cells can be cultured with differentiation-promoting hormonal stimuli, causing them to develop into cells that morphologically and functionally resemble mature adipocytes. In this study we have inhibited a panel of miRNAs in pre-adipocytes using antisense oligonucleotides and evaluated the effect on adipocyte differentiation. Combined with expression analysis of miRNAs in differentiating adipocytes by microarray, one miRNA, miR-143, was identified which normally promotes adipocyte differentiation. These results indicate that miRNAs do play a role in adipocyte differentiation and are potential therapeutic targets for obesity and metabolic diseases. EXPERIMENTAL PROCEDURESOligonucleotide Synthesis-Oligonucleotides were prepared using conventional phosphoramidite chemistry and...

MicroRNAs (miRNAs) are believed to play important roles in developmental and other cellular processes by hybridizing to complementary target mRNA transcripts. This results in either cleavage of the hybridized transcript or negative regulation of translation. Little is known about the regulation or pattern of miRNA expression. The predicted presence of numerous miRNA sequences in higher eukaryotes makes it highly likely that the expression levels of individual miRNA molecules themselves should play an important role in regulating multiple cellular processes. Therefore, determining the pattern of global miRNA expression levels in mammals and other higher eukaryotes is essential to help understand both the mechanism of miRNA transcriptional regulation as well as to help identify miRNA regulated gene expression. Here, we describe a novel method to detect global processed miRNA expression levels in higher eukaryotes, including human, mouse and rats, by using a high-density oligonucleotide array. Array results have been validated by subsequent confirmation of mir expression using northern-blot analysis. Major differences in mir expression have been detected in samples from diverse sources, suggesting highly regulated mir expression, and specific gene regulatory functions for individual miRNA transcripts. For example, five different miRNAs were found to be preferentially expressed in human kidney compared with other human tissues. Comparative analysis of surrounding genomic sequences of the kidney-specific miRNA clusters revealed the occurrence of specific transcription factor binding sites located in conserved phylogenetic foot prints, suggesting that these may be involved in regulating mir expression in kidney.

Ceramide induces cell death in response to many stimuli. Its mechanism of action, however, is not completely understood. Ceramide induces autophagy in mammalian cells maintained in rich media and nutrient permease downregulation in yeast. These observations suggested to us that ceramide might kill mammalian cells by limiting cellular access to extracellular nutrients. Consistent with this proposal, physiologically relevant concentrations of ceramide produced a profound and specific downregulation of nutrient transporter proteins in mammalian cells. Blocking ceramide-induced nutrient transporter loss or supplementation with the cell-permeable nutrient, methyl pyruvate, reversed ceramide-dependent toxicity. Conversely, cells became more sensitive to ceramide when nutrient stress was increased by acutely limiting extracellular nutrients, inhibiting autophagy, or deleting AMP-activated protein kinase (AMPK). Observations that ceramide can trigger either apoptosis or caspase-independent cell death may be explained by this model. We found that methyl pyruvate (MP) also protected cells from ceramide-induced, nonapoptotic death consistent with the idea that severe bioenergetic stress was responsible. Taken together, these studies suggest that the cellular metabolic state is an important arbiter of the cellular response to ceramide. In fact, increasing nutrient demand by incubating cells in high levels of growth factor sensitized cells to ceramide. On the other hand, gradually adapting cells to tolerate low levels of extracellular nutrients completely blocked ceramide-induced death. In sum, these results support a model where ceramide kills cells by inducing intracellular nutrient limitation subsequent to nutrient transporter downregulation.autophagy ͉ caspase-independent cell death ͉ daunorubicin ͉ bioenergetics ͉ sphingolipid C eramide and related sphingolipids play an evolutionarily conserved role in the cellular response to stress by regulating cell growth, differentiation, senescence, and survival (1). Uncovering the mechanisms by which ceramide regulates these processes is of paramount importance given the wide range of human diseases that result from altered ceramide metabolism including cancer, type II diabetes, and neurodegenerative disease (2-4). Ceramide plays a particularly well-established role in cancer. Decreasing cellular ceramide levels increases tumor growth and metastasis and can lead to multidrug resistance, a major cause of cancer treatment failure (2, 5, 6). The ability of ceramide to trigger programmed cell death in response to growth factor withdrawal, death receptor ligation, hypoxia, and chemotherapeutic drugs is likely integral to its role in suppressing cancer initiation and progression. Although many of the downstream, executioner pathways that are activated by ceramide are known, how ceramide triggers these pathways is not completely understood.Autophagy, a process by which cells catabolize their own components, is induced in ceramide-treated cells (7-9). Autophagy has been conserved through...

The small GTPase Rab7 promotes fusion events between late endosomes and lysosomes. Rab7 activity is regulated by extrinsic signals, most likely via effects on its guanine nucleotide exchange factor (GEF) or GTPase-activating protein (GAP). Based on their homology to the yeast proteins that regulate the Ypt7 GTP binding state, TBC1D15, and mammalian Vps39 (mVps39) have been suggested to function as the Rab7 GAP and GEF, respectively. We developed an effector pull-down assay to test this model. TBC1D15 functioned as a Rab7 GAP in cells, reducing Rab7 binding to its effector protein RILP, fragmenting the lysosome, and conferring resistance to growth factor withdrawal-induced cell death. In a cellular context, TBC1D15 GAP activity was selective for Rab7. TBC1D15 overexpression did not inhibit transferrin internalization or recycling, Rab7-independent processes that require Rab4, Rab5, and Rab11 activation. TBC1D15 was thus renamed Rab7-GAP. Contrary to expectations for a Rab7 GEF, mVps39 induced lysosomal clustering without increasing Rab7 GTP binding. Moreover, a dominantnegative mVps39 mutant fragmented the lysosome and promoted growth factor independence without decreasing Rab7-GTP levels. These findings suggest that a protein other than mVps39 serves as the Rab7 GEF. In summary, although only TBC1D15/Rab7-GAP altered Rab7-GTP levels, both Rab7-GAP and mVps39 regulate lysosomal morphology and play a role in maintaining growth factor dependence.The small GTPase Rab7 facilitates homotypic and heterotypic fusion reactions between late endosomes and lysosomes (1-3). Inhibiting Rab7 function produces lysosomal fragmentation, confers growth factor independence, and promotes transformation in vitro (4). Autophagy, antigen processing, and pathogen clearance are also Rab7-dependent processes (5-9). Consistent with its key role in maintaining cellular and organismal homeostasis, Rab7 activity is regulated by extrinsic signals (10), most likely through effects on guanine nucleotide exchange factors (GEFs) 2 and GTPase-activating proteins (GAPs). GEFs activate GTPases by facilitating the exchange of GDP for GTP (reviewed in Refs. 11,12). GAPs inactivate GTPases by accelerating the hydrolysis of the bound GTP to GDP. The nucleotide binding state regulates GTPase activity because GTPases only associate with their effector proteins when GTP-bound. Effector proteins produce the responses associated with GTPase activation. Several effector proteins for Rab7 have been identified (13-16). Defining the Rab7 GEF and GAP proteins would provide critical insight into how its function is regulated.Because membrane fusion is frequently studied using purified yeast vacuoles, much is known about the molecules that regulate Ypt7, the Rab7 ortholog in Saccharomyces cerevisiae (17)(18)(19). Gyp7 is the Ypt7 GAP, blocking vacuole fusion by promoting GTP hydrolysis by . The GEF for Ypt7 may be Vps39. Vps39 facilitates nucleotide exchange on Ypt7 in vitro (23). However, in other studies, Vps39 preferentially bound the GTP-bound form of Ypt7 sugge...

Cancer cells are hypersensitive to nutrient limitation because oncogenes constitutively drive glycolytic and tricarboxylic acid (TCA) cycle intermediates into biosynthetic pathways. Because the anaplerotic reactions that replace these intermediates are fueled by imported nutrients, the cancer cell’s ability to generate ATP becomes compromised under nutrient-limiting conditions. In addition, most cancer cells have defects in autophagy, the catabolic process that provides nutrients from internal sources when external nutrients are unavailable. Normal cells, in contrast, can adapt to nutrient stress that kills cancer cells by becoming quiescent and catabolic. We show that FTY720, a water soluble sphingolipid drug that is effective in many animal cancer models, selectively starves cancer cells to death by down-regulating nutrient transporter proteins. Consistent with a bioenergetic mechanism of action, FTY720 induced homeostatic autophagy. Cells were protected from FTY720 by cell permeable nutrients or by reducing nutrient demand, but blocking apoptosis was ineffective. Importantly, AAL-149, an FTY720 analog that lacks FTY720’s dose limiting toxicity, also triggered transporter loss and killed patient-derived leukemias while sparing cells isolated from normal donors. Because they target the metabolic profile of cancer cells rather than specific oncogenic mutations, FTY720 analogs like AAL-149 should be effective against many different tumor types, particularly in combination with drugs that inhibit autophagy.

RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional coactivator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein-protein interactions through a short tryptophancontaining peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39-U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35-U2AF65 and RBM39-SF3b155, the RBM39-UHM-U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM-ULM binding interface, providing a rationale for the known specificity of UHM-ULM interactions. This study therefore establishes a structural basis for specific UHM-ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.

The Rab7 GTPase promotes membrane fusion reactions between late endosomes and lysosomes. In previous studies, we demonstrated that Rab7 inactivation blocks growth factor withdrawal-induced cell death. These results led us to hypothesize that growth factor withdrawal activates Rab7. Here, we show that growth factor deprivation increased both the fraction of Rab7 that was associated with cellular membranes and the percentage of Rab7 bound to guanosine triphosphate (GTP). Moreover, expressing a constitutively GTP-bound mutant of Rab7, Rab7-Q67L, was sufficient to trigger cell death even in the presence of growth factors. This activated Rab7 mutant was also able to reverse the growth factor-independent cell survival conferred by protein kinase C (PKC) delta inhibition. PKCdelta is one of the most highly induced proteins after growth factor withdrawal and contributes to the induction of apoptosis. To evaluate whether PKCdelta regulates Rab7, we first examined lysosomal morphology in cells with reduced PKCdelta activity. Consistent with a potential role as a Rab7 activator, blocking PKCdelta function caused profound lysosomal fragmentation comparable to that observed when Rab7 was directly inhibited. Interestingly, PKCdelta inhibition fragmented the lysosome without decreasing Rab7-GTP levels. Taken together, these results suggest that Rab7 activation by growth factor withdrawal contributes to the induction of apoptosis and that Rab7-dependent fusion reactions may be targeted by signaling pathways that limit growth factor-independent cell survival.

Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. We immunoprecipitated U2AF2 to identify what mRNA transcripts were bound as a function of activation by TCR crosslinking and costimulation. In parallel, mass spectrometry revealed the proteins incorporated into the U2AF2-centered RNA/protein interactome. Molecules that retained interaction with the U2AF2 complex after RNAse treatment were designated as “central” interactome members (CIMs). Mass spectrometry also identified a second class of activation-induced proteins, “peripheral” interactome members (PIMs), that bound to the same transcripts but were not in physical association with U2AF2 or its partners. siRNA knockdown of two CIMs and two PIMs caused changes in activation marker expression, cytokine secretion, and gene expression that were unique to each protein and mapped to pathways associated with key aspects of T cell activation. While knocking down the PIM, SYNCRIP, impacts a limited but immunologically important set of U2AF2-bound transcripts, knockdown of U2AF1 significantly impairs assembly of the majority of protein and mRNA components in the activation-induced interactome. These results demonstrated that CIMs and PIMs, either directly or indirectly through RNA, assembled into activation-induced U2AF2 complexes and play roles in post-transcriptional regulation of genes related to cytokine secretion. These data suggest an additional layer of regulation mediated by the activation-induced assembly of RNA splicing interactomes that is important for understanding T cell activation.