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The transmembrane receptor CD44 conveys important signals from the extracellular microenvironment to the cytoplasm, a phenomena known as "outside-in" signaling. CD44 exists as several isoforms that result from alternative splicing, which differ only in the extracellular domain but yet exhibit different activities. CD44 is a binding partner for the membrane-cytoskeleton cross-linker protein ezrin. In this study, we demonstrate that only CD44 standard (CD44s) colocalizes and interacts with the actin cross-linkers ezrin and moesin using well-characterized cell lines engineered to express different CD44 isoforms. Importantly, we also show that the association CD44s-ezrin-actin is an important modulator of Fas-mediated apoptosis. The results highlight a mechanism by which signals from the extracellular milieu regulate intracellular signaling activities involved in programmed cell death.

Artificial endonucleases consisting of a Fokl cleavage domain tethered to engineered zinc-finger DNA-binding proteins have proven useful for stimulating homologous recombination in a variety of cell types. Because the catalytic domain of zinc-finger nucleases (ZFNs) must dimerize to become active, two subunits are typically assembled as heterodimers at the cleavage site. The use of ZFNs is often associated with significant cytotoxicity, presumably due to cleavage at off- target sites. Here we describe a structure- based approach to reducing off- target cleavage. Using in silico protein modeling and energy calculations, we increased the specificity of target site cleavage by preventing homodimerization and lowering the dimerization energy. Cell-based recombination assays confirmed that the modified ZFNs were as active as the original ZFNs but elicit significantly less genotoxicity. The improved safety profile may facilitate therapeutic application of the ZFN technology.

Novel highly potent CXCR4 inhibitors with good pharmacokinetic properties were designed and optimized starting from the naturally occurring beta-hairpin peptide polyphemusin II. The design involved incorporating important residues from polyphemusin II into a macrocyclic template-bound beta-hairpin mimetic. Using a parallel synthesis approach, the potency and ADME properties of the mimetics were optimized in iterative cycles, resulting in the CXCR4 inhibitors POL2438 and POL3026. The inhibitory potencies of these compounds were confirmed in a series of HIV-1 invasion assays in vitro. POL3026 showed excellent plasma stability, high selectivity for CXCR4, favorable pharmacokinetic properties in the dog, and thus has the potential to become a therapeutic compound for application in the treatment of HIV infections (as an entry inhibitor), cancer (for angiogenesis suppression and inhibition of metastasis), inflammation, and in stem cell transplant therapy.

Peptidyl–prolyl isomerases (PPIase) facilitate the cis–trans interconversion of the peptidyl–prolyl bond and in such way affect protein folding. Pin1 is a PPIase, which specifically recognizes phosphorylated S/T-P bonds. The transcription factor TFIIH mediates phosphorylation of the retinoic acid receptor alpha (RARα) at position Ser 77 . In the presence of retinoic acid ligand (RA), the Ser 77 non-phosphorylated receptor is suggested to undergo degradation through the proteasome pathway. Here we provide evidence that Pin1 is able to selectively destabilize RARα in a ligand independent-manner. We show that this is caused by RARα ubiquitination, which in turn is phosphorylation dependent. The single mutation Ser 77 >A completely abolishes RARα degradation whereas the mutation Ser 77 >E rescues this effect. In addition, we correlate RARα stability to Ser 77 phosphorylation required for the ligand independent transcriptional activity on fgf8 promoter. Finally, we show that the ligand-independent Ser 77 phosphorylation requires the genuine ligand-binding domain.

Dicer is a multi-domain RNase III-related endonuclease responsible for processing double-stranded RNA (dsRNA) to small interfering RNAs (siRNAs) during a process of RNA interference (RNAi). It also catalyses excision of the regulatory microRNAs from their precursors. In this work, we describe the purification and properties of a recombinant human Dicer. The protein cleaves dsRNAs into approximately 22 nucleotide siRNAs. Accumulation of processing intermediates of discrete sizes, and experiments performed with substrates containing modified ends, indicate that Dicer preferentially cleaves dsRNAs at their termini. Binding of the enzyme to the substrate can be uncoupled from the cleavage step by omitting Mg(2+) or performing the reaction at 4 degrees C. Activity of the recombinant Dicer, and of the endogenous protein present in mammalian cell extracts, is stimulated by limited proteolysis, and the proteolysed enzyme becomes active at 4 degrees C. Cleavage of dsRNA by purifed Dicer and the endogenous enzyme is ATP independent. Additional experiments suggest that if ATP participates in the Dicer reaction in mammalian cells, it might be involved in product release needed for the multiple turnover of the enzyme.

More than 100 copper/zinc superoxide dismutase 1 (SOD1) genetic mutations have been characterized. These mutations lead to the death of motor neurons in ALS. In its native form, the SOD1 protein is expressed as a homodimer in the cytosol. In vitro studies have shown that SOD1 mutations impair the dimerization kinetics of the protein, and in vivo studies have shown that SOD1 forms aggregates in patients with familial forms of ALS. In this study, we analyzed WT SOD1 and 9 mutant (mt) forms of the protein by non-invasive fluorescence techniques. Using microscopic techniques such as fluorescence resonance energy transfer, fluorescence complementation, image-based quantification, and fluorescence correlation spectroscopy, we studied SOD1 dimerization, oligomerization, and aggregation. Our results indicate that SOD1 mutations lead to an impairment in SOD1 dimerization and, subsequently, affect protein aggregation. We also show that SOD1 WT and mt proteins can dimerize. However, aggregates are predominantly composed of SOD1 mt proteins.

In eukaryotes, double-stranded (ds) RNA induces sequence-specific inhibition of gene expression, referred to as RNA interference (RNAi). In invertebrates, RNAi can be triggered effectively by either long dsRNAs or 21- to 23-nt-long short interfering (si) duplex RNAs, acting as effectors of RNAi. siRNAs recently have been shown to act as potent inducers of RNAi in cultured mammalian cells. However, studies of RNAi activated by long dsRNA are impeded by its nonspecific effects, mediated by dsRNA-dependent protein kinase PKR and RNase L. Here, we report that the RNAi response can be induced effectively by long dsRNA in nondifferentiated mouse cells grown in culture. Transfection of dsRNA into embryonal carcinoma (EC) P19 and F9 cells results in a sequence-specific decrease in the level of proteins expressed from either exogenous or endogenous genes. dsRNA-mediated inhibition of the reporter gene also occurs in mouse embryonic stem cells. The RNAi effect is mediated by siRNAs, which are generated by cleavage of dsRNA by the RNaseIII-like enzyme, Dicer. We demonstrate that extracts prepared from EC cells catalyze processing of dsRNA into ≈23-nt fragments and that Dicer localizes to the cytoplasm of EC and HeLa cells.

Retinoic acid (RA) is described as an inhibitor of prostate cancer cell growth. We utilized reverse transcription-polymerase chain reaction (RT-PCR) to analyze expression of different isoforms of fibroblast growth factor 8 (FGF8) in response to RA. Results in the prostate cancer cell line LNCaP show that whereas overall expression levels of FGF8 appear to remain constant, RA addition induces an inversion of the ratio between FGF8a and -b mRNAs. Along with this observed "isoform switch," unexpected expression of retinoic acid receptor alpha was detected. Although preliminary, these data allow one to hypothesize on the existence of a possible link between the morphogenic hormone RA and the regulation of the potent mitogen FGF8.

The main transcriptional regulator of the human immunodeficiency virus, the Tat protein, recognizes and binds to a small structured RNA element at the 5' end of every viral mRNA, termed TAR. On the basis of published structural data of the molecular interactions between TAR and Tat-related peptides, we defined requirements for potential low-molecular weight inhibitors of TAR recognition by the Tat protein. In accordance with the resulting concept, a series of compounds was synthesized. In vitro evaluation of their potential to directly interfere with Tat-TAR interaction was used to define a new chemical class of potent Tat antagonistic substances. The most active compound competed with Tat-TAR complexation with a competition dose CD50 of 22 nM in vitro and blocked HIV expression in a cellular Tat transactivation system with an IC50 of 1.2 microM. The close relation between structural features of the interaction between TAR and a new type of inhibitory agent, "In-PRiNts" (for inhibitor of protein-ribonucleotide sequences), such as CGP 40336A and those of the Tat-TAR complex was confirmed by RNase A footprinting and by two-dimensional NMR. Structural implications for the complex between this class of compounds and TAR RNA will be presented.

International audience; Classical target-based, high-throughput screening has been useful for the identification of inhibitors for known molecular mechanisms involved in the HIV life cycle. In this study, the development of a cell-based assay that uses a phenotypic drug discovery approach based on automated high-content screening is described. Using this screening approach, the antiviral activity of 26,500 small molecules from a relevant chemical scaffold library was evaluated. Among the selected hits, one sulfonamide compound showed strong anti-HIV activity against wild-type and clinically relevant multidrug resistant HIV strains. The biochemical inhibition, point resistance mutations and the activity of structural analogs allowed us to understand the mode of action and propose a binding model for this compound with HIV-1 reverse transcriptase.

665 M/S n° 6-7, vol. 18, juin-juillet 2002 > Le dosage de l’expression des genes est essentiel au bon fonctionnement cellulaire ainsi qu’au developpement et au maintien des organismes pluricellulaires. De fait, des mecanismes biologiques permettent d’activer ou de reprimer l’expression des genes sans affecter l’integrite du support de l’information genetique. Au cours des dernieres annees, les biologistes se sont notamment interesses aux phenomenes epigenetiques aboutissant a la repression de l’expression d’un gene. Ces regulations negatives, qui affectent aussi bien la transcription (TGS : inhibition epigenetique de la transcription) que les processus subsequents de l’expression des genes (stabilite des ARN messagers, PTGS : inhibition epigenetique post-transcriptionelle), sont communes a tous les eucaryotes [1]. Parmi les approches qui permettent d’etudier la fonction proprement dite d’un gene, l’une d’entre elles consiste a supprimer l’expression de ce dernier, dans des cellules ou dans un organisme. De nouvelles techniques, comme l’interference par ARN (ARNi [2]), fondees sur l’utilisation d’ARN double brin (ARNdb), sont en voie de developpement. La reaction ARNi detourne des enzymes impliquees dans le metabolisme d’ARNdb produits par les virus et les transposons. En effet, ces ARNdb de grande taille induisent des mecanismes cellulaires antiviraux ou des phenomenes de regulation de la transposition (Figure 1A). La reaction cellulaire met en jeu au niveau nucleaire des enzymes (ADAR, adenosine desaminase) capables de desaminer en inosine les adenines de l’ARNdb [3]. Ces modifications induisent la destructuration des ARNdb et la separation des deux brins d’ARN, ARN interference dans les cellules de mammiferes

The recent development of artificial endonucleases with tailored specificities has opened the door for a wide range of new applications, including the correction of mutated genes directly in the chromosome. This kind of gene therapy is based on homologous recombination, which can be stimulated by the creation of a targeted DNA double-strand break (DSB) near the site of the desired recombination event. Artificial nucleases containing zinc finger DNA-binding domains have provided important proofs of concept, showing that inserting a DSB in the target locus leads to gene correction frequencies of 1-18% in human cells. In this paper, we describe how zinc finger nucleases are assembled by polymerase chain reaction (PCR) and present two methods to assess these custom nucleases quickly in vitro and in a cell-based recombination assay.

The recent development of artificial endonucleases with tailored specificities has opened the door for a wide range of new applications, including the correction of mutated genes directly in the chromosome. This kind of gene therapy is based on homologous recombination, which can be stimulated by the creation of a targeted DNA double-strand break (DSB) near the site of the desired recombination event. Artificial nucleases containing zinc finger DNA-binding domains have provided important proofs of concept, showing that inserting a DSB in the target locus leads to gene correction frequencies of 1-18% in human cells. In this paper, we describe how zinc finger nucleases are assembled by polymerase chain reaction (PCR) and present two methods to assess these custom nucleases quickly in vitro and in a cell-based recombination assay.

Novel, highly potent CXCR4 inhibitors with good pharmacokinetic properties were obtained by applying PEM technology starting from the naturally occurring ?-hairpin peptide polyphemusin II. The design involved incorporation of key residues from polyphemusin II into a macrocyclic template-bound ?-hairpin mimetic. Using a parallel synthesis approach, the potency and ADME properties of the mimetics were optimized, resulting in CXCR4 inhibitors such as POL2438 and POL3026. Their activities were confirmed in a series of in vitro HIV-1 infection assays. Besides high selectivity for CXCR4, POL3026 had excellent plasma stability and favorable pharmacokinetic properties in dogs. In a murine model POL3026 was highly efficacious in hematopoietic stem cell mobilization. Hence, PEM-based CXCR4 inhibitors have the potential to become therapeutic agents for the treatment of HIV infections (as entry inhibitor), cancer (e.g. for inhibition of metastasis), stem cell transplant and inflammation.

Human immunodeficiency virus 1 (HIV-1) multiplication depends on a cellular protein, cyclophilin A (CyPA), that gets integrated into viral particles. Because CyPA is not required for cell viability, we attempted to block its synthesis in order to inhibit HIV-1 replication. For this purpose, we used antisense U7 small nuclear RNAs (snRNAs) that disturb CyPA pre-mRNA splicing and short interfering RNAs (siRNAs) that target CyPA mRNA for degradation. With dual-specificity U7 snRNAs targeting the 3' and 5' splice sites of CyPA exons 3 or 4, we obtained an efficient skipping of these exons and a strong reduction of CyPA protein. Furthermore, short interfering RNAs targeting two segments of the CyPA coding region strongly reduced CyPA mRNA and protein levels. Upon lentiviral vector-mediated transduction, prolonged antisense effects were obtained for both types of antisense RNAs in the human T-cell line CEM-SS. These transduced CEM-SS cells showed a delayed, and for the siRNAs also reduced, HIV-1 multiplication. Since the two types of antisense RNAs function by different mechanisms, combining the two approaches may result in a synergistic effect.

We previously reported that retinoids were inducing a complete switch in the expression of two isoforms from the fgf8 gene. In order to gain insight into the transcriptional mechanisms possibly involved in this regulation, we cloned and sequenced a fragment of genomic DNA encompassing 6 kb of the region 5' upstream of the fgf8 coding sequence and investigated its promoter elements. A comprehensive series of biochemical and cellular experiments determined two distinct functional regions cis-responsive to retinoids and/or their receptors: (i) a canonical RARE (type DR2) which is the cis target of a RARalpha-RXRalpha liganded heterodimer; and (ii) a completely novel type of response element composed of two half-binding sites separated by 87 nucleotides, which we demonstrate to be the target of an unliganded RARalpha homodimer phosphorylated on the Ser77 residue. Combined activities of these cis and trans-acting factors support a model of a complex regulation of fgf8 expression: by alternative binding to two distinct promoter elements, phosphorylated-unliganded-RARalpha homodimer or its liganded form have two distinct and mutually exclusive trans-activating activities, explaining the expression of two different isoforms of fgf8.

Claims about molecular mechanisms underlying the resistance to anti-hormones of prostate cancer cells find support in biological experiments, which involve hormone-independent activation of the androgen receptor's (AR) transcriptional activity. In order to test this hypothesis, we attempted to shut down the expression of AR by the means of target-directed antisense oligonucleotides. A set of 49 oligonucleotides matching sequences of the AR mRNA either in the coding sequence or in the 3' and 5' untranslated regions were synthesized and examined in a cellular AR-dependent reporter system. Five antisense oligonucleotides were identified as highly potent inhibitors of AR-driven gene expression in a cellular reporter assay. These five were further profiled using point-mutated control sequences for the assessment of AR inhibition. In addition the expression of another AR-driven gene, the modulator of PSA expression (gene for inhibition of prostate specific antigen, an endogenous, AR-driven gene) was examined. Finally, we observed that the hormone-independent but AR-mediated transactivation by IGF-1 could also be specifically shut-down by these antisense oligonucleotides. The selection of highly target-restricted antisense oligonucleotides in the prostate cancer cell line LNCaP provided tools to study a central role of the androgen receptor in growth regulation of prostatic cancer cell lines and could be of utility in cancer situations in vivo.

Correction of the genetic mutations that underlie genetic diseases remains an essential goal of gene therapy. Repair by homologous recombination (HR) is a promising therapeutic strategy. In mammalian cells, HR is a rare event that can be stimulated by creating a double strand break (DSB) near the site to be modified. A DSB at specific genomic location can be accomplished using customized zinc finger proteins fused to a FokI endonuclease catalytic domain (ZFP-FOKI). To target non-palindromic sequences, two ZFPs engineered for distinct sequences are needed. Only the asymmetric complex involving the two ZFP-FOKI proteins is able to catalyze DNA cleavage at the specific non-palindromic sequence. To analyze and optimize ZFP-FOKI fusion protein activity in mammalian cells, we developed a cellular assay based on co-transfection of a plasmid- based single strand annealing (SSA) recombination substrate. The DSB generated by ZFP-FOKI at the specific site, allows restoration of luciferase reporter gene activity by homologous recombination. Here we report the development of an assay system to analyze ZFP-FOKI protein activity and toxicity in mammalian cells. Using an inverted gradient concentration of vectors expressing ZFP-FOKI, we are able to characterize conditions for optimal activity of the asymmetric complex and toxicity of the expressed ZFP-FOKI proteins.