The LIM protein Ajuba promotes adipogenesis by enhancing PPARγ and p300/CBP interaction.

Adipocytes play a vital role in energy homeostasis and adipogenesis is a hierarchically regulated cellular differentiation process, in which the precursor mesenchymal stem cells are differentiated into mature adipocytes. Here, we report Ajuba is an important regulator of adipocyte differentiation by functioning as an obligate co-activator of PPARγ. Ajuba binds the DNA-binding domain of PPARγ via its preLIM region in a ligand-independent manner. Depletion of Ajuba in 3T3-L1 cells decreases PPARγ target gene expression and results in delayed adipogenic differentiation. Conversely, stable overexpression of Ajuba in 3T3-L1 cells increases PPARγ target gene expression and accelerates adipogenic differentiation. Mechanistic investigations demonstrate that Ajuba recruits p300/CBP via its LIM domain and facilitates p300/CBP binding to PPARγ. Moreover, Ajuba, PPARγ, p300/CBP can cooperatively occupy the PPARγ target promoters and concomitantly increases histone acetylation at these loci. Collectively, these data suggest that Ajuba is a co-activator constitutively associated with PPARγ and may be a potential therapeutic target for PPARγ-mediated metabolic disorders.

Characterization of the E-box binding affinity to snag-zinc finger proteins.

Members of the Snail/Gfi-1 domain family of zinc finger proteins are known to recognize the E-box sequence CANNTG, such as that found in the promoter of E-cadherin, however, no studies have shown that the internal "NN" dinucleotides can play a role in different binding affinities. We show via gel shift assays that only the sequences CACCTG and CAGGTG can be recognized more strongly by the SNAG-ZFP members such as Slug, Smuc, Snail, and Scratch while the other combinations of the internal nucleotides were bound weakly. All 16 possible dinucleotide combinations were tested by competition EMSAs to determine their relative binding affinities. The Kd value for the best-binding sequences was approximately 1.25 x 10(-6) M, while the other interactions were less effective. Our study has shown for the first time how different internal dinucleotide combinations of the E-box can be recognized differently by different transcription factors and also sheds light into how this transcription factor binding site may participate in DNA-protein interactions.

Regulating the neoplastic phenotype using engineered transcriptional repressors.

We have applied engineered transcriptional repressors to specifically inhibit disease gene-activated pathways in oncogenesis. We have demonstrated that synthetic repressors combining PAX3 DNA binding domains with different repression domains, KRAB or SNAG, are able to specifically inhibit malignant growth and suppress tumorigenesis in alveolar rhabdomyosarcoma tumor cells transformed by the translocation-derived chimeric transcriptional activator, PAX3-FKHR. We discuss the potential applications of the engineered repressor strategy that relate to target gene analysis, mechanisms of repression, cell regulation, and possible anti-viral and cancer therapy.

Hormone-dependent tumor regression in vivo by an inducible transcriptional repressor directed at the PAX3-FKHR oncogene.

In alveolar rhabdomyosarcomas (ARMSs), a specific chromosomal translocation creates a fusion transcription factor, PAX3-FKHR, that is oncogenic due to transcriptional activation. As a strategy for down-regulation of PAX3-FKHR target genes, we created conditional PAX3 repressors by fusing the PAX3 DNA-binding motifs to the hormone binding domain (HBD) of the estrogen receptor and to the KRAB repression domain. We validated proper expression, specific DNA binding, corepressor interaction, and nuclear localization for the KRAB-PAX3-HBD protein and showed it to be a 4-hydroxytamoxifen-dependent transcriptional repressor of transiently transfected and integrated PAX3 reporters in ARMS cells. We established ARMS cell lines that exhibited stable expression of the conditional PAX3 repressor proteins and used them to down-regulate the malignant growth under low serum or anchorage-independent conditions in a hormone-dependent manner. Terminal deoxynucleotidyl transferase-mediated nick end labeling assays revealed that hormonal activation of the PAX3 repressors induced extensive apoptosis that correlated with down-regulation of BCL-X(L) expression. SCID mice that were engrafted with the KRAB-PAX3-HBD ARMS cell lines and were implanted with 4-hydroxytamoxifen timed-release pellets exhibited suppression of tumor growth and an altered vascularity that was not observed in the control mice. These observations strongly suggest that we have directly repressed the PAX3 target genes that are deregulated by the PAX3-FKHR oncogene in ARMS.

An engineered PAX3-KRAB transcriptional repressor inhibits the malignant phenotype of alveolar rhabdomyosarcoma cells harboring the endogenous PAX3-FKHR oncogene.

The t(2;13) chromosomal translocation in alveolar rhabdomyosarcoma tumors (ARMS) creates an oncogenic transcriptional activator by fusion of PAX3 DNA binding motifs to a COOH-terminal activation domain derived from the FKHR gene. The dominant oncogenic potential of the PAX3-FKHR fusion protein is dependent on the FKHR activation domain. We have fused the KRAB repression module to the PAX3 DNA binding domain as a strategy to suppress the activity of the PAX3-FKHR oncogene. The PAX3-KRAB protein bound PAX3 target DNA sequences and repressed PAX3-dependent reporter plasmids. Stable expression of the PAX3-KRAB protein in ARMS cell lines resulted in loss of the ability of the cells to grow in low-serum or soft agar and to form tumors in SCID mice. Stable expression of a PAX3-KRAB mutant, which lacks repression function, or a KRAB protein alone, lacking a PAX3 DNA binding domain, failed to suppress the ARMS malignant phenotype. These data suggest that the PAX3-KRAB repressor functions as a DNA-binding-dependent suppressor of the transformed phenotype of ARMS cells, probably via competition with the endogenous PAX3-FKHR oncogene and repression of target genes required for ARMS tumorigenesis. The engineered repressor approach that directs a transcriptional repression domain to target genes deregulated by the PAX3-FKHR oncogene may be a useful strategy to identify the target genes critical for ARMS tumorigenesis.

Exogenous cdk4 overcomes reduced cdk4 RNA and inhibition of G1 progression in hematopoietic cells expressing a dominant-negative CBF - a model for overcoming inhibition of proliferation by CBF oncoproteins.

Core Binding Factor (CBF) is required for the development of definitive hematopoiesis, and the CBF oncoproteins AML1-ETO, TEL-AML1, and CBFbeta-SMMHC are commonly expressed in subsets of acute leukemia. CBFbeta-SMMHC slows the G1 to S cell cycle transition in hematopoietic cells, but the mechanism of this effect is uncertain. We have sought to determine whether inhibition of CBF-mediated trans-activation is sufficient to slow proliferation. We demonstrate that activation of KRAB-AML1-ER, a protein containing the AML1 DNA-binding domain, the KRAB repression domain, and the Estrogen receptor ligand binding domain, also slows G1, if its DNA-binding domain is intact. Also, exogenous AML1 overcame CBFbeta-SMMHC-induced inhibition of proliferation. Representational difference analysis (RDA) identified cdk4 RNA expression as an early target of KRAB-AML1 activation. Inhibition of CBF activities by KRAB-AML1-ER or CBFbeta-SMMHC rapidly reduced endogenous cdk4 mRNA levels, even in cells proliferating at or near control rates as a result of exogenous cdk4 expression. Over-expression of cdk4, especially a variant which cannot bind p16INK4a, overcame cell cycle inhibition resulting from activation of KRAB-AML1-ER, although cdk4 did not accelerate proliferation when expressed alone. These findings indicate that mutations which alter the expression of G1 regulatory proteins can overcome inhibition of proliferation by CBF oncoproteins. Oncogene (2000).

KAP-1 corepressor protein interacts and colocalizes with heterochromatic and euchromatic HP1 proteins: a potential role for Krüppel-associated box-zinc finger proteins in heterochromatin-mediated gene silencing.

Krüppel-associated box (KRAB) domains are present in approximately one-third of all human zinc finger proteins (ZFPs) and are potent transcriptional repression modules. We have previously cloned a corepressor for the KRAB domain, KAP-1, which is required for KRAB-mediated repression in vivo. To characterize the repression mechanism utilized by KAP-1, we have analyzed the ability of KAP-1 to interact with murine (M31 and M32) and human (HP1alpha and HP1gamma) homologues of the HP1 protein family, a class of nonhistone heterochromatin-associated proteins with a well-established epigenetic gene silencing function in Drosophila. In vitro studies confirmed that KAP-1 is capable of directly interacting with M31 and hHP1alpha, which are normally found in centromeric heterochromatin, as well as M32 and hHP1gamma, both of which are found in euchromatin. Mapping of the region in KAP-1 required for HP1 interaction showed that amino acid substitutions which abolish HP1 binding in vitro reduce KAP-1 mediated repression in vivo. We observed colocalization of KAP-1 with M31 and M32 in interphase nuclei, lending support to the biochemical evidence that M31 and M32 directly interact with KAP-1. The colocalization of KAP-1 with M31 is sometimes found in subnuclear territories of potential pericentromeric heterochromatin, whereas colocalization of KAP-1 and M32 occurs in punctate euchromatic domains throughout the nucleus. This work suggests a mechanism for the recruitment of HP1-like gene products by the KRAB-ZFP-KAP-1 complex to specific loci within the genome through formation of heterochromatin-like complexes that silence gene activity. We speculate that gene-specific repression may be a consequence of the formation of such complexes, ultimately leading to silenced genes in newly formed heterochromatic chromosomal environments.

Mechanism-Based Inhibitors: Development of a High Throughput Coupled Enzyme Assay to Screen for Novel Antimalarials.

Identifying potent enzyme inhibitors through a robust HTS assay is currently thought to be the most efficient way of searching for lead molecules. We have developed a HTS assay that mimics a crucial step in an essential metabolic pathway, the purine salvage pathway of the malarial parasite Plasmodium falciparum. In this assay we have used purified recombinant enzymes: hypoxanthine guanine phosphoribosyl transferase (HGPRT) and inosine monophosphate dehydrogenase (IMPDH) from the malarial parasite and the human host, respectively. These two enzymes, which work in tandem, are used to set up a coupled assay that is robust enough to meet the stringent criteria of an HTS assay. In the first phase of our screen we seem to have identified novel inhibitors that kill the parasite by inhibiting the salvage pathway of the parasite.

Structural characterization and fine chromosomal mapping of the human P2Y1 purinergic receptor gene (P2RY1).

Using P2Y1 specific oligonucleotide primers in a Polymerase Chain Reaction on human genomic DNA, we have amplified a region encoding the P2Y1 receptor Restriction analysis and Southern hybridization of the PCR product revealed that the entire open reading frame of the human P2Y1 receptor is coded by an intronless gene. We have previously localized the P2Y1 receptor gene to human chromosome 3. The gene was further localized to a region of chromosome 3 using a subchromosomal hybrid panel containing different segments of chromosome 3. Based on the specific PCR product obtained and its Southern hybridization to the human P2Y1 receptor cRNA, the P2Y1 receptor gene was mapped to human chromosome 3q25.

Identification and characterization of a generic DNA probe capable of detecting plasmodial infections in blood.

DNA-based detection systems are being rapidly adapted for diagnostic technologies. The currently available non-radioactive DNA techniques for malaria detection are primarily based on probes which are species-specific. The major requirement of a cross-species (generic) diagnostics is the identification of an universal probe which is long enough to be used in either PCR amplification or solid state capture of the hybrids, the two principal techniques currently used in the field of non-radioactive DNA detection. This paper describes a DNA sequence (pARC 178), originally obtained from P. falciparum genomic library, which is also present in other malarial species. Southern-blot analysis indicates that this sequence is derived from a repetitive DNA element. This DNA fragment encodes for a small RNA species of approximately 120 bases. PCR primers based on this sequence amplifies the expected size (157 bp) product from the genomic DNA isolated from P. falciparum, P. vivax, P. berghei, P. yoelii, P. vinckei and P. chabaudi thus confirming its generic nature. The utility of this probe is further demonstrated by its capability in successfully detecting P. falciparum and P. vivax infections in clinical samples when used in a PCR assay.

Molecular cloning of a novel P2 purinoceptor from human erythroleukemia cells.

Screening of a human erythroleukemia cell cDNA library with radiolabeled chicken P2Y3 cDNA at low stringency revealed a cDNA clone encoding a novel G protein-coupled receptor with homology to P2 purinoceptors. This receptor, designated P2Y7, has 352 amino acids and shares 23-30% amino acid identity with the P2Y1-P2Y6 purinoceptors. The P2Y7 cDNA was transiently expressed in COS-7 cells: binding studies thereon showed a very high affinity for ATP (37 +/- 6 nM), much less for UTP and ADP (approximately 1300 nM), and a novel rank order of affinities in the binding series studied of 8 nucleotides and suramin. The P2Y7 receptor sequence appears to denote a different subfamily from that of all the other known P2Y purinoceptors, with only a few of their characteristic sequence motifs shared. The P2Y7 receptor mRNA is abundantly present in the human heart and the skeletal muscle, moderately in the brain and liver, but not in the other tissues tested. The P2Y7 receptor mRNA was also abundantly present in the rat heart and cultured neonatal rat cardiomyocytes. The P2Y7 receptor is functionally coupled to phospholipase C in COS-7 cells transiently expressing this receptor. The P2Y7 gene was shown to be localized to human chromosome 14. We have thus cloned a unique member of the P2Y purinoceptor family which probably plays a role in the regulation of cardiac muscle contraction.

Cloning and chromosomal localization of the human P2Y1 purinoceptor.

We have isolated two types of human P2Y1 cDNA clones from the human erythro leukemia cell cDNA library. The sequence of both clones codes for the same 373 amino acid polypeptide and these clones differ only in the length of the 3' untranslated region. The long form of the cDNA has 1165 nt 3' untranslated region while the 3' untranslated region in the short form is only 258 nt. Both forms are, however, polyadenylated. A multiple human tissue northern blot indicated two transcripts of approximately 4.4 kb and 7.0 kb. The 4.4 kb mRNA is present in all the eight tissues, while the approximately 7.0 kb transcript is expressed only in placenta, skeletal muscle, and pancreas. Using oligonucleotide primers specific for the human P2Y1 purinergic receptor to amplify a region from genomic DNA from a panel of mouse/human somatic cell hybrid cell lines, we have localized the P2Y1 gene to human chromosome 3.

Development of specific DNA probes and their usage in the detection of Plasmodium vivax infection in blood.

The application of nucleic acid probes, in the detection of pathogenic micro-organisms, has become an integral part of diagnostic technologies. In this study, Plasmodium vivax-specific DNA probes have been identified by carrying out genomic subtractive hybridization. In this approach, the recombinant clones from a P. vivax genomic library are screened with radiolabelled human and P. falciparum DNA. The colonies which react with labelled P. falciparum and human DNA are eliminated and those which do not produce any autoradiographic signal have been subjected to further screening procedures. Three P. vivax specific DNA probes have been obtained by these repeated screenings. Further analyses indicate that these probes are specific and sensitive enough to detect P. vivax infection in clinical blood samples when used in a non-radioactive DNA hybridization assay.

A non-radioactive DNA diagnostic procedure for the detection of malarial infection: general application to genome with repetitive sequences.

A novel non-radioactive DNA diagnostic method has been developed to detect Plasmodium falciparum infection in whole blood. In this method a drop of blood from a finger prick is added to a lysing solution containing a biotinylated oligonucleotide whose sequence design is based on the repeated sequence of the parasite genome. The mixture is heated in a boiling water bath and then added to a microtitre plate where the 'target-bioprobe hybrids' are captured by the immobilized oligonucleotides. The plate is then washed to remove the coloured material and the biotinylated oligonucleotide retained on the plate is assayed by streptavidin-alkaline phosphatase conjugate. This method has also been tested in field trials by double-blind studies to detect P.falciparum infection in blood samples. Results indicate that this method is superior to the classical blood smear examination for its speed and its ease in large epidemiological surveys and is especially useful in identifying clinical malaria in endemic areas where the semi-immune population predominates. The method described can be of general application for the detection of any foreign pathogen in blood, other body fluids and tissue samples, provided the DNA probe employed constitutes a part of the repeated sequence of the genome and is unique.