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PubMed2002

Aceruloplasminemia: new clinical, pathophysiological and therapeutic insights.

Aceruloplasminemia is an autosomal recessive disease of iron overload associated with mutation(s) in the ceruloplasmin gene. We report here a new case of aceruloplasminemia in a woman who is a compound heterozygote for two new mutations. Besides this novel genotypic profile, this observation provides new insights on: (i) iron metabolism with normal erythroid repartition, in the absence of serum non-transferrin-bound iron and with an increase of 59Fe plasma clearance; (ii) hepatic abnormalities associated with the presence of iron-free foci; (iii) the therapeutic management of the disease, chronic subcutaneous infusion of deferrioxamine being remarkably effective at reducing hepatic iron overload.

Ceruloplasmin↗
PubMed2002

Rett syndrome. Current status and new vistas.

RS, the most common cause of profound cognitive impairment in girls and women, is composed of characteristic clinical features, including communication dysfunction, stereotypic movements, and pervasive growth failure. Neuropathologic findings indicate a failure of neuronal maturation with too small neurons and too few dendritic arbors and no evidence of a progressive neurodegenerative process. The combination of clinical and neuropathologic characteristics presents the profile of a neurodevelopmental disorder. Mutations in the gene MECP2, which encodes MeCP2, have been identified in 80% to 85% of girls and women with RS. Furthermore, the panorama of phenotypes with MECP2 mutations now extends far beyond RS to include normal girls and women, mild learning disability, autistic spectrum disorders, and X-linked mental retardation. These rapid advances in our understanding of RS over the past three decades have opened new avenues of study in developmental neurobiology.

Adult↗
PubMed2000

Role of side-chains in the cooperative beta-hairpin folding of the short C-terminal fragment derived from streptococcal protein G.

A short C-terminal fragment of immunoglobulin-binding domain of streptococcal protein G is known to form nativelike beta-hairpin at physiological conditions. To understand the cooperative folding of the short peptide, eight Ala-substituted mutants of the fragment were investigated with respect to their structural stabilities by analyzing temperature dependence of NMR signals. On comparison of the obtained thermodynamic parameters, we found that the nonpolar residues Tyr45 and Phe52 and the polar residues Asp46 and Thr49 are crucial for the beta-hairpin folding. The results suggest a strong interaction between the nonpolar side chains that participates in a putative hydrophobic cluster and that the polar side chains form a fairly rigid conformation around the loop (46-51). We also investigated the complex formation of the mutants with N-terminal fragment at the variety of temperature to get their thermal unfolding profiles and found that the mutations on the residues Asp46 and Thr49 largely destabilized the complexes, while substitution of Asp47 slightly stabilized the complex. From these results, we deduced that both the hydrophobic cluster formation and the rigidity of the loop (46-51) cooperatively stabilize the beta-hairpin structure of the fragment. These interactions which form a stable beta-hairpin may be the initial structural scaffold which is important in the early folding events of the whole domain.

Amino Acid Substitution↗
PubMed2002

Beyond the proton abstracting role of Glu-376 in medium-chain acyl-CoA dehydrogenase: influence of Glu-376-->Gln substitution on ligand binding and catalysis.

The active site residue, Glu-376, of medium-chain acyl-CoA dehydrogenase (MCAD) has been known to abstract the alpha-proton from acyl-CoA substrates during the course of the reductive half-reaction. The site-specific mutation of Glu-376-->Gln(E376Q) slows down the octanoyl-CoA-dependent reductive half-reaction of the enzyme by about 5 orders of magnitude due to impairment in the proton-transfer step. To test whether the carboxyl group of Glu-376 exclusively serves as the active site base (for abstracting the alpha-proton) during the enzyme catalysis, we undertook a detailed kinetic investigation of the enzyme-ligand interaction and enzyme catalysis, utilizing octanoyl-CoA/octenoyl-CoA as a physiological substrate/product pair and the wild-type and E376Q mutant enzymes as the catalysts. The transient kinetic data revealed that the E376Q mutation not only impaired the rate of octanoyl-CoA-dependent reduction of the enzyme-bound FAD, but also impaired the association and dissociation rates for the binding of the reaction product, octenoyl-CoA. Besides, the E376Q mutation correspondingly impaired the kinetic profiles for the quenching of the intrinsic protein fluorescence during the course of the above diverse (i.e., "chemistry" versus "physical interaction") processes. A cumulative account of the experimental data led to the suggestion that the carboxyl group of Glu-376 of MCAD is intimately involved in modulating the microscopic environment (protein conformation) of the enzyme's active site during the course of ligand binding and catalysis. Arguments are presented that the electrostatic interactions among Glu-376, FAD, and CoA-ligands are responsible for structuring the enzyme's active site cavity in the ground and transition states of the enzyme during the above physicochemical processes.

Acyl Coenzyme A↗
PubMed1999

Catalytic acid/base residues of glutamate racemase.

Glutamate racemase is a cofactor-independent enzyme that employs two active-site cysteine residues as acid/base catalysts during the interconversion of glutamate enantiomers. In a given reaction direction, a thiolate from one of the cysteines abstracts the alpha-proton, and the other cysteine thiol delivers a proton to the opposite face of the resulting carbanionic intermediate. This paper reports that the C73S and C184S mutants are still capable of racemizing glutamate with specificity constants about 10(3)-fold lower than those of the wild-type enzyme. A "one-base requiring" reaction, the elimination of water from N-hydroxyglutamate, has been used to deduce which thiol acts as the base for a given enantiomer. With D-N-hydroxyglutamate the C73S mutant is a much poorer catalyst than wild-type enzyme, whereas the C184S mutant is a somewhat better catalyst. This trend was reversed with L-N-hydroxyglutamate, suggesting that Cys73 is responsible for the deprotonation of D-glutamate and Cys184 is responsible for the deprotonation of L-glutamate. In addition, with C73S the Vmax/KM isotope effect on D-glutamate racemization was greater than that seen with wild-type enzyme, whereas the isotope effect with L-glutamate had decreased. The results were reversed with the C184S mutant. This is interpreted as being due to an asymmetry in the free energy profiles that is induced upon mutation, with the deprotonation step involving a serine becoming the more cleanly rate-determining of the two. These results support the above assignment and the notion that a carbanionic intermediate is formed during catalysis.

Amino Acid Isomerases↗
PubMed2003

Evidence that a single nucleotide polymorphism in the promoter of the G protein receptor kinase 3 gene is associated with bipolar disorder.

In a genome-wide linkage survey, we have previously shown evidence suggesting that the chromosome 22q12 region contains a susceptibility locus for bipolar disorder (BPD). Two independent family sets yielded lod scores suggestive of linkage at markers in this region near the gene G protein receptor kinase 3 (GRK3). GRK3 is an excellent candidate risk gene for BPD since GRK3 is expressed widely in the brain, and since GRKs play key roles in the homologous desensitization of G protein-coupled receptor signaling. We have also previously shown GRK3 expression to be induced by amphetamine in an animal model of mania using microarray-based expression profiling. To identify possible functional mutations in GRK3, we sequenced the putative promoter region, all 21 exons, and intronic sequence flanking each exon, in 14-22 individuals with BPD. We found six sequence variants in the 5'-UTR/promoter region, but no coding or obvious splice variants. Transmission disequilibrium analyses of one set of 153 families indicated that two of the 5'-UTR/promoter variants are associated with BPD in families of northern European Caucasian ancestry. A supportive trend towards association to one of these two variants (P-5) was then subsequently obtained in an independent sample of 237 families. In the combined sample, the P-5 variant had an estimated allele frequency of 3% in bipolar subjects, and displayed a transmission to non-transmission ratio of 26 : 7.7 (chi(2)=9.6, one-sided P value=0.0019). Altogether, these data support the hypothesis that a dysregulation in GRK3 expression alters signaling desensitization, and thereby predisposes to the development of BPD.

Animals↗
PubMed2005

The coenzyme specificity of Candida tenuis xylose reductase (AKR2B5) explored by site-directed mutagenesis and X-ray crystallography.

CtXR (xylose reductase from the yeast Candida tenuis; AKR2B5) can utilize NADPH or NADH as co-substrate for the reduction of D-xylose into xylitol, NADPH being preferred approx. 33-fold. X-ray structures of CtXR bound to NADP+ and NAD+ have revealed two different protein conformations capable of accommodating the presence or absence of the coenzyme 2'-phosphate group. Here we have used site-directed mutagenesis to replace interactions specific to the enzyme-NADP+ complex with the aim of engineering the co-substrate-dependent conformational switch towards improved NADH selectivity. Purified single-site mutants K274R (Lys274-->Arg), K274M, K274G, S275A, N276D, R280H and the double mutant K274R-N276D were characterized by steady-state kinetic analysis of enzymic D-xylose reductions with NADH and NADPH at 25 degrees C (pH 7.0). The results reveal between 2- and 193-fold increases in NADH versus NADPH selectivity in the mutants, compared with the wild-type, with only modest alterations of the original NADH-linked xylose specificity and catalytic-centre activity. Catalytic reaction profile analysis demonstrated that all mutations produced parallel effects of similar magnitude on ground-state binding of coenzyme and transition state stabilization. The crystal structure of the double mutant showing the best improvement of coenzyme selectivity versus wild-type and exhibiting a 5-fold preference for NADH over NADPH was determined in a binary complex with NAD+ at 2.2 A resolution.

Adenosine↗
PubMed2004

Beta-catenin expression in benign and malignant pilomatrix neoplasms.

BACKGROUND: Beta-catenin is a 92-kDa protein, initially identified as a coprecipitating species with the E-cadherin cell-cell adhesive complex. It plays a role in signal transduction in the Wnt signalling pathway and has been identified as an oncogene in colon cancer and melanoma. Exon 3 beta-catenin-activating mutations were found in 75% of cases of pilomatricoma (PM). Previous studies have shown that nuclear and/or cytoplasmic staining may correlate with beta-catenin gene mutation. OBJECTIVES: Because the immunohistochemical expression of beta-catenin in the nucleus or the cytoplasm correlates with beta-catenin mutation, we studied the immunohistochemical profile of beta-catenin expression in normal scalp hair follicles and in PM and pilomatrix carcinoma (PC). METHODS: We reviewed 21 cases of PM and five cases of PC using immunohistochemical staining with commercially available antibody in a standard fashion on formalin-fixed paraffin-embedded tissue samples. RESULTS: All 26 tumours displayed both nuclear and cytoplasmic staining in the basaloid cells with focal membranous staining. Shadow cells were negative in all tumours. Normal control sections from the scalp displayed nuclear reactivity of the matrical cells, mostly concentrated in the supramatrical zone of hair follicles. Membranous staining was present along the intercellular junctions of the epidermis and along the outer and inner root sheaths of hair follicles. We have found similar patterns of beta-catenin nuclear and cytoplasmic expression in both PM and PC. CONCLUSIONS: Despite the shared beta-catenin expression, the biological behaviour of PM and PC is markedly different. These two tumours probably share the activation of a common cellular pathway that could be related to their shared method of keratinization or a shared dysfunction of the cellular adhesion complex and consequently tumorigenesis. To the best of our knowledge, this is the first report on the beta-catenin immunohistochemical expression profile in PC.

Cell Nucleus↗
PubMed2003

A four-tiered transcriptional regulatory circuit controls flagellar biogenesis in Pseudomonas aeruginosa.

The single polar flagellum of Pseudomonas aeruginosa is an important virulence and colonization factor of this opportunistic pathogen. In this study, the annotation of the genes belonging to the fla regulon was updated and their organization was analysed in strains PAK and PAO1, representative type-a and type-b strains of P. aeruginosa respectively. The flagellar genes are clustered in three non-contiguous regions of the chromosome. A polymorphic locus flanked by flgJ and fleQ in Region I contains a glycosylation island in PAK. The expression and ordered assembly of the complex multicomponent flagellum is intricately regulated. Dedicated flagellar genes fleQ, fleS, fleR, fliA, flgM and fleN encode proteins that participate in the regulation of the flagellar transcriptional circuit. In addition, expression of the flagellum is coordinately regulated with other P. aeruginosa virulence factors by the alternative sigma factor sigma54, encoded by rpoN. In order to gain insight into the hierarchical regulation of flagellar genes, deletion mutations were constructed in fleQ, fleR, fliA and rpoN. The transcriptional impact of these mutations was examined by transcriptional profiling using a P. aeruginosa whole genome microarray. Analysis of the transcriptomes generated for each of these mutants indicates a four-tiered (Classes I-IV) hierarchy of transcriptional regulation. Class I genes are constitutively expressed and include the transcriptional regulator fleQ and the alternative sigma factor fliA (sigma28). Class II genes including fleSR, encoding a two-component regulatory system require FleQ and RpoN (sigma54) for their transcriptional activation. Class III genes are positively regulated by the activated response regulator FleR in concert with RpoN. The transcription of Class IV genes is dependent on the availability of free FliA following the export of the FliA specific antisigma factor FlgM through the basal body rod-hook structure (assembled from Class II and III gene products). Two previously uncharacterized genes, which are coordinately regulated with known flagellar genes have been identified by genome-wide analysis and their role in flagellar biogenesis was analysed.

Bacterial Proteins↗
PubMed1991

A single amino acid substitution strongly modulates the activity and substrate specificity of the mouse mdr1 and mdr3 drug efflux pumps.

Specific protein domains and amino acids responsible for the apparent capacity of P-glycoprotein (mdr) to recognize and transport a large group of structurally unrelated drugs have not been identified. We have introduced a single Ser----Phe substitution within the predicted TM11 domain of mdr1 (position 941) and mdr3 (position 939) and analyzed the effect of these substitutions on the drug-resistance profiles of these two proteins. Mutations at this residue drastically altered the overall degree of drug resistance conveyed by mdr1 and mdr3. The modulating effect of this mutation on mdr1 and mdr3 varied for the drugs tested: it was very strong for colchicine and adriamycin and moderate for vinblastine. For mdr1, the Ser941----Phe941 substitution produced a unique mutant protein that retained the capacity to confer vinblastine resistance but lost the ability to confer adriamycin and colchicine resistance. These results strongly suggest that the predicted TM11 domain of proteins encoded by mdr and mdr-like genes plays an important role in the recognition and transport of their specific substrates.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1999

Chloroquine resistance in Plasmodium falciparum and polymorphism of the CG2 gene.

A distinct genotype (designated Dd2-type profile) consisting of 12 point mutations and 3 repetitive regions of the CG2 gene, a candidate gene for chloroquine resistance, has been associated with in vitro resistance in laboratory-adapted strains of Plasmodium falciparum. The DNA sequence of clinical isolates, characterized by in vitro and in vivo tests, was analyzed to evaluate whether the genotype corresponds to the phenotype in naturally occurring parasites. Eight of 11 chloroquine-resistant isolates had the Dd2 genotype. One resistant isolate (by in vitro assay) with a sensitive CG2 genotype was sensitive in vivo. Two resistant isolates and 6 sensitive isolates were multiple infections with mixed alleles. No typical CG2 genotype was found corresponding to the chloroquine-sensitive isolates. These results suggest a strong association between the drug-resistant and CG2 genotypes and support the hypothesis that the CG2 gene may be implicated in chloroquine resistance.

Animals↗
PubMed1993

High-level quinolone resistance amongst clinical isolates of Escherichia coli and Klebsiella pneumoniae from Spain.

A recombinant plasmid containing gyr A encoding wild-type Escherichia coli quinolone susceptible DNA gyrase A subunits has been used as a broad host range gene probe. Strains expressing gyr A-mediated quinolone resistance become susceptible to quinolones upon insertion of the plasmid, whereas the plasmid without gyrA (pLA2917, vector) has no effect. Fifteen highly ciprofloxacin-resistant E. coli and three Klebsiella pneumoniae (MICs 2-64 mg/L) were isolated from clinical specimens in the Hospital de la Princesa, Madrid, Spain. Plasmid pNJR3-2 and pLA2917 were introduced into the clinical isolates by conjugation, and transconjugants selected with tetracycline or kanamycin (for which the plasmids encode resistance). Ten transconjugants from each mating, the original isolates, the gene probe and vector control were screened for susceptibility to nalidixic acid, ciprofloxacin, ofloxacin, norfloxacin, tetracycline, chloramphenicol, cefoxitin and trimethoprim. Lower MICs of quinolones were seen for the transconjugants of two K. pneumoniae isolates in the presence of the gene probe, suggesting that these isolates harboured mutations in gyr A. Plasmid profiles confirmed the presence of the probe. The susceptibility of the third K. pneumoniae strain and all E. coli isolates were unaffected by insertion of the plasmid, suggesting another mechanism was responsible for quinolone resistance.

4-Quinolones↗
PubMed2002

The control of spikelet meristem identity by the branched silkless1 gene in maize.

Most of the world's food supply is derived from cereal grains that are borne in a unique structure called the spikelet, the fundamental unit of inflorescence architecture in all grasses. branched silkless1 (bd1) is a maize mutation that alters the identity of the spikelet meristem, causing indeterminate branches to form in place of spikelets. We show that bd1 encodes a putative ERF transcription factor that is conserved in different grasses and is expressed in a distinct domain of the spikelet meristem. Its expression pattern suggests that signaling pathways regulate meristem identity from lateral domains of the spikelet meristem.

Alleles↗
PubMed2005

Pharmacodynamic modeling of the evolution of levofloxacin resistance in Staphylococcus aureus.

Previously, we demonstrated the importance of low-level-resistant variants to the evolution of resistance in Staphylococcus aureus exposed to ciprofloxacin in an in vitro system and developed a pharmacodynamic model which predicted the emergence of resistance. Here, we examine and model the evolution of resistance to levofloxacin in S. aureus exposed to simulated levofloxacin pharmacokinetic profiles. Enrichment of subpopulations with mutations in grlA and low-level resistance varied with levofloxacin exposure. A regimen producing average steady-state concentrations (Cavg ss) just above the MIC selected grlA mutants with up to 16-fold increases in the MIC and often additional mutations in grlA/grlB and gyrA. A regimen providing Cavg ss between the MIC and the mutant prevention concentration (MPC) suppressed bacterial numbers to the limit of detection and prevented the appearance of bacteria with additional mutations or high-level resistance. Regimens producing Cavg ss above the MPC appeared to eradicate low-level-resistant variants in the cultures and prevent the emergence of resistance. There was no relationship between the time concentrations remained between the MIC and the MPC and the degree of resistance or the presence or type of mutations that appeared in grlA/B or gyrA. Our pharmacodynamic model described the growth and levofloxacin killing of the parent strains and the most resistant grlA mutants in the starting cultures and correctly predicted conditions that enrich subpopulations with low-level resistance. These findings suggest that the pharmacodynamic model has general applicability for describing fluoroquinolone resistance in S. aureus and further demonstrate the importance of low-level-resistant variants to the evolution of resistance.

Anti-Infective Agents↗
PubMed2006

Genetic and clinical implications of the Val617Phe JAK2 mutation in 72 families with myeloproliferative disorders.

To study the prevalence of the Val617Phe JAK2 mutation in familial cases of myeloproliferative disorder (MPD) and its possible implication as a predisposing genetic factor, we analyzed 72 families including 174 patients (81 polycythemia vera [PV], 68 essential thrombocythemia [ET], 11 myelofibrosis with myeloid metaplasia [MMM], 12 chronic myeloid leukemia), 1 systemic mastocytosis, and 1 chronic myelomonocytic leukemia (CMML). The JAK2 mutation was found in three quarters of patients with PV and MMM and in half of patients with ET. Among 46 families with at least 2 cases of PV, ET, or MMM, the JAK2 mutation was absent in 6 families, heterogeneously distributed in 18, and present in all MPD patients in 22. Among these 22 families, the absence of the JAK2 mutation both in purified T and B cells in 13 unrelated patients and the observation of variable ratios of the JAK2 mutant allele in patient leucocytes indicated that the Val617Phe JAK2 mutation was acquired in familial MPDs. The JAK2 mutation was present in natural killer cells in two thirds of tested patients (27 of 40), suggesting its occurrence in a multipotent hematopoietic progenitor cell. The analysis of the hematologic profile showed that the homozygous JAK2 mutation confers a proliferative advantage and is associated with the progression of the hematologic disease.

Cohort Studies↗
PubMed2026

Identification of ultrasound-associated gene candidates in myeloid cells and construction of a prognostic risk model for acute myeloid leukemia.

BACKGROUND: Incorporating ultrasound (US) treatment sensitivity analysis may improve the treatment of acute myeloid leukemia (AML). METHODS: This study integrated single-cell and bulk datasets for analysis. Differential expression analysis between US-treated and control samples was performed using limma package. The AUCell package was used to calculate US-associated scores in the single-cell dataset. Differentially expressed genes (DEGs) between the specific groups were identified, followed by intersection analysis with previously identified DEGs. Univariate regression, Least Absolute Shrinkage and Selection Operator (LASSO) analysis (using the glmnet package), and stepwise multivariate regression (using the MASS package) were used to refine the candidate genes and to construct a risk model. The model genes were validated using in vitro experiments. Enrichment analysis was conducted using gene set enrichment analysis (GSEA), and immune infiltration was evaluate by single-sample GSEA (ssGSEA) and ESTIMATE algorithms. The correlations between RiskScores and drug sensitivity were analyzed by oncoPredict package. Finally, tumor mutational burden (TMB) and genomic mutations were compared between the risk groups. RESULTS: Nine prognostic signatures (SPINK2, HNRNPAB, SH3BGRL3, CLEC11A, ITGA4, RPL39L, MX1, HEXIM1, and MAP4K4) were identified. Particularly, low expression of SPINK2 attenuated the activity and invasion of AML cells. High-risk group had higher immune cell infiltration. Eight drugs were predicted to be correlated with the RiskScore model. DNMT3A and RUNX1 showed higher mutation frequencies in the high-risk group, whereas KIT and MUC16 showed higher mutation frequencies in the low-risk group. CONCLUSION: The RiskScore model established in this study provides a theoretical basis for clinically screening responsive populations and optimizing treatment strategies.

Humans↗
PubMedDate not supplied

Molecular mechanisms involved in the pathogenesis of gastric carcinoma: interactions between genetic alterations, cellular phenotype and cancer histotype.

Gastric cancer develops through the accumulation of multiple genetic lesions that involve oncogenes, tumor suppressor genes and DNA mismatch repair genes. Lauren's classification of gastric carcinoma does not correlate with cellular phenotypes expressed by neoplastic cells and gastric and intestinal cell differentiation markers are widely expressed in both types (intestinal and diffuse) of gastric carcinoma. In contrast, the study of the correlation between morphologic events and genetic alterations, which come about in the cancerogenetic process, seems to indicate the existence of distinct cancerogenetic pathways for the intestinal (or glandular) and diffuse type carcinoma, both originating from a HP-positive gastritis. In particular there seem to be three different profiles of cancerogenesis: 1) p53 mutations which accompany the onset of dysplasia and intestinal-type carcinoma; 2) DNA repair mechanism alterations conditioning microsatellite instability, seem mutually exclusive with regards to p53 mutations. Microsatellite instability correlates with antrally located intestinal-type carcinoma, with little metastatic tendency and a better prognosis; microsatellite instability frequently involves the TGF beta RII, IGF II R genes or the BAX proapoptotic gene, in as much as these contain microsatellite sequences; 3) alterations of E-cadherin, both with regards to mutations and abnormal expression. These lead to junctional and cell polarity loss and are primarily associated with diffuse type carcinoma, which is characterized by poorly cohesive neoplastic cells. Some tumors, initially arising as intestinal-type (glandular structure), acquire a mixed histotype during neoplastic progression, in which both the typical alterations of the intestinal cancerogenesis (p53, microsatellite instability) and those of the diffuse carcinoma (E-cadherin) coexist. The identification of a mixed histotype could have importance both in epidemiologic, pathogenetic and prognostic terms.

Animals↗