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PubMed2002

env chimeric virus technology for evaluating human immunodeficiency virus susceptibility to entry inhibitors.

We describe the development of chimeric virus technology (CVT) for human immunodeficiency virus (HIV) type 1 (HIV-1) env genes gp120, gp41, and gp160 for evaluation of the susceptibilities of HIV to entry inhibitors. This env CVT allows the recombination of env sequences derived from different strains into a proviral wild-type HIV-1 clone (clone NL4.3) from which the corresponding env gene has been deleted. An HIV-1 strain (strain NL4.3) resistant to the fusion inhibitor T20 (strain NL4.3/T20) was selected in vitro in the presence of T20. AMD3100-resistant strain NL3.4 (strain NL4.3/AMD3100) was previously selected by De Vreese et al. (K. De Vreese et al., J. Virol. 70:689-696, 1996). NL4.3/AMD3100 contains several mutations in its gp120 gene (De Vreese et al., J. Virol. 70:689-696, 1996), whereas NL4.3/T20 has mutations in both gp120 and gp41. Phenotypic analysis revealed that NL4.3/AMD3100 lost its susceptibility to dextran sulfate, AMD3100, AMD2763, T134, and T140 but not its susceptibility to T20, whereas NL4.3/T20 lost its susceptibility only to the inhibitory effect of T20. The recombination of gp120 of NL4.3/AMD3100 and gp41 of NL4.3/T20 or recombination of the gp160 genes of both strains into a wild-type background reproduced the phenotypic (cross-)resistance profiles of the corresponding strains selected in vitro. These data imply that mutations in gp120 alone are sufficient to reproduce the resistance profile of NL4.3/AMD3100. The same can be said for gp41 in relation to NL4.3/T20. In conclusion, we demonstrate the use of env CVT as a research tool in the delineation of the region important for the phenotypic (cross-)resistance of HIV strains to entry inhibitors. In addition, we obtained a proof of principle that env CVT can become a helpful diagnostic tool in assessments of the phenotypic resistance of clinical HIV isolates to HIV entry inhibitors.

Antiviral Agents↗

PubMed2000

Elevated levels of synthesis of over 20 proteins results after mutation of the Rhizobium leguminosarum exopolysaccharide synthesis gene pssA.

The protein expression profiles of Rhizobium leguminosarum strains in response to specific genetic perturbations in exopolysaccharide (EPS) biosynthesis genes were examined using two-dimensional gel electrophoresis. Lesions in either pssA, pssD, or pssE of R. leguminosarum bv. viciae VF39 or in pssA of R. leguminosarum bv. trifolii ANU794 not only abolished the capacity of these strains to synthesize EPS but also had a pleiotropic effect on protein synthesis levels. A minimum of 22 protein differences were observed for the two pssA mutant strains. The differences identified in the pssD and pssE mutants of strain VF39 were a distinct subset of the same protein synthesis changes that occurred in the pssA mutant. The pssD and pssE mutant strains shared identical alterations in the proteins synthesized, suggesting that they share a common function in the biosynthesis of EPS. In contrast, a pssC mutant that produces 38% of the EPS level of the parental strain showed no differences in its protein synthesis patterns, suggesting that the absence of EPS itself was contributing to the changes in protein synthesis and that there may be a complex interconnection of the EPS biosynthetic pathway with other metabolic pathways. Genetic complementation of pssA can restore wild-type protein synthesis levels, indicating that many of the observed differences in protein synthesis are also a specific response to a dysfunctional PssA. The relevance of these proteins, which are grouped as members of the pssA mutant stimulon, remains unclear, as the majority lacked a homologue in the current sequence databases and therefore possibly represent a novel functional network(s). These findings have illustrated the potential of proteomics to reveal unexpected higher-order processes of protein function and regulation that arise from mutation. In addition, it is evident that enzymatic pathways and regulatory networks are more interconnected and more sensitive to structural changes in the cell than is often appreciated. In these cases, linking the observed phenotype directly to the mutated gene can be misleading, as the phenotype could be attributable to downstream effects of the mutation.

Amino Acid Sequence↗

PubMed2004

Differential production of interleukin-10 and interleukin-12 in mononuclear cells from leprosy patients with a Toll-like receptor 2 mutation.

Toll-like receptor 2 (TLR2) is a key mediator of the immune response to mycobacterial infections, and mutations in TLR2 have been shown to confer susceptibility to infection with mycobacteria. This study investigated the profiles of cytokines, such as interferon (IFN)-gamma, interleukin (IL)-10, IL-12 and tumour necrosis factor (TNF)-alpha in response to Mycobacterium leprae in peripheral blood mononuclear cells (PBMC) with the TLR2 mutation Arg677Trp, a recently reported polymorphism that is associated with lepromatous leprosy. In leprosy patients with the TLR2 mutation, production of IL-2, IL-12, IFN-gamma, and TNF-alpha by M. leprae-stimulated PBMC were significantly decreased compared with that in groups with wild-type TLR2. However, the cells from patients with the TLR2 mutation showed significantly increased production of IL-10. There was no significant difference in IL-4 production between the mutant and wild-type during stimulation. Thus, these results suggest that the TLR2 signal pathway plays a critical role in the alteration of cytokine profiles in PBMC from leprosy patients and the TLR2 mutation Arg677Trp provides a mechanism for the poor cellular immune response associated with lepromatous leprosy.

Adult↗

PubMed2003

The interaction of the cap-binding complex (CBC) with eIF4G is dispensable for translation in yeast.

In eukaryotes, the m(7)GpppN cap structure is added to all nascent RNA polymerase II transcripts, and serves important functions at multiple steps of RNA metabolism. The predominantly nuclear cap-binding complex (CBC) binds to the cap during RNA synthesis. The predominantly cytoplasmic eukaryotic initiation factor 4F (eIF4F) is thought to replace CBC after export of mature mRNA to the cytoplasm, and mediates the bulk of cellular translation. Yeast as well as mammalian CBC interacts in vitro with eIF4G, a subunit of eIF4F. In this work, we investigate a potential role of this interaction during translation in yeast. We identify a mutation (DR548/9AA) in Tif4631p, one of two isoforms of yeast eIF4G, that abolishes its binding to CBC. Cells expressing this mutant protein as the sole source of eIF4G grow at wild-type rates, and bulk cellular translation, as assessed by metabolic labeling and polysome profile analysis, is unchanged. Importantly, we find that the DR548/9AA mutation neither diminishes nor delays the translation of newly induced reporter mRNA. Finally, microarray analysis reveals marked transcriptome alterations in CBC subunit deletion strains, whereas eIF4G point mutants have essentially a wild-type transcriptome composition. Collectively, these data suggest that in yeast, the phenotypic consequences of CBC deletions are separable from its interaction with eIF4G, and that the CBC-eIF4G interaction is dispensable for a potential "pioneering round" of translation in yeast.

Binding Sites↗

PubMed1994

Neuroanatomy of fragile X syndrome: the temporal lobe.

Fragile X syndrome, an X-linked genetic disorder caused by a mutation in the FMR-1 gene, is associated with a particular profile of abnormalities of behavior, learning, language, and memory, suggesting temporal lobe dysfunction. We undertook a quantitative neuroimaging study investigating the neuroanatomy of the temporal lobe in individuals with the fragile X mutation. The temporal lobe neuroanatomy of 15 young fragile X subjects was quantified and compared with that of 26 age- and IQ-matched control subjects. Analyses showed the right and left hippocampal volumes to be significantly larger in the fragile X group compared with the control group. Subjects with the fragile X mutation showed an age-related increase in volume of the hippocampus an age-related decrease in volume of the superior temporal gyrus. Along with the findings of previous imaging studies of fragile X subjects, the results of the present investigation are consistent with studies showing a nonrandom distribution of expression of the FMR-1 gene in the developing brain, with increased expression in the cerebellum, hippocampus, and specific cortical regions. The results also suggest involvement of temporal lobe regions in the behavioral and cognitive abnormalities associated with fragile X syndrome.

Adolescent↗

PubMed2005

The value of c-kit mutational analysis in a cytokeratin positive gastrointestinal stromal tumour.

The expression of cytokeratins in gastrointestinal stromal tumours (GISTs) is rare and may lead to diagnostic confusion when it occurs. This report describes a metastatic GIST that stained strongly for cytokeratins, CD117, and CD34 in a patient who was previously diagnosed with gastric epithelioid angiosarcoma. A review of both tumours showed the same histological and immunohistochemical profiles, and c-kit molecular analysis revealed an insertional mutation at codon 558 of exon 11 in both tumours. Thus, pathologists should be aware that GISTs can occasionally express cytokeratins, and that c-kit mutational investigations may have a key diagnostic role and may prevent diagnostic mistakes that could have important clinical implications.

Adult↗

PubMed2003

Detection of known mutations in hypertrophic cardiomyopathy using oligonucleotide microarrays assisted by improved base stacking hybridization.

With the assistance of improved base stacking hybridization, a low-density microarray, containing 12 capture probes, was used to identify 7 known hypertrophic cardiomyopathy-related mutations in the gene of MYH7 (beta-myosia heavy chain). The hybridization targets, amplified from 11 plasmids containing wild type or mutation sequences of MYH7 and healthy genomic DNA, were prepared by single-step fluorescence labeled asymmetric PCR. Six single base substitutions and a trinucleotide deletion were identified unambiguously, and the average discrimination ratio (Qmut) for artificial heterozygous samples was as high as 16.2.

Base Sequence↗

PubMed2005

Molecular cloning and expression profiling of optineurin in the rhesus monkey.

PURPOSE: It has been shown that mutations in the optineurin (OPTN) gene are involved in the etiology of adult-onset primary open-angle glaucoma (POAG). In view of close similarities between human and nonhuman primate ocular development and function, the rhesus monkey is considered a suitable model for human visual system research. Therefore, this study was conducted to clone the orthologue of the human OPTN gene in the rhesus monkey (Rh-OPTN) and to determine its genomic organization. A further purpose was to establish Rh-OPTN protein expression profiles and tissue distribution in the rhesus anterior segment, retina, and optic nerve. METHODS: The Rh-OPTN gene was cloned and its genomic structure determined. The mRNA expression pattern was examined by Northern blot analysis. The protein's cellular localization, ocular expression, and tissue distribution were established by immunolabeling. RESULTS: The Rh-OPTN gene has 13 exons and encodes for a 571-amino-acid protein. Both cDNA and amino acid sequences are 96% identical with the human OPTN. Northern blot analysis revealed prominent expression of two different transcripts in heart, brain, kidney, lung, spleen, skeletal muscle, and small intestine. Cellular and tissue distribution of Rh-OPTN protein were highly similar to its human and mouse homologous proteins. CONCLUSIONS: The optineurin gene and protein are evolutionary conserved between humans and the rhesus monkey. High similarity of ocular expression and tissue distribution between the two optineurin proteins suggests that this nonhuman primate is a suitable model for the pathophysiology and treatment of human glaucomatous optic neuropathy.

Amino Acid Sequence↗

PubMed2002

Differential display of expressed genes in pancreatic cancer cells.

Activating K-ras mutations occur in 80-95% of pancreatic cancers. The purpose of this study was to conduct an open, panoramic survey of gene expression, using K-ras status as the axis over which to sub-classify pancreatic cancers. Differential display was used to contrast mRNA purified from exponentially growing PANC-1 and Capan-2 cells (mutated K-ras) with Hs766T and BxPC-3 cells (wild-type). Differences were confirmed by Northern analysis. Twenty-five transcripts were differentially expressed by a factor of two or more. Four transcripts were over-expressed and twelve were under-expressed in the mutants relative to the wild-types. The transcripts most strikingly over-expressed by the mutant cell lines were MARCKS, DKFZp547C244, and RPLP2. The transcripts over-expressed by the wild-types were CEACAM6, cDNA AK026924, and myosin light chain-6. Profiling of gene expression with respect to K-ras mutation status may lead to new insights into pancreatic cancer pathogenesis, as well as to the identification of novel therapeutic targets.

Antigens, CD↗

PubMed2003

Characterisation of p53 status at the gene, chromosomal and protein levels in oesophageal adenocarcinoma.

p53 mutations and loss of heterozygosity have been commonly associated with oesophageal adenocarcinoma. In this investigation, the p53 status of a Welsh population of Barrett's-associated oesophageal adenocarcinomas were fully characterised at the gene sequence, chromosomal, mRNA and protein levels. In total, 31 tumours were examined for p53 gene sequence mutations using RFLP with sequencing, allelic loss of the gene was characterised by FISH, mRNA expression by p53 pathway signalling arrays and protein levels by p53 immunohistochemistry. In all, 9.6% of adenocarcinomas harboured p53 mutations, 24% displayed p53 allelic loss and 83% exhibited p53 protein accumulation. Point mutations and deletions of the gene did not coexist within the same samples. All samples containing p53 mutations also displayed positive immunostaining; however; in the majority of cases, p53 protein accumulation developed in the absence of mutations. The gene expression analysis demonstrated no differences in p53 and mdm-2 transcription levels between the p53 immunonegative and immunopositive samples, indicating other mechanisms underlie the proteins' overexpression. In conclusion, p53 mutations and deletions do not appear to be frequent events in oesophageal adenocarcinomas; however, abnormal accumulation of the protein is present in a vast majority of cases. P53 gene mutations are not the primary cause of protein overexpression--an alternative mechanism is responsible for the positive p53 immunohistochemistry detected.

Adenocarcinoma↗

PubMed1993

Energy transduction between membranes. TonB, a cytoplasmic membrane protein, can be chemically cross-linked in vivo to the outer membrane receptor FepA.

TonB, a cytoplasmic membrane protein, couples cytoplasmic membrane protonmotive force to active transport across the outer membrane of Escherichia coli. In vivo cross-linking studies were initiated to analyze TonB interactions with other cell envelope proteins. Four TonB-specific cross-linked complexes were detected with apparent molecular masses of 195, 77, 59, and 43.5 kDa. The 195-kDa complex was shown to contain both TonB and FepA, the outer membrane receptor for the siderophore enterochelin. The 195-kDa complex is absent in strains missing either TonB or FepA and can be detected by either TonB-specific or FepA-specific monoclonal antibodies. This is the first direct in vivo evidence that TonB can span the periplasmic space to interact physically with outer membrane receptors. Consistent with that observation, the outer membrane protease OmpT was shown to play a role in TonB turnover, both in the presence and absence of ExbB results in the rapid degradation of TonB. The absence of OmpT could be used to stabilize TonB in an exbB::Tn10 strain such that steady state levels of TonB protein are identical to a wild-type strain. Under those conditions, the absence of ExbB results in greatly reduced TonB activity, indicating that ExbB plays a direct role in energy transduction and probably secondarily protects TonB protein from proteolysis. The 59-kDa complex was absent in an exbB::Tn10 strain, suggesting either that ExbB is in the complex with TonB or that ExbB is required to form the 59-kDa complex. A tolQ nonsense mutation had no effect on the cross-linking profile observed, confirming that its participation in TonB-dependent phenomena is minor and most likely the result of evolutionary cross-talk.

Animals↗

PubMed2026

Molecular and immune profiling of HER2-low, HER2 ultra-low, and HER2-null male breast cancer.

BACKGROUND: HER2 expression is described along a biological continuum from null to positive and serves as a critical biomarker for therapeutic guidance in breast cancer (BC). While HER2-low and ultra-low categories have emerged as actionable targets for antibody-drug conjugates (ADCs) in female BC, their molecular and immune characteristics remain largely unexplored in male breast cancer. METHODS: We profiled 214 male breast tumors using next-generation sequencing and whole-transcriptome sequencing to assess mutational, transcriptomic, and immune landscapes. Tumor mutational burden (TMB) was defined as high if > 10 mutations/Mb. Immune cell fractions were inferred using Quantiseq deconvolution. RESULTS: Among 214 samples, 66 (30.8%) were HER2-null, 53 (24.8%) HER2 ultra-low, 80 (37.4%) HER2-low, and 15 (7.0%) HER2-positive. HER2 ultra-low tumors exhibited a higher prevalence of PIK3CA mutations (39.2% vs 22.6%, p ≤ 0.05) compared to HER2-null. No significant differences were observed in TMB-high frequency or PD-L1 expression across subgroups. Immune composition differed primarily between HER2-null and HER2-expressing subgroups: HER2-ultra-low tumors showed higher B-cell infiltration, whereas HER2-null tumors were enriched in neutrophils. Transcriptomic analysis revealed upregulation of selected stemness-associated genes (NANOG, KLF4, POU5F1) and CEACAM1 in HER2-null tumors, while HER2-low and HER2-ultra-low tumors were largely similar across most molecular and immune readouts in this cohort. CONCLUSIONS: HER2-null male breast cancer appears to represent the most biologically divergent subgroup within the HER2-negative spectrum, whereas HER2-low and HER2-ultra-low tumors were largely similar in this cohort. These findings support further investigation of HER2-null disease as a distinct biological state and provide hypothesis-generating data for biomarker development in this rare population.

Male↗

PubMed1995

Use of site-directed mutagenesis and alternative substrates to assign the prototropic groups important to catalysis by Escherichia coli aspartate aminotransferase.

The pH dependence of Escherichia coli aspartate aminotransferase (AATase) has been investigated by the use of site-directed mutants and alternative substrates. Inhibition of the enzyme by CHES and variations in ionic strength are proposed to explain some of the qualitative differences in the published pH dependence of pig cytosolic AATase kinetics [Velick, S. F., & Vavra, J. (1962) J. Biol. Chem. 237, 2109-2122; Kiick, D.M., & Cook, P.F. (1983) Biochemistry 22, 375-382]. The pKa values of the basic limbs in the kcat/KM profiles for the amino acids, L-Asp and L-cysteinesulfinate (L-CS), are identical, within error, to those of free substrates, (L-Asp, pKa = 9.6; L-CS, pKa = 9.0). This pKa therefore is assigned to the alpha-amino group of the substrate. Replacement of the active site base, Lys-258, with the weaker base, gamma-thia-Lys, does not alter the intrinsic pKa for the profiles of the Ki values for the maleate-E.PMP complexes or the kcat/K alpha-KGM values. The mutation Y225F results in an alkaline shift of the pKa in the kcat/K alph-KGM profile. This pKa is assigned to the C4' amino group of PMP. E. coli AATase, unlike pig cytosolic AATase, shows a pH dependence on kcat between pH 5 and 10 that arises from a change in the rate-determining step at pH extremes. C alpha proton abstraction is partially rate-determining at neutral pH values, but not at pH extremes.(ABSTRACT TRUNCATED AT 250 WORDS)

Aspartate Aminotransferases↗

PubMed2000

A tyramine receptor gene mutation causes a defective olfactory behavior in Drosophila melanogaster.

We characterized molecular profiles of a new olfactory mutant line, honoka (hono), which was found among 500 viable P-element insertion lines screened first by 5-bromo-4-chloro-3-indrolyl-beta-D-galactopyranoside (X-gal) staining on the third segment of the antenna, and then by behavioral assays to several pure chemicals. The behavioral responses of hono mutants to repellents such as ethyl acetate (EA), benzaldehyde (BZ) and 4-methylcycrohexanol (MCH), were reduced compared with those of a control strain. The location of the P-element insertion was determined to be about 100bp) upstream of the first exon of the tyramine receptor gene. The level of 3.6kb tyramine receptor mRNA expression was reduced in hono compared with that of wild-type flies. The tyramine receptor cDNA hybridized to the chromosomal division 79C-D, the same locus as the P-element insertion point in hono, and not to 99A-B, previously reported by Arakawa et al. (1990. Neuron 2, 343-354). Electrophysiological responses to octopamine and tyramine were examined by measuring the excitatory junctional potential (EJP) amplitude from larval body-wall muscles of the hono mutant. The hono was impaired with responding to tyramine, while displaying normal response to octopamine. These results indicate that tyramine has a functional role in the Drosophila olfactory system as a neurotransmitter or a neuromodulator, and hono is the first tyramine receptor mutant. This study provides the first step toward understanding of the molecular genetics of tyramine-mediated neural functions in Drosophila.

Acetates↗

PubMed1995

Interaction of host proteins with the plus-strand promoter of brome mosaic virus RNA-2.

The binding of five barley proteins (Mr: 37, 36, 35, 34, and 30 kDa) to the ICR2 motif present at the 5' end of brome mosaic virus (BMV) RNA-2 was identified using UV cross-linking. Evidence that the interaction is specific included the observation that these proteins did not recognize a similar-size RNA fragment transcribed from a nonviral (beta-glucuronidase) gene, nor did they bind to the 3' end of the plus strand of RNA-3. Replication-defective BMV RNA-2 mutants bearing substitution mutations at nucleotides 9 and 10 of the ICR2 motif were used to show that these positions were involved in the interaction of the five barley proteins with BMV RNA-2. Surprisingly, the profile of barley proteins interacting with the 3' end of the minus strand of RNA-2 was similar to that seen for the 5' end of the plus strand. Further, the profile of proteins binding to minus-sense probes bearing substitution mutations in the ICR2 region differed from that found for the wild-type sequence. These findings support the concept that host proteins are involved in genome replication and that their ability to interact with both plus and minus strands of the viral RNA is probably involved with the initiation of plus-strand synthesis.

Base Sequence↗

PubMed2004

Microarray analysis in cystic fibrosis.

DNA microarrays provide a versatile platform for applications including gene expression analysis and genotyping. In the case of cystic fibrosis (CF), DNA microarrays enable the measurement of gene expression levels of thousands of genes in parallel, and potentially therefore, to identify non-CFTR genes down- or up-regulated in CF, which could lead to insights into disease pathophysiology, as well as novel molecular markers and therapeutic strategies. Moreover, using optimised microarray protocols based on either primer extension analysis (i.e. minisequencing) or electronic hybridisation stringency control, the potential now exists to detect all relevant CFTR mutations on a single DNA microarray as a novel platform for CF screening.

Cystic Fibrosis↗

PubMed2001

Mutations in a new gene encoding a protein of the hair bundle cause non-syndromic deafness at the DFNB16 locus.

Hearing impairment affects about 1 in 1,000 children at birth. Approximately 70 loci implicated in non-syndromic forms of deafness have been reported in humans and 24 causative genes have been identified (see also http://www.uia.ac.be/dnalab/hhh). We report a mouse transcript, isolated by a candidate deafness gene approach, that is expressed almost exclusively in the inner ear. Genomic analysis shows that the human ortholog STRC (so called owing to the name we have given its protein-stereocilin), which is located on chromosome 15q15, contains 29 exons encompassing approximately 19 kb. STRC is tandemly duplicated, with the coding sequence of the second copy interrupted by a stop codon in exon 20. We have identified two frameshift mutations and a large deletion in the copy containing 29 coding exons in two families affected by autosomal recessive non-syndromal sensorineural deafness linked to the DFNB16 locus. Stereocilin is made up of 1,809 amino acids, and contains a putative signal petide and several hydrophobic segments. Using immunohistolabeling, we demonstrate that, in the mouse inner ear, stereocilin is expressed only in the sensory hair cells and is associated with the stereocilia, the stiff microvilli forming the structure for mechanoreception of sound stimulation.

Amino Acid Sequence↗

PubMed2005

ALBINO AND PALE GREEN 10 encodes BBMII isomerase involved in histidine biosynthesis in Arabidopsis thaliana.

We isolated an Arabidopsis albino and pale green 10 (apg10) mutant which exhibits pale green cotyledons and true leaves at the juvenile stage. We identified a valine to leucine change in BBMII (N'-[(5'-phosphoribosyl)-formimino]-5-aminoimidazole-4-carboxamide ribonucleotide) isomerase involved in histidine biosynthesis. The morphological abnormality of apg10 was recovered by histidine supplementation. The histidine limitation induced by apg10 mutation causes dynamic changes of the free amino acid profile, suggesting the existence of a cross-pathway regulatory mechanism of amino acid biosynthesis in plants. We also revealed that the APG10 knockout mutant exhibited embryo lethality, indicating the essential role of the Arabidopsis BBMII isomerase for plant growth.

Amino Acid Sequence↗