Antibody-mediated enzyme formation: Its legacy at age fifty-four.

Antibody-mediated enzyme formation is a phenomenon first described in 1968 and further studied by molecular Immunologists and Biochemists over the following five decades. The present review is made mainly by analyzing the 27 articles concerned with AMEF that appeared over the course of 47 years, commenting 16 original figures selected to be re-printed in AMEF's Legacy. We, the reviewers, started by revisiting our own "insider's" experience of discovery, and followed by considering all results, our own and of members of other AMEF Labs. We had planned to conclude the review by correlating the various AMEF mutants to a detailed knowledge of the consensus betaGal structure. However, we became aware of several "robust" papers, published between 1989 and 2014, by authors outside of AMEF Labs. We familiarly called this surge: "The Second Wave" and adorned it with a doodle in Hokusai style. We were thrilled and happy to take them on board and properly examined their data. A team of this second wave had imagined unique uses for AMEF, and new doors to modern biotechnology. Another one had used AMEF as Tool and Marker to attain high levels of crystallography, solving puzzles of conformation, and ultimate structure. Together, they doubled our motivation to review AMEF. Serendipity gives us back the pleasure of finding, a treat at any age.

The Impact on Genetic Testing of Mutational Patterns of CFTR Gene in Different Clinical Macrocategories of Cystic Fibrosis.

More than 2000 sequence variations of the cystic fibrosis transmembrane conductance regulator gene are known. The marked genetic heterogeneity, poor functional characterization of the vast majority of sequence variations, and an uncertain genotype-phenotype relationship complicate the definition of mutational search strategies. We studied the effect of the marked genetic heterogeneity detected in a case series comprising 610 patients of cystic fibrosis (CF), grouped in different clinical macrocategories, on the operative characteristics of the genetic test designed to fully characterize CF patients. The detection rate in each clinical macrocategory and at each mutational step was found to be influenced by genetic heterogeneity. The definition of a single mutational panel that is suitable for all clinical macrocategories proved impossible. Only for classic CF with pancreas insufficiency did a reduced number of mutations yield a detection rate of diagnostic value. All other clinical macrocategories required an extensive genetic search. The search for specific mutational classes appears to be useful only in specific CF clinical forms. A flowchart defining a mutational search that may be adopted for different CF clinical forms, optimized in respect to those already available, is proposed. The findings also have consequences for carrier screening strategies.

Correction: Atherogenic Dyslipidemia in Children: Evaluation of Clinical, Biochemical and Genetic Aspects.

[This corrects the article DOI: 10.1371/journal.pone.0120099.].

Atherogenic dyslipidemia in children: evaluation of clinical, biochemical and genetic aspects.

The precursors of atherogenic dyslipidemia (AD) are not well defined. Therefore, we investigated 62 non-obese, non-diabetic AD and 221 normolipemic children. Anthropometric parameters, blood pressure and biochemical measures were obtained in index children, their parents and all available siblings. The heritability (h(2)) of anthropometric and biochemical traits was estimated by SOLAR. Rare and common variants in APOA1 and LPL genes were screened by re-sequencing. Compared to normolipemic, AD children showed increased body mass index, waist circumference, plasma glucose, insulin, ApoB, HOMA-IR, hs-CRP and lower adiponectin (p<0.001 for all). Metabolic syndrome was present in 40% of AD while absent in controls. All traits (except adiponectin and hs-CRP) showed a strong familial aggregation, with plasma glucose having the highest heritability (89%). Overall, 4 LPL loss-of-function mutations were detected (p.Asp9Asn, p.Ser45Asn, p.Asn291Ser, p.Leu365Val) and their cumulative prevalence was higher in AD than in control children (0.073 vs. 0.026; P=0.038). The LPL p.S447* gain-of-function mutation, resulted to be less frequent in AD than in control children (0.064 vs. 0.126; P=0.082). No variant in the APOA1 gene was found. Our data indicate that AD is a rather common dyslipidemia in childhood; it associates with metabolic abnormalities typical of insulin resistant state and shows a strong familial aggregation. LPL variants may contribute to the development of AD phenotype.

A Genotypic-Oriented View of CFTR Genetics Highlights Specific Mutational Patterns Underlying Clinical Macrocategories of Cystic Fibrosis.

Cystic fibrosis (CF) is a monogenic disease caused by mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The genotype-phenotype relationship in this disease is still unclear, and diagnostic, prognostic and therapeutic challenges persist. We enrolled 610 patients with different forms of CF and studied them from a clinical, biochemical, microbiological and genetic point of view. Overall, there were 125 different mutated alleles (11 with novel mutations and 10 with complex mutations) and 225 genotypes. A strong correlation between mutational patterns at the genotypic level and phenotypic macrocategories emerged. This specificity appears to largely depend on rare and individual mutations, as well as on the varying prevalence of common alleles in different clinical macrocategories. However, 19 genotypes appeared to underlie different clinical forms of the disease. The dissection of the pathway from the CFTR mutated genotype to the clinical phenotype allowed to identify at least two components of the variability usually found in the genotype-phenotype relationship. One component seems to depend on the genetic variation of CFTR, the other component on the cumulative effect of variations in other genes and cellular pathways independent from CFTR. The experimental dissection of the overall biological CFTR pathway appears to be a powerful approach for a better comprehension of the genotype-phenotype relationship. However, a change from an allele-oriented to a genotypic-oriented view of CFTR genetics is mandatory, as well as a better assessment of sources of variability within the CFTR pathway.

Emergence of blaKPC-3-Tn4401a in Klebsiella pneumoniae ST512 in the municipal wastewater treatment plant and in the university hospital of a town in central Italy.

In this study, 20 carbapenem-resistant environmental Klebsiella pneumoniae strains were found to correlate with 18 clinical K. pneumoniae isolates from the teaching hospital of L'Aquila city, Italy. All strains analysed by multilocus sequence typing (MLST) were included in the same clone (ST512), and pulsed-field gel electrophoresis demonstrated a genetic relationship between the clinical isolates and most environmental strains. Both environmental and clinical strains harboured the same mobile genetic elements: transposon Tn4401a including a blaKPC-3 determinant; and a class 1 integron with the gene cassette aadA2.

A template for mutational data analysis of the CFTR gene.

BACKGROUND: Automated DNA sequencing produces large amounts of data that need to be analyzed by appropriate software. Personalization of software can be a difficult and time-consuming task, especially if a large number of mutations have to be analyzed. METHODS: The Applied BioSystems SeqScape software, based on the KB basecaller algorithm, is a versatile tool that can be used for mutational analysis and for data quality assessment of sequences belonging to any gene of interest. Using this software we analyzed over 1400 sequences of CFTR exons and adjacent intronic zones, representing over 500,000 bases. RESULTS: We present an up to date specific template and a linked set of instructions for automated labeling of all point mutations and polymorphisms of the CFTR gene, whose mutations cause cystic fibrosis (the most common genetic disease among Caucasian individuals). We also describe our refined software settings for mutational analysis, in order to keep to a minimum the need of manual validation. CONCLUSIONS: The use of our template greatly simplifies the mutational analysis of the CFTR gene, reducing human intervention. In our opinion, it might not only be useful to researchers that already perform CFTR mutational analysis by sequencing methods but it should also improve the approach in those laboratories that already use ABI PRISM instrumentation for a limited mutational analysis of the CFTR gene. Similar mutational templates can also be used for other disease causing genes, thus improving molecular genetics protocols.

Early demethylation of non-CpG, CpC-rich, elements in the myogenin 5'-flanking region: a priming effect on the spreading of active demethylation.

The dynamic changes and structural patterns of DNA methylation of genes without CpG islands are poorly characterized. The relevance of CpG to the non-CpG methylation equilibrium in transcriptional repression is unknown. In this work, we analyzed the DNA methylation pattern of the 5'-flanking of the myogenin gene, a positive regulator of muscle differentiation with no CpG island and low CpG density, in both C2C12 muscle satellite cells and embryonic muscle. Embryonic brain was studied as a non-expressing tissue. High levels of both CpG and non-CpG methylation were observed in non-expressing experimental conditions. Both CpG and non-CpG methylation rapidly dropped during muscle differentiation and myogenin transcriptional activation, with an active demethylation dynamics. Non-CpG demethylation occurred more rapidly than CpG demethylation. Demethylation spread from initially highly methylated short CpC-rich elements to a virtually unmethylated status. These short elements have a high CpC content and density, share some motifs and largely coincide with putative recognition sequences of some differentiation-related transcription factors. Our findings point to a dynamically controlled equilibrium between CpG and non-CpG active demethylation in the transcriptional control of tissue-specific genes. The short CpC-rich elements are new structural features of the methylation machinery, whose functions may include priming the complete demethylation of a transcriptionally crucial DNA region.

A new complex allele of the CFTR gene partially explains the variable phenotype of the L997F mutation.

PURPOSE: To evaluate the role of complex alleles, with two or more mutations in cis position, of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in the definition of the genotype-phenotype relationship in cystic fibrosis (CF), and to evaluate the functional significance of the highly controversial L997F CFTR mutation. METHODS: We evaluated the diagnosis of CF or CFTR-related disorders in 12 unrelated subjects with highly variable phenotypes. According to a first CFTR mutational analysis, subjects appeared to be compound heterozygotes for a classic mutation and the L997F mutation. A further CFTR mutational analysis was conducted by means of a protocol of extended sequencing, particularly suited to the detection of complex alleles. RESULTS: We detected a new [R117L; L997F] CFTR complex allele in the four subjects with the highest sweat test values and CF. The eight subjects without the complex allele showed the most varied biochemical and clinical outcome and were diagnosed as having mild CF, CFTR-related disorders, or even no disease. CONCLUSIONS: The new complex allele partially explains the variable phenotype in CF subjects with the L997F mutation. CFTR complex alleles are likely to have a role in the definition of the genotype-phenotype relationship in CF. Whenever apparently identical CFTR-mutated genotypes are found in subjects with divergent phenotypes, an extensive mutational search is mandatory.

Autoantibodies in patients with monoclonal gammopathies.

Although autoantibody activities are rather often associated to monoclonal gammopathies, only monoclonal immunoglobulins of the IgM isotype are really directed against autoantigens that are often polysaccharides or are formed by highly repetitive structures. This strict association is frequently revealed also by clinical manifestations of the autoimmune response generated by the monoclonal macroglobulin. Most monoclonal immunoglobulins of non-IgM isotype are instead totally inactive toward self-antigens, the autoantibody activity being instead associated, if present, to polyclonal immunoglobulins. Although the same BAFF/APRIL system is involved in perpetuation of humoral autoimmunity as well as in stimulation of clonal B-cell expansion, the autoimmune commitment of B cells of a non-IgM isotype is hardly compatible with their possible involvement in an uncontrolled proliferation pathway, whose prerequisite is the homing of these B cells to the bone marrow compartment. The IgM-secreting cells appear instead to possess a much lower tendency, and/or a looser requirement, for their homing in the bone marrow prior to their actual proliferation. This may explain the quite different consequences, in terms of autoimmunity, between IgM and non-IgM paraproteinemias.

Zidovudine inhibits protein kinase C activity in human chronic myeloid (K562) cells.

In this paper we show that human erythroleukaemia (K562) cells exhibited a significant inhibition of protein kinase C activity when cells were exposed to 40 micro M zidovudine in a time interval of 5-180 min., whereas prolonged treatment (24 hr) was uneffective. The addition of an excess of thymidine (125:1, mol:mol), in the cell suspension with or without zidovudine fully restored the protein kinase C activity. Interestingly, either in cell homogenates and in commercially purified rat brain protein kinase C, both zidovudine and its monophosphate derivative, caused inhibition that was higher than in intact cells. This inhibition reached a maximal value of 45% when zidovudine or zidovudine monophosphate were incubated with the pure commercial enzyme and in this case the addition of thymidine did not prevent the enzyme inhibition. The conclusions from these data are that either zidovudine or zidovudine monophosphate interact directly with the pure enzyme, causing inhibition, while in intact cells exposed to the drug, zidovudine monophosphate appears to be the main metabolite responsible for protein kinase C inhibition.

A 96-well formatted method for exon and exon/intron boundary full sequencing of the CFTR gene.

Full genotypic characterization of subjects affected by cystic fibrosis (CF) is essential for the definition of the genotype-phenotype correlation as well as for the enhancement of the diagnostic and prognostic value of the genetic investigation. High-sensitivity diagnostic methods, capable of full scanning of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, are needed to enhance the significance of these genetic assays. A method for extensive sequencing of the CFTR gene was optimized. This method was applied to subjects clinically positive for CF and to controls from the general population of central Italy as well as to a single subject heterozygous for a mild mutation and with an uncertain diagnosis. Some points that are crucial for the optimization of the method emerged: a 96-well format, primer project and purification, and amplicon purification. The optimized method displayed a high degree of diagnostic sensitivity; we identified a subset of 13 CFTR mutations that greatly enhanced the diagnostic sensitivity of common methods of mutational analysis. A novel G1244R disease causing mutation, leading to a CF phenotype with pancreatic sufficiency but early onset of pulmonary involvement, was detected in the subject with an uncertain diagnosis. Some discrepancies between our results and previously published CFTR sequence were found.

Regulation by cannabinoid receptors of anandamide transport across the blood-brain barrier and through other endothelial cells.

The endocannabinoid anandamide (AEA) has many neurovascular activities. However, it is not yet clear how AEA can be metabolized at the neurovascular interface, and how it can move through the vascular and the cerebral compartments. The results reported in this article show that isolated bovine brain microvessels, an ex vivo model of the blood-brain barrier, have detectable levels of endogenous AEA and possess the biochemical machinery to bind and metabolize it, i.e. type-1 and type-2 cannabinoid receptors (CB1R and CB2R), a selective AEA membrane transporter (AMT), an AEA-degrading fatty acid amide hydrolase, and the AEA-synthesizing enzymes N-acyltransferase and N-acyl-phosphatidylethanolamines-specific phospholipase D. We also show that activation of CB1R enhances AMT activity through increased nitric oxide synthase (NOS) activity and subsequent increase of NO production. AMT activity is instead reduced by activation of CB2R, which inhibits NOS and NO release. In addition, binding experiments and immunoelectronmicroscopy demonstrate that different endothelial cells vary in the expression of CB1R and CB2R on the luminal and/or abluminal sides. The different localization of CBRs can lead to a diverse effect on AMT activity on the luminal and abluminal membranes, suggesting that the distribution of these receptors may drive AEA directional transport through the blood-brain barrier and other endothelial cells.

A reassessment of semiquantitative analytical procedures for DNA methylation: comparison of bisulfite- and HpaII polymerase-chain-reaction-based methods.

Two techniques in particular are used to study site-specific DNA methylation: genomic sequencing after bisulfite modification and polymerase chain reaction after digestion by a methylation-sensitive endonuclease (usually HpaII). Only the former methodology assesses the methylation status of all the cytosine residues in the DNA sequence, but it is so complex and time consuming that the latter procedure, though limited to the restriction sites recognized by the endonuclease(s) used, is often preferred at least for a first analysis. In this work we investigate differences between these two techniques in the assessment of DNA methylation and offer some suggestions on how to avoid uncorrected results. Although there is substantial accordance in the results obtained using these different techniques, we observed a general overestimate for methylation levels above 30% and a general underestimate for methylation levels below this value using the HpaII/PCR technique in the study of methylation of the 5'-flanking region of the mouse myogenin gene in cultured muscle cells and mouse tissues.

Reduced circulating natural killer T cells and gamma/delta T cells in patients with systemic sclerosis.

OBJECTIVE: To evaluate peripheral blood mononuclear cells (PBMC) expressing natural killer (NK) cell surface markers (CD16 and CD56, in both CD3- and CD3+ cells) and g/d T cell receptors (TCR) involved in non-MHC-restricted cytotoxicity, assessing their possible relationship with clinical and laboratory variables in patients with systemic sclerosis (SSc). METHODS: We submitted 50 patients with SSc to detailed clinical and laboratory assessment, and also performed PBMC subset analyses by direct dual immunofluorescence and flow cytometry. RESULTS: No statistically significant differences were found in the percentages or the absolute numbers of total lymphocytes, of B cells, and of CD4+ T cells. The absolute number of CD8+ cells was lower (p < 0.03), while HLA-DR+ elements were higher in frequency (p < 0.03) in SSc patients than in healthy controls. SSc patients had lower values (both percentage and absolute number) of NK-T cells (p < 0.01 and p < 0.003, respectively) and of T cells expressing g/d TCR (p < 0.01 and p < 0.005, respectively); whereas NK cells were marginally but not significantly decreased. The absolute number of NK-T cells showed an inverse correlation to erythrocyte sedimentation rate values (p < 0.03; rs = -0.306), percentage of g-globulins (p < 0.01; rs = -0.353), and serum concentrations of IgG (p < 0.02; rs = -0.334). CONCLUSION: Impairment of NK-T cells and of T cells expressing g/d TCR may lead to downregulation of normal immune response, and seems to be important for immunological and inflammatory aspects of SSc.

High frequency of (TG)mTn variant tracts in the cystic fibrosis transmembrane conductance regulator gene in men with high semen viscosity.

OBJECTIVE: To evaluate a possible correlation between abnormal semen consistency and cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations and variant tracts. DESIGN: Study of CFTR mutations and variant tracts in men with high semen viscosity as compared with normospermic men. SETTING: University-based centers for andrology, clinical biochemistry, and cystic fibrosis. PATIENT(S): Forty-six male partners from infertile couples with sine causa high semen viscosity compared with 72 normospermic men. INTERVENTION(S): Semen sample collection. MAIN OUTCOME MEASURE(S): We obtained the (TG)mTn polymorphic tracts and a panel of 31 mutations of CFTR, semen viscosity, and semen variables. RESULT(S): The frequencies of the (TG)12 and T5 variant alleles were statistically significantly higher in men with high semen viscosity (17.4% and 7.6%, respectively) than in the normospermic control group (6.9% and 1.4%, respectively). The frequency of the genotypes carrying (TG)12 or T5 was statistically significantly higher in men with high semen viscosity (39.1%) than in the normospermic control group (16.7%). Four men with high semen viscosity showed the variant (TG)12T5 haplotype; one of these men presented variant tracts on both alleles. None of the normospermic controls showed a (TG)12T5 haplotype. CONCLUSION(S): Semen hyperviscosity could be considered a "minimal clinical expression" of cystic fibrosis; CFTR gene sequence variations may constitute the genetic basis for this disease.

Expression of OP4 (ORL1, NOP1) receptors in vascular endothelium.

Endothelial cells from rat brain microvessels, human aortic artery and human umbilical vein were examined, together with ex vivo rat brain capillaries and rat aortic ring sections, for the expression of opioid receptor-like OP-4 mRNA and protein. High levels of mRNA expression and an immunopositive reaction for the receptor protein were detected in the endothelial cells from primary and from established in vitro cultures, as well as in the intima of ex vivo rat aortic rings, where the signal was limited to the endothelial layer. Interaction of the OP4 receptor with its physiological ligand nociceptin caused, in cultured endothelial cells, the activation of a mitogen-activated protein (MAP) kinase cascade. Taken together, these results show that the OP4 receptor is synthesised and functionally expressed in endothelial cells, presumably as a starting point for some vasoactive mechanism(s).

Triacsin C inhibits the formation of 1H NMR-visible mobile lipids and lipid bodies in HuT 78 apoptotic cells.

Nuclear magnetic resonance-visible mobile lipids (ML) have been reported to accumulate during cell apoptosis in vitro and in vivo. The biogenesis, biochemical nature and structure of these lipids are still under debate. In this study, a human lymphoblastoid cell line, HuT 78, was induced to apoptosis by exposure to anti-Fas monoclonal antibodies (alpha-Fas mAb) followed by incubation for different time intervals (1-24 h, hypodiploid cell fraction, H, varying from 1% to over 60%) either in the presence or in the absence of 5.0 microM Triacsin C (TRC), specific inhibitor of long-chain acyl-CoA synthetase (ACS). The increase of ML in apoptotic cells correlated linearly with H and was associated with: (a) accumulation of intracellular lipid bodies, detected by confocal laser scanning microscopy in lipophilic dye-stained cells; (b) increases, detected by thin-layer chromatography in total lipid extracts, in the relative abundance of triacylglycerides (TAG) and cholesteryl esters (CE), with corresponding decreases of phospholipids (PL). TRC completely abolished both ML and lipid body formation in anti-Fas-treated apoptotic cells, with concomitant reversion of TAG, CE and PL to control levels, but did not alter cell viability nor did it inhibit apoptosis. ML signals detected during anti-Fas-induced apoptosis therefore appear to originate from neutral lipids assembled in intracellular lipid bodies, synthesised from cellular acyl-CoA pools.

Two-step formation of 1H NMR visible mobile lipids during apoptosis of paclitaxel-treated K562 cells.

Despite increasing evidence on the formation of 1H NMR-detectable mobile lipid (ML) domains in cells induced to programmed cell death by continuous exposure to anticancer drugs, the time course of ML generation during the apoptotic cascade has not yet been fully elucidated. The present study shows that ML formation occurs at two different stages of apoptosis induced in human erythroleukemia K562 cells by a brief (3 hr) exposure to paclitaxel (Taxol), an antitumour drug with a stabilising effect on microtubules, or to paclitaxel plus tyrphostin AG957, a selective inhibitor of the p210(BCR-ABL) tyrosine kinase activity. A first wave of ML generation was in fact detected in paclitaxel-treated cells at the onset of the effector phase (8-24hr after exposure to the drug), plateaued at 24-48 hr and was eventually followed by further ML accumulation during the degradative phase (48-72 hr). Addition of AG957 to paclitaxel shifted to the 3-8 hr interval in both the early ML production and the onset of apoptotic events, such as chromatin condensation, phosphatidylserine externalization, cytochrome c release and caspase-3 activation. A significant loss of mitochondrial membrane potential was almost concomitant with the second wave of ML accumulation, associated in both cell systems with the phase of terminal cell degeneration, likely connected to non-regulated degradation of cell lipid components.

The expression of native and oxidized LDL receptors in brain microvessels is specifically enhanced by astrocytes-derived soluble factor(s).

Ex vivo rat brain microvessels express receptors for native as well as for oxidized low-density lipoproteins. In brain microvessels-derived endothelial cells, the expression levels of both receptors were enhanced by co-cultivation with rat astrocytes, even in the absence of actual contact between the two cell types, suggesting a soluble factor(s)-based mechanism of induction. No modulation effect could be evidenced in a heterologous cellular system. Since both receptors were found to be expressed also in astrocytes, these cells are likely to contribute substantially to the lipoprotein management at the blood-brain barrier and in the brain compartment.