Lifestyle Risk Score: handling missingness of individual lifestyle components in meta-analysis of gene-by-lifestyle interactions

Recent studies consider lifestyle risk score (LRS), an aggregation of multiple lifestyle exposures, in identifying association of gene-lifestyle interaction with disease traits. However, not all cohorts have data on all lifestyle factors, leading to increased heterogeneity in the environmental exposure in collaborative meta-analyses. We compared and evaluated four approaches (Naïve, Safe, Complete and Moderator Approaches) to handle the missingness in LRS-stratified meta-analyses under various scenarios. Compared to “benchmark” results with all lifestyle factors available for all cohorts, the Complete Approach, which included only cohorts with all lifestyle components, was underpowered due to lower sample size, and the Naïve Approach, which utilized all available data and ignored the missingness, was slightly inflated. The Safe Approach, which used all data in LRS-exposed group and only included cohorts with all lifestyle factors available in the LRS-unexposed group, and the Moderator Approach, which handled missingness via moderator meta-regression, were both slightly conservative and yielded almost identical p values. We also evaluated the performance of the Safe Approach under different scenarios. We observed that the larger the proportion of cohorts without missingness included, the more accurate the results compared to “benchmark” results. In conclusion, we generally recommend the Safe Approach, a straightforward and non-inflated approach, to handle heterogeneity among cohorts in the LRS based genome-wide interaction meta-analyses.Subject terms: Genetics, Risk factors     

Controlled elimination of intracellular H(2)O(2): regulation of peroxiredoxin, catalase, and glutathione peroxidase via post-translational modification

The predominant enzymes responsible for elimination of hydrogen peroxide (H(2)O(2)) in cells are peroxiredoxins (Prxs), catalase, and glutathione peroxidases (GPxs). Evidence suggests that catalytic activities of certain isoforms of these H(2)O(2)-eliminating enzymes are extensively regulated via posttranslational modification. Prx I and Prx II become inactivated when phosphorylated on Thr(90) by cyclin B-dependent kinase Cdc2. In addition, the active-site cysteine of Prx I-IV undergoes a reversible sulfinylation (oxidation to cysteine sulfinic acid) in cells. Desulfinylation (reduction to cysteine) is achieved by a novel enzyme named sulfiredoxin. c-Abl and Arg nonreceptor protein tyrosine kinases associate with catalase in cells treated with H(2)O(2) by mechanisms involving the SH3 domains of the kinases and the Pro(293)PheAsnPro motif of catalase and activate catalase by phosphorylating it on Tyr(231) and Tyr(386). Similarily, GPx1 is activated by c-Abl- and Arg-mediated phosphorylation. The tyrosine phosphorylation is critical for ubiquitination-dependent degradation of catalase.     

Prion protein is ubiquitinated after developing protease resistance in the brains of scrapie-infected mice

Although the key event in the pathology of prion diseases is thought to be the conversion of cellular prion protein (PrP(C)) to the protease-resistant scrapie species termed PrP(Sc), the factors that contribute to neurodegeneration in scrapie-infected animals are poorly understood. One probable determinant could be when the accumulation of PrP(Sc) in infected brain overwhelms the ubiquitin-proteasome system and triggers the degenerative cascade. In the present study, it was found that in mouse brains infected with the ME7 scrapie strain, the level of ubiquitin protein conjugates increased significantly at approximately 144 days post-infection (pi) when clinical signs first become apparent. This elevation correlated with the detection of protease-resistant PrP(Sc) and a decline in two endopeptidase activities associated with proteasome function. However, ubiquitination of PrP was only detected at the terminal stage, 3 weeks after the development of clinical symptoms (approximately 165 days pi). These results suggest that ubiquitination of PrP is a late event phenomenon and this conjugation occurs after the formation of protease-resistant PrP(Sc). Whether this post-translational modification and the impairment of proteasome function are pivotal events in the pathogenesis of prion diseases remains to be determined.     

Real-time PCR assay for detection of fluoroquinolone resistance associated with grlA mutations in Staphylococcus aureus

Resistance to fluoroquinolones among clinical isolates of Staphylococcus aureus has become a clinical problem. Therefore, a rapid method to identify S. aureus and its susceptibility to fluoroquinolones could provide clinicians with a useful tool for the appropriate use of these antimicrobial agents in the health care settings. In this study, we developed a rapid real-time PCR assay for the detection of S. aureus and mutations at codons Ser-80 and Glu-84 of the grlA gene encoding the DNA topoisomerase IV, which are associated with decreased susceptibility to fluoroquinolones. The detection limit of the assay was 10 genome copies per reaction. The PCR assay was negative with DNA from all 26 non-S. aureus bacterial species tested. A total of 85 S. aureus isolates with various levels of fluoroquinolone resistance was tested with the PCR assay. The PCR assay correctly identified 100% of the S. aureus isolates tested compared to conventional culture methods. The correlation between the MICs of ciprofloxacin, levofloxacin, and gatifloxacin and the PCR results was 98.8%. The total time required for the identification of S. aureus and determination of its susceptibility to fluoroquinolones was about 45 min, including DNA extraction. This new rapid PCR assay represents a powerful method for the detection of S. aureus and its susceptibility to fluoroquinolones.     

Gamma interferon responses induced by a panel of recombinant and purified mycobacterial antigens in healthy,non-mycobacterium bovis BCG-vaccinated Malawian young adults

We have previously shown that young adults living in a rural area of northern Malawi showed greater gamma interferon (IFN-gamma) responses to purified protein derivatives (PPD) prepared from environmental mycobacteria than to PPD from Mycobacterium tuberculosis. In order to define the mycobacterial species to which individuals living in a rural African population have been exposed and sensitized, we tested T-cell recognition of recombinant and purified antigens from M. tuberculosis (38 kDa, MPT64, and ESAT-6), M. bovis (MPB70), M. bovis BCG (Ag85), and M. leprae (65 kDa, 35 kDa, and 18 kDa) in >600 non-M. bovis BCG-vaccinated young adults in the Karonga District of northern Malawi. IFN-gamma was measured by enzyme-linked immunosorbent assay (ELISA) in day 6 supernatants of diluted whole-blood cultures. The recombinant M. leprae 35-kDa and 18-kDa and purified native M. bovis BCG Ag85 antigens induced the highest percentages of responders, though both leprosy and bovine tuberculosis are now rare in this population. The M. tuberculosis antigens ESAT-6 and MPT64 and the M. bovis antigen MPB70 induced the lowest percentages of responders. One of the subjects subsequently developed extrapulmonary tuberculosis; this individual had a 15-mm-diameter reaction to the Mantoux test and responded to M. tuberculosis PPD, Ag85, MPT64, and ESAT-6 but not to any of the leprosy antigens. We conclude that in this rural African population, exposure to M. tuberculosis or M. bovis is much less frequent than exposure to environmental mycobacteria such as M. avium, which have antigens homologous to the M. leprae 35-kDa and 18-kDa antigens. M. tuberculosis ESAT-6 showed the strongest association with the size of the Mantoux skin test induration, suggesting that among the three M. tuberculosis antigens tested it provided the best indication of exposure to, or infection with, M. tuberculosis.     

Structural control of immunogenicity. II. Antibody synthesis and cellular immunity in response to immunization with mono-epsilon-oligo-L-lysines

A detailed evaluation of the capacity of mono-ε-DNP-oligo-L-lysines to initiate anti-DNP antibody synthesis and a state of delayed hypersensitivity in guinea-pigs is presented. Peptides containing as few as two lysine residues elicit the production of significant amounts of anti-DNP antibody when they are administered as Freund''s complete adjuvant emulsions. Under these immunization conditions, the serum concentration of anti-DNP antibody is dependent on the chain length of the peptide, and on the amount and kind of mycobacteria in the adjuvant; guinea-pigs lacking the PLL gene produce amounts of anti-DNP antibody indistinguishable from that produced by guinea-pigs possessing this gene. On the other hand, when guinea-pigs are immunized with either 1-ε-DNP-tetra-L-lysine or 1-ε-DNP-nona-L-lysine without the use of mycobacterial adjuvant, anti-DNP antibody is produced only by guinea-pigs receiving the nona-L-lysine and only by those animals possessing the PLL gene.Delayed hypersensitivity results from immunizing PLL+ guinea-pigs with mono-ε-DNP-octa and nona-lysines but not from immunization with mono-ε-DNP-hexa-lysine; PLL— animals do not exhibit delayed hypersensitivity to any of these compounds.The data suggest that antibody synthesis to positively charged compounds may proceed as a result of formation of charge complexes with mycobacterial proteins; under such immunization conditions the intrinsic immunogenicity of a compound is more reliably revealed by the induction or elicitation of cellular immune responses. On this basis, a definite discontinuity in the degree of immunogenicity of the mono-ε-DNP-oligo-L-lysines occurs as the peptides are lengthened from six to eight residues.     

Translocation (X;20) involving the inactive X chromosome in a patient with myeloproliferative disorder

We report a patient with an unclassifiable myeloproliferative disorder and the rare t(X;20)(q13;q13.3) as the sole cytogenetic abnormality. The breakpoint on Xq is consistent with other reports of translocations involving the X chromosome with breakpoints that cluster to Xq13 and association with myeloid disorders. Late replication studies demonstrated the inactive X chromosome was involved in this translocation. The critical event in patients with myeloproliferative disease and deletion of 20q appears to be the loss of tumor suppressor genes. This may also be the mechanism in this patient with a potential cryptic deletion associated with the translocation. Alternatively, spreading of X inactivation into the derivative chromosome 20 provides a second mechanism for the loss of function of tumor suppressor genes on 20q. The finding in this patient of t(X;20) together with three others reported in the literature indicates that this may represent a primary non-random abnormality associated with myeloid malignancy, which may take on clinical significance with the accumulation of more cases.     

Analysis of IFN-kappa expression in pathologic skin conditions: downregulation in psoriasis and atopic dermatitis.

Interferon-kappa (IFN-kappa) is a type I IFN expressed by keratinocytes, monocytes and dendritic cells (DCs). In human keratinocytes, it is produced in response to double-stranded RNA (dsRNA) and other IFNs and protects from viral infections. In monocytes and DCs, IFN-kappa induces tumor necrosis factor-alpha (TNF-alpha) and interleukin-10 (IL-10) and inhibits lipopolysaccharide (LPS)-induced IL-12. In this study, we evaluated IFN-kappa expression in skin lesions of patients with common immune-mediated inflammatory disorders using immunohistochemical techniques. IFN-kappa was not detectable in healthy skin but was strongly expressed in allergic contact dermatitis and lichen planus-affected skin. IFN-kappa was localized mainly in basal and suprabasal keratinocytes and in some leukocytes infiltrating the dermis. In contrast, IFN-kappa expression in psoriatic or atopic dermatitis (AD) pidermis was weak and detectable in only 2 of 5 patients examined. Consistently, cultured keratinocytes and monocytes obtained from psoriatic and AD patients expressed null or low levels of IFN-kappa in response to IFN-gamma, which strongly upregulates IFN-kappa in normal keratinocytes. IFN-kappa accumulated in keratinocyte cytoplasm and plasma membrane, and only limited amounts were released extracellularly. Soluble IFN-kappa did not influence keratinocyte proliferation or chemokine and membrane molecule expression, and only its membrane-associated form activated IFN-stimulated response element (ISRE) signaling. Given the difference in IFN-kappa expression levels in the skin disorders examined, IFN-kappa presence or deficiency might have different pathogenetic consequences depending also on other disease-specific intrinsic alterations.     

Molecular epidemiology of rotaviral infection in South Indian children with acute diarrhea from 1995-1996 to 1998-1999

The distribution of VP7 (G-) and VP4 (P-) genotypes among 126 rotavirus strains from South Indian children, < 5 years of age and with acute diarrhoea, presenting to a single hospital during the months to November and December, from 1995 to 1998, was studied. Multiplex hemi-nested G- and P-typing polymerase chain reactions determined 101 (80%) G types and 78 (61%) P types, respectively. In order of frequency, the commonest G types were G1, G4, G2, G9, G3, and G8, and P types were P1B[4], P1A[8], and P2A[6] and the most common G:P combinations were G1:P1A[8], G1:P1B[4], G2P1B[4] and G4:P1A[8]. G1, G2, and G4 types were seen in all years. The single G3 isolate was seen in 1998. The single G8 isolate and the 5 G9 isolates were seen in 1997, after a period of heavy rain. Sequence analysis showed that the G8 isolate was related most closely to the bovine strain A5, and the G9 strains were distinct from the nonpathogenic Indian isolate 116E and similar to G9s isolated in Mysore and the United Kingdom described previously.