Identification of Genes Whose Expression Profile Is Associated with Non-Progression towards AIDS Using eQTLs

Background

Many genome-wide association studies have been performed on progression towards the acquired immune deficiency syndrome (AIDS) and they mainly identified associations within the HLA loci. In this study, we demonstrate that the integration of biological information, namely gene expression data, can enhance the sensitivity of genetic studies to unravel new genetic associations relevant to AIDS.

Methods

We collated the biological information compiled from three databases of expression quantitative trait loci (eQTLs) involved in cells of the immune system. We derived a list of single nucleotide polymorphisms (SNPs) that are functional in that they correlate with differential expression of genes in at least two of the databases. We tested the association of those SNPs with AIDS progression in two cohorts, GRIV and ACS. Tests on permuted phenotypes of the GRIV and ACS cohorts or on randomised sets of equivalent SNPs allowed us to assess the statistical robustness of this method and to estimate the true positive rate.

Results

Eight genes were identified with high confidence (p = 0.001, rate of true positives 75%). Some of those genes had previously been linked with HIV infection. Notably, ENTPD4 belongs to the same family as CD39, whose expression has already been associated with AIDS progression; while DNAJB12 is part of the HSP90 pathway, which is involved in the control of HIV latency. Our study also drew our attention to lesser-known functions such as mitochondrial ribosomal proteins and a zinc finger protein, ZFP57, which could be central to the effectiveness of HIV infection. Interestingly, for six out of those eight genes, down-regulation is associated with non-progression, which makes them appealing targets to develop drugs against HIV.     

Diversity of bacteriocinogenic lactic acid bacteria isolated from Mediterranean fish viscera

Nine lactic acid bacteria strains showing bacteriocin-like activity were isolated from various fresh fish viscera. The following species were identified based on 16S rDNA sequences: Enterococcus durans (7 isolates), Lactococcus lactis (1) and Enterococcus faecium (1). These strains were active against Listeria innocua and other LAB. Random amplified polymorphic DNA analyses showed four major patterns for the E. durans species. PCR analyses revealed a nisin gene in the genome of the Lc. lactis strain. Genes coding enterocins A, B and P were found in the genome of the E. faecium isolate. Enterocins A and B genes were also present in the genome of E. durans GM19. Hence, this is the first report describing E. durans strains producing enterocins A and B. Electrospray ionization mass spectrometry revealed that the purified bacteriocin produced by the E. durans GMT18 strain had an exact molecular mass of 6,316.89 Da. This bacteriocin was designated as durancin GMT18. Edman sequencing failed to proceed; suggesting that durancin GTM18 may contain terminal lanthionine residues. Overall, the results obtained revealed the presence of a variety of enterococci in Mediterranean fish viscera, as evidenced by their genetic profiles and abilities to produce different bacteriocins. These strains could be useful for food biopreservation or as probiotics.     

Selective alteration at the growth-hormone- releasing-hormone nerve terminals during aging in GHRH-green fluorescent protein mice

Growth hormone (GH) secretion decreases spontaneously during lifespan, and the resulting GH deficiency participates in aging-related morbidity. This deficiency appears to involve a defect in the activity of hypothalamic GH-releasing hormone (GHRH) neurons. Here, we investigated this hypothesis, as well as the underlying mechanisms, in identified GHRH neurons from adult ( approximately 13 weeks old) and aged ( approximately 100 weeks old) transgenic GHRH-green fluorescent protein mice, using morphological, biochemical and electrophysiological methods. Surprisingly, the spontaneous action potential frequency was similar in adult and aged GHRH neurons studied in brain slices. This was explained by a lack of change in the intrinsic excitability, and simultaneous increases in both stimulatory glutamatergic- and inhibitory GABAergic-synaptic currents of aged GHRH neurons. Aging did not decrease GHRH and enhanced green fluorescent protein contents, GHRH neuronal number or GHRH-fibre distribution, but we found a striking enlargement of GHRH-positive axons, suggesting neuropeptide accumulation. Unlike in adults, autophagic vacuoles were evident in aged GHRH-axonal profiles using electron microscopy. Thus, GHRH neurons are involved in aging of the GH axis. Aging had a subtle effect at the nerve terminal level in GHRH neurons, contrasting with the view that neuronal aging is accompanied by more widespread damage.     

CD25 Appears Non Essential for Human Peripheral Treg Maintenance In Vivo

Background

IL-2 has been reported to be critical for peripheral T_reg survival in mouse models. Here, we examined T_reg maintenance in a series of paediatric liver transplant recipients who received basiliximab, a therapeutic anti-CD25 monoclonal antibody.

Methodology/Principal Findings

FoxP3⁺ CD4 T cells were analyzed by flow cytometry before liver grafting and more than 9 months later. We found that in vivo CD25 blockade did not lead to T_reg depletion: the proportion of FoxP3⁺ cells among CD4 T cells and the level of FoxP3 expression were both unchanged. IL-2Rβ expression was enhanced in FoxP3⁺ cells both before and after basiliximab treatment, while the level of IL-2Rγ expression was similar in T_regs and non-T_regs. No significant change in the weak or absent expression of IL-7Rα and IL-15Rα expression on FoxP3⁺ cells was observed. Although the proportion of FoxP3⁺ cells among CD4 T cells did not vary, food allergies occurred more rapidly after liver grafting in patients who received basiliximab, raising questions as to T_reg functionality in vivo in the absence of functional CD25.

Conclusions

CD25 appears non essential for human T_reg peripheral maintenance in vivo. However, our results raise questions as to T_reg functionality after therapeutic CD25 targeting.     

Adhesion molecules (ICAM-1 and VCAM-1) and diabetic retinopathy in type 2 diabetes

The expression of intercellular adhesion molecule (ICAM-1) and vascular cell adhesion molecule (VCAM-1) were studied in the conjunctiva of diabetic patients with and without retinopathy. All patients underwent a complete ophthalmic examination including ocular fundus and retinal fluorescein angiography. The indirect immunoperoxidase method was performed on 15 normal conjunctivas taken during cataract surgery (group 1), on 40 eyes of 40 patients with type 2 diabetes without diabetic retinopathy (DR) (group 2) and 13 eyes of 13 patients with DR (group 3). ICAM-1 and VCAM-1 are located in epithelial cells, vascular endothelial cells and in stromal cells. Our results show a statistically significant increase in the immunohistochemical expression of these proteins in the conjunctiva of diabetic patients with and without DR in comparison with normal conjunctiva (P = 0.001). Noteworthy, ICAM-1 and VCAM-1 are upregulated in the conjunctiva of diabetic patients with and without retinopathy, reflecting the inflammatory nature of this condition and suggesting a possible role for these mediators in the pathogenesis of diabetic microangiopathy.     

Proteome analysis reveals novel proteins associated with proliferation and differentiation of the colorectal cancer cell line Caco-2

Here, we describe a proteomics approach to study protein expression changes in differentiating Caco-2 cells. Caco-2 is a colorectal carcinoma cell line, which upon differentiation loses its tumorigenic phenotype and displays characteristics of mature enterocytes, including brush borders with microvilli. Cells were grown in culture flasks and harvested at different stages of differentiation (days post-confluence: -3, 0, 3, 7, 10, 14, and 18). Two-dimensional gel electrophoresis was used to analyse proteome changes. Approximately 1400 protein spots were detected within the Caco-2 proteome, within the pH 4-7 range. Two-dimensional gel electrophoresis allowed for the detection of 18 proteins from which the levels of expression were found to be associated with differentiation. Of these proteins, 11 were identified by means of MALDI-TOF or NANO-ESI-MS/MS mass spectrometry and include liver fatty acid binding protein (FABL), three forms of alpha-enolase (ENOA), nucleoside diphosphate kinase A (NDKA), cofilin-1 (COF1), translationally controlled tumour protein (TCTP), mitochondrial 60-kDa heat shock protein (CH60), probable protein disulfide isomerase (ER60), creatine kinase B (KCRB), and glutathione S-transferase alpha (GTA1). Thus, proteomics revealed that the differentiation-related change in phenotype of Caco-2 involves changes in a variety of distinct biochemical pathways. Some of these proteins have not been shown before to be associated with Caco-2 differentiation (ER60; COF1; CH60; NDKA; TCTP and ENOA). Therefore, processes related to protein folding and disulfide bridge formation, cytoskeleton formation and maintenance, nucleotide metabolism, glycolysis as well as tumorigenesis-associated proteins may be involved in Caco-2 differentiation. Changes in the expression of CH60, TCTP, GTA1, NDKA, and FABL have also been reported to be associated with in vivo colon carcinogenesis. These findings illustrate that a combination of proteomics and cell culture is a useful approach to find markers for Caco-2 differentiation, which could contribute to the comprehension of the process of colon carcinogenesis.     

Evidence for the utility of the Bm86 antigen from Boophilus microplus in vaccination against other tick species

The Bm86 antigen, as originally identified in Boophilus microplus, is the basis of commercial tick vaccines against this tick species. The potential for using this antigen or homologues of the antigen in vaccination against other tick species has been assessed. We have conducted vaccine trials in cattle using the B. microplus-derived recombinant Bm86 vaccine (TickGARD) using pairs of vaccinated calves and control calves. These were infested with B. microplus and Boophilus decoloratus larvae simultaneously. For both species, the numbers of engorged female adult ticks, their weight and egg-laying capacity were all reduced, leading to a reduction in reproductive capacity of 74% for B. microplus and 70% for B. decoloratus. Hyalomma anatolicum anatolicum ticks were fed both as immatures as well as adults on vaccinated calves and non-vaccinated controls. There was an overall 50% reduction in the total weight of nymphs engorging on vaccinated calves, and a suggestion of a subsequent effect on feeding adults. For Hyalomma dromedarii there was a 95% reduction in the number of nymphs engorging and a further 55% reduction in weight of those ticks surviving. Rhipicephalus appendiculatus and Amblyomma variegatum ticks were fed simultaneously both as immatures and subsequently as adults. There was no evidence for a significant vaccination effect. Finally, the amino acid sequence of a Bm86 homologue found in H. a. anatolicum unequivocally demonstrated the conservation of this molecule in this species. Our strategy for the development of multivalent anti-tick vaccines is discussed in relation to these findings.     

Anaerobic digestion of palm oil mill effluent and condensation water waste: an overall kinetic model for methane production and substrate utilization

The process of anaerobic digestion is viewed as a series of reactions which can be described kinetically both in terms of substrate utilization and methane production. It is considered that the rate limiting factor in the digestion of complex wastewaters is hydrolysis and this cannot be adequately described using a Monod equation. In contrast readily assimilable wastewaters conform well to this approach. A generalized equation has thus been derived, based on both the Monod and Contois equations, which serves extreme cases. The model was verified experimentally using continuous feed anaerobic digesters treating palm oil mill effluent (POME) and condensation water from a thermal concentration process. POME represents a complex substrate comprising of unhydrolyzed materials whereas the condensation water is predominantly short chain volatile fatty acids. Substrate removal and methane production in both cases could be predicted accurately using the generalized equation presented.List of Symbols A (=K_skY/K_h) Kinetic parameter - B Specific methane yield, 1 of CH₄/g of substrate added B₀ Maximum specific methane yield, 1 of CH₄/g of substrate added at infinity - C Empirical constant in Contois equation - F Volumetric substrate removal rate, g/l day - k Hydrolysed substrate transport rate coefficient, 1/days - K (=YC) Kinetic parameter in Chen-Hashimoto equation - K _h Substrate hydrolysis rate coefficient, 1/days - K _s Half-saturation constant for hydrolysed substrate, g/l - M _v Volumetric methane production rate, 1 of CH₄/l day - MS Mineral solids, g/l - MSS Mineral suspended soilds, g/l - POME Palm oil mill effluent - R (=S_r/S_T0) Refractory coefficient - S _h Concentration of hydrolysed substrate, g/l - S _u Intracellular concentration of hydrolysed substrate, g/l - S ₀ Input biodegradable substrate concentration, g/l - S Biodegradable substrate concentration in the effluent or in the digester, g/l - S _r Refractory feed substrate concentration, g/l - S _T0 (=S₀+S_r) Total feed substrate concentration, g/l - S _T (S+S_r) Total substrate concentration in the effluent, g/l - TS Total solids, g/l - TSS Total suspended solids, g/l - VFA Total volatile fatty acids, g/l - VS Volatile solids, g/l - VSS Volatile suspended solids, g/l - X Biomass concentration, g/l - Y Biomass yield coefficient, biomass/substrate mass - Hydraulic retention time, days. - Specific growth rate of microorganisms, l/days - _m Maximum specific growth rate of microorganisms, l/days The authors wish to express their gratitude to the Departamento de Postgrado y Especialización del CSIC and to the Consejería de Educación y Ciencia de la Junta de Andalucia for their financial support of this work.