T cells from Programmed Death-1 deficient mice respond poorly to Mycobacterium tuberculosis infection

Background

Programmed Death-1 (PD-1; CD279) receptor molecule is widely believed to be a negative regulator predominantly expressed by exhausted/activated mouse T cells. Upon interaction with its ligands, PD-L1 and PD-L2, PD-1 inhibits activation of T cells and cytokine production, which has been documented in various viral and fungal infections as well as in vitro studies. Therefore, inhibition of T cell responses by PD-1 resulted in disease resistance in a variety of mouse infection models studied heretofore.

Methodology/Principal Findings

Here, we report that PD-1 deficient (PD-1^−/−) mice infected with Mycobacterium tuberculosis (M. tb) H37Rv by the aerosol route have increased susceptibility as compared with their wild type littermates. Surprisingly, M. tb antigen-specific T cell proliferation was dramatically reduced in PD-1 deficient animals compared with wild-type littermates, and this was due to increased numbers of regulatory T cells (Tregs) and recruitment of mesenchymal stem cells. Furthermore, PD-1^−/− mice exhibited decreases in the autophagy-induced LC3-B marker protein in macrophages.

Conclusions/Significance

Our findings suggest that PD-1 does not play an inhibitory role during M. tb infection and instead promotes mycobacterial clearance in mice.     

Mannose-6-phosphate regulates destruction of lipid-linked oligosaccharides

Mannose-6-phosphate (M6P) is an essential precursor for mannosyl glycoconjugates, including lipid-linked oligosaccharides (LLO; glucose(3)mannose(9)GlcNAc(2)-P-P-dolichol) used for protein N-glycosylation. In permeabilized mammalian cells, M6P also causes specific LLO cleavage. However, the context and purpose of this paradoxical reaction are unknown. In this study, we used intact mouse embryonic fibroblasts to show that endoplasmic reticulum (ER) stress elevates M6P concentrations, leading to cleavage of the LLO pyrophosphate linkage with recovery of its lipid and lumenal glycan components. We demonstrate that this M6P originates from glycogen, with glycogenolysis activated by the kinase domain of the stress sensor IRE1-α. The apparent futility of M6P causing destruction of its LLO product was resolved by experiments with another stress sensor, PKR-like ER kinase (PERK), which attenuates translation. PERK's reduction of N-glycoprotein synthesis (which consumes LLOs) stabilized steady-state LLO levels despite continuous LLO destruction. However, infection with herpes simplex virus 1, an N-glycoprotein-bearing pathogen that impairs PERK signaling, not only caused LLO destruction but depleted LLO levels as well. In conclusion, the common metabolite M6P is also part of a novel mammalian stress-signaling pathway, responding to viral stress by depleting host LLOs required for N-glycosylation of virus-associated polypeptides. Apparently conserved throughout evolution, LLO destruction may be a response to a variety of environmental stresses.     

Oxidative Stress is Associated with Genetic Polymorphisms in One-Carbon Metabolism in Coronary Artery Disease

In view of growing body of evidence favouring the association of aberrations in one-carbon metabolism and oxidative stress in the aetiology of coronary artery disease (CAD), we investigated the risk associated with polymorphisms regulating the folate uptake and transport such as the glutamate carboxypeptidase II (GCPII) C1561T, reduced folate carrier 1 (RFC1) G80A and cytosolic serine hydroxymethyltransferase (cSHMT) C1420T. We further evaluated the impact of seven putatively functional polymorphisms of this pathway on oxidative stress markers. Genotyping was performed on 288 CAD cases and 266 healthy controls along with the dietary folate assessment. GCPII C1561T polymorphism was found to be an independent risk factor (OR 2.71, 95% CI 1.47–4.98) for CAD, whereas cSHMT C1420T conferred protection (OR 0.51, 95% CI 0.37–0.70). Oxidative stress markers like the plasma levels of malondialdehyde, protein carbonyls and 8-oxo-deoxyguanosine were significantly increased and total glutathione was significantly decreased in CAD cases. Elevated oxidative stress was observed in subjects carrying GCPII 1561T and MTRR 66A-variant alleles and low oxidative stress was observed in the subjects carrying cSHMT 1420T and TYMS 5′-UTR 2R allele. GCPII C1561T, MTHFR C677T and MTRR A66G polymorphisms were observed to influence the homocysteine levels (P < 0.05). SHMT and TYMS variants were found to decrease oxidative stress by increasing the folate pool (r = 0.38, P = 0.003) and also by increasing the antioxidant status (r = 0.28, P = 0.03). Influence of dietary folate status was not observed. Overall, this study revealed elevated oxidative stress that was associated with the aberrations in one-carbon metabolism which could possibly influence the CAD risk.     

Edge effects in calling variants from targeted amplicon sequencing

Background

Analysis of targeted amplicon sequencing data presents some unique challenges in comparison to the analysis of random fragment sequencing data. Whereas reads from randomly fragmented DNA have arbitrary start positions, the reads from amplicon sequencing have fixed start positions that coincide with the amplicon boundaries. As a result, any variants near the amplicon boundaries can cause misalignments of multiple reads that can ultimately lead to false-positive or false-negative variant calls.

Results

We show that amplicon boundaries are variant calling blind spots where the variant calls are highly inaccurate. We propose that an effective strategy to avoid these blind spots is to incorporate the primer bases in obtaining read alignments and post-processing of the alignments, thereby effectively moving these blind spots into the primer binding regions (which are not used for variant calling). Targeted sequencing data analysis pipelines can provide better variant calling accuracy when primer bases are retained and sequenced.

Conclusions

Read bases beyond the variant site are necessary for analysis of amplicon sequencing data. Enzymatic primer digestion, if used in the target enrichment process, should leave at least a few primer bases to ensure that these bases are available during data analysis. The primer bases should only be removed immediately before the variant calling step to ensure that the variants can be called irrespective of where they occur within the amplicon insert region.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1073) contains supplementary material, which is available to authorized users.     

20-Iodo-14,15-epoxyeicosa-8(Z)-enoyl-3-azidophenylsulfonamide: photoaffinity labeling of a 14,15-epoxyeicosatrienoic acid receptor

Endothelium-derived epoxyeicosatrienoic acids (EETs) relax vascular smooth muscle by activating potassium channels and causing membrane hyperpolarization. Recent evidence suggests that EETs act via a membrane binding site or receptor. To further characterize this binding site or receptor, we synthesized 20-iodo-14,15-epoxyeicosa-8(Z)-enoyl-3-azidophenylsulfonamide (20-I-14,15-EE8ZE-APSA), an EET analogue with a photoactive azido group. 20-I-14,15-EE8ZE-APSA and 14,15-EET displaced 20-(125)I-14,15-epoxyeicosa-5(Z)-enoic acid binding to U937 cell membranes with K(i) values of 3.60 and 2.73 nM, respectively. The EET analogue relaxed preconstricted bovine coronary arteries with an ED(50) comparable to that of 14,15-EET. Using electrophoresis, 20-(125)I-14,15-EE8ZE-APSA labeled a single 47 kDa band in U937 cell membranes, smooth muscle and endothelial cells, and bovine coronary arteries. In U937 cell membranes, the 47 kDa radiolabeling was inhibited in a concentration-dependent manner by 8,9-EET, 11,12-EET, and 14,15-EET (IC(50) values of 444, 11.7, and 8.28 nM, respectively). The structurally unrelated EET ligands miconazole, MS-PPOH, and ketoconazole also inhibited the 47 kDa labeling. In contrast, radiolabeling was not inhibited by 8,9-dihydroxyeicosatrienoic acid, 5-oxoeicosatetraenoic acid, a biologically inactive thiirane analogue of 14,15-EET, the opioid antagonist naloxone, the thromboxane mimetic U46619, or the cannabinoid antagonist AM251. Radiolabeling was not detected in membranes from HEK293T cells expressing 79 orphan receptors. These studies indicate that vascular smooth muscle, endothelial cells, and U937 cell membranes contain a high-affinity EET binding protein that may represent an EET receptor. This EET photoaffinity labeling method with a high signal-to-noise ratio may lead to new insights into the expression and regulation of the EET receptor.     

Protective effect of ellagic acid against TCDD-induced renal oxidative stress: Modulation of CYP1A1 activity and antioxidant defense mechanisms

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) belongs to toxicologically important class of poly halogenated aromatic hydrocarbons and produce wide variety of adverse effects in humans. The present study investigated the protective effect of ellagic acid, a natural polyphenolic compound against TCDD-induced nephrotoxicity in Wistar rats. TCDD-induced nephrotoxicity was reflected in marked changes in the histology of kidney, increase in levels of kidney markers (serum urea, serum creatinine) and lipid peroxides. A significant increase in activity of phase I enzyme CYP1A1 with concomitant decline in the activities of phase II enzymes [non-enzymic antioxidant and various enzymic antioxidants such as superoxide dismutase, catalase, glutathione peroxidase, glutathione-s-transferase] was also observed. In addition, TCDD treated rats showed alterations in ATPase enzyme activities such as Na⁺ K⁺-ATPase, Mg²⁺ ATPase and Ca²⁺ ATPase. Oral pre-treatment with ellagic acid prevented TCDD-induced alterations in levels of kidney markers. Ellagic acid pre-treatment significantly counteracted TCDD-induced oxidative stress by decreasing CYP1A1 activity and enhancing the antioxidant status. Furthermore, ellagic acid restored TCDD-induced histopathological changes and alterations in ATPase enzyme activities. The results of the present study show that significant protective effect rendered by ellagic acid against TCDD-induced nephrotoxicity might be attributed to its antioxidant potential.     

The Patient Health Questionnaire-9: Validation among Patients with Glaucoma

Background

Depression and anxiety are two common normal responses to a chronic disease such as glaucoma. This study analysed the measurement properties of the depression screening instrument - Patient Health Questionnaire-9 (PHQ-9) using Rasch analysis to determine if it can be used as a measure.

Methods

In this hospital-based cross-sectional study, the PHQ-9 was administered to primary glaucoma adults attending a glaucoma clinic of a tertiary eye care centre, South India. All patients underwent a comprehensive clinical evaluation. Patient demographics and sub-type of glaucoma were abstracted from the medical record. Rasch analysis was used to investigate the following properties of the PHQ-9: behaviour of the response categories, measurement precision (assessed using person separation reliability, PSR; minimum recommended value 0.80), unidimensionality (assessed using item fit [0.7–1.3] and principal components analysis of residuals), and targeting.

Results

198 patients (mean age ± standard deviation  = 59.83±12.34 years; 67% male) were included. The native PHQ-9 did not fit the Rasch model. The response categories showed disordered thresholds which became ordered after category reorganization. Measurement precision was below acceptable limits (0.62) and targeting was sub-optimal (−1.27 logits). Four items misfit that were deleted iteratively following which a set of five items fit the Rasch model. However measurement precision failed to improve and targeting worsened further (−1.62 logits).

Conclusions

The PHQ-9, in its present form, provides suboptimal assessment of depression in patients with glaucoma in India. Therefore, there is a need to develop a new depression instrument for our glaucoma population. A superior strategy would be to use the item bank for depression but this will also need to be validated in glaucoma patients before deciding its utility.