Publisher Correction: Innate-like functions of natural killer T cell subsets result from highly divergent gene programs.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Innate-like functions of natural killer T cell subsets result from highly divergent gene programs.

Natural killer T cells (NKT cells) have stimulatory or inhibitory effects on the immune response that can be attributed in part to the existence of functional subsets of NKT cells. These subsets have been characterized only on the basis of the differential expression of a few transcription factors and cell-surface molecules. Here we have analyzed purified populations of thymic NKT cell subsets at both the transcriptomic level and epigenomic level and by single-cell RNA sequencing. Our data indicated that despite their similar antigen specificity, the functional NKT cell subsets were highly divergent populations with many gene-expression and epigenetic differences. Therefore, the thymus 'imprints' distinct gene programs on subsets of innate-like NKT cells that probably impart differences in proliferative capacity, homing, and effector functions.

A gene-specific non-enhancer sequence is critical for expression from the promoter of the small heat shock protein gene αB-crystallin.

BACKGROUND: Deciphering of the information content of eukaryotic promoters has remained confined to universal landmarks and conserved sequence elements such as enhancers and transcription factor binding motifs, which are considered sufficient for gene activation and regulation. Gene-specific sequences, interspersed between the canonical transacting factor binding sites or adjoining them within a promoter, are generally taken to be devoid of any regulatory information and have therefore been largely ignored. An unanswered question therefore is, do gene-specific sequences within a eukaryotic promoter have a role in gene activation? Here, we present an exhaustive experimental analysis of a gene-specific sequence adjoining the heat shock element (HSE) in the proximal promoter of the small heat shock protein gene, αB-crystallin (cryab). These sequences are highly conserved between the rodents and the humans. RESULTS: Using human retinal pigment epithelial cells in culture as the host, we have identified a 10-bp gene-specific promoter sequence (GPS), which, unlike an enhancer, controls expression from the promoter of this gene, only when in appropriate position and orientation. Notably, the data suggests that GPS in comparison with the HSE works in a context-independent fashion. Additionally, when moved upstream, about a nucleosome length of DNA (-154 bp) from the transcription start site (TSS), the activity of the promoter is markedly inhibited, suggesting its involvement in local promoter access. Importantly, we demonstrate that deletion of the GPS results in complete loss of cryab promoter activity in transgenic mice. CONCLUSIONS: These data suggest that gene-specific sequences such as the GPS, identified here, may have critical roles in regulating gene-specific activity from eukaryotic promoters.

Comparison of clinical characteristics between Korean and Western normal-tension glaucoma patients.

PURPOSE: To detect potential differences in the phenotypes between Western normal-tension glaucoma (NTG) and Korean NTG. DESIGN: A retrospective, cross-sectional study. METHODS: One hundred eighty-four NTG eyes of 71 patients of the Jules Stein Eye Institute, University of California, Los Angeles, and 113 patients of the Seoul National University Hospital, Seoul, Korea, were studied after reviewing medical charts retrospectively. All eligible patients from both institutions who were evaluated between July 2007 and June 2008 were included. The groups were matched for stage of glaucoma severity based on the visual field mean deviation value. All patients underwent a complete ophthalmic examination, Humphrey perimetry, Heidelberg Retina Tomography, Stratus optical coherence tomography, and pachymetry. Structural and functional parameters between the 2 groups were compared. RESULTS: There were no statistically significant differences in the baseline intraocular pressure, disc area, frequency of disc hemorrhage, or peripapillary atrophy (P > .05). Cup-shape measure (by Heidelberg Retina Tomography), average RNFL thickness (by Stratus optical coherence tomography), and central corneal thickness were significantly different (P < .002). The eyes of Korean NTG patients showed higher values for cup-shape measure, higher average RNFL thicknesses, and thinner central corneal thicknesses than Western NTG patients. The difference was significant (P < .001) while controlling for age, sex, disc area, mean deviation, pattern standard deviation, and spherical equivalent with multivariate analysis. CONCLUSIONS: Korean NTG patients showed steeper cup shapes, thicker RNFL thickness, and thinner central corneal thickness compared with Western NTG patients with similar amounts of visual field loss. This result may help clinicians understand the clinical characteristics of NTG patients and points to the heterogeneous character of the glaucomas.

Cell-type-dependent access of HSF1 and HSF4 to αB-crystallin promoter during heat shock.

Epithelial cells and fibroblasts both express heat shock transcription factors, HSF1 and HSF4, yet they respond to heat shock differentially. For example, while HSP70 is induced in both cell types, the small heat shock protein, αB-crystallin gene (CRYAB) that contains a canonical heat shock promoter, is only induced in fibroblasts. A canonical heat shock promoter contains three or more inverted repeats of the pentanucleotide 5'-nGAAn-3' that make the heat shock element. It is known that, in vitro, promoter architecture (the order and spacing of these repeats) impacts the interaction of various heat shock transcription factors (HSFs) with the heat shock promoter, but in vivo relevance of these binding preferences so far as the expression is concerned is poorly understood. In this report, we first establish cell-type-dependent differential expression of CRYAB in four established cell lines and then working with adult human retinal pigment epithelial cells and NIH3T3 fibroblasts and employing chromatin immunoprecipitation, attempt to relate expression to promoter occupancy by HSF1 and HSF4. We show that HSF4 occupies only CRYAB and not HSP70 promoter in epithelial cells, while HSF1 occupies only HSP70 promoter in both cell types, and cryab promoter, only in heat shocked fibroblasts; HSF4, on the other hand, is never seen on these two promoters in NIH3T3 fibroblasts. This comparative analysis with CRYAB and HSP70 demonstrates that differential heat shock response is controlled by cell-type-dependent access of HSFs (HSF1 and HSF4) to specific promoters, independent of the promoter architecture.

Validation of point-wise exponential regression to measure the decay rates of glaucomatous visual fields.

PURPOSE: This study was conducted to validate a recently described technique for measuring the rates of visual field (VF) decay in glaucoma. METHODS: A pointwise exponential regression (PER) model was used to calculate average rates of faster and slower deteriorating VF components, and that of the entire VF. Rapid progressors had a faster component rate of >25%/year. Mean deviation (MD) and visual field index (VFI) forecasts were calculated by (1) extrapolation of linear regression of MD and VFI, and (2) calculation de novo from the PER-predicted final thresholds. RESULTS: The mean (± SD) years of follow-up and number of VFs were 9.2 (± 2.7) and 13.7 (± 5.8), respectively. The median rates of the decay were -0.1 and 3.6 (%/year) for the slower and the faster components, respectively. The "rapid progressors" (32% of eyes) had a mean decay rate of 52.2%/year. In comparison with actual values, the average absolute difference and the mean squared error for MD forecasts with linear extrapolation of indices were 3.58 dB and 31.91 dB(2), and with the de novo recalculation from PER predictions were 2.95 dB and 17.49 dB(2), respectively. Similar results were obtained for VFI forecasts. Comparisons of the prediction errors for both the MD and VFI favored the PER forecasts (P < 0.001). CONCLUSIONS: PER for measuring rates of VF decay is a robust indicator of rates across a wide range of disease severity and can predict future global indices accurately. The identification of "rapid progressors" identifies high-risk patients for appropriate treatment.

Pointwise rates of visual field progression cluster according to retinal nerve fiber layer bundles.

PURPOSE: To explore whether pointwise rates of visual field progression group together in patterns consistent with retinal nerve fiber layer (RNFL) bundles. METHODS: Three hundred eighty-nine eyes of 309 patients from the Advanced Glaucoma Intervention Study with ≥6 years of follow-up and ≥12 reliable visual field exams were selected. Linear and exponential regression models were used to estimate pointwise rates of change over time. Clustering of pointwise rates of progression was investigated with hierarchical cluster analysis using Pearson's correlation coefficients as distance measure and an average linkage scheme for building the hierarchy with cutoff value of r > 0.7. RESULTS: The average mean deviation (±SD) was -10.9 (±5.4). The average (±SD) follow-up time and number of visual field exams were 8.1 (±1.1) years and 15.7 (±3.0), respectively. Pointwise rates of progression across the visual field grouped into clusters consistent with anatomic patterns of RNFL bundles with both linear (10 clusters) and exponential (six clusters) regression models. One hundred forty-four (37%) eyes progressed according to the two-omitting pointwise linear regression model. CONCLUSIONS: ointwise rates of change in glaucoma patients cluster into regions consistent with RNFL bundle patterns. This finding validates the clinical significance of such pointwise rates. The correlations among pointwise rates of change can be used for spatial filtering purposes, facilitating detection or prediction of glaucoma progression.

ORAI1 deficiency impairs activated T cell death and enhances T cell survival.

ORAI1 is a pore subunit of Ca(2+) release-activated Ca(2+) channels that mediate TCR stimulation-induced Ca(2+) entry. A point mutation in ORAI1 (ORAI1(R91W)) causes SCID in human patients that is recapitulated in Orai1(-/-) mice, emphasizing its important role in the immune cells. In this study, we have characterized a novel function of ORAI1 in T cell death. CD4(+) T cells from Orai1(-/-) mice showed robust proliferation with repetitive stimulations and strong resistance to stimulation-induced cell death due to reduced mitochondrial Ca(2+) uptake and altered gene expression of proapoptotic and antiapoptotic molecules (e.g., Fas ligand, Noxa, and Mcl-1). Nuclear accumulation of NFAT was severely reduced in ORAI1-deficient T cells, and expression of ORAI1 and a constitutively active mutant of NFAT recovered cell death. These results indicate NFAT-mediated cell death pathway as one of the major downstream targets of ORAI1-induced Ca(2+) entry. By expressing various mutants of ORAI1 in wild-type and Orai1(-/-) T cells to generate different levels of intracellular Ca(2+), we have shown that activation-induced cell death is directly proportional to the intracellular Ca(2+) concentration levels. Consistent with the in vitro results, Orai1(-/-) mice showed strong resistance to T cell depletion induced by injection of anti-CD3 Ab. Furthermore, ORAI1-deficient T cells showed enhanced survival after adoptive transfer into immunocompromised hosts. Thus, our results demonstrate a crucial role of the ORAI1-NFAT pathway in T cell death and highlight the important role of ORAI1 as a major route of Ca(2+) entry during activated T cell death.

A method to measure and predict rates of regional visual field decay in glaucoma.

PURPOSE: This study was conducted to measure the rate of visual field (VF) decay in glaucoma, to separate faster and slower components of decay, and to predict the rate of VF decay. METHODS: Patients who had primary glaucoma and 6 or more years of follow-up were included. Thresholds at each VF location were regressed with linear, quadratic, and exponential models. The best model was used to parse the VF into slower and faster rate components. Two independent cohorts (glaucoma [n = 87] and cataract [n = 38]) were used to determine the technique's ability to distinguish areas of glaucomatous VF changes from those caused by cataract. VF forecasts, derived from the first half of follow-up, were compared with actual VF thresholds at the end of follow-up. RESULTS: The mean (±SD) years of follow-up and number of VFs for the main cohort (389 eyes of 309 patients) were 8.2 (±1.1) years and 15.7 (±3.0), respectively. The proportions of best fits were linear 2%, quadratic 1%, and exponential 97%. Proportions of eyes with exponential rates of decay ≥10% for the entire visual field (VF), faster components, and slower components were 20%, 56%, and 4%, respectively. The difference in decay rates between the faster and slower components was greater in the independent glaucoma cohort (19% ± 10%) than in the cataract cohort (5% ± 5%; P < 0.001). Test location forecasts significantly correlated with measured values (r(2) = 0.67; P < 0.001). CONCLUSIONS: This method isolates faster and slower components of VF decay in glaucoma, can identify patients who are fast progressors, and can predict patterns of future VF loss with appropriate confidence intervals. (ClinicalTrials.gov number, NCT00000148.).

Lactobacillus bulgaricus prevents intestinal epithelial cell injury caused by Enterobacter sakazakii-induced nitric oxide both in vitro and in the newborn rat model of necrotizing enterocolitis.

Enterobacter sakazakii is an emerging pathogen that has been associated with outbreaks of necrotizing enterocolitis (NEC) as well as infant sepsis and meningitis. Our previous studies demonstrated that E. sakazakii induces NEC in a newborn rat model by inducing enterocyte apoptosis. However, the mechanisms responsible for enterocyte apoptosis are not known. Here we demonstrate that E. sakazakii induces significant production of nitric oxide (NO) in rat intestinal epithelial cells (IEC-6) upon infection. The elevated production of NO, which is due to increased expression of inducible NO synthase, is responsible for apoptosis of IEC-6 cells. Notably, pretreatment of IEC-6 cells with Lactobacillus bulgaricus (ATCC 12278) attenuated the upregulation of NO production and thereby protected the cells from E. sakazakii-induced apoptosis. Furthermore, pretreatment with L. bulgaricus promoted the integrity of enterocytes both in vitro and in the infant rat model of NEC, even after challenge with E. sakazakii. Infection of IEC-6 cells with E. sakazakii upregulated several genes related to apoptosis, cytokine production, and various signaling pathways, as demonstrated by rat gene array analysis, and this upregulation was subdued by pretreatment with L. bulgaricus. In agreement with these data, L. bulgaricus pretreatment protected newborn rats infected with E. sakazakii from developing NEC, resulting in improved survival.

Profiling motility signal-specific genes in primary human keratinocytes.

Regulation of human keratinocyte (HK) migration is critical for skin wound healing. Profiling HK migration-specific genes could help us gain a comprehensive understanding of the process. The main challenge is to separate genes that are unrelated to migration, but simultaneously induced by the same growth factor. In this study, we took advantage of a unique response of HKs to transforming growth factor-beta (TGF-beta), which inhibits proliferation but not migration of HKs, to suppress selectively the proliferation-related genes. Furthermore we stimulated HKs independently with TGF-alpha or insulin and identified the common genes and eliminated TGF-alpha- or insulin-specific genes. Under these conditions, we obtained profiles of the immediate-early genes (IEGs, at 30 minutes), early genes (EGs, at 60 minutes), and delayed-early genes (DEGs, at 120 minutes) by microarray analyses, followed by quantitative real-time reverse transcription-PCR (QRT-PCR) validation and functional characterization by RNA interference (RNAi). Our results revealed the following: (1) 25 upregulated and 1 downregulated IEGs; (2) 58 upregulated and 15 downregulated EGs, and (3) 13 upregulated and 3 downregulated DEGs in both TGF-alpha- and insulin-stimulated HKs. Three genes, all encoding secreted molecules, were investigated in HK migration. These cell motility-specific gene profiles may prove useful to skin wound healing.

Intragraft gene expression profile associated with the induction of tolerance.

BACKGROUND: Xenotransplantation holds the promise of providing an unlimited supply of donor organs for terminal patients with organ failure. Pre-existing natural antibodies to the Galalpha1,3Galbeta1,4GlcNac-R (alphaGal) carbohydrate xenoantigen, however, bind rapidly to the graft endothelium and initiate hyperacute rejection of wild type pig grafts in humans. Experimental procedures designed to prevent xenoantibody-mediated rejection have been tested in gal knockout mice. These mice produce anti-gal xenoantibodies and are widely used as small animal models for xenotransplantation research. In this model, chimerism for cells expressing the gal carbohydrate can be achieved by transplantation of mixed cells or by transduction of bone marrow cells with viral vectors expressing a functional alpha1,3 galactosyltransferase gene. Chimerism induces tolerance to heart grafts expressing alphaGal. The mechanisms by which tolerance is achieved include systemic changes such as clonal deletion and/or anergy. Intragraft changes that occur during the early stages of tolerance induction have not been characterized. RESULTS: Cytoprotective genes heme oxygenase-1 (HO-1), Bcl2, and A20 that have been reported to contribute to long-term graft survival in various models of accommodation were not expressed at high levels in tolerant heart grafts. Intragraft gene expression at both early (Day 10) and late (>2 month) time points after heart transplant were examined by real-time PCR and microarray analysis was used to identify changes associated with the induction of tolerance. Intragraft gene expression profiling using microarray analysis demonstrated that genes identified in the functional categories of stress and immunity and signal transduction were significantly up-regulated in early tolerant grafts compared with syngeneic control grafts. Biological process classification showed lower binomial p-values in the categories of "response to biotic stimulus, defense response, and immune response" suggesting that up-regulated genes identified in these grafts promote survival in the presence of an immune response. The expression of the incompatible carbohydrate antigen (alphaGal) was reduced by 2 months post-transplant when compared with the expression of this gene at Day 10 post-transplant. These results suggest that the gal carbohydrate antigen is downmodulated over time in grafts that demonstrate tolerance. CONCLUSION: Our study suggests that tolerance is associated with intragraft gene expression changes that render the heart resistant to immune-mediated rejection. Genes associated with stress and immunity are up-regulated, however cytoprotective genes HO-1, Bcl2 and A20 were not up-regulated. The expression of the gal carbohydrate, the key target initiating an immune response in this model, is down-regulated in the post-transplant period.

Nuclear receptor ERR alpha and coactivator PGC-1 beta are effectors of IFN-gamma-induced host defense.

Macrophage activation by the proinflammatory cytokine interferon-gamma (IFN-gamma) is a critical component of the host innate response to bacterial pathogenesis. However, the precise nature of the IFN-gamma-induced activation pathway is not known. Here we show using genome-wide expression and chromatin-binding profiling that IFN-gamma induces the expression of many nuclear genes encoding mitochondrial respiratory chain machinery via activation of the nuclear receptor ERR alpha (estrogen-related receptor alpha, NR3B1). Studies with macrophages lacking ERR alpha demonstrate that it is required for induction of mitochondrial reactive oxygen species (ROS) production and efficient clearance of Listeria monocytogenes (LM) in response to IFN-gamma. As a result, mice lacking ERR alpha are susceptible to LM infection, a phenotype that is localized to bone marrow-derived cells. Furthermore, we found that IFN-gamma-induced activation of ERR alpha depends on coactivator PGC-1 beta (peroxisome proliferator-activated receptor gamma coactivator-1 beta), which appears to be a direct target for the IFN-gamma/STAT-1 signaling cascade. Thus, ERR alpha and PGC-1 beta act together as a key effector of IFN-gamma-induced mitochondrial ROS production and host defense.

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation.

BACKGROUND: Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal transduction pathways. For example, although all three of these ligands induce proliferation, only stimulation through the B cell antigen receptor (BCR) induces apoptosis in resting splenic B cells. In order to define the common and unique biological responses to ligand stimulation, we compared the gene expression changes induced in normal primary B cells by a panel of ligands using cDNA microarrays and a statistical approach, CLASSIFI (Cluster Assignment for Biological Inference), which identifies significant co-clustering of genes with similar Gene Ontology annotation. RESULTS: CLASSIFI analysis revealed an overrepresentation of genes involved in ion and vesicle transport, including multiple components of the proton pump, in the BCR-specific gene cluster, suggesting that activation of antigen processing and presentation pathways is a major biological response to antigen receptor stimulation. Proton pump components that were not included in the initial microarray data set were also upregulated in response to BCR stimulation in follow up experiments. MHC Class II expression was found to be maintained specifically in response to BCR stimulation. Furthermore, ligand-specific internalization of the BCR, a first step in B cell antigen processing and presentation, was demonstrated. CONCLUSION: These observations provide experimental validation of the computational approach implemented in CLASSIFI, demonstrating that CLASSIFI-based gene expression cluster analysis is an effective data mining tool to identify biological processes that correlate with the experimental conditional variables. Furthermore, this analysis has identified at least thirty-eight candidate components of the B cell antigen processing and presentation pathway and sets the stage for future studies focused on a better understanding of the components involved in and unique to B cell antigen processing and presentation.

Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands.

We examined the major patterns of changes in gene expression in mouse splenic B cells in response to stimulation with 33 single ligands for 0.5, 1, 2, and 4 h. We found that ligands known to directly induce or costimulate proliferation, namely, anti-IgM (anti-Ig), anti-CD40 (CD40L), LPS, and, to a lesser extent, IL-4 and CpG-oligodeoxynucleotide (CpG), induced significant expression changes in a large number of genes. The remaining 28 single ligands produced changes in relatively few genes, even though they elicited measurable elevations in intracellular Ca(2+) and cAMP concentration and/or protein phosphorylation, including cytokines, chemokines, and other ligands that interact with G protein-coupled receptors. A detailed comparison of gene expression responses to anti-Ig, CD40L, LPS, IL-4, and CpG indicates that while many genes had similar temporal patterns of change in expression in response to these ligands, subsets of genes showed unique expression patterns in response to IL-4, anti-Ig, and CD40L.

Unravelling the signal-transduction network in B lymphocytes.

The Alliance for Cellular Signaling has chosen the mouse B lymphocyte as a model system to understand basic principles that govern cellular signalling. Progress to that end has focused initially on establishing a reproducible experimental cell system and characterizing essential signalling responses. Although unravelling this complex network will take years, findings revealed in the interim will prove immensely useful to the scientific community at large.