应用 PPIN分析肝移植临床耐受患者PBMC基因表达特点

应用生物信息学方法分析肝移植临床耐受患者PBMC基因表达特征,筛选临床耐受关键基因。从GEO数据库获取19个肝移植临床耐受病例及22个非临床耐受病例基因表达谱数据。应用DAVID网络软件进行差异基因功能注释与聚类分析;通过Cytoscape软件的MiMI插件构建蛋白质相互作用网络(PPIN)筛选肝移植临床耐受关键基因。差异基因涉及蛋白质及RNA代谢、免疫应答、膜结构调节等复杂生物过程。PPIN网络分析获得10个临床耐受核心基因。我们的研究表明:肝移植临床耐受涉及外周血免疫细胞复杂的基因表达调控机制及蛋白质间相互作用;RNA的转录后加工及蛋白质降解在免疫耐受的形成中发挥了重要作用;RBM8A、DHX9、CBL、IKBKB、CSNK2A1、HSPA8等核心基因发挥重要的免疫调节功能。     

On the evolution of heavy-metal tolerant populations in Armeria maritima: evidence from allozyme variation and reproductive barriers

The process of ecological differentiation leading to the evolution of heavy-metal tolerant populations in Armeria maritima was studied by comparing population genetic structure and pattern of gene flow between populations growing on heavy-metal contaminated against non-contaminated sites using allozyme markers. In addition the evolution of reproductive isolation among populations was studied by measuring pollen fertility in interpopulational hybrids. The allozyme data suggested that in A. maritima multiple independent evolutionary origins of heavy-metal tolerant populations have occurred in the absence of strong genetic bottlenecks. The pattern of gene flow among populations was consistent with the model of isolation by distance with considerable gene flow between neighbor populations, and no reduction of gene flow between tolerant and non-tolerant populations. Hence it appears that substantial gene flow has not hampered genetic differentiation, probably because of the high selection pressure for heavy-metal tolerance. The pattern of reproductive isolation among populations suggests that evolution of heavy-metal tolerant populations has not triggered the development of reproductive barriers against non-tolerant populations. However, partial reproductive isolation has occurred under geographic separation.     

Transient expression of human interleukin-2 and interferon-γ genes is regulated by interaction between distinct cell subsets

The level of transient expression of human IL-2 and IFN-γ genes, we show, is regulated by dynamic interaction between two functionally distinct cell populations. One is able to express these genes, while the other, bearing one of several specific surface markers, actively inhibits their expression. Defined cell subsets were isolated from PBMC and tonsil cells using immunomagnetic beads coated with monoclonal antibodies directed against surface markers. Depletion of CD8, CD11a (Leu15), or Leu8 subsets led to a pronounced superinduction of IL-2 and IFN-γ gene expression when the remaining cell population was stimulated with mitogen (PHA) or antigen (SEB). Thus, a 10-fold increase in production of IFN-γ was observed after removal of CD11a (Leu15) cells constituting only a small percentage of the total cell population. By contrast, depletion of cells expressing CD19, a B cell marker, did not yield any superinduction. Conversely, CD8, CD11a (Leu15), or Leu8 cell subsets, but not CD19 cells, each inhibited the induction of IL-2 and IFN-γ gene expression almost completely in depleted or total cell populations from which they were derived. Gene expression occurring within one cell subset could be effectively inhibited by cells from a second subset. Introduction of inhibitory cells (Leu8) into a population that actively expressed IL-2 and IFN-γ mRNA resulted in an immediate cessation of gene expression. This suppression involves a soluble mediator, since the culture medium in which such cells were activated exerted a similarly effective inhibition.     

Analysis of the underlying cellular mechanisms of anti-CD154-induced graft tolerance: the interplay of clonal anergy and immune regulation

Although it has been shown that CD4(+)CD25(+) regulatory T cells (T(reg)) contribute to long-term graft acceptance, their impact on the effector compartment and the mechanism by which they exert suppression in vivo remain unresolved. Using a CD4(+) TCR transgenic model for graft tolerance, we have unveiled the independent contributions of anergy and active suppression to the fate of immune and tolerant alloreactive T cells in vivo. First, it is shown that anti-CD154-induced tolerance resulted in the abortive expansion of the alloreactive, effector T cell pool. Second, commensurate with reduced expansion, there was a loss of cytokine production, activation marker expression, and absence of memory T cell markers. All these parameters defined the tolerant alloreactive T cells and correlated with the inability to mediate graft rejection. Third, the tolerant alloreactive T cell phenotype that is induced by CD154 was reversed by the in vivo depletion of T(reg). Reversal of the tolerant phenotype was followed by rapid rejection of the allograft. Fourth, in addition to T(reg) depletion, costimulation of the tolerant alloreactive T cells or activation of the APC compartment also reverted alloreactive T cell tolerance and restored an activated phenotype. Finally, it is shown that the suppression is long-lived, and in the absence of anti-CD154 and donor-specific transfusion, these T(reg) can chronically suppress effector cell responses, allowing long-lived graft acceptance.     

Internal desynchronization of circadian rhythms and tolerance to shift work

Intolerance to shift work may result from individual susceptibility to an internal desynchronization. Some shift workers (SW) who show desynchronization of their circadian rhythms (e.g., sleep-wake, body temperature, and grip strength of both hands) exhibit symptoms of SW intolerance, such as sleep alteration, persistent fatigue, sleep medication dependence, and mood disturbances, including depression. Existing time series data previously collected from 48 male Caucasian French SW were reanalyzed specifically to test the hypothesis that internal synchronization of circadian rhythms is associated with SW intolerance and symptoms. The entry of the subjects into the study was randomized. Three groups were formed thereafter: SW with good tolerance (n=14); SW with poor tolerance, as evident by medical complaints for at least one year (n=19); and former SW (n=15) with very poor tolerance and who had been discharged from night work for at 1.5 yr span but who were symptom-free at the time of the study. Individual and longitudinal time series of selected variables (self-recorded sleep-wake data using a sleep log, self-measured grip strength of both hands using a Colin Gentile dynamometer, and oral temperature using a clinical thermometer) were gathered for at least 15 days, including during one or two night shifts. Measurements were performed 4-5 times/24 h. Power spectra used to quantify the prominent period (tau) and t-test, chi square, and correlation coefficient were used as statistical tools. The mean (+/-SEM) age of SW with good tolerance was greater than that of SW with poor tolerance (44.9+/-2.1 yrs vs. 40.1+/-2.6 yrs, p<.001) and of former SW discharged from night work (very poor tolerance; 33.4+/-1.7, p<.001). The shift-work duration (yrs) was longer in SW with good than poor tolerance (19.9+/-2.2 yrs vs. 15.7+/-2.2; p<0.002) and former SW (10.7+/-1.2; p<.0001). The correlation between subject age and shift-work duration was stronger in tolerant SW (r=0.97, p<.0001) than in non-tolerant SW (r=0.80, p<0.001) and greater than that of former SW (r=0.72, p<.01). The mean sleep-wake rhythm tau was 24 h for all 48 subjects. The number of desynchronized circadian rhythms (tau differing from 24 h) was greater in non-tolerant than in tolerant SW (chi square=38.9, p<.0001). In Former SW (i.e., 15 individuals assessed in follow-up studies done 1.5 to 20 yrs after return to day work), both symptoms of intolerance and internal desynchronization were reduced or absent. The results suggest that non-tolerant SW are particularly sensitive to the internal desynchronization of their circadian time organization.     

Amplification and rearrangement of a prokaryotic metallothionein locus smt in Synechococcus PCC 6301 selected for tolerance to cadmium.

Metal-tolerant cyanobacteria have been isolated from metal-polluted aquatic environments and also selected in culture, but no genes which confer metal tolerance have been described. To investigate the possibility that amplification of a prokaryotic metallothionein gene (smtA), or rearrangement of the smt locus, could be involved in the development of Cd tolerance in Synechococcus PCC 6301, Cd-tolerant lines were selected by stepwise adaptation of a Synechococcus culture. An increase in smtA gene copy number and the appearance of unique additional smtA restriction fragments (both larger and smaller) were detected in these tolerant lines (tolerant to 0.8 microM Cd, 1.3 microM Cd and 1.7 microM Cd). Stepwise adaptation was repeated by using a culture of Synechococcus PCC 6301 inoculated from a single plated colony to obtain four new lines (tolerant to 1.4 microM Cd, 1.8 microM Cd, 2.6 microM Cd and 3.2 microM Cd). Amplification of the smtA gene and development of unique smtA restriction fragments (larger and smaller) were once again detected in these tolerant lines. Amplification and rearrangement of the smt locus were only detected in the seven Cd-tolerant lines, with no evidence of amplification or rearrangement in the non-tolerant lines from which they were derived. As a control, another gene, psaE, was also monitored in these cell lines. There was no evidence of amplification or rearrangement of psaE in the non-tolerant or any of the Cd-tolerant lines.     

Differential Gene Expression from Genome-Wide Microarray Analyses Distinguishes Lohmann Selected Leghorn and Lohmann Brown Layers

The Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) layer lines have been selected for high egg production since more than 50 years and belong to the worldwide leading commercial layer lines. The objectives of the present study were to characterize the molecular processes that are different among these two layer lines using whole genome RNA expression profiles. The hens were kept in the newly developed small group housing system Eurovent German with two different group sizes. Differential expression was observed for 6,276 microarray probes (FDR adjusted P-value <0.05) among the two layer lines LSL and LB. A 2-fold or greater change in gene expression was identified on 151 probe sets. In LSL, 72 of the 151 probe sets were up- and 79 of them were down-regulated. Gene ontology (GO) enrichment analysis accounting for biological processes evinced 18 GO-terms for the 72 probe sets with higher expression in LSL, especially those taking part in immune system processes and membrane organization. A total of 32 enriched GO-terms were determined among the 79 down-regulated probe sets of LSL. Particularly, these terms included phosphorus metabolic processes and signaling pathways. In conclusion, the phenotypic differences among the two layer lines LSL and LB are clearly reflected in their gene expression profiles of the cerebrum. These novel findings provide clues for genes involved in economically important line characteristics of commercial laying hens.     

A new aluminum tolerance gene located on rye chromosome arm 7RS

Rye has one of the most efficient groups of genes for aluminum tolerance (Alt) among cultivated species of Triticeae. This tolerance is controlled by, at least, three independent and dominant loci (Alt1, Alt2, and Alt3) located on chromosome arms 6RS, 3RS, and 4RL, respectively. The segregation of Alt genes and several random amplified polymorphic DNA (RAPD), Secale cereale inter-microsatellite (SCIM), and Secale cereale microsatellite (SCM) markers in three F(2) between a tolerant cultivar (Ailés) and a non-tolerant inbred line (Riodeva) were studied. The segregation ratio obtained for aluminum tolerance in the three F(2) populations analyzed was 3:1 (tolerant:non-tolerant), indicating that tolerance is controlled by one dominant locus. SCIM811(1376) was linked to an Alt gene in the three F(2) populations studied, and three different SCIMs and one RAPD (SCIM811(1376), SCIM812(626), SCIM812(1138), and OPQ4(725)) were linked to the Alt gene in two F(2) populations. This result indicated that the same Alt gene was segregating in the three crosses. SCIM819(1434) and OPQ4(578) linked to the tolerance gene in one F(2) population were located using wheat-rye ditelosomic addition lines on the 7RS chromosome arm. The Alt locus is mapped between SCIM819(1434) and the OPQ4(578) markers. Two microsatellite loci (SCM-40 and SCM-86), previously located on chromosome 7R, were also linked to the Alt gene. Therefore, the Alt gene segregating in these F(2) populations is new and probably could be orthologous to the Alt genes located on wheat chromosome arm 4DL, on barley chromosome arm 4HL, on rye chromosome arm 4RL, and rice chromosome 3. This new Alt gene located on rye chromosome arm 7RS was named Alt4. A map of rye chromosome 7R with the Alt4 gene, 16 SCIM and RAPD, markers and two SCM markers was obtained.     

Selective adaptation to copper of populations ofAgrostis tenuis andFestuca rubra (Poaceae)

Populations ofAgrostis Tenuis andFestuca rubra, tolerant and non-tolerant towards Zn and Pb, were studied in regard to their adaptability by natural selection, towards a third metal (Cu) and the time required for the appearance of such tolerance. It was found that Zn and Pb tolerant and non-tolerant populations are likely to select the character of Cu-tolerance within the course of only one generation. More specifically, Zn and Pb tolerant populations show a better adaptability compared with non-tolerant ones. The amount of tolerance to copper obtained by artificial selection is comparable with that of populations growing naturally on copper mines.     

Neuropilin-1 Expression Is Induced on Tolerant Self-Reactive CD8+ T Cells but Is Dispensable for the Tolerant Phenotype

Establishing peripheral CD8⁺ T cell tolerance is vital to avoid immune mediated destruction of healthy self-tissues. However, it also poses a major impediment to tumor immunity since tumors are derived from self-tissue and often induce T cell tolerance and dysfunction. Thus, understanding the mechanisms that regulate T cell tolerance versus immunity has important implications for human health. Signals received from the tissue environment largely dictate whether responding T cells become activated or tolerant. For example, induced expression and subsequent ligation of negative regulatory receptors on the surface of self-reactive CD8⁺ T cells are integral in the induction of tolerance. We utilized a murine model of T cell tolerance to more completely define the molecules involved in this process. We discovered that, in addition to other known regulatory receptors, tolerant self-reactive CD8⁺ T cells distinctly expressed the surface receptor neuropilin-1 (Nrp1). Nrp1 was highly induced in response to self-antigen, but only modestly when the same antigen was encountered under immune conditions, suggesting a possible mechanistic link to T cell tolerance. We also observed a similar Nrp1 expression profile on human tumor infiltrating CD4⁺ and CD8⁺ T cells. Despite high expression on tolerant CD8⁺ T cells, our studies revealed that Nrp1 had no detectable role in the tolerant phenotype. Specifically, Nrp1-deficient T cells displayed the same functional defects as wild-type self-reactive T cells, lacking in vivo cytolytic potential, IFNγ production, and antitumor responses. While reporting mostly negative data, our findings have therapeutic implications, as Nrp1 is now being targeted for human cancer therapy in clinical trials, but the precise molecular pathways and immune cells being engaged during treatment remain incompletely defined.     

Characterization of alfalfa (Medicago sativa L.) plants regenerated from selected NaCl tolerant cell lines

Selection of stable, NaCl tolerant alfalfa (Medicago sativa L.) cell lines was accomplished by a step-up selection procedure, whereby cell lines originally selected for tolerance at 0.5% NaCl were subsequently selected at 1.0% NaCl. Sodium chloride tolerant cell lines retained tolerance following four subcultures (16 weeks) on control media (0% NaCl). Plants were regenerated from selected NaCl tolerant cell lines of three initial genotypes, one diploid (2n=2x=16) and two tetraploids (2n=4x=32). In addition, plants were regenerated from control cell lines maintained on 0% NaCl media for the same duration. Plants regenerated from NaCl tolerant cell lines were characterized by extensive somaclonal variation compared to plants regenerated from control lines. Morphologically, all plants regenerated from NaCl tolerant cell lines are abnormal and many (44.7%) were extreme dwarfs (maximum height of 5 cm). The grossly aberrant phenotypes prevented an in-depth characterization of many of the plants regenerated from NaCl tolerant cell lines. Most plants regenerated from NaCl tolerant cell lines had unbalanced polyploid chromosome sets with the most extreme cytogenetic variant having 106 chromosomes. In contrast, 98.5% of the plants regenerated from control cell lines were euploid (85% were tetraploid, 15% were octoploid). Isozyme phenotypes of the plants from NaCl tolerant cell lines were also extensively altered, compared to plants from control cell lines. In vitro NaCl tolerance was maintained following plant regeneration for nine of the 12 regenerants tested. Importantly, whole plant NaCl tolerance was expressed in two of the seven regenerated plants tested at the whole plant level; however, only one of these plants has flowered and is both male and female sterile; the other plant has never flowered. Although NaCl tolerant alfalfa cell lines are efficiently selected, the extensive somaclonal variation that accompanied the selection was a deterrent to successful recovery of heritable NaCl tolerance.     

Identification of key genes and pathways associated with different immune statuses of hepatitis B virus infection

We aimed to identify key genes and pathways associated with different immune statuses of hepatitis B virus (HBV) infection. The gene expression and DNA methylation profiles were analysed in different immune statuses of HBV infection. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) were identified, followed by their functional and integrative analyses. The differential expression of IgG Fc receptors (FcγRs) in chronic HBV‐infected patients and immune cells during different stages of HBV infection was investigated. Toll‐like receptor (TLR) signalling pathway (including TLR6) and leucocyte transendothelial migration pathway (including integrin subunit beta 1) were enriched during acute infection. Key DEGs, such as FcγR Ib and FcγR Ia, and interferon‐alpha inducible protein 27 showed correlation with alanine aminotransferase levels, and they were differentially expressed between acute and immune‐tolerant phases and between immune‐tolerant and immune‐clearance phases. The integrative analysis of DNA methylation profile showed that lowly methylated and highly expressed genes, including cytotoxic T lymphocyte‐associated protein 4 and mitogen‐activated protein kinase 3 were enriched in T cell receptor signalling pathway during acute infection. Highly methylated and lowly expressed genes, such as Ras association domain family member 1 and cyclin‐dependent kinase inhibitor 2A were identified in chronic infection. Furthermore, differentially expressed FcγR Ia, FcγR IIa and FcγR IIb, CD3^?CD56⁺CD16⁺ natural killer cells and CD14^highCD16⁺ monocytes were identified between immune‐tolerant and immune‐clearance phases by experimental validation. The above genes and pathways may be used to distinguish different immune statuses of HBV infection.     

Phenotypically and functionally distinct subsets of natural killer cells in human PBMCs

Human natural killer (NK) cells are one major component of lymphocytes that mediate early protection against viruses and tumor cells, and play an important role in immune regulatory functions. In this study, we demonstrated that human NK cells could be divided into four subsets, CD56hi CD16(-), CD56lo CD16(-), CD56+CD16+ and CD56(-)CD16+, based on the expression of cell surface CD56 and CD16 molecules. Phenotypic analysis of NK cell subsets indicated that the expression of activation markers, adhesion molecules, memory cell markers, inhibitory and activating receptors, and intracellular proteins (granzyme B and perforin) were heterogeneous. Following interleukin (IL)-2 stimulation, interferon-gamma was preferentially produced by CD56+CD16(-) NK cells and this subset showed more proliferative capacity. The cytolytic activity of both CD56+CD16(-) and CD56+/-CD16+ subsets could be augmented in response to IL-2. The data provided a new definition for NK cell subsets demonstrating their phenotypic and functional diversity and possible stage of NK cell differentiation in peripheral blood.