A genome-wide regulatory network identifies key transcription factors for memory CD8+ T-cell development

Memory CD8[superscript +] T-cell development is defined by the expression of a specific set of memory signature genes. Despite recent progress, many components of the transcriptional control of memory CD8[superscript +] T-cell development are still unknown. To identify transcription factors and their interactions in memory CD8[superscript +] T-cell development, we construct a genome-wide regulatory network and apply it to identify key transcription factors that regulate memory signature genes. Most of the known transcription factors having a role in memory CD8[superscript +] T-cell development are rediscovered and about a dozen new ones are also identified. Sox4, Bhlhe40, Bach2 and Runx2 are experimentally verified, and Bach2 is further shown to promote both development and recall proliferation of memory CD8[superscript +] T cells through Prdm1 and Id3. Gene perturbation study identifies the interactions between the transcription factors, with Sox4 positioned as a hub. The identified transcription factors and insights into their interactions should facilitate further dissection of molecular mechanisms underlying memory CD8[superscript +] T-cell development.Singapore-MIT AllianceNational Institutes of Health (U.S.) (Grant AI69208)National Cancer Institute (U.S.) (Koch Institute Support (core) Grant P30-CA14051

Defining species specific genome differences in malaria parasites

<p>Abstract</p> <p>Background</p> <p>In recent years a number of genome sequences for different <it>plasmodium </it>species have become available. This has allowed the identification of numerous conserved genes across the different species and has significantly enhanced our understanding of parasite biology. In contrast little is known about species specific differences between the different genomes partly due to the lower sequence coverage and therefore relatively poor annotation of some of the draft genomes particularly the rodent malarias parasite species.</p> <p>Results</p> <p>To improve the current annotation and gene identification status of the draft genomes of <it>P. berghei</it>, <it>P. chabaudi </it>and <it>P. yoelii</it>, we performed genome-wide comparisons between these three species. Through analyses via comparative genome hybridizations using a newly designed pan-rodent array as well as in depth bioinformatics analysis, we were able to improve on the coverage of the draft rodent parasite genomes by detecting orthologous genes between these related rodent parasite species. More than 1,000 orthologs for <it>P. yoelii </it>were now newly associated with a <it>P. falciparum </it>gene. In addition to extending the current core gene set for all plasmodium species this analysis also for the first time identifies a relatively small number of genes that are unique to the primate malaria parasites while a larger gene set is uniquely conserved amongst the rodent malaria parasites.</p> <p>Conclusions</p> <p>These findings allow a more thorough investigation of the genes that are important for host specificity in malaria.</p

Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy

<p>Abstract</p> <p>Background</p> <p>The design of long oligonucleotides for spotted DNA microarrays requires detailed attention to ensure their optimal performance in the hybridization process. The main challenge is to select an optimal oligonucleotide element that represents each genetic locus/gene in the genome and is unique, devoid of internal structures and repetitive sequences and its Tm is uniform with all other elements on the microarray. Currently, all of the publicly available programs for DNA long oligonucleotide microarray selection utilize various combinations of cutoffs in which each parameter (uniqueness, Tm, and secondary structure) is evaluated and filtered individually. The use of the cutoffs can, however, lead to information loss and to selection of suboptimal oligonucleotides, especially for genomes with extreme distribution of the GC content, a large proportion of repetitive sequences or the presence of large gene families with highly homologous members.</p> <p>Results</p> <p>Here we present the program OligoRankPick which is using a weighted rank-based strategy to select microarray oligonucleotide elements via an integer weighted linear function. This approach optimizes the selection criteria (weight score) for each gene individually, accommodating variable properties of the DNA sequence along the genome. The designed algorithm was tested using three microbial genomes <it>Escherichia coli</it>, <it>Saccharomyces cerevisiae </it>and the human malaria parasite species <it>Plasmodium falciparum</it>. In comparison to other published algorithms OligoRankPick provides significant improvements in oligonucleotide design for all three genomes with the most significant improvements observed in the microarray design for <it>P. falciparum </it>whose genome is characterized by large fluctuations of GC content, and abundant gene duplications.</p> <p>Conclusion</p> <p>OligoRankPick is an efficient tool for the design of long oligonucleotide DNA microarrays which does not rely on direct oligonucleotide exclusion by parameter cutoffs but instead optimizes all parameters in context of each other. The weighted rank-sum strategy utilized by this algorithm provides high flexibility of oligonucleotide selection which accommodates extreme variability of DNA sequence properties along genomes of many organisms.</p

Antibiotics induce polarization of pleural macrophages to M2-like phenotype in patients with tuberculous pleuritis

Pleural macrophages play critical roles in pathogenesis of tuberculous pleuritis, but very little is known about their response to anti-tuberculosis antibiotics treatment. Here, we examined whether and how pleural macrophages change in phenotype, transcription and function following antibiotics treatment in patients with tuberculous pleuritis. Results show pro-inflammatory cytokines were down-regulated significantly post antibiotic treatment in the pleural effusions and pleural macrophages up-regulated markers characteristic of M2 macrophages such as CD163 and CD206. Differential expression analysis of transcriptomes from four paired samples before and after treatment identified 230 treatment-specific responsive genes in pleural macrophages. Functional analysis identified interferon-related pathway to be the most responsive genes and further confirmed macrophage polarization to M2-like phenotype. We further demonstrate that expression of a significant fraction of responsive genes was modulated directly by antibiotics in pleural macrophages in vitro. Our results conclude that pleural macrophages polarize from M1-like to M2-like phenotype within a mean of 3.5 days post antibiotics treatment, which is dependent on both pleural cytokine environment and direct modulatory effects of antibiotics. The treatment-specific genes could be used to study the roles of pleural macrophages in the pathogenesis of tuberculous pleuritis and to monitor the response to antibiotics treatment

LILRB3 (ILT5) is a myeloid cell checkpoint that elicits profound immunomodulation.

Despite advances in identifying the key immunoregulatory roles of many of the human leukocyte immunoglobulin-like receptor (LILR) family members, the function of the inhibitory molecule LILRB3 (ILT5, CD85a, LIR3) remains unclear. Studies indicate a predominant myeloid expression; however, high homology within the LILR family and a relative paucity of reagents have hindered progress toward identifying the function of this receptor. To investigate its function and potential immunomodulatory capacity, a panel of LILRB3-specific monoclonal antibodies (mAbs) was generated. LILRB3-specific mAbs bound to discrete epitopes in Ig-like domain 2 or 4. LILRB3 ligation on primary human monocytes by an agonistic mAb resulted in phenotypic and functional changes, leading to potent inhibition of immune responses in vitro, including significant reduction in T cell proliferation. Importantly, agonizing LILRB3 in humanized mice induced tolerance and permitted efficient engraftment of allogeneic cells. Our findings reveal powerful immunosuppressive functions of LILRB3 and identify it as an important myeloid checkpoint receptor

Vitamin D₃-vitamin D receptor axis suppresses pulmonary emphysema by maintaining alveolar macrophage homeostasis and function

Background: Chronic obstructive pulmonary disease (COPD) is characterized by emphysema and/or obstructive bronchiolitis. Deficiency in vitamin D3 (VD3), which regulates gene expression through binding to vitamin D receptor (VDR), is associated with high risks of COPD susceptibility. Alveolar macrophages (AM), which are generated during early ontogeny and maintained in alveoli by self-renewal in response to cytokine GM-CSF, are positively correlated with severity of emphysema. However, whether and how VD3, VDR and AM interact to contribute to COPD pathogenesis at the molecular and cellular levels are largely unknown. Methods: We used systems biology approaches to analyze gene expression in mouse macrophages from different tissues to identify key transcription factors (TF) for AM and infer COPD disease genes. We used RNA-seq and ChIP-seq to identify genes that are regulated by VD3 in AM. We used VDR-deficient (Vdr−/−) mice to investigate the role of VD3-VDR axis in the pathogenesis of COPD and characterized the transcriptional and functional alterations of Vdr−/− AM. Findings: We find that VDR is a key TF for AM and a COPD disease gene. VDR is highly expressed in AM and in response to VD3 inhibits GM-CSF-induced AM proliferation. In Vdr−/− AM, genes involved in proliferation and immune response are upregulated. Consistently, Vdr−/− mice progressively accumulate AM and concomitantly develop emphysema without apparent infiltration of immune cells into the lung tissue. Intratracheal transfer of Vdr−/− AM into wildtype mice readily induces emphysema. The production of reactive oxygen species at basal level and in response to heme or lipopolysaccharide is elevated in Vdr−/− AM and suppressed by VD3 in wildtype AM. Interpretation: These results show that the VD3-VDR axis is critical to counteract GM-CSF-induced AM proliferation and defect in this regulation leads to altered AM homeostasis and function. Our findings identify that VD3 deficiency contributes to emphysema by altering AM function without contributing to bronchiolitis. Our findings also suggest possibilities of modulating the VD3-VDR axis for inhibiting emphysema in COPD patients.National Institutes of Health (U.S.) (Grant AI69208)National Institutes of Health (U.S.) (Grant CA197605)National Institutes of Health (U.S.) (Grant NS104315)National Cancer Institute (U.S.) (Grant P30-CA14051

Effect of anodic oxidation of 2024-T3 aluminum alloy on interface properties of metal fiber laminates

Interlaminar fracture failure is the main factor restricting the development and application of fiber metal laminates. In this paper, the interlayer bonding properties of 2024-T3 aluminum alloy plates with different surface treatments were compared and studied through lap-shear experiments. Compared with the aluminum plate treated with acid and alkali corrosion, the interlaminar shear strength of the aluminum plate after sulfuric acid anodization increased by 34.3%. After different surface treatments, experimental stressstrain curves of 2024-T3 aluminum alloys reveal the enhancement mechanism and changing trend of interlaminar shear strength

Verifications of microarray results by quantitative real-time PCR and example of oligonucleotide selection for highly homologous genes

<p><b>Copyright information:</b></p><p>Taken from "Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy"</p><p>http://www.biomedcentral.com/1471-2105/8/350</p><p>BMC Bioinformatics 2007;8():350-350.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2099447.</p><p></p> The bar graph indicates mRNA abundance ratios between two developmental stages (schizont/trophozoite) of the IDC for 10 genes measured by microarray and by real-time RT-PCR. The expression data were obtained using the total RNA isolations from the trophozoite and schizont stage. Each measurement was carried three times and the standard error for each measurement is indicated. . The uniqueness score distributions along the two highly homologous histone 3 genes. The uniqueness is represented by the BLAST score of each 70 nt window along the histone genes (H3 and H3.3) to its second best target in the genome. The red arrow indicates the position of oligonucleotide selected by OligoRankPick in each gene

Overall profiles of the uniqueness and GC content of oligonucleotide microarray elements in the 12 designed theoretical microarray sets

<p><b>Copyright information:</b></p><p>Taken from "Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy"</p><p>http://www.biomedcentral.com/1471-2105/8/350</p><p>BMC Bioinformatics 2007;8():350-350.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2099447.</p><p></p> Four algorithms OligoRankPick, ArrayoligoSelector, OligoPicker, and OligoArray2.1 were used to design long oligonucleotide DNA microarray sets for , and . Contour plots illustrate oligonucleotide density plotted of along the uniqueness scores (second target ) and GC contents. The oligonucleotide density is is calculated as -log10(N/N) (N ~ number of oligonucletide in a given area and N~ number of oligonucleotide in the most dense area)and displayed using the indicated by the color based scale