Transcript imaging of the development of human T helper cells using oligonucleotide arrays (original) (raw)
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Distinct gene expression profiles of human type 1 and type 2 T helper cells
Genome biology, 2001
The development and activation of CD4+ helper T cell (Th) subsets with distinct patterns of unbalanced production of cytokines play an important part in infectious, allergic and autoimmune diseases. Human neonatal cord blood CD4+ Th cells can be polarized into type 1 or type 2-like effector cells in vitro by culturing them in the presence of interleukin (IL)-12 or IL-4, respectively. We have exploited this experimental system to identify marker genes that are differentially expressed by polarized Th1 and Th2 cells. An oligonucleotide microarray specifically designed to screen for inflammation-related candidate genes was used and the differential expression was further validated with a quantitative real-time RT-PCR method. In addition to the previously described marker genes of Th cells, we report subtle changes in the expression of several other genes that represent growth factors, receptors and other signaling molecules in polarized Th1 and Th2 cell subsets. Additionally, we descri...
Journal of Immunological Methods, 2006
Identification of key factors mediating the differentiation of naïve CD4 + T helper cells into Th1 and Th2 subsets is important for understanding the molecular mechanisms of the development of autoimmune diseases as well as asthma and allergy. Functional importance of a given gene in the initiation of human T helper cell differentiation has been hard to study due to the difficulty in transfecting primary resting human T lymphocytes. In this study we have successfully transfected human primary CD4 + T helper cells using Amaxa's Nucleofection technology. To overcome the background caused by untransfected cells, we have developed a system for enriching nucleofected unstimulated human primary T helper cells that express the gene of interest. This is achieved by introducing a plasmid construct containing a bicistronic unit coding for a truncated mouse MHC class l H-2K k cell surface marker followed by selection of H-2K k positive cells using antibody coated beads. We demonstrate that the nucleofected and enriched H-2K k positive T helper cells differentiate into Th1 and Th2 cells as well as the non-transfected control cells. We also show that by using this novel method, introduction of an shRNA targeting Stat6, a key molecule driving the Th2 cell development, results in impaired Th2 cell differentiation, as expected. The method described here, enables fast and feasible preparation of highly pure transfected primary CD4 + T cell cultures ideal for studying the influence of overexpression or knockdown of a given gene on T helper cell differentiation and other primary human T cell functions.
Allergy, 2008
Background: Allergic diseases are thought to involve dysregulated activation of T cells including CD4+ lymphocytes. T‐cell activation results in changes in gene expression, but the optimal method to study gene expression profiles in T cells, and how this changes over time, are not known.Methods: Circulating CD4+ T cells were obtained from subjects with atopic asthma, nonatopic asthma or nonallergic controls, and total mRNA was rapidly isolated. Atopy was defined as positive skin prick test to one of nine allergens. Gene expression was analyzed using hybridization and Affymetrix® oligonucleotide arrays (Hu133A and Hu133B chips, n = 84), or by reverse transcription‐polymerase chain reaction (RT‐PCR) with a pathway‐targeted array (Human Th1–Th2–Th3 RT2 ProfilerTM PCR Array, Superarray, n = 16).Results: Using Affymetrix arrays, it was difficult to discern a dominant allergy‐associated profile because of heterogeneity in gene expression profiles. In contrast, a Th2‐like signature was ...
JMIR bioinformatics and biotechnology, 2023
Background: T helper (Th) 9 cells are a novel subset of Th cells that develop independently from Th2 cells and are characterized by the secretion of interleukin (IL)-9. Studies have suggested the involvement of Th9 cells in variable diseases such as allergic and pulmonary diseases (eg, asthma, chronic obstructive airway disease, chronic rhinosinusitis, nasal polyps, and pulmonary hypoplasia), metabolic diseases (eg, acute leukemia, myelocytic leukemia, breast cancer, lung cancer, melanoma, pancreatic cancer), neuropsychiatric disorders (eg, Alzheimer disease), autoimmune diseases (eg, Graves disease, Crohn disease, colitis, psoriasis, systemic lupus erythematosus, systemic scleroderma, rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, atopic dermatitis, eczema), and infectious diseases (eg, tuberculosis, hepatitis). However, there is a dearth of information on its involvement in other metabolic, neuropsychiatric, and infectious diseases. Objective: This study aims to identify significant differentially altered genes in the conversion of Th2 to Th9 cells, and their regulating microRNAs (miRs) from publicly available Gene Expression Omnibus data sets of the mouse model using in silico analysis to unravel various pathogenic pathways involved in disease processes. Methods: Using differentially expressed genes (DEGs) identified from 2 publicly available data sets (GSE99166 and GSE123501) we performed functional enrichment and network analyses to identify pathways, protein-protein interactions, miR-messenger RNA associations, and disease-gene associations related to significant differentially altered genes implicated in the conversion of Th2 to Th9 cells. Results: We extracted 260 common downregulated, 236 common upregulated, and 634 common DEGs from the expression profiles of data sets GSE99166 and GSE123501. Codifferentially expressed ILs, cytokines, receptors, and transcription factors (TFs) were enriched in 7 crucial Kyoto Encyclopedia of Genes and Genomes pathways and Gene Ontology. We constructed the protein-protein interaction network and predicted the top regulatory miRs involved in the Th2 to Th9 differentiation pathways. We also identified various metabolic, allergic and pulmonary, neuropsychiatric, autoimmune, and infectious diseases as well as carcinomas where the differentiation of Th2 to Th9 may play a crucial role. Conclusions: This study identified hitherto unexplored possible associations between Th9 and disease states. Some important ILs, including CCL1 (chemokine [C-C motif] ligand 1), CCL20 (chemokine [C-C motif] ligand 20), IL-13, IL-4, IL-12A, and IL-9; receptors, including IL-12RB1, IL-4RA (interleukin 9 receptor alpha), CD53 (cluster of differentiation 53), CD6 (cluster of differentiation 6), CD5 (cluster of differentiation 5), CD83 (cluster of differentiation 83), CD197 (cluster of differentiation 197), IL-1RL1 (interleukin 1 receptor-like 1), CD101 (cluster of differentiation 101), CD96 (cluster of differentiation 96), CD72 (cluster of differentiation 72), CD7 (cluster of differentiation 7), CD152 (cytotoxic T lymphocyte-associated protein 4), CD38 (cluster
Profiling of differential gene expression in activated, allergen-specific human Th2 cells
Genes & Immunity, 2001
Th2 cells play a pivotal role in the pathogenesis of allergic diseases, including asthma, but the molecular basis of the Th1/Th2 dichotomy and the precise molecular pathways leading to Th2-dominant immune responses are still unclear. To this end, we have combined suppression subtractive hybridization (SSH) and high throughput analysis of cDNA arrays spotted with IMAGE clones to determine the profile of differential gene expression in human allergen-specific Th2 cells. Allergen-stimulated Th2 cells were used as the tester, and either resting Th2 cells or stimulated Th1 cells were used as the driver. SSH was used to equalize different mRNA levels and remove common sequences between the tester and the driver. Comparison of cDNA arrays probed with subtracted tester and non-subtracted driver provided a profile of Th2selective gene expression. Analysis of 77 sequence-confirmed and differentially expressed genes in Th2 cells showed predominant EST sequences, representing 80% of sequences analyzed. The pattern of gene expression in 19 selected sequences was further analyzed in additional Th1 and Th2 clones. A total of 15 sequences showed predominant expression in Th2 cells, while the remaining four EST sequences showed no detectable amplification signal. The database containing Th2-selective genes will further our understanding of Th2 cell function and the genetic basis of allergic diseases. Genes and Immunity (2001) 2, 88-98.
Selective expression of an interleukin-12 receptor component by human T helper 1 cells
Immunology Letters, 1997
Interleukin-12 (IL-12), a heterodimeric cytokine produced by activated monocytes and dendritic cells, plays a crucial role in regulating interferon (IFN)-␥ production and in the generation of IFN-␥-producing T helper 1 (Th1) cells. Here we show that the IL-12 receptor (IL-12R)  2 subunit, a recently cloned binding and signal transducing component of the IL-12R, is expressed on human Th1 but not Th2 clones and is induced during differentiation of human naive cells along the Th1 but not the Th2 pathway. IL-12 and type I but not type II interferons induce expression of the IL-12R  2 chain during in vitro T cell differentiation after antigen receptor triggering. The selective expression and regulation of the IL-12R  2 subunit may help to understand the basis of Th1/Th2 differentiation and may provide therapeutic options for altering the Th1/Th2 balance in several immuno-pathological conditions such as autoimmune diseases and allergies.
PREDICTION OF REGULATORY TRANSCRIPTION FACTORS IN T HELPER CELL DIFFERENTIATION AND MAINTENANCE
Genome Informatics 2009 - Proceedings of the 9th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2009), 2010
Naive T-helper (Th) cells differentiate into distinct lineages including Th1, Th2, Th17 and regulatory T (Treg) cells. Each of these Th-lineages has specific functions in immune defense and T cell homeostasis. Th cell fate decisions and commitment are dependent on the kind and strength of T cell stimulation and the subsequent gene expression profiles.
BMC Genomics, 2008
Background T-cell activation is an essential step of the immune response and relies on the tightly controlled orchestration of hundreds of genes/proteins, yet the cellular and molecular events underlying this complex process are not fully understood, especially at the genome-scale. Significantly, a comparative genome-scale transcriptional analysis of two T-cell subsets (CD4+ and CD8+) against each other and against the naturally mixed population (CD3+ cells) remains unexplored. Results Comparison of the microarray-based gene expression patterns between CD3+ T cells, and the CD4+ and CD8+ subsets revealed largely conserved, but not identical, transcriptional patterns. We employed a Gene-Ontology-driven transcriptional analysis coupled with protein abundance assays in order to identify novel T-cell activation genes and cell-type-specific genes associated with the immune response. We identified potential genes involved in the communication between the two subsets (including IL23A, NR4A...
Identification of global regulators of T-helper cell lineage specification
Genome medicine, 2015
Activation and differentiation of T-helper (Th) cells into Th1 and Th2 types is a complex process orchestrated by distinct gene activation programs engaging a number of genes. This process is crucial for a robust immune response and an imbalance might lead to disease states such as autoimmune diseases or allergy. Therefore, identification of genes involved in this process is paramount to further understand the pathogenesis of, and design interventions for, immune-mediated diseases. We aimed at identifying protein-coding genes and long non-coding RNAs (lncRNAs) involved in early differentiation of T-helper cells by transcriptome analysis of cord blood-derived naïve precursor, primary and polarized cells. Here, we identified lineage-specific genes involved in early differentiation of Th1 and Th2 subsets by integrating transcriptional profiling data from multiple platforms. We have obtained a high confidence list of genes as well as a list of novel genes by employing more than one prof...