| 1. |
- Chemin, Karine, et al.
(author)
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EOMES-positive CD4+ T cells are increased in PTPN22 (1858T) risk allele carriers.
- 2018
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In: European Journal of Immunology. - : Wiley. - 0014-2980 .- 1521-4141. ; 48:4, s. 655-669
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Journal article (peer-reviewed)abstract
- The presence of the PTPN22 risk allele (1858T) is associated with several autoimmune diseases including rheumatoid arthritis (RA). Despite a number of studies exploring the function of PTPN22 in T cells, the exact impact of the PTPN22 risk allele on T-cell function in humans is still unclear. In this study, using RNA sequencing, we show that, upon TCR-activation, naïve human CD4+ T cells homozygous for the PTPN22 risk allele overexpress a set of genes including CFLAR and 4-1BB, which are important for cytotoxic T-cell differentiation. Moreover, the protein expression of the T-box transcription factor Eomesodermin (EOMES) was increased in T cells from healthy donors homozygous for the PTPN22 risk allele and correlated with a decreased number of naïve CD4+ T cells. There was no difference in the frequency of other CD4+ T cell subsets (Th1, Th17, Tfh, Treg). Finally, an accumulation of EOMES+CD4+ T cells was observed in synovial fluid of RA patients with a more pronounced production of Perforin-1 in PTPN22 risk allele carriers. Altogether, we propose a novel mechanism of action of PTPN22 risk allele through the generation of cytotoxic CD4+ T cells and identify EOMES+CD4+ T cells as a relevant T-cell subset in RA pathogenesis.
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| 2. |
- Houtman, Miranda, et al.
(author)
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Five commercially-available antibodies react differentially with allelic forms of human HLA-DR beta chain
- 2022
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In: Molecular Immunology. - : Elsevier BV. - 0161-5890 .- 1872-9142. ; 152, s. 106-110
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Journal article (peer-reviewed)abstract
- Allelic variants of HLA-DRB1 have been associated with a variety of autoimmune and infectious diseases. Although the precise molecular mechanisms by which HLA-DRB1 alleles predispose to a particular disease are currently unclear, it has been shown that mRNA expression levels of HLA-DRB1 are dependent on the different alleles. We aimed to measure HLA-DR beta chain levels in peripheral blood mononuclear cells of individuals carrying HLA-DRB1*03:01/*04:01 and HLA-DRB1*03:01/*15:01 alleles by western blotting, using five commercially-available HLA-DRB antibodies. We observed highly heterogeneous binding of the tested antibodies to the different allelic forms of the HLA-DR beta chain. Overall, we show that current immunological research that employs available antibodies to detect HLA-DR beta chains is biased towards detection of specific variants of the protein; this may cause significant discrepancy in quantification of protein expression in a heterogeneous human population.
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| 3. |
- Houtman, Miranda
(author)
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Gene expression profiling in autoimmune diseases : a story of ups and downs
- 2018
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Doctoral thesis (other academic/artistic)abstract
- Autoimmune diseases are believed to arise from a combination of genetic and environmental factors that affect normal function of immune cells. In this thesis, we studied the functional role of genetic variants, in peripheral blood cells, that relate to rheumatoid arthritis (RA) and myositis by gene expression profiling. Genome wide association studies have identified numerous susceptibility loci for autoimmune diseases, however, the precise mechanisms of how these loci lead to increased risk of autoimmunity remain mostly unknown. We therefore aimed to increase our understanding of the involvement of the susceptibility loci PTPN2, PTPN22 and HLA-DRB1 in the pathogenesis of RA. For the PTPN2 locus, we show that the long non-coding RNA (lncRNA) LINC01882 encoded on this locus can be linked to RA. We found that the genetic variants in the PTPN2 locus are associated with the expression of several lncRNAs, but not with the expression of PTPN2. By silencing LINC01882 in Jurkat T cells, we identified that LINC01882 might play a role in T-cell activation by regulating IL-2 levels, an important cytokine in RA. In addition, we show a new role for the PTPN22 risk allele in the context of RA through the generation of CD4+ T cells with cytotoxic characteristics. We found that genes related to T-cell survival and cytotoxic T-cell differentiation were differentially expressed between PTPN22 risk and non-risk allele carriers. This led us to identify an increased frequency of EOMES+CD4+ T cells in healthy individuals carrying the PTPN22 risk allele. Furthermore, we identified a difference in the expression of HLA-DRB1 and certain HLA-DQ genes between healthy individuals carrying RA HLA-DRB1 risk (*04:01) and non-risk (*15:01) alleles. These differences in gene expression were observed in different cell types, including CD4+ and CD8+ T cells. This data suggests that HLA-DRB and HLA-DQ levels, and potentially their corresponding proteins, might support loss of immune tolerance in RA patients carrying HLA-DRB1*04:01 alleles. In addition, we aimed to differentiate involvement of CD4+ and CD8+ T cells in the myositis subgroups, polymyositis (PM) and dermatomyositis (DM), by studying gene expression. We found two genes that were differentially expressed in CD4+ T cells of patients with PM compared to DM, whereas we identified 176 genes that were differentially expressed in CD8+ T cells of patients with PM compared to DM. Several of these genes were related to lymphocyte migration and regulation of T-cell differentiation. These results add to the evidence that different immune mechanisms are involved in patients with PM compared to patients with DM. In summary, this thesis presents several new mechanisms for the RA susceptibility loci PTPN2, PTPN22 and HLA-DRB1. As these susceptibility loci are shared between several autoimmune diseases, these results can be implicated in the pathogenesis of other autoimmune diseases as well. We further suggest that different immune mechanisms are involved in subgroups of RA and myositis patients. These results could ultimately lead to the identification of more specific therapeutic targets for different autoimmune diseases.
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| 4. |
- Houtman, Miranda, et al.
(author)
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Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients
- 2021
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In: Frontiers in Immunology. - : Frontiers Media S.A.. - 1664-3224. ; 12
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Journal article (peer-reviewed)abstract
- HLA-DRB1 alleles have been associated with several autoimmune diseases. For anti-citrullinated protein antibody positive rheumatoid arthritis (RA), HLA-DRB1 shared epitope (SE) alleles are the major genetic risk factors. In order to study the genetic regulation of major histocompatibility complex (MHC) Class II gene expression in immune cells, we investigated transcriptomic profiles of a variety of immune cells from healthy individuals carrying different HLA-DRB1 alleles. Sequencing libraries from peripheral blood mononuclear cells, CD4+ T cells, CD8+ T cells, and CD14+ monocytes of 32 genetically pre-selected healthy female individuals were generated, sequenced and reads were aligned to the standard reference. For the MHC region, reads were mapped to available MHC reference haplotypes and AltHapAlignR was used to estimate gene expression. Using this method, HLA-DRB and HLA-DQ were found to be differentially expressed in different immune cells of healthy individuals as well as in whole blood samples of RA patients carrying HLA-DRB1 SE-positive versus SE-negative alleles. In contrast, no genes outside the MHC region were differentially expressed between individuals carrying HLA-DRB1 SE-positive and SE-negative alleles, thus HLA-DRB1 SE alleles have a strong cis effect on gene expression. Altogether, our findings suggest that immune effects associated with different allelic forms of HLA-DR and HLA-DQ may be associated not only with differences in the structure of these proteins, but also with differences in their expression levels.
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| 5. |
- Houtman, Miranda, et al.
(author)
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T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus
- 2018
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In: Journal of Autoimmunity. - : ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD. - 0896-8411 .- 1095-9157. ; 90, s. 28-38
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Journal article (peer-reviewed)abstract
- Non-coding SNPs in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) locus have been linked with several autoimmune diseases, including rheumatoid arthritis, type I diabetes, and inflammatory bowel disease. However, the functional consequences of these SNPs are poorly characterized. Herein, we show in blood cells that SNPs in the PTPN2 locus are highly correlated with DNA methylation levels at four CpG sites downstream of PTPN2 and expression levels of the long non-coding RNA (IncRNA) LINC01882 downstream of these CpG sites. We observed that LINC01882 is mainly expressed in T cells and that anti-CD3/CD28 activated naive CD4(+) T cells downregulate the expression of LINC01882. RNA sequencing analysis of LINC01882 knockdown in Jurkat T cells, using a combination of antisense oligo-nucleotides and RNA interference, revealed the upregulation of the transcription factor ZEB1 and kinase MAP2K4, both involved in IL-2 regulation. Overall, our data suggests the involvement of LINC01882 in T cell activation and hints towards an auxiliary role of these non-coding SNPs in autoimmunity associated with the PTPN2 locus.
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