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Monozygotic twins discordant for common variable immunodeficiency reveal impaired DNA demethylation during naïve-to-memory B-cell transition.

Rodríguez-Cortez VC, Del Pino-Molina L, Rodríguez-Ubreva J, Ciudad L, Gómez-Cabrero D, Company C, Urquiza JM, Tegnér J, Rodríguez-Gallego C, López-Granados E, Ballestar E - Nat Commun (2015)

Bottom Line: Common variable immunodeficiency (CVID), the most frequent primary immunodeficiency characterized by loss of B-cell function, depends partly on genetic defects, and epigenetic changes are thought to contribute to its aetiology.Individual analysis confirms hypermethylation of these genes.Our results not only indicate a role for epigenetic alterations in CVID but also identify relevant DNA methylation changes in B cells that could explain the clinical manifestations of CVID individuals.

View Article: PubMed Central - PubMed

Affiliation: Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avda Gran Via 199-203, 08908L'Hospitalet de Llobregat, Barcelona, Spain.

ABSTRACT
Common variable immunodeficiency (CVID), the most frequent primary immunodeficiency characterized by loss of B-cell function, depends partly on genetic defects, and epigenetic changes are thought to contribute to its aetiology. Here we perform a high-throughput DNA methylation analysis of this disorder using a pair of CVID-discordant MZ twins and show predominant gain of DNA methylation in CVID B cells with respect to those from the healthy sibling in critical B lymphocyte genes, such as PIK3CD, BCL2L1, RPS6KB2, TCF3 and KCNN4. Individual analysis confirms hypermethylation of these genes. Analysis in naive, unswitched and switched memory B cells in a CVID patient cohort shows impaired ability to demethylate and upregulate these genes in transitioning from naive to memory cells in CVID. Our results not only indicate a role for epigenetic alterations in CVID but also identify relevant DNA methylation changes in B cells that could explain the clinical manifestations of CVID individuals.

No MeSH data available.


Related in: MedlinePlus

Comparison of the expression and histone modification levels of aforementioned selected genes in different B-cell subsets in healthy donors and CVID patients.(a) Box and whisker plots showing quantitative RT–PCR analysis comparing mRNA levels of the selected genes in different B-cell subsets in five CVID patients and four healthy controls. HPRT1 was used for normalization. Grey boxes represent expression levels in CVID patients. The bottom and top of the box are the first and third quartiles, respectively, the band inside the box is the median and the ends of the whiskers represent the minimum and maximum of all of the data. Student's t-test comparisons with a P value above 0.05 are considered with a nonsignificant difference (n.s.). (b) ChIP assays for two histone modifications, one activating marks (H3K4me3, blue bars) and one repressive mark (H3K27me3, red bars) focusing on the same regions were changes in DNA methylation were identified. The values correspond to relative enrichment of the bound fraction with respect to input. Negative control (immunoprecipitated with IgG) samples are also shown. The comparison corresponds to a technical triplicate of one CVID individual and one healthy control. Error bars correspond to s.d.
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f4: Comparison of the expression and histone modification levels of aforementioned selected genes in different B-cell subsets in healthy donors and CVID patients.(a) Box and whisker plots showing quantitative RT–PCR analysis comparing mRNA levels of the selected genes in different B-cell subsets in five CVID patients and four healthy controls. HPRT1 was used for normalization. Grey boxes represent expression levels in CVID patients. The bottom and top of the box are the first and third quartiles, respectively, the band inside the box is the median and the ends of the whiskers represent the minimum and maximum of all of the data. Student's t-test comparisons with a P value above 0.05 are considered with a nonsignificant difference (n.s.). (b) ChIP assays for two histone modifications, one activating marks (H3K4me3, blue bars) and one repressive mark (H3K27me3, red bars) focusing on the same regions were changes in DNA methylation were identified. The values correspond to relative enrichment of the bound fraction with respect to input. Negative control (immunoprecipitated with IgG) samples are also shown. The comparison corresponds to a technical triplicate of one CVID individual and one healthy control. Error bars correspond to s.d.

Mentions: Demethylation of these genes is compatible with the increased expression levels of these genes and the function of their products in memory cells. These results are also in agreement with the progressive loss of methylation and gain of expression during B-cell differentiation22. We used quantitative real-time PCR (QRT–PCR) to measure mRNA levels of these genes, and observed that normal individuals exhibit increasing levels of genes such as BCL2L1, KCNC4 and CORO1B in the naive-to-switched memory B-cell transition, confirming a relationship between DNA demethylation and gain of expression (Fig. 4a). In fact, analysis of histone modifications in the sequences containing the CpG sites undergoing demethylation showed an increase in the activating histone mark H3K4me3 during naive to memory cell differentiation in genes such as BCL2L1 and PIK3CD (Fig. 4b), indicating a relationship between DNA methylation, histone modifications and gene expression and a less clear correlation for the repressive mark H3K27me3 (Fig. 4b).


Monozygotic twins discordant for common variable immunodeficiency reveal impaired DNA demethylation during naïve-to-memory B-cell transition.

Rodríguez-Cortez VC, Del Pino-Molina L, Rodríguez-Ubreva J, Ciudad L, Gómez-Cabrero D, Company C, Urquiza JM, Tegnér J, Rodríguez-Gallego C, López-Granados E, Ballestar E - Nat Commun (2015)

Comparison of the expression and histone modification levels of aforementioned selected genes in different B-cell subsets in healthy donors and CVID patients.(a) Box and whisker plots showing quantitative RT–PCR analysis comparing mRNA levels of the selected genes in different B-cell subsets in five CVID patients and four healthy controls. HPRT1 was used for normalization. Grey boxes represent expression levels in CVID patients. The bottom and top of the box are the first and third quartiles, respectively, the band inside the box is the median and the ends of the whiskers represent the minimum and maximum of all of the data. Student's t-test comparisons with a P value above 0.05 are considered with a nonsignificant difference (n.s.). (b) ChIP assays for two histone modifications, one activating marks (H3K4me3, blue bars) and one repressive mark (H3K27me3, red bars) focusing on the same regions were changes in DNA methylation were identified. The values correspond to relative enrichment of the bound fraction with respect to input. Negative control (immunoprecipitated with IgG) samples are also shown. The comparison corresponds to a technical triplicate of one CVID individual and one healthy control. Error bars correspond to s.d.
© Copyright Policy - open-access
Related In: Results  -  Collection

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f4: Comparison of the expression and histone modification levels of aforementioned selected genes in different B-cell subsets in healthy donors and CVID patients.(a) Box and whisker plots showing quantitative RT–PCR analysis comparing mRNA levels of the selected genes in different B-cell subsets in five CVID patients and four healthy controls. HPRT1 was used for normalization. Grey boxes represent expression levels in CVID patients. The bottom and top of the box are the first and third quartiles, respectively, the band inside the box is the median and the ends of the whiskers represent the minimum and maximum of all of the data. Student's t-test comparisons with a P value above 0.05 are considered with a nonsignificant difference (n.s.). (b) ChIP assays for two histone modifications, one activating marks (H3K4me3, blue bars) and one repressive mark (H3K27me3, red bars) focusing on the same regions were changes in DNA methylation were identified. The values correspond to relative enrichment of the bound fraction with respect to input. Negative control (immunoprecipitated with IgG) samples are also shown. The comparison corresponds to a technical triplicate of one CVID individual and one healthy control. Error bars correspond to s.d.
Mentions: Demethylation of these genes is compatible with the increased expression levels of these genes and the function of their products in memory cells. These results are also in agreement with the progressive loss of methylation and gain of expression during B-cell differentiation22. We used quantitative real-time PCR (QRT–PCR) to measure mRNA levels of these genes, and observed that normal individuals exhibit increasing levels of genes such as BCL2L1, KCNC4 and CORO1B in the naive-to-switched memory B-cell transition, confirming a relationship between DNA demethylation and gain of expression (Fig. 4a). In fact, analysis of histone modifications in the sequences containing the CpG sites undergoing demethylation showed an increase in the activating histone mark H3K4me3 during naive to memory cell differentiation in genes such as BCL2L1 and PIK3CD (Fig. 4b), indicating a relationship between DNA methylation, histone modifications and gene expression and a less clear correlation for the repressive mark H3K27me3 (Fig. 4b).

Bottom Line: Common variable immunodeficiency (CVID), the most frequent primary immunodeficiency characterized by loss of B-cell function, depends partly on genetic defects, and epigenetic changes are thought to contribute to its aetiology.Individual analysis confirms hypermethylation of these genes.Our results not only indicate a role for epigenetic alterations in CVID but also identify relevant DNA methylation changes in B cells that could explain the clinical manifestations of CVID individuals.

View Article: PubMed Central - PubMed

Affiliation: Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avda Gran Via 199-203, 08908L'Hospitalet de Llobregat, Barcelona, Spain.

ABSTRACT
Common variable immunodeficiency (CVID), the most frequent primary immunodeficiency characterized by loss of B-cell function, depends partly on genetic defects, and epigenetic changes are thought to contribute to its aetiology. Here we perform a high-throughput DNA methylation analysis of this disorder using a pair of CVID-discordant MZ twins and show predominant gain of DNA methylation in CVID B cells with respect to those from the healthy sibling in critical B lymphocyte genes, such as PIK3CD, BCL2L1, RPS6KB2, TCF3 and KCNN4. Individual analysis confirms hypermethylation of these genes. Analysis in naive, unswitched and switched memory B cells in a CVID patient cohort shows impaired ability to demethylate and upregulate these genes in transitioning from naive to memory cells in CVID. Our results not only indicate a role for epigenetic alterations in CVID but also identify relevant DNA methylation changes in B cells that could explain the clinical manifestations of CVID individuals.

No MeSH data available.


Related in: MedlinePlus