| Literature DB >> 31824477 |
Susana L Silva1,2,3, Mariana Fonseca1,2, Marcelo L M Pereira4, Sara P Silva1,2,3, Rita R Barbosa1, Ana Serra-Caetano1,2, Elena Blanco5,6, Pedro Rosmaninho1,2, Martin Pérez-Andrés5,6, Ana Berta Sousa1,2,3, Alexandre A S F Raposo1,2, Margarida Gama-Carvalho4, Rui M M Victorino1,2,3, Lennart Hammarstrom7, Ana E Sousa1,2.
Abstract
Monozygotic twins provide a unique opportunity to better understand complex genetic diseases and the relative contribution of heritable factors in shaping the immune system throughout life. Common Variable Immunodeficiency Disorders (CVID) are primary antibody defects displaying wide phenotypic and genetic heterogeneity, with monogenic transmission accounting for only a minority of the cases. Here, we report a pair of monozygotic twins concordant for CVID without a family history of primary immunodeficiency. They featured a remarkably similar profile of clinical manifestations and immunological alterations at diagnosis (established at age 37) and along the subsequent 15 years of follow-up. Interestingly, whole-exome sequencing failed to identify a monogenic cause for CVID, but unraveled a combination of heterozygous variants, with a predicted deleterious impact. These variants were found in genes involved in relevant immunological pathways, such as JUN, PTPRC, TLR1, ICAM1, and JAK3. The potential for combinatorial effects translating into the observed disease phenotype is inferred from their roles in immune pathways, namely in T and B cell activation. The combination of these genetic variants is also likely to impose a significant constraint on environmental influences, resulting in a similar immunological phenotype in both twins, despite exposure to different living conditions. Overall, these cases stress the importance of integrating NGS data with clinical and immunological phenotypes at the single-cell level, as provided by multi-dimensional flow-cytometry, in order to understand the complex genetic landscape underlying the vast majority of patients with CVID, as well as those with other immunodeficiencies.Entities:
Keywords: CVID; WES; flow-cytometry; genetics; monozygotic twins; polygenic disease
Year: 2019 PMID: 31824477 PMCID: PMC6882918 DOI: 10.3389/fimmu.2019.02503
Source DB: PubMed Journal: Front Immunol ISSN: 1664-3224 Impact factor: 7.561
Figure 1Immune phenotype at CVID diagnosis at age 37 in the MZ twins. (A) Representative plots of the flow-cytometry analysis of switched-memory B cells (top), CD21lowCD38low B cells (middle) and transitional B cells (bottom). Numbers represent the percentage of the given population within CD19+ cells (3.0%/4.2% in case-1/case-2, respectively). (B) Frequency of naïve and memory subpopulations, expression of activation marker HLA-DR+, and frequency of cells producing IL-2, IL-4, IFN-γ, and IL-17 within CD4 and CD8 T cells (1,777/1,380 lymphocytes/μL; CD4 T cells 42.2%/43.6%; CD8 T cells 44.1%/39.8%; in cases 1/2, respectively) (C) Lymphoproliferative responses upon culture with antigens (top) and mitogens (bottom) in comparison with healthy adult individuals.
Figure 2Supervised flow-cytometric analysis of blood lymphocytes in MZ twins concordant for CVID at age 50. (A) Principal component analysis (PCA) multidimensional view of the distribution of major lymphocyte subsets analyzed with the EuroFlow PID orientation tube in 1 × 106 peripheral blood leukocytes. (B) Distribution of memory B cells according to the surface membrane expression of the IgH-isotypes (IgM, IgD, IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2) in 5 × 106 peripheral blood leukocytes analyzed from an age-matched healthy donor and the two twins with CVID (7, 8, 26).
Selected SNVs with impact in the immune system identified by WES.
| chr19:17952472 T/C | ENST00000428406 | T321A | NA | NA | PD | T | Member of Janus kinase family of tyrosine kinases; Cytokine receptor-mediated intracellular signal transduction | |
| chr19:10394792 G/A | ENST00000264832 | G241R | rs1799969 | 0,1102 | PD | D | Cell surface glycoprotein with major role in cell-cell adhesion, in endothelia and immune cells | |
| chr19:10395468 G/A | ENST00000423829 | R397Q | rs5497 | 0,0006 | PD | D | ||
| chr1:59248405 C/G | ENST00000371222 | G113A | rs1462279538 | NA | PD | D | Transcription Factor AP-1 interacts with specific target DNA sequences to regulate gene expression in the immune system | |
| chr1:235972992 G/T | ENST00000536965 | P376T | rs770362521 | 3 ×10−5 | PD | T | Regulates intracellular protein trafficking in endosomes; Mutations associated with Chediak-Higashi syndrome with impaired cytotoxic lymphocyte function ( | |
| chr4: 38799956; NM_003263.4:c.497del | ENST00000308979 | K166fs | rs761749628 | 0,0003454 | NA | D | Member of the Toll-like receptor family, with a role in pathogen recognition and activation of innate immunity. Identified as a critical mediator of intestinal immunity | |
| chr10:54531242 G/A | ENST00000373968 | R52C | rs5030737 | 0,076 | PD | D | Belongs to collectin family. Important element in the innate immune system Variants associated with susceptibility to autoimmunity and infections ( | |
| chr1:198665917 C/G | ENST00000352140 | C77G | rs17612648 | 0,016 | S | N/A | Important for efficient T and B-cell antigen receptor signal transduction CD45RA persistence in memory T cells in alternative splicing defect |
HGVS, human genome variation society; NA, not available; MAF, minor allele frequency; EUR, European; PD, probably damaging; S, synonimous; T, tolerated; D, deleterious.
Figure 3Identified genetic variants and predicted functional impact on B and T-cell activation pathways. (A) Family tree of the patients. The sectors and color patterns represent the 8 genetic variants identified in the 7 listed genes, and their presence/absence in both the progenitors and the children of the two siblings. Each sector corresponds to one specific variant. Paternally inherited variants are represented on the left, and maternal variants on the right, with a color code per gene, next to the gene ID and identified variant (in parenthesis). The black dotted pattern highlights the maternal variant in the case of ICAM, for which the patients have two altered alleles. (B) Role of affected genes in T and B-cell activation processes. The figure represents a generic lymphoid cell with the major membrane receptors, signaling molecules and transcription factors (identified by their names) and intracellular signaling pathways (identified by arrows) involved in the activation process. Red and green arrows represent the final stages of the lymphocyte activation pathways leading to the expression of genes that promote anergy (red) or survival/proliferative responses (green) within the cell nucleus. The top half of cell highlights proteins and processes specific for T cell activation and the bottom half those specific for B-cell activation. The names of proteins encoded by genes that present potentially pathogenic variants are presented in orange. The figure compiles all the information that was retrievable from pathways databases and literature search regarding the connections between genes presented in (A) and the B and T cell activation pathways. Of these 7 genes, LYST did not present any connection to these processes, whereas two others (MBL2 and TLR1) have reported functions in lymphocyte activation but their connection to signaling pathways remains unclear and are thus not represented in the figure.