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Centrum für Chronische Immundefizienz - CCI

Research Group "Genetic basis of immunodeficiency"

Prof. Dr. Bodo Grimbacher

The research group „Genetic basis of immunodeficiency“ focuses on the genetics and molecular pathophysiology of primary immunodeficiencies.

Research Areas

The Molecular and Genetic Causes of Primary Immunodeficiencies

Many primary immunodeficiencies represent an “Experiment of Nature” (Robert Good), by having genetic alterations in their genomic code impairing immunocompetence. Interestingly enough, in recent years it became clear that:

  • The very same mutation causing the immunodeficiency can also cause immune dysregulation/autoimmunity/autoinflammation
  • Mutations in one and the same gene can lead to many different phenotypes, and may often even have a substantially reduced penetrance
  • A very similar phenotype in different individuals (even within the same family) may have different (mono-)genetic causes.

Common Variable Immunodeficiency (CVID) presents as a widely heterogeneous disorder in clinical as well as genetic terms. Monogenetic defects have been identified in only a proportion of cases (approximately 25%). Whereas, the majority of CVID patients still lacks a definite molecular diagnosis. Epigenetic factors point to be contributing to disease pathogenesis.

DNA-Methylation and histone posttranslational modifications play a role not only in transcription and DNA repair, but also in the maintenance of repressive chromatin. B and T cell differentiation are accompanied by highly coordinated and cumulative demethylation processes.

Through the combination of immunophenotyping, the power of genomic sequencing and state-of-the-art bioinformatic analysis our lab is currently working in the generation of DNA methylation profiles using Whole genome Bisulfite Sequencing (WGBS) analysis and, histone posttranslational imprint using Chromatin immunoprecipitation (ChIP) methods in successive subsets of B and T cells in CVID patients with unknown etiology.

In addition, we investigate the perturbations of the enhancer repertoire in different B cell subsets in CVID patients carrying mutation in TNFRSF13B compared to their healthy relatives harboring the same mutation and healthy controls without TNFRSF13B mutation. For this purpose we use assay for transposase accessibility chromatin using sequencing (ATAC-seq), a method for mapping chromatin accessibility genome-wide and RNA sequencing, a method to analyze continuously changing cellular transcriptomes.

The genetic research on hyper-IgE syndromes (HIES) and the genetic susceptibility to Staphylococcus and Candida infections dates back to my postdoc period. Here, I first described that HIES is a multisystem disease (NEJM, 1999), but can also be an autosomal-recessive trait (J. Pediatrics, 2004). It took more than 10 years to identify the first genetic defect for HIES, being heterozygous dominant-negative mutations in STAT3 (NEJM, 2007). Interestingly, also heterozygous gain-of-function mutations in STAT1 (J Clin Immunol, 2016) cause a similar but more limited phenotype, chronic mucocutaneous candidiasis. We are currently in the process of evaluating different gene editing protocols for a possible gene therapy approaches to genetically cure these patients (Dr. Manfred Fliegauf). A most recent discovery is that the transcription factor ZNF341 regulates STAT3, but probably not STAT1 transcript levels (Dr. Stefanie Frey-Jakobs).

Hyper-Immunoglobulin E syndrome (HIES) is a complex chronic primary immunodeficiency found to be quite rare (incidence 1:1 Mio). It presents as a defect of the immune response and is characterized by both immunological and non-immunological manifestations. Immunological manifestations include highly elevated serum IgE levels, eosinophilia, recurrent bacterial and fungal infections, eczema, skin infections, and pneumonia. Non-immunological manifestations include a characteristic facial appearance, scoliosis, retained primary teeth, joint hyperextensibility, recurrent bone fractures following minimal trauma, and craniosynostosis. Most cases of HIES are sporadic, but both autosomal dominant (AD-HIES) and autosomal recessive (AR-HIES) inheritance has been observed.

Autosomal Dominant HIES

We and others discovered in 2007 that heterozygous mutations of the Signal Transducer and Activator of Transcription 3 (STAT3) are a causal factor for most AD-HIES cases. These mutations lead to the production of STAT3 mutant forms, which function negative-dominantly over the wild-type STAT3. STAT3 is involved in multiple JAK-STAT signaling pathways and plays a key role in the production of a broad range of cytokines, one of which is IL-6, a regulator of Th17 cells. Defective signaling due to mutations in STAT3 therefore leads to the failure of Th17 cell development in AD-HIES patients. Interestingly, 30% of AD-HIES patients do not show STAT3 mutations; hence, further genetic causes of AD-HIES remain to be elucidated.

Autosomal Recessive HIES

Homozygous mutations of the Dedicator Of Cytokinesis 8 (DOCK8) gene have been shown to be responsible for many, although not all, cases of autosomal recessive HIES (AR-HIES). DOCK8 belongs to a family of guanine nucleotide exchange factors (GEFs) that are responsible for the activation of small G proteins, therefore a crucial part of intracellular signaling networks that when defective lead to phenotypes seen in HIES patients.

In 2014, mutations in PGM3 (Phosphoglucomutase 3) another gene involved in protein glycosylation as a causal factor for AR-HIES has been identified by us (J Allergy Clin Immunol., 2014) and others. Further research regarding its pathogenesis is currently being performed.

Recently, we identified ZNF341 another so far unknown gene as disease-causing for HIES. ZNF341, a transcription factor, binds to the STAT3 promoter and induces STAT3 transcription and translation (Science Immunology, 2018). Hence, patients with homozygous nonsense mutations in ZNF341 represent a phenocopy of STAT3- like hyper-IgE-syndrome. Although ZNF341 targets STAT3 and thereby influences immune-homeostasis, this transcription factor is not exclusively controlling STAT3. Thus, the impact of other ZNF341 target genes with regard to a more complex regulatory mechanism remains to be investigated.

Homozygous nonsense mutations in ZNF341 cause HIES with reduced Th17 cell numbers in patient PBMCs.

(A-D) Pedigrees and genotypes with the nonsense mutated (mut) alleles g.32345116C>T (c.904C>T; p.Arg302*) for Families A-C and g.32349795C>T (c.1156C>T; p.Arg386*) for Family D. Heterozygous carriers are unaffected. Wt, wild-type. Circles, female; squares, male; filled symbols, affected individuals with HIES; open symbols, healthy members; slash, deceased individual; double horizontal lines, consanguinity; black dot, miscarriage. (E) Both mutations predict premature termination of translation. (F) Flow cytometry of PBMCs demonstrate reduced Th17 cell counts on the basis of CD45RA-CCR6+CCR4+CXCR3- of CD3+CD4+ in patients (n=6; triangles, Family A; squares, Family D) compared to healthy donor controls (HD; n=8; open circles) (left). In contrast to controls (n=11), patient PBMCs (n=6) fail to differentiate into IL17+ cells (CD3+CD4+CD45RO+) upon in vitro stimulation (d4) with Th17 polarizing cytokines IL-1β and IL-6 plus T cell activation/expansion (right). Significance was determined using Mann-Whitney test. (G) ZNF341 is a 854 amino acids “zinc-finger-only” transcription factor with twelve C2H2 motifs (vertical boxes). R302* and R386* (arrows) delete zinc fingers 2-12 and 4-12, respectively. A putative nuclear localization sequence (NLS; blue) is retained in the R386* mutant. Numbers indicate amino acid positions in NP 001269862. from Science Immunology, 2018

Nevertheless, we further aim to discover novel genetic defects underlying the phenotypes of HIES patients who do not carry mutations in known HIES genes. Therefore, we study the clinical and immunological cellular phenotype of patients by flow cytometry and perform mutational analysis (linkage analysis, next generation sequencing, and Sanger sequencing) to detect the disease causing mutation. The pathomechanism by which the detected mutations lead to HIES is then further evaluated by various techniques such as Western blotting, RT-qPCR, overexpression systems, or ChIP sequencing.

LRBA deficiency, firstly described by our group in 2012 (Lopez-Herrera et al, Am J Hum Genet), is an early-onset primary immunodeficiency (PID) and immune dysregulation syndrome caused by biallelic mutations in LRBA that abolish its protein expression. Clinically, LRBA deficiency presents with a broad clinical phenotype including mostly autoimmune cytopenias, enteropathy, recurrent infections, and hypogammaglobulinemia, accompanied by reduced expression of CTLA-4 as well as diminished numbers of regulatory T cells (Tregs), switched memory B cells, and plasmablasts (Gámez-Díaz et al., J Allergy Clin Immunol. 2016). LRBA plays an essential role in the expression, function, and trafficking of CTLA-4 in Tregs, thereby controlling T-cell mediated immune responses (Lo et al., Science, 2015). However, the exact function of LRBA in other immune cells is not yet fully understood. Interestingly, LRBA deficiency mouse models do not mirror the human LRBA deficiency, as Lrba null mice do not present any clinical signs of disease and do not develop overt autoimmunity despite low levels of CTLA-4, reduced frequency of IL-10-producing B cells, and increased numbers of T follicular helper cells (Gámez-Díaz L et al., Immunol Cell Biol. 2017). In addition, Lrba null mice have a normal B- and T lymphocyte development and normal humoral immune responses against T-dependent as well as T-independent antigens.

Intestinal, pulmonary, and splenic alterations in LRBA-deficient patients

  • A, Colonoscopy in patient 105-1 revealed severe circular inflammation in the rectum, numerous ulcerations, and mucosal edema and erythema.
  • B, Magnetic resonance image from patient 109 showing marked splenomegaly.
  • C, High- resolution chest computed tomographic scan from patient 105-1 showing atypical, partly conflating patchy alveolar consolidations in both lungs.
  • D, Marked regression of alveolar consolidation 2 years after therapy and slight bilateral ground-glass infiltrates.

Our group focuses in the elucidation of the pathomechanisms of LRBA deficiency using in vivo and in vitro models, aiming for the development of future targeted therapies that improve the survival and quality of life of LRBA-deficient patients. In addition, we screen for LRBA deficiency based on LRBA protein detection by flow cytometry in activated peripheral blood mononuclear cells (PBMCs) from patients with clinical diagnosis of Common Variable Immunodeficiency (CVID) and Inflammatory Bowel Disease (IBD)-like phenotypes. Moreover, we sequence LRBA together with additional 130 genes by next generation sequencing on an Illumina MiSeq, aiming for the identification of biallelic mutations in LRBA providing a final diagnosis of this disease.

Reduced CTLA-4 expression in LRBA deficiency

LRBA binds with high affinity to the tail of CTLA-4 which is expressed constitutively in regulatory T cells (Tregs) or upon activation in conventional T cells. The LRBA- CTLA-4 interaction is required to guide CTLA-4 containing vesicles to the cell surface in order to capture and engulf the co-stimulatory molecules CD80 and CD86 from the antigen presenting cells (APC), thereby effectively controlling T-cell activation. In the absence of LRBA the adaptor protein AP-1 binds to CTLA-4 leading to its lysosomal degradation.

Our research work from the past years on LRBA deficiency has produced the following first and last author publications:

  1. Gámez-Díaz L et al., Frontiers Immunology. 2018.
  2. Gámez-Díaz L et al., Immunol Cell Biol. 2017.
  3. Gámez-Díaz L et al., J Allergy Clin Immunol. 2016.
  4. López-Herrera G et al., Am J Hum Genet. 2012

In addition, we have collaborated in the following publications related to LRBA deficiency:

  1. De Bruyne M et al., J Allergy Clin Immunol. 2018.
  2. Sharapova SO et al., J Clin Immunol. 2018.
  3. Seidel M et al., J Allergy Clin Immunol. 2017.
  4. Bakhtiar S et al., Frontiers Immunology. 2017.
  5. Schreiner F et al., J Clin Endocrinol Metab. 2016.
  6. Revel-Vilk S et al., Clin Immunol. 2015.
  7. Seidel MG et al., J Allergy Clin Immunol. 2015.
  8. Serwas NK et al., Inflamm Bowel Dis. 2015

Finally, our work on LRBA deficiency has been funded by the Bundesministerium für Bildung und Forschung (BMBF), the Deutsche Forschungsgemeinschaft (DFG), the Jeffrey Modell Foundation and the Fritz Thyssen Stiftung.

C. albicans pattern recognition via membrane receptors of monocytes/macrophages and dendritic cells. Pattern recognition receptors include Toll-like receptors (TLR2, TLR4, TLR6) and C-type lectin receptors (Dectin-1, Dectin-2, Mannose receptor, DC-SIGN) that recognize molecular structures of microbial pathogens like C. albicans. This leads to the activation of intracellular signaling cascades (such as the Dectin-1-Syk-CARD9 signaling pathway) that induce the production of proinflammatory cytokines initiating the adaptive immune response via activation and differentiation of specific immune cells.

Chronic mucocutaneous candidiasis (CMC) constitutes a primary immunodeficiency characterized by an enhanced susceptibility to recurrent fungal infections. CMC is associated with persistent or recurrent Candida infections of the skin, nail and mucous membranes. Additional clinical manifestations may include autoimmune disease, endocrinopathy, or an increased susceptibility to bacterial infections as well as secondary complications, such as aneurysms and carcinomas. Depending on the underlying genetic defect, the clinical presentations may offer a heterogeneous picture.

The role of Th17 cell cytokines in Candida control. Th17 cells play an important role in maintaining Candida immunity by secretion of cytokines IL-17A, IL17-F, IL-21 and IL-22 that stimulate the expression of antimicrobial peptides (ß-defensins, S100, lactoferrin). Further, IL-17 induces neutrophil-attracting factors (MIP, G-CSF) which are required for activation of polymorphonuclear neutrophils (PMNs) and recruitment to mucosal sites leading to pathogen clearance.

During recent years, great advances towards a better understanding of the pathomechanisms leading to development of mucocutaneous candidiasis have been made. It has been established that especially the IL-17/Th17 pathway plays a crucial role in antifungal immunity: Th17 cells produce IL-17A, IL-17F, IL-21 and IL-22, which in turn induce the production of antimicrobial peptides, such as defensins, S100 or lactoferrin, as well as the recruitment of neutrophils to mucosal sites, thus playing an important role in maintaining the mucosal tissue barrier and preventing mucosal infection.

Host defense against fungal pathogens and dysregulation in disease. Intracellular signaling pathways consist of numerous immunomodulatory proteins that ensure effective immune responses after exposure to fungal pathogens. In patients with CMC, dysregulation of a particular pathway is caused by severe mutations in associated genes that result in reduced expression or absence of the protein product. In detail, CARD9 deficiency (mutations in CARD9), IL-17RA deficiency (mutations in IL-17RA), IL-17F deficiency (mutations in IL-17F), hyper IgE syndrome (mutations in STAT3) and APS-1/APECED (mutations in AIRE) are associated with CMC.

The importance of the IL17/Th17 axis is underlined by a growing number of known genetic defects, which affect this very pathway. In particular, mutations in IL-17F, IL-17RA, STAT1 ACT1, CARD9, as well as IL12B and IL12RB1 have been established to predispose to CMC. Furthermore, a number of genetic defects in innate immune components, such as PRKCD and Dectin1 are indirectly linked to this pathway.

The contributions of our group are the following:

STAT1:

  1. Depner M. et al., J Clin Immunol., 2016
  2. Toubiana J. et al, Blood, 2016
  3. Kobbe R. et al, Gene, 2016
  4. Frans G. et al., J Allergy Clin Immunol., 2016

CARD9:

  1. Lanternier F. et al., New Engl J Med, 2013
  2. Glocker E. et al., New Engl J Med, 2009

The work on CMC performed by our group is funded by the German Center for Infection Research (DZIF). We use targeted candidate gene sequencing in order to elucidate the particular genetic alterations of patients suffering from Candida infections. In detail, a PCR-based DNA target enrichment using the Agilent SureSelect technology followed by next generation sequencing on an Illumina MiSeq is performed. In addition, we perform functional assays aiming to link the genetic defect to an immunological phenotype. With this information we further seek to determine the prognosis and to find the best suited treatment options for each individual patient.

In addition, we search for novel genetic defects in patients and families with CMC in which a monogenetic defect has not yet been identified. To this end, we use methods such as linkage analysis, whole exome sequencing as well as whole genome sequencing.

Figure 1: The pathophysiology of CTLA-4 insufficiency

CTLA-4 is a negative immune regulator constitutively expressed on regulatory T cells (Treg cells) and plays essential roles in peripheral tolerance and prevention of autoimmune disease (Figure 1). Heterozygous germline mutations in CTLA4 lead to haploinsufficiency, impaired ligand binding, or impaired CTLA-4 homodimerization. Human cytotoxic-T-lymphocyte-antigen-4 (CTLA-4) insufficiency, which was first reported in 2014 by our group (Schubert. D et al., Nat. Med, 2014), is characterized by hypogammaglobulinemia, recurrent infections, enteropathy, and autoimmune conditions such as autoimmune thrombocytopenia, autoimmune hemolytic anemia, and arthritis (Figure 2).

Figure 2: Tissue infiltration in patients with CTLA4 mutations. (a,b) Duodenal biopsies (b) stained for CD4. (c) High-resolution chest computed tomography can of the lungs. Arrows point to granulomatous-lymphocytic. (d) Pulmonary lymphoid brotic lesions stained for CD4 in pulmonary biopsy. (e) Magnetic resonance imaging (MRI) of the pelvic area with two enlarged lymph nodes (arrows). (f) Bone marrow biopsy stained for CD4. (g) MRI of gadolinium-enhanced lesion (arrows) in the cerebellum. (h) Resected cerebellar lesion stained for CD3. Scale bars, 50 μm (a, b, d, f, h), 20mm (c) and 50mm (e). (Schubert et al. Nature Medicine. 2014)

Our group has collected clinical information of more than 200 CTLA-4 insufficient individuals including affected CTLA4 mutation carriers who have severe symptoms, and unaffected CTLA4 mutation carriers who do not require specific medical care, hence documenting a reduced penetrance of the heterozygous mutations in CTLA4. Our world-wide observational longitudinal study showcased the natural history of the disease, defined the immunological phenotypes, and documented the variable outcome of targeted therapies with abatacept, rituximab, sirolimus, and hematopoietic stem cell transplantation. The study on the CTLA4 cohort also confirmed the reduction of total CD4+ T cell numbers, the low number of naive T cells, and reduced CTLA-4 expression levels in Treg cells in affected mutation carriers (Schwab G. et al., J Allergy Clin Immunol, 2018).

Figure 3: The incomplete penetrance of of CTLA-4 insufficiency mutations

Interestingly, the penetrance of CTLA-4 insufficiency mutations is only at about 70% (Figure 3). The incomplete penetrance brings up a new question: what factors trigger or modify the disease-onset in the affected CTLA4 mutation carriers? These factors are still unknown. In our current work, we follow various hypotheses on additional genomic, epigenetic, or environmental factors are associated with the disease-onset.

The contribution of our group to this research topic include the following publications:

  1. Schubert. D et al., Nat. Med. 2014
  2. Greil C et al., J Clin Immunol. 2017
  3. Navarini AA. et al., J Allergy Clin Immunol. 2017
  4. Schwab G. et al., J Allergy Clin Immunol. 2018
  5. Lougaris V. et al., J Clin Immunol. 2018
  6. Egg D. et al., Front Immunol. 2018

The work performed by our group is funded by the Federal Ministry of Education and Research (BMBF), and the German Research Foundation (DFG) via the Sonderforschungsbereich IMPATH (SFB1160). To identify the modifier(s), we will i) study the epigenetic status of T cell populations including Treg cells, ii) record the individual pathogen exposure history of patients, and iii) analyze the microbiome, comparing the results among three groups: affected and unaffected CTLA4 mutation carriers and wild-type healthy donors.

Ad i) To determine the methylation status of the FOXP3 locus, we perform bisulfite pyrosequencing of CpG islands in the FOXP3 promoter and enhancer, such as the Treg-specific demethylated region (TSDR) which is methylated in conventional T cells but fully demethylated in Treg. In the case in which there is no difference in FOXP3 methylation, we perform genome-wide bisulfite sequencing, ATAC sequencing, and single cell RNA-sequencing on naïve T cells, effector T cells, and Treg cells.

Ad ii) To investigate the pathogens exposed to CTLA-4 insufficient patients, we will measure the level of serum immunoglobulin or the viral load by using direct detection method including but not limited to the following viruses and pathogens: EBV, CMV, HSV1/2, HHV6, human parvovirus B19, H. pylori, and T. gondii. In addition, we will sequence the TCR of organ-infiltrating T lymphocytes in affected mutation carriers and attempt to detect a specific antigen which triggers disease progression.

Ad iii) With regard to the microbiome analysis, the association between the dysbiosis of gut microbiota and autoimmunity is known. Our previous results showed a reduced microbial diversity in CVID patients with enteropathy. On the basis of these data, we performed bacterial 16S rRNA-sequencing in CTLA4 mutation carriers using universal bacterial primers and compared the groups.

Figure 4: Immunological phenotyping

We continue to collect the prospective and long-term follow-up documentation of the clinical and immunological phenotypes, the complications, the treatment, and the outcome of patients with CTLA-4 insufficiency (Figure 4). This research might reveal new functions of CTLA-4 and an understanding of disease modifiers, which will lead to the prevention and the treatment of not only CTLA4 insufficiency, but also other immune dysregulation disorders.

Common variable immunodeficiency (CVID) is the most prevalent symptomatic primary antibody deficiency (PAD), with recurrent infections, mostly in the upper respiratory tract. Genetic defects are identified in approximately 20% of CVID patients. Among these, heterozygous mutations in NFKB1 or NFKB2 collectively account for up to 10% of the monogenic forms. The transcription factors of the NFKB family play important roles in many biological processes including the immune system, by mediating transcriptional responses to a multitude of stimuli. NFKB1 encodes the transcription factor precursor p105 which is processed to p50 (canonical pathway), whereas NFKB2 encodes p100/p52 (non-canonical pathway).

The basic principle of NF-κB signaling

The NF-κB signaling network is highly complex and operative in most cell types. (left) The canonical NF-κB1 pathway integrates signals from receptors (TCR, BCR, TNF-R and TLRs in lymphocytes), co-stimulators, and metabolites (e.g. glutamine). Processing of the C-terminal half converts the NF-κB1 precursor p105 into the mature p50, which assembles with RelA (also known as p65) and the inhibitory protein IκBα an inactive cytoplasmic trimer. Pathway stimulation activates upstream kinases, which leads to phosphorylation, polyubiquitination and degradation of IκBα. Subsequently, the heteromeric transcriptional activator p50/RelA is released from its inhibitor, translocates to the nucleus, and activates its target genes. (right) Activation of the non-canonical NF-κB2 pathway occurs through BAFF receptor signaling, CD40 or the lymphotoxin-beta receptor. Pathway stimulation leads to proteasomal degradation of the inhibitory C-terminal half of the p100 precursor thereby releasing the active p52/RelB transcription factor. Homodimers of p50/p50 and p52/p52 are not equipped with a transactivation domain and therefore act as transcriptional repressors (not shown).

We are evaluating the pathogenic relevance of NFKB1 and NFKB2 variants and assign them into distinct categories according to specific molecular defects. Known pathogenic mutations in NFKB1 typically affect the N-terminal half of the protein and predict the expression of severely truncated, non-functional proteins which undergo rapid decay and cause p50 haploinsufficiency. Truncating mutation in the central part of the protein predict skipping of the precursor stage and expression and constitutive nuclear localization of p50-like proteins. The effect of frequently occurring missense variants (single amino acid changes) however is largely unknown. Most known disease-causing mutations in NFKB2 cause expression of non-processable p100 precursor proteins and thus p52 haploinsufficiency. Proximally truncating precursor-skipping mutations associated with expression of p52-like nuclear proteins are also known.

NFKB1 mutations can be assigned to at least four categories

Schematic protein structure of the p105 precursor with the N-terminal Rel homology domain (RHD), the central nuclear localization sequence (NLS) and the glycine-rich region (GRR), and the C-terminal Ankyrin-repeat domain (ANK) and the death domain (DD). The mature p50 comprises the N-terminal half of p105. Numbers indicate amino acid positions. Depending on the type and the localization of a given mutation (indicated by horizontal black bars), miscellaneous protein functions and/or diverse signaling processes might be involved. Due to the complexity of NF-kB signaling, this concept is not exhaustive. (adapted from Fliegauf & Grimbacher JACI 2018;142(4):1062-1065.)

Characterization of the phenotypic consequences of NFKB1 mutations

Analysis of the clinical and immunological phenotype of affected PAD patients with damaging heterozygous NFKB1 mutations has revealed an incomplete penetrance and an age-dependent disease severity associated with inborn defects of immune regulation. Patients are characterized by hypo-gammaglobulinemia, reduced switched memory B cells as well as respiratory and gastrointestinal. In addition, autoimmunity, lymphoproliferation, non-infectious enteropathy, opportunistic infections, autoinflammation and malignancy are frequently occurring. Increased susceptibility to bacterial, viral and fungal infections is typical and autoantibodies are detectable in a large proportion.

Despite an unmet medical need, no targeted treatment is available for this rare condition. Current treatment protocols include immunoglobulin replacement and application of immunosuppressive agents. However, Abatacept (a CTLA4 fusion protein) appears as a promising option.

In a research collaboration with Merck KGaA Darmstadt we therefore investigate, whether the observed autoinflammation and the increased frequency of viral infections (both reminiscent of interferonopathies) is associated with altered Type 1 interferon expression pattern in innate immune cells. Since the observed autoimmune disease is indicative of defective regulatory T cells (Tregs), we also aim at a detailed characterization and phenotyping of Tregs (and effector T cell subsets) in patients with damaging NFKB1 mutations. We furthermore analyze whether a second genetic alteration (either somatic or germline) accounts for the observed incomplete and age-dependent penetrance. In addition, we are testing whether the increased frequency of cytopenia in these patients is mediated by autoantibodies.

Studying NF-κB signalling in health and disease combining optogenetics and mathematical modelling

The activation of NF-κB1 in the canonical pathway depends on the activation of an upstream kinase (IKK), which in turns triggers the degradation of IκBα, the cytosolic inhibitor of NF-κB1. As a consequence, NF-κB1 enters the nucleus and regulates its target genes, including IκBα itself. The transcriptional activation of its own inhibitor establishes a negative feedback loop that leads to NF-κB1 oscillations. In numerous patients with primary antibody deficiencies (PAD), heterozygous mutations in NFKB1 are predicted to result in inappropriate p105/p50 ratios and to cause impaired NF-κB1 dynamics. In this study supported by the German Research Foundation (DFG) under Germany's Excellence Strategy (CIBSS – EXC-2189 – Project ID 390939984) we aim at a detailed analysis of the spatio-temporal regulation of the canonical NF-κB signal oscillation (including mathematical modelling), at identifying molecular switches (e.g. small molecules) to manipulate NF-κB activity in order to develop targeted therapies for human disease and at establishing optogenetic tools to control NF-κB1 signalling and its target gene expression.

The contributions of our group are the following:

  1. Klemann C. et al., Frontiers Immunology. 2019
  2. Fliegauf M. et al., Clin Immunol. 2018
  3. Lougaris V. et al., Clin Immunol. 2017
  4. Lougaris V. et al., J Allergy Clin Immunol. 2017
  5. Keller B. et al., J Allergy Clin Immunol. 2017
  6. Fliegauf M. et al., Am J Hum Genet. 2015

Figure 1: Geographic distribution of centers in Germany in Oct. 2018 and Nov. 2013. Centers that are located in the same city are subsumed under the city’s name. Point markers are proportional to the number of reported patients.

Electronic registries that collect patient data are a central asset for rare disease research. These registries make it possible to analyze the epidemiology and natural course of primary immunodeficiencies, identify factors affecting the clinical course, and evaluate the impact of therapeutic strategies. Furthermore, they are important for studies investigating genotype-phenotype correlations. While single centers often have very limited cohort sizes, patient registries make it possible to define larger cohorts based on common clinical features and use these for genetic studies. Thereby, they provide researchers with sufficient numbers of cases for genetic research and clinical trials.

PID-NET Registry (German national registry for primary immunodeficiency)

We have realized that there is a need for establishing patient registries both within Freiburg as well as on the national and international level. In 2009, we set up an internal registry for our outpatient clinics which is used by physicians and study assistants to report clinical findings in a well-defined and structured way. The registry enables researchers in the Center for Chronic Immunodeficiencies to quickly identify patients with specific features and analyze their data. It is also a data source for Health Services Research.

The German national registry for primary immunodeficiencies (PID-NET registry) is part of the PID-NET consortium (www.pid-net.org) which was funded by the German Federal Ministry of Education and Research between 2009 and 2018 (BMBF, grants 01GM0896, 01GM1111B, 01GM1517C, and 01EO1303). The PID-NET registry is further supported by the European Society for Immunodeficiency (ESID), the Care-for-Rare Foundation, PROimmun e.V., CSL-Behring, and LFB.

On the top of the objectives mentioned above, the registry is also intended for establishing links between medical centers within Germany and beyond. As of March 2019, the national registry contains data on 3.043 patients. The distribution of patients at PID centers in Germany is visualized in Figure 1.

The national PID-Net registry is embedded within the European PID registry of the European Society for Immunodeficiencies (ESID, www.esid.org). The ESID Registry was established by Prof. Bodo Grimbacher in 2004 and is coordinated by the head of the ESID Registry Working Party. It is hosted and developed at the CCI and currently (March 2019) holds data on more than 21,669 patients from 30 countries. The ESID Registry also maintains active ties with the United States' USIDNET Registry and the Latin American LASID Registry, as well as registries in Asia and Australia. Thereby, the contribution of the CCI to the German national registry provides links to immunodeficiency centers around the globe.

The distribution of the registered patients in the ESID registry are regularly updated and published on the ESID “Reporting Website” (https://esid.org/Working-Parties/Registry-Working-Party/Reporting-website).

Important Publications:

  1. Schütz K. et al., J Clin Immunol. 2018
  2. Seidel MG. et al., J Allergy Clin Immunol. 2019
  3. Odnoletkova I. et al., Orphanet J Rare Dis. 2018
  4. Gathmann B. et al., J Allergy Clin Immunol. 2014
  5. Gathmann B. et al., Clin Exp Immunol. 2013
  6. Gathmann B. et al., Clin Exp Immunol. 2009

Multi-organ autoimmune diseases belong to the “ultra-rare” disorders and have only recently been recognized being caused by monogenetic mutations in immune-regulatory genes. Patients are typically characterized by multi-organ inflammation including, but not limited to the bone marrow, gut, lungs, kidneys, skin, and the central nervous system (CNS). Genes recently added to the list include CTLA4, LRBA, NFκB1, NFκB2, STAT3, and LAT. This cohort of patients provides a frontier in medicine, as these rare monogenetic disorders are highly instructive for understanding and treating also more prevalent polygenic autoimmune disorders.

Our research in recent years has shown that autoimmune diseases involving several organs in one patient can be caused by genetic mutations in a single gene. This monogenetic mutation may completely disrupt homeostasis of the immune system of affected individuals causing lifethreatening autoimmune complications such as autoimmune (ai) thrombocytopenia, ai hemolytic anemia, ai enterocolitis, ai encephalitis, ai interstitial lung disease, type-1 diabetes, ai thyroiditis, vitiligo, and many others. However, most interestingly, not all mutation carriers necessarily become sick (termed reduced penetrance), and when becoming sick, not always the same organs are involved (termed variable expressivity). Currently, we do not know all monogenetic causes of multi-organ autoimmunity, and we do not understand why some known mutations cause a reduced penetrance and what determines their disease expressivity. Some mutation carriers stay quite healthy throughout their lives, despite carrying the very same disease-causing mutation as their relative who died in childhood. What are the protective factors? Are there susceptibility factors? Are these factors genetic or are they epigenetic, or even environmental? We need to know these factors to better advise our families smitten by these devastating genetic traits. To this end, we will

  • identify novel genetic causes of multi-organ autoimmune disease
  • create a patient registry capable of holding data entered by the treating physician but also supported by data-entry by the patient (e.g. for up-to-date drug dosing or disease symptom severity)
  • create a biobank across Germany for the rare samples of these rare patients
  • research the pathophysiology on these conditions to better understand the molecular pathomechanisms which we need to tackle in order to restore immune homeostasis
  • study whether there are epigenetic factors influencing disease penetrance and expressivity
  • study whether replacing CTLA4-Fc is safe and efficient in patients with a disease-causing mutation in CTLA4

Projects:

  1. Coordination of GAIN Prof. Dr. med. Bodo Grimbacher, Freiburg
  2. Registry of the German multi-organ Auto-Immunity Network (GAIN-registry) Dr. med. Dipl. Inf. Gerhard Kindle, Freiburg PD Dr. rer. nat. Alexandra Nieters, Freiburg
  3. Consortial Biobank for patients with Inborn Errors of Multi-Organ Autoimmune Diseases Prof. Dr. rer. nat. Thomas Illig, Hanover
  4. CTLA4 insufficiency Prof. Dr. med. Bodo Grimbacher, Freiburg
  5. Immune dysregulation due to NFKB1D defects Prof. Dr. med. Klaus Warnatz, Freiburg
  6. STAT3 gain-of-function (GOF) associated disease Prof. Dr. med. Stephan Ehl, Freiburg
  7. Initial description of human DGKζ -deficiency PD Dr. med. Dr. sci. nat. Fabian Hauck, Munich
  8. The role of GARP in monogenic traits of multi-organ autoimmunity PD Dr. Alla Skapenko, Munich Prof. Dr. med. Hendrik Schulze-Koops, Munich
  9. Monogenetic immune dysregulation syndromes and their effect on the plasma cell compartment Prof. Dr. med. Bimba Franziska Hoyer, Kiel Prof. Dr. rer. nat. Andreas Radbruch, Berlin
  10. Identification of epigenetic factors in multi-organ autoimmunity Dr. rer. nat. Faranaz Atschekzei, Hanover Prof. Dr. med. Reinhold Ernst Schmidt, Hanover
  11. Safety and Efficacy of abatacept (s.c.) in patients with CTLA4 insufficiency and LRBA deficiency (ABACHAI) Prof. Dr. med. Bodo Grimbacher, Freiburg

Figure 1: crosstalk between intestinal and systemic immune response: correct gut colonization (1) is necessary to guarantee efficient systemic immunity (2).

In addition to infections, a large number (~50%) of patients with primary immunodeficiency develop non-infectious complications, including malignancies, autoimmunity and systemic inflammation. The exact mechanisms triggering autoimmunity and systemic inflammation in immunodeficient patients are still largely unknown. In the last decade experimental evidence accumulated indicating that the gut microbiome plays a prominent role in shaping the immune system. The gut flora directs the development of the immune system (Figure 1) and is central for immune tolerance and homeostasis. Additionally, the immune system influences the composition of the microbiota. This said, it comes without surprise that increasing evidence suggests a possible connection between immune dysregulation and the gut microbiota. However, the following central questions remain unanswered: Can the microbiome cause immune dysregulation by itself? Are changes in the microbiota a consequence or a cause of the immune dysregulation? What is the role of the microbiome as a modifier for disease severity in primary immunodeficiency with defined genetic defects ?

Figure 2: Impact of gut microbiome on primary immunodeficiency: experimental workflow.

To answer these questions, we are conducting a longitudinal study involving a large cohort of PID patients accumulating large microbiome (16s RNA sequencing), clinical, and immunological datasets. The analysis and integration of these datasets (Figure 2) will in turn influence the design of mechanistic studies.

Translational impact: Immunosuppressive medicines, such as glucocorticoids, still represent effective first-line therapies to treat inflammation and autoimmunity in primary immunodeficiency patients, however they come with considerable side effects. Therefore, a desirable “side” effect of a better understanding of the interplay between the gut microbiota and the immunopathology of primary immunodeficiency could be the design of therapeutic strategies aiming for a better standard of care and drugs to treat inflammatory and autoimmune complications. The development of a translational approach to the gut microbiome would largely benefit from the detailed description of the temporal and kinetic impact of the microbiota on the host immune system, and therefore, as mentioned above requires a considerable cohort of patients.

The human immune system controls how we respond to infections and other diseases. However, its functioning differs substantially between individuals. Certain people have mild or severe immune defects, which makes them prone to infections, autoimmunity and cancer. Some of these immunodeficiencies are monogenetic and relatively well understood. But in many cases the molecular cause is entirely unknown, which makes these rare diseases difficult to diagnose and treat.

In this project, we will use cutting-edge multi-omics profiling and integrative bioinformatics analysis to dissect the molecular pathways underlying common variable immunodeficiency (CVID, ORPHA: #1572), an archetypical rare primary antibody deficiency (PAD) where impaired B cell function causes recurrent infections. A subset of CVID individuals (~25%) display one or several monogenetic variants known to be associated with PADs. We will use such genetically resolved cases to identify recurrent epigenomic, transcriptomic and/or proteomic aberrations underlying CVID, and we will exploit the identified patterns to improve the diagnosis, stratification and mechanistic understanding of CVID patients with unknown genetic and/or non-genetic causes. We will also include patients with selective IgA deficiency (IgAD) due to its likely role as preamble of CVID, opening up the potential for accurate molecular diagnostics and disease stratification at an early stage.

In this project, key leaders (Prof. Dr. Bodo Grimbacher, Freiburg, Germany; Prof. Dr. Lennart Hammarström, Stockholm, Schweden; Dr. Esteban Ballestar, Barcelona, Spain; Dr. Roger Geiger, Bellinzona, Switzerland; Prof. Dr. Christoph Bock, Vienna, Austria) in the fields of CVID, immunology, genetics, epigenetics, proteomics and bioinformatics have joined forces to provide a novel and systematic classification of CVID patients based on the molecular dissection of affected cellular pathways. Our approach will directly benefit PAD patients and provide a perspective for personalized management of PAD based on multi-omics technologies that are cost-effective and ready to be used by clinical immunology and rare diseases experts.

Publications

PubMed

CV

since 2011Scientific Director and Consultant, Center for Chronic Immunodeficiency, Medical Center - University of Freiburg
2006-2011Consultant and Marie-Curie Research Group Leader, Department of Immunology, Royal Free Hospital, University College London, UK
2006Habilitation in Internal Medicine, Medical Center - University of Freiburg (Prof. Dr. H.H. Peter)
2000-2006Physician, Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg
1997-2000 Postdoc, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA (Dr. Jennifer Puck)
1995-1997AiP in Internal Medicine, Medical Center - University of Freiburg
1995MD degree, Medical Center - University of Freiburg (Prof. Dr. H.H. Peter)
1988-1995Study of Medicine in Aachen, Freiburg, and Hamburg

Team

Group Leader
Bodo Grimbacher bodo.grimbacher@uniklinik-freiburg.de 270-77731

Office
Teresa Sprangteresa.sprang@uniklinik-freiburg.de270-77732

Scientists
Alla Bulashevska alla.bulashevska@uniklinik-freiburg.de 270-77563
Manfred Fliegauf manfred.fliegauf@uniklinik-freiburg.de 270-77735
Stefanie Frey-Jakobs stefanie.frey-jakobs@uniklinik-freiburg.de 270-77561
Laura Gamez laura.gamez@uniklinik-freiburg.de 270-77742
Noriko Mitsuiki noriko.mitsuiki@uniklinik-freiburg.de 270-77729
Michele Proietti michele.proietti@uniklinik-freiburg.de 270-77769

PhD Students
Nadezhda Camacho Ordonez nadezhda.camacho.ordonez@uniklinik-freiburg.de
Zoya Eskandarian zoya.eskandarian@uniklinik-freiburg.de 270-77561
Neftali Jose Ramirez neftali.ramirez@uniklinik-freiburg.de
Linlin Yang linlin.yang@uniklinik-freiburg.de 270-77742

MSc Students
Theresa Stauß theresa.stauss@uniklinik-freiburg.de

MD Students
Svenja Abel svenja.abel@uniklinik-freiburg.de
Carla Arteaga carla.arteaga@uniklinik-freiburg.de
Mirjam Bayer
Mark Depner
David Egg david.egg@uniklinik-freiburg.de
Felicitas Felber felicitas.felber@uniklinik-freiburg.de
Annemarie Gabrysch annemarie.gabrysch@uniklinik-freiburg.de
Alexa Gagas
Julia Hartberger julia.hartberger@uniklinik-freiburg.de
Valentina Holter
Fiona Jäger fiona.jaeger@uniklinik-freiburg.de
Sandra Jendrossek sandra.jendrossek@uniklinik-freiburg.de
Nils Klammer nils.klammer@uniklinik-freiburg.de
Máté Krausz mate.krausz@uniklinik-freiburg.de
Johannes Kühn johannes.kuehn@uniklinik-freiburg.de
Lea Mollner
Christina Nöltner christina.noeltner@uniklinik-freiburg.de
Larissa Pietsch larissa.pietsch@uniklinik-freiburg.de
Johanna Schepp johanna.schepp@uniklinik-freiburg.de
Philipp Scheuerlein philipp.scheuerlein@uniklinik-freiburg.de
Cornelia van Schewick cornelia.vanschewick@uniklinik-freiburg.de
Charlotte Schwab charlotte.schwab@uniklinik-freiburg.de
Johannes Sperlich johannes.sperlich@uniklinik-freiburg.de

Technicians
Mary Buchta mary.buchta@uniklinik-freiburg.de 270-77737
Hanna Haberstroh hanna.haberstroh@uniklinik-freiburg.de
Katrin Hübscher katrin.huebscher@uniklinik-freiburg.de 270-77733
Pavla Mrovecova pavla.mrovecova@uniklinik-freiburg.de 270-77737
Jessica Rojas jessica.rojas@uniklinik-freiburg.de 270-77733

Physicians
Aleksandra Hirsch aleksandra.hirsch@uniklinik-freiburg.de
Jan Pruszak jan.pruszak@uniklinik-freiburg.de 203-5121
Ina Caroline Rump ina.caroline.rump@uniklinik-freiburg.de

Others
Sabine El-Helou sabine.el-helou@uniklinik-freiburg.de 270-34450
Daniel Fix daniel.fix@uniklinik-freiburg.de

Linlin Yang, Desiée Schubert, Laura Gamez, Sophie Jung, Tiziana Lorenzini, Manfred Fliegauf, Michele Proietti, Andrés Caballero (left), Jessica Rojas, Katrin Hübscher, Hanna Haberstroh, Bodo Grimbacher, Pavla Mrovecova, Ingrid Werder, Stefanie Frey-Jakobs, Alla Bulashevska, Christina Nöltner, Nadezhda Ordonez (left to right)

Contact

Prof. Dr. med. Bodo Grimbacher

MEDICAL CENTER - UNIVERSITY OF FREIBURG
Center for Chronic Immunodeficiency
at Center for Translational Cell Research

Breisacher Str. 115
79106 Freiburg
Germany

Phone: +49 (0)761 270-77731
Fax: +49 (0)761 270-77744
bodo.grimbacher@uniklinik-freiburg.de