Characterization of Human FOXN1 Mutations Uncovers both Loss- and Gain-of-Function Outcomes

Thymus hypoplasia is reported for individuals with autosomal recessive, compound heterozygous and single allelic FOXN1 mutations. FOXN1 is the master transcriptional regulator of thymus epithelial cell development. Autosomal recessive mutations in FOXN1 lead to a Nude/SCID phenotype due to the ensuing T cell lymphopenia and impaired hair follicle extrusion. Targeted exome and whole genome sequencing for patients with low TRECs (measure of T cell output) has increased the number of diverse FOXN1 mutations to over 40. The consequence of these FOXN1 mutations on patients is varied and somewhat complicated by some individuals having only a transient delay in T cell development that corrects over time. We compared the functions of the FOXN1 mutants with luciferase reporter assays and nuclear localization experiments. For selected FOXN1 mutations, mice were developed to genocopy these to assess impacts on thymopoiesis. We identify partial and complete loss-of-function mutations along with gain-of-function and dominant negatives. Comparative analyses of murine thymopoiesis reveal some compound het Foxn1 mutations cause a transient thymus hypoplasia while others cause a permanent small thymus. Taken together, our findings establish FOXN1 genotype-phenotype relationships and suggest rapid functional screening approaches can be used to define the impact of different mutations of clinical relevance.

Supported by grants from NIH (R01AI114523,  R21AI144140) and the Jeffrey Modell Foundation (MdlM, CAW)

22q11.2 Deletion Syndrome Causes a Thymus Hypoplasia Corrected by Mesenchymal Cell Replacement

Thymus hypoplasia occurs in several clinical conditions including 22q11.2 deletion syndrome (22q11.2DS). 22q11.2DS is the most common human microdeletion disorder, affecting 1/4000. Thymuses from 60–70% 22q11.2DS patients are small and produce fewer T cells than normal. For individuals with a severe hypoplasia, an allogenic thymus tissue graft is needed to restore thymopoiesis. To determine the molecular mechanisms contributing to a small thymus in 22q11.2DS, we compared the development of the thymus in embryos from various 22q11.DS mouse models, normal controls and Foxn1 mutant mice. Reaggregate fetal thymic organ culture assays reveal that replacing mesenchymal cells from 22q11.2del hypoplastic lobes with normal ones restores tissue expansion and thymopoiesis. Thymic epithelial cells used as substitutes cannot. This is distinct from the Foxn1 mutant mice, wherein defective thymic epithelial cell functions lead to thymus hypoplasia/aplasia. Single cell RNA sequencing of normal and hypoplastic thymus lobes revealed differential expression of transcripts that primarily impacted 5 distinct mesenchymal cell subsets in 22q11.2DS. These transcripts are involved in cell-cell interactions, collagen deposition and growth. Elevated levels of collagen are present in the hypoplastic thymus tissues, suggesting a structural restriction. Mesenchymal and epithelial cell differentiation/expansion assays reveal a selective reduction in mesenchymal tissue expansion due to 22q11.2DS

Supported by grants from the National Institutes of Health (R01AI114523, R21AI144140) and the Jeffrey Modell Foundation (MdlM, CAW)

22q11.2 Deletion Syndrome (DiGeorge) and Mutations in Forkhead Box N1 (FOXN1) cause a Thymic Hypoplasia through distinct Developmental Processes

Patients with 22q11.2 deletion syndrome and those with mutations in the Forkhead Box N1(FOXN1) transcription factor (Nude/SCID) can both present with a thymic hypoplasia that results in a severe T cell lymphopenia. In both clinical conditions, the thymic anlage fails to develop properly within the 3rdpharyngeal pouch during embryogenesis. We characterized the development of the thymus in mouse models of 22q11.2 deletion syndrome (22q11.2del) and a new set of mice with mutations in Foxn1that genocopied a SCID patient with novel compound heterozygous mutations in FOXN1. Both sets of mice develop hypoplastic thymic lobes. An analysis of thymopoiesis in embryos revealed distinct development problems. The hypoplastic thymii from the 22q11.2del mice were primarily sized restricted, with normal percentages of all thymocyte subsets apparent. This contrasted a severe deficiency of thymocytes due to the Foxn1mutations, which primarily affected the development and expansion of thymic epithelial cells. Comparative gene expression analyses of e13.5 fetal thymii revealed differentially regulated transcripts that define the basis of the hypoplasia. A dysregulated mesenchymal cell signature was apparent in the 22q11.2del model, which contrasted the epithelial transcript disruption due to the Foxn1mutations. These results suggest different strategies are necessary to correct the thymic tissue abnormalities in patients who present with thymic hypoplasias due to their congenital disorders.

Serum Antibody Profiling Healthy Toddlers Reveals Low, Intermediate and High Response Cohorts

During their first two years of life, infant/toddlers produce their own antibodies in response to diverse environmental exposures, infections, and vaccinations. The specificity of these antibodies towards self-antigens, infections, and vaccine components and how they vary among individuals is poorly characterized. We developed a new antigen array comprising autoantigens, infectious agents, and vaccine antigens to assess the serum antibody specificities among a cohort of >150 health toddlers. An analysis of their responses reveals a stratification of healthy toddlers into 3 groups, low, intermediate, and high responders. Among those 16% that are high responders, their serum IgGs were able to bind a diverse array of self-antigens as well as infectious agents. Longitudinal follow-up suggests this pattern is relatively stable over time. Comparing clinical data reveals a significant correlation with the high IgG responder cohort and a family history of asthma and maternal gestational diabetes. Targeted DNA sequencing in the high responder group revealed a strong genetic association signal at the HLA locus, with polymorphisms at this locus associated with high ANA and IgG titers to many antigens. Findings from this study may provide insights into the natural history of human autoantibody formation.

Profiling Serum Antibody Specificities in Infants Reveals a Significant Number with Autoreactive Antibodies

The antibody repertoire of an infant develops in response to infections, environmental exposures, and vaccinations. By adulthood, many will produce antibodies that react against self-antigens, often causal to autoimmune diseases such as lupus erythematosus. Limited scientific literature exists as to whether such autoreactive antibodies develop early in infancy. For this reason, the antibody specificities in the serum of healthy infants at 1 and 2 years of age was analyzed. Screening in a cohort of 82 infants revealed that 23 (28%) had moderate to high titered antibodies directed to diverse self-antigens. These numbers are consistent with observed ANA positivity in adults. Ongoing custom targeted DNA sequencing analysis will assess the genetic load of known autoimmune risk alleles in the ANA positive infants. Relationships between the antibody specificities and the genetic risk alleles assembled for each infant will be presented. The comparisons will include clinical information; sex, ethnicity, growth records, vaccination status, infectious history, antibiotic and antiviral treatments, disease status, and family history. Genomic analysis of infants with autoantibodies may facilitate implementation of a new wellness screen to identify antibody positive infants that have significant genetic predisposition and therefore are at risk for developing diverse immune system abnormalities including autoimmune disorders.

Compound Heterozygous Mutations in Forkhead Box N1 (FOXN1) Lead to a Severe Immunodeficiency but Normal Hair and Nail Development in Patients

Patients with mutations in the Forkhead Box N1 (FOXN1) transcription factor are born with a severe T-cell lymphopenia in conjunction with alopecia and nail dystrophy (OMIM # 600838). The T-cell lymphopenia results from the impaired development and/or function of the thymic epithelial cells (TECs). TECs are essential regulators of positive and negative selection of developing thymocytes. We report on 3 independent patients with compound heterozygous mutations in FOXN1. All 3 patients had a severe T cell lymphopenia. However, each had normal hair growth and nail bed formation, suggesting that the compound heterozygous mutations result in clinical presentations distinct from classic cases. To determine how the mutations impact murine Foxn1 function, transcriptional reporter assays and protein expression studies were done. Only one of the mutations affected the transcriptional activity of murine Foxn1, with Western blot analyses indicating that this mutation caused production of a truncated protein. CRISPR/Cas9 technologies were used to create mouse lines with compound heterozygous mutations in Foxn1. The mice are currently being intercrossed. The impact of the compound heterozygous Foxn1 mutations on T cell development in the thymus will be presented. Findings from this study may suggest novel therapeutic strategies at restoring thymopoiesis in different clinical settings.

MIR205HG is a Long Noncoding RNA with Distinct Functions in the Thymus versus the Anterior Pituitary

MicroRNAs (miRNAs) are processed from primary RNA transcripts (pri-miRNAs) encoded in host genes. Several miRNAs including miR-205 are present within long noncoding RNAs (lncRNAs). MiR-205 is an epithelial-specific miRNA that supports thymopoiesis by positively regulating Forkhead Box N1 (Foxn1) expression. We assessed whether the host gene for miR-205, MIR205HG, has independent functions as a lncRNA. The more severe stress-induced thymic atrophy reported in miR-205-deficient mice is also evident in MIR205HG knockout lines. However, MIR205HG knockouts have a small stature phenotype. A new set of miR-205KI mice did not have this phenotype. The smaller mouse size of the MIR205HG null animals is partly a consequence of reduced levels of endocrine hormones produced by the anterior pituitary. In addition, the MIR205HG null animals had abnormal development of the lacrimal and harderian glands that produce eye secretions. Transcriptome analyses revealed that MIR205HG regulates gene expression in the anterior pituitary unlike miR-205. In contrast, transcripts regulated by miR-205 and MIR205HG in the epithelial cells of the skin and thymus overlap significantly. These data indicate that MIR205HG has a specific function as a lncRNA in the anterior pituitary in addition to its primary role as the host gene for miR-205 in thymic epithelial cells.

Characterization of the Thymic Hypoplasia in Mouse Models of 22q11.2 Deletion Syndrome (DiGeorge Syndrome)

Patients with 22q11.2 deletion syndrome have variable, multi-system disorders including a thymic hypoplasia, cardiac anomalies, and hypoparathyroidism. Over 90% have a deletion of 2.5 Mb on chromosome 22q11.2, affecting protein coding genes, microRNAs, long noncoding RNAs, and pseudogenes. 50%~70% have some degree of thymic hypoplasia (DiGeorge syndrome), resulting in a T cell lymphopenia. Successful transplantation of thymic tissue in patients with a thymic aplasia suggests stromal tissue abnormalities. The thymic stroma consists of thymic epithelial cells (TEC), mesenchymal cells, and endothelial populations. We are exploring the TEC-mesenchyme-endothelial interactions during thymus organogenesis in the mouse model of 22q11.2 deletion syndrome (Df1/+). Comparative transcriptome analyses of hypoplastic and normal thymic lobes from embryos revealed a unique mesenchymal cells mRNA expression signature, including reduced levels of the PDGFRa. PDGFRaH2B-EGFP heterozygous mice that have lower level of PDGFRa expression are being crossed with the Df1/+ model to ascertain whether the hypoplasia is influenced by this receptor. Additional mouse models with prominent penetrance of thymic hypoplasia are being used to determine how Tbx1 (encoded on 22q11.2) influences pharyngeal pouch mesenchymal-TEC development. The results from the study will likely lead to novel approaches for thymus reconstitution in various clinical settings.

A Long Noncoding RNA, lncRNA205, and an Embedded MicroRNA, MiR-205 have Overlapping and Distinct Contributions to Thymopoiesis and Development

MiR-205 is an epithelial-specific microRNA (miR) that supports thymopoiesis. This miR positively regulates Forkhead Box N1 (Foxn1) transcription factor expression. MiR-205 is embedded in a long noncoding RNA (lncRNA), termed MIR205HG in humans. Several lncRNAs that contain miRs have independent functional roles in tissue development and/or regeneration. We characterized the transcriptome assembly of the murine locus containing miR-205 and the larger lncRNA. Conditional knockout mice that harbored a targeted deletion of the proximal region of the lncRNA, with miR-205 sequences retained, were developed. The phenotypes in these mice were compared to those with a miR-205 deficiency. The more severe stress-induced thymic atrophy reported in miR-205-deficient mice, compared to littermate controls, is also evident in lncRNA205 knockout lines. In contrast, a lncRNA205 deficiency results in a smaller mouse stature, which may be coupled with a reduced fat but normal lean mass. These phenotypic differences are explained, in part, by the differential regulation of the lncRNA transcript relative to the pre-mature miR-205. Interferon and IL-22, cytokines released following inflammation, transiently reduce miR-205 while increasing the lncRNA. This is partly determined by the DNp63 transcription factor, which controls miR-205 expression. Gene expression comparisons are being undertaken to reveal how the transcriptome is differentially regulated by these two non-coding RNA species. Further, the mechanism by which these noncoding RNAs regulate Foxn1 is being elucidated. Taken together, these findings suggest both overlapping and independent functions for the lncRNA205 and the embedded miR-205.

Patients with Compound Heterozygous Mutations in Forkhead Box N1 have a Severe Immunodeficiency while Maintaining Normal Skin and Hair Development

Forkhead Box N1 (FoxN1) is an epithelial-specific transcription factor essential for the development of the thymus. Patients with mutations in Foxn1 (OMIM # 600838) are born with a severe T-cell lymphopenia that presents in combination with alopecia and nail dystrophy. The nude mouse, which developed from a spontaneous genetic mutation in Foxn1, phenocopies the human disease. We report on 3 independently identified patients that presented with low to absent circulating T cells. Genetic workup of these patients revealed mutations in Foxn1. Each patient had distinct compound heterozygous mutations that were localized in the distal exons of Foxn1. These were predicted to maintain Foxn1 expression while adversely affect its function. Of significance, each patient had normal hair and skin, without any evidence of nail dystrophy, distinct from previously reported phenotypes. To better define the molecular mechanisms leading to this novel clinical presentation, we used CRISPR/Cas techniques to introduce the corresponding mutations in the mouse Foxn1 sequence. We will present data on the phenotypes of these mice, using intercrosses between individual mutant mice. Comparative transcriptome analyses of fetal thymii from these mice will reveal how the Foxn1 mutations impacts thymic epithelial gene expression and function compared to normal Foxn1. Our findings may lead to better understanding of the role of Foxn1 epithelial cell development and function in both the thymus and skin.

Signature Gene Expression Patterns Revealed in Hypoplastic Thymii from Mouse Models of DiGeorge-22q11.2 Deletion Syndrome

Chromosome 22q11.2 deletion syndrome (22q11.2 ΔS) is the most common microdeletion disorder reported (1/4000). Individuals with this deletion have variable, multi-system disorders including thymic hypoplasia, cardiac anomalies, hypoparathyroidism, and/or dysmorphic facial features. Over 90% of patients have a deletion of 2.4 Mb, which comprises 90 genes, 50% protein coding and the remainder microRNAs, long noncoding RNAs and pseudogenes. The principal cause of the development defects is a haploinsufficiency of the T-box 1 transcription factor (Tbx1). Between 40–60% of patients have some degree of thymic hypoplasia, resulting in systemic T cell lymphopenia. Defects in the thymic stromal tissue is the underlying cause of the hypoplasia. We analyzed the thymic tissue in the mouse models of 22q11.2 ΔS (Df1/+). Comparative transcriptome analyses of hypoplastic and normal-sized lobes derived from the same Df1/+ embryo revealed a signature mRNA expression pattern unique to hypoplastic lobes. Ingenuity pathway analysis uncovered selective pathways compromised in the hypoplastic lobes. Fetal thymic organ culture and reaggregate cultures are currently being used to identify the genes essential for the specification and expansion of the thymic stroma. In addition, normal and hypoplastic thymii, including some from 22q11.2 ΔS patients, are being characterized for the expression of the over- and under-represented genes identified in the mouse model. Findings from these studies may lead to better strategies for improving human thymopoiesis in patients with conditions including 22q11.2 and 10p syndromes, those undergoing chemoablative treatments, and other conditions leading to a thymic hypoplasia and ensuing T cell lymphopenia.

MiR-205 Supports Thymopoiesis Following Stress by Positively Regulating Foxn1 Expression

T cells are a critical component of the adaptive immune system, developing within the thymus. Immature thymocytes interact with an interconnected meshwork of thymic epithelial cells (TECs) to establish the T cell repertoire. The developmental process is extremely stress sensitive, as the thymus can undergo a rapid involution in response to diverse inflammatory conditions, and a more prolonged hypoplasia during aging. The type of stress predicates whether TECs, thymocytes, and/or myeloid cell populations are affected. Several microRNAs (miRs) have been identified in the thymus based on their ability to mitigate the stress damage. We identified miR-205 as a stress responsive miR specifically expressed in TECs. Mice generated with a conditional ablation of miR-205 in TECs exhibit an age and sex-dependent thymic hypoplasia beginning at 8 weeks. Under stress conditions involving a type I interferon response (dsRNA mimic; polyI:C), the TEC-miR-205 deficient mice had a severe thymic atrophy compared to littermate controls. The TEC-miR-205 deficient mice displayed a delayed recovery of single positive CD4 and CD8 thymocytes, likely resulting from a block in the cortical TEC expansion. qPCR and gene expression comparisons revealed that the miR-205 deficient TECs had significant changes in chemokine/chemokine receptor and antigen processing pathways. MiR-205 positively regulated Foxn1 transcription factor expression, the master regulator of TEC development and function. Interestingly, miR-205 is encoded within a long non-coding RNA (lncRNA), 4631405K08Rik. Current experiments will reveal the mechanisms by which the miR and lncRNA are transcriptionally regulated, and how these affect Foxn1 expression to support thymopoiesis.

Mycobacterium tuberculosis produces small noncoding RNAs during infections to regulate mycobacterial and eukaryotic gene expression

Mycobacterium tuberculosis (Mtb) presently infects 1/3 of the World’s population, causing both active and latent pulmonary tuberculosis (TB). The pathogenic mechanisms used by Mtb remain poorly defined. We used a small RNA sequencing strategy on RNA extracted from Mtb-infected THP-1 macrophages to characterize the changes in eukaryotic microRNAs (miRs) and identify any mycobacterially-encoded small RNAs. A large number of mammalian microRNAs were differentially regulated during the infection course. Target prediction programs indicated that the mRNAs regulated by the miRs were involved in immune processes, metabolic pathways, cell communication, and developmental events. In addition, 35 Mtb-encoded small RNAs (18–30 nucleotides, mRs) were discovered. Several of the Mtb-encoded mRs were detected in lung tissue biopsies from TB infected monkeys. The 100–150 nucleotides surrounding the 35 Mtb-encoded small RNAs had extensive secondary RNA folding capabilities, including hairpins and antisense stretches more characteristic of eukaryotic pre-microRNAs. Two such small RNAs, Mtb-mR-1 and Mtb-mR-6 were transcribed in Mycobacterium avium complex and Mtb in a hairpin loop and antisense sequence-dependent manner. These mRs were not expressed in Mycobacterium smegmatis, revealing a restricted expression to pathogenic strains. Mtb-encoded mR-1 and mR-6 modulated both prokaryotic and eukaryotic gene expression. Taken together, our findings reveal potentially novel pathogenic processes utilized by Mtb during infections.