ImSpectR - R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data

SUMMARY

An effective immune system is characterized by a diverse immune repertoire. There is a strong demand for accurate and quantitative methods to assess the diversity of the immune repertoire for various (pre-)clinical applications, including the diagnosis and prognosis of primary immune deficiencies, or to assess the response to therapy. Current strategies for immune diversity assessment generally comprise the visual inspection of the length distribution of rearranged T- and B-cell receptors. Visual inspections, however, are prone to subjective assessments and thus lead to biases. Here, we introduce ImSpectR, a unified approach to quantify immunodiversity using either spectratype, repertoire sequencing or single cell RNA sequencing data. ImSpectR scores various types of deviations from the expected length distribution and integrates these into one measure, allowing for robust quantitative comparisons of immune diversity across individuals or conditions.

AVAILABILITY

R-package is available for download on GitHub at https://github.com/martijn-cordes/ImSpectR.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Clinico-immunological heterogeneity in Comèl-Netherton syndrome

BACKGROUND

Comèl-Netherton syndrome (CN) is characterized by atopic-eczema-like skin abnormalities combined with linear ichthyotic lesions, hair shaft abnormalities and atopy with high IgE levels.

OBJECTIVE

Five children with CN are described. In 2 of the 3 CN patients still alive, analysis of cytokines regulating IgE synthesis was performed.

METHODS

In peripheral blood mononuclear cells and cultures of purified T cells, mRNA expression and protein production of interleukin 4 (IL-4), IL-13, IL-5 and interferon gamma were analysed. The results were compared with the values in age-matched atopic dermatitis patients and healthy children.

RESULTS

The 5 CN patients showed striking differences in disease severity and evolution. Marked differences were found in several cytokines in the 2 analysed CN patients. Low percentages of natural killer cells were observed in both CN patients.

CONCLUSION

The regulation of IgE production in patients with CN is varied and complex. The CN patients were heterogeneous in terms of Th2 skewing.

Selective development of a strong Th2 cytokine profile in high-risk children who develop atopy: risk factors and regulatory role of IFN-gamma, IL-4 and IL-10

BACKGROUND

The immunological processes in early life and their relation to allergic sensitization leading to a Th2 cytokine profile are still not well understood.

OBJECTIVE

To analyse the environmental and genetic risk factors and immunological responses at birth in relation to the development of atopic disease at 12 months of age in a longitudinal study of high-risk children.

METHODS

High-risk children were followed from birth till 12 months of age. Mononuclear cells obtained at birth and 6 and 12 months thereafter were analysed for their proliferative and cytokine responses after polyclonal and allergen-specific stimulation.

RESULTS

At 12 months of age 25% children had developed an atopic disease. Two atopic parents, parental smoking and atopic dermatitis of at least one of the parents were significant risk factors. In cord blood of newborns who developed atopy, an increased percentage of CD4+CD45RO+ cells and an increased polyclonal-stimulated proliferation were observed. Furthermore, an impaired allergen-induced, but not polyclonal-stimulated IFN-gamma production was found, suggesting a regulatory defect. At 6 and 12 months of age, a strong Th2 profile (characterized by increased levels of IL-4, IL-5, and IL-13) after both polyclonal and, to a lesser extent, allergen-specific stimulation was found in the children developing atopy. Allergen-induced IL-10 production at 12 months of age was only observed in the non-atopic children.

CONCLUSION

Our data indicate that the first 6 months of life represent a critical time window for the initiation of immunological changes resulting in the development of atopy. The selective development of a Th2 cytokine profile in high-risk children who develop atopy is due to increased production of Th2 cytokines, possibly caused by impaired allergen-induced IFN-gamma production in the neonatal period. Furthermore, the decreased allergen-induced IL-10 levels observed in the atopic children at 12 months of age may result in a lack of down-regulation of the inflammatory process.

Markers for early sensitization and inflammation in relation to clinical manifestations of atopic disease up to 2 years of age in 133 high-risk children

BACKGROUND

The combination of genetic susceptibility and environmental factors induce allergic sensitization and subsequently local inflammation, resulting in atopic manifestations.

OBJECTIVE

To examine whether immunological features reflecting sensitization (total and specific IgE levels, allergen-induced proliferative responses and skin tests) and markers of inflammation (plasma sE-selectin and blood eosinophils) are related to the clinical expression of atopy and whether they precede atopic disease in children up to 2 years of age.

METHODS

The development of these markers during the first 2 years of life was studied prospectively in 133 newborns at high risk to develop atopic disease.

RESULTS

The prevalence of atopic disease increased from 25% at 12 months to 32% at 24 months of age. The children with food allergy at 12 months, who all had atopic dermatitis (AD), turned out to have asthma-like disease in 40% and AD in 100% at the age of 24 months. Total IgE levels increased with time and from 12 months onward levels started to differ markedly between atopics and nonatopics. Food-specific IgE antibodies were significantly associated with AD (relative risk [RR] = 2.39), food (RR = 1.32) and upper-airway allergy (RR = 1.20), and house dust mite-specific IgE antibodies with upper-airway allergy (RR = 5.00). A positive skin test was significantly associated with AD (RR = 2.90) and food allergy (RR = 1.36). The inflammation markers investigated, were not related to the clinical expression or preceded atopic disease at 2 years of age in high-risk children.

CONCLUSION

Positive skin tests and specific IgE to food or inhalant allergens were related to the clinical expression of different atopic diseases. The combination of AD and food allergy at 12 months reflected the strongest risk factor in this high risk cohort for the development of asthma-like disease at 24 months of age.

Differential mRNA expression and production of interleukin-4 and interferon-gamma in stimulated peripheral blood mononuclear cells of house-dust mite-allergic patients

Optimal culture conditions were established for the analysis of interleukin-4 (IL-4) and interferon-gamma (IFN-gamma) mRNA expression and protein production, as well as proliferative capacity of peripheral blood mononuclear cells (PBMC). These culture conditions permitted the analysis of differences in the responses of house-dust mite (HDM) allergic patients and healthy controls after polyclonal and allergen-specific stimulation. Proliferative responses were optimal when PBMC were cultured in RPMI, whereas for studying mRNA expression by RT-PCR and protein production by ELISA, PBMC should be stimulated in Yssels's medium. Blood holding period influenced the cytokine mRNA expression and proliferative capacity of primarily the unstimulated cells. It is thus crucial to isolate PBMC as soon as possible, and in any event no later than 7 hours after blood collection. Proliferative responses to Dermatophagoides pteronyssinus-extract were observed in HDM allergic patients (mean stimulation index (SI) = 5.3+/-0.75), but not in non-allergic subjects (mean SI = 2.3+/-0.21). After D. pteronyssinus-specific stimulation, IL-4 mRNA expression was significantly (p = 0.03) increased in HDM-allergic subjects compared to non-allergic subjects. No significant differences were found in IFN-gamma mRNA expression between HDM-allergic and non-allergic subjects. Both IFN-gamma (p = 0.04) and IL-4 (p = 0.06) protein production were increased after D. pteronyssinus-specific stimulation in HDM-allergic subjects compared to non-allergic subjects. Our data suggest activation of both Th1 and Th2-like cells, as well as CD8+ T cells in allergic patients. Furthermore, analysis of possible functional differences in PBMC between allergic and non-allergic patients, necessitates polyclonal and allergen-specific stimulation of PBMC. Moreover, proliferative responses as well as cytokine mRNA expression and protein production should be studied under optimal culture conditions to highlight the often subtle differences.

Levels of soluble intercellular adhesion molecule-1, soluble E-selectin, tumor necrosis factor-alpha, and soluble tumor necrosis factor receptor p55 and p75 in atopic children

During inflammation, membrane expression of adhesion molecules and tumor necrosis factor (TNF)-receptors (TNF-R) are increased, and soluble forms of these molecules are released. This study analyzed plasma levels of sICAM-1 and sE-selectin as well as TNF-alpha, sTNF-R55, and sTNF-R75 in nonallergic (NAA) and allergic asthma patients (AA), atopic dermatitis patients (AD), and healthy children (HC) by ELISA. Plasma levels of sICAM-1, sE-selectin, and sTNF-R, but not TNF-alpha, were detectable, but were not significantly different between the patient groups and healthy children. In the AA group, a significant correlation (rs = 0.78, P = 0.008) was found between sICAM-1 and sE-selectin levels. Furthermore, a significant correlation was found between sTNF-R55 and sTNF-R75 levels in the AA group (rs = 0.70, P = 0.025) and in the AD group (rs = 0.69, P = 0.027). In AD patients, a significant correlation was observed between sE-selectin and the disease severity, as measured by the SCORAD index (rs = 0.73, P = 0.038). Our data demonstrate that plasma levels of sICAM-1, sE-selectin, TNF-alpha, sTNF-R55, and sTNF-R75 were not different between atopic and nonatopic children during a stable phase of the disease. In AD patients, levels of sE-selectin seemed to be related to clinical severity of the disease.

T cells subsets and cytokines in allergic and non-allergic children. II. Analysis and IL-5 and IL-10 mRNA expression and protein production

Interleukin 5 (IL-5) has an enhancing effect on IL-4 induced immunoglobulin E (IgE) synthesis. Furthermore, IL-5 plays an important role in the differentiation, recruitment, activation and survival of eosinophils. IL-10 has a downmodulating effect on interferon gamma (IFN-gamma) production and can exert strong anti-inflammatory activities. Therefore, we analysed whether differences were present in IL-5 and IL-10 mRNA expression and protein production between T cells of children with allergic and non-allergic asthma, atopic dermatitis and healthy control children. We demonstrated significant increases in IL-5 mRNA expression and protein production in different T cell fractions of children with allergic and non-allergic asthma and children with atopic dermatitis as compared to healthy controls. This indicates that IL-5 is not only involved in allergy, but also plays a role in the inflammatory process of non-allergic asthma. Interestingly, IL-10 mRNA expression by purified T cells of children with allergic and non-allergic asthma and children with atopic dermatitis was strongly decreased as compared with that of healthy controls. In the peripheral blood mononuclear cell (PBMC) fraction, IL-10 mRNA expression was comparable between the four groups. We hypothesize that this decreased T cell derived IL-10 expression results in a lack of immunosuppression of the inflammatory process in these diseases. However, a role of monocyte derived IL-10 cannot be ruled out.

T cell subsets and cytokines in allergic and non-allergic children. I. Analysis of IL-4, IFN-gamma and IL-13 mRNA expression and protein production

Interleukin 4 (IL-4) and IL-13 are key cytokines inducing switching to immunoglobulin E (IgE), whereas interferon gamma (IFN-gamma) acts inhibitory on this process. We analysed whether differences existed in IL-4, IFN-gamma and IL-13 mRNA expression and protein production between T cells of children with allergic and non-allergic asthma, atopic dermatitis and health control children. IL-4 mRNA expression was increased in stimulated T cells of children with allergic asthma and atopic dermatitis, but not in those with non-allergic asthma as compared with healthy controls. Thus the increase in IL-4 expression can be considered as an underlying mechanism of the allergic disease process and not so much of the asthmatic state of the children. In unstimulated T cells of children with atopic dermatitis increased IFN-gamma mRNA expression with a reduced IFN-gamma protein production was found, indicating a post-translational defect in IFN-gamma. Differences in IL-13 expression between the groups were not significant, but IL-13 was significantly correlated with the height of the radio-allergo-sorbent test (RAST) class and with the severity scoring of atopic dermatitis (SCORAD) index. This indicates the clinical relevance of IL-13 for the degree of allergen-specific sensitization and severity of atopic dermatitis. In conclusion, the imbalance in IL-4 and IFN-gamma secretion in patients with atopic dermatitis may reflect general T cell activation in the presence of an intrinsic defect of IFN-gamma secretion.

Development of immune functions related to allergic mechanisms in young children

The newborn immune system differs quantitatively and functionally from that of adults. Development of the immune system has important implications for childhood diseases. The immaturity of the immune system in the first years of life may contribute to failure of tolerance induction and in the development of allergic disease. T cell function is diminished, especially the capacity to produce cytokines; production of interferon (IFN)-gamma, and IL-4 is strongly reduced. IFN-gamma has been found to be even lower in cord blood of newborns with a family history of atopy. Differences in other cell types (natural killer cells, antigen-presenting cells, and B cells) could also play a role in the development of allergic disease. Current data suggest that irregularities in IgE synthesis, helper T cell subsets (Th1, Th2, CD45RA, and CD45RO), cytokines (IL-4, IFN-gamma), and possibly other cell types may play a role in the development of allergy in childhood. Moreover, the role of cell surface molecules, like co-stimulatory molecules (CD28, CD40L), activation markers (CD25), and adhesion molecules (LFA-1/ICAM-1, VLA-4/ VCAM-1) is also discussed. These variables are modulated by genetic (relevant loci are identified on chromosome 5q, 11q, and 14) and environmental forces (allergen exposure, viral infections, and smoke). The low sensitivity of current predictive factors for the development of allergic diseases, such as cord blood IgE levels, improves in combination with family history and by measurement of in vitro responses of lymphocytes and skin reactivity to allergens. New therapeutic approaches are being considered on the basis of our current understanding of the immunopathology of allergic disease, for instance cytokine therapy and vaccination with tolerizing doses of allergen or peptides.

Differential adherence of murine hematopoietic stem cell subsets to fibronectin

Growth and differentiation of hematopoietic stem cells occur in close contact with the cells and extracellular-matrix (ECM) proteins of the hematopoietic microenvironment. We observed the role of fibronectin, a matrix glycoprotein proposed to be involved in the attachment of hematopoietic cells and in the binding of stem cell subsets to bone marrow stroma, for this study. Murine bone marrow cells (BMC) were allowed to adhere to surfaces coated with human plasma fibronectin. Using the cobblestone-area-forming cells (CAFC) assay, adherent and nonadherent cell fractions were tested for their quantity of primitive and less primitive stem cell subsets. The CAFC assay is based on a time-dependent clone formation in pre-established, bone marrow-derived, irradiated stromal layers under limiting dilution conditions, and it allows in vitro enumeration of day-12 colony-forming unit-spleen (CFU-S12) (CAFC-10) and more primitive cells with long-term repopulating abilities (LTRA) (CAFC-28/35). We observed that the majority of primitive CAFC-28/35 adhered to fibronectin, while only a minority of CFU-S-like CAFC-10 did. The adherence of primitive stem cells to fibronectin could partially be blocked by high molar concentrations of oligopeptides containing the essential amino acid sequence of the central cell-binding domain of fibronectin, RGD. Adherence of the small subpopulation of CAFC-10 to fibronectin could almost entirely be prevented by oligopeptides organized in a specific fashion. These data suggest a role for RGD-binding integrins in the adherence of hematopoietic stem cells.

Selective advantage of normal erythrocyte production after bone marrow transplantation of alpha-thalassemic mice

Anemia resulting from alpha-thalassemia in mice was corrected by transplantation of normal bone marrow cells following sublethal total body irradiation, resulting in partial hematopoietic chimerism with a preponderance of normal peripheral blood red cells. Peripheral blood red cell chimerism in recipients of graded numbers of bone marrow cells from sex-mismatched donors, determined by cytometric analysis, was directly compared with immature hematopoietic cell (CFU-S) chimerism and peripheral blood white cell chimerism. The latter two were assessed by fluorescent in situ hybridization with a murine Y-chromosome-specific probe. Peripheral blood white cell chimerism consistently corresponded with immature hematopoietic cell chimerism, emphasizing the selective advantage of normal red cell production in partially chimeric alpha-thalassemic mice.

Stable multilineage hematopoietic chimerism in alpha-thalassemic mice induced by a bone marrow subpopulation that excludes the majority of day-12 spleen colony-forming units

We have investigated the contribution of highly purified day-12 spleen colony-forming units (CFU-S-12) as well as more primitive cells to sustained blood cell production using in vivo and in vitro assays that allow frequency analysis. Normal or day-6 post-5-fluorouracil light-density bone marrow (BM) was sorted on the basis of differences in rhodamine-123 (Rh123) retention or wheat germ agglutinin (WGA) affinity and tested in vivo using a recently developed alpha-thalassemic chimeric mouse model. In addition, short-term and long-term clonal activity was assessed in vitro using a limiting dilution-type long-term BM culture, the cobblestone area forming cell assay. When sublethally irradiated alpha-thalassemic mice were transplanted with as many as 281 purified WGAbright CFU-S-12, derived from a fraction containing 95% of all CFU-S-12 from day-6 post-5-fluorouracil light-density BM of wild-type mice, detectable chimerism was not observed at 6 months posttransplantation. In contrast, only three CFU-S-12 were included in the Rh123dull and WGAdim subpopulations that induced 29% to 58% and 21% to 31% stable multilineage donor-type chimerism of erythrocytes and leukocytes, respectively. The Rh123dull and WGAdim cells were up to 240-fold enriched for long-term repopulating ability (LTRA) as compared with unseparated BM. A comparable level of chimerism was found in the different hematopoietic organs and at the level of BM CFU-S-12. The frequency of the LTRA unit capable of inducing a 10% sustained level of donor-type erythrocytes was calculated to be 1 to 2 per 10(5) BM cells. Several reports have suggested that LTRA and spleen colony formation could be capacities of the same stem cell subset. However, the present results show that the majority of CFU-S-12 have only short-term repopulating ability and are physically separable from more primitive stem cells with long-term multilineage reconstituting capacities.

Loss of long-term repopulating ability in long-term bone marrow culture

We have studied the maintenance of stem cells with long-term multilineage repopulating ability from murine bone marrow, cultured on a pre-established bone marrow-derived stromal cell layer, both in a qualitative and quantitative way. Female bone marrow cells were cultured for a period of 1-4 weeks and compared with uncultured cells for their ability to establish and maintain a level of 50% chimerism in a sex-mismatched bone marrow transplantation model. Chimerism was determined in nucleated cells using fluorescence in situ hybridization with a murine Y-chromosome-specific probe. We observed a rapid decline in the ability of cultured marrow cells to repopulate the blood, bone marrow, spleen, and thymus of sublethally irradiated male recipients. After 4 weeks of culture only 5% of the long-term repopulating ability of the inoculated bone marrow cells remained. The remaining long-term repopulating cells, however, had similar qualities to establish and maintain long-term engraftment compared to fresh bone marrow, as judged from their ability to give stable chimerism over a period of 6 months. These observations are relevant for the therapeutic applications of long-term bone marrow cultures in purging protocols prior to autologous bone marrow transplantation of acute and chronic myeloid leukemic patients, and for the use of long-term marrow cultures when introducing foreign genetic material in hematopoietic stem cells.

Wheat germ agglutinin affinity of murine hemopoietic stem cell subpopulations is an inverse function of their long-term repopulating ability in vitro and in vivo

Hemopoietic stem cells show extensive heterogeneity with respect to their proliferative potential and activity. We have recently reported that the accepted technique for sorting stem cells on the basis of high affinity for the lectin wheat germ agglutinin (WGA) did not select for cells initiating long-term production of new stem cells on a stromal layer in vitro. We have therefore reinvestigated the expression of cell surface sialic acid residues in the hemopoietic stem cell compartment by sorting murine bone marrow cells on the basis of affinity for WGA. Frequency analysis of long-term bone marrow culture initiating stem cells was done using the cobblestone-area-forming cell (CAFC) assay with limiting dilution set-up. In vivo stem cell quality was determined by spleen colony formation, marrow-repopulating ability (MRA) and long-term repopulating ability (LTRA) using sex-mismatched hemopoietic chimerism. The data indicate that MRA and LTRA in vivo and in vitro are among the most WGA-dim cells. In contrast, the enrichment factors for splenic colony-forming units (CFU-S) at day 12 and transient CAFC increase with increasing WGA affinity. These characteristics allowed us to concentrate LTRA cells 590- to 850-fold over their activity in normal bone marrow without significant enrichment of day-12 CFU-S. The data reveal that WGA affinity is an inverse function of the primitiveness of murine hemopoietic stem cells and that long-term production of blood cells in vivo and in vitro is provided for by primitive cells that are physically separable from the vast majority of day-12 CFU-S. In addition the data reveal, that the CAFC frequency at day 28-35 of a graft strongly correlates with the number of cells required to induce 40% donor-type chimerism at 15 months post-transplantation and thus predicts the in vivo LTRA of a graft.

Use of limiting-dilution type long-term marrow cultures in frequency analysis of marrow-repopulating and spleen colony-forming hematopoietic stem cells in the mouse

We have developed an in vitro clonal assay of murine hematopoietic precursor cells that form spleen colonies (CFU-S day 12) or produce in vitro clonable progenitors in the marrow (MRA cells) of lethally irradiated mice. The assay is essentially a long-term bone marrow culture in microtiter wells containing marrow-derived stromal "feeders" depleted for hematopoietic activity by irradiation. To test the validity of the assay as a quantitative in vitro stem cell assay, a series of unsorted and physically sorted bone marrow cells were simultaneously assayed in vivo and overlaid on the feeders in a range of concentrations, while frequencies of cells forming hematopoietic clones (cobblestone area forming cells, CAFC) were calculated by means of Poisson statistics. Linear regression analysis of the data showed high correlations between the frequency of CFU-S day 12 and CAFC day 10, and between MRA cells and CAFC day 28. A majority of MRA activity and CAFC day 28 was separable from CFU-S day 12 and CAFC day 10. This correlation study validates the CAFC system as a clonal assay facilitation both the quantitative assessment of a series of subsets in the hematopoietic stem cell hierarchy and the study of single long-term repopulating cells in vitro.

Transferrin receptor expression and the regulation of placental iron uptake

Placental transferrin receptors, located at the apical side of syncytiotrophoblast, mediate placental iron uptake. Regulation of transferrin receptors on the fetal-maternal exchange area could be a major determinant in the regulation of trans-placental iron transport. Transferrin receptor expression in cultured human term cytotrophoblasts is on a much lower level than in choriocarcinoma cells, with a higher proportion of receptors located on the cell surface. Differentiation of cells, either due to longer culture periods or to 8-bromo-cAMP treatment does not lead to an increase of transferrin receptor expression. In vitro, the level of expression is largely regulated by the cellular density in the culture dishes. Low cellular occupancy of the dish leads to a high level of transferrin receptors. Treatment with iron-sources results in a down regulation of transferrin receptors. Thus, though the level of transferrin receptors in cultured normal trophoblast is at a constant level, unaffected by differentiation, high levels of maternal transferrin-iron availability can lead to a decrease in placental iron uptake. This feed-back mechanism makes placental iron uptake independent of maternal iron stores.