Pathogenetic mechanisms of immune dysregulation and hematopoietic disorders

Pathogenetic mechanisms of immune dysregulation and hematopoietic disorders Abstract The aim of my work was to introduce whole exome sequencing (WES) and a routine algorithm for data analysis in pediatric patients with suspected inborn error of immunity (IEI) or hematopoiesis. A clear molecular diagnosis based on genetic testingwas achieved in 25% of patients. Additionally, novel mutations not previously described in the pathogenesis of IEI or hematopoietic failure were revealed in 9% of the patients. Validation experiments were designed to confirm the causality of the identified mutations in the pathogenesis of the disease, based on literature review and known mechanisms of immune system development and regulation in these patients. Thanks to WES, we were able to elucidate the cause of two new congenital diseases - megaloblastic anemia due to a homozygous mutation of the SLC19A1 gene and immune dysregulation syndrome with autoimmune and autoinflammatory manifestations due to an X-linked mutation of the TLR8 gene in monozygotic twins with chronic autoimmune hemolytic anemia (AIHA). In five additional patients, novel mutations in the STAT3, SPTA1, SAMD9 and XIAP genes were identified and their causality in the pathogenesis of hematopoietic failure or IEI was demonstrated. In one patient with an atypical...Patogenetické mechanismy imunitní dysregulace a hematopoetických onemocnění Abstrakt Cílem mé práce bylo zavedení vyšetření pomocí celoexomového sekvenování (WES) a rutinního algoritmu analýzy získaných dat u dětských pacientů s podezřením na vrozenou poruchu imunity (IEI) nebo selhání kostní dřeně. Kromě jasné molekulární diagnózy na základě genetického vyšetření, které bylo dosaženo u 25 % pacientů, tvoří část výsledků (9 %) také pacienti, u nichž toto vyšetření odhalilo nové mutace, které nebyly dosud popsány v patogenezi IEI nebo selhání krvetvorby. U těchto pacientů byly na základě literárních rešerší a známých mechanismů vývoje a regulace imunitního systému navrženy validační experimenty, za účelem potvrzení kauzality identifikovaných mutací v patogenezi onemocnění. Díky WES se podařilo objasnit příčinu dvou nových vrozených onemocnění - megaloblastické anémie na podkladě homozygotní mutace genu SLC19A1 a syndromu imunitní dysregulace s autoimunitními a autoinflammatorními projevy na podkladě X-vázané mutace genu TLR8 u monozygotických dvojčat s chronickou autoimunitní hemolytickou anémií (AIHA). U pěti dalších pacientů se podařilo identifikovat nové mutace v genech STAT3, SPTA1, SAMD9 a XIAP a prokázat jejich kauzalitu v patogenezi selhání krvetvorby nebo IEI. U jedné pacientky s netypickým fenotypem...Department of Paediatric Haematology and OncologyKlinika dětské hematologie a onkologie2. lékařská fakultaSecond Faculty of Medicin

Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS

Assessment of clonality, marker identification and measurement of minimal residual disease (MRD) of immunoglobulin (IG) and T cell receptor (TR) gene rearrangements in lymphoid neoplasms using next-generation sequencing (NGS) is currently under intensive development for use in clinical diagnostics. So far, however, there is a lack of suitable quality control (QC) options with regard to standardisation and quality metrics to ensure robust clinical application of such approaches. The EuroClonality-NGS Working Group has therefore established two types of QCs to accompany the NGS-based IG/TR assays. First, a central polytarget QC (cPT-QC) is used to monitor the primer performance of each of the EuroClonality multiplex NGS assays; second, a standardised human cell line-based DNA control is spiked into each patient DNA sample to work as a central in-tube QC and calibrator for MRD quantification (cIT-QC). Having integrated those two reference standards in the ARResT/Interrogate bioinformatic platform, EuroClonality-NGS provides a complete protocol for standardised IG/TR gene rearrangement analysis by NGS with high reproducibility, accuracy and precision for valid marker identification and quantification in diagnostics of lymphoid malignancies.This work was supported by Ministry of Health of the Czech Republic, grant no. 16-34272A; computational resources were provided by the CESNET LM2015042 and the CERIT Scientific Cloud LM2015085, provided under the programme “Projects of Large Research, Development, and Innovations Infrastructures”. Analyses in Prague (JT, EF and MS) were supported by Ministry of Health, Czech Republic, grant no. 00064203, and by PRIMUS/17/MED/11. Analyses in the Monza (Centro Ricerca Tettamanti, SS, AG and GC) laboratory were supported by the Italian Association for Cancer Research (AIRC) and Comitato Maria Letizia Verga

EuroFlow Standardized Approach to Diagnostic Immunopheneotyping of Severe PID in Newborns and Young Children

The EuroFlow PID consortium developed a set of flow cytometry tests for evaluation of patients with suspicion of primary immunodeficiency (PID). In this technical report we evaluate the performance of the SCID-RTE tube that explores the presence of recent thymic emigrants (RTE) together with T-cell activation status and maturation stages and discuss its applicability in the context of the broader EuroFlow PID flow cytometry testing algorithm for diagnostic orientation of PID of the lymphoid system. We have analyzed peripheral blood cells of 26 patients diagnosed between birth and 2 years of age with a genetically defined primary immunodeficiency disorder: 1

Pathogenetic mechanisms of immune dysregulation and hematopoietic disorders

Pathogenetic mechanisms of immune dysregulation and hematopoietic disorders Abstract The aim of my work was to introduce whole exome sequencing (WES) and a routine algorithm for data analysis in pediatric patients with suspected inborn error of immunity (IEI) or hematopoiesis. A clear molecular diagnosis based on genetic testingwas achieved in 25% of patients. Additionally, novel mutations not previously described in the pathogenesis of IEI or hematopoietic failure were revealed in 9% of the patients. Validation experiments were designed to confirm the causality of the identified mutations in the pathogenesis of the disease, based on literature review and known mechanisms of immune system development and regulation in these patients. Thanks to WES, we were able to elucidate the cause of two new congenital diseases - megaloblastic anemia due to a homozygous mutation of the SLC19A1 gene and immune dysregulation syndrome with autoimmune and autoinflammatory manifestations due to an X-linked mutation of the TLR8 gene in monozygotic twins with chronic autoimmune hemolytic anemia (AIHA). In five additional patients, novel mutations in the STAT3, SPTA1, SAMD9 and XIAP genes were identified and their causality in the pathogenesis of hematopoietic failure or IEI was demonstrated. In one patient with an atypical..

The TREC/KREC Assay for the Diagnosis and Monitoring of Patients with DiGeorge Syndrome

<div><p></p><p>DiGeorge syndrome (DGS) presents with a wide spectrum of thymic pathologies. Nationwide neonatal screening programs of lymphocyte production using T-cell recombination excision circles (TREC) have repeatedly identified patients with DGS. We tested what proportion of DGS patients could be identified at birth by combined TREC and kappa-deleting element recombination circle (KREC) screening. Furthermore, we followed TREC/KREC levels in peripheral blood (PB) to monitor postnatal changes in lymphocyte production.</p><p>Methods</p><p>TREC/KREC copies were assessed by quantitative PCR (qPCR) and were related to the albumin control gene in dry blood spots (DBSs) from control (n = 56), severe immunodeficiency syndrome (SCID, n = 10) and DGS (n = 13) newborns. PB was evaluated in DGS children (n = 32), in diagnostic samples from SCID babies (n = 5) and in 91 controls.</p><p>Results</p><p>All but one DGS patient had TREC levels in the normal range at birth, albeit quantitative TREC values were significantly lower in the DGS cohort. One patient had slightly reduced KREC at birth. Postnatal DGS samples revealed reduced TREC numbers in 5 of 32 (16%) patients, whereas KREC copy numbers were similar to controls. Both TREC and KREC levels showed a more pronounced decrease with age in DGS patients than in controls (p<0.0001 for both in a linear model). DGS patients had higher percentages of NK cells at the expense of T cells (p<0.0001). The patients with reduced TREC levels had repeated infections in infancy and developed allergy and/or autoimmunity, but they were not strikingly different from other patients. In 12 DGS patients with paired DBS and blood samples, the TREC/KREC levels were mostly stable or increased and showed similar kinetics in respective patients.</p><p>Conclusions</p><p>The combined TREC/KREC approach with correction via control gene identified 1 of 13 (8%) of DiGeorge syndrome patients at birth in our cohort. The majority of patients had TREC/KREC levels in the normal range.</p></div

Quantitative levels of TRECs (A) KRECs (B), relative T cell (CD3^pos) counts (C), relative B cell (CD19^pos) counts (D), absolute T cell counts (E), absolute B cell counts (F), absolute lymphocyte counts (G) and relative NK cell (CD3^negCD16^posCD56^pos) counts (H) in relation to age (x-axis) in patients with DiGeorge syndrome (black diamonds) and in controls (empty diamonds).

<p>Lines show linear regression analyses for patients (full lines) and controls (dotted lines).</p

TREC and KREC numbers expressed as copies per microgram of DNA in A) neonatal dry blood spots B) peripheral blood in children (0–18 years) for controls, patients with DiGeorge syndrome and patients with severe combined immunodeficiency (SCID).

<p>Grey areas represent the abnormal TREC/KREC range.</p

Quantitative TREC/KREC levels expressed as number of copies per microgram of DNA in A) neonatal dry blood spots B) peripheral blood for control children vs. children with DiGeorge syndrome (0–18 years).

<p>Quantitative TREC/KREC levels expressed as number of copies per microgram of DNA in A) neonatal dry blood spots B) peripheral blood for control children vs. children with DiGeorge syndrome (0–18 years).</p

EuroFlow standardized approach to diagnostic immunopheneotyping of severe PID in newborns and young children

The EuroFlow PID consortium developed a set of flow cytometry tests for evaluation of patients with suspicion of primary immunodeficiency (PID). In this technical report we evaluate the performance of the SCID-RTE tube that explores the presence of recent thymic emigrants (RTE) together with T-cell activation status and maturation stages and discuss its applicability in the context of the broader EuroFlow PID flow cytometry testing algorithm for diagnostic orientation of PID of the lymphoid system. We have analyzed peripheral blood cells of 26 patients diagnosed between birth and 2 years of age with a genetically defined primary immunodeficiency disorder: 15 severe combined immunodeficiency (SCID) patients had disease-causing mutations in RAG1 or RAG2 (n = 4, two of them presented with Omenn syndrome), IL2RG (n = 4, one of them with confirmed maternal engraftment), NHEJ1 (n = 1), CD3E (n = 1), ADA (n = 1), JAK3 (n = 3, two of them with maternal engraftment) and DCLRE1C (n = 1) and 11 other PID patients had diverse molecular defects [ZAP70 (n = 1), WAS (n = 2), PNP (n = 1), FOXP3 (n = 1), del22q11.2 (DiGeorge n = 4), CDC42 (n = 1) and FAS (n = 1)]. In addition, 44 healthy controls in the same age group were analyzed using the SCID-RTE tube in four EuroFlow laboratories using a standardized 8-color approach. RTE were defined as CD62L+CD45RO-HLA-DR-CD31+ and the activation status was assessed by the expression of HLA-DR+. Naïve CD8+ T-lymphocytes and naïve CD4+ T-lymphocytes were defined as CD62L+CD45RO-HLA-DR-. With the SCID-RTE tube, we identified patients with PID by low levels or absence of RTE in comparison to controls as well as low levels of naïve CD4+ and naïve CD8+ lymphocytes. These parameters yielded 100% sensitivity for SCID. All SCID patients had absence of RTE, including the patients with confirmed maternal engraftment or oligoclonally expanded T-cells characteristic for Omenn syndrome. Another dominant finding was the increased numbers of activated CD4+HLA-DR+ and CD8+HLA-DR+ lymphocytes. Therefore, the EuroFlow SCID-RTE tube together with the previously published PIDOT tube form a sensitive and complete cytometric diagnostic test suitable for patients suspected of severe PID (SCID or CID) as well as for children identified via newborn screening programs for SCID with low or absent T-cell receptor excision circles (TRECs).MBa was supported by Grant Agency of the Charles university (GAUK 316218); MBl by ZonMW project 543002002 (SONNET study); VK by project NV19-05-00332 from Ministry of Health, and TK by project LO1604 from Ministry of Education, Youth and Sports Czech Republic and cytometer instrument was supported by EU-Prague project CZ.2.16/3.1.00/24505. MP-A was supported by a grant from Fundación Mutua Madrileña (Madrid, Spain). The EuroFlow Consortium received support from the FP6-2004-LIFESCIHEALTH-5 program of the European Commission (grant LSHB-CT-2006-018708) as Specific Targeted Research Project (STREP).Peer reviewe