Crazy Sequential Representations: Base 13 (0000 up to CCCC)

Abstract not available

Crazy Sequential Representations: Base 13 (0000 up to CCCC)

Abstract not available

Bronchial Epithelial Cells and Peptidases: Modulation by cytokincs and glucocorticoids ill vitro and in asthma

The airways can be divided in the upper respiratory tract, including the nose, the pharynx, and the larynx. and the lower respiratory tract. consisting of the trachea, bronchi, bronchioles, and alveoli. This structure provides an enormous surface area where the exchange of oxygen and carbon dioxide. the function of the lungs, can take place. Respiratory diseases may affect onc or more of the different parts of the airways. For example, emphysema is characterized by a decreased number of alveoli which also have a reduced elasticity. On the other hand, asthma, the main focus of this thesis, is considered to be a disease affecting predominantly the bronchi and bronchioli

Robust FCS Parsing: Exploring 211,359 Public Files

When it comes to data storage, the field of flow cytometry is fairly standardized, thanks to the flow cytometry standard (FCS) file format. The structure of FCS files is described in the FCS specification. Software that strictly complies with the FCS specification is guaranteed to be interoperable (in terms of exchange via FCS files). Nowadays, software interoperability is crucial for eco system, as FCS files are frequently shared, and workflows rely on more than one piece of software (e.g., acquisition and analysis software). Ideally, software developers strictly follow the FCS specification. Unfortunately, this is not always the case, which resulted in various nonconformant FCS files being generated over time. Therefore, robust FCS parsers must be developed, which can handle a wide variety of nonconformant FCS files, from different resources. Development of robust FCS parsers would greatly benefit from a fully fledged set of testing files. In this study, readability of 211,359 public FCS files was evaluated. Each FCS file was checked for conformance with the FCS specification. For each data set, within each FCS file, validated parse results were obtained for the TEXT segment. Highly space efficient testing files were generated. FlowCore was benchmarked in depth, by using the validated parse results, the generated testing files, and the original FCS files. Robustness of FlowCore (as measured by testing against 211,359 files) was improved by re-implementing the TEXT segment parser. Altogether, this study provides a comprehensive resource for FCS parser development, an in-depth benchmark of FlowCore, and a concrete proposal for improving FlowCore

Antigen receptor sequencing of paired bone marrow samples shows homogeneous distribution of acute lymphoblastic leukemia subclones

In B-cell precursor acute lymphoblastic leukemia, the initial leukemic cells share the same antigen receptor gene rearrangements. However, due to ongoing rearrangement processes, leukemic cells with different gene rearrangement patterns can develop, resulting in subclone formation. We studied leukemic subclones and their distribution in the bone marrow and peripheral blood at diagnosis

High CD33-antigen loads in peripheral blood limit the efficacy of gemtuzumab ozogamicin |(Mylotarg®) treatment in acute myeloid leukemia patients

Gemtuzumab ozogamicin (Mylotarg®) induces remission in approximately 30% of relapsed AML patients. We previously demonstrated that gemtuzumab infusion results in near-complete CD33 saturation in peripheral blood, and that saturating gemtuzumab levels result in continuous binding and internalization of gemtuzumab due to renewed CD33 expression. We now demonstrate that a high CD33-antigen load in peripheral blood is an independent adverse prognostic factor, likely due to peripheral consumption of gemtuzumab. Indeed, CD33 saturation in bone marrow is significantly reduced (40-90% saturation) as compared with CD33 saturation in corresponding peripheral blood samples (>90%). In vitro, such reduced CD33 saturation levels were strongly related with reduced cell kill. Apparently, high CD33-antigen loads in blood consume gemtuzumab and thereby limit its penetration into bone marrow. Consequently, CD33 saturation in bone marrow is reduced, which hampers efficient cell kill. Therefore, gemtuzumab should be administered at higher or repeated doses, or, preferably, after reduction of the leukemic cell burden by classical chemotherapy

Increased group 2 innate lymphoid cells in peripheral blood of adults with mastocytosis

Background: Systemic mastocytosis is a hematological disease in which aberrant mast cells accumulate because of gain-of-function mutations in the KIT receptor. Group 2 innate lymphoid cells (ILC2s) are effector cells of type 2 immune responses that also express KIT and colocalize with mast cells at barrier tissue sites. In mouse models, mast cell-ILC2 crosstalk can drive local inflammation. However, a possible role for ILC2s in the pathophysiology of mastocytosis remains unexplored. Objective: We sought to characterize circulating ILC2s in a clinically diverse cohort of patients with mastocytosis. Methods: We included 21 adults with systemic mastocytosis and 18 healthy controls. Peripheral blood ILC2 abundance and phenotype were analyzed by flow cytometry and correlated to clinical characteristics, including the presence of the D816V KIT mutation. Results: ILC2 levels were significantly higher in D816V+ patients with mastocytosis compared with D816V− patients or healthy controls. We observed increased proportions of KIT+ ILC2s among patients with mastocytosis, regardless of D816V status. Patients with skin involvement and itch showed the highest levels of ILC2s, which was independent from atopy or serum tryptase levels. Allele-specific quantitative PCR showed that the vast majority of ILC2s did not carry the D816V mutation. Conclusions: Our findings suggest a role for ILC2s and pathogenic ILC2-mast cell crosstalk in mastocytosis. We hypothesize that a high cutaneous D816V+

Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin

Newborns are unable to mount antibody responses towards certain antigens. This has been related to the restricted repertoire of immunoglobulin (Ig) genes of their B cells. The mechanisms underlying the restricted fetal Ig gene repertoire are currently unresolved. We here addressed this with detailed molecular and cellular analysis of human precursor-B cells from fetal liver, fetal bone marrow (BM), and pediatric BM. In the absence of selection processes, fetal B-cell progenitors more frequently used proximal V, D and J genes in complete IGH gene rearrangements, despite normal Ig locus contraction. Fewer N-nucleotides were added in IGH gene rearrangements in the context of low TdT and XRCC4 expression. Moreover, fetal progenitor-B cells expressed lower levels of IL7Rα than their pediatric counterparts. Analysis of progenitor-B cells from IL7Rα-deficient patients revealed that TdT expression and N-nucleotides additions in Dh-Jh junctions were dependent on functional IL7Rα. Thus, IL7Rα affects TdT expression, and decreased expression of this receptor underlies at least in part the skewed Ig repertoire formation in fetal B-cell precursors. These new insights provide a better understanding of the formation of adaptive immunity in the developing fetus

Next-generation antigen receptor sequencing of paired diagnosis and relapse samples of B-cell acute lymphoblastic leukemia: Clonal evolution and implications for minimal residual disease target selection

Antigen receptor gene rearrangements are frequently applied as molecular targets for detection of minimal residual disease (MRD) in B-cell precursor acute lymphoblastic leukemia patients. Since such targets may be lost at relapse, appropriate selection of antigen receptor genes as MRD-PCR target is critical. Recently, next-generation sequencing (NGS) – much more sensitive and quantitative than classical PCR-heteroduplex approaches – has been introduced for identification of MRD-PCR targets. We evaluated 42 paired diagnosis-relapse samples by NGS (IGH, IGK, TRG, TRD, and TRB) to evaluate clonal evolution patterns and to design an algorithm for selection of antigen receptor gene rearrangements most likely to remain stable at relapse. Overall, only 393 out of 1446 (27%) clonal rearrangements were stable between diagnosis and relapse. If only index clones with a frequency >5% at diagnosis were taken into account, this number increased to 65%; including only index clones with an absolute read count >10,000, indicating truly major clones, further increased the stability to 84%. Over 90% of index clones at relapse were also present as index clone at diagnosis. Our data provide detailed information about the stability of antigen receptor gene rearrangements, based on which we propose an algorithm for selecting stable MRD-PCR targets, successful in >97% of patients