CD34-positive early stages of human T-cell differentiation

SifiNet: a robust and accurate method to identify feature gene sets and annotate cells

SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multi-omic cellular profiles. It is conveniently available as an open-source R package.

SifiNet: A robust and accurate method to identify feature gene sets and annotate cells

SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multiomic cellular profiles. It is conveniently available as an open-source R package.

A simple model system enabling human CD34(+) cells to undertake differentiation towards T cells

Background

Channelling the development of haematopoietic progenitor cells into T lymphocytes is dependent upon a series of extrinsic prompts whose temporal and spatial sequence is critical for a productive outcome. Simple models of human progenitor cells development depend in the main on the use of xenogeneic systems which may provide some limitations to development.

Methods and Findings

Here we provide evidence that a simple model system which utilises both human keratinocyte and fibroblast cell lines arrayed on a synthetic tantalum coated matrix provides a permissive environment for the development of human CD34⁺ haematopoietic cells into mature CD4⁺ or CD8⁺ T lymphocytes in the presence of Interleukin 7 (IL-7), Interleukin 15 (IL-15) and the Fms-like tyrosine kinase 3 ligand (Flt-3L). This system was used to compare the ability of CD34⁺ cells to produce mature thymocytes and showed that whilst these cells derived from cord blood were able to productively differentiate into thymocytes the system was not permissive for the development of CD34⁺ cells from adult peripheral blood.

Conclusions/Significance

Our study provides direct evidence for the capacity of human cord blood CD34⁺ cells to differentiate along the T lineage in a simple human model system. Productive commitment of the CD34⁺ cells to generate T cells was found to be dependent on a three-dimensional matrix which induced the up-regulation of the Notch delta-like ligand 4 (Dll-4) by epithelial cells.

BIOMED-1 concerted action report: flow cytometric characterization of CD7+ cell subsets in normal bone marrow as a basis for the diagnosis and follow-up of T cell acute lymphoblastic leukemia (T-ALL)

The European BIOMED-1 Concerted Action was initiated in 1994 to improve and standardize the flow cytometric detection of minimal residual disease (MRD) in acute leukemia (AL). Three different protocols were defined to identify the normal subsets of B, T and myeloid cells in bone marrow (BM), and were applied to the different types of AL in order to study aberrant immunophenotypes. Using sensitive acquisition methods ('live gate') T cell subsets in normal BM could be identified with five triple-stains: CD7/CD5/CD3, CD7/CD4/CD8, CD7/CD2/CD3, CD7/CD38/CD34 and TdT/CD7/surface or cytoplasmic (cy)CD3 (antibodies conjugated with FITC/PE/PECy5 or PerCP, respectively). The identification of T cell subsets in BM allowed definition of 'empty spaces' (ie areas of flow cytometric plots where normally no cells are found). All studied T-ALL cases (n = 65) were located in 'empty spaces' and could be discriminated from normal T cells. The most informative triple staining was TdT/CD7/cyCD3, which was aberrant in 91% of T-ALL cases. In most cases, two or more aberrant patterns were found. Apparently the immunophenotypes of T-ALL differ significantly from normal BM T cells. This is mostly caused by their thymocytic origin, but also the neoplastic transformation might have affected antigen expression patterns. Application of the five proposed marker combinations in T-ALL contributes to standardized detection of MRD, since cells persistent or reappearing in the 'empty spaces' can be easily identified in follow-up BM samples during and after treatment.

Functional and Phenotypic Analysis of Thymic CD34+CD1a− Progenitor-Derived Dendritic Cells: Predominance of CD1a+ Differentiation Pathway

Whether thymic dendritic cells (DC) are phenotypically and functionally distinct from the monocyte lineage DC is an important question. Human thymic progenitors differentiate into T, NK, and DC. The latter induce clonal deletion of autoreactive thymocytes and therefore might be different from their monocyte-derived counterparts. The cytokines needed for the differentiation of DC from thymic progenitors were also questioned, particularly the need for GM-CSF. We show that various cytokine combinations with or without GM-CSF generated DC from CD34+CD1a− but not from CD34+CD1a+ thymocytes. CD34+ thymic cells generated far fewer DC than their counterparts from the cord blood. The requirement for IL-7 was strict whereas GM-CSF was dispensable but nonetheless improved the yield of DC. CD14+ monocytic intermediates were not detected in these cultures unless macrophage-CSF (M-CSF) was added. Cultures in M-CSF generated CD14−CD1a+ DC precursors but also CD14+CD1a− cells. When sorted and recultured in GM-CSF, CD14+ cells down-regulated CD14 and up-regulated CD1a. TNF-α accelerated the differentiation of progenitors into DC and augmented MHC class II transport to the membrane, resulting in improved capacity to induce MLR. The trafficking of MHC class II molecules was studied by metabolic labeling and immunoprecipitation. MHC class II molecules were transported to the membrane in association with invariant chain isoforms in CD14+ (monocyte)-derived and in CD1a+ thymic-derived DC but not in monocytes. Thus, thymic progenitors can differentiate into DC along a preferential CD1a+ pathway but have conserved a CD14+ maturation capacity under M-CSF. Finally, CD1a+-derived thymic DC and monocyte-derived DC share very close Ag-processing machinery.

Expression of CD10 on lymphoid cells associated with thymoma

BACKGROUND

The thymoma is a mixture, in varying proportions, of epithelial and lymphoid cells. The aim of this study was to detect immature T-lineage components of lymphoid cells infiltrating thymoma tissue.

METHODS

Tissue-infiltrating lymphoid cells (N = 10) and normal thymocytes (TC, N = 3) were retrieved from surgical specimens. The surface antigens of these lymphocytes were examined with flow cytometry.

RESULTS

CD3 was detected on 48 +/- 19% of tissue-infiltrating lymphoid cells and 66 +/- 16% of TC, while CD19 was expressed on neither. CD4 and CD8 were co-expressed on 70 +/- 21% of Tissue-infiltrating lymphoid cells and 68 +/- 28% of TC. CD10 was expressed on 22 +/- 10% of tissue-infiltrating lymphoid cells, but was not expressed on TC (5 +/- 3%, p = 0.0003). Two-color analysis showed that the CD10+ fraction was weakly stained with CD3. It was also stained with anti-CD38 and anti-CD4, but not with anti-CD34.

CONCLUSIONS

Tissue-infiltrating lymphoid cells included CD10-positive T-lineage cells. This fraction corresponds to very immature thymocyte subsets. These observations suggest that the epithelial component of a thymoma either inhibits the normal differentiation of T-lineage cells, or attracts immature T-lineage cells of bone-marrow origin.

Human CD34(+) thymocyte maturation: pre-T and NK cell differentiation on neonatal thymic stromal cell culture

The development of a simple assay for studying human T and NK lymphopoiesis from CD34 progenitors is of great interest. T and NK cells arise from a common CD34(+) immature precursor. While T cell maturation is dependent on interactions and cytokines provided by thymic stromal cells. NK maturation does not require the thymic microenvironment and primarily takes place extrathymically. In addition to models using a mouse thymic microenvironment, in vitro assays based on coculture on human fetal thymic stroma have been described. As an alternative source of fetal thymic tissue we studied the capacity of neonatal thymic epithelial cell enriched stroma to support T and NK cell differentiation. While in the fetal-based assays on NK cells were observed under the conditions used for T cell differentiation, neonatal stroma can generate CD3/TcR+ as well as CD56(+)3(-)8(+)NKR-P1(+)NK cells from both CD34(+)1(-) and CD34(+)1(+) thymocyte precursors. However, following acquisition of CD3/TcR, T-lineage cells disappeared from the culture after 2-3 weeks as a consequence of the outgrowth of the NK cells. These CD56(+)3(-) NK cells appeared to be functionally immature as they required incubation with IL2 or IL15 to lyse K562 target cells. Our data offer a simple and reliable assay for studying the reconstitution potential of T and NK cell progenitors on a monolayer of thymic epithelial cells.

The role of interleukin-7 in early T-cell development

Interleukin-7 (IL-7) is a non redundant cytokine in thymic T-cell development. It binds to a dimeric receptor consisting of a specific IL-7Ralpha and a gamma-common subunit that it shares with the receptors for IL-2, 4, 9, 13 and 15. IL-7 is critical for early T-cell development but it also acts on immature B-cells and mature T-cells, and leads to secondary cytokine release. Its mechanisms of action in early T-cell development may be multiple. There is direct evidence to support a mechanistic involvement in TCR-gamma rearrangement that drives further TCR-gammadelta thymocyte commitment and maturation. There is indirect evidence for a role of IL-7 in TCR-beta rearrangement. It may however also act as a survival factor for TCR-beta rearranging thymocytes while the critical commitment selections are effected by other factors. The effects of IL-7 in fetal thymus organ culture are dose dependent, with a biphasic response: low doses of IL-7 are necessary for normal TCR-alphabeta thymocyte development but high doses block TCR-alphabeta maturation in favor of TCR-gammadelta development. A good understanding of the dose response of IL-7 in thymocyte development, mature T-cell stimulation, and of the release of secondary cytokines will be important for planning successful clinical trials with IL-7.

Enhanced Megakaryocyte and Erythroid Development From Normal Human CD34+ Cells: Consequence of Enforced Expression of SCL

The product of the SCL gene is a basic helix-loop-helix (bHLH) transcription factor that is essential for the development of hematopoietic stem cells in both the embryo and the adult. However, once the stem cell compartment is established, the function of SCL in subsequent differentiation and commitment events within normal hematopoietic cells remains undefined. The aim of the current study was to investigate this role using purified normal human hematopoietic CD34+ cells. An SCL retrovirus was used to transduce CD34+ cells isolated from human bone marrow, peripheral blood, and umbilical cord blood. Enforced expression of SCL increased by a median of twofold the number of erythroid colonies, with an increase in both colony size and the rate of hemoglobinization. Unexpectedly, enforced expression in CD34+ cells also significantly increased the number of megakaryocyte colonies, but with no impact on the size of colonies. There was no consistent effect on the number nor size of granulocyte-macrophage (GM) colonies. The proliferative effect of enforced SCL expression on erythroid cells was attributed to a shortened cell cycle time; the self-renewal capacity of erythroid or GM progenitors was unchanged, as was survival of cells within colonies. These results demonstrate a role for SCL in determining erythroid and megakaryocyte differentiation from normal human hematopoietic CD34+ cells.

Enhanced Megakaryocyte and Erythroid Development From Normal Human CD34+ Cells: Consequence of Enforced Expression of SCL

The product of the SCL gene is a basic helix-loop-helix (bHLH) transcription factor that is essential for the development of hematopoietic stem cells in both the embryo and the adult. However, once the stem cell compartment is established, the function of SCL in subsequent differentiation and commitment events within normal hematopoietic cells remains undefined. The aim of the current study was to investigate this role using purified normal human hematopoietic CD34+ cells. An SCL retrovirus was used to transduce CD34+ cells isolated from human bone marrow, peripheral blood, and umbilical cord blood. Enforced expression of SCL increased by a median of twofold the number of erythroid colonies, with an increase in both colony size and the rate of hemoglobinization. Unexpectedly, enforced expression in CD34+ cells also significantly increased the number of megakaryocyte colonies, but with no impact on the size of colonies. There was no consistent effect on the number nor size of granulocyte-macrophage (GM) colonies. The proliferative effect of enforced SCL expression on erythroid cells was attributed to a shortened cell cycle time; the self-renewal capacity of erythroid or GM progenitors was unchanged, as was survival of cells within colonies. These results demonstrate a role for SCL in determining erythroid and megakaryocyte differentiation from normal human hematopoietic CD34+ cells.

Cellular immune responses of human cadaver donor bone marrow cells and their susceptibility to commonly used immunosuppressive drugs in transplantation

BACKGROUND

The cascade of immunological effects brought about by donor bone marrow cell (DBMC) infusions in human organ transplantation, especially in the context of continuous pharmacologic immunosuppression, is not fully understood. Yet, in inbred rodents and even primates, administration of specific bone marrow cells has caused a state of acquired immunologic tolerance.

METHODS

In vitro mixed lymphocyte culture (MLC) and cell-mediated lympholysis (CML) culture systems were used to compare the responding and regulatory properties of DBMC and individual bone marrow cell subsets versus spleen cells in the presence or absence of pharmacologic immunosuppression.

RESULTS

In the absence of immunosuppressive drugs, the DBMC proliferated in MLC and in response to phytohemagglutinin, but to a lower magnitude than donor spleen cells. In CML assays, DBMC failed to function as cytotoxic cells. Removal of both CD3+ and CD34+ cells together (not just singly) had to occur for complete abrogation of the proliferative response of DBMC evoked in the presence of allogeneic stimulating cells. Testing several experimental variables using flow cytometric analysis led to the conclusion that when purified DBMC CD34+ cells were placed in coculture with irradiated allogeneic peripheral blood mononuclear cells, such CD34+ cells give rise both to CD3- TCRalphabeta+ as well as to dimly staining CD3+ TCRalphabeta+ cells. Low pharmacologic concentrations of tacrolimus/cyclosporine (CsA) and mycophenolic acid (MPA) singly or in combination had no effect on the spontaneous proliferation of DBMC and had significantly less inhibitory activity on MLC responses of DBMC and its purified CD3+ or CD34+ subpopulations, compared with the responses of spleen cells. Moreover, the previously described regulatory effects of DBMC on the MLC responses of peripheral blood or splenic responding cells were not inhibited by these immunosuppressive drugs.

CONCLUSIONS

Taken together, these results support the notion that in vitro DBMC subpopulations, which proliferate as responding cells in co-culture with x-irradiated allogeneic cells and which cause regulatory effects when added as a third component to MLC reactions, seem to be culture-generated lymphoid cell lineage(s) progeny of CD34+ cells. This possibly includes unique CD3+ "primitive" (dimly staining) T cells, which are not as inhibited in their function by tacrolimus/CsA and MPA, as are postthymic (splenic) T cells.

Cytokine-induced cytotoxic function expressed by lymphocytes of the innate immune system: distinguishing characteristics of NK and LAK based on functional and molecular markers

Several molecular events are now identifiable during the activation, recognition, and killing by natural killer (NK) cells that are distinct from those differentiated in response to cytokines during the generation of lymphokine-activated killer (LAK) cells or during lymphocyte proliferation. Because LAK and MHC-unrestricted killing activities also include the prototypic NK targets as part of their broad recognition spectra, accurate identification of the complete function being studied is critical. In many publications, past and present, only NK-sensitive target cells were used (K562, Molt-4, others), and, therefore, the results do not necessarily indicate whether the effectors are NK or have differentiated into LAK cells. Such a consideration becomes critical when the effectors are grown in interleukin-2 (IL-2), and an attempt is made to define receptor recognition, signal transduction pathways, and specificity at the molecular level. In some instances, effector cells are likely to have stopped, therefore merely expressing NK activity, and have also acquired LAK function. The identified receptors may not have been unique to NK cells or NK function. Not until the targets employed are also confirmed to be NK sensitive, and the effectors do not kill NK-resistant targets can the results of molecular studies be proposed to represent aspects unique to NK. Reports of the use of IL-2-expanded NK clones are most likely providing data concerning the biology of LAK and not of classic NK. The classic NK activity surveying our blood apparently performs an important function, including the ability to respond rapidly to certain cytokines and to acquire additional functions and receptors for use in destroying a vast array of target cells. It is critical for scientists to appreciate the functional distinctions and to identify the molecules and pathways unique to each of these curious cytolytic systems.

CD34-positive early human thymocytes: T cell receptor and cytokine receptor gene expression

CD34, a stem cell marker, has been shown to be expressed on human CD3-CD4-CD8- (triple-negative; TN) thymocytes. Phenotypic and functional analyses suggest the following differentiation sequence: CD34+1-3-4-8(-)--> CD34+1+3-4 +/- 8(-)-->CD34-1+3-4+8(+/-)-->CD34-1++3-4+8+. In this report, we examined cytokine receptor gene expression on these subsets by reverse transcription-polymerase chain reaction analysis (RT-PCR). We were able to detect interleukin-7 receptor (IL-7R), c-kit and IL-2R gamma in all CD34+ thymocyte subsets, consistent with previous functional studies. We found IL-1R, granulocyte/macrophage colony-stimulating factor receptor-alpha and IL-4R transcripts in CD3- and CD34+ subsets. Secondly, we investigated T cell receptor (TCR)-delta and -beta gene rearrangement and transcription in CD34+ thymocytes. Our results show that a full-length TCR-delta transcript and the recombination activating genes RAG-1 and RAG-2 mRNA were already expressed in the CD34+1- subset. Mature V beta-containing TCR transcripts were also detected in the CD34+1+ subset, but not in the CD1- fraction. Furthermore, PCR analysis of D-J beta gene rearrangements showed that > or = 70% of CD34+1- cells are in a TCR beta germ-line configuration, although D-J beta recombination had already started in this population.