MHC class II and c-kit expression allows rapid enrichment of T-cell progenitors from total bone marrow cells

OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks

MOTIVATION

Reverse engineering of gene regulatory networks remains a central challenge in computational systems biology, despite recent advances facilitated by benchmark in silico challenges that have aided in calibrating their performance. A number of approaches using either perturbation (knock-out) or wild-type time-series data have appeared in the literature addressing this problem, with the latter using linear temporal models. Nonlinear dynamical models are particularly appropriate for this inference task, given the generation mechanism of the time-series data. In this study, we introduce a novel nonlinear autoregressive model based on operator-valued kernels that simultaneously learns the model parameters, as well as the network structure.

RESULTS

A flexible boosting algorithm (OKVAR-Boost) that shares features from L2-boosting and randomization-based algorithms is developed to perform the tasks of parameter learning and network inference for the proposed model. Specifically, at each boosting iteration, a regularized Operator-valued Kernel-based Vector AutoRegressive model (OKVAR) is trained on a random subnetwork. The final model consists of an ensemble of such models. The empirical estimation of the ensemble model's Jacobian matrix provides an estimation of the network structure. The performance of the proposed algorithm is first evaluated on a number of benchmark datasets from the DREAM3 challenge and then on real datasets related to the In vivo Reverse-Engineering and Modeling Assessment (IRMA) and T-cell networks. The high-quality results obtained strongly indicate that it outperforms existing approaches.

AVAILABILITY

The OKVAR-Boost Matlab code is available as the archive: http://amis-group.fr/sourcecode-okvar-boost/OKVARBoost-v1.0.zip.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44 K Agilent microarray

Background

Salmonella enterica serovar Enteritidis (SE) is one of the most common food-borne pathogens that cause human salmonellosis and usually results from the consumption of contaminated poultry products. The mechanism of SE resistance in chickens remains largely unknown. Previously, heterophils isolated from broilers with different genetic backgrounds (SE-resistant [line A] and -susceptible [line B]) have been shown to be important in defending against SE infections. To dissect the interplay between heterophils and SE infection, we utilized large-scale gene expression profiling.

Results

The results showed more differentially expressed genes were found between different lines than between infection (SE-treated) and non-infection (control) samples within line. However, the numbers of expressed immune-related genes between these two comparisons were dramatically different. More genes related to immune function were down-regulated in line B than line A. The analysis of the immune-related genes indicated that SE infection induced a stronger, up-regulated gene expression of line heterophils A than line B, and these genes include several components in the Toll-like receptor (TLR) signaling pathway, and genes involved in T-helper cell activation.

Conclusion

We found: (1) A divergent expression pattern of immune-related genes between lines of different genetic backgrounds. The higher expression of immune-related genes might be more beneficial to enhance host immunity in the resistant line; (2) a similar TLR regulatory network might exist in both lines, where a possible MyD88-independent pathway may participate in the regulation of host innate immunity; (3) the genes exclusively differentially expressed in line A or line B with SE infection provided strong candidates for further investigating SE resistance and susceptibility. These findings have laid the foundation for future studies of TLR pathway regulation and cellular modulation of SE infection in chickens.

Primitive hematopoietic cell populations reside in the spleen: Studies in the pig, baboon, and human

OBJECTIVE

We previously observed high levels (>40%) of multilineage hematopoietic cell chimerism following spleen transplantation across full MHC barriers in immunosuppressed miniature swine. We therefore investigated the spleen as a source of hematopoietic progenitor cells (HPCs).

MATERIALS AND METHODS

Specific cell-surface markers were used to identify HPCs in the spleen and bone marrow (BM) of young adult (n = 15) and fetal (n = 9) miniature swine by flow cytometry. Hoechst dye-effluxing side population (SP) cells were analyzed in adult spleen, BM, and blood for their expression of c-kit. Functional HPC activity of varying repopulation potential in vitro was investigated by the ability of spleens and BM to give rise to colony-forming units (CFUs) and cobblestone area-forming cells (CAFCs) in long-term stromal cultures. Studies were also carried out on baboon and human spleens and BM.

RESULTS

Spleen c-kit+ cells co-expressed more lymphoid markers, but equal myeloid markers, when compared with BM c-kit+ cells. BM and spleen both contained significant percentages of c-kit+ SP cells. Although the frequency of early-forming CFUs in the spleen was only 0.1 to 1.3% of that in the BM, the frequency of CAFCs developing after 8 weeks in culture was comparable to that of BM. Secondary CFUs in long-term culture-initiating cell assays confirmed the presence of long-term repopulating cells at comparable frequencies in spleen and BM. Similar findings were found with regard to baboon and human spleen cells.

CONCLUSION

The adult spleen is a relatively rich source of very primitive HPCs, possibly hematopoietic stem cells (HSCs), and may be of therapeutic value.

Avian HSC emergence, migration, and commitment toward the T cell lineage

To date three sites of emergence of hemopoietin cells have been identified during early avian development: the yolk sac, the intraaortic clusters and recently the allantois. However, the contributions of the hematopoietic stem cell (HSC) populations generated by these different sites to definitive hematopoiesis and their migration routes are not fully unraveled. Experimental embryology as well as the establishment of the genetic cascades involved in HSC emergence help now to draw a better scheme of these processes.

Stem cell activity of porcine c-kit+ hematopoietic cells

OBJECTIVE

A marker for hematopoietic stem cells (HSCs) of pigs, which are considered to be the most suitable donors for clinical xenotransplantation, has not yet been identified. In this study, we examined the HSC activity of porcine c-kit+ bone marrow cells (BMCs).

METHODS

The HSC activity of porcine c-kit+ BMCs was evaluated both in vitro using colony-forming unit (CFU) and cobblestone area-forming cell (CAFC) assays and in vivo in nonobese diabetic/severe combined immunodeficiency transgenic (NOD/SCID-Tg) mice carrying porcine cytokine transgenes.

RESULTS

Purified c-kit+ BMCs were substantially enriched for both CFUs and CAFCs in vitro and their transplantation led to long-term porcine hematopoiesis in vivo in mice. Although porcine chimerism was detectable in the peripheral blood of NOD/SCID-Tg mice receiving porcine c-kit- BMCs at early time points after transplantation, the levels were markedly lower than those in mice receiving purified c-kit+ BMCs (0.2%+/-0.14% vs 7.7%+/-1.6% and 0.17%+/-0.17% vs 5.6%+/-2.1% at weeks 3 and 6, respectively). Importantly, all mouse recipients of porcine c-kit+ BMCs showed durable multilineage chimerism (>19 weeks), whereas no recipients of porcine c-kit- BMCs sustained long-term engraftment. Moreover, porcine HSCs that had engrafted for 19 weeks in the recipients of porcine c-kit+ BMCs gave rise to clonogenic progenitors in vitro and reconstituted porcine hematopoiesis in secondary recipients.

CONCLUSION

The present study demonstrates that c-kit is an essential marker of both long-term-repopulating HSCs and progenitor cells with early engraftment capacity.

Myeloid-lymphoid initiating cells (ML-IC) are highly enriched in the rhodamine-c-kit(+)CD33(-)CD38(-) fraction of umbilical cord CD34(+) cells

OBJECTIVE

The study of hematopoietic stem cells (HSC) is limited by lack of specific markers for HSC. Rhodamine 123 (Rho) is one of the substrates of P-glycoprotein (Pgp), and the presence of active Pgp can be shown by the efflux of Rho. Rho can also be used to measure the mitochondrial transmembrane potential (energy state) of a cell. We reasoned that selection of hematopoietic progenitors using a combination of Rho efflux and phenotypic markers might be superior to use of phenotypic markers alone.

MATERIALS AND METHODS

We used the myeloid-lymphoid initiating cell (ML-IC) assay as functional measure of primitive progenitors. Umbilical cord blood CD34(+)CD33(-)CD38(-), CD34(+)CD33(-)CD38(-)Rho(-), and CD34(+)CD33(-)CD38(-)Rho(-)c-kit(+) cells were sorted singly onto AFT024 feeders to assess their capacity to become ML-IC.

RESULTS

The frequency of ML-IC in CD34(+)CD33(-)CD38(-)Rho(-) cells was significantly higher (15 +/- 0.4%) than that in CD34(+)CD33(-)CD38(-) cells (6.2 +/- 0.9%, p < 0.05). However, the frequency of long-term culture-initiating cells (LTC-IC) (17 +/- 3% vs 12 +/- 1.5%) and natural killer culture-initiating cells (NK-IC) (25 +/- 3% vs 20 +/- 4%) was similar in the two populations. Following the treatment of CD34(+)CD33(-)CD38(-)Rho(-) cells with verapamil, which blocks Pgp function, no increase in ML-IC was detected compared with CD34(+)CD33(-)CD38(-) cells (6 +/- 0.7%), suggesting that differences in the energy state, which is reflected by Rho staining after verapamil treatment, cannot be used as a criterion to identify human HSC. Further selection of CD34(+)CD33(-)CD38(-)Rho(-) cells based on expression of c-kit significantly increased the frequency of ML-IC, LTC-IC and NK-IC by 1.75-, 1.3-, and 1.8-fold, respectively.

CONCLUSION

Combining the function of Pgp and phenotypic features of hematopoietic progenitors enriches the frequency of cord blood ML-IC to greater than 25%. Use of such enriched populations will allow us to characterize the biological behavior of human HSC.

Stem cell factor: laboratory and clinical aspects

Stem cell factor is an essential haemopoietic progenitor cell growth factor with proliferative and anti-apoptotic functions. Molecular biologists have now dissected some of the various pathways through which this cytokine signals to the nucleus. At the same time, new molecules have become available which can inhibit SCF signalling. This provides an exciting prospect for the treatment of Kit+ malignancies such as acute myeloblastic leukaemia. The capacity of SCF to synergize with other cytokines has been exploited in the ex vivo expansion of haemopoietic progenitors and dendritic cells, which may also hold therapeutic promise. In this review the last 5 years' literature on these issues is reviewed and collated.

Lnk adaptor: novel negative regulator of B cell lymphopoiesis

Originally thought to have the functions now ascribed to the linker for activation of T cells protein (LAT), Lnk is coming into its own as an adaptor protein that mediates signaling through several receptor pathways. An essential role for Lnk in B cell development and maturation was recently uncovered by Perlmutter and colleagues. Rudd discusses the role of Lnk in B cells and hypothesizes a mechanism whereby Lnk, and its closely related protein family members, the adaptor molecules containing pleckstrin homology (PH) and Src-homology 2 (SH2) domains (APS), and Src-homology 2-B protein (SH2-B), may mediate signal promotion or attenuation.

MHC class II beta-chain and alphaIIbbeta3 integrin are expressed on T-cell progenitors in embryonic bone marrow

The RR5 monoclonal antibody (mAb) was obtained after immunization of mice with hemopoietic cells from chicken embryos. The cDNA encoding the protein recognized by RR5 was cloned using COS-7 cells transfected with an embryonic bone marrow (BM) cDNA library. The epitope recognized by the RR5 mAb was located on the non-polymorphic MHC class II beta-chain molecule. In the embryonic BM, RR5 labeled 50% of the c-kit expressing cells. Previous experiments have shown that the T-cell progenitors are present in the MHC class II(+)/c-kit(+) BM population along with myeloid progenitors and that T-cell and myeloid progenitors also express the integrin alphaIIbbeta3. In this study, using intrathymic cell transfer experiments in chicks, we have tested the T-cell differentiation potential of MHC class II/alphaIIbbeta3 double positive cells. It proved to be similar to that of the c-kit/MHC class II positive cells. However, injection of triple positive cells resulted in a selection of cells with an increased T-cell potential. Most of the MHC class II positive cells which do not express c-kit are prone to apoptosis, indicating that these progenitors might need a survival signal via c-kit. Interestingly, the MHC class II positive progenitors lose this expression after intrathymic transfer. Taken together our data suggest that the presence of the MHC class II beta-chain molecule on the surface of BM progenitor cells could be implicated in differentiation toward myeloid and lymphoid lineages.