Transcriptional regulation of hemopoiesis

Morinda citrifolia fruit extract enhances the resistance of Penaeus vannamei to Vibrio parahaemolyticus infection

Vibrio parahaemolyticus is a gram-negative facultative anaerobic bacterium implicated as the causative agent of several shrimp diseases. As part of the effort to provide biocontrol and cost-effective treatments, this research was designed to elucidate the effect of Morinda citrifolia fruit extract on the immunity of Penaeus vannamei postlarvae (PL) to V. parahaemolyticus. The methanol extract of M. citrifolia was vacuum evaporated, and the bioactive compounds were detected using gas chromatography‒mass spectrometry (GC‒MS). Thereafter, P. vannamei PL diets were supplemented with M. citrifolia at different concentrations (0, 10, 20, 30, 40, and 50 mg/g) and administered for 30 days before 24 h of exposure to the bacterium V. parahaemolyticus. A total of 45 bioactive compounds were detected in the methanol extract of M. citrifolia, with cyclononasiloxane and octadecamethyl being the most abundant. The survival of P. vannamei PLs fed the extract supplement was better than that of the control group (7.1-26.7% survival greater than that of the control group) following V. parahaemolyticus infection. Shrimp fed 50 mg/g M. citrifolia had the highest recorded survival. The activities of digestive and antioxidant enzymes as well as hepatopancreatic cells were significantly reduced, except for those of lipase and hepatopancreatic E-cells, which increased following challenge with V. parahaemolyticus. Histological assessment of the hepatopancreas cells revealed reduced cell degeneration following the administration of the plant extracts (expecially those fed 50 mg/g M. citrifolia) compared to that in the control group. Therefore, the enhanced immunity against V. parahaemolyticus infection in P. vannamei could be associated with the improved hepatopancreas health associated with M. citrifolia fruit extract supplementation.

An Integrative Transcriptomic Analysis of Systemic Juvenile Idiopathic Arthritis for Identifying Potential Genetic Markers and Drug Candidates

Systemic juvenile idiopathic arthritis (sJIA) is a rare subtype of juvenile idiopathic arthritis, whose clinical features are systemic fever and rash accompanied by painful joints and inflammation. Even though sJIA has been reported to be an autoinflammatory disorder, its exact pathogenesis remains unclear. In this study, we integrated a meta-analysis with a weighted gene co-expression network analysis (WGCNA) using 5 microarray datasets and an RNA sequencing dataset to understand the interconnection of susceptibility genes for sJIA. Using the integrative analysis, we identified a robust sJIA signature that consisted of 2 co-expressed gene sets comprising 103 up-regulated genes and 25 down-regulated genes in sJIA patients compared with healthy controls. Among the 128 sJIA signature genes, we identified an up-regulated cluster of 11 genes and a down-regulated cluster of 4 genes, which may play key roles in the pathogenesis of sJIA. We then detected 10 bioactive molecules targeting the significant gene clusters as potential novel drug candidates for sJIA using an in silico drug repositioning analysis. These findings suggest that the gene clusters may be potential genetic markers of sJIA and 10 drug candidates can contribute to the development of new therapeutic options for sJIA.

Immunostimulatory Effects of Live Lactobacillus sakei K040706 on the CYP-Induced Immunosuppression Mouse Model

Our previous studies have shown that heat-killed Lactobacillus sakei K040706 exerts immunostimulatory and anti-inflammatory activities in macrophages, cyclophosphamide (CYP)-treated mice, and dextran sulfate sodium–induced colitis mice. However, the immunostimulatory effects of live Lactobacillus sakei K040706 (live K040706) against CYP-induced immunosuppression and its underlying molecular mechanisms remain unknown. Therefore, we investigated the immunostimulatory effects of live K040706 (10⁸ or 10⁹ colony forming unit (CFU)/day, p.o.) in CYP-induced immunosuppressed mice. Oral administration of live K040706 prevented the CYP-induced decreases in body weight, thymus index, natural killer (NK) cell activity, T and B cell proliferation, and cytokine (interferon (IFN)-γ, interleukin (IL)-2, and IL-12) production. The administration of live K040706 also exerted positive effects on the gut microbiota of CYP-induced mice, resulting in a microbiota composition similar to that of normal mice. Moreover, live K040706 significantly enhanced IL-6 and granulocyte-macrophage colony-stimulating factor (GM-CSF) production in the splenocytes and Peyer’s patch (PP) cells of mice and increased bone marrow (BM) cell proliferation. Taken together, our data indicate that live K040706 may effectively accelerate recovery from CYP-induced immunosuppression, leading to activation of the immune system. Therefore, live K040706 may serve as a potential immunomodulatory agent against immunosuppression.

Transcriptome Analysis Provides Insights into the Markers of Resting and LPS-Activated Macrophages in Grass Carp (Ctenopharyngodon idella)

Macrophages are very versatile immune cells, with the characteristics of a proinflammatory phenotype in response to pathogen-associated molecular patterns. However, the specific activation marker genes of macrophages have not been systematically investigated in teleosts. In this work, leukocytes (WBC) were isolated using the Percoll gradient method. Macrophages were enriched by the adherent culture of WBC, then stimulated with lipopolysaccharide (LPS). Macrophages were identified by morphological features, functional activity and authorized cytokine expression. Subsequently, we collected samples, constructed and sequenced transcriptomic libraries including WBC, resting macrophage (Mø) and activated macrophage (M(LPS)) groups. We gained a total of 20.36 Gb of clean data including 149.24 million reads with an average length of 146 bp. Transcriptome analysis showed 708 differential genes between WBC and Mø, 83 differentially expressed genes between Mø and M(LPS). Combined with RT-qPCR, we proposed that four novel cell surface marker genes (CD22-like, CD63, CD48 and CD276) and two chemokines (CXCL-like and CCL39.3) would be emerging potential marker genes of macrophage in grass carp. Furthermore, CD69, CD180, CD27, XCL32a.2 and CXCL8a genes can be used as marker genes to confirm whether macrophages are activated. Transcriptome profiling reveals novel molecules associated with macrophages in C. Idella, which may represent a potential target for macrophages activation.

A novel viral responsive protein (MjVRP) from Marsupenaeus japonicus haemocytes is involved in white spot syndrome virus infection

A viral responsive protein (MjVRP) was characterized from Marsupenaeus japonicus haemocytes. In amino acid homology and phylogenetic tree analyses, MjVRP clustered in the same group with the viral responsive protein of Penaeus monodon (PmVRP15), showing 34% identity. MjVRP transcripts were mainly expressed in haemocytes and the lymphoid organ. Western blotting likewise showed that MjVRP was strongly expressed in haemocytes and the lymphoid organ. Immunostaining detected MjVRP within the cytosol next to the perinuclear region in some haemocytes. Experimental challenge with white spot syndrome virus (WSSV) significantly up-regulated the mRNA level of MjVRP in the M. japonicus haemocytes at 6 and 48 h. Flow cytometry and indirect immunofluorescence assays revealed that the ratio of MjVRP⁺ haemocytes significantly increased 24 and 48 h post-WSSV infection. These results suggest that MjVRP⁺ haemocytes have a supporting role in the pathogenesis of WSSV.

Characterization of a Kunitz-type protease inhibitor (MjKuPI) reveals the involvement of MjKuPI positive hemocytes in the immune responses of kuruma shrimp Marsupenaeus japonicus

Serine proteases and their inhibitors play vital roles in biological processes. Serine protease inhibitors, including Kunitz-type protease inhibitors play important roles not only in physiological process (i.e. blood clotting and fibrinolysis) but also in immune responses. In this study, we characterized a Kunitz-type protease inhibitor, designated MjKuPI, from kuruma shrimp Marsupenaeus japonicus. An expression profile showed that MjKuPI was mainly expressed in hemocytes. Immunostaining revealed that some hemocytes expressed MjKuPI (MjKuPI(+) hemocytes) and others did not (MjKuPI(-) hemocytes). Injection of shrimp with Vibrio penaeicida and white spot syndrome virus (WSSV) upregulated the mRNA level of MjKuPI, and a flow cytometry analysis revealed that the proportion of MjKuPI(+) hemocytes increased significantly 24 h after injection. Together, these results suggest that MjKuPI and MjKuPI(+) hemocytes have a role in the innate immune system of kuruma shrimp.

Goldfish (Carassius auratus L.) as a model system to study the growth factors, receptors and transcription factors that govern myelopoiesis in fish

The process of myeloid cell development (myelopoiesis) in fish has mainly been studied in three cyprinid species: zebrafish (Danio rerio), ginbuna carp (Carassius auratus langsdorfii) and goldfish (C. auratus, L.). Our studies on goldfish myelopoiesis have utilized in vitro generated primary kidney macrophage (PKM) cultures and isolated primary kidney neutrophils (PKNs) cultured overnight to study the process of macrophage (monopoiesis) and neutrophil (granulopoiesis) development and the key growth factors, receptors, and transcription factors that govern this process in vitro. The PKM culture system is unique in that all three subpopulations of macrophage development, namely progenitor cells, monocytes, and mature macrophages, are simultaneously present in culture unlike mammalian systems, allowing for the elucidation of the complex mixture of cytokines that regulate progressive and selective macrophage development from progenitor cells to fully functional mature macrophages in vitro. Furthermore, we have been able to extend our investigations to include the development of erythrocytes (erythropoiesis) and thrombocytes (thrombopoiesis) through studies focusing on the progenitor cell population isolated from the goldfish kidney. Herein, we review the in vitro goldfish model systems focusing on the characteristics of cell sub-populations, growth factors and their receptors, and transcription factors that regulate goldfish myelopoiesis.

hnRNP K in PU.1-containing complexes recruited at the CD11b promoter: a distinct role in modulating granulocytic and monocytic differentiation of AML-derived cells

PU.1 is essential for the differentiation of haemopoietic precursors and is strongly implicated in leukaemogenesis, yet the protein interactions that regulate its activity in different myeloid lineages are still largely unknown. In the present study, by combining fluorescent EMSA (electrophoretic mobility-shift assay) with MS, we reveal the presence of hnRNP K (heterogeneous nuclear ribonucleoprotein K) in molecular complexes that PU.1 forms on the CD11b promoter during the agonist-induced maturation of AML (acute myeloid leukaemia)-derived cells along both the granulocytic and the monocytic lineages. Although hnRNP K and PU.1 act synergistically during granulocytic differentiation, hnRNP K seems to have a negative effect on PU.1 activity during monocytic maturation. Since hnRNP K acts as a docking platform, integrating signal transduction pathways to nucleic acid-directed processes, it may assist PU.1 in activating or repressing transcription by recruiting lineage-specific components of the transcription machinery. It is therefore possible that hnRNP K plays a key role in the mechanisms underlying the specific targeting of protein-protein interactions identified as mediators of transcriptional activation or repression and may be responsible for the block of haemopoietic differentiation.

Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models

MOTIVATION

Blood cell development is thought to be controlled by a circuit of transcription factors (TFs) and chromatin modifications that determine the cell fate through activating cell type-specific expression programs. To shed light on the interplay between histone marks and TFs during blood cell development, we model gene expression from regulatory signals by means of combinations of sparse linear regression models.

RESULTS

The mixture of sparse linear regression models was able to improve the gene expression prediction in relation to the use of a single linear model. Moreover, it performed an efficient selection of regulatory signals even when analyzing all TFs with known motifs (>600). The method identified interesting roles for histone modifications and a selection of TFs related to blood development and chromatin remodelling.

AVAILABILITY

The method and datasets are available from http://www.cin.ufpe.br/~igcf/SparseMix.

CONTACT

igcf@cin.ufpe.br

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Is there a direct role for erythrocytes in the immune response?

Erythrocytes are highly abundant circulating cells in the vertebrates, which, with the notable exception of mammals, remain nucleated throughout the entire life cycle. The major function associated with these cells is respiratory gas exchange however other functions including interaction with the immune system have been attributed to these cells. Many viral, prokaryotic and eukaryotic pathogens directly target this cell type and across the vertebrate group a significant number of related pathologies have been reported. Across the primary literature mechanisms of interaction, invasion and replication between viruses and erythrocytes have been well described however the functional response of the erythrocyte has been poorly studied. A fragmented series of reports spanning the vertebrates suggests that these cells are capable of functional responses to viral infection. In contrast, in-depth proteomic studies using human erythrocytes have strongly progressed throughout the past decade providing a rich source of information related to protein expression and potential function. Furthermore information at the gene expression level is becoming available. Here we provide a review of erythrocyte-pathogen interactions, erythrocyte functions in immunity and propose in light of recent -omics research that the nucleated erythrocytes may have a direct role in the immune response.

Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models

BACKGROUND

The differentiation process from stem cells to fully differentiated cell types is controlled by the interplay of chromatin modifications and transcription factor activity. Histone modifications or transcription factors frequently act in a multi-functional manner, with a given DNA motif or histone modification conveying both transcriptional repression and activation depending on its location in the promoter and other regulatory signals surrounding it.

RESULTS

To account for the possible multi functionality of regulatory signals, we model the observed gene expression patterns by a mixture of linear regression models. We apply the approach to identify the underlying histone modifications and transcription factors guiding gene expression of differentiated CD4+ T cells. The method improves the gene expression prediction in relation to the use of a single linear model, as often used by previous approaches. Moreover, it recovered the known role of the modifications H3K4me3 and H3K27me3 in activating cell specific genes and of some transcription factors related to CD4+ T differentiation.

PU.1 and partners: regulation of haematopoietic stem cell fate in normal and malignant haematopoiesis

During normal haematopoiesis, cell development and differentiation programs are accomplished by switching ‘on’ and ‘off’ specific set of genes. Specificity of gene expression is primarily achieved by combinatorial control, i.e. through physical and functional interactions among several transcription factors that form sequence-specific multiprotein complexes on regulatory regions (gene promoters and enhancers). Such combinatorial gene switches permit flexibility of regulation and allow numerous developmental decisions to be taken with a limited number of regulators. The haematopoietic-specific Ets family transcription factor PU.1 regulates many lymphoid- and myeloid-specific gene promoters and enhancers by interacting with multiple proteins during haematopoietic development. Such protein–protein interactions regulate DNA binding, subcellular localization, target gene selection and transcriptional activity of PU.1 itself in response to diverse signals including cytokines, growth factors, antigen and cellular stresses. Specific domains of PU.1 interact with many protein motifs such as bHLH, bZipper, zinc fingers and paired domain for regulating its activity. This review focuses on important protein–protein interactions of PU.1 that play a crucial role in regulation of normal as well as malignant haematopoiesis. Precise delineation of PU.1 protein-partner interacting interface may provide an improved insight of the molecular mechanisms underlying haematopoietic stem cell fate regulation. Its interactions with some proteins could be targeted to modulate the aberrant signalling pathways for reversing the malignant phenotype and to control the generation of specific haematopoietic progeny for treatment of haematopoietic disorders.

Development of macrophages of cyprinid fish

The innate immune responses of early vertebrates, such as bony fishes, play a central role in host defence against infectious diseases and one of the most important effector cells of innate immunity are macrophages. In order for macrophages to be effective in host defence they must be present at all times in the tissues of their host and importantly, the host must be capable of rapidly increasing macrophage numbers during times of need. Hematopoiesis is a process of formation and development of mature blood cells, including macrophages. Hematopoiesis is controlled by soluble factors known as cytokines, that influence changes in transcription factors within the target cells, resulting in cell fate changes and the final development of specific effector cells. The processes involved in macrophage development have been largely derived from mammalian model organisms. However, recent advancements have been made in the understanding of macrophage development in bony fish, a group of organisms that rely heavily on their innate immune defences. Our understanding of the growth factors involved in teleost macrophage development, as well as the receptors and regulatory mechanisms in place to control them has increased substantially. Furthermore, model organisms such as the zebrafish have emerged as important instruments in furthering our understanding of the transcriptional control of cell development in fish as well as in mammals. This review highlights the recent advancements in our understanding of teleost macrophage development. We focused on the growth factors identified to be important in the regulation of macrophage development from a progenitor cell into a functional macrophage and discuss the important transcription factors that have been identified to function in teleost hematopoiesis. We also describe the findings of in vivo studies that have reinforced observations made in vitro and have greatly improved the relevance and importance of using teleost fish as model organisms for studying developmental processes.

Transcription Factor Expression in Cell Lines Derived from Natural Killer-Cell and Natural Killer-Like T-Cell Leukemia-Lymphoma

Although a number of transcription factors (TFs) have been identified that play a pivotal role in the development of hematopoietic lineages, only little is known about factors that may influence development and lineage commitment of natural killer (NK) or NK-like T (NKT)-cells. Obviously to fully appreciate the NK- and NKT-cell differentiation process, it is important to identify and characterize the TFs effecting the NK- and NKT-cell lineage. Furthermore, these TFs may play a role in NK- or NKT-cell leukemias, in which the normal differentiation program is presumably disturbed. The present study analyzed the expression of the following 13 TFs: AML1, CEBPA, E2A, ETS1, GATA1, GATA2, GATA3, IKAROS, IRF1, PAX5, PU1, TBET and TCF1 in 7 malignant NK-cell lines together with 5 malignant NKT-cell lines, 5 T-cell acute lymphoblastic leukemia (ALL) cell lines including 3 gamma/delta T-cell receptor (TCR) type and 2 alpha/beta TCR type, and 3 B-cell precursor (BCP) leukemia cell lines. AML1, E2A, ETS1, IKAROS and IRF1 were found to be positive for all cell lines tested whereas GATA1 turned out to be universally negative. CEBPA, PAX5 and PU1 were negative for all cell lines tested except in the three positive BCP-cell lines. GATA2 was positive for 3/5 T-cell lines but negative for the other cell lines. GATA3 was positive for 7/7 NK-, 4/5 NKT-, 5/5 T- and 2/3 BCP-cell lines. TBET was positive for all NK- and NKT-cell lines and negative for all T- and BCP-cell lines except one BCP-cell line. In contrast to the expression of TBET, TCF1 was negative for all NK- and NKT-cell lines, being positive for 4/5 T- and 1/3 BCP-cell lines. Expression analysis of TFs revealed that NK- and NKT-cell lines showed identical profiles, clearly distinct from those of the other T-ALL or BCP-ALL leukemia-derived cell lines..

Cell-mediated immunity in arthropods: Hematopoiesis, coagulation, melanization and opsonization

The functions of hemocytes in innate immune response are reviewed with emphasized on their roles in coagulation, melanization and opsonization. Also the ways in which hemocytes are produced in and released from hematopoietic tissue are discussed.

Development of goldfish macrophages in vitro

Over 100 years after the first description of macrophages by Metchnikoff, there are still questions as to the mechanisms leading to the heterogeneity of their lineage. Current views are based on the mononuclear phagocyte system (MPS) theory, where all mammalian macrophages are derived from circulating blood monocytes and ultimately from hematopoietic stem cells in the bone marrow. Our studies on the regulation of fish macrophage development, suggested that teleosts have alternate pathways of monopoiesis, which undoubtedly contribute to macrophage heterogeneity in the goldfish. Macrophage heterogeneity has been attributed to a network of positive and negative regulators of macrophage development, including soluble mediators known as colony-stimulating factors of which two (M-CSF and GM-CSF) promote formation and growth of mature macrophages. In contrast to our knowledge of CSFs and their receptors in mammals, there is no published information about fish macrophage CSFs. Since fish macrophages generate their own growth factors, it is reasonable to assume that pathways of fish macrophage development and hematopoiesis may be distinct from those of mammalian macrophages. More importantly, the presence of fish progenitor/stem cells and developing macrophages in long-term cultures, allowed us to address pathways of macrophage differentiation, which could not be addressed in mammalian macrophage culture systems. Characterization of primary kidney macrophage (PKM) cultures from goldfish hematopoietic tissues (kidney) indicated that three distinct subpopulations developed in response to endogenous macrophage growth factors. These macrophage subpopulations expressed several differentiation markers, including the hematopoietic stem cell antigen AC133, c-kit, granulin, CD63, macrosialin, c/EBPbeta, legumain, and the colony-stimulating factor receptor-1 (CSF-1R). In the goldfish, there appeared to be a stringent control between those early progenitors that self-renewed, and those that were recruited into the maturation pathways. We report that upon commitment, goldfish macrophages developed through two distinct differentiation pathways: one consistent with the "classical" pathway (MPS) of macrophage development (progenitors-->monocytes-->mature macrophages), and an "alternate" pathway (AP-macrophages) where mature macrophages appeared to rapidly develop from early progenitors in the absence of an intermediate monocyte stage. AP-macrophages represent a unique subset of spontaneously growing cells. Their self-renewal was promoted by endogenous macrophage growth factors (MGF), and effectively controlled by a novel soluble form of the CSF-1R (sCSF-1R). The discovery of sCSF-1R in the goldfish highlights the inherent complexity in the hematopoietic regulatory machinery of teleosts.

The hematopoietic system: a new niche for the renin–angiotensin system

The role of the renin-angiotensin system was previously thought to be restricted to the cardiovascular system. It now appears that this system also has important functions in other tissues. Hematopoiesis can be affected by inhibitors of the renin system in patients and in various experimental models. The renin system, particularly angiotensin II, has a role in different stages of hematopoiesis, notably during the first wave in the chick embryo (primitive hematopoiesis) and in the human adult (definitive hematopoiesis). In addition, the renin-angiotensin system in mice is involved in reconstitutive hematopoiesis following experimental irradiation; inhibition of this system improved the hematopoietic recovery in this situation. The clinical relevance and therapeutic applications of these findings offer a new area of clinical research. In this article, we review the evidence for a role for the renin system in the control of hematopoiesis at its different stages.

Induction of human LTBP-3 promoter activity by TGF-beta1 is mediated by Smad3/4 and AP-1 binding elements

Latent TGF-beta binding proteins (LTBPs) are extracellular matrix glycoproteins, which are essential for the targeting and activation of TGF-betas. LTBP-3 regulates the bioavailability of TGF-beta especially in the bone. To understand the regulation of LTBP-3 expression, we have isolated and characterized the promoter region of human LTBP-3 gene. The GC-rich TATA-less promoter contained several transcription initiation sites and putative binding sites for multiple sequence specific transcription factors including Sp1, AP-1, c-Ets, MZF-1, Runx1 and members of the GATA-family. Reporter gene analyses of the promoter indicated that it was more active in MG-63 than in Saos-2 osteosarcoma cells, suggesting that it is regulated as the endogenous gene. TGF-beta1 stimulated the transcriptional activity of LTBP-3 promoter in MG-63 cells, while certain other bone-derived growth factors and hormones were ineffective. TGF-beta1 increased LTBP-3 mRNA levels accordingly. Analyses of deletion constructs of the promoter and mutational deletion of specific transcription factor binding sites indicated that Smad3/4 and AP-1 binding sites mediated the TGF-beta1 response. The involvement of AP-1 activity was further indicated by decreased TGF-beta responsiveness of the LTBP-3 promoter in the presence of a MEK/Erk signaling pathway inhibitor. Our results suggest an important new role for TGF-beta1 in the regulation of its binding protein, LTBP-3.

Impaired maturation of myeloid progenitors in mice lacking novel Polycomb group protein MBT-1

Polycomb group (PcG) proteins participate in DNA-binding complexes with gene-repressing activity, many of which have been highlighted for their involvement in hematopoiesis. We have identified a putative PcG protein, termed MBT-1, that is associated with Rnf2, an in vivo interactor of PcG proteins. MBT-1 structurally resembles the H-L(3)MBT protein, whose deletion is predicted to be responsible for myeloid hematopoietic malignancies. The human MBT-1 gene is located on chromosome 6q23, a region frequently deleted in leukemia cells, and shows a transient expression spike in response to maturation-inducing stimuli in myeloid leukemia cells. MBT-1(-/-) myeloid progenitor cells exhibit a maturational deficiency but maintain normal proliferative activities. This results in the accumulation of immature myeloid progenitors and hence, a marked decrease of mature myeloid blood cells, causing the MBT-1(-/-) mice to die of anemia during a late embryonic stage. Together, we conclude that MBT-1 specifically regulates the maturational advancement of myeloid progenitor cells during transitions between two developmental stages. We also show that MBT-1 appears to influence myelopoiesis by transiently enhancing p57(KIP2) expression levels.

Transcription factor expression in B-cell precursor-leukemia cell lines: preferential expression of T-bet

A number of transcription factors (TFs) have been reported that play crucial roles in hematopoiesis. However, only little is known about how these factors are involved in the mechanisms of hematopoietic development and lineage commitment. To investigate the roles of TFs in human B-cell precursors (BCPs), the present study analyzed the expression of the following 16 hematopoietic TFs: AML1, C/EBPalpha, C/EBPbeta, C/EBPgamma, C/EBPepsilon, E2A, Ets-1, GATA-1, GATA-2, GATA-3, Ikaros, IRF-1, Pax5, PU.1, T-bet and TCF-1 in 30 human BCP-leukemia cell lines. All BCP-leukemia cell lines were found to be positive for the expression of AML1, C/EBPgamma, E2A, Ets-1, IRF-1, Pax5 and PU.1 at the mRNA level. The mRNA expression of C/EBPalpha, C/EBPbeta, C/EBPepsilon, GATA-2, Ikaros, T-bet and TCF-1 was detected in 2 to 29 of the cell lines. Eight BCP-cell lines showed positivity for the dominant negative Ikaros isoform Ik6, while others were positive for expression of Ik1, 2, 3 and 4. GATA-1 and GATA-3 were universally negative. The expression of C/EBPalpha, PU.1 and T-bet was positive at the protein level in five, 29 and four out of 30 BCP-cell lines, respectively. Cell lines were stimulated with interleukin (IL)-7 and/or interferon (IFN)-gamma to investigate the regulation of TF expression. T-bet was clearly induced in the two cell lines NALM-19 and NALM-29 after stimulation. C/EBPbeta and IRF-1 were up-regulated in both cell lines and TCF-1 was down-regulated in NALM-19. No significant changes were observed for the other 12 TFs. The present report could provide useful information in the study of the role of TFs on normal and malignant human BCPs.

Association between single nucleotide polymorphisms in deoxycytidine kinase and treatment response among acute myeloid leukaemia patients

Development of resistance to 1-beta-arabinofuranosylcytosine (AraC) is a major obstacle in the treatment of patients with acute myeloid leukaemia (AML). Deficiency of functional deoxycytidine kinase (dCK) plays an important role in AraC resistance in vitro. We screened 5378 bp sequences of the dCK gene, including all exons and the 5' flanking region, and identified two single nucleotide polymorphisms (SNPs) in the regulatory region (rSNPs) with high allele frequencies. These two rSNPs (-201C>T and -360C>G) formed two major haplotypes. Genotyping with sequencing and MassARRAY system among 122 AML patients showed that those with -360CG/-201CT and -360GG/-201TT compound genotypes (n = 41) displayed a favourable response to chemotherapy whereas those with -360CC/-201CC (n = 81) tended to have a poor response (P = 0.025). Moreover, real-time quantitative reverse transcriptase-polymerase chain reaction showed that patients with -360CG/-201CT and -360GG/-201TT genotypes expressed higher level of dCK mRNA compared to those with the -360CC/-201CC genotype (P = 0.0034). Luciferase-reporter assay showed that dCK 5' regulatory region bearing -360G/-201T genotype alone had an eight-fold greater transcriptional activation activity compared to that with -360C/-201C genotype, whereas co-transfection of both -360G/-201T and -360C/-201C constructs mimicked the heterozygous genotype, which exhibited a four-fold greater activity compared to that with -360C/-201C. These results indicate that rSNP haplotypes of dCK gene may serve as a genetic marker for predicting drug responsiveness, which will be beneficial in establishing more effective AML chemotherapeutic regimens.

HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development

Hematopoiesis describes the process of the normal formation and development of blood cells, involving both proliferation and differentiation from stem cells. Abnormalities in this developmental program yield blood cell diseases, such as leukemia. Although, in recent years, extensive molecular research in normal hematopoietic development has characterized transcription factors and their binding sites in the target gene promoters, the information generated is highly fragmented. In order to integrate this important regulatory information with the corresponding genomic sequences, we have developed a new database called Hematopoiesis Promoter Database (HemoPDB). HemoPDB is a comprehensive resource focused on transcriptional regulation during hematopoietic development and associated aberrances that result in malignancy. HemoPDB (version 1.0) contains 246 promoter sequences and 604 experimentally known cis-regulatory elements of 187 different transcription factors, with links to published references. Orthologous promoters from different species are linked with each other and displayed in the same database record, accompanied by a visual image of the promoters and corresponding annotations of cis-regulatory elements. HemoPDB may be searched for the promoter of a specific gene, transcription factors and target genes, and genes that are expressed in a certain cell type or lineage, through a user-friendly web interface at http://bioinformatics.med.ohio-state.edu/HemoPDB. Links to the documentation and other technical details are provided on this website.

Gene-expression profiling of CD34+cells from various hematopoietic stem-cell sources reveals functional differences in stem-cell activity

The replacement of bone marrow (BM) as a conventional source of stem cell (SC) by umbilical cord blood (UCB) and granulocyte-colony stimulating factor-mobilized peripheral blood SC (PBSC) has brought about clinical advantages. However, several studies have demonstrated that UCB CD34(+) cells and PBSC significantly differ from BM CD34(+) cells qualitatively and quantitatively. Here, we quantified the number of SC in purified BM, UCB CD34(+) cells, and CD34(+) PBSC using in vitro and in vivo assays for human hematopoietic SC (HSC) activity. A cobblestone area-forming cell (CAFC) assay showed that UCB CD34(+) cells contained the highest frequency of CAFC(wk6) (3.6- to tenfold higher than BM CD34(+) cells and PBSC, respectively), and the engraftment capacity in vivo by nonobese diabetic/severe combined immunodeficiency repopulation assay was also significantly greater than BM CD34(+), with a higher proportion of CD45(+) cells detected in the recipients at a lower cell dose. To understand the molecular characteristics underlying these functional differences, we performed several DNA microarray experiments using Affymetrix gene chips, containing 12,600 genes. Comparative analysis of gene-expression profiles showed differential expression of 51 genes between BM and UCB CD34(+) SC and 64 genes between BM CD34(+) cells and PBSC. These genes are involved in proliferation, differentiation, apoptosis, and engraftment capacity of SC. Thus, the molecular expression profiles reported here confirmed functional differences observed among the SC sources. Moreover, this report provides new insights to describe the molecular phenotype of CD34(+) HSC and leads to a better understanding of the discrepancy among the SC sources.

Genomic structure of mouse PIR-A6, an activating member of the paired immunoglobulin-like receptor gene family

The gene for one of the activating members of the paired Ig-like receptor family, Pira6, was isolated from a genomic library and sequenced. The first of 9 exons in the approximately 8.2 kb Pira6 gene encodes the 5' untranslated region, the translation initiation site, and approximately half of the signal sequence. The second exon encodes the rest of the signal sequence, exons 3-8 each encode a single Ig-like extracellular domain, and exon 9 encodes the transmembrane region, cytoplasmic tail and 3' UTR with four polyadenylation signals and six mRNA instability sequences. A soluble form of PIR-A6 may be generated by alternative splicing. The exonic sequences account for approximately 42% of the Pira6 gene and approximately 34% for the single inhibitory Pirb gene, thus defining Pira and Pirb as genes with relatively short intronic sequences. Extensive sequence homology was found between Pira6 and Pirb from approximately 2 kb upstream of the ATG initiation site to the beginning of intron 8. The Pir genes appear to be distributed in three regions of the proximal end of chromosome 7 based on the present data and an analysis of currently available mouse genomic sequence databases. One region contains a single Pir gene which is almost identical to Pira6, and the other two contain multiple Pir genes in opposite transcriptional orientations. Potential binding sites for hemopoiesis-specific and ubiquitous transcription factors were identified upstream of the Pira6 transcription start sites that reside within the initiator consensus sequence motif. These results provide important clues to the coordinate regulation observed for PIR-A and PIR-B expression during hematopoiesis.

Cloning and characterization of a proliferation-associated cytokine-inducible protein, CIP29

We identified a novel erythropoietin (Epo)-induced protein (CIP29) in lysates of human UT-7/Epo leukemia cells using two-dimensional gel analysis and cloned its full-length cDNA. CIP29 contains 210 amino acids with a predicted MW of 24 kDa, and has a N-terminal SAP DNA-binding motif. CIP29 expression was higher in cancer and fetal tissues than in normal adult tissues. CIP29 mRNA expression is cytokine regulated in hematopoietic cells, being up-regulated by Epo in UT7/Epo cells, and by thrombopoietin (Tpo), FLT3 ligand (FL) and stem cell factor (SCF) in primary human CD34(+) cells. Up-regulation of CIP29 in UT7/Epo cells by Epo was associated with cell cycle progression but not with antiapoptosis. Epo withdrawal reduced CIP29 expression concomitant with cell cycle arrest. Overexpression of CIP29-GFP in HEK293 cells enhances cell cycle progression. CIP29 appears to be a new cytokine regulated protein involved in normal and cancer cell proliferation.