Determination of genes involved in the process of implantation: application of GeneChip to scan 6500 genes

Dynamic evolution of endogenous retrovirus-derived genes expressed in bovine conceptuses during the period of placentation

In evolution of mammals, some of essential genes for placental development are known to be of retroviral origin, as syncytin-1 derived from an envelope (env) gene of an endogenous retrovirus (ERV) aids in the cell fusion of placenta in humans. Although the placenta serves the same function in all placental mammals, env-derived genes responsible for trophoblast cell fusion and maternal immune tolerance differ among species and remain largely unidentified in the bovine species. To examine env-derived genes playing a role in the bovine placental development comprehensively, we determined the transcriptomic profiles of bovine conceptuses during three crucial windows of implantation periods using a high-throughput sequencer. The sequence reads were mapped into the bovine genome, in which ERV candidates were annotated using RetroTector^© (7,624 and 1,542 for ERV-derived and env-derived genes, respectively). The mapped reads showed that approximately 18% (284 genes) of env-derived genes in the genome were expressed during placenta formation, and approximately 4% (63 genes) were detected for all days examined. We verified three env-derived genes that are expressed in trophoblast cells by polymerase chain reaction. Out of these three, the sequence of env-derived gene with the longest open reading frame (named BERV-P env) was found to show high expression levels in trophoblast cell lines and to be similar to those of syncytin-Car1 genes found in dogs and cats, despite their disparate origins. These results suggest that placentation depends on various retrovirus-derived genes that could have replaced endogenous predecessors during evolution.

Differential gene expression profiling of mouse uterine luminal epithelium during periimplantation

Uterine luminal epithelium (LE) is critical for establishing uterine receptivity. Microarray analysis of gestation day 3.5 (D3.5, preimplantation) and D4.5 (postimplantation) LE from natural pregnant mice identified 382 upregulated and 245 downregulated genes in the D4.5 LE. Gene Ontology annotation grouped 186 upregulated and 103 downregulated genes into 22 and 15 enriched subcategories, respectively, in regulating DNA-dependent transcription, metabolism, cell morphology, ion transport, immune response, apoptosis, signal transduction, and so on. Signaling pathway analysis revealed 99 genes in 21 significantly changed signaling pathways, with 14 of these pathways involved in metabolism. In situ hybridization confirmed the temporal expression of 12 previously uncharacterized genes, including Atp6v0a4, Atp6v0d2, F3, Ggh, Tmprss11d, Tmprss13, Anpep, Fxyd4, Naip5, Npl, Nudt19, and Tpm1 in the periimplantation uterus. This study provides a comprehensive picture of the differentially expressed genes in the periimplantation LE to help understand the molecular mechanism of LE transformation upon establishment of uterine receptivity.

Physiological and molecular determinants of embryo implantation

Embryo implantation involves the intimate interaction between an implantation-competent blastocyst and a receptive uterus, which occurs in a limited time period known as the window of implantation. Emerging evidence shows that defects originating during embryo implantation induce ripple effects with adverse consequences on later gestation events, highlighting the significance of this event for pregnancy success. Although a multitude of cellular events and molecular pathways involved in embryo-uterine crosstalk during implantation have been identified through gene expression studies and genetically engineered mouse models, a comprehensive understanding of the nature of embryo implantation is still missing. This review focuses on recent progress with particular attention to physiological and molecular determinants of blastocyst activation, uterine receptivity, blastocyst attachment and uterine decidualization. A better understanding of underlying mechanisms governing embryo implantation should generate new strategies to rectify implantation failure and improve pregnancy rates in women.

Cystathionine β-synthase deficiency causes infertility by impairing decidualization and gene expression networks in uterus implantation sites

Hyperhomocysteinemia has been reported in human reproduction as a risk factor for early pregnancy loss, preeclampsia, and congenital birth defects like spina bifida. Female infertility was also observed in cystathionine beta synthase-deficient mice ( Cbs-KO) as an animal model for severe hyperhomocysteinemia. The aim for the present research was to elucidate the time-point of pregnancy loss and to pinpoint gene and cellular changes involved in the underlying pathological mechanism. By mating 90-day-old wild-type and Cbs-KO female mice with their homologous male partners, we found that pregnancy loss in Cbs-KO occurred between the 8th and 12th gestation day during placenta formation. DNA microarrays were carried out on uterus from implantation and interimplantation samples obtained on day 8. The results allowed us to select genes potentially involved in embryo death; these were individually confirmed by RT-qPCR, and their expressions were also followed throughout pregnancy. We found that changes in expression of Calb1, Ttr, Expi, Inmt, Spink3, Rpgrip1, Krt15, Mt-4, Gzmc, Gzmb, Tdo2, and Afp were important for pregnancy success, since a different regulation in Cbs-KO mice was found. Also, differences in relationships among selected genes were observed, indicating a dysregulation of these genes in Cbs-KO females. In conclusion, our data provide more information on the gene expression cascade and its timely regulated process required for a successful pregnancy. In addition, we unveil new potential avenues to explore further investigations in pregnancy loss.

Gene expression profiling of mouse aborted uterus induced by lipopolysac charide

To identify genes that participate in the abortion process, normal pregnant uteri were compared to lipopolysaccharide (LPS)-induced abortion uteri. At day 6 of pregnancy, mice were treated with LPS at various time points to induce an abortion. Total RNAs were applied to a cDNA microarray to analyze genes with altered expression. At the early stage (2 hours) of LPS-induced abortion, upregulated genes were mainly composed of immune responsive genes, including Ccl4, Ccl2, Cxcl13, Gbp3, Gbp2, Mx2, H2-Eb1, Irf1 and Ifi203. Genes related to toll-like receptor signaling were also overexpressed. At late stages of abortion (12-24 hours), many genes were suppressed rather than activated, and these were mainly related to the extracellular matrix, cytoskeleton, and anti-apoptosis. Altered expression of several selected genes was confirmed by real time reverse transcription-polymerase chain reaction. The results demonstrated that many known genes were altered in the LPS-treated pregnant uterus, implying that the molecular mechanisms of the genes involved in LPS-induced abortion are complicated. Further analysis of this expression profile will help our understanding of the pathophysiological basis for abortion.

The postimplantation embryo differentially regulates endometrial gene expression and decidualization

Transcriptomal changes in the uterine endometrium induced in response to the implanting embryo remain largely unknown. In this study, using Affymetrix mRNA expression microarray analysis, we identified genes differentially expressed in the murine endometrium in the presence or absence of the embryo. Compared with the pseudopregnant deciduoma induced by a mechanical stimulus in the absence of an embryo, approximately 1500 genes (753 up-regulated, 686 down-regulated; P < 0.05) were differentially expressed by at least 1.2-fold in the uterine decidua of pregnancy. Most of these genes fall into five major biological categories that include binding (45%), catalysis (24%), signal transduction (10%), transcriptional regulators (5%), and transporters (5%). This strong, embryo-induced transcriptomal impact represented approximately 10% of the total number of genes expressed in the decidualizing endometrium. Validation studies with mRNA and protein confirmed existence of the phylogenetically conserved, embryo-regulated genes involved in the following: 1) hemostasis and inflammation; 2) interferon signaling; 3) tissue growth and remodeling; and 4) natural killer cell function. Interestingly, whereas expression of many growth factors and their cognate receptors were not different between the decidual and deciduomal endometria, a number of proteases that degrade growth factors were selectively up-regulated in the decidual tissue. Increased expression of IGF and activin A neutralizing factors (i.e. HtrA1 and Fstl3) correlated with reduced stromal cell mitosis, tissue growth, and mitogenic signaling in the decidual endometrium. These results support the hypothesis that the implanting murine embryo takes a proactive role in modulating endometrial gene expression and development during early gestation.

Evidence for the immunostimulatory effects of low-dose orally delivered human IFN-alpha in cattle

Orally delivered interferon-alpha (IFN-alpha) has been associated with systemic protection against various disorders in humans and animals. In an attempt to understand how IFN-alpha delivers a systemic signal following its local oral administration, the present study aimed at identifying genes differentially regulated in bovine peripheral blood through the use of cDNA microarrays following oral therapy with IFN-alpha. We identified thousands of genes to be IFN-alpha regulated. Of these, about 8.5% had a minimum 4-fold degree of change, the majority of which represented novel IFN-stimulated genes (ISG). Several upregulated ISGs were transcripts with key and diverse biologic functions, including antigen processing and presentation, leukocyte migration, lymphocyte activation, immune effector and modulation functions, apoptosis, and hematopoiesis. Interestingly, IFN-alpha expression itself was not modulated in bovine peripheral blood, suggesting that the blood levels of IFN-alpha are not the hallmark of the immunostimulatory effects of oral IFN-alpha therapy. Rather, IFN-alpha seems to interact with local mucosal lymphoid cells in the gastrointestinal tract. This interaction may initiate a signaling cascade eventually leading to the transcriptional induction of ISGs, which in turn encode immunostimulatoiry proteins. Thus, ISGs, through the proteins they encode, may potentially perform critical immune modulation functions.

Analysis of uteroplacental-specific molecules and their functions during implantation and placentation in the bovine

In cattle, the mechanisms underlying implantation and placental development are still unclear. Synepitheliochorial placentation in cattle is noninvasive, and thus generates limited interest in terms of degradation and remodeling of endometrial tissues. The overall purpose of this study was three-fold: (1) to examine the gene circuitry around the implantation window, (2) to understand development of the placenta during the peri-implantation period by using a uteroplacental cDNA microarray, and (3) to study the roles of molecules involved in endometrial remodeling. Bovine trophoblastic binucleate cell-specific molecules, such as pregnancy-associated glycoproteins (PAGs), placental lactogen (PL), and prolactin-related proteins (PRPs), were markedly expressed in binucleate cells (BNCs) around implantation. The expression of PRP-1 was specific to the caruncular (CAR) area of the gravid uterine horn. Gelatinases (MMP-2 and -9) in association with heparanase may be central to endometrial remodeling. In situ hybridization analyses of PAGs, PRPs, PL, and heparanase suggested that BNCs expressed these molecules simultaneously. Future studies will further investigate the specific roles of these molecules in placentogenesis. The uteroplacental cDNA microarray presented cascades of molecular signatures not only for the endometrium but also for the intricate dialogue at the level of the feto-maternal interface in cattle. Placentome morphogenesis potentially parallels the dynamic multigenic circuitry and regulates the cell cycle in the endometrium. The roles of BNCs and their secreted molecules remain an enigma, particularly with regard to the adhesion process and endometrial remodeling, which is the focus of this study.

Gene expression and maintenance of pregnancy in bovine: roles of trophoblastic binucleate cell-specific molecules

Cell to cell interaction plays a pivotal role in the regulation of placentogenesis and exchange of stage-specific developmental signals between the fetal and maternal units. Specifically, these interactions are paramount for programmed fetal growth, maternal adaptation to pregnancy and coordination of parturition. However, little is known about the precise regulation of placentation and maintenance of gestation in cattle. Therefore, the aim of the present study was to decipher the complex networks of cell communication to gain an insight into the multifaceted developmental process and understand the profound consequences of flawed communication. In the ruminant, the binucleate cell plays a central role in forming the structures and secretions at the fetomaternal interface that are crucial in establishing and maintaining pregnancy. Herein, we summarise differences in the abundance of specific RNA transcripts in the bovine cotyledon and caruncle using global gene expression profiling and further investigate the relationship of mRNA abundance for selected pregnancy-specific genes of interest (identified from microarray studies) that are localised exclusively to the binucleate cell, such as placental lactogen, prolactin-related proteins and pregnancy-associated glycoproteins. The results suggest that a well-orchestrated transcriptional command from binucleate cells is pivotal to the establishment and progression of pregnancy in cattle.

Molecular mechanisms involved in progesterone receptor regulation of uterine function

The ovarian steroid hormone progesterone is a major regulator of uterine function. The actions of this hormone is mediated through its cognate receptor, the progesterone receptor, Pgr. Ablation of the Pgr has shown that this receptor is critical for all female reproductive functions including the ability of the uterus to support and maintain the development of the implanting mouse embryo. High density DNA microarray analysis has identified direct and indirect targets of Pgr action. One of the targets of Pgr action is a member of the Hedgehog morphogen Indian Hedgehog, Ihh. Ihh and members of the Hh signaling cascade show a coordinate expression pattern in the mouse uterus during the preimplantation period of pregnancy. The expression of Ihh and its receptor Patched-1, Ptc1, as well as, down stream targets of Ihh-Ptch1 signaling, such as the orphan nuclear receptor COUP-TF II show that this morphogen pathway mediates communication between the uterine epithelial and stromal compartments. The members of the Ihh signaling axis may function to coordinate the proliferation, vascularization and differentiation of the uterine stroma during pregnancy. This analysis demonstrates that progesterone regulates uterine function in the mouse by coordinating the signals from the uterine epithelium to stroma in the preimplantation mouse uterus.

Effects of urinary and recombinant gonadotrophins on gene expression profiles during the murine peri-implantation period

BACKGROUND

Controlled ovarian stimulation (COS) with urinary gonadotrophins but not recombinant gonadotrophins, adversely affect the implantation process. In this study, we investigated the effects of urinary and recombinant gonadotrophins on gene expression profiles at implantation sites during the mouse peri-implantation period and the possible molecular mechanisms involved in the detrimental effects of urinary gonadotrophins using microarray technology.

METHODS

Adult female CD1 mice were treated with (i) urinary human FSH (hFSH) and urinary HCG, (ii) recombinant hFSH and recombinant human LH or (iii) saline. Gene expression profiling with GeneChip mouse genome 430 2.0 arrays, containing 45 101 probe sets, was performed using implantation sites on embryonic day 5. Data were statistically analysed using Significance Analysis of Microarrays. Ten genes from the microarray analysis were selected for validation using quantitative RT-PCR (qRT-PCR). A parallel group of pregnant mice was allowed to give birth to study the effect of gonadotrophins on resorption.

RESULTS

Urinary gonadotrophins differentially up-regulated the expression of 30 genes, increased resorption and reduced litter size, whereas recombinant gonadotrophins did not. Nine of the 10 genes were confirmed by qRT-PCR.

CONCLUSIONS

Urinary gonadotrophins, but not recombinant gonadotrophins, exerted differential effects on gene expression during the murine peri-implantation period. These findings might contribute to improve protocols for COS, leading to higher successful pregnancy rates.

Decidual stromal cell response to paracrine signals from the trophoblast: amplification of immune and angiogenic modulators

During the invasive phase of implantation, trophoblasts and maternal decidual stromal cells secrete products that regulate trophoblast differentiation and migration into the maternal endometrium. Paracrine interactions between the extravillous trophoblast and the maternal decidua are important for successful embryonic implantation, including establishing the placental vasculature, anchoring the placenta to the uterine wall, and promoting the immunoacceptance of the fetal allograph. To our knowledge, global crosstalk between the trophoblast and the decidua has not been elucidated to date, and the present study used a functional genomics approach to investigate these paracrine interactions. Human endometrial stromal cells were decidualized with progesterone and further treated with conditioned media from human trophoblasts (TCM) or, as a control, with control conditioned media (CCM) from nondecidualized stromal cells for 0, 3, and 12 h. Total RNA was isolated and processed for analysis on whole-genome, high-density oligonucleotide arrays containing 54,600 genes. We found that 1374 genes were significantly upregulated and that 3443 genes were significantly downregulated after 12 h of coincubation of stromal cells with TCM, compared to CCM. Among the most upregulated genes were the chemokines CXCL1 (GRO1) and IL8,CXCR4, and other genes involved in the immune response (CCL8 [SCYA8], pentraxin 3 (PTX3), IL6, and interferon-regulated and -related genes) as well as TNFAIP6 (tumor necrosis factor alpha-induced protein 6) and metalloproteinases (MMP1, MMP10, and MMP14). Among the downregulated genes were growth factors, e.g., IGF1, FGF1, TGFB1, and angiopoietin-1, and genes involved in Wnt signaling (WNT4 and FZD). Real-time RT-PCR and ELISAs, as well as immunohistochemical analysis of human placental bed specimens, confirmed these data for representative genes of both up- and downregulated groups. The data demonstrate a significant induction of proinflammatory cytokines and chemokines, as well as angiogenic/static factors in decidualized endometrial stromal cells in response to trophoblast-secreted products. The data suggest that the trophoblast acts to alter the local immune environment of the decidua to facilitate the process of implantation and ensure an enriched cytokine/chemokine environment while limiting the mitotic activity of the stromal cells during the invasive phase of implantation.

Wide genomic analysis of human endometrial receptivity: new times, new opportunities

Microarray technology has broadened the insight into many research fields allowing scientists to analyse the expression of many genes in quick and efficient experiments aimed at translating these findings into clinical applications. In reproductive medicine, researchers have exploited microarrays to increase understanding of the molecular mechanisms involved in endometrial receptivity and how a possible therapeutic translation can be feasible. In the last 4 years, several studies have focused on the genomics of the human endometrium in different physiological and pathological conditions, and these studies have generated a large amount of information about the regulation and dysregulation of the window of implantation (WOI) genes in fertile, subfertile and refractory conditions. However, the key molecules/mechanisms in endometrial receptivity remain to be elucidated. In this comprehensive review, we have analysed the available results obtained in our own and other laboratories, defining the genomic profile of the receptive endometrium in different situations and its possible clinical application.

Large-scale gene expression studies of the endometrium: what have we learnt?

The endometrium is a dynamic tissue that undergoes coordinated changes under the influence of steroid hormones. This results in proliferation and differentiation culminating in a receptive state, followed by menstruation and endometrial repair. These functions involve complex interactions between the epithelium, stroma and leucocytes in the endometrium. Understanding the underlying causes of endometrial disorders, such as infertility, endometriosis and heavy menstrual bleeding, therefore represents a considerable challenge. Recently developed techniques, such as differential display and DNA microarrays permit the abundance of thousands of mRNA transcripts within cells or tissues to be measured simultaneously. This provides a new approach to understanding the complex interactions that underlie both healthy and disease states. Responses of the endometrium to hormones or drugs can be studied and the response of the system as an integrated whole can be assessed. Comparisons of endometrium from healthy women and those with endometrial dysfunction have advanced our understanding of key areas of endometrial physiology, including infertility, receptivity, endometriosis and cancer. Using this approach, novel genes controlling specific endometrial functions like receptivity have been identified for functional testing. This paper will review the impact of these techniques for transcript profiling on our understanding of selected areas of endometrial biology and discuss the potential applications in future.

Mining the mouse transcriptome of receptive endometrium reveals distinct molecular signatures for the luminal and glandular epithelium

Epithelia coat most tissues where they sense and respond to the environment and participate in innate immune responses. In the adult mouse uterus, columnar epithelium lines the central lumen and the glands that penetrate the underlying stroma. A nidatory surge of estrogen causes differentiation of the luminal epithelium to the receptive state that permits blastocyst attachment and allows subsequent implantation. Here, using laser-capture microdissection to isolate the luminal and glandular epithelia separately, we have profiled gene expression 2 h before embryo attachment to determine whether there are unique roles for these two epithelial structures in this process. Although most genes were expressed in both compartments, there was greater expression of 153 and 118 genes in the lumen and glands, respectively. In the luminal epithelium, there is enrichment in lipid, metal-ion binding, and carbohydrate-metabolizing enzymes, whereas in the glands, immune response genes are emphasized. In situ hybridization to uterine sections obtained from mice during the preimplantation period validated these data and indicated an array of previously undocumented genes expressed with unique patterns in these epithelia. The data show that each epithelial compartment has a distinct molecular signature and that they act differentially and synergistically to permit blastocyst implantation.

Monozygotic Twin Model Reveals Novel Embryo-Induced Transcriptome Changes of Bovine Endometrium in the Preattachment Period1

Initiation and maintenance of pregnancy are critically dependent on an intact embryo-maternal communication in the preimplantation period. To get new insights into molecular mechanisms underlying this complex dialog, a holistic transcriptome study of endometrium samples from Day 18 pregnant vs. nonpregnant twin cows was performed. This genetically defined model system facilitated the identification of specific conceptus-induced changes of the endometrium transcriptome. Using a combination of subtracted cDNA libraries and cDNA array hybridization, 87 different genes were identified as upregulated in pregnant animals. Almost one half of these genes are known to be stimulated by type I interferons. For the ISG15ylation system, which is assumed to play an important role in interferon tau (IFNT) signaling, mRNAs of four potential components (IFITM1, IFITM3, HSXIAPAF1, and DTX3L) were found at increased levels in addition to ISG15 and UBE1L. These results were further substantiated by colocalization of these mRNAs in the endometrium of pregnant animals shown by in situ hybridization. A functional classification of the identified genes revealed several different biological processes involved in the preparation of the endometrium for the attachment and implantation of the embryo. Specifically, elevated transcript levels were found for genes involved in modulation of the maternal immune system, genes relevant for cell adhesion, and for remodeling of the endometrium. This first systematic study of maternal transcriptome changes in response to the presence of an embryo on Day 18 of pregnancy in cattle is an important step toward deciphering the embryo-maternal dialog using a systems biology approach.

Serial analysis of gene expression in mouse uterus at the implantation site

Although oligonucleotide chips, cDNA microarrays, differential display reverse transcription-PCR, and other approaches have been used to screen implantation-related molecules, the mechanism by which embryo implantation occurs is still unknown. The aim of this study was to profile the differential gene expression between interimplantation site and implantation site in mouse uterus on day 5 of pregnancy by serial analysis of gene expression (SAGE). In our two SAGE libraries of 11-bp tags, the total numbers of tags sequenced were 48,121 for the interimplantation site and 50,227 for the implantation site. There were 1,039 tags specifically expressed at interimplantation site, and 1,252 tags specifically expressed at the implantation site. Based on the p value, there were 195 tags significantly up-regulated at the interimplantation site and 261 tags significantly up-regulated at the implantation site, of which 100 genes were single matched at the interimplantation site and 127 genes were single matched at the implantation site, respectively. By reverse transcription-PCR, the tag ratio between the implantation site and interimplantation site was verified on 14 significantly changed genes. Using in situ hybridization, 1810014L12Rik, Psmb5, Cd63, Npm1, Fads3, and Tagln2 were shown to be highly expressed at the implantation site compared with the interimplantation site. Compared with the interimplantation site, Ddx39 was strongly expressed in the subluminal stromal cells at the implantation site on day 5 of pregnancy. Ddx39 expression at the implantation site was specifically induced by active blastocysts. Additionally, Ddx39 expression was significantly up-regulated by estrogen in the ovariectomized mice. In our SAGE data, many implantation-related genes were identified in mouse uterus. Our data could be a valuable source for future study on embryo implantation.

A guide to issues in microarray analysis: application to endometrial biology

Within the last decade, the development of DNA microarray technology has enabled the simultaneous measurement of thousands of gene transcripts in a biological sample. Conducting a microarray study is a multi-step process; starting with a well-defined biological question, moving through experimental design, target RNA preparation, microarray hybridisation, image acquisition and data analysis – finishing with a biological interpretation requiring further study. Advances continue to be made in microarray quality and methods of statistical analysis, improving the reliability and therefore appeal of microarray analysis for a wide range of biological questions. The purpose of this review is to provide both an introduction to microarray methodology, as well as a practical guide to the use of microarrays for gene expression analysis, using endometrial biology as an example of the applications of this technology. While recommendations are based on previous experience in our laboratory, this review also summarises the methods currently considered to be best practice in the field.

Amplicon secondary structure prevents target hybridization to oligonucleotide microarrays

DNA microarrays that are used as end-point detectors for PCR assays are typically composed of short (15-25 mer) oligonucleotide probes bound to glass. When designing these detectors, we have frequently encountered situations where a probe would not hybridize to its complementary, terminally labeled PCR amplicon. To determine if failures could be explained by general phenomenon such as secondary structure, we designed a microarray to detect eight regions of the Escherichia coli 16S rDNA gene. We then amplified eight amplicons of different lengths using a biotin conjugated, antisense primer. Amplicons were then hybridized to the microarray and detected using a combination of signal amplification and fluorescence. In most cases, probe sequences complementary to the 5' region of the amplified products (sense orientation) did not hybridize to their respective amplicon. We tested for positional bias and showed that a biotin conjugated sense primer mirrored the same probe failures. Nick translated products, however, hybridized to all probes. Because nick translation generates many labeled fragments of random length, we concluded that this method disrupted secondary structure that otherwise prevented the amplicons from hybridizing to their respective probes. We also show that nick translation does not compromise detector sensitivity even when used with long PCR amplicons (ca. 1.5 kbp). Despite the increased cost of the nick translation, we concluded that this labeling strategy will reduce the time needed to design new assays as well as avoid possible false negatives during field applications. Alternative labeling strategies are also discussed.

Gene expression profiling during the embryonic development of mouse brain using an oligonucleotide-based microarray system

We analyzed gene expression profiles in embryonic day 12, 15, 18 and postnatal day 0 mouse brains by utilizing a GeneChip microarray. Significant differential expression was observed in 1413 of 12,422 (11.4%) represented on the chip. Then, 397 genes known to be related to neural development and functions were selected and analyzed in more detail. Clustering of the differentially expressed genes in terms of gene function and their temporal expression patterns indicated an aspect of the genetic foundation that underlies cellular events. Moreover, we identified a novel gene that encodes a putative protein kinase, Ebr kinase, which is differentially expressed in the developing brain.

Uterine extracellular matrix components are altered during defective decidualization in interleukin-11 receptor alpha deficient mice

BACKGROUND

Implantation of the embryo and successful pregnancy are dependent on the differentiation of endometrial stromal cells into decidual cells. Female interleukin-11 receptor alpha (IL-11Ralpha) deficient mice are infertile due to disrupted decidualization, suggesting a critical role for IL-11 and its target genes in implantation. The molecular targets of IL-11 in the uterus are unknown, but it is likely that IL-11 signaling modifies the expression of other genes important in decidualization. This study aimed to identify genes regulated by IL-11 during decidualization in mouse uterus, and to examine their expression and localization as an indication of functional significance during early pregnancy.

METHODS

Decidualization was artificially induced in pseudopregnant wild type (IL11Ra+/+) and IL-11Ralpha deficient (IL11Ra-/-) littermates by oil injection into the uterine lumen, and gene expression analyzed by NIA 15K cDNA microarray analysis at subsequent time points. Quantitative real-time RT-PCR was used as an alternative mRNA quantitation method and the expression and cellular localization of the protein products was examined by immunohistochemistry.

RESULTS

Among 15,247 DNA probes, 13 showed increased and 4 decreased expression in IL11Ra-/- uterus at 48 h of decidualization. These included 4 genes encoding extracellular matrix proteins; collagen III alpha1, secreted acidic cysteine-rich glycoprotein (SPARC), biglycan and nidogen-1 (entactin). Immunohistochemistry confirmed increased collagen III and biglycan protein expression in IL11Ra-/- uterus at this time. In both IL11Ra-/- and wild type uterus, collagen III and biglycan were primarily localized to the outer connective tissue and smooth muscle cells of the myometrium, with diffuse staining in the cytoplasm of decidualized stromal cells.

CONCLUSION

These data suggest that IL-11 regulates changes in the uterine extracellular matrix that are necessary for decidualization.

Alteration of the timing of implantation by in vivo gene transfer: delay of implantation by suppression of nuclear factor kappaB activity and partial rescue by leukemia inhibitory factor

Nuclear factor kappaB (NF-kappaB) is activated in the murine endometrium during implantation period [Am. J. Reprod. Immunol. 51 (2004) 16]. Transient transfection of IkappaBalpha mutant (IkappaBalphaM) cDNA into the mouse uterine cavity using hemagglutinating virus of Japan envelope vector suppressed uterine NF-kappaB activity less than half of that observed in control on days 3.5 and 4.5 p.c. IkappaBalphaM cDNA transfection led to significant delay of implantation. After IkappaBalphaM cDNA transfection, LIF mRNA expression in the uterus was significantly suppressed on days 3.5 and 4.5 p.c. Co-transfection of LIF cDNA with IkappaBalphaM cDNA in the uterus partially rescued the delay of implantation induced by suppression of NF-kappaB activity. Taken together, these findings indicate that NF-kappaB activation determines the timing of the implantation, at least in part, via control of LIF expression.

Use of DNA array to screen blastocyst genes potentially involved in the process of murine implantation

Conceptus implantation to the mother's uterus is a complex series of events involving coordinated expression of numerous genes at both the embryonic and the uterine sides. Since there are no suitable in vivo or in vitro experimental models, sequential changes occurring during the peri-implantation periods have not been well characterized. Using GeneChip technology and a recently introduced murine in vitro model of implantation, the expression of embryonic genes was examined before and after attachment to the uterine stromal cells. Instead of RNA or mRNA, amplified cRNA was subjected to the GeneChip analysis because amounts of mRNA in each blastocyst were minimal. Among 6,500 gene transcripts examined, changes in mRNA levels for 802 genes were identified. Of these detections, transcripts previously unsuspected were changes in a group of tumor suppressor and stress-induced genes, whose transcripts increased as embryos attached to the membrane. Validity of the data was evaluated using reverse transcription-polymerase chain reaction and in situ hybridization analyses, both of which confirmed developmental changes in selected gene expressions during pre- and post-attachment periods. The present data suggest that GeneChip technology would be very useful for finding genes previously unsuspected, and this method should be used as an initial step, particularly as a screening tool, toward the dissection of complex mechanisms such as the processes of implantation.

Molecular cues to implantation

Successful implantation is the result of reciprocal interactions between the implantation-competent blastocyst and receptive uterus. Although various cellular aspects and molecular pathways of this dialogue have been identified, a comprehensive understanding of the implantation process is still missing. The receptive state of the uterus, which lasts for a limited period, is defined as the time when the uterine environment is conducive to blastocyst acceptance and implantation. A better understanding of the molecular signals that regulate uterine receptivity and implantation competency of the blastocyst is of clinical relevance because unraveling the nature of these signals may lead to strategies to correct implantation failure and improve pregnancy rates. Gene expression studies and genetically engineered mouse models have provided valuable clues to the implantation process with respect to specific growth factors, cytokines, lipid mediators, adhesion molecules, and transcription factors. However, a staggering amount of information from microarray experiments is also being generated at a rapid pace. If properly annotated and explored, this information will expand our knowledge regarding yet-to-be-identified unique, complementary, and/or redundant molecular pathways in implantation. It is hoped that the forthcoming information will generate new ideas and concepts for a process that is essential for maintaining procreation and solving major reproductive health issues in women.

Determination of Genes Involved in the Early Process of Embryonic Implantation in Rhesus Monkey (Macaca mulatta) by Suppression Subtractive Hybridization1

Embryonic implantation is a temporally and spatially restricted process that involves a precise cross talk between the embryo and the receptive maternal endometrium. Underlying the complex changes in the uterus during implantation is the alteration in gene expression pattern, which is not fully understood for the primates. In the present study, suppression subtractive hybridization (SSH) was performed to screen genes that were differentially expressed in the implantation site of the pregnant rhesus monkey, and a subtractive cDNA library was constructed. Furthermore, with dot blot analysis, reverse Northern blot analysis, and semiquantitative reverse transcription-polymerase chain reaction, 76 of 376 clones randomly selected from the library were proven to be differentially expressed in the implantation site. With DNA sequencing and BLAST analysis against the GenBank/EMBL database, it was demonstrated that the cDNA fragments carried by 73 clones shared high homology with 31 human genes. Among them, 15 positive clones represented the S100A10 gene and 10 positive ones corresponded with the secreted frizzled-related protein 4 gene. The other two clones shared homology with one human EST. There was one clone homologous to a human DNA sequence, which indicated that it might be a novel gene. To our knowledge, this is the first report to determine genes involved in the early implantation stage in the rhesus monkey with high throughput technology.

A molecular basis for embryo apposition at the luminal epithelium

To obtain a gene expression profile during embryo apposition to the luminal epithelium, we isolated mouse luminal epithelium from implantation (IM) and interimplantation (INTER) sites using laser capture microdissection (LCM), and analyzed their gene expression by microarray analysis. IM and INTER sites were sampled on day 4.5 after mating of female mice with fertile males (day 0.5 = vaginal plug). RNA was extracted, amplified, labeled, and hybridized to microarrays and results were analyzed using the significance analysis of microarrays (SAM) method. Comparison of IM and INTER sites by SAM identified 73 genes most highly ranked at IM, while 13 genes most highly expressed at the INTER sites, within the estimated false discovery rate (FDR) of 0.163. Among 73 genes at IM, 20 were ESTs or were of unknown function, and the remain 53 genes had known functions mainly relating to cellular structuring and others such as cell cycling, gene/protein expression, immune responses, invasion, metabolism, oxidative stress, or signal transduction. Specifically, of the 24 structural genes, 14 were implicated in extracellular matrix and tissue remodeling. Meanwhile, of the 13 genes that were highly expressed at INTER, eight were ESTs or of unknown function, and the remaining five were implicated in metabolism, signal transduction, and gene/protein expression. Among these 58 (53 + 5) genes with known functions, 13 genes (22.4%) were associated with Ca2+ for their function. Results of the present study suggest that (1) at IM sites, active tissue remodeling is occurring for embryo invasion while the INTER sites are relatively quiescent and (2) Ca2+ may be a vital regulatory factor in the apposition process. Investigations of human homologues of those genes expressed in the mouse luminal epithelium during apposition may help to understand the implantation process and/or implantation failure in humans.

NF-κB Activation at Implantation Window of the Mouse Uterus

PROBLEM

Nuclear factor kappa B (NF-kappaB) is one candidate transcriptional modulator, which might regulate many kinds of molecules that play sequential roles at implantation in the endometrium. However, temporal and spatial activation of NF-kappaB at implantation window is unknown.

METHODS

Activation of NF-kappaB in the mouse uterus was determined by electrophoretic mobility shift assays. Localization of p50 and p65, components of NF-kappaB, was analyzed by immunohistochemistry.

RESULTS

NF-kappaB was activated in the proestrus and estrus phases in non-pregnant uterus. In the pregnant uterus, NF-kappaB was activated after day 1.5 post-coitum, and the activation continued during implantation period. The immunoreactivities of p50 and p65 were mainly localized in endometrial epithelium, and were weaker in endometrial stroma cells.

CONCLUSION

NF-kappaB activity is dynamically regulated during the sexual cycle as well as during the implantation period in the endometrium, where the biochemical interaction between mother and conceptus first occurs.

Microarray Expression Profiling Reveals Candidate Genes for Human Uterine Receptivity

The endometrium undergoes cyclic changes in response to circulating ovarian steroid hormones as it prepares for implantation. This dynamic tissue is well suited to microarray expression profiling for elucidation of molecular players participating in the maturation of the endometrium and during the process of implantation. Recent advances in sequencing the human and mouse genomes and the availability of microarray technology and bioinformatic analyses have made elucidating these molecular participants and dialogs a reality. Analysis of the window of implantation, a temporal and spatially unique period in which the endometrium is receptive to embryonic implantation, has revealed numerous processes to be occurring simultaneously or sequentially. These include cell cycle regulation, angiogenesis, immune modulation of implantation, defense mechanisms put into place by antibacterial agents and detoxicants, secretion of unique products, transport of ions and water, growth factor actions, steroid hormone action and metabolism, and production of extracellular matrix proteins, unique cell surface glycoproteins, and a variety of transcription factors, to name a few. Several groups have recently conducted studies with human endometrium, and remarkable similarities exist with mouse. Also, many genes and gene families involved in the unique differentiation process of stromal cell decidualization are conserved. In addition, infertility associated with endometriosis is partly implantation-based, and gene profiling of such tissue during the window of implantation has revealed additional insight into mechanisms underlying infertility in this disorder. Global profiling of genes in the endometrium, decidua, and at the interface between the trophoblast and the decidua, has provided remarkable in sight into endometrial maturation and implantation.

Immune-responsive gene 1 is a novel target of progesterone receptor and plays a critical role during implantation in the mouse

The steroid hormone progesterone (P) is a critical regulator of uterine receptivity during blastocyst implantation. The hormone acts through nuclear P receptors (PRs) to modulate the expression of specific gene networks in various uterine cell types. To identify the P-regulated pathways underlying uterine receptivity, we previously used oligonucleotide microarrays to analyze uterine mRNA profiles at the time of implantation in response to RU486, a PR antagonist. We reported that the mRNA corresponding to the immune-responsive gene 1 (Irg1), a previously described lipopolysaccharide-inducible gene, is one of the several mRNAs that are markedly down-regulated by RU486 in the preimplantation uterus. In the present study, we performed in situ hybridization to show that P stimulates Irg1 mRNA synthesis in the luminal epithelial cells of uteri of ovariectomized wild-type but not PR knockout mice. We also report that Irg1 mRNA was induced in the luminal epithelium of pregnant uterus between d 3 and 5, overlapping the window of implantation. To investigate the function of Irg1 during implantation, we administered sense or antisense oligodeoxynucleotides into preimplantation mouse uteri. Treatment with antisense oligodeoxynucleotides led to suppression in Irg1 mRNA expression without affecting unrelated mRNAs in the pregnant uterus. This intervention was also accompanied by impairment in embryo implantation, indicating that the phenotype is linked to the suppression of Irg1 mRNA. Collectively, our studies identified Irg1 as a novel target of PR in the pregnant uterus and also revealed that it is a critical regulator of the early events leading to implantation.

Characterization of gene expression profiles in early bovine pregnancy using a custom cDNA microarray

Gene expression analysis comparing nonpregnant with pregnant bovine uteri, including placenta, was performed with a custom cDNA microarray containing 1,933 independent genes. These genes were classified into six categories according to biological function, as follows: cell and tissue structural dynamics (108 genes), intercellular communication (221), intracellular metabolism (265), cell cycle and apoptosis (26), regulation of gene expression (113), expressed sequence tag (EST) and function unknown (617), and uncomplemented genes (583 clones). This array possessed bovine placental/endometrial specificity, as it included many pregnancy-specific molecules, such as pregnancy-associated glycoprotein-1 (PAGs), placental lactogen (PLs), and prolactin-related protein-1 (PRPs). A total of 77 genes were induced and 12 repressed in the placenta/endometrium. Our results point to a fundamental role for bovine placental-specific genes such as PAGs, PLs, and PRPs, in implantation and placentogenesis, and document that cDNA microarray analysis from bovine placenta/endometrium is possible and is a specific tool for monitoring genome-wide gene expression during the establishment and maintenance of pregnancy.

Enhanced expression of uterine stathmin during the process of implantation and decidualization in rats

We used the library subtraction technique to identify genes specifically expressed in the rat uterus during early pregnancy. One such gene was that for stathmin, a factor that is associated with tubulin binding and the destabilization of microtubules. Stathmin was expressed at higher levels in implantation sites than in interimplantation sites on d 6 and 7 of pregnancy; the levels on d 6 and 7 were higher in implantation sites than in the entire uterus on d 3-5 of pregnancy or in nonpregnant uteri. Intense expression of stathmin mRNA was primarily limited to the subluminal stromal cells at the implantation site. Expression was also detected in the decidual zones and was accentuated during the period of decidualization (d 7-12). In the delayed implantation pregnant rat model, uterine stathmin expression was low, but increased after implantation induced by administration of 17beta-estradiol to the progesterone-primed animal. Further, decidualization in the pseudopregnant rat, induced by intrauterine infusion of oil, enhanced stathmin expression. Stathmin expression clearly increases in the uterus when stimulated by embryo implantation and decidualization and may play a role in the early stages of pregnancy.

Aquaporin water channel genes are differentially expressed and regulated by ovarian steroids during the periimplantation period in the mouse

The periimplantation period is marked by edematous changes in the uterus. In the mouse, increased uterine vascular permeability occurs in response to estrogen and certain vasoactive mediators, but the mechanisms that regulate fluid transport during implantation are not fully understood. Aquaporins (AQPs) are a family of membrane channel proteins that facilitate bulk water transport. To assess their role in implantation, we examined the expression of AQPs 0-9 in the mouse uterus on d 1-8 of pregnancy. Our results show distinct uterine expression patterns for AQP1, AQP4, and AQP5. AQP1 is localized to the inner circular myometrium throughout the periimplantation period. AQP4 is highly expressed in the luminal epithelium on d 1 of pregnancy but barely detectable at the time of implantation. AQP5 is expressed at low levels in the glandular epithelium during early pregnancy but is markedly increased on d 5. By immunohistochemistry, AQP5 is localized in the basolateral region of the uterine glands. Treatment of adult ovariectomized mice with replacement steroids demonstrates an estrogen-induced shift in AQP1 signals from the myometrium to the uterine stromal vasculature, suggesting a role in uterine fluid imbibition. In contrast, AQP5 is induced only in estrogen-treated, progesterone-primed uteri. We also observed expression of AQP8 in the inner-cell mass and AQP9 in the mural trophectoderm of the implanting blastocyst. Collectively, these results suggest that members of the AQP family are involved in embryo and uterine fluid homeostasis during implantation.

Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the preimplantation uterus

Human infertility and recurrent pregnancy loss caused by implantation defects are poorly understood. Hoxa-10-deficient female mice have severe infertility and recurrent pregnancy loss due to defective uterine implantation. Gene expression profiling experiments reveal that Hoxa-10 is an important regulator of two critical events in implantation: stromal cell proliferation and local immunosuppression. At the time of implantation, Hoxa-10 mediates the progesterone-stimulated proliferation of uterine stromal cells. Hoxa-10 mutants express a stromal cell proliferation defect that is accompanied by quantitative or spatial alterations in the expression of two cyclin-dependent kinase inhibitor genes, p57 and p15. Hoxa-10 deficiency also leads to a severe local immunological disturbance, characterized by a polyclonal proliferation of T cells, that occurs in place of the normal progesterone-mediated immunosuppression in the periimplantation uterus.

Human endometrial receptivity: a genomic approach

The endometrium is a specialized tissue, hormonally-regulated, that is non-adhesive for embryos throughout most of the menstrual cycle in humans and other primates. Thus, endometrial receptivity is a self-limited period in which the endometrial epithelium (EE) acquires a functional and transient ovarian steroid-dependent status. The luminal EE acquires the ability to adhere (receptivity) the developing human blastocyst during this period due mainly to the presence of progesterone after appropriate 17beta-oestradiol priming. This status is a key element for embryonic implantation and appears to be closely associated with morphological and biochemical changes of EE cells. This specific time window is thought to be open after 4-5 days and closes after 9-10 days of progesterone production or administration, creating a physiological window of receptivity limited to days 19-24 of the menstrual cycle in humans. The scientific knowledge of the endometrial receptivity process is fundamental for the understanding of the human reproduction, but, so far, none of the proposed biochemical markers for endometrial receptivity have been proved clinically useful. In this work new strategies are presented based on molecular biology technologies that aim to clarify the fragmented information in this field using differential display, quantitative PCR and cDNA microarray analysis of endometrial epithelial-derived cell lines and endometrial samples to investigate the hierarchy at the mRNA level of molecules implicated in the process of endometrial receptivity.

Detection of HBV, HCV and HBV YMDD mutants by DNA microarray

AIM: To investigate the effect of DNA microarray in detection of hepatitis B virus (HBV), hepatitis C virus (HCV) and HBV YMDD mutants.

METHODS: HBV and HCV in 40 serum samples were detected by mixed microarray and quantitative determination method as well; 20 serum samples from patients with hepatitis B treated with lamivudine were detected by microarray loaded HBV YMDD mutants gene, and were simultaneously tested with mismatched PCR and DNA sequencing for comparison.

RESULTS: The coincident rate of mixed microarray and quantitative determination of HBV DNA was 85% (34/40). The detectable rate of HBV by mixed microarray was 83% (19/23); 2 of 17 samples showed false positive reaction. The coincident rate of mixed microarray and HCV RNA quantitative determination was 85% (34/40). The detectable rate of HCV by mixed microarray was 58% (7/12). One of 28 samples showed false positive reaction. The coincident rate of HBV YMDD mutants microarray and mismatched PCR was 70% (14/20). Mixed infection of wild and mutant HBV or different mutants were detected by microarray.

CONCLUSION: Mixed microarray has high sensitivity and low non-specificity in detection of HBV, but has lower sensitivity and higher specificity in detection of HCV. Detection of HBV YMDD mutants and mixed infection with microarray had higher sensitivity and specificity.

A genomic approach to identify novel progesterone receptor regulated pathways in the uterus during implantation

The cellular actions of steroid hormone progesterone (P) are mediated via its nuclear receptors, which regulate the expression of specific target genes. The identity of gene networks that are regulated by the P receptors (PRs) in the uterus at various stages of the reproductive cycle and pregnancy, however, remain largely unknown. In this study, we have used oligonucleotide microarrays to identify mRNAs whose expression in the pregnant mouse uterus is modulated by RU486, a well-characterized PR antagonist, which is also an effective inhibitor of implantation. We found that, in response to RU486, expression of mRNAs corresponding to 78 known genes was down-regulated at least 2-fold in the preimplantation mouse uterus. The PR regulation of several of these genes was ascertained by administering P to ovariectomized wild-type and PR knockout (PRKO) mice. Detailed spatio-temporal analysis of these genes in the pregnant uterus indicated that their expression in the epithelium and stroma could be correlated with the expression of PR in those cell types. Furthermore, time-course studies suggested that many of these genes are likely primary targets of PR regulation. We also identified 70 known genes that were up-regulated at least 2-fold in the pregnant uterus in response to RU486. Interestingly, initial examination of a number of RU486-inducible genes reveals that their uterine expression is also regulated by estrogen. The identification of several novel PR-regulated gene pathways in the reproductive tract is an important step toward understanding how P regulates the physiological events leading to implantation.

Hormonal genomics

The availability of the human genomic sequence is changing the way in which biological questions are addressed. Based on the prediction of genes from nucleotide sequences, homologies among their encoded amino acids can be analyzed and used to place them in distinct families. This serves as a first step in building hypotheses for testing the structural and functional properties of previously uncharacterized paralogous genes. As genomic information from more organisms becomes available, these hypotheses can be refined through comparative genomics and phylogenetic studies. Instead of the traditional single-gene approach in endocrine research, we are beginning to gain an understanding of entire mammalian genomes, thus providing the basis to reveal subfamilies and pathways for genes involved in ligand signaling. The present review provides selective examples of postgenomic approaches in the analysis of novel genes involved in hormonal signaling and their chromosomal locations, polymorphisms, splicing variants, differential expression, and physiological function. In the postgenomic era, scientists will be able to move from a gene-by-gene approach to a reconstructionistic one by reading the encyclopedia of life from a global perspective. Eventually, a community-based approach will yield new insights into the complexity of intercellular communications, thereby offering us an understanding of hormonal physiology and pathophysiology.

Global gene expression analysis to identify molecular markers of uterine receptivity and embryo implantation

Infertility and spontaneous pregnancy losses are an enduring problem to women's health. The establishment of pregnancy depends on successful implantation, where a complex series of interactions occurs between the heterogeneous cell types of the uterus and blastocyst. Although a number of genes are implicated in embryo-uterine interactions during implantation, genetic evidence suggests that only a small number of them are critical to this process. To obtain a global view and identify novel pathways of implantation, we used a dual screening strategy to analyze the expression of nearly 10,000 mouse genes by microarray analysis. Comparison of implantation and interimplantation sites by a conservative statistical approach revealed 36 up-regulated genes and 27 down-regulated genes at the implantation site. We also compared the uterine gene expression profile of progesterone-treated, delayed implanting mice to that of mice in which delayed implantation was terminated by estrogen. The results show up-regulation of 128 genes and down-regulation of 101 genes after termination of the delayed implantation. A combined analysis of these experiments showed specific up-regulation of 27 genes both at the implantation site and during uterine activation, representing a broad diversity of molecular functions. In contrast, the majority of genes that were decreased in the combined analysis were related to host immunity or the immune response, suggesting the importance of these genes in regulating the uterine environment for the implanting blastocyst. Collectively, we identified genes with recognized roles in implantation, genes with potential roles in this process, and genes whose functions have yet to be defined in this event. The identification of unique genetic markers for the onset of implantation signifies that genome-wide analysis coupled with functional assays is a promising approach to resolve the molecular pathways required for successful implantation.

Gene expression microarrays: a 21st century tool for directed vaccine design

DNA microarray technology is a new and powerful tool that allows the simultaneous analysis of a large number of nucleic acid hybridization experiments in a rapid and efficient fashion. The development of the DNA microarray chip has been driven by modern techniques of microelectronic fabrication, miniaturization and integration to produce what is referred to as "laboratory-on-chip" devices. The application of DNA chip technology includes the comprehensive analysis of multiple gene mutations and expressed sequences with regard to newer drug designs, host-pathogen interactions and the design of new vaccines. An advantage of microarray technology is that it can assist researchers to better define and understand the expression profile of a given genotype associated with disease, adverse effects from exposure to certain stimuli, or the ability to understand or predict immune responses to specific antigens. This paper briefly reviews DNA microarray technology and its implications with special reference to vaccine design. The technical aspects comprising array manufacturing and design, array hybridization, formatting, scanning and data handling are also briefly discussed.

Selective down-regulation of high-affinity IgE receptor (FcepsilonRI) alpha-chain messenger RNA among transcriptome in cord blood-derived versus adult peripheral blood-derived cultured human mast cells

Substantial numbers of human mast cells (MCs) were generated from umbilical cord blood (CB) and from adult peripheral blood (PB). A single CB progenitor produced 15 436 MCs, whereas a single PB progenitor produced 807 MCs on average. However, PB-derived MCs were far more active than CB-derived MCs in terms of high-affinity IgE receptor (FcepsilonRI)-mediated reactions. One million sensitized PB-derived MCs released 3.6 microg histamine, 215 pg IL-5, and 14 ng granulocyte macrophage-colony-stimulating factor (GM-CSF), whereas 10(6) sensitized CB-derived MCs released only 0.8 microg histamine, 31 pg IL-5, and 0.58 ng GM-CSF on anti-IgE challenge. However, ionophore A23 187 released similar levels of histamine from the 2 MC types. PB-derived MCs highly expressed surface FcepsilonRI alpha chain, and CB-derived MCs almost lacked it in the absence of IgE. PB-derived MCs expressed approximately 5 times higher levels of messenger RNA (mRNA) for FcepsilonRI alpha chain than CB-derived MCs, but mRNAs for beta and gamma chains of the receptors were equally expressed. Among the approximately 5600 kinds of full-length human genes examined by using the high-density oligonucleotide probe-array system, FcepsilonRIalpha was ranked the fifth most increased transcript in PB-derived MCs. The 4 other increased transcripts were unrelated to MC function. These results suggest that IgE-mediated reactions may be restricted during early infancy through the selective inhibition of FcepsilonRIalpha transcription, which is probably committed at progenitor stages and is, at least in part, cytokine-insensitive.