Factors affecting the gene expression of in vitro cultured human preimplantation embryos

STUDY QUESTION

What is the relative effect of common environmental and biological factors on transcriptome changes during human preimplantation development?

SUMMARY ANSWER

Developmental stage and maternal age had a larger effect on the global gene expression profile of human preimplantation embryos than the culture medium or oxygen concentration used in in vitro culture.

WHAT IS KNOWN ALREADY

Studies on mouse and bovine embryos have shown that different conditions in the in vitro culture of embryos can lead to changes in transcriptome profiles. For humans, an effect of developmental stage on the transcriptome profile of embryos has been demonstrated, but studies on the effect of maternal age or culture conditions are lacking.

STUDY DESIGN, SIZE, DURATION

Donated, good quality, day 4 cryopreserved human preimplantation embryos (N = 89) were randomized to be cultured in one of two culture media (G5 medium or HTF medium) and one of two oxygen concentrations (5% or 20%), with stratification for maternal age. Next to these variables, developmental stage after culture was taken into account in the analysis.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Embryos that developed to morula or blastocyst stage during these 2 days whose amplified mRNA passed our quality control criteria for microarray hybridization were individually examined for genome-wide gene expression (N = 37).

MAIN RESULTS AND THE ROLE OF CHANCE

Based on the number of differentially expressed genes (DEGs), developmental stage (3519 DEGs) and maternal age (1258 DEGs) had a larger effect on the global gene expression profile of human preimplantation embryos than either tested culture medium (596 DEGs) or oxygen concentration (492 DEGs) used during in vitro culture. Interactions between the factors were found, indicating that culture conditions might have a different effect depending on the developmental stage or the maternal age of the embryos. Affected pathways included metabolism, cell cycle processes and oxidative phosphorylation.

LIMITATIONS, REASONS FOR CAUTION

Culture of embryos for only 2 days might have limited the effect on global gene expression by the investigated culture conditions. Earlier stages of development (Day 0 until Day 4) were not analyzed and these embryos might respond differently to the experimental conditions. The freezing and thawing procedures might have had an effect on gene expression. RT-PCR validation was not performed due to scarcity of the material.

WIDER IMPLICATIONS OF THE FINDINGS

Our results show that when studying gene expression in single human preimplantation embryos under various experimental conditions, one should take into account the confounding effect of biological variables, such as developmental stage and maternal age. This makes these experiments different from gene expression experiments where these variables can be tightly controlled, for example when using cell lines.

STUDY FUNDING/COMPETING INTERESTS

This study received no external funding and there were no competing interests.

Purified Timothy grass pollen major allergen Phl p 1 may contribute to the modulation of allergic responses through a pleiotropic induction of cytokines and chemokines from airway epithelial cells

By definition, allergens are proteins with the ability to elicit powerful T helper lymphocyte type 2 (Th2) responses, culminating in immunoglobulin (Ig)E antibody production. Why specific proteins cause aberrant immune responses has remained largely unanswered. Recent data suggest that there may be several molecular paths that may affect allergenicity of proteins. The focus of this study is the response of airway epithelium to a major allergen from Phleum pratense Phl p 1. Instead of focusing on a few genes and proteins that might be affected by the major allergen, our aim was to obtain a broader view on the immune stimulatory capacity of Phl p 1. We therefore performed detailed analysis on mRNA and protein level by using a microarray approach to define Phl p 1-induced gene expression. We found that this allergen induces modulation and release of a broad range of mediators, indicating it to be a powerful trigger of the immune system. We were able to show that genes belonging to the GO cluster 'cell communication' were among the most prominent functional groups, which is also reflected in cytokines and chemokines building centres in a computational model of direct gene interaction. Further detailed comparison of grass pollen extract (GPE)- and Phl p 1-induced gene expression might be beneficial with regard to the application of single components within diagnosis and immunotherapy.

Timothy grass pollen extract-induced gene expression and signalling pathways in airway epithelial cells

BACKGROUND

Grass pollen allergy is one of the most common allergies worldwide and airborne allergens are the major cause of allergic rhinitis. Airway epithelial cells (AECs) are the first to encounter and respond to aeroallergens and are therefore interesting targets for the development of new therapeutics. Our understanding of the epithelial contribution to immune responses is limited as most studies focus on only a few individual genes or proteins.

OBJECTIVE

To describe in detail the Timothy grass pollen extract (GPE)-induced gene expression in AECs.

METHODS

NCI-H292 cells were exposed to GPE for 24 h, and isolated RNA and cell culture supernatants were used for microarray analysis and multiplex ELISA, respectively.

RESULTS

Eleven thousand and seven hundred fifty-eight transcripts were affected after exposure to GPE, with 141 genes up-regulated and 121 genes down-regulated by more than threefold. The gene ontology group cell communication was among the most prominent categories. Network analysis revealed that a substantial part of regulated genes are related to the cytokines IL-6, IL-8, IL-1A, and the transcription factor FOS. After analysing significantly regulated signalling pathways, we found, among others, epidermal growth factor receptor 1, IL-1, Notch-, and Wnt-related signalling members. Unexpectedly, we found Jagged to be down-regulated and an increased release of IL-12, in line with a more Th1-biased response induced by GPE.

CONCLUSION AND CLINICAL RELEVANCE

Our data show that the stimulation of AECs with GPE results in the induction of a broad response on RNA and protein level by which they are able to affect the initiation and regulation of local immune responses. Detailed understanding of GPE-induced genes and signalling pathways will allow us to better define the pathogenesis of the allergic response and to identify new targets for treatment.

Comparative transcriptomic responses to chronic cadmium, fluoranthene, and atrazine exposure in Lumbricus rubellus

Transcriptional responses of a soil-dwelling organism (the earthworm Lumbricus rubellus) to three chemicals, cadmium (Cd), fluoranthene (FA), and atrazine (AZ), were measured following chronic exposure, with the aim of identifying the nature of any shared transcriptional response. Principal component analysis indicated full or partial separation of control and exposed samples for each compound but not for the composite set of all control and exposed samples. Partial least-squares discriminant analysis allowed separation of the control and exposed samples for each chemical and also for the composite data set, suggesting a common transcriptional response to exposure. Genes identified as changing in expression level (by the least stringent test for significance) following exposure to two chemicals indicated a substantial number of common genes (> 127). The three compound overlapping gene set, however, comprised only 25 genes. We suggest that the low commonality in transcriptional response may be linked to the chronic concentrations (approximately 10% EC50) and chronic duration (28 days) used. Annotations of the three compound overlapping gene set indicated that genes from pathways most often associated with responses to environmental stress, such as heat shock, phase I and II metabolism, antioxidant defense, and cation balance, were not represented. The strongest annotation signature was for genes important in mitochondrial function and energy metabolism.

Comparison of expression profiles induced by dust mite in airway epithelia reveals a common pathway

BACKGROUND

Airway epithelial cells have shown to be active participants in the defense against pathogens by producing signaling and other regulatory molecules in response to the encounter.

METHODS

In previous manuscripts, we have studied the effect of house dust mite (HDM) extract on both an epithelial cell-line (H292) and primary nasal epithelial cell. When we compare these responses we conclude that the H292 cells more closely resemble nasal epithelium of healthy controls (share 107 probe-sets) than of allergic individuals (share 17 probe-sets).

RESULTS

Interestingly, probably because of an absent intraindividual variation between samples, more probe-sets (8280) change expression significantly in H292 than in either healthy (555) or allergic (401) epithelium.

CONCLUSIONS

A direct comparison of all the responses in these epithelial cells reveals a core-response to HDM of just 29 genes. These genes (CCL20, IL-8, CXCL2, CXCL1, IL-1B, AREG, TNFAIP3, HBEGF, PTGS2, BMP2, LDLR, PLAUR, PLAU, NFKB2, NFKB1, JUN, ATF3, EGR1, NPC1, TICAM1, EPHA2, CTGF, DUSP1, SPRY1, TLR-3, complement factor C3, IVNS1ABP, SerpinB3, and PSAT1) have described links with allergy or inflammation and may even describe the well-established relationship between viral infections and allergic exacerbations or allergy development.

[Nitrous-oxide sedation indispensable in the dental care of anxious people and the mentally impaired]

The long-term occupational exposure to high concentrations of nitrous oxide in health-care workers in a Dutch hospital, with probable adverse effects on their offspring, has triggered a discussion about the benefits and risks of nitrous oxide. In Dutch dentistry, nitrous-oxide sedation is a valuable and indispensable aid in the treatment of patients with challenging behaviour, such as those with mental impairment or in extremely-anxious adults and children. Nitrousoxide sedation can be used without risk to the dental team, provided that measures are taken for sufficient scavenging and room ventilation. A possible ban on nitrous oxide would be a major setback for specialty-care dentistry in the Netherlands.

The oedema-protective effect of Lycra support stockings

BACKGROUND

Oedema may be an early sign of chronic venous insufficiency (CVI), but swelling of the lower legs is a common phenomenon in many people. The distinction between physiological swelling and CVI is not clear. There is a gradual transition between healthy legs and the early stages of CVI. In case of CVI, medical elastic compression stockings are used in order to prevent oedema completely. In case of healthy people without demonstrable CVI, no medical stockings are required in the prevention of oedema but stockings exerting less compression.

OBJECTIVE

The aim of this study was to investigate the effect of mild compression on the development of swelling of the legs and the effect on subjective complaints in healthy subjects.

METHODS

The diurnal volume change (DVC) of the lower legs during full working days was monitored with an optical leg volume meter in 118 healthy volunteers (60 males, 58 females) without objective symptoms of CVI. The DVCs after wearing two kinds of class I support stockings (X: average pressure at the ankle of almost 14 mm Hg; Y: almost 18 mm Hg) were compared with the DVC after wearing a control stocking (Z: almost 6 mm Hg). Also, the effect on subjective feelings of the legs was noted.

RESULTS

It appeared that healthy people have a mean daily volume increase of the legs of 2.3% in females and 1.6% in males. Mild compression stockings reduced this daily increase with 31 and 18% in males and females, respectively, by stocking X and 37 and 32% by stocking Y. Subjective feelings occurred in 57% of all cases. A beneficial effect on subjective feelings, in particular of tired and swollen legs, was found. A difference in this beneficial effect between stocking X and Y was not obvious.

CONCLUSIONS

Mild compression stockings reduce diurnal oedema and unpleasant feelings of the legs in healthy individuals.

The outcome of an additional patch-test reading on days 6 or 7

In a retrospective study (period 1997-1998), the usefulness of an additional patch-test reading on day (D) 6 or 7 was investigated. In 62 out of 760 patients (8.2%), 77 late-positive reactions, those manifest after D3, were seen. 4 late reactions of allergens of which a related allergen reacted earlier (at D2 or D3) in the same patient were not incorporated in the study as late-positive. Allergens most involved in producing late-positive reactions were nickel sulfate (20 reactions), neomycin sulfate (7), tixocortol-21-pivalate (5), p.t. butylphenol formaldehyde resin (5) and Cl+ Me isothiazolinone (5). Special attention is paid to ?+ reactions at D6 or D7, because these reactions could add extra information to the outcome of patch-test readings, considering that this might be a group of allergens that has been positive between D3 and D6/7 or become positive later on. When this group is included, the total number of late-positive reactions is 105 in 88 out of 760 patients (11.6%). By doing D3 readings in combination with D6 or D7 readings only, one would miss 24 positive reactions. However, we concluded that it was preferable to have a reading on D2 and D3. An extra reading on D6 or D7 is very useful as it gives additional information in 8.2% of patch-tested patients.

Species-specific responses to metals in organically enriched river water, with emphasis on effects of humic acids

Invertebrate communities in polluted rivers are often exposed to a wide variety of compounds. Due to complex interactions, 'pollution tolerant' species are not necessarily the most tolerant species to toxicants tested under standard laboratory conditions. It was hypothesized that the distribution of species in polluted rivers is not only dependent on the tolerance of species to toxicants, but also on species-specific capacities to modify or compensate for negative effects of toxicants. To test this hypothesis, species-specific responses to metals in organically enriched river water were studied under controlled conditions. The zebra mussel Dreissena polymorpha and the midge Chironomus riparius were exposed to metal-polluted water from the River Dommel. Additionally, the (interactive) effects of metals and humic acids (HA) on both species were evaluated. In spite of a lower tolerance of Chironomus riparius to metals in laboratory studies, the midge was the most tolerant of the two test species to metal-polluted site water. The results indicated that the sensitivities of the two test species determined in laboratory tests were inversely related to their sensitivities to polluted river water. In accordance with these results, midge larvae were protected from copper (Cu) toxicity by HA, while metal toxicity was not reduced (Cu) or even amplified (cadmium) by HA for the zebra mussel. Thus, the presence of (naturally occurring) HA in site water may partly account for discrepancies between responses of species to bioassays and toxicity tests. It is suggested that these differences in responses to metals in site water are strongly influenced by species-specific preferences for organic compounds (like HA). It is concluded that the response to organic compounds present in site water largely determines whether a species is classified as 'pollution tolerant' or 'pollution sensitive'.

Polymorphism of C4 and CYP21 genes in various primate species

To study the genetic heterogeneity of the C4 and CYP21 genes in selected primate species we used the technique of restriction fragment length polymorphism (RFLP). Genomic DNA was digested using several restriction endonucleases and filters were hybridized with a 500 bp BamHI/KpnI fragment derived from the 5' section of a human C4-cDNA and with a 1700 bp BamHI obtained from a human CYP21 gene. Abundant RFLP heterogeneity was observed for the C4 genes within a rhesus monkey population but not for the chimpanzee colony analyzed. Duplicated C4-CYP21 clusters can be traced back in humans, but also in chimpanzees, orang-utans and rhesus monkeys. Thus, duplication of the basic C4-CYP21 cluster in primates may have happened more than 30 million years ago. Non-duplicated C4-CYP21 regions were found for the gorilla and orang-utan. Apart from this, shortened C4A and C4B genes were observed in chimpanzees, orang-utans and rhesus monkeys, whereas the so-called long variety of the C4A gene appears to be present in humans and orang-utans. This ancestral modification, resulting from an insertion of a 6.5 kb intron in the C4A gene, therefore predates at least speciation of human and orang-utan which is estimated to have taken place more than 12 million years ago.