Comparative Analysis of Shapley Values Enhances Transcriptomics Insights across Some Common Uterine Pathologies.

Uterine pathologies pose a challenge to women's health on a global scale. Despite extensive research, the causes and origin of some of these common disorders are not well defined yet. This study presents a comprehensive analysis of transcriptome data from diverse datasets encompassing relevant uterine pathologies such as endometriosis, endometrial cancer and uterine leiomyomas. Leveraging the Comparative Analysis of Shapley values (CASh) technique, we demonstrate its efficacy in improving the outcomes of the classical differential expression analysis on transcriptomic data derived from microarray experiments. CASh integrates the microarray game algorithm with Bootstrap resampling, offering a robust statistical framework to mitigate the impact of potential outliers in the expression data. Our findings unveil novel insights into the molecular signatures underlying these gynecological disorders, highlighting CASh as a valuable tool for enhancing the precision of transcriptomics analyses in complex biological contexts. This research contributes to a deeper understanding of gene expression patterns and potential biomarkers associated with these pathologies, offering implications for future diagnostic and therapeutic strategies.

Fractal Dimension Analysis in Neurological Disorders: An Overview.

Fractal analysis has emerged as a powerful tool for characterizing irregular and complex patterns found in the nervous system. This characterization is typically applied by estimating the fractal dimension (FD), a scalar index that describes the topological complexity of the irregular components of the nervous system, both at the macroscopic and microscopic levels, that may be viewed as geometric fractals. Moreover, temporal properties of neurophysiological signals can also be interpreted as dynamic fractals. Given its sensitivity for detecting changes in brain morphology, FD has been explored as a clinically relevant marker of brain damage in several neuropsychiatric conditions as well as in normal and pathological cerebral aging. In this sense, evidence is accumulating for decreases in FD in Alzheimer's disease, frontotemporal dementia, Parkinson's disease, multiple sclerosis, and many other neurological disorders. In addition, it is becoming increasingly clear that fractal analysis in the field of clinical neurology opens the possibility of detecting structural alterations in the early stages of the disease, which highlights FD as a potential diagnostic and prognostic tool in clinical practice.

Cross-disorder analysis of endometriosis and its comorbid diseases reveals shared genes and molecular pathways and proposes putative biomarkers of endometriosis.

RESEARCH QUESTION: Women with endometriosis are considered to be at higher risk of several chronic diseases, such as autoimmune disorders, gynaecological cancers, asthma/atopic diseases and cardiovascular and inflammatory bowel diseases. Could the study of endometriosis-associated comorbidities help to identify potential biomarkers and target pathways of endometriosis? DESIGN: A systematic review was performed to identify all possible endometriosis-associated comorbid conditions. Next, this list of disorders was coded into MeSH terms, and the gene expression profiles were downloaded from the Phenopedia database and subsequently analysed following a systems biology approach. RESULTS: The results identified a group of 127 candidate genes that were recurrently expressed in endometriosis and its closest comorbidities and that were defined as 'endometriosis sibling disorders' (ESD). The enrichment analysis showed that these candidate genes are principally involved in immune and drug responses, hormone metabolism and cell proliferation, which are well-known hallmarks of endometriosis. The expression of ESD genes was then validated on independent sample cohorts (n = 207 samples), in which the involvement of 16 genes (AGTR1, BDNF, C3, CCL2, CD40, CYP17A1, ESR1, IGF1, IGF2, IL10, MMP1, MMP7, MMP9, PGR, SERPINE1 and TIMP2) in endometriosis was confirmed. Several of these genes harbour polymorphisms that associate to either endometriosis or its comorbid conditions. CONCLUSIONS: The study results highlight the molecular processes underlying the aetiopathogenesis of endometriosis and its comorbid conditions, and identify putative endometriosis biomarkers.

DNA methylation changes in endometrium and correlation with gene expression during the transition from pre-receptive to receptive phase.

The inner uterine lining (endometrium) is a unique tissue going through remarkable changes each menstrual cycle. Endometrium has its characteristic DNA methylation profile, although not much is known about the endometrial methylome changes throughout the menstrual cycle. The impact of methylome changes on gene expression and thereby on the function of the tissue, including establishing receptivity to implanting embryo, is also unclear. Therefore, this study used genome-wide technologies to characterize the methylome and the correlation between DNA methylation and gene expression in endometrial biopsies collected from 17 healthy fertile-aged women from pre-receptive and receptive phase within one menstrual cycle. Our study showed that the overall methylome remains relatively stable during this stage of the menstrual cycle, with small-scale changes affecting 5% of the studied CpG sites (22,272 out of studied 437,022 CpGs, FDR < 0.05). Of differentially methylated CpG sites with the largest absolute changes in methylation level, approximately 30% correlated with gene expression measured by RNA sequencing, with negative correlations being more common in 5' UTR and positive correlations in the gene 'Body' region. According to our results, extracellular matrix organization and immune response are the pathways most affected by methylation changes during the transition from pre-receptive to receptive phase.

Maternal Pre-Pregnancy Obesity Is Associated with Altered Placental Transcriptome.

Maternal obesity has a major impact on pregnancy outcomes. There is growing evidence that maternal obesity has a negative influence on placental development and function, thereby adversely influencing offspring programming and health outcomes. However, the molecular mechanisms underlying these processes are poorly understood. We analysed ten term placenta's whole transcriptomes in obese (n = 5) and normal weight women (n = 5), using the Affymetrix microarray platform. Analyses of expression data were carried out using non-parametric methods. Hierarchical clustering and principal component analysis showed a clear distinction in placental transcriptome between obese and normal weight women. We identified 72 differentially regulated genes, with most being down-regulated in obesity (n = 61). Functional analyses of the targets using DAVID and IPA confirm the dysregulation of previously identified processes and pathways in the placenta from obese women, including inflammation and immune responses, lipid metabolism, cancer pathways, and angiogenesis. In addition, we detected new molecular aspects of obesity-derived effects on the placenta, involving the glucocorticoid receptor signalling pathway and dysregulation of several genes including CCL2, FSTL3, IGFBP1, MMP12, PRG2, PRL, QSOX1, SERPINE2 and TAC3. Our global gene expression profiling approach demonstrates that maternal obesity creates a unique in utero environment that impairs the placental transcriptome.

Endometrial transcriptome analysis indicates superiority of natural over artificial cycles in recurrent implantation failure patients undergoing frozen embryo transfer.

Little consensus has been reached on the best protocol for endometrial preparation for frozen embryo transfer (FET). It is not known how, and to what extent, hormone supplementation in artificial cycles influences endometrial preparation for embryo implantation at a molecular level, especially in patients who have experienced recurrent implantation failure. Transcriptome analysis of 15 endometrial biopsy samples at the time of embryo implantation was used to compare two different endometrial preparation protocols, natural versus artificial cycles, for FET in women who have experienced recurrent implantation failure compared with fertile women. IPA and DAVID were used for functional analyses of differentially expressed genes. The TRANSFAC database was used to identify oestrogen and progesterone response elements upstream of differentially expressed genes. Cluster analysis demonstrated that natural cycles are associated with a better endometrial receptivity transcriptome than artificial cycles. Artificial cycles seemed to have a stronger negative effect on expression of genes and pathways crucial for endometrial receptivity, including ESR2, FSHR, LEP, and several interleukins and matrix metalloproteinases. Significant overrepresentation of oestrogen response elements among the genes with deteriorated expression in artificial cycles (P < 0.001) was found; progesterone response elements predominated in genes with amended expression with artificial cycles (P = 0.0052).

Gene expression profiling to investigate tyrosol-induced lifespan extension in Caenorhabditis elegans.

PURPOSE: We have previously reported that tyrosol (TYR) promotes lifespan extension in the nematode Caenorhabditis elegans, also inducing a stronger resistance to thermal and oxidative stress in vivo. In this study, we performed a whole-genome DNA microarray in order to narrow down the search for candidate genes or signaling pathways potentially involved in TYR effects on C. elegans longevity. METHODS: Nematodes were treated with 0 or 250 µM TYR, total RNA was isolated at the adult stage, and derived cDNA probes were hybridized to Affymetrix C. elegans expression arrays. Microarray data analysis was performed, and relative mRNA expression of selected genes was validated using qPCR. RESULTS: Microarray analysis identified 208 differentially expressed genes (206 over-expressed and two under-expressed) when comparing TYR-treated nematodes with vehicle-treated controls. Many of these genes are linked to processes such as regulation of growth, transcription, reproduction, lipid metabolism and body morphogenesis. Moreover, we detected an interesting overlap between the expression pattern elicited by TYR and those induced by other dietary polyphenols known to extend lifespan in C. elegans, such as quercetin and tannic acid. CONCLUSIONS: Our results suggest that important cellular mechanisms directly related to longevity are influenced by TYR treatment in C. elegans, supporting our previous notion that this phenol might act on conserved genetic pathways to increase lifespan in a whole organism.

Fractals in the neurosciences, Part II: clinical applications and future perspectives.

It has been ascertained that the human brain is a complex system studied at multiple scales, from neurons and microcircuits to macronetworks. The brain is characterized by a hierarchical organization that gives rise to its highly topological and functional complexity. Over the last decades, fractal geometry has been shown as a universal tool for the analysis and quantification of the geometric complexity of natural objects, including the brain. The fractal dimension has been identified as a quantitative parameter for the evaluation of the roughness of neural structures, the estimation of time series, and the description of patterns, thus able to discriminate different states of the brain in its entire physiopathological spectrum. Fractal-based computational analyses have been applied to the neurosciences, particularly in the field of clinical neurosciences including neuroimaging and neuroradiology, neurology and neurosurgery, psychiatry and psychology, and neuro-oncology and neuropathology. After a review of the basic concepts of fractal analysis and its main applications to the basic neurosciences in part I of this series, here, we review the main applications of fractals to the clinical neurosciences for a holistic approach towards a fractal geometry model of the brain.

Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium.

BACKGROUND: 'Omics' high-throughput analyses, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, are widely applied in human endometrial studies. Analysis of endometrial transcriptome patterns in physiological and pathophysiological conditions has been to date the most commonly applied 'omics' technique in human endometrium. As the technologies improve, proteomics holds the next big promise for this field. The 'omics' technologies have undoubtedly advanced our knowledge of human endometrium in relation to fertility and different diseases. Nevertheless, the challenges arising from the vast amount of data generated and the broad variation of 'omics' profiling according to different environments and stimuli make it difficult to assess the validity, reproducibility and interpretation of such 'omics' data. With the expansion of 'omics' analyses in the study of the endometrium, there is a growing need to develop guidelines for the design of studies, and the analysis and interpretation of 'omics' data. METHODS: Systematic review of the literature in PubMed, and references from relevant articles were investigated up to March 2013. RESULTS: The current review aims to provide guidelines for future 'omics' studies on human endometrium, together with a summary of the status and trends, promise and shortcomings in the high-throughput technologies. In addition, the approaches presented here can be adapted to other areas of high-throughput 'omics' studies. CONCLUSION: A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.

MicroRNAs miR-30b, miR-30d, and miR-494 regulate human endometrial receptivity.

MicroRNAs (miRNAs) act as important epigenetic posttranscriptional regulators of gene expression. We aimed to gain more understanding of the complex gene expression regulation of endometrial receptivity by analyzing miRNA signatures of fertile human endometria. We set up to analyze miRNA signatures of receptive (LH + 7, n = 4) versus prereceptive (LH + 2, n = 5) endometrium from healthy fertile women. We found hsa-miR-30b and hsa-miR-30d to be significantly upregulated, and hsa-miR-494 and hsa-miR-923 to be downregulated in receptive endometrium. Three algorithms (miRanda, PicTar, and TargetScan) were used for target gene prediction. Functional analyses of the targets using Ingenuity Pathways Analysis and The Database for Annotation, Visualization and Integrated Discovery indicated roles in transcription, cell proliferation and apoptosis, and significant involvement in several relevant pathways, such as axon guidance, Wnt/ß-catenin, ERK/MAPK, transforming growth factor ß (TGF-ß), p53 and leukocyte extravasation. Comparison of predicted miRNA target genes and our previous messenger RNA microarray data resulted in a list of 12 genes, including CAST, CFTR, FGFR2, and LIF that could serve as a panel of genes important for endometrial receptivity. In conclusion, we suggest that a subset of miRNAs and their target genes may play important roles in endometrial receptivity.

El Genoma en los Cordados: Introducción a la Genómica Comparada / The Genome in the Chordates: Introduction to Comparative Genomics

El objetivo del presente trabajo es describir brevemente conceptos de la genómica de los cordados así como de la genómica comparada y sus aspectos éticos. El genoma de los cordados cambió ligeramente dando lugar al genoma de los vertebrados, entre ellos el de los mamíferos, entre los que se incluye el ser humano. La genómica comparada estudia las semejanzas y diferencias entre genomas de diferentes organismos; trata de explicar la información proporcionada por la selección natural para entender la función y los procesos evolutivos que actúan sobre los genomas. La complejidad de los procesos evolutivos constituye todo un desafío a la hora de analizar e interpretar la información biológica generada; en este sentido, la Bioinformática y la Biología Computacional proporcionan un amplio abanico de técnicas estadísticas, matemáticas y algorítmicas para el análisis de datos biológicos. Un reto clave es analizar el caudal de datos de secuencias de ADN con el fin de comprender la información almacenada en términos de estructura, función y evolución proteicas. En Biología computacional BLAST y ClustalW2 son las herramientas más empleadas para el análisis de alineamientos múltiples de secuencias. La Genómica está resultando clave también en el campo de la medicina; conocer la cartografía del genoma humano proporciona una valiosa información a tener en cuenta a la hora de detectar genes implicados en ciertas enfermedades. Esto conlleva que en la actualidad nos centremos más en la predicción de patologías que en la prevención, por lo que la tendencia es que en el futuro la Medicina Genómica acabe desbancando a la Medicina Preventiva. El Proyecto Genoma Humano presenta diversas aplicaciones que, al no tener una clara cobertura legal, traen consigo un nuevo paradigma con problemas éticos, sociales y legales que la comunidad científica trata de resolver para compaginar los aspectos morales con el progreso en la investigación.

The aim of this paper is to briefly describe concepts of genomics of chordates and comparative genomics and its ethical aspects. The genome of chordates changed slightly resulting in the genome of vertebrates, including mammals. The human being belongs to the phylum chordates. Comparative genomics studies the similarities and differences between genomes of different organisms, trying to explain the information provided by natural selection to understand the function and evolutionary processes that act on genomes. Evolutive processes' complexity is considered a major challenge in terms of analyzing and interpreting all the biological information generated; in this sense, Bioinformatics and Computational Biology provide an enormous range of statistical, mathematical and algorythmical techniques for biological data analyses. A key challenge for bioinformatics is to analyze the flow of DNA sequence data to understand the information stored in terms of structure, function and protein evolution. BLAST and ClustalW2 tools are used for the analysis of multiple sequence alignments in Computational Biology. Genomics is also playing a key role in Medicine; human genome's cartography provides valuable information to detect genes involved in certain diseases. It entails that nowadays it is better to focus on prediction much more than on prevention. The current tendency is that in the future Genomic Medicine will displace Preventive Medicine. The Human Genome Project implies diverse applications that do not have clear legal coverage. This brings a new paradigm with ethical, social and legal problems that the scientific community is trying to resolve in order to combine morality and research progress.

Hormonal and molecular characterization of follicular fluid, cumulus cells and oocytes from pre-ovulatory follicles in stimulated and unstimulated cycles.

BACKGROUND: The use of ovarian stimulation, to stimulate a multi-follicular response for assisted reproduction treatments, may force the production of oocytes from follicles that do not reach optimal maturation, possibly yielding oocytes that are not fully competent. The present study aimed to define the follicular environment and oocyte competence of unstimulated pre-ovulatory follicles, to compare it with that of similar-sized stimulated follicles. For this purpose, we analyzed the follicular hormonal milieu, the oocyte meiotic spindle, the embryo development and the cumulus cells gene expression (GE) profiles. METHODS AND RESULTS: The study population was divided in two groups: (i) 42 oocyte donors undergoing unstimulated cycles and (ii) 18 oocyte donors undergoing controlled ovarian stimulation cycles (COS). Follicular fluid was analyzed to quantify the concentrations of estradiol (E2), progesterone (P), FSH, LH, testosterone (T) and androstendione (Δ4). T was higher in the COS group, while Δ4, E2 and LH were significantly higher in unstimulated cycles. The cumulus oophorus cells (CC) surrounding the oocyte were removed and their GE profiles were analyzed with microarrays. There were 18 differentially expressed genes in CC: 7 were up-regulated and 11 were down-regulated in the COS cycles. The microarray was validated by qRT-PCR. The analysis of spindle structure revealed no significant differences between the groups, except for the parameter of length which presented differences. The fertilization ability and embryo morphology on Days 2, 3 and 4 did not show any significant differences between groups. CONCLUSIONS: The use of ovarian stimulation induces changes in the follicular fluid and in CC GE that may affect immune processes, meiosis and ovulation pathways. Although these differences do not seem to relate to early-stage embryo morphology, the implications of some of the molecules, especially ALDH1A2, CTSL and ZNF33B at the CC level, deserve to be addressed in future studies.

Medicina genómica: aspectos éticos, legales y sociales del genoma humano / Genomic medicine: ethical, legal and social aspects of the human genome / Medicina genômica: aspectos éticos, legais e sociais do genoma humano

La Medicina Genómica es el uso de la información de los genomas y sus derivados (ARN, proteínas y metabolitos) que permite guiar la toma de decisiones médicas, es un componente clave de la medicina personalizada. La Medicina Genómica permite conocer la cartografía del genoma humano y proporciona una valiosa información a tener en cuenta a la hora de detectar genes implicados en ciertas enfermedades. Esto conlleva a que en la actualidad nos centremos más en la predicción de patologías que en la prevención, por lo que la tendencia es que en el futuro la Medicina Genómica acabe desbancando a la Medicina Preventiva. El Proyecto Genoma Humano presenta diversas aplicaciones que, al no tener una clara cobertura legal, traen consigo un nuevo paradigma con problemas éticos, sociales y legales que la comunidad científica trata de resolver para compaginar los aspectos morales con el progreso en la investigación. El objetivo del presente trabajo es describir brevemente los aspectos éticos, legales y sociales del Genoma Humano...

Genomic Medicine and its different forms of application (personalized or individualized medicine, which are part of pharmacogenomics, toxicogenomics and nutrigenomics, and predictive, regenerative placement, molecular and reproductive medicine), without a doubt have transformed the modern cine and are a new paradigm. This article aims to review the various forms of genomic medicine, since its benefits to human health and substantial changes in the approach to health-disease process, as well as the problems and paradoxes associated to be addressed from bioethics and Law...

A Medicina Genômica é o uso da informação dos genomas e seus derivados (ARN, proteínas e metabólitos) e permite guiar a tomada de decisões médicas; é um componente-chave da medicina personalizada. A Medicina Genômica permite conhecer a cartografia do genoma humano, proporciona uma valiosa informação a ser considerada na hora de detectar genes implicados em certas doenças. Isto leva a que atualmente nos concentremos mais na predição de patologias que na prevenção, sendo que a tendência é que no futuro a Medicina Genômica acabe desbancando a Medicina Preventiva. O Projeto Genoma Humano apresenta diversas aplicações, que se não tiverem uma clara cobertura legal trazem consigo um novo paradigma, com problemas éticos, sociais e legais que a comunidade científica tenta resolver para compaginar os aspectos morais com o progresso na pesquisa. O objetivo do presente trabalho é descrever brevemente os aspectos éticos, legais e sociais do Genoma Humano...

A genomic diagnostic tool for human endometrial receptivity based on the transcriptomic signature.

OBJECTIVE: To create a genomic tool composed of a customized microarray and a bioinformatic predictor for endometrial dating and to detect pathologies of endometrial origin. To define the transcriptomic signature of human endometrial receptivity. DESIGN: Two cohorts of endometrial samples along the menstrual cycle were used: one to select the genes to be included in the customized microarray (endometrial receptivity array [ERA]), and the other to be analyzed by ERA to train the predictor for endometrial dating and to define the transcriptomic signature. A third cohort including pathological endometrial samples was used to train the predictor for pathological classification. SETTING: Healthy oocyte donors and patients. PATIENT(S): Healthy fertile women (88) and women with implantation failure (5) or hydrosalpinx (2). INTERVENTION(S): Human endometrial biopsies. MAIN OUTCOME MEASURE(S): The gene expression of endometrial biopsies. RESULT(S): The ERA included 238 selected genes. The transcriptomic signature was defined by 134 genes. The predictor showed a specificity of 0.8857 and sensitivity of 0.99758 for endometrial dating, and a specificity of 0.1571 and a sensitivity of 0.995 for the pathological classification. CONCLUSION(S): This diagnostic tool can be used clinically in reproductive medicine and gynecology. The transcriptomic signature is a potential endometrial receptivity biomarkers cluster.

The bone marrow-derived human mesenchymal stem cell: potential progenitor of the endometrial stromal fibroblast.

The cellular sources that contribute to the renewal of human endometrium are largely unknown. It has been suggested that endometrial stem cells originate from bone marrow-derived mesenchymal stem cells (MSC), with subsequent development into endometrial stromal fibroblasts (hESF). We hypothesized that if bone marrow-derived MSC contribute to endometrial regeneration and are progenitors of hESF, their treatment with agents known to regulate hESF differentiation could promote their differentiation down the stromal fibroblast lineage. To this end, we treated bone marrow-derived MSC with estradiol and progesterone, bone morphogenetic protein 2 (BMP2), and activators of the protein kinase A (PKA) pathway and investigated specific markers of hESF differentiation (decidualization). Furthermore, we investigated the transcriptome of these cells in response to cAMP and compared this to the transcriptome of hESF decidualized in response to activation of the PKA pathway. The data support the idea that MSC can be differentiated down the hESF pathway, as evidenced by changes in cell shape and common expression of decidual markers and other genes important in hESF differentiation and function, and that bone marrow-derived MSC may be a source of endometrial stem/progenitor cells. In addition, we identified MSC-specific markers that distinguish them from other fibroblasts and, in particular, from hESF, which is of biologic relevance and practical value to the field of endometrial stem cell research.

The protein kinase A pathway-regulated transcriptome of endometrial stromal fibroblasts reveals compromised differentiation and persistent proliferative potential in endometriosis.

Intrinsic abnormalities in transplanted eutopic endometrium are believed to contribute to the pathogenesis of pelvic endometriosis. Herein we investigated transcriptomic differences in human endometrial stromal fibroblasts (hESFs) from women with (hESF(endo)) vs. without (hESF(nonendo)) endometriosis, in response to activation of the protein kinase A (PKA) pathway with 8-bromoadenosine-cAMP (8-Br-cAMP). hESF(nonendo) (n = 4) and hESF(endo) (n = 4) were isolated from eutopic endometrium and treated +/- 0.5 mm 8-Br-cAMP for 96 h. Purified total RNA was subjected to microarray analysis using the whole-genome Gene 1.0 ST Affymetrix platform. A total of 691 genes were regulated in cAMP-treated hESF(nonendo) vs. 158 genes in hESF(endo), suggesting a blunted response to cAMP/PKA pathway activation in women with disease. Real-time PCR and ELISA validated the decreased expression of decidualization markers in hESF(endo) compared with hESF(nonendo). In the absence of disease, 8-Br-cAMP down-regulated progression through the cell cycle via a decrease in cyclin D1, cyclin-dependent kinase 6, and cell division cycle 2 and an increase in cyclin-dependent kinase inhibitor 1A. However, cell cycle components in hESF(endo) were not responsive to 8-Br-cAMP, resulting in persistence of a proliferative phenotype. hESF(endo) treated with 8-Br-cAMP exhibited altered expression of immune response, extracellular matrix, cytoskeleton, and apoptosis genes. Changes in phosphodiesterase expression and activity were not different among experimental groups. These data support that eutopic hESF(endo) with increased proliferative potential can seed the pelvic cavity via retrograde menstruation and promote establishment, survival, and proliferation of endometriosis lesions, independent of hydrolysis of cAMP and likely due to an inherent abnormality in the PKA pathway.

Embryologic outcome and secretome profile of implanted blastocysts obtained after coculture in human endometrial epithelial cells versus the sequential system.

OBJECTIVE: To compare embryologic and clinical outcomes in terms of preimplantation development, implantation, pregnancy rates, and secretome profile of implanted blastocysts from the preimplantation genetic diagnosis program grown in sequential versus endometrial epithelial cell (EEC) coculture system. DESIGN: Retrospective clinical study and prospective experimental study. SETTING: In vitro fertilization clinical unit and university research laboratory. INTERVENTION(S): Blastomere biopsy, embryo culture, blastocyst transfer, and protein analysis of the media conditioned from implanted embryos obtained from coculture and sequential systems. MAIN OUTCOME MEASURE(S): Clinical study: blastocyst, implantation, and gestation rates in own and donated oocytes. Experimental study: differential protein analysis of implanted embryos grown in coculture system versus sequential system. RESULT(S): Of the 12,377 embryos analyzed, the blastocyst rates were 56.0% versus 45.9% in the coculture versus the sequential system, respectively, with own oocytes. With ovum donation, the rates were 70.5% versus 56.4%, respectively. Reproductive outcomes in terms of pregnancy rates (39.1% vs. 27.5%) and implantation rates (33.3% vs. 20.9%,) were statistically higher in EEC coculture versus sequential media. Furthermore, the protein profile of the EEC coculture versus the sequential system was obtained. Interleukin-6 (IL-6) was the most secreted protein by the EEC culture. Further ELISA experiments showed that the IL-6 present in the sequential medium diminished in implanted blastocysts. CONCLUSION(S): The coculture system favors blastocyst development and implantation rates, given the contribution of the factors secreted by endometrial epithelial cells, such as IL-6.

Controlled ovarian stimulation induces a functional genomic delay of the endometrium with potential clinical implications.

CONTEXT: Controlled ovarian stimulation induces morphological, biochemical, and functional genomic modifications of the human endometrium during the window of implantation. OBJECTIVE: Our objective was to compare the gene expression profile of the human endometrium in natural vs. controlled ovarian stimulation cycles throughout the early-mid secretory transition using microarray technology. METHOD: Microarray data from 49 endometrial biopsies obtained from LH+1 to LH+9 (n=25) in natural cycles and from human chorionic gonadotropin (hCG) +1 to hCG+9 in controlled ovarian stimulation cycles (n=24) were analyzed using different methods, such as clustering, profiling of biological processes, and selection of differentially expressed genes, as implemented in Gene Expression Pattern Analysis Suite and Babelomics programs. RESULTS: Endometria from natural cycles followed different genomic patterns compared with controlled ovarian stimulation cycles in the transition from the pre-receptive (days LH/hCG+1 until LH/hCG+5) to the receptive phase (day LH+7/hCG+7). Specifically, we have demonstrated the existence of a 2-d delay in the activation/repression of two clusters composed by 218 and 133 genes, respectively, on day hCG+7 vs. LH+7. Many of these delayed genes belong to the class window of implantation genes affecting basic biological processes in the receptive endometrium. CONCLUSIONS: These results demonstrate that gene expression profiling of the endometrium is different between natural and controlled ovarian stimulation cycles in the receptive phase. Identification of these differentially regulated genes can be used to understand the different developmental profiles of receptive endometrium during controlled ovarian stimulation and to search for the best controlled ovarian stimulation treatment in terms of minimal endometrial impact.

Localization of S-nitrosoglutathione and expression of S-nitrosoglutathione reductase in pea plants under cadmium stress.

S-nitrosoglutathione (GSNO) is considered a natural nitric oxide (NO.) reservoir and a reactive nitrogen intermediate in animal cells, but little is known about this molecule and its metabolism in plant systems. In this work, using pea plants as a model system, the presence of GSNO in collenchyma cells was demonstrated by an immunohistochemical method. When pea plants were grown with a toxic Cd concentration (50 microM) the content of GSNO in collenchyma cells was drastically reduced. Determination of the nitric oxide (NO.) and gluthathione contents in leaves by confocal laser scanning microscopy and HPLC, respectively, showed a marked decrease of both compounds in plants treated with cadmium. The analysis of the S-nitrosoglutathione reductase (GSNOR) activity and its transcript expression in leaves showed a reduction of 31% by cadmium. These results indicate that GSNO is associated with a specific plant cell type, and this metabolite and its related catabolic activity, GSNOR, are both down-regulated under Cd stress.