- Open Access
Functional genomics of the pregnant uterus: from expectations to reality, a compilation of studies in the myometrium
BMC Pregnancy and Childbirth volume 7, Article number: S4 (2007)
Studies on the human myometrium have reported on different microarrays containing different sets of genes or ESTs. However each study profiled only a small number of patients due to various constraints. More profiling information would be an addition to our knowledge base of parturition.
We compiled from five human studies, transcriptional differences between the non pregnant myometrium (NP), preterm myometrium (PTNIL), term myometrium not in labor (TNIL) and term myometrium in labor (TIL). Software modules developed by the Draghici's group at Wayne State University (Detroit, MI, USA) were used to propose a hierarchical list of several KEGG pathways most likely adjusted to changes observed in microarray experiments.
The differential expression of 118 genes could be dispatched in 14 main KEGG pathways that were the most representative of the changes seen in NP and PTNIL, versus TNIL or TIL. Despite the potential of multiple pitfalls inherent to the use of the microarray technology, gene module analysis of the myometrial transcriptome reveals the activation of precise signaling pathways, some of which may have been under evaluated.
The remodelling and maturation processes that the uterus undergoes in pregnancy appear clearly as phenomena which last during the full course of gestation. It is attested by the nature of the main signaling pathways represented, in the comparison of the PTNIL versus TNIL uterus. Comparatively, the onset of labor is a phenomenon which remains less well characterized by these methods of analysis, possibly because it is a phenomenon occurring in too short a window to have been grasped by the studies carried out up to now.
The common hallmark of recently published papers referring to functional genomics is their enthusiastic tone on expectations. The near-entire genomic sequence of the human and several model animals has given the opportunity to flesh out the relationships between genes, phenotypes and global transcriptional status at unprecedented speed and scale . The microarray technology allows the examination of the function of thousands of genes at once and in parallel, thereby providing an "assay" of the transcriptional status of cells or tissues in a wide variety of physiological or pathophysiological situations . Computational methods allow the identification of genes differentially expressed across cell types, developmental stages or pathological conditions; genes expressed in a coordinated manner across a set of conditions and to delineate clusters of genes sharing coherent expression features . These techniques open up new areas of unrecognized molecular networks and yet unidentified players in the anabolic-catabolic balance in intracellular signaling cascades which have been so far hardly investigated in the context of preterm labor.
From past studies in domestic animals, it has amply been demonstrated that during pregnancy the production/withdrawal of sex steroids, notably that of progesterone which is thought to actively block the transformation of the myometrium to a contractile phenotype, govern the precise timing of labor onset . Steroids modulate transcription by interacting with specific response elements in the promoter regions of target genes to recruit the basic transcriptional complex. Although it is not yet definitively established whether functional progesterone withdrawal is indeed a pivotal event in the human parturition cascade , all the preceding elements point to the fact that transcriptome studies of the myometrium, fetal membranes or placenta, should be a valuable approach to decipher the mechanisms involved in human parturition. In the course of the last 6 years, a number of transcriptomic studies on the preterm versus term pregnant human uterus [6–12] or fetal membranes [13–17] have been published.
Studies on the human myometrium have reported on different microarrays containing different sets of genes or ESTs. However each study profiled only a small number of patients due to various constraints. More gene expression profiling information would be an addition to our knowledge base of parturition. We compiled from human studies [7–9, 12, 18], transcriptional differences between the preterm myometrium (PTNIL), term myometrium not in labor (TNIL) and term myometrium in labor (TIL).
To translate lists of hundreds of genes differentially regulated in the conditions under study into a clearer understanding, we used combinations of searches through the literature referenced in public databases (Table 1) and the Onto-Tools software developed by the Draghici's group at Wayne State University (Detroit, MI, USA) . The Onto-Express module helps to recognize functional profiles (using gene ontology terms) for the categories: biochemical function; biological process; cellular role; cellular component; molecular function, and chromosome location . The Pathway-Express module helps data mining – proposing on the basis of a computational method a hierarchical list of several KEGG pathways [21, 22] most likely adjusted to changes observed in microarray experiments [23, 24]. KEGG is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information . Input data files for use with the Onto-Tools software modules were built on gene lists reported in published papers or, when available, on the complete gene expression data set, deposited as supplemental data at a public Internet site [7–9, 12, 18].
Genomic studies of the uterus remain scarce and accounted for approximately 1% of the total of genomic studies published in the past 6 years. Studies in pregnancy represented about 1/3 of the total studies on the uterus and studies specifically dedicated to the myometrium were even fewer (Figure 1).
In the myometrium, the differential expression of 118 genes could be distributed in 14 main KEGG pathways that were the most representative of the changes seen in NP versus TNIL, or PTNIL versus TNIL or TIL. It is to notice that expression of genes involved in growth and cytoskeletal remodeling of myometrial cells was critically modified in the comparison of the non pregnant versus pregnant uterus, until term. Conversely, limited changes in gene transcription, characterized the transition between the term and term in labor stages in the myometrium. Interestingly, genes involved in apoptosis were only expressed in advanced gestation and their changes clearly anticipated the onset of labor (Table 2).
Table 3 lists the genes expressed in the uterus for the MAPK signaling pathway which is a good example of a pathway whose changes remain active until the end of pregnancy. An overall picture of the general trend of changes in gene expression pertaining to the 14 KEGG pathways that characterize the transition of the preterm versus term uterus is summarized in Figure 2.
Drawbacks and limitations inherent to the use of Onto-Tools or of their cognate alternatives for ontological analysis have been discussed. These limitations remain to the present day, questions over the robustness of array data and the criteria under which their conclusions were drawn have been made . A recent review by Allison et al. , has the merit of proposing simple sound recommendations for future microarrays analysis methods.
Despite the potential of pitfalls inherent to the use of the microarray technology (review in ), gene module analysis of the myometrial transcriptome reveals the activation of precise signaling pathways, some of which may have been under evaluated. Thus, the remodelling and maturation processes that the uterus undergoes in pregnancy appear clearly as phenomena which last during the full course of gestation. It is attested by the nature of the main signaling pathways represented, in the comparison of the PTNIL versus TNIL uterus. Comparatively, the onset of labor is a phenomenon which remains less well described by these methods of analysis, possibly because it is a phenomenon occurring in too short a window to have been grasped by the few studies carried out up to now.
Also, although the myometrium is considered to be a relatively homogeneous tissue, some of its largest changes at term occurred in genes that were not normally associated with muscle. This is consistent with animal studies which better allow to explore the global pattern of gene expression and their co-regulation on the basis of their genomic location over the full time-course of myometrial transformation or following experimentally-controlled infection [28–31].
Today, a main handicap with high throughput methods is the capacity for each individual research group to handle samples and data. These methods indeed suggested a number of potentially new biochemical markers of preterm labor , some of which, for example, could be detected in circulating immune-cells. However, all studies, notably in the human, have suffered from several limitations, among which are the limited size of samples which hardly can be considered as representative of even a small population; the regular inconsistency in nomenclature usage or terminology in reference to the molecules studied; the lack of integrated databases to compile different studies and the underestimation of heterogeneity of the tissue exposed to the microarray analysis.
Genomic studies of the pregnant uterus, like in other domains, widen our comprehension of the structural and metabolic transformations which affect the myometrium from the beginning of pregnancy until parturition. Although the studies so far published remain a few numbers, they throw light on the urgent need to constitute a Working Group to standardize the techniques, terminology and experimental plans as well as to design new integrated databasing protocols. In this respect we have much to learn from those who anticipated the burst of genome biology . Access to dedicated databases by researchers and clinicians will be critical to progress in biomarker identification for the major obstetrical concern, namely the preterm birth.
cell adhesion molecules
expressed sequence tags
G-protein coupled membrane receptors
Janus kinases/Signal transducers and activators of transcription
Kyoto Encyclopedia of Genes and Genomes
mitogen-activated protein kinase
Online Mendelian Inheritance in Man
preterm not in labor
transforming growth factor
term myometrium in labor
term not in labor
- Wnt protein/signaling:
wingless-type protein/signaling. Gene names, see  for detailed names of genes listed in this article.
White KP: Functional genomics and the study of development, variation and evolution. Nat Rev Genet. 2001, 2 (7): 528-537. 10.1038/35080565.
Dunckley T, Coon KD, Stephan DA: Discovery and development of biomarkers of neurological disease. Drug Discov Today. 2005, 10 (5): 326-334. 10.1016/S1359-6446(04)03353-7.
Claverie JM: Computational methods for the identification of differential and coordinated gene expression. Hum Mol Genet. 1999, 8 (10): 1821-1832. 10.1093/hmg/8.10.1821.
Bosc MJ, Germain G, Nicolle A, Mouren M, Philibert D, Baulieu EE: Control of birth in rats by RU 486, an antiprogesterone compound. J Reprod Fertil. 1987, 79 (1): 1-8.
Mesiano S: Myometrial progesterone responsiveness and the control of human parturition. J Soc Gynecol Investig. 2004, 11 (4): 193-202. 10.1016/j.jsgi.2003.12.004.
Aguan K, Carvajal JA, Thompson LP, Weiner CP: Application of a functional genomics approach to identify differentially expressed genes in human myometrium during pregnancy and labour. Mol Hum Reprod. 2000, 6 (12): 1141-1145. 10.1093/molehr/6.12.1141.
Charpigny G, Leroy MJ, Breuiller-Fouche M, Tanfin Z, Mhaouty-Kodja S, Robin P, Leiber D, Cohen-Tannoudji J, Cabrol D, Barberis C, et al: A functional genomic study to identify differential gene expression in the preterm and term human myometrium. Biol Reprod. 2003, 68 (6): 2289-2296. 10.1095/biolreprod.102.013763.
Bethin KE, Nagai Y, Sladek R, Asada M, Sadovsky Y, Hudson TJ, Muglia LJ: Microarray analysis of uterine gene expression in mouse and human pregnancy. Mol Endocrinol. 2003, 17 (8): 1454-1469. 10.1210/me.2003-0007.
Rehman KS, Yin S, Mayhew BA, Word RA, Rainey WE: Human myometrial adaptation to pregnancy: cDNA microarray gene expression profiling of myometrium from non-pregnant and pregnant women. Mol Hum Reprod. 2003, 9 (11): 681-700. 10.1093/molehr/gag078.
Bailey J, Europe-Finner GN: Identification of human myometrial target genes of the c-Jun NH2-terminal kinase (JNK) pathway: the role of activating transcription factor 2 (ATF2) and a novel spliced isoform ATF2-small. J Mol Endocrinol. 2005, 34 (1): 19-35. 10.1677/jme.1.01608.
Bailey J, Tyson-Capper AJ, Gilmore K, Robson SC, Europe-Finner GN: Identification of human myometrial target genes of the cAMP pathway: the role of cAMP-response element binding (CREB) and modulator (CREMalpha and CREMtau2alpha) proteins. J Mol Endocrinol. 2005, 34 (1): 1-17. 10.1677/jme.1.01594.
Havelock JC, Keller P, Muleba N, Mayhew BA, Casey BM, Rainey WE, Word RA: Human myometrial gene expression before and during parturition. Biol Reprod. 2005, 72 (3): 707-719. 10.1095/biolreprod.104.032979.
Marvin KW, Keelan JA, Eykholt RL, Sato TA, Mitchell MD: Expression of angiogenic and neurotrophic factors in the human amnion and choriodecidua. Am J Obstet Gynecol. 2002, 187 (3): 728-734. 10.1067/mob.2002.125286.
Ognjanovic S, Bryant-Greenwood GD: Pre-B-cell colony-enhancing factor, a novel cytokine of human fetal membranes. Am J Obstet Gynecol. 2002, 187 (4): 1051-1058. 10.1067/mob.2002.126295.
Tashima LS, Yamamoto SY, Yasuda M, Millar LK, Bryant-Greenwood GD: Decidual relaxins: gene and protein up-regulation in preterm premature rupture of the membranes by complementary DNA arrays and quantitative immunocytochemistry. Am J Obstet Gynecol. 2002, 187 (3): 785-797. 10.1067/mob.2002.125763.
Keelan JA, Blumenstein M, Helliwell RJ, Sato TA, Marvin KW, Mitchell MD: Cytokines, prostaglandins and parturition–a review. Placenta. 2003, 24 (Suppl A): S33-46. 10.1053/plac.2002.0948.
Ogita K, Kimura T, Nakamura H, Koyama S, Tsujie T, Tomiie M, Tsutsui T, Shimoya K, Wada Y, Koyama M, et al: Differential expression and localization of decorin in human choriodecidual membrane during preterm and term pregnancy. Am J Reprod Immunol. 2004, 51 (3): 204-210. 10.1111/j.1600-0897.2004.00143.x.
Esplin MS, Fausett MB, Peltier MR, Hamblin S, Silver RM, Branch DW, Adashi EY, Whiting D: The use of cDNA microarray to identify differentially expressed labor-associated genes within the human myometrium during labor. Am J Obstet Gynecol. 2005, 193 (2): 404-413. 10.1016/j.ajog.2004.12.021.
Intelligent Systems and Bioinformatics Laboratory. [http://vortex.cs.wayne.edu/Projects.html]
Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA: Global functional profiling of gene expression. Genomics. 2003, 81 (2): 98-104. 10.1016/S0888-7543(02)00021-6.
Kanehisa M: A database for post-genome analysis. Trends Genet. 1997, 13 (9): 375-376. 10.1016/S0168-9525(97)01223-7.
Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28 (1): 27-30. 10.1093/nar/28.1.27.
Khatri P, Draghici S: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics. 2005, 21 (18): 3587-3595. 10.1093/bioinformatics/bti565.
Khatri P, Sellamuthu S, Malhotra P, Amin K, Done A, Draghici S: Recent additions and improvements to the Onto-Tools. Nucleic Acids Res. 2005, W762-765. 10.1093/nar/gki472. 33 Web Server
The KEGG Pathway Database. [http://www.genome.jp/kegg/pathway.html]
Allison DB, Cui X, Page GP, Sabripour M: Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet. 2006, 7 (1): 55-65. 10.1038/nrg1749.
Tarca AL, Romero R, Draghici S: Analysis of microarray experiments of gene expression profiling. Am J Obstet Gynecol. 2006, 195 (2): 373-388. 10.1016/j.ajog.2006.07.001.
Wu WX, Zhang Q, Ma XH, Unno N, Nathanielsz PW: Suppression subtractive hybridization identified a marked increase in thrombospondin-1 associated with parturition in pregnant sheep myometrium. Endocrinology. 1999, 140 (5): 2364-2371. 10.1210/en.140.5.2364.
Muhle RA, Pavlidis P, Grundy WN, Hirsch E: A high-throughput study of gene expression in preterm labor with a subtractive microarray approach. Am J Obstet Gynecol. 2001, 185 (3): 716-724. 10.1067/mob.2001.117183.
Girotti M, Zingg HH: Gene expression profiling of rat uterus at different stages of parturition. Endocrinology. 2003, 144 (6): 2254-2265. 10.1210/en.2002-0196.
Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR: Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005, 6 (2): R12-10.1186/gb-2005-6-2-r12.
Breuiller-Fouche M, Germain G: Gene and protein expression in the myometrium in pregnancy and labor. Reproduction. 2006, 131 (5): 837-850. 10.1530/rep.1.00725.
Lewis SE: Gene Ontology: looking backwards and forwards. Genome Biol. 2005, 6 (1): 103-10.1186/gb-2004-6-1-103.
Online Mendelian Inheritance in Man. [http://www.ncbi.nlm.nih.gov/omim/]
We wish to acknowledge the sponsorship of Ferring, PerkinElmer and Serono, who helped to cover publishing charges of the article. We are also indebted to the financial support and organization by the EU project SAFE (The Special Non-Invasive Advances in Fetal and Neonatal Evaluation Network, LSHB-CT-2004-503243) of the 2005 and 2006 PTL workshops, where data of this article were presented as oral communications.
This article has been published as part of BMC Pregnancy and Childbirth Volume 7, Supplement 1, 2007: Proceedings of the First and Second European Workshops on Preterm Labour of the Special Non-Invasive Advances in Fetal and Neonatal Evaluation (SAFE) Network of Excellence. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2393/7?issue=S1.
The authors declare that they have no competing interests.
MBF carried out the searches through the literature referenced in public databases and helped to draft the manuscript. GC participated in the design of the study and helped to perform the statistical analysis. GG conceived the study, contributed to its statistical analysis and finalized the draft of the manuscript. All authors read and approved the final manuscript.
Michèle Breuiller-Fouche, Gilles Charpigny contributed equally to this work.