Strategy for elucidating differentially expressed genes in leiomyomata identified by microarray technology

Integrated analysis reveals candidate mRNA and their potential roles in uterine leiomyomas

AIM

Uterine leiomyomas (UL) are the most common pelvic tumors, and the etiology and pathophysiology are not well understood. We aimed to elucidate the genes responsible for UL development.

METHODS

Integrated analyses of four datasets of mRNA profiling for UL were performed. Functional annotation of differentially expressed genes (DEG) was used to systematically characterize the global expression profiles. The UL-specific protein-protein interaction network was constructed.

RESULTS

Integrated analysis led to the discovery of 2167 DEG (1042 upregulated and 1125 downregulated). The aberrant expression of NAV2, KIF5C, DCX, CAPN6, COL4A2, ALDH1A1, and DPT may play important roles in UL tumorigenesis. In addition, the dysregulation of MEST, LGALS3, and TLR3 may be involved in the progression of UL by a common mechanism. Functional annotation showed that extracellular matrix receptor interaction may be more active and cause the extracellular matrix abnormally formed in UL. Moreover, focal adhesion and cell adhesion molecules may play roles in the development of UL. Furthermore, chemokine signaling pathway and cytokine-cytokine receptor interaction were most probably involved in the development of UL.

CONCLUSION

In conclusion, our study observed that a set of aberrantly expressed genes and the related biochemical pathways may lead to transformation of normal myometrium in pathological focuses.

Missense mutations in exon 2 of the MED12 gene are involved in IGF-2 overexpression in uterine leiomyoma

Uterine leiomyoma (UL), the most common benign tumour found in females, is associated with many recurrent genetic aberrations, such as translocations, interstitial deletions and specific germline mutations. Among these, mutations affecting exon 2 of the mediator complex subunit 12 (MED12) gene are commonly detected in the majority of ULs. Mutational analysis of the MED12 gene, performed on 36 UL samples, revealed that 12 leiomyomas (33.4%) exhibited heterozygous missense mutations in codon 44 of exon 2 of the MED12 gene, four leiomyomas (11.1%) showed internal in-frame deletions, and two leiomyomas (5.5%) exhibited deletions involving intron 1-exon 2 junction, which caused a predicted loss of the splice acceptor. No mutations were detected in uterine myometrium (UM) and pseudocapsule (PC) samples, including those from women with a MED12 mutation in UL. These data showed that the PC is a healthy tissue that surrounds the UL to maintain UM integrity. Analysis of insulin-like growth factor 2 (IGF-2) and collagen type IV alpha 2 (COL4A2) mRNA expression levels in the same set of ULs revealed that only those with MED12 missense mutations expressed significantly higher levels of IGF-2 mRNA. In contrast, MED12 gene status does not appear to affect mRNA expression levels of the COL4A2 gene. On the basis of this finding, we suggest that the MED12 status stratifies the ULs into two mutually exclusive pathways of leiomyoma genesis, one with IGF-2 overexpression and the other with no IGF-2 activation. The occurrence of IGF-2 overexpression could be therapeutically targeted for the non-surgical treatment of leiomyomas.

Gene expression analysis reveals an angiogenic profile in uterine leiomyoma pseudocapsule

The pseudocapsule (PC) of the uterine leiomyoma (UL) is an anatomic entity that surrounds the myoma separating it from the myometrium (UM). Although a number of microarray experiments have identified differences in gene expression profile in the UL when compared with the UM, there is a lack of systematic studies on the PC. In this study, quantitative RT-PCR analysis was performed on 18 matched PC, UL and UM specimens and results showed that the PC displays a specific gene expression profile. The low expression level of insulin-like growth factor (IGF-2), a fibroid specific marker, that we found in the PC and the UM when compared with the UL, clearly indicates that the PC is in structural continuity with the UM. However, the significant increase in endoglin expression level in PC with respect to the UL and UM indicates that an active neoangiogenesis is present in PC. Conversely, other angiogenic factors such as von Willebrand factor (vWF) and vascular endothelial growth factor A (VEGF-A) seem to have little influence on the PC angiogenesis. Because the endoglin is preferentially expressed in proliferating endothelial cells, whereas the vWF and VEGF-A are preferentially expressed in preexisting endothelial cells, our idea is that the angiogenic activity in the PC is linked to wound healing. The angiogenic activity is also sustained by intermediate expression level of cystein-rich angiogenesis inducer 61, connective tissue growth factor and collagen 4α2 genes all involved in the neoangiogenesis, that we detected in the PC. Taken together our data demonstrate that the specific expression pattern observed in the PC could be the response of the uterine wall's smooth cells to the tension imposed by the tumor. As a consequence, a neovascular structure is generated involving regenerative processes. For these reasons, we suggest that the laparoscopic intracapsular myomectomy (LIM), a new surgical technique that preserves the PC during the UL removal, should always be preferred, to favor a faster and proper uterine healing.

Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma

Background

Uterine leiomyomas, or fibroids, represent the most common benign tumor of the female reproductive tract. Fibroids become symptomatic in 30% of all women and up to 70% of African American women of reproductive age. Epigenetic dysregulation of individual genes has been demonstrated in leiomyoma cells; however, the in vivo genome-wide distribution of such epigenetic abnormalities remains unknown.

Principal Findings

We characterized and compared genome-wide DNA methylation and mRNA expression profiles in uterine leiomyoma and matched adjacent normal myometrial tissues from 18 African American women. We found 55 genes with differential promoter methylation and concominant differences in mRNA expression in uterine leiomyoma versus normal myometrium. Eighty percent of the identified genes showed an inverse relationship between DNA methylation status and mRNA expression in uterine leiomyoma tissues, and the majority of genes (62%) displayed hypermethylation associated with gene silencing. We selected three genes, the known tumor suppressors KLF11, DLEC1, and KRT19 and verified promoter hypermethylation, mRNA repression and protein expression using bisulfite sequencing, real-time PCR and western blot. Incubation of primary leiomyoma smooth muscle cells with a DNA methyltransferase inhibitor restored KLF11, DLEC1 and KRT19 mRNA levels.

Conclusions

These results suggest a possible functional role of promoter DNA methylation-mediated gene silencing in the pathogenesis of uterine leiomyoma in African American women.

Activin-A and myostatin response and steroid regulation in human myometrium: disruption of their signalling in uterine fibroid

CONTEXT

Investigation of activin-A (A) and myostatin (M) in human myometrium (HM) and leiomyoma (HL) will explain their involvement in human myometrial pathophysiology.

OBJECTIVE

We aimed to investigate A and M response and steroid regulation in HM. We also evaluated A and M expression and response in HL.

DESIGN

Tissues were analyzed and cultured.

PATIENTS

Patients included fertile (in proliferative phase) and menopausal women undergoing hysterectomy.

INTERVENTIONS

HM explant cultures were treated with A and M (for Smad-7 mRNA quantification) or estrogen and progesterone (for A and M mRNA quantification). A and M expression levels were also evaluated in menopausal (physiological absence of steroids) HM specimens. A and M and their receptors were evaluated in HL (n = 8, diameter 5-8 cm) compared with their matched HM. HL explants cultures were treated with A and M (for Smad7 mRNA quantification), and, to explain the absence of response, the levels of follistatin, follistatin-related gene (FLRG), and Cripto were evaluated.

RESULTS

A and M increased Smad7 expression in HM explants. A and M mRNAs were both reduced after estradiol treatment, unchanged after progesterone treatment, but were higher in menopausal than fertile (in proliferative phase) specimens. A, M, and FLRG were expressed at higher levels in HL compared with adjacent HM, whereas the receptors, follistatin, and Smad7 mRNAs resulted unchanged. Cripto mRNA was expressed only in HL.

CONCLUSIONS

A and M act on human HM and are regulated by steroids. In HL there is an increase of A, M, FLRG, and Cripto expression.

Transforming growth factor beta3 regulates the versican variants in the extracellular matrix-rich uterine leiomyomas

Uterine leiomyoma are common, benign tumors that are enriched in extracellular matrix. The tumors are characterized by a disoriented and loosely packed collagen fibril structure similar to other diseases with disrupted Transforming growth factor beta (TGF-beta) signaling. Here we characterized TGF-beta3 signaling and the expression patterns of the critical extracellular matrix component versican in leiomyoma and myometrial tissue and cell culture. We also demonstrate the regulation of the versican variants by TGF-beta3. Using leiomyoma and matched myometrium from 15 patients, messenger RNA (mRNA) from leiomyoma and myometrium was analyzed by semiquantitative real time reverse transcription-polymerase chain reaction (RT-PCR), while protein analysis was done by western blot. Transforming growth factor beta3 transcripts were increased 4-fold in leiomyoma versus matched myometrium. Phosphorylated-TGF-beta RII and phosphorylated-Smad 2/3 complex were greater in leiomyoma as documented by Western blot. The inhibitor Smad7 transcripts were decreased 0.44-fold. The glycosaminoglycan (GAG)-rich versican variants were elevated in leiomyoma versus myometrial tissue: specifically V0 (4.27 +/- 1.12) and V1 (2.01 +/- 0.27). Treatment of leiomyoma and myometrial cells with TGF-beta3 increased GAG-rich versican variant expression 7 to 12 fold. Neutralizing TGF-beta3 antibody decreased the expression of the GAG-rich versican variants 2 to 8 fold in leiomyoma cells. Taken together, the aberrant production of excessive and disorganized extracellular matrix that defines the leiomyoma phenotype involves the activation of the TGF-beta signaling pathway and excessive production of GAG-rich versican variants.

Genic expression of the uterine leiomyoma in reproductive-aged women after treatment with goserelin

OBJECTIVE

To identify the genes presenting different expression in uterine leiomyomas after goserelin treatment.

DESIGN

Retrospective analyses of tissue obtained in a prospective clinical study.

SETTING

School of Medicine of the University of São Paulo.

PATIENT(S)

30 nulliparous black women aged 20 to 45 years with symptoms of uterine leiomyoma, uterine volume over 300 mL, and surgical indications for myomectomy.

INTERVENTION(S)

Fifteen patients were given a monthly dose of 3.6 mg of goserelin over 3 months before surgery (group A), and 15 patients underwent surgery without any previous treatment (group B). Five random samples from each group were analyzed using the microarray technique with the Affymetrix platform (GeneChip Rat Genome 230 2.0 Array).

MAIN OUTCOME MEASURE(S)

Quantification of transcript expression levels of uterine fibroids in patients treated or not treated with goserelin.

RESULT(S)

Of the total of 47,000 sequences that were analyzed, representing approximately 38,500 human genes already characterized, we found a differential expression of 174 genes. Of these, 70 were up-regulated (33 genes with known function) and 104 were down-regulated (65 genes with known function) in samples from group A (treated) when compared with group B (nontreated).

CONCLUSION(S)

The genic expression of uterine leiomyomas changes in women who have had goserelin treatment when compared with nontreated patients.

Expression of insulin-like growth factors (IGFs) and IGF signaling: molecular complexity in uterine leiomyomas

OBJECTIVE

To study whether dysregulation of insulin-like growth factors (IGFs) and IGF signaling are common molecular changes in symptomatic leiomyomas (fibroids) and whether IGFs are associated with large fibroids.

DESIGN

Examination of IGFs and IGF pathway genes in a large cohort of fibroids at transcriptional and translational levels. Mechanisms leading to alterations of IGFs and related genes were also analyzed.

SETTING

University clinical research laboratory.

PATIENT(S)

Hysterectomies for symptomatic fibroids were collected: 180 cases from paraffin-embedded tissues and 50 cases from fresh-frozen tissues.

INTERVENTION(S)

Tissue microarray and immunohistochemistry, DNA methylation analysis, reverse-transcriptase polymerase chain reaction, and Western blot.

MAIN OUTCOME MEASUREMENT(S)

Transcription and translation analyses of IGF-1/2, p-AKT, p-S6K, and TSC1/2 in fibroids and matched myometrium.

RESULT(S)

Insulin-like growth factors and downstream effectors were dysregulated in approximately one third of fibroids. All except for IGF-2 seemed to be abnormally regulated at translation levels. Up-regulation of IGF-2 messenger RNAs was contributed by all four alternating slicing promoters. There was a positive correlation of IGF-1 and p-AKT over-expression with fibroid size. Insulin-like growth factor 1 but not IGF-2 levels directly correlated with activation of p-AKT and p-S6K.

CONCLUSION(S)

Altered expressions of IGFs and their related downstream proteins were found in one third of fibroids. Large fibroids show high levels of IGF-1 and p-AKT activity compared with small ones.

Sample size calculation for microarray experiments with blocked one-way design

Background

One of the main objectives of microarray analysis is to identify differentially expressed genes for different types of cells or treatments. Many statistical methods have been proposed to assess the treatment effects in microarray experiments.

Results

In this paper, we consider discovery of the genes that are differentially expressed among K (> 2) treatments when each set of K arrays consists of a block. In this case, the array data among K treatments tend to be correlated because of block effect. We propose to use the blocked one-way ANOVA F-statistic to test if each gene is differentially expressed among K treatments. The marginal p-values are calculated using a permutation method accounting for the block effect, adjusting for the multiplicity of the testing procedure by controlling the false discovery rate (FDR). We propose a sample size calculation method for microarray experiments with a blocked one-way design. With FDR level and effect sizes of genes specified, our formula provides a sample size for a given number of true discoveries.

Conclusion

The calculated sample size is shown via simulations to provide an accurate number of true discoveries while controlling the FDR at the desired level.

Activating transcription factor 3 gene expression suggests that tissue stress plays a role in leiomyoma development

OBJECTIVE

To determine whether expression of the stress response gene ATF3 and related members of activator protein complex-1, cJun and cFos, were altered in leiomyoma compared with myometrium, and whether this difference might correlate with leiomyoma size or race.

DESIGN

Laboratory study.

SETTING

University hospital.

PATIENT(S)

Fifteen women undergoing hysterectomy for symptomatic leiomyoma.

INTERVENTION(S)

Tissue procurement, RNA isolation, reverse-transcriptase polymerase chain reaction, real-time reverse-transcriptase polymerase (RT-PCR) chain reaction, immunohistochemistry, Western blot.

MAIN OUTCOME MEASURE(S)

Expression of mRNA and protein in leiomyoma and patient-matched myometrium.

RESULT(S)

mRNA transcripts of ATF3 were decreased in leiomyoma compared with matched myometrium by both RT-PCR and real-time RT-PCR. The decrease was greater than fivefold in a majority of samples. The reduction seen in ATF3 mRNA expression did not show a correlation with race and leiomyoma size. Surprisingly, immunohistochemistry and Western blot analysis demonstrated an elevation of ATF3 protein expression by a mean of 2.9-fold. Transcripts of related AP-1 genes, cJun and cFos, were significantly decreased by a mean of -29.57 for cJun and -23.78 for cFos, but there was no significant change in protein expression of the two transcription factors.

CONCLUSIONS

Alterations in ATF3 gene expression resemble the response to mechanical and ischemic stress reported in other tissues. Results suggested that ATF3 protein expression was increased in leiomyoma, and may reflect increased tissue stress.

Gene expression profiling of multiple leiomyomata uteri and matched normal tissue from a single patient

OBJECTIVE

To identify differentially expressed genes between fibroid and adjacent normal myometrium in an identical hormonal and genetic background.

DESIGN

Array analysis of three leiomyomata and matched adjacent normal myometrium in a single patient.

SETTING

University of Colorado Hospital.

PATIENT(S)

A single female undergoing medically indicated hysterectomy for symptomatic fibroids.

INTERVENTIONS(S)

mRNA isolation and microarray analysis, reverse-transcriptase polymerase chain reaction, Western blotting, and immunohistochemistry.

MAIN OUTCOME MEASURE(S)

Changes in mRNA and protein levels in leiomyomata and matched normal myometrium.

RESULT(S)

Expression of 197 genes was increased and 619 decreased significantly by at least twofold, in leiomyomata relative to normal myometrium. Expression profiles between tumors were similar and normal myometrial samples showed minimal variation. Changes in, and variation of, expression of selected genes were confirmed in additional normal and leiomyoma samples from multiple patients.

CONCLUSION(S)

Analysis of multiple tumors from a single patient confirmed changes in expression of genes described in previous, apparently disparate, studies, and identified novel targets. Gene expression profiles in leiomyomata are consistent with increased activation of mitogenic pathways and inhibition of apoptosis. Down-regulation of genes implicated in invasion and metastasis, of cancers, was observed in fibroids. This expression pattern may underlie the benign nature of uterine leiomyomata and may aid in the differential diagnosis of leiomyosarcoma.

Mechanical homeostasis is altered in uterine leiomyoma

OBJECTIVE

Uterine leiomyoma produce an extracellular matrix (ECM) that is abnormal in its volume, content, and structure. Alterations in ECM can modify mechanical stress on cells and lead to activation of Rho-dependent signaling and cell growth. Here we sought to determine whether the altered ECM that is produced by leiomyoma was accompanied by an altered state of mechanical homeostasis.

STUDY DESIGN

We measured the mechanical response of paired leiomyoma and myometrial samples and performed immunogold, confocal microscopy, and immunohistochemical analyses.

RESULTS

Leiomyoma were significantly stiffer than matched myometrium. The increased stiffness was accompanied by alteration of the ECM, cell shape, and cytoskeleton in leiomyoma, compared with myometrial samples from the same uterus. Levels of AKAP13, a protein that is known to activate Rho, were increased in leiomyoma compared to myometrium. AKAP13 was associated with cytoskeletal filaments of immortalized leiomyoma cells.

CONCLUSION

Leiomyoma cells are exposed to increased mechanical loading and show structural and biochemical features that are consistent with the activation of solid-state signaling.

Effects of a protein kinase C inhibitor on the initial development of ectopic implants in a syngeneic mouse model of endometriosis

OBJECTIVE

To evaluate the effect of protein kinase C inhibition on surgically induced endometriosis in mice.

DESIGN

Prospective, randomized study.

SETTING

Academic facility.

ANIMALS

Sixty adult female C57BJ6 mice.

INTERVENTION(S)

On day -7, oral gavage of a vehicle alone or of a protein kinase C inhibitor (100 mg/kg/day, once a day) was started and continued for 1 week in donor groups A and B, respectively. On day 0, uterine fragments from donor group A were implanted into recipient mice. Recipient mice were divided randomly into two groups: group 1 (vehicle) and group 2 (protein kinase C inhibitor). Uterine fragments from donor group B were implanted into recipient mice, and they were divided randomly into two groups: group 3 (vehicle) and group 4 (protein kinase C inhibitor). Oral gavage of a protein kinase C inhibitor (100 mg/kg/day, once a day) or vehicle was continued for 1 week.

MAIN OUTCOME MEASURE(S)

Presence and number of ectopic implants.

RESULT(S)

The number of mice that developed ectopic implants was significantly lower in groups 3 (40%) and 4 (30%) than in group 1 (100%). The number of ectopic implants was significantly lower in groups 2, 3, and 4 than in group 1.

CONCLUSION(S)

Protein kinase C inhibitor use partially prevented the development of ectopic implants in a mouse model of endometriosis.

Compensatory alterations in energy homeostasis characterized in uterine tumors from hereditary leiomyomatosis and renal cell cancer

OBJECTIVE

To determine the molecular alterations that maintain energy homeostasis in hereditary leiomyomatosis and renal cell cancer (HLRCC) uterine tumors with disrupted fumarate hydratase, compared with nonsyndromic uterine tumors.

DESIGN

Laboratory study.

SETTING

Tertiary academic university hospital.

PATIENT(S)

Eleven nonsyndromic leiomyoma-myometrium pairs and three HLRCC leiomyoma-myometrium pairs were obtained from patients who were recruited at national and military research centers in the United States.

INTERVENTION(S)

Molecular analysis.

MAIN OUTCOME MEASURE(S)

Hereditary leiomyomatosis and renal cell cancer and nonsyndromic leiomyomas were compared with patient-matched myometrium for relative glycolysis and Krebs cycle gene expression.

RESULT(S)

By microarray analysis, we confirmed that fumarate hydratase messenger RNA (mRNA) was underexpressed in HLRCC fibroids, compared with matched myometrium. Consistent with the possibility that alterations in fumarate hydratase represented a change to a more anaerobic state, we found that HLRCC fibroids overexpressed genes such as phosphofructokinase, aldolase, phosphoglycerate kinase, enolase, and pyruvate kinase. Expression of these genes was not altered in nonsyndromic leiomyomas. Furthermore, there were no overt changes in expression of Krebs cycle enzyme gene expression, with the exception of fumarate hydratase.

CONCLUSION(S)

Our findings demonstrate that alterations in fumarate hydratase are compensated for by increases in glycolysis enzyme expression in HLRCC.

Retinoic acid pathway genes show significantly altered expression in uterine fibroids when compared with normal myometrium

Fibroids are benign neoplasms of myometrial smooth muscle cells (SMC). Despite being the most common tumor in humans, their etiology is poorly understood. Recent microarray studies have demonstrated that multiple members of the retinoid pathway are differentially expressed between myometrium and fibroids. The aim of this present study was to investigate gene expression of members of the retinoid pathway in matched myometrium and fibroids. We have demonstrated differential gene expression of two binding proteins [cellular retinol-binding proteins (CRBP) 1 and 2], three enzymes [alcohol dehydrogenase 1 (ADH1), aldehyde dehydrogenase (ALDH1) and retinol dehydrogenase (RODH)] and two receptors [retinoid X receptors (RXR) alpha and gamma] involved in the retinoid pathway by real-time PCR. There were no differences in gene expression for retinoid receptors RARalpha, beta, gamma and RXRbeta, and for the metabolizing enzyme cytochrome P450, family 26 subfamily A. We confirmed results for ADH1, ALDH1, CRBP1 and CRABP2 at the protein level by western blot. Using immunohistochemistry these proteins were mostly localized to myometrial and fibroid SMC. An exception to this was ALDH1 protein, which displayed strong staining localized to cells of the connective tissue, presumably fibroblasts, with a striking differential expression pattern between myometrium and fibroids. These results demonstrate that the retinoid pathway is altered in fibroids when compared with normal myometrium and specifically identify ALDH1 in fibroid fibroblasts. These alterations can lead to aberrant retinoic acid (RA) production and signaling, and alter the expression of RA target genes, which may be an important step in fibroid development.

Uterine leiomyomas express a molecular pattern that lowers retinoic acid exposure

OBJECTIVE

To analyze expression of the retinoic acid signaling pathway genes that are involved in retinol metabolism, transport, transcriptional activation, and transcriptional products in spontaneous human leiomyomas.

DESIGN

Laboratory study of human leiomyoma and patient-matched myometrial tissue.

PATIENT(S)

Eight women undergoing hysterectomy for symptomatic leiomyomas.

INTERVENTION(S)

Confirmation of an altered retinoic acid pathway analyzed by microarray, real time reverse transcription-polymerase chain reaction, Western blot, immunohistochemistry, and high-performance liquid chromatography (HPLC).

MAIN OUTCOME MEASURE(S)

Gene and protein expression.

RESULT(S)

Regardless of patient demographics and leiomyoma location and size, we found decreased expression of the major genes involved in retinoic acid pathway including alcohol dehydrogenase-1 (-3.97- +/- 0.03-fold), aldehyde dehydrogenase-1 (-3.1- +/- 0.07-fold), cellular retinol binding protein-1 (-2.62- +/- 0.04-fold), and cellular retinoic acid binding protein-1 (-2.42- +/- 0.20-fold). Cytochrome P450 (CYP 26A1), which is responsible for retinoic acid metabolism, was highly up-regulated in leiomyomas (+5.4- +/- 0.53-fold). Nuclear receptors demonstrated a complex pattern of under-expression (RARalpha, RARbeta, RXRalpha, RXRgamma) and over-expression (RARgamma, RXRbeta) at both the mRNA and protein level. Differences in protein amounts were confirmed by Western blot. Finally, a reduced amount of cellular ATRA and 9-cis retinoic acid was confirmed by HPLC in leiomyomas compared with myometrial tissues.

CONCLUSION(S)

Molecular alterations in the retinoic acid pathway of leiomyomata result in a decrease in retinoic acid exposure.

The effect of the readthrough acetylcholinesterase variant (AChE-R) on uterine muscle and leiomyomas

Acetylcholine signaling and acetylcholinesterase (AChE) function(s) are pivotal elements in muscle development. The effects of the stimulus-dependent readthrough AChE variant, AChE-R, on leiomyomas and normal myometrium proliferation were assessed in vivo and in vitro. Histological preparations and cell cultures therefrom were obtained during hysterectomies or myomectomies and included both the leiomyoma sample and the adjacent normal uterine muscle as control. In situ hybridization procedures were performed using AChE cRNA probes complementary to the human AChE-R transcript. Antibodies against the AChE-R variant served for immunohistochemical staining. To determine the biological function of AChE-R on the uterine muscle cell cultures, we used a synthetic peptide representing the potentially cleavable morphogenically active C-terminus of AChE-R (ARP). Cell proliferation was assessed using the incorporation of 5'-bromo-2-deoxyuridine (BrDU). Leiomyomas expressed an excess of AChE-R mRNA and the AChE-R protein compared with the normal myometrium. Cell cultures originating from leiomyomas proliferated significantly faster than cultures from the adjacent myometrium (P = 0.027 at BrDU incorporation). Addition of ARP (2-200 nM) caused a dose-dependent decrease in the proliferation of cell cultures from both leiomyomas and the myometrium. The effect on the myometrium reached statistical significance (at 20 and 200 nM, P = 0.02), whereas the variability of the rapidly proliferating primary cultures was high and precluded statistical significance in the leiomyoma cultures. AChE-R is involved in the proliferation of the myometrium. The inhibitory effect of ARP on the myometrium may suggest a future therapeutic role of ARP.

Human myometrium and leiomyomas express gonadotropin-releasing hormone 2 and gonadotropin-releasing hormone 2 receptor

OBJECTIVE

To determine the presence or absence of a second form of GnRH (GnRH2) and corresponding receptor (GnRHR2) in human uterine myometrium and leiomyomata.

DESIGN

Evaluation of human leiomyoma and patient-matched myometrium of differential mRNA and protein expression of GnRH2 and GnRHR2.

SETTING

University hospital.

PATIENT(S)

Eight women undergoing medically indicated hysterectomy for symptomatic fibroids.

INTERVENTION(S)

Microarray analysis, reverse-transcriptase polymerase chain reaction (RT-PCR), real-time RT-PCR, and immunohistochemistry.

MAIN OUTCOME MEASURE(S)

Expression of mRNA and protein in leiomyoma and patient-matched myometrium.

RESULT(S)

Microarray analysis demonstrated expression, and we confirmed the findings by RT-PCR. Real-time RT-PCR demonstrated equivalent expression of the genes in leiomyoma compared with patient-matched myometrium (0.99-fold for GnRH2 and 1.28-fold for GnRHR2). Immunohistochemistry confirmed the expression of GnRH2 protein in both leiomyoma and myometrium.

CONCLUSION(S)

A second form of GnRH and corresponding receptor exists in the fibroid and myometrium. We speculate that an autocrine loop exists. Our findings provide further evidence that GnRH agonists may interact directly with GnRH receptors present in uterine fibroids.

Novel method to characterize primary cultures of leiomyoma and myometrium with the use of confirmatory biomarker gene arrays

OBJECTIVE

To develop a rapid biomarker method for confirming that leiomyoma and myometrium primary cultures maintain the molecular phenotype of the progenitor tissues.

DESIGN

Confirmation of primary cultures from leiomyoma and myometrium tissues.

SETTING

University hospital.

PATIENT(S)

Women undergoing hysterectomy for symptomatic leiomyomas.

INTERVENTION(S)

Primary cell cultures, reverse-transcriptase polymerase chain reaction (RT-PCR), microarray, real time RT-PCR, and immunofluorescence.

MAIN OUTCOME MEASURE

Relative messenger RNA and protein expression in leiomyoma and myometrial cell cultures.

RESULT(S)

We developed primary cell cultures from human leiomyoma and patient-matched myometrium obtained from hysterectomy specimens. In the primary cultures, we confirmed the presence of smooth muscle-specific alpha-actin as well as filamentous actin. Based on microarray analysis, we expected and confirmed, in the progenitor tissue and derived primary cultures, an overexpression of versican (8.31 fold +/- 2.2 SEM and 4.3 fold +/- 1.01 SEM, respectively), transforming growth factor beta-3 (5.66 fold +/- 0.82 SEM and 4.92 fold +/- 0.58 SEM, respectively), and cytochrome P450-26A1 (6.76 fold +/- 0.80 SEM and 6.17 fold +/- 2.02 SEM, respectively), and an underexpression of dermatopontin (-5.6 fold +/- 1.82 SEM and -3.41 +/- 1.20 SEM, respectively).

CONCLUSION(S)

Primary cell cultures offer a reliable in vitro model system for leiomyoma disease, if confirmed. Analysis of a gene array that distinguishes between myometrium and leiomyoma molecular phenotypes offers a rapid and reliable confirmation method, and provides confidence that in vitro findings resemble in vivo disease.

Expression profile of several genes in human myometrium and uterine leiomyoma

OBJECTIVE

To screen several genes that are differentially expressed in uterine leiomyoma and matched unaffected myometrium by using microarray-based hybridization and real-time polymerase chain reaction analyses.

DESIGN

Screen by arrays for < or =2,400 known genes in leiomyoma and control myometrium.

SETTING

University clinical research laboratory.

PATIENT(S)

Four patients with leiomyoma scheduled for surgery during the proliferative phase.

INTERVENTION(S)

Four paired samples of leiomyoma and adjacent myometrium were obtained from patients undergoing hysterectomy.

MAIN OUTCOME MEASURE(S)

Fold-changes in expression of leiomyoma and matched myometrium (L/M).

RESULT(S)

A comparison of expression patterns revealed 73 genes significantly up- or down-regulated in each paired tissue sample, of which 30 genes showed increased expression (mean L/M of >2) and 43 showed decreased expression (mean L/M of <0.5) in leiomyoma compared with normal myometrium. When considering only growth factors, pleiotropin (PTN) was expressed 3.5-fold more in leiomyomas compared with in myometrium. No other growth factors were similarly affected. In addition, real-time polymerase chain reaction analysis correlated well with microarray data.

CONCLUSION(S)

Data obtained from the present study suggest that several genes are selectively overexpressed in leiomyomas compared with in myometrium. Increased expression of growth factor PTN may represent a promising target for therapy.

A new hypothesis about the origin of uterine fibroids based on gene expression profiling with microarrays

This article will discuss some recent insights based on our microarray studies that have emphasized the role the extracellular matrix, transforming growth factor beta, and collagen structure in fibroid formation. These studies led to appreciation of molecular similarities between fibroids and keloids. Collectively, these observations suggest a model of fibroid development based on an abnormal response to tissue repair, resulting in disordered healing and formation of an altered extracellular matrix.

Spatial differences in biologic activity of large uterine leiomyomata

OBJECTIVE

To evaluate the growth pattern of the large uterine leiomyomata (ULM), we examined the spatial gene distributions, vessel density, proliferative activity, and hyaline degeneration.

DESIGN

Tissue sections from three-dimensional large ULM, matched myometrium, and small ULM were collected and microarrayed. The spatial difference of the tumor activity was mapped in large ULM.

SETTING

University clinical research laboratory.

PATIENT(S)

Hysterectomy specimens from 7 patients with large (>10 cm) ULM and 3 patients with large (>10 cm) uterine leiomyosarcomas.

INTERVENTION(S)

Tissue microarray analysis by the immunohistochemistry.

MAIN OUTCOME MEASURE(S)

Selected gene products, vessel density, and the percentage of hyaline degeneration were all scored in tissue cores/sections of large and small ULM against matched myometrium.

RESULT(S)

We found that there was a spherical spatial difference of the tumor activities in large ULM. The tumor region next to the periphery, the most biologically active zone, demonstrated higher levels of gene expression, a higher density of vessels, a higher proliferative rate and a lower level of hyaline degeneration. The large ULM have higher levels of gene products (except for estrogen and progesterone receptors) than small ULM.

CONCLUSION(S)

In comparison of the spatial patterns of the gene activity between the large ULM and the large uterine leiomyosarcoma, the large ULM illustrate a growth pattern of nutritional dependence.

Expression profile of the tumorigenic factors associated with tumor size and sex steroid hormone status in uterine leiomyomata

OBJECTIVE

To use tissue microarray in combination with dendrogram cluster analysis to characterize some potential tumorigenic factors in association with tumor size and sex steroid hormone status in uterine leiomyomata.

DESIGN

Expression analysis of 21 selected potential tumorigenic factors in 60 patients with uterine leiomyomata.

SETTING

University clinical research laboratory.

PATIENT(S)

Hysterectomy specimens from 60 patients with uterine leiomyomata of different ages and tumor sizes.

INTERVENTION(S)

Tissue cores from normal myometrium and leiomyomata were examined by immunohistochemistry.

MAIN OUTCOME MEASURE(S)

Semiquantitative immunointensity was scored and analyzed by net gain and loss between normal myometrium and leiomyomata and integrated into dendrogram cluster tree view.

RESULT(S)

We found that upregulation of estrogen and progesterone receptors was reverse associated with tumor size. Upregulation of some factors (HMGA2, sex steroid receptor cofactors, proteins in insulin pathway, and CD24) were identified in a group of patients in their later forties, were associated with large fibroids, and were weakly affected by the SSH status (illustrated by endometrial phases and menopause). Downregulation of tuberin and glucocorticoid receptor was mostly isolated in a second group of women at their late reproductive age.

CONCLUSION(S)

Analyses of the sex steroid hormone receptors and the nonsex steroid hormone factors in leiomyomata and the matched myometrium showed different expression patterns in different tumor sizes and patients' ages. A group of patients in their late forties with the larger leiomyomata contributes largely by upregulation of nonsex steroid hormone factors. Adenomyosis is a protective factor preventing large leiomyomata.

Ethnic differences in expression of the dysregulated proteins in uterine leiomyomata

BACKGROUND

Black ethnicity is one of the risk factors for uterine leiomyomata (ULM). Little is known about the ethnic differences in leiomyoma-associated gene products in women with uterine leiomyomata.

METHODS

A total of 120 hysterectomies with ULM were collected from black, Asian, Hispanic and white women (30 cases from each group). Twenty-two gene products were selected for the study. The expressions of the selected dysregulated gene products were measured by the semiquantification and the immunoscores were normalized by matched myometrium.

RESULTS

The relative expressions of progesterone receptor A (PR-A) (up-regulation), retinoid acid receptor alpha (down-regulation), and retinoid X receptor alpha (RXRalpha) (no change) in leiomyomata compared to normal myometrium in black women were significantly different compared to other ethnic groups (P < 0.05). About one-third of ULM from black women subclustered together in association with a group of up-regulated gene products. Many other gene products, including local growth factors, insulin-like growth factor (IGF)-signalling proteins, and cell proliferation markers, were dysregulated in ULM but showed non-significant differences between the ethnic groups.

CONCLUSIONS

There are substantial differences of the sex steroid receptors and other nuclear receptors between black women and other ethnic groups. Based on tissue microarray data, there are at least two broad groups of leiomyomata presented by the dysregulation of different groups of gene products. One is dominated by up-regulation of amplified in breast cancer 1, CD24, hamartin, human mobility group gene 2, IGF2, PR-A and RXR, and the other is characterized by up-regulation of epithelial growth factor receptor, down-regulation of hamartin, PR-A and tuberin.

Gene expression studies provide clues to the pathogenesis of uterine leiomyoma: new evidence and a systematic review

BACKGROUND

Uterine leiomyomas are extremely common and a major cause of pelvic pain, bleeding, infertility, and the leading indication for hysterectomy. Familial and epidemiological studies provide compelling evidence that genetic alterations play an important role in leiomyoma development.

METHODS

Using Affymetrix U133A GeneChip we analysed expression profiles of 22,283 genes in paired samples of leiomyoma and adjacent normal myometrium. We compared our results with previously published data on gene expression in uterine leiomyoma and identified the overlapping gene alterations.

RESULTS

We detected 80 genes with average differences of > or = 2-fold and false discovery rates of < 5% (14 overexpressed and 66 underexpressed). A comparative analysis including eight previous gene expression studies revealed eight prominent genes (ADH1, ATF3, CRABP2, CYR61, DPT, GRIA2, IGF2, MEST) identified by at least five different studies, eleven genes (ALDH1, CD24, CTGF, DCX, DUSP1, FOS, GAGEC1, IGFBP6, PTGDS, PTGER3, TYMS) reported by four studies, twelve genes (ABCA, ANXA1, APM2, CCL21, CDKN1A, CRMP1, EMP1, ESR1, FY, MAP3K5, TGFBR2, TIMP3) identified by three studies, and 40 genes reported by two different studies.

CONCLUSIONS

Review of gene expression data revealed concordant changes in genes regulating retinoid synthesis, IGF metabolism, TGF-beta signaling and extracellular matrix formation. Gene expression studies provide clues to the relevant pathways of leiomyoma development.

Expression profile of tuberin and some potential tumorigenic factors in 60 patients with uterine leiomyomata

Human uterine leiomyomata are the most common tumors in women of reproductive age. The pathogenesis of leiomyomata remains unknown. An animal model of Eker rats with deleted tuberous sclerosis complex gene 2 (tuberin) shows increased incidence of leiomyomata. The role of tuberin in human leiomyomata is unknown. In this study, we designed a tissue microarray with tissue cores of leiomyomata and the matched myometrium from 60 hysterectomy specimens. We examined the expression of tuberin and tuberous sclerosis complex gene 1 product hamartin, proteins of the insulin-signaling pathway, steroid receptors and some of their cofactors, and human mobility group gene A2 by immunohistochemistry. We found that nearly half of the cases displayed either reduction or loss of tuberin in leiomyomata compared with matched normal myometrium. No change of hamartin was noted. Furthermore, a significant reduction of glucocorticoid receptor was found in leiomyomata with reduced tuberin. The proteins insulin like growth factor 1, insulin-like growth factor receptor beta, AKT kinase, and phosphatidylinositol 3-kinase were upregulated. Nearly half of leiomyomata show upregulation of human mobility group gene A2, along with the steroid receptor cofactors. Our findings suggest that there are two broad groups of uterine leiomyomata. One group is associated with an alteration of tuberin and glucocorticoid receptor. The other group is associated with upregulation of human mobility group gene A2 and steroid receptor cofactors.

Proteomics: Analysis of Spectral Data

The goal of disease-related proteogenomic research is a complete description of the unfolding of the disease process from its origin to its cure. With a properly selected patient cohort and correctly collected, processed, analyzed data, large scale proteomic spectra may be able to provide much of the information necessary for achieving this goal. Protein spectra, which are one way of representing protein expression, can be extremely useful clinically since they can be generated from blood rather than from diseased tissue. At the same time, the analysis of circulating proteins in blood presents unique challenges because of their heterogeneity, blood contains a large number of different abundance proteins generated by tissues throughout the body. Another challenge is that protein spectra are massively parallel information. One can choose to perform top-down analysis, where the entire spectra is examined and candidate peaks are selected for further assessment. Or one can choose a bottom-up analysis, where, via hypothesis testing, individual proteins are identified in the spectra and related to the disease process. Each approach has advantages and disadvantages that must be understood if protein spectral data are to be properly analyzed. With either approach, several levels of information must be in tegrated into a predictive model. This model will allow us to detect disease and it will allow us to discover therapeutic interventions that reduce the risk of disease in at-risk individuals and effectively treat newly diagnosed disease.

Comparative ultrastructure of collagen fibrils in uterine leiomyomas and normal myometrium

OBJECTIVE

To examine the ultrastructural characteristics of extracellular matrix and mature collagen fibrils in uterine leiomyomas and compare them with those in adjacent normal myometrium.

DESIGN

Analysis of paired leiomyoma-myometrium in surgical specimens.

SETTING

Research center and tertiary care center.

SUBJECT(S)

Women undergoing medically indicated hysterectomy for symptomatic uterine leiomyomas.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Appearance and spatial orientation of the collagen fibrils in leiomyomas compared with myometrium.

RESULT(S)

Observation of specimens at x 12,500 magnification indicated that collagen fibrils were more abundant, loosely packed, and arrayed in a nonparallel manner in leiomyomas compared with myometrium. Random areas were examined at x 6,500 to x 64,000 magnification and revealed collagen fibrils of equal diameter in both leiomyomas and myometrium. However, an ordered and regular barbed appearance was present in collagen fibrils from myometrium but was lacking in leiomyomas.

CONCLUSION(S)

Leiomyomas contain an abnormal collagen fibril structure and orientation, which suggests that the well-regulated fibril formation in myometrium is altered in leiomyomas. Alterations in collagen genes may play a role in the pathogenesis of leiomyomas.

Molecular characterization of uterine fibroids and its implication for underlying mechanisms of pathogenesis

OBJECTIVE

To identify genes involved in fibroid development by performing global expression profiling on tissues of normal myometrium and uterine leiomyoma origin using Affymetrix HG-U133A GeneChip microarrays.

DESIGN

Whole-genome analysis of mRNA levels in leiomyoma and normal myometrium tissue samples.

SETTING

University research laboratory.

PATIENT(S)

Eight patients of varying age and race undergoing surgery for symptomatic fibroids.

INTERVENTION(S)

After tissue collection of five tumors and five normals from human pathological specimens, labeled cRNA was generated and hybridized to the oligonucleotide-composed arrays.

MAIN OUTCOME MEASURE(S)

Quantification of transcript expression levels in uterine fibroids relative to normal myometrium.

RESULT(S)

Model-based expression analysis revealed that of the 22,500 transcripts represented on the arrays, 226 genes were found to be dysregulated by a > or =1.5-fold change between leiomyoma and normal myometrium. Moreover, our research identified many dysregulated apoptosis-related genes, of particular interest was TRAIL and Ask1, and also found numerous differentially expressed proliferation genes, including TGFB1, PDGFC, and two dual specificity phosphatases.

CONCLUSION(S)

These results indicate that these genes may play a significant role in the development of leiomyomas from normal uterine tissue. We hypothesize that the deregulation of apoptotic and proliferative processes is pivotal to fibroid development.

Increased expression of calcium-binding protein S100 in human uterine smooth muscle tumours

S100 proteins belong to the EF-hand Ca(2+ )-binding protein family and regulate a variety of cellular processes via interaction with different target proteins. Several diseases, including cancer and melanoma, are related to the abnormal expression of S100 proteins, which are expressed in cell- and tissue-specific manners. We investigated the expression of S100 family members in human uterine smooth muscle tumours. Expression of six members of the S100 protein family: S100A1, A4, A6, A7, A10 and A11, was found in human uterine leiomyoma and myometrium tissue, but expression of other members was not detected by RT-PCR. Real-time PCR showed that S100A11 expression was significantly increased in leiomyoma compared with myometrium. Suppression of S100A11 by small interfering RNA (siRNA) led to apoptosis, and the overexpression of S100A11 inhibited apoptosis in human uterine smooth muscle tumour cells. These findings suggest that S100A11 has an anti-apoptotic function and is related to the process of growth of human uterine leiomyoma.

Reduced dermatopontin expression is a molecular link between uterine leiomyomas and keloids

Uterine leiomyomas are prevalent estrogen-responsive clonal tumors, but the specific genetic alterations that contribute to their development have not been elucidated. To identify genes involved in the formation of leiomyomas, we used global expression profiling to compare clonal tumors with normal myometrium. Contrary to expectation, genes involved in estrogen action were not differentially expressed between leiomyoma and normal myometrium. Genes encoding extracellular-matrix proteins were prominently featured, suggesting their involvement in formation of a myofibroblast phenotype. Analysis of the extracellular matrix in the leiomyomas revealed a disordered collagen fibril orientation. Expression of the collagen-binding protein dermatopontin was found to be consistently decreased in leiomyoma by both reverse transcriptase-polymerase chain reaction (RT-PCR) and real-time RT-PCR (mean underexpression = 9.41-fold) regardless of leiomyoma size, leiomyoma location, patient race, and patient age. This expression pattern was observed in 11 subjects and a total of 23 leiomyoma:myometrium pairs. Decreased expression of dermatopontin was also associated with keloid formation, a fibrotic disease that shares epidemiologic similarities with leiomyoma. Immunohistochemical studies of leiomyomas and keloids demonstrated reduced levels of dermatopontin in both tissues. In addition, ultrastructural analysis revealed that the orientation of the collagen fibrils in the keloid tissues strongly resembled that in the leiomyomas. Reduction in dermatopontin was associated with an increase in transforming growth factor-beta3 (TGFB3) mRNA levels in leiomyomas, whereas other genes involved in dermatopontin signaling were not differentially expressed. These findings suggest that leiomyoma development involves a myofibroblast cell phenotype characterized by dysregulation of genes encoding extracellular-matrix proteins. In particular, decreased expression of dermatopontin represents a molecular link between the leiomyoma and keloid phenotypes.