Profiling of differentially expressed genes in human uterine leiomyomas

The effect of N-acetyl cysteine on the volume of uterine leiomyoma: A randomized clinical trial

OBJECTIVE

To conduct a clinical trial to investigate the effect of N-acetyl cysteine (NAC), a non-hormonal drug, on the volume of leiomyoma, the most common benign tumor in women.

METHODS

This study is a randomized clinical trial, which was performed in Semnan, Iran. Eligible women who were diagnosed with uterine leiomyoma using vaginal ultrasound were randomly assigned to receive NAC or placebo for 12 weeks. The change in the volume of Leiomyoma was considered to be the main variable in the efficacy evaluation. Reduction in the leiomyoma volume was calculated after intervention and data were entered in SPSS version 23.

RESULTS

Fifty individuals were enrolled in our study. 25 women received NAC, while 25 women took placebo. The mean volume of leiomyoma in group A was 5.71 cm³ and in group B was 6.56 cm³ . The mean rate of volume reduction in the A and B groups was 25.25 % and 1.08 %, respectively, which demonstrated a significant difference between the two groups (P < 0.004).

CONCLUSION

Although this trial recommends the use of NAC as a non-hormonal drug in the treatment of leiomyoma of the uterus, the possibility of treatment failure in controlling abnormal uterine bleeding cannot be ignored. Nevertheless, we can say it is feasible and effective in the reduction of leiomyoma volume.

New Insights of Uterine Leiomyoma Pathogenesis: Endocannabinoid System

Background

The aim of this study was to determine if components of the endocannabinoid system are modulated in uterine leiomyomas (fibroids). Components studied included cannabinoid receptors 1 (CB1) and 2 (CB2); the G protein-coupled receptor GPR55; transient potential vanilloid receptor 1 (TRPV1) and the endocannabinoid modulating enzymes N-acylphosphatidylethanolamine-specific phospholipase D (NAPE-PLD) and fatty acid amide hydrolase (FAAH), and their N-acylethanolamine (NAE) ligands: N-arachidonylethanolamine (AEA), N-oleoylethanolamine (OEA), and N-palmityolethanaolamine (PEA).

Material/Methods

Transcript levels of CB1, CB2, TRPV1, GPR55, NAPE-PLD, and FAAH were measured using RT-PCR and correlated with the tissue levels of the 3 NAEs in myometrial tissues. The tissues studied were: 1) fibroids, 2) myometrium adjacent/juxtaposed to the fibroid lesions, and 3) normal myometrium. Thirty-seven samples were processed for NAE measurements and 28 samples were used for RT-PCR analyses.

Results

FAAH expression was significantly lower in fibroids, resulting in a NAPE-PLD: FAAH ratio that favors higher AEA levels in pre-menopausal tissues, whilst PEA levels were significantly lower, particularly in post-menopausal women, suggesting PEA protects against fibroid pathogenesis. The CB1: CB2 ratio was lower in fibroids, suggesting that loss of CB1 expression affects the fibroid cell phenotype. Significant correlations between reduced FAAH, CB1, and GPR55 expression and PEA in fibroids indicate that the loss of these endocannabinoid system components are biomarkers of leiomyomata.

Conclusions

Loss of expression of CB1, FAAH, GPR55, and PEA production are linked to the pathogenesis of uterine fibroids and further understanding of this might eventually lead to better disease indicators or the development of therapeutic potentials that might eventually be used in the management of uterine fibroids.

Subtype-Specific Tumor-Associated Fibroblasts Contribute to the Pathogenesis of Uterine Leiomyoma

Recent genomic studies have identified subtypes of uterine leiomyoma (LM) with distinctive genetic alterations. Here, we report the elucidation of the biological characteristics of the two most prevalent uterine leiomyoma subtypes, MED12-mutant (MED12-LM) and HMGA2-overexpressing (HMGA2-LM) uterine leiomyomas. Because each tumor carries only one genetic alteration, both subtypes are considered to be monoclonal. Approximately 90% of cells in HMGA2-uterine leiomyoma were smooth muscle cells (SMC) with HMGA2 overexpression. In contrast, MED12-LM consisted of similar numbers of SMC and non-SMC, which were mostly tumor-associated fibroblasts (TAF). Paradoxically, TAF carried no mutations in MED12, suggesting an interaction between SMC and TAF to coordinate their growth. The higher amount of extracellular matrix in MED12-LM than HMGA2-LM was partially due to the high concentration of collagen-producing TAF. SMC growth in a xenograft assay was driven by progesterone in both uterine leiomyoma subtypes. In contrast, TAF in MED12-LM proliferated in response to estradiol, whereas progesterone had no effect. The high concentration of estrogen-responsive TAF in MED12-LM explains the inconsistent discoveries between in vivo and in vitro studies on the mitogenic effect of estrogen and raises questions regarding the accuracy of previous studies utilizing MED12-LM cell culture. In addition, the differential effects of estradiol and progesterone on these uterine leiomyoma subtypes emphasize the importance of subtypes and genotypes in designing nonsurgical therapeutic strategies for uterine leiomyoma. Cancer Res; 77(24); 6891-901. ©2017 AACR.

Association of genetic variations in RTN4 3'-UTR with risk of uterine leiomyomas

This pilot case-control study was conducted to test the hypothesis that the TATC (rs71682890) and CAA (rs34917480) insertion/deletion polymorphisms of RTN4 3'-UTR are associated with the susceptibility to uterine leiomyoma (UL). The study recruited 286 premenopausal women with UL and 450 unrelated postmenopausal women not presenting the disease as control subjects. The polymorphisms of rs71682890 and rs34917480 were genotyped with the method of polymerase chain reaction polyacrylamide gel electrophoresis (PCR - PAGE). No statistically significant association was observed between the TATC insertion/deletion polymorphism and UL risk. However, increased UL risk was identified to be significantly associated with CAA insertion/deletion polymorphism in the recessive and codominant model. The present study provided evidence for the first time that CAA polymorphism in RTN4 3'-UTR, but not TATC polymorphism may be involved in susceptibility to UL.

Expression of p53 and p21(WAF-1), apoptosis, and proliferation of smooth muscle cells in normal myometrium during the menstrual cycle: implication of DNA damage and repair for leiomyoma development

Uterine leiomyoma is the most common tumor in the female genital tract, although its pathogenesis remains unclear. Molecular analyses have demonstrated that each leiomyoma nodule is monoclonal and harbors various DNA abnormalities, suggesting that DNA damage in normal smooth muscle cells plays an important role in the pathogenesis of leiomyoma. The aim of this study is to evaluate precisely when and where DNA damage occurs in the myometrium. The localization of damaged, apoptotic, and proliferating cells was evaluated by immunohistochemical staining of p53, p21(WAF-1), TUNEL, and the cell proliferation marker, Ki-67, in normal myometrium during the menstrual cycle. p53-positive cells and p21(WAF-1)-positive cells were observed during the follicular phase, mostly in the submucosal layer of the myometrium. TUNEL-positive cells were sporadically identified in this layer during either the menstrual or follicular phase. In contrast, the number of Ki-67-positive cells was higher in the luteal phase. These results suggest that DNA damage, repair, and apoptosis occur cyclically in normal myometrium during the follicular phase. In addition, smooth muscle cells proliferate in the luteal phase, which may be a vulnerable period for DNA damage. Thus, these cyclic events during the menstrual cycle may contribute to a high incidence of leiomyoma development.

Fibroid-associated heavy menstrual bleeding: correlation between clinical features, Doppler ultrasound assessment of vasculature, and tissue gene expression profiles

Despite the prevalence of uterine fibroids (Fs), few studies have investigated the links between clinical features and the cellular or molecular mechanisms that drive F growth and development. Such knowledge will ultimately help to differentiate symptomatic from asymptomatic Fs and could result in the development of more effective and individualized treatments. The aim of this study was to investigate the relationship between ultrasound appearance, blood flow, and angiogenic gene expression in F, perifibroid (PM), and distant myometrial (DM) tissues. We hypothesized that angiogenic gene expression would be increased in tissues and participants that showed increased blood flow by Doppler ultrasound. The study was performed using Doppler ultrasound to measure blood flow prior to hysterectomy, with subsequent tissue samples from the F, PM, and DM being investigated for angiogenic gene expression. Overall, PM blood flow (measured as peak systolic velocity [PSV]) was higher than F blood flow, although significant heterogeneity was seen in vascularity and blood flow between different Fs and their surrounding myometrium. We did not find any correlation between PSV and any other clinical or molecular parameter in this study. We identified 19 angiogenesis pathway-related genes with significant differences in expression between F and DM, and 2 genes, matrix metalloproteinase 9 (MMP9) and Neuropilin 2 (NRP2), that were significantly different between F and PM. These results are consistent with subtle differences between PM and DM. Understanding the differences between symptomatic versus asymptomatic Fs may eventually lead to more effective treatments that directly target the source of heavy menstrual bleeding.

Characterization of the uterine leiomyoma microRNAome by deep sequencing

MicroRNAs (miRNAs) are a class of small non-coding RNAs, which are negative regulators of gene expression. Many genes in human uterine leiomyoma (ULM) are aberrantly expressed and in some cases this can be due to dysregulation of miRNAs. Here we present the first study to determine genome-wide miRNA expression patterns in uterine leiomyoma and myometrium using Solexa high-throughput sequencing. We found more than 50 miRNAs, which were differentially expressed, and furthermore we extend the list of putative new miRNA genes. The top five significantly de-regulated miRNAs in ULMs that we found in our libraries were miR-363, miR-490, miR-137, miR-217 and miR-4792. We also observed "isomiRs" with higher copy number than referenced mature miRNA specific for the leiomyoma libraries, which have a potential role in tumorigenesis. The microRNA transcriptomes obtained in this study deliver insights and further expand our understanding the role of small RNAs in uterine leiomyoma development.

Molecular Genetics of Mesenchymal Tumors of the Female Genital Tract

Mesenchymal tumors of the female genital tract are a heterogeneous group of neoplasms that can be classified based on cellular differentiation into 3 main groups: smooth muscle tumors, endometrial stromal tumors, and other differentiated and undifferentiated tumors. Genomic analysis techniques have revealed important genetic aberrations such as the t(7;17) translocation, resulting in JAZF1-JJAZ1 gene fusion, characteristic of endometrial stromal tumors. These analyses have demonstrated genetic complexity and heterogeneity in many mesenchymal tumor types. This article focuses on current understanding of the molecular genetics of mesenchymal tumors of the female genital tract, with emphasis on diagnostic and prognostic molecular features.

Phylogenetic modeling of heterogeneous gene-expression microarray data from cancerous specimens

The qualitative dimension of gene expression data and its heterogeneous nature in cancerous specimens can be accounted for by phylogenetic modeling that incorporates the directionality of altered gene expressions, complex patterns of expressions among a group of specimens, and data-based rather than specimen-based gene linkage. Our phylogenetic modeling approach is a double algorithmic technique that includes polarity assessment that brings out the qualitative value of the data, followed by maximum parsimony analysis that is most suitable for the data heterogeneity of cancer gene expression. We demonstrate that polarity assessment of expression values into derived and ancestral states, via outgroup comparison, reduces experimental noise; reveals dichotomously expressed asynchronous genes; and allows data pooling as well as comparability of intra- and interplatforms. Parsimony phylogenetic analysis of the polarized values produces a multidimensional classification of specimens into clades that reveal shared derived gene expressions (the synapomorphies); provides better assessment of ontogenic pathways and phyletic relatedness of specimens; efficiently utilizes dichotomously expressed genes; produces highly predictive class recognition; illustrates gene linkage and multiple developmental pathways; provides higher concordance between gene lists; and projects the direction of change among specimens. Further implication of this phylogenetic approach is that it may transform microarray into diagnostic, prognostic, and predictive tool.

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.

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.

Physical mapping of distinct 7q22 deletions in uterine leiomyoma and analysis of a recently annotated 7q22 candidate gene

Uterine leiomyoma (UL) is a benign, smooth muscle tumor of the uterus affecting a significant proportion of women of reproductive age. Deletions involving chromosome 7q22 are common in UL and vary in length. Previously reported 7q22 deletion intervals were physically mapped using information from the recently completed human genome sequence. Four distinct deletion intervals, which included a microdeletion reported by our laboratory, were identified. This microdeletion contains two known genes, ORC5L and LHFPL3. The single deleted marker in the microdeletion was mapped within the LHFPL3 locus. The ORC5L gene has been studied in UL. Conversely, LHFPL3 has been annotated only recently, and has therefore not been studied in UL. The predicted LHFPL3 protein sequence contained a polyalanine domain, and a signature sequence for the PMP22 Claudin protein family. Members of this family are transmembrane proteins with roles in differentiation, proliferation, and extracellular matrix formation, and have been implicated in other tumors. Differences in LHFPL3 expression were observed in both human and Eker rat UL. Our results provide evidence for four distinct 7q22 deletion intervals, each with multiple candidate genes, including the recently identified LHFPL3 gene.

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.

Absolute enrichment: gene set enrichment analysis for homeostatic systems

The Gene Set Enrichment Analysis (GSEA) identifies sets of genes that are differentially regulated in one direction. Many homeostatic systems will include one limb that is upregulated in response to a downregulation of another limb and vice versa. Such patterns are poorly captured by the standard formulation of GSEA. We describe a technique to identify groups of genes (which sometimes can be pathways) that include both up- and down-regulated components. This approach lends insights into the feedback mechanisms that may operate, especially when integrated with protein interaction databases.

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.

In vitro culture significantly alters gene expression profiles and reduces differences between myometrial and fibroid smooth muscle cells

Cultured myometrial (M) and fibroid (F) smooth muscle cells (SMCs) have been widely used as a model for the study of F growth. The aim of this study was to compare gene expression profiles using microarrays between six paired M and F tissues from hysterectomy specimens, as well as cells isolated from the same tissues and cultured for up to three passages. A total of 2055 genes were differentially expressed by ANOVA between all experimental groups. Among them, 128 genes were found to be statistically different between M and F tissues. More than 1100 genes were significantly changed between tissues and cultured cells, with 648 genes common between both M and F cells at P0 and P3. Expression profiles of six genes including estrogen receptor-alpha (ERalpha) and progesterone receptor (PR) were also validated using real-time PCR. These data demonstrate that large changes occur in SMC gene expression in culture, reducing differences between M and F cells. They also show that ERalpha and PR levels are reduced in cells compared with whole tissue. These results indicate that although M and F cell cultures provide an important tool to study these tumours, in vitro studies must be carefully planned and evaluated to provide meaningful results.