Expression and imprinting of insulin-like growth factor II (IGF2) and H19 genes in uterine leiomyomas

Long Non-coding RNAs Involved in Resistance to Chemotherapy in Ovarian Cancer

Ovarian cancer (OC) accounts for more than 150,000 deaths worldwide every year. Patients are often diagnosed at an advanced stage with metastatic dissemination. Although platinum- and taxane-based chemotherapies are effective treatment options, they are rarely curative and eventually, the disease will progress due to acquired resistance. Emerging evidence suggests a crucial role of long non-coding RNAs (lncRNAs) in the response to therapy in OC. Transcriptome profiling studies using high throughput approaches have identified differential expression patterns of lncRNAs associated with disease recurrence. Furthermore, several aberrantly expressed lncRNAs in resistant OC cells have been related to increased cell division, improved DNA repair, up-regulation of drug transporters or reduced susceptibility to apoptotic stimuli, supporting their involvement in acquired resistance. In this review, we will discuss the key aspects of lncRNAs associated with the development of resistance to platinum- and taxane-based chemotherapy in OC. The molecular landscape of OC will be introduced, to provide a background for understanding the role of lncRNAs in the acquisition of malignant properties. We will focus on the interplay between lncRNAs and molecular pathways affecting drug response to evaluate their impact on treatment resistance. Additionally, we will discuss the prospects of using lncRNAs as biomarkers or targets for precision medicine in OC. Although there is still plenty to learn about lncRNAs and technical challenges to be solved, the evidence of their involvement in OC and the development of acquired resistance are compelling and warrant further investigation for clinical applications.

Analyzing large gene expression and methylation data profiles using StatBicRM: statistical biclustering-based rule mining

Microarray and beadchip are two most efficient techniques for measuring gene expression and methylation data in bioinformatics. Biclustering deals with the simultaneous clustering of genes and samples. In this article, we propose a computational rule mining framework, StatBicRM (i.e., statistical biclustering-based rule mining) to identify special type of rules and potential biomarkers using integrated approaches of statistical and binary inclusion-maximal biclustering techniques from the biological datasets. At first, a novel statistical strategy has been utilized to eliminate the insignificant/low-significant/redundant genes in such way that significance level must satisfy the data distribution property (viz., either normal distribution or non-normal distribution). The data is then discretized and post-discretized, consecutively. Thereafter, the biclustering technique is applied to identify maximal frequent closed homogeneous itemsets. Corresponding special type of rules are then extracted from the selected itemsets. Our proposed rule mining method performs better than the other rule mining algorithms as it generates maximal frequent closed homogeneous itemsets instead of frequent itemsets. Thus, it saves elapsed time, and can work on big dataset. Pathway and Gene Ontology analyses are conducted on the genes of the evolved rules using David database. Frequency analysis of the genes appearing in the evolved rules is performed to determine potential biomarkers. Furthermore, we also classify the data to know how much the evolved rules are able to describe accurately the remaining test (unknown) data. Subsequently, we also compare the average classification accuracy, and other related factors with other rule-based classifiers. Statistical significance tests are also performed for verifying the statistical relevance of the comparative results. Here, each of the other rule mining methods or rule-based classifiers is also starting with the same post-discretized data-matrix. Finally, we have also included the integrated analysis of gene expression and methylation for determining epigenetic effect (viz., effect of methylation) on gene expression level.

Gene expression patterns of insulin-like growth factor 2 in human uterine fibroid tissues: a genetic study with clinical correlations

BACKGROUND/AIMS

We investigated insulin-like growth factor 2 (IGF-2) gene activity in human uterine fibroid tissue. Results of the genetic testing were correlated with clinical data.

METHODS

We obtained samples from patients treated for uterine fibroid and from patients undergoing hysterectomy due to other indications (control group). The examined group (with fibroid) contained 101 cases, while the control group was similar with 110 patients. Gene expression values were determined using the standard PCR technique. Clinical data were available from the computer database of the department.

RESULTS

IGF-2 gene expression was significantly higher in the fibroid group. There was no correlation between increase in gene activity and the number of tumors. History of previous uterine fibroid did not seem to predict IGF-2 gene activity in the current fibroid tumor tissue. IGF-2 gene expression did not correlate with cumulative duration of lactation following prior pregnancies.

CONCLUSION

IGF-2 gene activity is significantly increased in leiomyoma tissue compared to normal myometrium. Familial aggregation of uterine fibroids is not significantly associated with increased IGF-2 gene activity; other genes may have a stronger etiological role. It appears that the genetic factors potentially important in the development of familiar uterine leiomyoma are not related to the IGF-2 gene.

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.

Differential expression of selected gene products in uterine leiomyomata and adenomyosis

Gene products estrogen receptor alpha, progesterone receptor-A, retinoid X receptor alpha, insulin-like growth factor-II, insulin-like growth factor I receptor beta, platelet-derived growth factor, epithelial growth factor receptor, and BCL-2 were examined by immunohistochemistry with the aid of a tissue microarray from 46 hysterectomies with adenomyosis and leiomyomata. With appropriate internal controls, there were significant differences in gene expression between adenomyosis and leiomyomata.

Altered imprinting, promoter usage, and expression of insulin-like growth factor-II gene in gestational trophoblastic diseases

OBJECTIVE

We aimed to understand the involvement of imprinted genes in the pathogenesis of gestational trophoblastic diseases (GTD) such as hydatidiform mole (H-mole) and gestational trophoblastic tumors (GTT).

METHODS

An allelic-typing assay was performed using a PCR-RFLP-based method for identification of heterozygous informative cases. The usage of insulin-like growth factor-II (IGF2) promoters was examined by RT-PCR using promoter-specific primers. The mRNA expression of IGF2 and H19 was quantified using a densitometer.

RESULTS

The imprinting of IGF2 and H19 was maintained in all normal placenta tissues (n = 15) but relaxed in GTD (n = 47). Loss of imprinting (LOI) of IGF2 was in the order of GTT (57%) > complete H-mole (43%) > partial H-mole (25%). Similarly, LOI of H19 was in the order of GTT (40%) > complete H-mole (18%) > partial H-mole (0%). Promoter usage pattern of IGF2 changed with gestation stage of normal placentae and GTD. In normal placentae, the usage of promoter P1 was higher than that of P4 in the first trimester but lowered in the full term. H-mole and GTT predominantly used promoter P1 with relative silencing of promoter P4. Although normal early placenta and various GTD tissues showed the similar usage of IGF2 promoter P1, GTT tissues revealed the higher expression levels of IGF2 but a down-regulation of H19 relative to the normal early placentae.

CONCLUSIONS

These results suggest that LOI, deregulation of IGF2 promoters, and the altered expression levels of IGF2 and H19 genes might be associated with the progression of GTD.

Insights from gene arrays on the development and growth regulation of uterine leiomyomata

OBJECTIVE

To use microarray analysis as an unbiased approach to identify genes involved in the induction and growth of uterine leiomyomata.

DESIGN

Screen by arrays for up to 12,000 genes in leiomyoma (L) and control myometrium (M) from nine patients.

SETTING

University research laboratories.

PATIENT(S)

Nine patients in the follicular and luteal phases of the menstrual cycle.

INTERVENTION(S)

mRNA from L and M was converted to biotin-labeled cRNA and hybridized to cDNA oligonucleotide sequences on the arrays.

MAIN OUTCOME MEASURE(S)

Greater than two-fold change in gene expression between leiomyoma and matched myometrium.

RESULT(S)

Prominent among the 67 genes overexpressed in L relative to M were dlk or Pref-1, doublecortin, JM27, ionotropic glutamate receptor subunit 2, apolipoprotein E3, IGF2, semaphorin F, myelin proteolipid protein, MEST, frizzled, CRABP II, stromelysin-3, and TGFbeta3. The genes dlk, IGF2, and MEST are paternally expressed imprinted genes, and the others are involved in tissue differentiation and growth. Prominent among the 78 genes down-regulated in L relative to M were alcohol dehydrogenases 1alpha-gamma, tryptase, dermatopontin, thrombospondin, coxsackievirus receptor, nur77, and c-kit.

CONCLUSION(S)

Arrays offer large-scale screening of mRNA expression, which will help us differentiate between the genes and metabolic pathways necessary for leiomyoma growth and those regulating myometrial contractions.

Alterations in promoter usage and expression levels of insulin-like growth factor-II and H19 genes in cervical carcinoma exhibiting biallelic expression of IGF-II

Biallelic expression of insulin-like growth factor-II (IGF2) has been reported to be associated with progression of several tumors. Here, we report that the promoter usage and expression levels of IGF2 and H19 were altered in cervical carcinoma showing loss of imprinting. The imprinting status was examined in 32 cervical carcinomas and their matched normal tissues. Loss of imprinting (LOI) of IGF2 was observed in seven of 18 (39%) informative cases. LOI of H19 gene was detected in five of 14 informative cases. The usage of promoter P1 was observed in LOI tumors of IGF2, but not in the tumors showing maintenance of IGF2 imprinting (MOI) and in the normal cervical tissues. Unlike MOI tumors, some LOI tumors revealed the lack of IGF2 transcription from promoter P3. LOI tumors of IGF2 showed an increased expression level of IGF2 but a down-regulation of H19 relative to the normal tissues whereas MOI tumors did not reveal significant alterations. These results suggest that promoter P1 could be involved in the biallelic expression of IGF2 and that the altered expression levels of IGF2 and H19 gene might be associated with the progression of cervical carcinoma showing biallelic expression of IGF2.