MicroRNA expression profiling of mature ovarian teratomas

The Human Pre-miRNA Distance Distribution for Exploring Disease Association

MicroRNAs (miRNAs), playing an important role in cell differentiation, development, gene regulation, and apoptosis, have attracted much attention in recent years. miRNAs were shown to be involved in the mechanisms of various diseases, and certainly, they can be employed as useful disease biomarkers. The phylogenetic tree analysis of miRNA biomarkers is a useful tool to investigate the association between various diseases as well as the association between viruses and disease. In addition to the phylogenetic tree analysis, a more advanced study is to use the miRNA distance distribution to evaluate the similarity of the miRNA biomarkers. The mature miRNA distance distribution based on mature miRNA sequences has been derived. The averages of the pairwise distances of miRNA biomarkers for several associated diseases were shown to be smaller than the overall mean of all miRNAs, which indicates the high similarity of miRNA biomarkers for associated diseases. In addition to the mature miRNA, the precursor miRNA (pre-miRNA) may be more useful to explore the similarity of miRNAs because the mature miRNA duplex is released from the pre-miRNA. Therefore, in this study, the distance distributions based on human pre-miRNA stem-loop sequences were derived. The 1917 human miRNA stem-loop sequences in the miRBase dataset were used to derive the pre-miRNA distance distribution, and this is the first study to provide the distance distribution based on the human pre-miRNAs. The similarity of miRNA biomarkers for several associated diseases or vaccines was examined using the derived distribution, and the results show that the similarity of pre-miRNA biomarkers may be a feasible way to help explore the disease association.

The distance distribution of human microRNAs in MirGeneDB database

MicroRNAs (miRNAs) are small single-stranded non-coding RNAs around 22 nucleotide lengths found in organisms, playing an important role in cell differentiation, development, gene regulation, and apoptosis. The distance of disease miRNA biomarkers has been used to explore the association between various diseases as well as the association between virus and disease in the literature. To date, there have been no studies on deriving the distribution of the pairwise distance of human miRNAs. As the pairwise distance of miRNA biomarkers might be a useful tool in studying the disease association, in this paper, the distance distributions of human miRNAs were derived such that they could be used to measure the closeness between miRNAs. Two distance models were used to calculate the pairwise distances of 567 Homo sapiens miRNA genes accessed from the MirGeneDB database. These miRNA pairwise distances were fitted by the normal distribution, gamma distribution, empirical cumulative distribution, and the kernel density estimation method. This is the first study to provide the distance distribution of human miRNAs. The similarity of miRNA biomarkers for several diseases was examined using the derived distributions.

MicroRNAs in Differentiation of Embryoid Bodies and the Teratoma Subtype of Testicular Cancer

BACKGROUND

Testicular germ cell tumours (TGCTs) are the most frequent tumour type among young, adult men. TGCTs can be efficiently treated, but metastases of the teratoma subtype, for which there are no circulating biomarkers, represent a challenge.

MATERIALS AND METHODS

Global microRNA expression in teratoma tissue and embryoid bodies was assessed using next-generation sequencing. Levels of microRNAs identified as potential biomarkers were obtained from serum of patients with teratoma and matched healthy men.

RESULTS

We identified miR-222-5p, miR-200a-5p, miR-196b-3p and miR-454-5p as biomarker candidates from the tumour tissue and embryoid body screening but the expression of these microRNAs was very low in serum and not statistically different between patients and controls. miR-375-3p was highly expressed, being highest in patients with teratoma (p=0.012) but the levels of expression in serum from these patients and healthy controls overlapped. miR-371a-3p was not expressed in serum from patients with pure teratoma, only in patients with mixed tumours.

CONCLUSION

The microRNA profiles of the teratoma subtype of TGCT and embryoid bodies were obtained and assessed for candidate circulating biomarkers, but none with high sensitivity and specificity for teratoma were identified in our study. We conclude that neither the proposed teratoma marker miR-375-3p nor miR-371a-3p are suitable as circulating teratoma markers.

Single Cell Gene Transcriptome Analysis of Ovarian Mature Teratomas

Teratoma is a type of germ cell tumor that originates from totipotential germ cells that are present in gonads, which can differentiate into any of the cell types found in adult tissues. Ovarian teratomas are usually mature cystic teratomas (OMCTs, also known as dermoid cysts). Chromosome studies in OMCTs show that the chromosomes are uniformly homozygous with karyotype of 46, XX, indicating that they may be parthenogenic tumors that arise from a single ovum after thefirst meiotic division. However, the tissues in OMCTs have been known to be morphologically and immunophenotypically identical to the orthotopic tissues. Currently, expression profiles of tissue components in OMCTs are not known. To identify whether OMCT tissues are expressionally similar to or different from the orthotopic tissues, we adopted single-cell RNA-sequencing (scRNA-seq), and analyzed transcriptomes of individual cells in heterogenous tissues of two OMCTs. We found that transcriptome profiles of the OMCTs at single cell level were not significantly different from those of normal cells in orthotopic locations. The present data suggest that parthenogeneticlly altered OMCTs may not alter expression profiles of inrivirual tissue components in OMCTs.

Phylogenetic Analysis to Explore the Association Between Anti-NMDA Receptor Encephalitis and Tumors Based on microRNA Biomarkers

MicroRNA (miRNA) is a small non-coding RNA that functions in the epigenetics control of gene expression, which can be used as a useful biomarker for diseases. Anti-NMDA receptor (anti-NMDAR) encephalitis is an acute autoimmune disorder. Some patients have been found to have tumors, specifically teratomas. This disease occurs more often in females than in males. Most of them have a significant recovery after tumor resection, which shows that the tumor may induce anti-NMDAR encephalitis. In this study, I review microRNA (miRNA) biomarkers that are associated with anti-NMDAR encephalitis and related tumors, respectively. To the best of my knowledge, there has not been any research in the literature investigating the relationship between anti-NMDAR encephalitis and tumors through their miRNA biomarkers. I adopt a phylogenetic analysis to plot the phylogenetic trees of their miRNA biomarkers. From the analyzed results, it may be concluded that (i) there is a relationship between these tumors and anti-NMDAR encephalitis, and (ii) this disease occurs more often in females than in males. This sheds light on this issue through miRNA intervention.

A transcriptional target of androgen receptor, miR-421 regulates proliferation and metabolism of prostate cancer cells

Prostate cancer is one of the most common malignancies, and microRNAs have been recognized to be involved in tumorigenesis of various kinds of cancer including prostate cancer (PCa). Androgen receptor (AR) plays a core role in prostate cancer progression and is responsible for regulation of numerous downstream targets including microRNAs. This study identified an AR-repressed microRNA, miR-421, in prostate cancer. Expression of miR-421 was significantly suppressed by androgen treatment, and correlated to AR expression in different prostate cancer cell lines. Furthermore, androgen-activated AR could directly bind to androgen responsive element (ARE) of miR-421, as predicted by bioinformatics resources and demonstrated by ChIP and luciferase reporter assays. In addition, over-expression of miR-421 markedly supressed cell viability, delayed cell cycle, reduced glycolysis and inhibited migration in prostate cancer cells. According to the result of miR-421 target genes searching, we focused on 4 genes NRAS, PRAME, CUL4B and PFKFB2 based on their involvement in cell proliferation, cell cycle progression and metabolism. The expression of these 4 downstream targets were significantly repressed by miR-421, and the binding sites were verified by luciferase assay. Additionally, we explored the expression of miR-421 and its target genes in human prostate cancer tissues, both in shared microarray data and in our own cohort. Significant differential expression and inverse correlation were found in PCa patients.

Novel roles for LIX1L in promoting cancer cell proliferation through ROS1-mediated LIX1L phosphorylation

Herein, we report the characterization of Limb expression 1-like, (LIX1L), a putative RNA-binding protein (RBP) containing a double-stranded RNA binding motif, which is highly expressed in various cancer tissues. Analysis of MALDI-TOF/TOF mass spectrometry and RNA immunoprecipitation-sequencing of interacting proteins and the microRNAs (miRNAs) bound to LIX1L revealed that LIX1L interacts with proteins (RIOK1, nucleolin and PABPC4) and miRNAs (has-miRNA-520a-5p, −300, −216b, −326, −190a, −548b-3p, −7–5p and −1296) in HEK-293 cells. Moreover, the reduction of phosphorylated Tyr¹³⁶ (pTyr¹³⁶) in LIX1L through the homeodomain peptide, PY136, inhibited LIX1L-induced cell proliferation in vitro, and PY136 inhibited MKN45 cell proliferation in vivo. We also determined the miRNA-targeted genes and showed that was apoptosis induced through the reduction of pTyr¹³⁶. Moreover, ROS1, HCK, ABL1, ABL2, JAK3, LCK and TYR03 were identified as candidate kinases responsible for the phosphorylation of Tyr¹³⁶ of LIX1L. These data provide novel insights into the biological significance of LIX1L, suggesting that this protein might be an RBP, with implications for therapeutic approaches for targeting LIX1L in LIX1L-expressing cancer cells.

Selective microRNA-Offset RNA expression in human embryonic stem cells

Small RNA molecules, including microRNAs (miRNAs), play critical roles in regulating pluripotency, proliferation and differentiation of embryonic stem cells. miRNA-offset RNAs (moRNAs) are similar in length to miRNAs, align to miRNA precursor (pre-miRNA) loci and are therefore believed to derive from processing of the pre-miRNA hairpin sequence. Recent next generation sequencing (NGS) studies have reported the presence of moRNAs in human neurons and cancer cells and in several tissues in mouse, including pluripotent stem cells. In order to gain additional knowledge about human moRNAs and their putative development-related expression, we applied NGS of small RNAs in human embryonic stem cells (hESCs) and fibroblasts. We found that certain moRNA isoforms are notably expressed in hESCs from loci coding for stem cell-selective or cancer-related miRNA clusters. In contrast, we observed only sparse moRNAs in fibroblasts. Consistent with earlier findings, most of the observed moRNAs derived from conserved loci and their expression did not appear to correlate with the expression of the adjacent miRNAs. We provide here the first report of moRNAs in hESCs, and their expression profile in comparison to fibroblasts. Moreover, we expand the repertoire of hESC miRNAs. These findings provide an expansion on the known repertoire of small non-coding RNA contents in hESCs.

The analysis of microRNA-34 family expression in human cancer studies comparing cancer tissues with corresponding pericarcinous tissues

Recently many studies have focused on the microRNA-34 (miR-34) family expression in various cancers; nevertheless, the controversial results of these studies still exist in identifying miR-34 members as new biomarkers of cancers. Therefore, we carried out this comprehensive meta-analysis of published studies that compared the miR-34 family expression profiles between cancer tissues and paired neighboring noncancerous tissues to systemically evaluate the findings globally and address the inconsistencies of pertinent literatures. The data included in this article were collected from Embase, PubMed and Web of Science up to December 2013. To overcome the difficulties that many raw data were unavailable and study methods were different, a vote-counting strategy was adopted to identify consistent markers in our analysis. Ultimately, a total of 23 cancers were reported in the 61 eligible studies, of which 46 studies provided fold-change value information. In the consistently reported cancer types, non-small cell lung cancer (NSCLC), glioma and nasopharyngeal carcinoma (NPC) ranked at the top with down-regulated feature. Cervical neoplasm was consistently reported to be over-expressed in the panel of each member of miR-34s. Subgroup analysis of miR-34 family expression demonstrated that colorectal cancer (CRC), gastric cancer (GC), hepatocellular carcinoma (HCC) and prostate cancer (PCa) were most frequently reported with inconsistent regulations. Our meta-analysis showed that miR-34 family members could be expected to become potential diagnostic and prognostic biomarkers in some types of human cancers. Further well-designed and larger sample studies are surely warranted to identify the role of the miR-34 family in the occurrence and development of tumors.

Inflammatory myofibroblastic tumor of the bladder - an unexpected case coexisting with an ovarian teratoma

Inflammatory myofibroblastic tumors (IMTs) mainly occur in children and young adults, usually in the first two decades of life. IMT-type tumors belong to neoplasms of an intermediate biologic potential with considerable rate of local recurrence and in some cases that able to create metastases. Presented case is the first IMT coexisting with the other neoplasm. In our paper we are going to present a peculiar case of an IMT of the bladder coexisting with an ovarian teratoma, and to discuss its pathogenesis, histological picture and differential diagnosis. A 19-year-old female was admitted to the Gynecological Department and during the surgery, two independent, non-adjacent tumors were found. To settle the diagnosis, a FISH examination with the ALK1 break apart probe was carried out. It confirmed the rearrangement of the chromosome 2p23. Morphologic and immunophenotypic similarities between an IMT and other malignant tumors of the bladder may lead to diagnostic errors and an unnecessary radical cystectomy as a result. The therapy of choice is only total excision of the tumor.

VIRTUAL SLIDES

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1937487606122622.

Identification of predictive biomarkers for early diagnosis of larynx carcinoma based on microRNA expression data

The abnormal expression of microRNAs (miRNAs) plays a key role in tumorigenesis. In order to identify potential miRNA biomarkers for early diagnosis of larynx carcinoma, we employed a miRNA microarray technique and applied bioinformatic algorithms to characterize miRNA classifiers in early larynx carcinoma and normal esophageal mucosa tissue samples from 69 patients who were selected retrospectively for this study. We identified 47 miRNAs that were significantly differentially expressed in primary larynx tumor tissues compared to normal tissues using a SAM algorithm. Of these, 30 were up-regulated and 17 down-regulated in early larynx cancer, including hsa-miR-657, which was overexpressed, and hsa-miR-1287, which was underexpressed. These two candidate miRNA biomarkers were combined as a single classifier to recognize the biological characteristics in early larynx carcinoma. Real-time quantitative reverse-transcription PCR validated the microarray results in both trial and test samples. The hsa-miR-657-hsa-miR-1287 classifier displayed high sensitivity and specificity for discriminating between early larynx carcinoma and normal mucosa tissues, suggesting they may be suitable as potential predictive biomarkers for the early diagnosis of larynx carcinoma.