miRNA microarray profiling in patients with androgenic alopecia and the effects of miR-133b on hair growth.

OBJECTIVE: Androgenetic alopecia (AGA), a common alopecia, is often accompanied by abnormal expression of multiple miRNAs. This study aims to investigate abnormally expressed miRNAs in patients with AGA and their specific molecular mechanism. METHODS: miRNA microarray profiling and qRT-PCR validation were used to screen and verify abnormally expressed miRNAs in patients with AGA. Human hair follicles (HFs) were treated with different concentrations of dihydrotestosterone (DHT, 10-5, 10-6, 10-7 and 10-8 mol/L) for 10 days. The effects of DHT on HF growth, proliferation, and miRNA expression in cultured HFs were investigated using immunofluorescence staining and qRT-PCR. Moreover, human dermal papilla cells (HDPCs) were treated/transfected with a Wnt/ß-catenin pathway activator and/or miR-133b mimic, and then the CCK-8 assay was used to evaluate HDPC proliferation. qRT-PCR and Western blotting were used to measure the expression of Versican, ALP and ß-catenin RESULTS: miRNA microarray profiling identified 43 miRNAs that were significantly differentially expressed in AGA patients, and qRT-PCR verified that 8 miRNAs were significantly differentially expressed. The expression of miR-133b was abnormally high in AGA patients. DHT (10-5 mol/L) inhibited human HF growth and upregulated miR-133b expression, and DHT (10-7 mol/L) induced human HF growth and downregulated miR-133b expression. HDPC proliferation was inhibited, and the expression of ß-catenin was downregulated in the miR-133b mimic-transfected group compared with the control group (P < 0.05). Wnt/ß-catenin pathway activator treatment significantly promoted HDPC proliferation and upregulated the expression of ß-catenin (P < 0.05). In addition, the proliferation of HDPCs was not significantly different between the group cotreated with a Wnt/ß-catenin pathway activator and miR-133b mimic, and the control group (P > 0.05), but the expression of Versican and ALP was suppressed in the cotreatment group (P < 0.05) CONCLUSION: Our data indicated that patients with androgenic alopecia have specific miRNA expression profiles and that the abnormal expression of miR-133b may inactivate the Wnt/ß-catenin pathway and ultimately regulate hair growth.

Microarray profiling analysis identifies the mechanism of miR-200b-3p/mRNA-CD36 affecting diabetic cardiomyopathy via peroxisome proliferator activated receptor-γ signaling pathway.

OBJECTIVE: Current study focused on the influence of miR-200b-3p on cardiocyte apoptosis of diabetic cardiomyopathy (DCM) by regulating CD36 and peroxisome proliferator-activated receptor γ (PPAR-γ) signaling pathway. METHODS: Bioinformatic analysis was used to analyze differentially expressed microRNA (miRNAs), messenger RNAs (mRNAs) and activated pathways in DCM. And then quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to verify expression of miR-200b-3p and CD36 in DCM model rats and glucose treated H9c2 cell line. Luciferase reporter assay was used to verify the transcriptional regulation of agomiR-200b-3p and investigate the relationship between miR-200b-3p and CD36. Flow cytometry was performed to assess cardiocyte apoptosis in different interference conditions. Echocardiography was used to illustrate the ejection fraction rate and fraction shortening rate of DCM model rats. Next, hematoxylin-eosin (H&E) staining assay was carried out to reveal structures of cardiocyte tissues with transfection in different conditions. Masson trichrome staining was used to evaluate myocardial fibrosis. Western blot analysis was used to detect the expression levels of PPAR-γ signaling-related protein PPAR-γ and Bcl-2. RESULTS: miR-200b-3p was low-expressed while CD36 was overexpressed in DCM. AgomiR-200b-3p could inhibit the expression of CD36 to regulate cardiocyte apoptosis in DCM. CD36 activated PPAR-γ signaling pathway in DCM. Silencing CD36 or GW9662 treatment protect rat against DCM. CONCLUSION: miR-200b-3p targeted CD36 to regulate cardiocyte apoptosis of DCM by activating PPAR-γ signaling pathway.

Nam Dia long, a Vietnamese folk formula, induces apoptosis in MCF-7 cells through various mechanisms of action.

BACKGROUND: The holistic approach of traditional medicine renders the identification of its mechanisms of action difficult. Microarray technology provides an efficient way to analyze the complex genome-wide gene expression of cells treated with mixtures of medicinal ingredients. We performed transcriptional profiling of MCF-7 cells treated with Nam Dia Long (NDL), a Vietnamese traditional formula, to explore the mechanism of action underlying the apoptosis inducing effect of this formula reported in a previous study. METHODS: MCF-7 cells were treated with aqueous extracts of NDL at the IC50 concentration for 24, 36 and 48 h. Total RNAs at 24 h and 48 h were subsequently extracted, reverse transcribed and submitted to microarray expression profiling using the Human HT-12 v4.0 Expression Bead Chip (Illumina). Functional analyses were performed using the Database for Annotation, Visualization and Integrated Discovery and the Ingenuity Pathways Analysis. The expression level from selected genes at the three time points were assessed by quantitative real-time RT-PCR and Western blot. RESULTS: Fifty-four and 601 genes were differentially expressed at 24 and 48 h of NDL treatment, respectively. Genes with altered expression at 24 h were mostly involved in cell responses to xenobiotic stress whereas genes differentially expressed at 48 h were related to endoplasmic reticulum stress, DNA damage and cell cycle control. Apoptosis of NDL treated MCF-7 cells resulted from a combination of different mechanisms including the intrinsic and extrinsic pathways, cell cycle arrest- and oxidative stress-related cell death. CONCLUSION: NDL elicited a two-stage response in MCF-7 treated cells with apoptosis as the ultimate result. The various mechanisms inducing apoptosis reflected the complexity of the formula composition.

Changes in gene methylation patterns in neonatal murine hearts: Implications for the regenerative potential.

BACKGROUND: The neonatal murine heart is able to regenerate after severe injury; this capacity however, quickly diminishes and it is lost within the first week of life. DNA methylation is an epigenetic mechanism which plays a crucial role in development and gene expression regulation. Under investigation here are the changes in DNA methylation and gene expression patterns which accompany the loss of regenerative potential. RESULTS: The MeDIP-chip (methylated DNA immunoprecipitation microarray) approach was used in order to compare global DNA methylation profiles in whole murine hearts at day 1, 7, 14 and 56 complemented with microarray transcriptome profiling. We found that the methylome transition from day 1 to day 7 is characterized by the excess of genomic regions which gain over those that lose DNA methylation. A number of these changes were retained until adulthood. The promoter genomic regions exhibiting increased DNA methylation at day 7 as compared to day 1 are significantly enriched in the genes critical for heart maturation and muscle development. Also, the promoter genomic regions showing an increase in DNA methylation at day 7 relative to day 1 are significantly enriched with a number of transcription factors binding motifs including those of Mfsd6l, Mef2c, Meis3, Tead4, and Runx1. CONCLUSIONS: The results indicate that the extensive alterations in DNA methylation patterns along the development of neonatal murine hearts are likely to contribute to the decline of regenerative capabilities observed shortly after birth. This conclusion is supported by the evidence that an increase in DNA methylation in the neonatal murine heart from day 1 to day 7 occurs in the promoter regions of genes playing important roles in cardiovascular system development.

Microarray profiling analysis of long non-coding RNAs expression in tendinopathy: identification for potential biomarkers and mechanisms.

The role of lncRNAs in pathologies of tendinopathy has not been researched so far, this study aims to identify the role and potent mechanism of lncRNAs in tendinopathy with a bioinformatic analysis. The gene profile of GSE26051 based on the platform of Affymetrix Human Genome U133B Array condensed was downloaded from Gene Expression Omnibus. A total of 46 specimens (including 23 normal samples and 23 tendinopathy specimens) were available. Compared with the control samples, differentially expressed genes (DEGs) of tendinopathy was identified the by packages in R. The selected DEGs were further analysed using bioinformatics methods including co-expression and enrichment analysis to detect the potential role of lncRNAs. A total of 40 different expressed lncRNAs were identified. However, most of the identified lncRNAs have not been researched before. And this study only annotate one of the identified lncRNAs successfully, the LOC100507027 (myoregulin), with the potential role in regulating skeletal muscle tissue development and skeletal muscle organ development.

Global gene expression profiling of telangiectasial tissue from patients with hereditary hemorrhagic telangiectasia.

UNLABELLED: Hereditary hemorrhagic telangiectasia (HHT), the most common inherited vascular disorder, is predominantly caused by mutations in ENG and ACVRL1, which are part of the transforming growth factor beta (TGF-ß) signaling pathway. HHT is characterized by the presence of mucocutaneous telangiectases and arteriovenous malformations in visceral organs, primarily the lungs, brain and liver. The most common symptom in HHT is epistaxis originating from nasal telangiectasia, which can be difficult to prevent and can lead to severe anemia. The clinical manifestations of HHT are extremely variable, even within family members, and the exact mechanism of how endoglin and ALK1 haploinsufficiency leads to HHT manifestations remains to be identified. OBJECTIVES: The purpose of this study was to detect significantly differentially regulated genes in HHT, and try to elucidate the pathways and regulatory mechanisms occurring in the affected tissue of HHT patients, in order to further characterize this disorder and hypothesize on how telangiectases develop. By microarray technology (Agilent G3 Human GE 8x60), we performed global gene expression profiling of mRNA transcripts from HHT nasal telangiectasial (n = 40) and non-telangiectasial (n = 40) tissue using a paired design. Comparing HHT telangiectasial and non-telangiectasial tissue, significantly differentially expressed genes were detected using a paired t-test. Gene set analysis was performed using GSA-SNP. In the group of ENG mutation carriers, we detected 67 differentially expressed mRNAs, of which 62 were down-regulated in the telangiectasial tissue. Gene set analysis identified the gene ontology (GO) terms vasculogenesis, TGF-ß signaling, and Wnt signaling as differentially expressed in HHT1. Altered Wnt signaling might be related to HHT pathogenesis and a greater understanding of this may lead to the discovery of therapeutic targets in HHT.

Transcriptome analysis reveals involvement of thiopurine S-methyltransferase in oxidation-reduction processes.

Thiopurine S-methyltransferase (TPMT) is an important enzyme involved in the deactivation of thiopurines and represents a major determinant of thiopurine-related toxicities. Despite its well-known importance in thiopurine metabolism, the understanding of its endogenous role is lacking. In the present study, we aimed to gain insight into the molecular processes involving TPMT by applying a data fusion approach to analyze whole-genome expression data. The RNA profiling was done on whole blood samples from 1017 adult male and female donors to the Estonian biobank using Illumina HTv3 arrays. Our results suggest that TPMT is closely related to genes involved in oxidoreductive processes. The in vitro experiments on different cell models confirmed that TPMT influences redox capacity of the cell by altering S-adenosylmethionine (SAM) consumption and consequently glutathione (GSH) synthesis. Furthermore, by comparing gene networks of subgroups of individuals, we identified genes, which could have a role in regulating TPMT activity. The biological relevance of identified genes and pathways will have to be further evaluated in molecular studies.

The cytotoxic activities of the major diterpene extracted from Salvia multicaulis (Bardakosh) are mediated by the regulation of heat-shock response and fatty acid metabolism pathways in human leukemia cells.

BACKGROUND: Leukemia is one of the most lethal cancers worldwide and represents the sixth-leading cause of cancer deaths. The results of leukemia treatment have not been as positive as desired, and recurrence is common. PURPOSE: Thus, there is an urgent requirement for the development of new therapeutic drugs. Salvia multicaulis (Bardakosh) is a widespread species that contains multiple phytochemical components with anti-cancer activities. METHODS: We isolated and characterized the major diterpene candesalvone B methyl ester from S. multicaulis and investigated its action as a cytotoxic agent towards sensitive and drug-resistant leukemia cells by the resazurin reduction assay. Additionally, the targeted genes and the affected molecular mechanisms attributed to the potent cytotoxic activities were discovered by transcriptome-wide mRNA expression profiling. The targets predicted to be regulated by candesalvone B methyl ester in each cell line were confirmed by qRT-PCR, molecular docking, microscale thermophoresis, and western blotting. Moreover, cell cycle distribution and apoptosis were analyzed by flow cytometry. RESULTS: Candesalvone B methyl ester was cytotoxic with IC50 values of 20.95 ± 0.15 µM against CCRF-CEM cells and 4.13 ± 0.10 µM against multidrug-resistant CEM/ADR5000 leukemia cells. The pathway enrichment analysis disclosed that candesalvone B methyl ester could regulate the heat-shock response signaling pathway via targeting heat shock factor 1 (HSF1) in CCRF-CEM cells and ELOVL fatty acid elongase 5 (ELOVL5) controls the fatty acid metabolism pathway in CEM/ADR5000 cells. Microscale thermophoresis showed the binding of candesalvone B methyl ester with HSF1 and ELOVL5, confirming the results of molecular docking analysis. Down-regulation of both HSF1 and ELOVL5 by candesalvone B methyl ester as detected by both western blotting and RT-qPCR was related to the reversal of drug resistance in the leukemia cells. Furthermore, candesalvone B methyl ester increased the arrest in the sub-G1 phase of the cell cycle in a dose-dependent manner from 1.3 % to 32.3 % with concomitant induction of apoptosis up to 29.0 % in CCRF-CEM leukemic cells upon inhibition of HSF1. CONCLUSION: Candesalvone B methyl ester isolated from S. multicaulis exerted cytotoxicity by affecting apoptosis, cell division, and modulation of expression levels of genes contributing to the heat stress signaling and fatty acid metabolism pathways that could relieve drug resistance of leukemia cells.

Microarray profiling of circular RNAs in LPS-induced Beas-2B cells and identification of circ_2979 as a potential biomarker for ARDS.

Acute respiratory distress syndrome (ARDS) is a major cause of high mortality and morbidity in critically ill patients. Circular RNAs (CircRNAs) are widely expressed in numerous tissues and are associated with various diseases. However, the role of circRNAs in ARDS remains unclear. In this study, we found that cell viability and proliferation were reduced in lipopolysaccharide (LPS)-induced Beas-2B cells. Microarray analysis identified 1131 differentially expressed circRNAs in LPS-treated Beas-2B cells, with 623 circRNAs significantly upregulated and 508 circRNAs strongly downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed significant enrichment and indicated potential functions and pathways of differentially expressed circRNAs. Reverse transcription-polymerase chain reaction (RT-PCR) analysis confirmed that expression of circ_2979, circ_5438, circ_4557 and circ_2066 in LPS-induced Beas-2B cells was consistent with the results obtained by RNA sequencing (RNA-seq). Additionally, we recruited 17 patients with ARDS and 13 healthy volunteers and found that expression of circ_2979 in serum was significantly increased in the patients with ARDS compared with healthy volunteers. Spearman's analyses indicated that circ_2979 was correlated with partial pressure of carbon dioxide in arterial blood (PaCO2), the ratio of partial pressure of arterial oxygen to the fraction of inspired oxygen (PaO2/FiO2), interleukin 2 receptor (IL-2R) and fibrinogen (FIB). The results suggested that circRNAs may play an important role in the progression of ARDS, and that circ_2979 may serve as a diagnosis and prognosis biomarker for ARDS.

Identification of Brain Regions Activated by Sevoflurane and Propofol and Regional Changes in Gene Expression.

General anesthetics have different efficacies and side effect incidences based on their mechanism of action. However, detailed comparative studies of anesthetics are incomplete. In this study, target brain regions and gene expression changes in these brain regions were determined for sevoflurane and propofol to understand the mechanisms that cause differences among anesthetics. Rats were anesthetized with sevoflurane or propofol for 1 hr, and brain regions with anesthesia-induced changes in neuronal activity were examined by immunohistochemistry and in situ hybridization for c-Fos. Among the identified target brain regions, gene expression analysis was performed in the habenula, the solitary nucleus and the medial vestibular nucleus from laser microdissected samples. Genes altered by sevoflurane and propofol were different and included genes involved in the incidence of postoperative nausea and vomiting and emergence agitation, such as Egr1 and Gad2. GO enrichment analysis showed that the altered genes tended to be evenly distributed in all functional category. The detailed profiles of target brain regions and induced gene expression changes of sevoflurane and propofol in this study will provide a basis for analyzing the effects of each anesthetic agent and the risk of adverse events.

Gene Expression-Based Signature Can Predict Sorafenib Response in Kidney Cancer.

Sorafenib is a tyrosine kinase inhibitory drug with multiple molecular specificities that is approved for clinical use in second-line treatments of metastatic and advanced renal cell carcinomas (RCCs). However, only 10-40% of RCC patients respond on sorafenib-containing therapies, and personalization of its prescription may help in finding an adequate balance of clinical efficiency, cost-effectiveness, and side effects. We investigated whether expression levels of known molecular targets of sorafenib in RCC can serve as prognostic biomarker of treatment response. We used Illumina microarrays to profile RNA expression in pre-treatment formalin-fixed paraffin-embedded (FFPE) samples of 22 metastatic or advanced RCC cases with known responses on next-line sorafenib monotherapy. Among them, nine patients showed partial response (PR), three patients-stable disease (SD), and 10 patients-progressive disease (PD) according to Response Evaluation Criteria In Solid Tumors (RECIST) criteria. We then classified PR + SD patients as "responders" and PD patients as "poor responders". We found that gene signature including eight sorafenib target genes was congruent with the drug response characteristics and enabled high-quality separation of the responders and poor responders [area under a receiver operating characteristic curve (AUC) 0.89]. We validated these findings on another set of 13 experimental annotated FFPE RCC samples (for 2 PR, 1 SD, and 10 PD patients) that were profiled by RNA sequencing and observed AUC 0.97 for 8-gene signature as the response classifier. We further validated these results in a series of qRT-PCR experiments on the third experimental set of 12 annotated RCC biosamples (for 4 PR, 3 SD, and 5 PD patients), where 8-gene signature showed AUC 0.83.

Profiling Long Non-coding RNA expression Using Custom-Designed Microarray.

Long non-coding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. The abnormal expression of lncRNAs has been implicated in a range of many human diseases, including cancer. To date, a small number of functional lncRNAs have been well characterized. lncRNA expression profiling may help to identify useful molecular biomarkers and targets for novel therapeutic approaches. In this chapter, we describe a highly efficient lncRNA expression profiling method using a custom-designed microarray.

Comprehensive analysis of lncRNA and mRNA based on expression microarray profiling reveals different characteristics of osteoarthritis between Tibetan and Han patients.

BACKGROUND: Osteoarthritis (OA) is thought to be the most prevalent chronic joint disease, especially in Tibet of China. Here, we aimed to explore the integrative lncRNA and mRNA landscape between the OA patients of Tibet and Han. METHODS: The lncRNA and mRNA expression microarray profiling was performed by SurePrint G3 Human Gene Expression 8x60K v2 Microarray in articular cartilage samples from OA patients of Han nationality and Tibetans, followed by GO, KEGG, and trans-regulation and cis-regulation analysis of lncRNA and mRNA. RESULTS: We found a total of 117 lncRNAs and 297 mRNAs differently expressed in the cartilage tissues of Tibetans (n = 5) comparing with those of Chinese Han (n = 3), in which 49 lncRNAs and 158 mRNAs were upregulated, and 68 lncRNAs and 139 mRNAs were downregulated. GO and KEGG analysis showed that several unreported biological processes and signaling pathways were particularly identified. LncRNA-mRNA co-expression analysis revealed a remarkable lncRNA-mRNA relationship, in which OTOA may play a critical role in the different mechanisms of the OA progression between Tibetans and Chinese Han. CONCLUSION: This study identified different lncRNA/mRNA expression profiling between OA patients of Tibetans and Han, which were involved in many characteristic biological processes and signaling pathways.

Identification of candidate biomarkers of liver hydatid disease via microarray profiling, bioinformatics analysis, and machine learning.

OBJECTIVES: Liver echinococcosis is a severe zoonotic disease caused by Echinococcus (tapeworm) infection, which is epidemic in the Qinghai region of China. Here, we aimed to explore biomarkers and establish a predictive model for the diagnosis of liver echinococcosis. METHODS: Microarray profiling followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis was performed in liver tissue from patients with liver hydatid disease and from healthy controls from the Qinghai region of China. A protein-protein interaction (PPI) network and random forest model were established to identify potential biomarkers and predict the occurrence of liver echinococcosis, respectively. RESULTS: Microarray profiling identified 1152 differentially expressed genes (DEGs), including 936 upregulated genes and 216 downregulated genes. Several previously unreported biological processes and signaling pathways were identified. The FCGR2B and CTLA4 proteins were identified by the PPI networks and random forest model. The random forest model based on FCGR2B and CTLA4 reliably predicted the occurrence of liver hydatid disease, with an area under the receiver operator characteristic curve of 0.921. CONCLUSION: Our findings give new insight into gene expression in patients with liver echinococcosis from the Qinghai region of China, improving our understanding of hepatic hydatid disease.

Transcriptomic alterations in malignant pleural mesothelioma cells in response to long­term treatment with bullfrog sialic acid­binding lectin.

Malignant pleural mesothelioma (MPM) is a universally lethal type of cancer that is increasing in incidence worldwide; therefore, the development of new drugs for MPM is an urgent task. Bullfrog sialic acid­binding lectin (cSBL) is a multifunctional protein that has carbohydrate­binding and ribonuclease activities. cSBL exerts marked antitumor activity against numerous types of cancer cells, with low toxicity to normal cells. Although in vitro and in vivo studies revealed that cSBL was effective against MPM, the mechanism by which cSBL exerts antitumor effects is not fully understood. To further understand the mechanism of action of cSBL, the present study aimed to identify the key molecules whose expression was affected by cSBL. The present study established cSBL­resistant MPM cells. Microarray analyses revealed that there were significant pleiotropic changes in the expression profiles of several genes, including multiple genes involved in metabolic pathways in cSBL­resistant cells. Furthermore, the expression of some members of the aldo­keto reductase family was revealed to be markedly downregulated in these cells. Among these, it was particularly interesting that cSBL action reduced the level of AKR1B10, which has been reported as a biomarker candidate for MPM prognosis. These findings revealed novel aspects of the effect of cSBL, which may contribute to the development of new therapeutic strategies for MPM.

Distinctive patterns of microRNA expression in extraocular muscles.

The extraocular muscles (EOMs) are a unique group of muscles that are anatomically and physiologically distinct from other muscles. We and others have shown that EOMs have a unique transcriptome and proteome. Here we investigated the expression pattern of microRNAs (miRNAs), as they may play a role in generating the unique EOM allotype. We isolated RNA and screened LC Sciences miRNA microarrays covering the sequences of miRBase 10.0 to define the microRNAome of normal mouse EOM and tibialis anterior (TA) limb muscle. Seventy-four miRNAs were found to be differentially regulated (P value <0.05) of which 31 (14 upregulated, 17 downregulated) were differentially regulated at signal strength >500. Muscle-specific miRNAs miR-206 and miR-499 were upregulated and miR-1, miR-133a, and miR-133b were downregulated in EOM. Quantitative PCR (qPCR) analysis was used to validate the differential expression. Bioinformatic tools were used to identify potential miRNA-mRNA-protein interactions and integrate data with previous transcriptome and proteomic profiling data. Luciferase assays using cotransfection of precursor miRNAs with reporter constructs containing the 3'-untranslated region of predicted target genes were used to validate targeting by identified miRNAs. The definition of the EOM microRNAome complements existing transcriptome and proteome data about the molecular makeup of EOM and provides further insight into regulation of muscle genes. These data will also help to further explain the unique EOM muscle allotype and its differential sensitivity to diseases such as Duchenne muscular dystrophy and may assist in development of therapeutic strategies.

Microarray analysis of long non-coding RNA and mRNA expression profiles in diabetic cardiomyopathy using human induced pluripotent stem cell-derived cardiomyocytes.

AIM: This study aims to investigate the altered expression signature of long non-coding RNAs, mRNAs and deregulated pathways related to diabetic cardiomyopathy disease pathogenesis. METHOD: We utilize the previously established in vitro diabetic cardiomyopathy model of human induced pluripotent stem cell-derived human cardiomyocytes to perform long non-coding RNA and mRNA expression analysis on glucose (11 mM), endothelin-1 (10 nM) and cortisol (1 µM) stimulated human induced pluripotent stem cell-derived human cardiomyocytes to interrogate diabetic cardiomyopathy associated RNA expression profile. RESULT: Out of 20,730 mRNAs and 40,173 long non-coding RNAs being screened, 2046 long non-coding RNAs and 1582 mRNAs were differentially regulated (fold change > 2, p < 0.05) between diabetic cardiomyopathy and control group, of which more than half were intergenic and antisense long non-coding RNAs. Most of the coding transcripts were associated with processes like inflammation, structural reorganization, metabolism, smooth muscle contraction, focal adhesion and repair contributing towards the development of diabetic cardiomyopathy. The subgroup analysis further revealed 411 long non-coding RNAs being co-expressed with neighbouring genes. However, our coding-non-coding co-expression analysis showed an overall 48,155 co-expression network connections. In addition to that, the long non-coding RNAs with highest network connections were profoundly enriched for focal adhesion, cell-matrix adhesion and muscle contraction. CONCLUSION: These results provide comprehensive data about the pathways and regulatory mechanisms associated with diabetic cardiomyopathy and indicate that long non-coding RNAs may play a crucial role in diabetic cardiomyopathy.

MicroRNA Microarray Profiling in Infantile Hemangiomas.

Objective: MicroRNAs are short, noncoding RNA molecules that negatively regulate the stability and translational efficiency of target mRNAs. They are critical regulators of growth and development. Our aim was to identify microRNAs involved in the growth and regulation of infantile hemangiomas. In addition, we searched for the presence of Piwi-interacting RNAs in hemangioma tissue as another regulator of infantile hemangiomas. Methods: RNA was extracted from hemangioma specimens from 3 clinical, age-based categories: proliferative (N = 16), quiescent (N = 8), and involuting (N = 9). RNAs from human dermal microvascular endothelial cells were used as controls. MicroRNA microarray was performed, and the expression profiles of the hemangiomas and endothelial cells were compared using the t test. 5' End-labeling of RNA of our hemangioma specimens was performed for Piwi-interacting RNA detection. Results: Analysis confirmed statistically significant downregulated (N = 18) and upregulated (N = 15) microRNAs. Piwi-interacting RNA analysis did not detect Piwi-interacting RNA transcripts in the hemangioma specimens. Conclusions: The differential expression of microRNAs found in our hemangioma specimens provides insight into the regulation of hemangioma formation and proliferation, quiescence, and fibrofatty involution. Piwi-interacting RNA transcripts were not detected in the hemangioma specimens. These novel findings will help in establishing new therapeutic and diagnostic initiatives for these tumors.

Global methylation patterns in primary plasma cell leukemia.

Primary plasma cell leukemia (pPCL) is a rare and very aggressive variant of multiple myeloma (MM). Specific clinical, biological and molecular patterns distinguish pPCL from MM. Here, we performed a genome-wide methylation analysis by high-density array in 14 newly diagnosed pPCL patients along with 60 MMs, and 5 patients affected by monoclonal gammopathy of uncertain significance (MGUS). Our analysis revealed a global hypomethylation profile associated with pPCL. Additionally, differential methylation patterns were found related to distinct chromosomal aberrations and DIS3 mutations, affecting genes with roles in bone metabolism, cell migration, transcription regulation or DNA damage response. When compared with MM patients, pPCL showed a distinct methylation profile mostly characterized by hypomethylated probes specific for genes involved in several processes like cell adhesion and migration. Furthermore, decreasing methylation levels were evidenced for genes significantly modulated in the progressive phases of plasma cell dyscrasias, from MGUS to MM and pPCL. Overall, our data provide new insights into the molecular characterization of pPCL, thus being potentially useful in the prognostic stratification or identification of novel molecular targets.

Antineoplastic activity of isoliquiritigenin, a chalcone compound, in androgen-independent human prostate cancer cells linked to G2/M cell cycle arrest and cell apoptosis.

Isoliquiritigenin is a natural chalcone derived from Glycyrrhiza, which has been reported to have anti-tumor activity in recent years. Here, we investigate the anticancer efficacy and associated mechanisms of isoliquiritigenin in human prostate cancer PC-3 and 22RV1 cells. Isoliquiritigenin (25-50µM) inhibited cell proliferation, induced cell apoptosis, and caused G2/M cell cycle arrest in vitro. This agent also repressed the growth of PC-3 xenograft tumors in vivo with the results of hematoxylin/eosin staining and immunohistochemistry staining showing differences between isoliquiritigenin-treated groups and control group. Next, we used microarray transcriptional profiling to identify isoliquiritigenin-regulated genes on PC-3 prostate cancer cells. Multiple genes involved in cell cycle, DNA damage, and apoptosis signaling pathways were changed remarkably with the treatment of isoliquiritigenin. Molecular studies revealed that G2/M arrest was associated with a decrease in cyclin B1, cyclin-dependent kinase 1 (CDK1), and phosphorylated CDK1 (Thr14, Tyr15, and Thr161), whereas the expression of 14-3-3σ and growth arrest and DNA damage-inducible 45 alpha (GADD45A) was increased. The complexes of cyclin B1-CDK1 were also examined to show a decrease in the binding of CDK1 with cyclin B1. In addition, treatment with relatively high concentrations of isoliquiritigenin induced apoptosis, mainly associated with enhancing apoptosis regulator (Bax/Bcl-2) ratio. Collectively, these findings indicate that isoliquiritigenin modulates cyclin B1-CDK1 for G2/M arrest, together with an alteration of cell cycle regulators and apoptotic factors in human prostate cancer cells. However, we observed pleiotropic effects for isoliquiritigenin in microarray results, suggesting that other biological mechanisms also contribute to its efficacy, which could be of interest for future investigations.