Search

miRNAs are noncoding RNAs with abnormal expression in breast cancer; their expression in high-risk benign breast tissue may relate to breast cancer risk. We examined miRNA profiles in contralateral unaffected breasts (CUB) of patients with breast cancer and validated resulting candidates in two additional sample sets. Expression profiles of 754 mature miRNAs were examined using TaqMan Low Density Arrays in 30 breast cancer samples [15 estrogen receptor (ER)-positive and 15 ER-negative] and paired CUBs and 15 reduction mammoplasty controls. Pairwise comparisons identified miRNAs with significantly differential expression. Seven candidate miRNAs were examined using qRT-PCR in a second CUB sample set (40 cases, 20 ER+, 20 ER−) and 20 reduction mammoplasty controls. Further validation was performed in 80 benign breast biopsy (BBB) samples; 40 from cases who subsequently developed breast cancer and 40 from controls who did not. Logistic regression, using tertiles of miRNA expression, was used to discriminate cases from controls. Seven miRNAs were differentially expressed in tumors and CUBs versus reduction mammoplasty samples. Among them, miR-18a and miR-210 were validated in the second CUB set, showing significantly higher expression in tumor and CUBs than in reduction mammoplasty controls. The expression of miR-18a and miR-210 was also significantly higher in BBB cases than in BBB controls. When both miR-18a and miR-210 were expressed in the upper tertiles in BBB, OR for subsequent cancer was 3.20, P = 0.023. miR-18a and miR-210 are expressed at higher levels in CUBs of patients with breast cancer, and in BBB prior to cancer development, and are therefore candidate breast cancer risk biomarkers. Cancer Prev Res; 10(1); 89–97. ©2016 AACR.

Supplemental Figure 1. Validation of miR-214*, miR-124, miR-193a-3p, miR-485a-3p and miR-671-3p in independent sample set of tumor (ER+T and ER-T) and matching contralateral breast (ER+C, ER-C) compared to reduction mammoplasty controls. Supplemental Figure 2. Expression of ER in (A) CUB validation samples and (B) BBB samples. (A) There is no significant difference between ER+ CUB (ER+C) or ER- CUB (ER-C) and controls. Only the tumor samples (ER+T, ER-T) showed the significant difference vs controls. *** P

Supplementary Table S4.

Supplementary Figure S2.

Supplementary Legends.

Ependymoma, a rare pediatric tumor originating from ependymal cells located in the lining of ventricular surfaces in the brain, presents great challenges in treatment despite advances in neurosurgical techniques. In order to identify new molecular biomarkers that could improve clinical management and outcomes, we have used RNA-seq to profile the Whole Transcriptome of three ependymoma samples and one normal control brain tissue, producing a total of 2.5 Gigabases of sequencing data. Different protein-coding gene databases were interrogated for known annotated genes to calculate RPKM and Fold Changes (FGs) for each clustered gene. Using this approach, we were able to identify Differentially Expressed Genes (DEGs) in ependymomas. KEGG pathways and Gene Ontology (GO) categories enriched in the DEGs were analyzed using Enrichr, and protein interaction networks were then built using MetaCore™. Thirty differentially expressed protein-coding genes associated with neurogenesis were identified by TaqMan Real-Time PCR, 17 of these showing statistically significant differential expression. Based on these results, we have identified IGF-2 as highly over-expressed in ependymomas and that this is due to loss of DNA methylation in its promoter region. In conclusion, we believe that some of these genes, specially IGF-2, may be of clinical importance, opening new avenues for disease management and new therapies. Keywords: Ependymomas, Transcriptome analysis, Expression, Big data analytics, Epigenetic regulation, Potential biomarkers.

Over the past few decades, the number of health and 'omics-related data' generated and stored has grown exponentially. Patient information can be collected in real time and explored using various artificial intelligence (AI) tools in clinical trials; mobile devices can also be used to improve aspects of both the diagnosis and treatment of diseases. In addition, AI can be used in the development of new drugs or for drug repurposing, in faster diagnosis and more efficient treatment for various diseases, as well as to identify data-driven hypotheses for scientists. In this review, we discuss how AI is starting to revolutionize the life sciences sector.

Breast cancer (BC) is the most frequently diagnosed female cancer and second leading cause of death. Despite the discovery of many antineoplastic drugs for BC, the current therapy is not totally efficient. In this study, we investigated the potential of repurposing the well-known diabetes type II drug liraglutide to modulate epigenetic modifications in BC cells lines in vitro and in vivo via Ehrlich mice tumors models. The in vitro results revealed a significant reduction on cell viability, migration, DNMT activity and displayed lower levels of global DNA methylation in BC cell lines after liraglutide treatment. The interaction between liraglutide and the DNMT enzymes resulted in a decrease profile of DNA methylation for the CDH1, ESR1 and ADAM33 gene promoter regions and, consequently, increased their gene and protein expression levels. To elucidate the possible interaction between liraglutide and the DNMT1 protein, we performed an in silico study that indicates liraglutide binding in the catalytic cleft via hydrogen bonds and salt bridges with the interdomain contacts and disturbs the overall enzyme conformation. The in vivo study was also able to reveal that liraglutide and the combined treatment of liraglutide and paclitaxel or methotrexate were effective in reducing tumor growth. Moreover, the modulation of CDH1 and ADAM33 mouse gene expression by DNA demethylation suggests a role for liraglutide in DNMT activity in vivo. Altogether, these results indicate that liraglutide may be further analysed as a new adjuvant treatment for BC.

Purpose: miRNAs are non-coding RNAs that are abnormally expressed in breast cancer, with critical roles in cancer due to their regulation of large gene networks. miRNA expression in benign high-risk breast tissue has never been evaluated, but it may provide information about early dysregulation events that contribute to breast cancer risk. The contralateral unaffected breast (CUB) of women with unilateral breast cancer is in high-risk for the second primary cancer. Thus, we examined miRNA expression profiles in tumor and the matching CUBs to seek potential miRNA biomarkers for breast cancer risk. Methods: FFPE tissues of breast cancer and their matching CUB tissues were sectioned. The areas of tumor and normal ductal epithelium were outlined and then dissected using laser microdissection system. Total RNA was extracted for miRNA profiling studies. Expression profiles of 754 mature miRNAs were examined using TaqMan Low Density Arrays assays in 30 paired breast cancer and CUB samples (15 with ER+ tumors, 15 with ER- tumors) and 15 reduction mammoplasty (RM) controls, matched by age, race and menopausal status. ANOVA test was performed to examine the differential expression among groups and pairwise comparison with Sidak adjustment was used for multiple comparison. Seven candidate miRNAs were then examined in an independent CUB sample set (20 with ER+ tumors, 20 with ER- tumors) and 20 RM controls. Further independent validation was performed using qRT-PCR in 80 benign breast biopsy (BBB) samples: 40 from women who subsequently developed breast cancer (cases) and 40 from those who did not (controls). Logistic regression analysis and receiver operating characteristic (ROC) analysis were performed using combinations of the expression of multiple miRNAs to establish models discriminating cases from controls. Results: Seven miRNAs (miR-18a, miR-210, miR-214*, miR-124, miR-193a-3p, miR485-3p and miR-671-3p) were found to be differentially expressed in breast cancer and CUB samples vs. RM samples in the discovery sample set. Among them, miR-18a and miR-210 were validated in a second, independent CUB sample set. The expression of miR-18a and miR-210 were significantly higher in tumor (regardless ER status) compared to CUBs and RM controls. The expression levels in CUBs were significantly higher than in RM. We then examined miR expression in case BBB samples, and confirmed that expression of miR-18a and miR-210 were increased compared with controls. ROC analysis using miR-18a and miR-210 discriminated high-risk cases from standard-risk controls with OR 2.44, P = 0.022. Conclusion: The expression of miR-18a and miR-210 were elevated in breast cancer, in matched CUBs, and in BBB predating cancer diagnosis. These data provide strong support for the hypothesis that miR-18a and miR-210 expression in BBB is an indicator of increased risk of breast cancer. Given the high expression in tumors, they are also potential cancer detection biomarkers. Citation Format: Wang J, Shidfar A, Costa FF, Scholtens D, Bischof JM, Sullivan ME, Ivancic D, Soares MB, Khan SA. Expression of miR-18a and miR-210 in normal breast tissue as candidate markers of breast cancer risk [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-07-02.

The constant demand for new antibiotic drugs has driven efforts by the scientific community to prospect for peptides with a broad spectrum of action. In this context, antimicrobial peptides (AMPs) have acquired great scientific importance in recent years due to their ability to possess antimicrobial and immunomodulatory activity. In the last two decades, plants have attracted the interest of the scientific community and industry as regards their potential as biofactories of heterologous proteins. One of the most promising approaches is the use of viral vectors to maximize the transient expression of drugs in the leaves of the plant Nicotiana benthamiana. Recently, the MagnifectionTM expression system was launched. This sophisticated commercial platform allows the assembly of the viral particle in leaf cells and the systemic spread of heterologous protein biosynthesis in green tissues caused by Agrobacterium tumefaciens “gene delivery method”. The system also presents increased gene expression levels mediated by potent viral expression machinery. These characteristics allow the mass recovery of heterologous proteins in the leaves of N. benthamiana in 8 to 10 days. This system was highly efficient for the synthesis of different classes of pharmacological proteins and contains enormous potential for the rapid and abundant biosynthesis of AMPs.

Objective.To identify differentially expressed microRNA (miRNA) in muscle biopsies (MBx) from 15 untreated children with juvenile dermatomyositis (JDM) compared with 5 controls.Methods.Following MBx miRNA profiling, differentially expressed miRNA and their protein targets were validated by quantitative real-time PCR (qRT-PCR) and immunological assay. The association of miRNA-10a and miRNA-10b with clinical data was evaluated, including Disease Activity Score (DAS), von Willebrand factor antigen (vWF:Ag), nailfold capillary end row loops, duration of untreated disease, and tumor necrosis factor (TNF)-α-308A allele.Results.In JDM, 16/362 miRNA were significantly differentially expressed [false discovery rate (FDR) < 0.05]. Among these, miRNA-10a was the most downregulated miRNA in both FDR and ranking of fold change: miRNA-10a = −2.27-fold, miRNA-10b = −1.80-fold. Decreased miRNA-10a and miRNA-10b expressions were confirmed using qRT-PCR: −4.16 and −2.59 fold, respectively. The qRT-PCR documented that decreased miRNA-10a expression was related to increased vascular cell adhesion molecule 1 in 13 of these JDM cases (correlation −0.67, p = 0.012), unlike miRNA-10b data (not significant). Concurrent JDM plasma contained increased levels of interleukin (IL) 6 (p = 0.0363), IL-8 (p = 0.0005), TNF-α (p = 0.0011), and monocyte chemoattractant proteins 1 (p = 0.0139). Decreased miRNA-10a, but not miRNA-10b, was associated with the TNF-α-308A allele (p = 0.015). In the 15 JDM, a trend of association of miRNA-10a (but not miRNA-10b) with vWF:Ag and DAS was observed.Conclusion.MiRNA-10a downregulation is an important element in untreated JDM muscle pathophysiology. We speculate that muscle miRNA expression in adult dermatomyositis differs from muscle miRNA expression in untreated childhood JDM.

Aggressive tumor cells express a plastic, multipotent phenotype similar to embryonic stem cells. However, the absence of major regulatory checkpoints in these tumor cells allows aberrant activation of embryonic signaling pathways, which seems to contribute to their plastic phenotype. Emerging evidence showing the molecular cross-talk between two major stem cell signaling pathways Nodal and Notch suggests a promising therapeutic strategy that could target aggressive tumor cells on the basis of their unique plasticity, and provide new insights into the mechanisms underlying the re-emergence of developmental signaling pathways during tumor progression.

Despite the advances in tumor identification and treatment, cancer remains the primary driver of death around the world. Also, regular treatments for the disease are incapable of targeting particular cancer types at different stages since they are not specifically focused on harmful cells since they influence both solid and tumor cells, causing side effects and undesirable symptoms. Therefore, novel strategies should be developed to treat this disease. Several efforts have been made in this direction to find more effective alternatives to cancer treatment, such as the use of antimicrobial peptides (AMPs) with antitumoral activity, nanocarriers and natural compounds from a variety of sources. AMPs are more specific to their targets because of electrostatic interaction between AMPs and the cancer cells' plasma membrane. Nanocarriers may be used for the delivery of non-soluble drugs, which are poorly stable or require a controlled release. In addition, natural compounds have been a rich source of anti-cancer agents for decades. In this review, these three approaches will be discussed, showing recent advances and advantages of using these strategies to treat cancer as well as the combination of these approaches increasing anticancer activity.

Opinion article written by Speaker for the II International Scientific Meeting of Instituto Evandro Chagas, held from October 25 to 27, 2017, in Ananindeua, Para, Brazil. All the articles of this modality were analyzed by the Scientific Committee of the Event and, later, by the Editors of RPAS.

Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death among women worldwide. Metastasis remains a major challenge for the clinical management and prognosis of patients with cancer. The metalloprotease MMP-9 plays a critical role in the first step of metastasis through extracellular matrix degradation. In this study, our goal was to determine the effect of epigenetic mechanisms in the promoter and intragenic region of this gene and to correlate it to the levels of expression of MMP9 in breast cancer cell lines. We have identified that MMP9 was highly expressed in the breast cancer cell lines MCF7 and MDA-MB-436 after 5-aza-2'-deoxycytidine (5-azadC) treatment. Sequencing of the promoter region as well as the CGI intronic CpG islands showed a specific sequence in CGI2, between CpGs 12-30 that was demethylated after 5-azadC treatment. This specific region was studied in breast cancer samples that revealed similar results with demethylation in positive MMP-9 breast cancer samples. Furthermore, the histone methylation marker of open chromatin (H3K4me3) was found in the promoter and intronic regions of MMP9 after 5-azadC treatment. Taken together these results showed a mechanism of DNA methylation and gene expression regulation by epigenetic marks present in the intronic DNA region of MMP9.

Breast cancer is a heterogeneous disease with differences in its clinical, molecular and biological features. Traditionally, immunohistochemical markers together with clinicopathologic parameters are used to classify breast cancer and to predict disease outcome. Triple-negative breast cancer (TNBC) is a particular type of breast cancer that is defined by a lack of expression of hormonal receptors and the HER2 gene. Most cases of TNBC also have a basal-like phenotype (BLBC) with expression of cytokeratin 5/6 and/or EGFR. A basal marker alone is insufficient for a better understanding of the tumor biology of TNBC. In that regard, the ADAM33 gene is silenced by DNA hypermethylation in breast cancer, which suggests that ADAM33 might be useful as a molecular marker. In the present study, we have produced monoclonal antibodies against the ADAM33 protein and have investigated the role of ADAM33 protein in breast cancer. We used 212 breast tumor samples and lower levels of ADAM33 were correlated with TNBC and basal-like markers. A lower level of ADAM33 was also correlated with shorter overall survival and metastasis-free survival and was considered an independent prognostic factor suggesting that ADAM33 is a novel molecular biomarker of TNBC and BLBC that might be useful as a prognostic factor.

In order to study the role of galectin-3 in tumor angiogenesis associated with tumor-associated macrophages (TAM) and tumor parenchyma, the galectin-3 expression was reconstituted in Tm1 melanoma cell line that lacks this protein. Galectin-3-expressing cells (Tm1G3) and mock-vector transfected cells (Tm1N3) were injected into wild-type (WT) and galectin-3 knockout (KO) C57Bl/6 mice. Tumors originated from Tm1G3 were larger in tumor volume with enlarged functional vessels, decreased necrotic areas, and increased vascular endothelial growth factor (VEGF) protein levels. Galectin-3-nonexpressing-cells injected into WT and KO showed increased levels of transforming growth factor beta 1 (TGFβ1) and, in WT animals this feature was also accompanied by increased VEGFR2 expression and its phosphorylation. In KO animals, tumors derived from galectin-3-expressing cells were infiltrated by CD68(+)-cells, whereas in tumors derived from galectin-3-nonexpressing-cells, CD68(+) cells failed to infiltrate tumors and accumulated in the periphery of the tumor mass. In vitro studies showed that Tm1G3 secreted more VEGF than Tm1N3 cells. In the latter case, TGFβ1 induced VEGF production. Basal secretion of VEGF was higher in WT-bone marrow-derived macrophages (BMDM) than in KO-BMDM. TGFβ1 induced secretion of VEGF only in WT-BMDM. Tm1G3-induced tumors had the Arginase I mRNA increased, which upregulated alternative macrophage (M2)/TAM induction. M2 stimuli, such as interleukin-4 (IL4) and TGFβ1, increased Arginase I protein levels and galectin-3 expression in WT- BMDM, but not in cells from KO mice. Hence, we report that galectin-3 disruption in tumor stroma and parenchyma decreases angiogenesis through interfering with the responses of macrophages to the interdependent VEGF and TGFβ1 signaling pathways.

Advances in Information Technology (IT) have enhanced our ability to gather, collect and analyze information from individuals and specific groups of people online. The emergence of online networks has facilitated connections between individuals by leveraging data exchange in a variety of fields. Online networking in life sciences transforms data collection into actionable information that will improve individual and population health, deliver effective therapies and, consequently, reduce the cost of healthcare. These novel tools might also have a direct impact in personalized medicine programs, since the adoption of new products by health care professionals in life sciences and peer-to-peer learning could be improved using social networks and big data analytics. However, one of the main concerns of information exchange online is data privacy. In this article, we will review how online networks and big data analytics are impacting the life sciences sector.

MicroRNAs (miRNAs) are short non-coding RNA transcripts that have the ability to regulate the expression of target genes, and have been shown to influence the development of various tumors. The purpose of our study is to identify aberrantly expressed miRNAs in retinoblastoma for the discovery of potential therapeutic targets for this disease, and to gain a greater understanding of the mechanisms driving retinoblastoma progression. We report 41 differentially expressed miRNAs (p

Maturity Onset Diabetes of the Young (MODY) is a heterogeneous group of genetic diseases characterized by a primary defect in insulin secretion and hyperglycemia, non-ketotic disease, monogenic autosomal dominant mode of inheritance, age at onset less than 25 years, and lack of auto-antibodies. It accounts for 2-5% of all cases of non-type 1 diabetes. MODY subtype 2 is caused by mutations in the glucokinase (GCK) gene. In this study, we sequenced the GCK gene of two volunteers with clinical diagnosis for MODY2 and we were able to identify four mutations including one for a premature stop codon (c.76C>T). Based on these results, we have developed a specific PCR-RFLP assay to detect this mutation and tested 122 related volunteers from the same family. This mutation in the GCK gene was detected in 21 additional subjects who also had the clinical features of this genetic disease. In conclusion, we identified new GCK gene mutations in a Brazilian family of Italian descendance, with one due to a premature stop codon located in the second exon of the gene. We also developed a specific assay that is fast, cheap and reliable to detect this mutation. Finally, we built a molecular ancestry model based on our results for the migration of individuals carrying this genetic mutation from Northern Italy to Brazil.

miRNAs are noncoding RNAs with abnormal expression in breast cancer; their expression in high-risk benign breast tissue may relate to breast cancer risk. We examined miRNA profiles in contralateral unaffected breasts (CUB) of patients with breast cancer and validated resulting candidates in two additional sample sets. Expression profiles of 754 mature miRNAs were examined using TaqMan Low Density Arrays in 30 breast cancer samples [15 estrogen receptor (ER)-positive and 15 ER-negative] and paired CUBs and 15 reduction mammoplasty controls. Pairwise comparisons identified miRNAs with significantly differential expression. Seven candidate miRNAs were examined using qRT-PCR in a second CUB sample set (40 cases, 20 ER+, 20 ER−) and 20 reduction mammoplasty controls. Further validation was performed in 80 benign breast biopsy (BBB) samples; 40 from cases who subsequently developed breast cancer and 40 from controls who did not. Logistic regression, using tertiles of miRNA expression, was used to discriminate cases from controls. Seven miRNAs were differentially expressed in tumors and CUBs versus reduction mammoplasty samples. Among them, miR-18a and miR-210 were validated in the second CUB set, showing significantly higher expression in tumor and CUBs than in reduction mammoplasty controls. The expression of miR-18a and miR-210 was also significantly higher in BBB cases than in BBB controls. When both miR-18a and miR-210 were expressed in the upper tertiles in BBB, OR for subsequent cancer was 3.20, P = 0.023. miR-18a and miR-210 are expressed at higher levels in CUBs of patients with breast cancer, and in BBB prior to cancer development, and are therefore candidate breast cancer risk biomarkers. Cancer Prev Res; 10(1); 89–97. ©2016 AACR.

BCR-ABL-negative myeloproliferative neoplasms (MPNs) are most frequently characterized by the JAK2V617F gain-of-function mutation, but several studies showed that JAK2V617F may not be the initiating event in MPN development, and recent publications indicate that additional alterations such as chromatin modification and microRNA (miRNA) deregulation may have an important role in MPN pathogenesis. Here we report that 61 miRNAs were significantly deregulated in CD34+ cells from MPN patients compared with controls (P

The future of drug design and the development of new therapeutics will rely on our ability to unravel the complexities of the epigenome in normal and disease states. Proper epigenetic regulation is essential for normal differentiation in embryogenesis and development. Conversely, abnormal epigenetic regulation is a feature of complex diseases, including cancer, diabetes, heart disease and other pathologies. Epigenetic therapies hold promise for a wide range of biological applications, from cancer treatment to the establishment of induced pluripotent stem cells. The creation of more specific and effective epigenetic therapies, however, requires a more complete understanding of epigenomic landscapes. Here, we give a historical overview of the epigenomics field and how epigenetic modifications can affect embryo development and disease etiology. We also discuss the impact of current and future epigenetic drugs.

Fabricio F Costa1,2, Luciano S Foly1, Marcelo P Coutinho11DataGenno Interactive Research Ltd., Itaperuna, Rio de Janeiro, Brazil; 2Cancer Biology and Epigenomics Program, Children's Memorial Research Center, Northwestern University's Feinberg School of Medicine, Chicago, IL, USAAbstract: Clinical genetics is one of the most challenging fields in medicine, with thousands of children born every year with congenital defects that have no satisfactory diagnosis. There are more than 6,000 known single-gene disorders that can cause birth defects or diseases in approximately 1 in every 200 births. Clinical and molecular information on genetic diseases and syndromes are widespread in the literature, and there are few databases combining this information. Therefore, it is very challenging for health care professionals and researchers to translate the latest advances in science and medicine into effective clinical interventions and new treatments. In order to overcome this obstacle and promote networking, we are building DataGenno, an online medical and scientific portal. DataGenno has been developed to be a source of information on genetic diseases and syndromes for the needs of all heath care professionals and researchers. Our database will be able to integrate both clinical and molecular aspects of genetic diseases in a fully interactive environment. DataGenno’s system already contains clinical and molecular information for 300 diseases, with approximately 6,000 signs and symptoms of these diseases in a database combined with a search engine. Our main goal is to cover all genetic diseases described to date, providing not only clinical information such as morphological and anatomical features but also the most comprehensive molecular genetics/genomics features and available testing information. We are also developing ways to connect DataGenno’s portal with Electronic Health Records in order to improve the efficiency of patient care. Additionally, DataGenno’s system and search engine will be able to provide tools that will facilitate the discovery and description of new genetic syndromes. In conclusion, we believe that DataGenno's portal will be a helpful and innovative tool for health care professionals, scientists, genetic counselors, and other professionals in the clinical genetics field.Keywords: genetic diseases, signs and symptoms, molecular genetics, genomics, search engine, database

Despite a considerable amount of effort by different groups to evaluate the genetic traits associated with complex diseases by genome-wide association studies (GWAS), just a few regions, mainly linked to protein-coding genes, were identified. Recently, studies from different groups have implicated new classes of long non-coding RNAs (ncRNAs) to important molecular mechanisms. Additionally, high-throughput transcriptome analyses of different cell types have shown that an unexpected amount of genomic DNA is transcribed. I am writing to propose that the majority of the regions that do not clearly correspond to a 'gene' controlling certain traits might be ncRNAs or other regulatory transcripts that are still unknown. These regions will need to be carefully examined in the future.

The mechanism(s) behind folate rescue of neural tube closure are not well understood. In this study we show that maternal intake of folate prior to conception reverses the proliferation potential of neural crest stem cells in homozygous Splotch embryos (Sp(-/-)) via epigenetic mechanisms. It is also shown that the pattern of differentiation seen in these cells is similar to wild-type (WT). Cells from open caudal neural tubes of Sp(-/-) embryos exhibit increased H3K27 methylation and decreased expression of KDM6B possibly due to up-regulation of KDM6B targeting micro-RNAs such as miR-138, miR-148a, miR-185, and miR-339-5p. In our model, folate reversed these epigenetic marks in folate-rescued Sp(-/-) embryos. Using tissue from caudal neural tubes of murine embryos we also examined H3K27me2 and KDM6B association with Hes1 and Neurog2 promoters at embryonic day E10.5, the proliferative stage, and E12.5, when neural differentiation begins. In Sp(-/-) embryos compared with WT, levels of H3K27me2 associated with the Hes1 promoter were increased at E10.5, and levels associated with the Neurog2 promoter were increased at E12.5. KDM6B association with Hes1 and Neurog2 promoters was inversely related to H3K27me2 levels. These epigenetic changes were reversed in folate-rescued Sp(-/-) embryos. Thus, one of the mechanisms by which folate may rescue the Sp(-/-) phenotype is by increasing the expression of KDM6B, which in turn decreases H3K27 methylation marks on Hes1 and Neurog2 promoters thereby affecting gene transcription.

Fabricio F CostaCancer Biology and Epigenomics Program, Children’s Memorial Research Center and Northwestern University’s Feinberg School of Medicine, 2430 N. Halsted St, Box 220, Chicago, IL, USAAbstract: The identification of all epigenetic modifications implicated in gene expression is the next step for a better understanding of human biology in both normal and pathological states. This field is referred to as epigenomics, and it is defined as epigenetic changes (ie, DNA methylation, histone modifications and regulation by noncoding RNAs such as microRNAs) on a genomic scale rather than a single gene. Epigenetics modulate the structure of the chromatin, thereby affecting the transcription of genes in the genome. Different studies have already identified changes in epigenetic modifications in a few genes in specific pathways in cancers. Based on these epigenetic changes, drugs against different types of tumors were developed, which mainly target epimutations in the genome. Examples include DNA methylation inhibitors, histone modification inhibitors, and small molecules that target chromatin-remodeling proteins. However, these drugs are not specific, and side effects are a major problem; therefore, new DNA sequencing technologies combined with epigenomic tools have the potential to identify novel biomarkers and better molecular targets to treat cancers. The purpose of this review is to discuss current and emerging epigenomic tools and to address how these new technologies may impact the future of cancer management.Keywords: genomics, epigenomics, epigenetics, DNA methylation, histone modifications, new technologies, cancer management

The cystic fibrosis transmembrane conductance regulator (CFTR) gene is driven by a promoter that cannot alone account for the temporal and tissue-specific regulation of the gene. This has led to the search for additional regulatory elements that cooperate with the basal promoter to achieve coordinated expression. We previously identified two alternative upstream exons of the gene that were mutually exclusive of the first exon, and one of which showed temporal regulation in the human and sheep lung. We now demonstrate that this alternative splice product generates a stable protein, which initiates translation at an ATG in exon 4, and thus lacks the N terminus of CFTR. The other splice variant inhibits translation of the protein. In a search for the promoter used by the upstream exons, we identified a novel element that contributes to the activity of the basal CFTR promoter in airway epithelial cells, but does not function independently. Finally, we demonstrate that, in primary airway cells, skin fibroblasts, and both airway and intestinal cell lines, the CFTR promoter is unmethylated, irrespective of CFTR expression status. Thus, methylation is not the main cause of inactivation of CFTR transcription.

Purpose: To understand the changes in gene expression in polycythemia vera (PV) progenitor cells and their relationship to JAK2V617F. Experimental Design: Messenger RNA isolated from CD34+ cells from nine PV patients and normal controls was profiled using Affymetrix arrays. Gene expression change mediated by JAK2V617F was determined by profiling CD34+ cells transduced with the kinase and by analysis of leukemia cell lines harboring JAK2V617F, treated with an inhibitor. Results: A PV expression signature was enriched for genes involved in hematopoietic development, inflammatory responses, and cell proliferation. By quantitative reverse transcription-PCR, 23 genes were consistently deregulated in all patient samples. Several of these genes such as WT1 and KLF4 were regulated by JAK2, whereas others such as NFIB and EVI1 seemed to be deregulated in PV by a JAK2-independent mechanism. Using cell line models and comparing gene expression profiles of cell lines and PV CD34+ PV specimens, we have identified panels of 14 JAK2-dependent genes and 12 JAK2-independent genes. These two 14- and 12-gene sets could separate not only PV from normal CD34+ specimens, but also other MPN such as essential thrombocytosis and primary myelofibrosis from their normal counterparts. Conclusions: A subset of the aberrant gene expression in PV progenitor cells can be attributed to the action of the mutant kinase, but there remain a significant number of genes characteristic of the disease but deregulated by as yet unknown mechanisms. Genes deregulated in PV as a result of the action of JAK2V617F or independent of the kinase may represent other targets for therapy. Clin Cancer Res; 16(17); 4339–52. ©2010 AACR.

Aggressive tumor cells express a plastic, multipotent phenotype similar to embryonic stem cells. However, the absence of major regulatory checkpoints in these tumor cells allows aberrant activation of embryonic signaling pathways, which seems to contribute to their plastic phenotype. Emerging evidence showing the molecular cross-talk between two major stem cell signaling pathways Nodal and Notch suggests a promising therapeutic strategy that could target aggressive tumor cells on the basis of their unique plasticity, and provide new insights into the mechanisms underlying the re-emergence of developmental signaling pathways during tumor progression. [Cancer Res 2009;69(18):7131–4]

AACR Annual Meeting-- Apr 18-22, 2009; Denver, CO PARP, a nuclear enzyme that detects and binds to DNA single-strand breaks (SSBs), functions as an important modulator of base excision repair (BER). PARP is also involved in cellular recovery from ionizing radiation (IR)-induced DNA damage by initiating a signaling network responsible for the preservation of genomic stability. PARP binds to and protects the SSBs induced by radiation from deteriorating into more deleterious double-strand breaks (DSB) during DNA replication. As a result, PARP inhibitors are being developed for cancer therapy due to their ability to sensitize cells to DNA-damaging agents. The purpose of this study was to determine whether MK-4827, a novel PARP-1 and PARP-2 inhibitor developed by Merck & Co., Inc., enhances radiosensitivity in two NSCLC cell lines, A549 (p53 wild type) and H1299 (p53 null). We examined the effect of MK-4827 and ionizing radiation on clonogenic survival and showed that a 1-hour pretreatment followed by a 24-hour post-radiation treatment with 1 \#956;M MK-4827 substantially increased the radiosensitivity of A549 cells (Dose Enhancement Factor (DEF) of 1.3) and to a lesser extent for H1299 cells (DEF = 1.15). Results from an analysis of DSB repair demonstrated that treatment with MK-4827 significantly increased the number of radiation-induced DSBs, detected on the basis of \#947;-H2AX foci, in A549 at early times after irradiation compared to radiation only controls. However, measurement of PARP enzyme activity, based on incorporation of biotinylated poly(ADP-ribose) onto histone proteins, showed that MK-4827 dramatically reduced PARP enzymatic activity in both the A549 and H1299 cell lines within 1 hour. Overall, we conclude that by inhibiting PARP activity with MK-4827, the BER pathway is compromised, leading to the conversion of radiation-induced SSBs into the more detrimental DSBs, which ultimately results in enhanced cell death. Reasons to explain the differences in response between the two cell lines are not understood at this time but may be due to the difference in p53 status or our observation that the H1299 cells typically have a smaller proportion of cells in S-phase compared to A549 cells. Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 5546.

Non-coding RNAs (ncRNAs) have been recently implicated in several molecular mechanisms in eukaryotes. They are a group of transcripts with no protein-coding potential that may have multiple functions and in many cases they have been associated with diseases. Some companies have already started to launch platforms such as arrays and products on the basis of new DNA sequencing technologies aimed at identifying and studying different types of ncRNAs but this represents just a small step toward the understanding of this new area of research. The private sector should start paying more attention to ncRNAs in order to improve the pipeline for drug discovery, drug development and facilitate the identification of new diagnostic and prognostic markers.

Pharmacogenomic studies emphasize the use of genomic information to enhance success in finding new medicines and also to improve those that are already used in clinics. Therefore, this field has a special interest in knowing how patients metabolize drugs depending on their genetic background. Most of the studies so far have focused on the impact of single genetic differences on drug metabolism. However, this may be only the tip of the iceberg in terms of how interpatient variability can influence the response to drugs. For example, control of gene expression by microRNAs (miRNAs) and alternative splicing are cellular mechanisms that have an effect on proteome diversity and have already been implicated in complex diseases such as cancer, arthritis and others. Changes in the sequence of a miRNA and/or variations in the miRNA target region of a transcript can have a major impact on post-transcriptional regulation. Events of alternative splicing can occur in more than half of the human genes, thereby changing the sequence of key proteins related to drug resistance, activation and metabolism. Furthermore, alternative splicing and miRNAs can work together to differentially control genes. This perspective article will highlight recent exciting discoveries in pharmacogenomics and also discuss how players such as miRNAs and alternative splicing may affect the way we design and apply future therapies.

Aggressive cancer cells and pluripotent stem cells converge in their capacity for self-renewal, proliferation and plasticity. Recent studies have capitalized on these similarities by demonstrating that tumors arise from specific cancer stem cell populations that, in a manner reminiscent of normal stem cells, are able to both self-renew and give rise to a heterogeneous tumor population. This stem cell like function of aggressive cancer cells is likely attributable to the ectopic expression of embryonic factors such as Nodal and Cancer Testis Specific Antigens (CTAs), which maintain a functional plasticity by promoting pluripotency and immortality. During development, the expression of these embryonic factors is tightly regulated by a dynamic array of mediators, including the spatial and temporal expression of inhibitors such as Lefty, and the epigenetic modulation of the genome. In aggressive cancer cells, particularly melanoma, this balance of regulatory mediators is disrupted, leading to the aberrant expression of pluripotency-associated genes. By exposing aggressive cancer cells to embryonic microenvironments, this balance of regulatory mediators is restored, thereby reprogramming tumor cells to a more benign phenotype. These stem cell-derived mediators, as well as the genes they regulate, provide therapeutic targets designed to specifically differentiate and eradicate aggressive cancers.

In the last ten years, several RNAs with no protein-coding potential have been accumulating in RNA databases and are in need of further molecular characterization. At the same time, examples of non-coding RNAs (ncRNAs) such as microRNAs, small RNAs, small interfering RNAs (siRNAs) and medium/large RNAs with various functions have been described in the literature. Recent evidence points to a widespread role of these molecules in eukaryotic cells, suggesting that the majority of the new ncRNA examples might have specific functions. The aim of this review is to describe several new functional ncRNAs that have been recently identified and characterized, providing some clues that these molecules might not be produced by chance or as by-products of transcription as has been speculated.

In the multistep process of cancer development, the concept that cancer stem cells are derived from normal stem cells that have gradually accumulated various genetic and epigenetic defects is gaining strong evidence. A number of investigations have identified molecular markers that, under normal conditions, are responsible for stem cell homeostasis but are also expressed in tumor “stem cell-like” subpopulations. In this regard, it was recently reported that a group of tumor-specific antigens known as cancer/testis antigens (CTAs) are expressed in human MSCs. It has long been stated that in normal tissue these antigens are exclusively expressed in germ cell precursors; however, based on these results, we suggest that CTAs are expressed at earlier stages during embryogenesis. The tumor-restricted expression of CTAs has led to several immunotherapeutic trials targeting some of these proteins. The clinical implications that these trials may have on the normal stem cell pools, as well as the immunologic properties of these cells, is to date poorly studied and should be considered.

The completion of the human, mouse and other eukaryotic genomes were important scientific milestones, but they were just small steps towards the understanding of eukaryotic biology. Recent transcriptome analysis and different experimental approaches have identified a surprisingly large number of non-coding RNAs (ncRNAs) in eukaryotic cells. ncRNAs comprise microRNAs, anti-sense transcripts and other Transcriptional Units containing a high density of stop codons and lacking any extensive "Open Reading Frame". They have been shown to regulate gene expression by novel mechanisms such as RNA interference, gene co-suppression, gene silencing, imprinting and DNA demethylation. It is becoming clear that these novel RNAs perform critical functions during development and cell differentiation. There is also mounting evidence of their involvement in cancer and neurological diseases. Together, all this information indicates that ncRNAs are emerging as a new class of functional transcripts in eukaryotes. Therefore, great challenges lie in the years ahead: understanding the molecular biology of higher organisms will require revealing all proteins (Proteome), all ncRNAs (RNome) and their interactions (Interactome) in the complex molecular scenario within eukaryotic cells.

Altered cell adhesion is causally involved in tumor progression, and the identification of novel adhesion molecules altered in tumors is crucial for our understanding of tumor biology and for the development of new prognostic and therapeutic strategies. Here, we provide evidence for the epigenetic downregulation in breast tumors of the A Desintegrin And Metalloprotease domain 23 gene (ADAM 23), a member of a new family of surface molecules with roles in cell-cell adhesion and/or cell-matrix interactions. We examined the mRNA expression and methylation status of the 5' upstream region of the ADAM23 gene in different breast tumor cell lines as well as in primary breast tumors. We found ADAM23 5' hypermethylation in eight out of 12 (66.7%) tumor cell lines and in nine out of 13 (69.2%) primary tumors. Promoter hypermethylation was strongly associated with reductions in both mRNA and protein expression, with a threshold of 40-60% of modified CpG dinucleotides being required for the complete silencing of ADAM23 mRNA expression. Treatment of MCF-7 and SKBR-3 cell lines with 5'-Aza-2'-deoxycytidine led to a reactivation of ADAM23 mRNA expression and a marked decrease in the methylation level. It is worth noting that primary breast tumors with a more advanced grade showed a higher degree of methylation, suggesting that the adhesion molecule ADAM23 may be downregulated during the progression of breast cancer. Oncogene (2004) 23, 1481-1488. doi:10.1038/sj.onc.1207263 Published online 8 December 2003

Aim: This study was undertaken to contribute to knowledge of the immunological profile of Down syndrome and alopecia areata patients. Material and Methods: Observational, case series study, with comparison group. The following data were computed: gender, age, karyotype, previous disease and immunological profile: complete blood count, Blood Sedimentation Rate (BSR), cellular and humoral immunity and autoimmunity. Frequency, central trends and dispersion measurements for descriptive analysis. The nonparametric χ2 test and Fisher Exact test for exploratory analyses; significance level for p value < 0.05. Results: Eighty-three Down Syndrome (DS) patients were evaluated: 21 with Alopecia Areata (AA) and 62 without it. The average age of patients with AA was 13.3 years (SD ± 5.0) and of DS without AA was 12.2 (SD ± 5.3); 94.7% presented free trisomy. The predominant previous illness was hypothyroidism, which occurred only in DS patients with AA (3/21). Hemogram was normal in 40.9% and the most frequent alteration was an increase of hematocrit (22.9%). The BSR was elevated in 71.1%. About cellular immunity, the principal abnormality was the decrease in CD4. Immunoglobulin electrophoresis was normal in 100.0%; DS patients showed normal levels of IgA in 100.0% of cases, of IgM in 98.8% and IgG, in 85.5%. Complement C4 and C3 were decreased in 67.4% and in 9.6% of the patients, respectively. The majority of studied antibodies were non reagent, but the presence of antiperoxidase antibody was significant in DS patients with AA. Conclusion: There was no significant difference between the groups, related to their immunological profile, except for the presence of antiperoxidase antibody that maybe associated with the presence of hypothyroidism in DS patients with AA. Perhaps some of the findings are justified by the small sample; the authors suggest further studies with a larger sample and with HLA testing in order to understand the mechanism of AA in DS.

The advent and improvement of high-throughput sequencing over the past decade leveraged the study of whole genomes and transcriptomes of different organisms at lower costs. In transcriptomics, RNA-Seq expands our capacity to understand gene expression in different tissues and pathologies, and how alternative splicing might affect the final protein sequence. Here, we discuss the association of using transcriptome and proteome high-throughput data to foster drug discovery. Using this innovative strategy, some research groups have already identified computationally predicted novel peptides derived from putative splice variants in experimental human proteome data. These discoveries provide new opportunities for targeted drug development.

This study was undertaken to better understand clinical characteristics, environmental and physical events in Down syndrome (DS) and alopecia areata (AA). This cross-sectional study included 18 DS patients who were currently presenting or had presented AA. We evaluated gender, age, location and type of AA, presence of autoimmune disease or atopy, AA in first-degree relatives, and environmental, physical, and clinical intercurrences. The mean age of study subjects was 11.6 (SD ± 5.5) years and mean age at AA onset 7.2 (2.5 to 15.2) years. The duration of alopecia episodes varied, with a mean of 2.7 (0.1 to 18.7) years. Recurrence of AA was reported in 27.7% (5/18) of subjects, with a mean number of recurrences of 3.6. Localized type AA was seen in 83.4% of individuals, with the most frequent location on the scalp (100%). Seven of the individuals presented atopy. Fourteen individuals had undergone environmental and/or clinical intercurrences. In conclusion, the most frequent presentation of AA in DS is the non-recurrent, localized form on the scalp, with a varied period of duration. Changes in the individuals' routine occurred in more than half of the study group. We suggest further studies of the psychology and immunogenetics in the etiopathology of AA in DS.

The increasing availability and growth rate of biomedical information, also known as 'big data', provides an opportunity for future personalized medicine programs that will significantly improve patient care. Recent advances in information technology (IT) applied to biomedicine are changing the landscape of privacy and personal information, with patients getting more control of their health information. Conceivably, big data analytics is already impacting health decisions and patient care; however, specific challenges need to be addressed to integrate current discoveries into medical practice. In this article, I will discuss the major breakthroughs achieved in combining omics and clinical health data in terms of their application to personalized medicine. I will also review the challenges associated with using big data in biomedicine and translational science.

Invasive ductal carcinoma (IDC) and invasive lobular breast carcinoma (ILC) are the most common malignancies compromising the breast tissue in women worldwide. ILCs tend to form metastasisin remote locations, such as the gastrointestinal tract, peritoneal surface and retroperitoneum, compared with IDCs that move preferentially to the lymph nodes, lung, pleura, liver, brain and bones. The histological characteristics of these two tumors are very similar and there is no useful molecular marker to differentiate IDC from ILC to date. In this study, we cloned and expressed ADAM33 recombinant protein cystein rich domain in order to produce polyclonal antibodies and used it as a new immnunohistochemical molecular biomarker that specifically recognizes the ILC breast cancer subtype.

Advances in information technology have improved our ability to gather, collect and analyze information from individuals online. Social networks can be seen as a nonlinear superposition of a multitude of complex connections between people where the nodes represent individuals and the links between them capture a variety of different social interactions. The emergence of different types of social networks has fostered connections between individuals, thus facilitating data exchange in a variety of fields. Therefore, the question posed now is "can these same tools be applied to life sciences in order to improve scientific and medical research?" In this article, I will review how social networks and other web-based tools are changing the way we approach and track diseases in biomedical research.

IntroductionWe have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression of miRNAs have been correlated with many human cancers.Materials and methodsWe have utilized TaqMan Low Density Arrays to evaluate the expression of 365 miRNAs in ependymomas and normal brain tissue. We first demonstrated the similarity of expression profiles of paired frozen tissue (FT) and paraffin-embedded specimens (FFPE). We compared the miRNA expression profiles of 34 FFPE ependymoma samples with 8 microdissected normal brain tissue specimens enriched for ependymal cells. miRNA expression profiles were then correlated with tumor location, histology and other clinicopathological features.ResultsWe have identified miRNAs that are over-expressed in ependymomas, such as miR-135a and miR-17-5p, and down-regulated, such as miR-383 and miR-485-5p. We have also uncovered associations between expression of specific miRNAs which portend a worse prognosis. For example, we have identified a cluster of miRNAs on human chromosome 14q32 that is associated with time to relapse. We also found that miR-203 is an independent marker for relapse compared to the parameters that are currently used. Additionally, we have identified three miRNAs (let-7d, miR-596 and miR-367) that strongly correlate to overall survival.ConclusionWe have identified miRNAs that are differentially expressed in ependymomas compared with normal ependymal tissue. We have also uncovered significant associations of miRNAs with clinical behavior. This is the first report of clinically relevant miRNAs in ependymomas.

Melanoma progression requires deregulation of gene expression by currently uncharacterized epigenetic mechanisms. A mouse model based on changes in cell microenvironment was developed by our group to study melanocyte malignant transformation. Melanoma cell lines (4C11- and 4C11+) were obtained as result of 5 sequential anchorage blockades of non-tumorigenic melan-a melanocytes. Melan-a cells submitted to 4 de-adhesion cycles were also established (4C), are non-tumorigenic and represent an intermediary phase of tumor progression. The aim of this work was to identify factors contributing to epigenetic modifications in early and later phases of malignant transformation induced by anchorage impediment. Epigenetic alterations occur early in tumorigenesis; 4C cell line shows changes in global and gene-specific DNA methylation and histone marks. Many histone modifications differ between melan-a, 4C, 4C11- (non-metastatic melanoma cell line) and 4C11+ (metastatic melanoma cell line) which could be associated with changes in gene and microRNA expression. These epigenetic alterations seem to play a key role in malignant transformation since melanocytes treated with 5-Aza-2'-deoxycytidine before each anchorage blockade do not transform. Some epigenetic changes seem to be also responsible for the maintenance of malignant phenotype, since melanoma cell lines (4C11- and 4C11+) treated in vitro with 5-Aza-2'-deoxycytidine or Trichostatin A showed reduction of tumor growth in vivo. Changes in gene expression reflecting cell adaptation to new environment were also observed. We propose a model in which sustained microenvironmental stress in melanocytes results in epigenetic reprogramming. Thus, after adaptation, cells may acquire epigenetic marks that could contribute to the establishment of a malignant phenotype.