Asociación del resultado auditivo final, en pacientes con hipoacusia súbita, a la respuesta a glucocorticoides in vitro / Association of the final hearing result, in patients with sudden hearing loss, to the response to glucocorticoids in vitro

Introducción: La hipoacusia súbita (HS) es poco frecuente y su etiopatogenia no está definida. La terapia con corticoides es de elección en base a recomendaciones de expertos por sus efectos teóricos y no en base a utilidad clínica demostrada. Objetivo: Evaluar si existe correlación entre el resultado auditivo final, de pacientes con HS tratados con corticoides, y la respuesta in vitro de sus leucocitos a corticoides, medida como diferencias en la expresión relativa de genes blanco del receptor de glucocorticoides. Material y Método: Estudio de casos (recuperación total) y controles (no recuperados) de pacientes con HS tratados con corticoides en el Hospital Clínico de la Universidad de Chile, durante 2017-2019. Se obtuvo DNA que fue almacenado en el Biobanco de Tejidos y Fluidos de la Universidad de Chile (BTUCH). Se purificaron y cultivaron leucocitos mononucleares de sangre periférica, expuestos in vitro a hidrocortisona. Se determinó la diferencia en la expresión relativa de genes blanco (IGFBP1, CAT, HSD17B12, APOA2), por Q-RTPCR, entre ambos grupos. Resultados: Se reclutaron 35 pacientes; se incluyeron para análisis 23: 11 casos y 12 controles, con edad promedio de 54,9 y 50,8 años respectivamente, distribución homogénea de sexo. No hubo diferencia estadísticamente significativa en la expresión relativa de los genes blanco, a la exposición in vitro a corticoides, entre ambos grupos. Conclusión: En nuestro estudio, modelo, y sistema de evaluación no se evidenciaron efectos de los corticoides. No podemos descartar que, con un número mayor de pacientes, otros genes blanco u otros protocolos de estudio podrían detectarse diferencias.

Introduction: Sudden hearing loss (SHL) is rare and its etiopathogenesis is still not clear. Corticosteroid therapy is of choice based on expert recommendations due to its theoretical effects and no based on proved clinical efficacy. Objectives: To assess whether there is a correlation between the final auditory outcome of patients with SHL treated with corticosteroids and the in vitro response of their leukocytes to corticosteroids, measured as differences in the relative expression of glucocorticoid receptor target genes. Material and Method: Case-control (total recovery and not recovered respectively) study of patients with SHL treated with corticosteroids at Clinical Hospital Universidad de Chile between 2017 and 2019. DNA was obtained and stored in the Biobanco de Tejidos y Fluidos de la Universidad de Chile (BTUCH). Peripheral blood mononuclear leukocytes were purified and cultured and then exposed to hydrocortisone. The difference in the relative expression of target genes (GFBP1, CAT, HSD17B12, APOA2), by Q-RTPCR was determined. Results: Thirty-five patients were recruited, 24 were included for the analysis: 11 cases and 12 controls, with and average age of 54.9 and 50.,8 years respectively, homogeneous sex distribution. There was no statistically significant difference in the relative expression of the target genes, upon in vitro exposure to corticosteroids, between both groups. Conclusion: In our study, model and evaluation system, no effects of corticosteroids were evidenced. With a larger number of patients, other target genes or other study protocols, we cannot rule out that differences could be detected.

A nine-gene signature as prognostic biomarker in gastric cancer by bioinformatics analysis.

PURPOSE: The prognosis of advanced gastric cancer (GC) remains poor. It is urgent and necessary to find suitable prognostic markers. miR-619-5p is highly expressed in GC. However, the value of miR-619-5p and its target genes as prognostic biomarkers of GC is unclear. METHODS: RT-PCR was performed to verify the expression of miR-619-5p in GC cell lines and their exosomes. Western blotting and transmission electron microscope were used to identify exosomes. The target genes of miR-619-5p were predicted by RNA22 and TargetScan. The differentially expressed genes (DEGs) and prognosis-related genes (PRGs) were obtained using The Cancer Genome Atlas (TCGA) database. The DAVID database was used to analyse pathway enrichment and functional annotation of common target genes. The STRING database and Cytoscape software were used to screen key genes and visualize their functional modules. The survival analysis was conducted using TCGA and Kaplan-Meier Plotter (KMP) databases. Finally, a prognostic model was constructed on the foundation of the key genes to assess the reliability of the screening process. RESULTS: The expression of miR-619-5p in GC cells and their exosomes was proved to be significantly higher than that in normal cell lines. There are 129 common target genes involved in 3 pathways and 28 functional annotations. Finally, nine key target genes of GC (BRCA1, RAD51, KIF11, ERCC6L, BRIP1, TIMELESS, CDC25A, CLSPN and NCAPG2) were identified, and a prognostic model was successfully constructed with a good predictive ability. CONCLUSIONS: The model of 9-gene signature could effectively predict the prognosis of GC, and have great potential to be novel prognostic factors and therapeutic targets for patients with GC.

Differential Expression of miRNAs Involved in Response to Candidatus Liberibacter asiaticus Infection in Mexican Lime at Early and Late Stages of Huanglongbing Disease.

Huanglongbing (HLB) is one of the most destructive diseases threatening citriculture worldwide. This disease has been associated with α-proteobacteria species, namely Candidatus Liberibacter. Due to the unculturable nature of the causal agent, it has been difficult to mitigate the disease, and nowadays a cure is not available. MicroRNAs (miRNAs) are key regulators of gene expression, playing an essential role in abiotic and biotic stress in plants including antibacterial responses. However, knowledge derived from non-model systems including Candidatus Liberibacter asiaticus (CLas)-citrus pathosystem remains largely unknown. In this study, small RNA profiles from Mexican lime (Citrus aurantifolia) plants infected with CLas at asymptomatic and symptomatic stages were generated by sRNA-Seq, and miRNAs were obtained with ShortStack software. A total of 46 miRNAs, including 29 known miRNAs and 17 novel miRNAs, were identified in Mexican lime. Among them, six miRNAs were deregulated in the asymptomatic stage, highlighting the up regulation of two new miRNAs. Meanwhile, eight miRNAs were differentially expressed in the symptomatic stage of the disease. The target genes of miRNAs were related to protein modification, transcription factors, and enzyme-coding genes. Our results provide new insights into miRNA-mediated regulation in C. aurantifolia in response to CLas infection. This information will be useful to understand molecular mechanisms behind the defense and pathogenesis of HLB.

Systems biology approach identifies key genes and related pathways in childhood obesity.

BACKGROUND: Childhood obesity is triggered by a complex interplay of environmental, genetic, and epigenetic factors; however, the molecular mechanisms behind this disease are not completely elucidated. Thus, the aim of this study was to investigate molecular mechanisms involved in childhood obesity by implementing a systems biology approach. METHODS: Experimentally validated and computationally predicted genes related to childhood obesity were downloaded from DisGeNET database. A protein-protein interaction (PPI) network was constructed using the STRING database and analyzed at Cytoscape web-tool. Hub-bottleneck genes and functional clusters were identified through CytoHubba and MCODE plugins, respectively. Functional enrichment analyses were performed based on Gene Ontology terms and KEGG Pathways. RESULTS: The DisGeNET search retrieved 191 childhood obesity-related genes. The resulting PPI network contained 12 hub-bottleneck genes (INS, LEP, STAT3, POMC, ALB, TNF, BDNF, CAT, GCG, PPARG, VEGFA, and ADIPOQ) and 4 functional clusters, with cluster 1 showing the highest interaction score. Genes at this cluster were enriched at inflammation, carbohydrate, and lipid metabolism pathways. With exception of POMC, all hub-bottleneck genes were found in cluster 1, which contains highly connected genes that possibly play key roles in obesity-related pathways. CONCLUSIONS: Our systems biology approach revealed a set of highly interconnected genes associated with childhood obesity, providing comprehensive information regarding genetic and molecular factors involved in the pathogenesis of this disease.

Expression and DNA methylation profiles of EZH2-target genes in plasma exosomes and matched primary tumor tissues of the patients with diffuse large B-cell lymphoma.

AIMS: Diffuse large B-cell lymphoma (DLBCL) is the most common type of aggressive lymphoma. This study was designed to compare epigenetic alterations observed in Enhancer of Zeste Homolog 2 (EZH2)-target genes between plasma-derived exosomes and primary tumors in DLBCL patients. MAIN METHODS: Exosomes were isolated from plasma of 21 DLBCL patients and 21 controls. We analyzed the methylation status of the target genes using methylation-specific PCR. We also examined whether the exosomes and the tumor samples contained transcripts of the target genes. KEY FINDINGS: We found that CDKN2A and CDKN2B were methylated in both plasma exosomes and primary tumor tissue samples. None of the transcripts were found in the exosomes except CDKN1B which was expressed in 8 (38%) of the exosome samples. SIGNIFICANCE: This study showed that plasma exosomes might preferably package certain target molecules from primary tumors and the exosomes containing dual methylated DNAs of CDKN2A and CDKN2B, or CDKN1B transcript may contribute to DLBCL pathogenesis.

Differential expression profiles of miRNAs and their putative targets in Schistosoma mansoni during its life cycle

BACKGROUND Schistosomiasis is a disease caused by Schistosoma. Due to its complex life cycle, evolutionary position and sexual dimorphism, schistosomes have several mechanisms of gene regulation. MicroRNAs (miRNAs) are short endogenous RNAs that regulate gene expression at the post-transcriptional level by targeting mRNA transcripts. OBJECTIVES Here, we tested 12 miRNAs and identified their putative targets using a computational approach. METHODS We performed the expression profiles of a set of miRNAs and their putative targets during the parasite's life cycle by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). FINDINGS Our results showed differential expression patterns of the mature miRNAs sma-miR-250; sma-miR-92a; sma-miR-new_4-3p; sma-miR-new_4-5p; sma-miR-new_5-5p; sma-miR-new_12-5p; sma-miR-new_13-3p and sma-miR-new_13-5p. Interestingly, many of the putative target genes are linked to oxidative phosphorylation and are up-regulated in adult-worms, which led us to suggest that miRNAs might play important roles in the post-transcriptional regulation of genes related to energetic metabolism inversion during parasite development. It is noteworthy that the expression of sma-miR-new_13-3p exhibited a negative correlation on SmNADH:ubiquinone oxidoreductase complex I. MAIN CONCLUSIONS Our analysis revealed putative miRNA genes related to important biological processes, such as transforming growth factor beta (TGF-β) signaling, proteasome regulation, glucose and lipid metabolism, immune system evasion and transcriptional regulation.

A meta-analysis of microRNA networks regulated by melatonin in cancer: Portrait of potential candidates for breast cancer treatment.

Melatonin is a ubiquitous molecule with a broad spectrum of functions including widespread anti-cancer activities. Identifying how melatonin intervenes in complex molecular signaling at the gene level is essential to guide proper therapies. Using meta-analysis approach, herein we examined the role of melatonin in regulating the expression of 46 microRNAs (miRNAs) and their target genes in breast, oral, gastric, colorectal, and prostate cancers, and glioblastoma. The deregulated miRNA-associated target genes revealed their involvement in the regulation of cellular proliferation, differentiation, apoptosis, senescence, and autophagy. Melatonin changes the expression of miRNA-associated genes in breast, gastric, and oral cancers. These genes are associated with cellular senescence, the hedgehog signaling pathway, cell proliferation, p53 signaling, and the hippo signaling pathway. Conversely, colorectal and prostate cancers as well as glioblastoma and oral carcinoma present a clear pattern of less pronounced changes in the expression of miRNA-associated genes. Most notably, colorectal cancer displayed a unique molecular change in response to melatonin. Considering breast cancer network complexity, we compared the genes found during the meta-analysis with RNA-Seq data from breast cancer-bearing mice treated with melatonin. Mechanistically, melatonin upregulated genes associated with immune responses and apoptotic processes, whereas it downregulated genes involved in cellular aggressiveness/metastasis (eg, mitosis, telomerase activity, and angiogenesis). We further characterized the expression profile of our gene subsets with human breast cancer and found eight upregulated genes and 16 downregulated genes that were appositively correlated with melatonin. Our results pose a multi-dimension network of tumor-associated genes regulated by miRNAs potentially targeted by melatonin.

Deregulated microRNAs Are Associated with Patient Survival and Predicted to Target Genes That Modulate Lung Cancer Signaling Pathways.

(1) Background: Although the advances in diagnostic and treatment strategies, lung cancer remains the leading cause of cancer-related deaths, worldwide, with survival rates as low as 16% in developed countries. Low survival rates are mainly due to late diagnosis and the lack of effective treatment. Therefore, the identification of novel, clinically useful biomarkers is still needed for patients with advanced disease stage and poor survival. Micro(mi)RNAs are non-coding RNAs and potent regulators of gene expression with a possible role as diagnostic, prognostic and predictive biomarkers in cancer. (2) Methods: We applied global miRNA expression profiling analysis using TaqMan® arrays in paired tumor and normal lung tissues (n = 38) from treatment-naïve patients with lung adenocarcinoma (AD; n = 23) and lung squamous cell carcinoma (SCC; n = 15). miRNA target genes were validated using The Cancer Genome Atlas (TCGA) lung AD (n = 561) and lung SCC (n = 523) RNA-Seq datasets. (3) Results: We identified 33 significantly deregulated miRNAs (fold change, FC ≥ 2.0 and p < 0.05) in tumors relative to normal lung tissues, regardless of tumor histology. Enrichment analysis confirmed that genes targeted by the 33 miRNAs are aberrantly expressed in lung AD and SCC, and modulate known pathways in lung cancer. Additionally, high expression of miR-25-3p was significantly associated (p < 0.05) with poor patient survival, when considering both tumor histologies. (4) Conclusions: miR-25-3p may be a potential prognostic biomarker in non-small cell lung cancer. Genes targeted by miRNAs regulate EGFR and TGFß signaling, among other known pathways relevant to lung tumorigenesis.

MicroRNA expression in relation with clinical evolution of osteosarcoma.

Osteosarcoma is the most common malignant bone tumor. Early diagnosis remains a major challenge, mainly because of the lack of specific biomarkers. We performed miRNAs expression analysis through qPCR in affected and paired healthy bone derived from osteosarcoma patients. Hierarchical clustering using the top ten miRNAs with differential expression showed two main clusters. One integrated by patients with the presence of metastasis or relapse and the other without these complications. Further pathway enrichment analysis reduced to four main miRNAs, hsa-miR-486-3p, hsa-miR-355-5p, hsa-miR-34a-5p and hsa-miR-1228-3p. Afterwards, we compared patients with and without metastasis, the function enrichment analysis along with review of relevant literature, showed that hsa-miR-93-5p and hsa-miR-28-5p were associated with metastasis development. Our results support the relevance of miRNAs in the pathogenesis of osteosarcoma and contribute with evidence regarding the potential role of miRNAs as potential biomarkers. More studies are needed to define the most informative miRNAs in osteosarcoma patients.

Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.

Some organism-specific databases about regulation in bacteria have become larger, accelerated by high-throughput methodologies, while others are no longer updated or accessible. Each database homogenize its datasets, giving rise to heterogeneity across databases. Such heterogeneity mainly encompasses different names for a gene and different network representations, generating duplicated interactions that could bias network analyses. Abasy (Across-bacteria systems) Atlas consolidates information from different sources into meta-curated regulatory networks in bacteria. The high-quality networks in Abasy Atlas enable cross-organisms analyses, such as benchmarking studies where gold standards are required. Nevertheless, network incompleteness still casts doubts on the conclusions of network analyses, and available sampling methods cannot reflect the curation process. To tackle this problem, the updated version of Abasy Atlas presented in this work provides historical snapshots of regulatory networks. Thus, network analyses can be performed at different completeness levels, making possible to identify potential bias and to predict future results. We leverage the recently found constraint in the complexity of regulatory networks to develop a novel model to quantify the total number of regulatory interactions as a function of the genome size. This completeness estimation is a valuable insight that may aid in the daunting task of network curation, prediction, and validation. The new version of Abasy Atlas provides 76 networks (204,282 regulatory interactions) covering 42 bacteria (64% Gram-positive and 36% Gram-negative) distributed in 9 species (Mycobacterium tuberculosis, Bacillus subtilis, Escherichia coli, Corynebacterium glutamicum, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pyogenes, Streptococcus pneumoniae, and Streptomyces coelicolor), containing 8459 regulons and 4335 modules. Database URL: https://abasy.ccg.unam.mx/.

Fungal-host interactions: insights into microRNA in response to Paracoccidioides species

BACKGROUND Paracoccidioides spp. causes paracoccidioidomycosis (PCM), an important and frequent systemic mycosis that occurs in Latin America. The infectious process begins with contact between the fungus and lung cells, and the molecular pattern of this interaction is currently poorly understood. MicroRNAs (miRNAs) are small non-coding RNAs that regulate the gene expression in many biological processes, including in the infections. OBJECTIVE This study aimed to analyse the expression of miRNAs in lung cells as response to infection by Paracoccidioides spp. METHODS A quantitative real-time polymerase chain reaction (RT-qPCR) based screening was employed to verify differentially expressed miRNAs in human lung cells infected with three different species; Paracoccidioides lutzii, Paracoccidioides americana, and Paracoccidioides brasiliensis. Furthermore, the in silico predictions of target genes and pathways for miRNAs were obtained. FINDINGS The results showed that miRNAs identified in the lung cells were different according to the species studied. However, based on the predicted targets, the potential signaling pathways regulated by miRNAs are common and related to adhesion, actin cytoskeleton rearrangement, apoptosis, and immune response mediated by T cells and TGF-β. MAIN CONCLUSIONS In summary, this study showed the miRNAs pattern of epithelial cells in response to infection by Paracoccidioides species and the potential role of these molecules in the regulation of key pathogenesis mechanisms of PCM.

Loss of canonical Wnt signaling is involved in the pathogenesis of Alzheimer's disease.

Alzheimer's disease (AD) is the most common form of dementia in the older population, however, the precise cause of the disease is unknown. The neuropathology is characterized by the presence of aggregates formed by amyloid-ß (Aß) peptide and phosphorylated tau; which is accompanied by progressive impairment of memory. Diverse signaling pathways are linked to AD, and among these the Wnt signaling pathway is becoming increasingly relevant, since it plays essential roles in the adult brain. Initially, Wnt signaling activation was proposed as a neuroprotective mechanism against Aß toxicity. Later, it was reported that it participates in tau phosphorylation and processes of learning and memory. Interestingly, in the last years we demonstrated that Wnt signaling is fundamental in amyloid precursor protein (APP) processing and that Wnt dysfunction results in Aß production and aggregation in vitro. Recent in vivo studies reported that loss of canonical Wnt signaling exacerbates amyloid deposition in a transgenic (Tg) mouse model of AD. Finally, we showed that inhibition of Wnt signaling in a Tg mouse previously at the appearance of AD signs, resulted in memory loss, tau phosphorylation and Aß formation and aggregation; indicating that Wnt dysfunction accelerated the onset of AD. More importantly, Wnt signaling loss promoted cognitive impairment, tau phosphorylation and Aß1-42 production in the hippocampus of wild-type (WT) mice, contributing to the development of an Alzheimer's-like neurophatology. Therefore, in this review we highlight the importance of Wnt/ß-catenin signaling dysfunction in the onset of AD and propose that the loss of canonical Wnt signaling is a triggering factor of AD.

Circulating miR-215-5p and miR-642a-5p as potential biomarker for diagnosis of osteosarcoma in Mexican population.

Osteosarcoma is the most common malignant bone neoplasia affecting individuals in the second decade of life. The survival rate has not been improved during the last 25 years, in part because of the lack of specific markers. The microRNAs have been identified as important regulators of gene expression, experimental evidence suggests these molecules as key players in cancer development and progression. To identify miRNAs differentially expressed in serum from patients with osteosarcoma compared to healthy donors in Mexican population. Fifteen osteosarcoma patients and fifteen age and sex matched healthy individuals were recruited. Two pools of total RNA extracted from serum per study group were prepared and the miRNA expression profiles were analyzed through TaqMan Low Density Arrays. Validation was carried out through RT-qPCR using individual TaqMan assays for those miRNAs differentially expressed. Fifteen miRNAs were differentially expressed in osteosarcoma patients compared to healthy controls. Overexpression of miR-215-5p and miR-642a-5p was confirmed by validation through RT-qPCR. The expression analysis of miRNAs from serum in osteosarcoma patients revealed differential expression of miR-215-5p and miR-642a-5p. Both microRNAs are potential markers for osteosarcoma diagnosis.

Wnt signaling loss accelerates the appearance of neuropathological hallmarks of Alzheimer's disease in J20-APP transgenic and wild-type mice.

Alzheimer's disease (AD) is a neurodegenerative pathology characterized by aggregates of amyloid-ß (Aß) and phosphorylated tau protein, synaptic dysfunction, and spatial memory impairment. The Wnt signaling pathway has several key functions in the adult brain and has been associated with AD, mainly as a neuroprotective factor against Aß toxicity and tau phosphorylation. However, dysfunction of Wnt/ß-catenin signaling might also play a role in the onset and development of the disease. J20 APPswInd transgenic (Tg) mouse model of AD was treated i.p. with various Wnt signaling inhibitors for 10 weeks during pre-symptomatic stages. Then, cognitive, biochemical and histochemical analyses were performed. Wnt signaling inhibitors induced severe changes in the hippocampus, including alterations in Wnt pathway components and loss of Wnt signaling function, severe cognitive deficits, increased tau phosphorylation and Aß1-42 peptide levels, decreased Aß42/Aß40 ratio and Aß1-42 concentration in the cerebral spinal fluid, and high levels of soluble Aß species and synaptotoxic oligomers in the hippocampus, together with changes in the amount and size of senile plaques. More important, we also observed severe alterations in treated wild-type (WT) mice, including behavioral impairment, tau phosphorylation, increased Aß1-42 in the hippocampus, decreased Aß1-42 in the cerebral spinal fluid, and hippocampal dysfunction. Wnt inhibition accelerated the development of the pathology in a Tg AD mouse model and contributed to the development of Alzheimer's-like changes in WT mice. These results indicate that Wnt signaling plays important roles in the structure and function of the adult hippocampus and suggest that inhibition of the Wnt signaling pathway is an important factor in the pathogenesis of AD. Read the Editorial Highlight for this article on page 356.

Molecular phylogeny and revision of the false violin spiders (Araneae: Drymusidae) of Africa

The family Drymusidae includes 16 cryptic spiders that build irregular webs in dark places. The family is distributed in South Africa, the Neotropical and Andean regions. Here, we use a molecular approach to infer the relationships of Drymusidae using three mitochondrial (COI, 16S, 12S) and three nuclear (H3, 28S, 18S) markers. Our preferred analyses support Drymusidae and its American and African clades, which emerge as sister groups. Our analyses suggest a Gondwanan distribution of Drymusidae and a Westward radiation of Izithunzi gen. nov. within South Africa, but both hypotheses remain to be thoroughly tested. We describe Izithunzi gen. nov. for the African species. All previous African species are redescribed and new combinations are proposed: Izithunzi capense (Simon) comb. nov., Izithunzi productum (Purcell) comb. nov. and Izithunzi silvicola (Purcell) comb. nov. Two new species are described: Izithunzi lina sp. nov. (known from both sexes) and Izithunzi zondii sp. nov. (known only from females). The male of I. productum (Purcell) comb. nov. is also described for the first time. We consider Loxosceles valida Lawrence, 1964, a junior synonym of I. capense (Simon) comb. nov. (new synonymy). We also provide a dichotomous key for Izithunzi gen. nov. species.

Inhibition of Wnt signaling induces amyloidogenic processing of amyloid precursor protein and the production and aggregation of Amyloid-ß (Aß)42 peptides.

Alzheimer's disease (AD) is the most common neurodegenerative disorder and the most frequent cause of dementia in the aged population. According to the amyloid hypothesis, the amyloid-ß (Aß) peptide plays a key role in the pathogenesis of AD. Aß is generated from the amyloidogenic processing of amyloid precursor protein and can aggregate to form oligomers, which have been described as a major synaptotoxic agent in neurons. Dysfunction of Wnt signaling has been linked to increased Aß formation; however, several other studies have argued against this possibility. Herein, we use multiple experimental approaches to confirm that the inhibition of Wnt signaling promoted the amyloidogenic proteolytic processing of amyloid precursor protein. We also demonstrate that inhibiting Wnt signaling increases the production of the Aß42 peptide, the Aß42 /Aß40 ratio, and the levels of Aß oligomers such as trimers and tetramers. Moreover, we show that activating Wnt signaling reduces the levels of Aß42 and its aggregates, increases Aß40 levels, and reduces the Aß42 /Aß40 ratio. Finally, we show that the protective effects observed in response to activation of the Wnt pathway rely on ß-catenin-dependent transcription, which is demonstrated experimentally via the expression of various 'mutant forms of ß-catenin'. Together, our findings indicate that loss of the Wnt signaling pathway may contribute to the pathogenesis of AD.

Computational identification and comparative analysis of miRNA precursors in three palm species.

MAIN CONCLUSION: In the present study, miRNA precursors in the genomes of three palm species were identified. Analyzes of sequence conservation and biological function of their putative targets contribute to understand the roles of miRNA in palm biology. MicroRNAs are small RNAs of 20-25 nucleotides in length, with important functions in the regulation of gene expression. Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnological tools in palm trees breeding. The goal of this study is the identification of miRNA precursors in the genomes of these species and their possible biological roles suggested by the mature miRNA-based regulation of target genes. Mature miRNA sequences from Arabidopsis thaliana, Oryza sativa, and Zea mays available at the miRBase were used to predict microRNA precursors in the palm genomes. Three hundred and thirty-eight precursors, ranging from 76 to 220 nucleotide (nt) in size and distributed in 33 families were identified. Moreover, we also identified 266 miRNA precursors of Musa acuminata, which are phylogenetically close to palms species. To understand the biological function of palm miRNAs, 374 putative miRNA targets were identified. An enrichment analysis of target-gene function was carried out using the agriGO tool. The results showed that the targets are involved in plant developmental processes, mainly regulating root development. Our findings contribute to increase the knowledge on microRNA roles in palm biology and could help breeding programs of palm trees.

TargetCompare: A web interface to compare simultaneous miRNAs targets.

UNLABELLED: MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue. AVAILABILITY: http://lghm.ufpa.br/targetcompare.

Perfil de metilación de genes supresores de tumores APAF1, ASSP1, p73 y FHIT en pacientes con leucemia linfoblástica aguda infantil / Detection of hypermethylation in tumor suppressor genes APAF1, ASSP1, p73 and FHIT in childhood acute lymphoblastic leukemia

La leucemia linfoblástica aguda (LLA), es la neoplasia mas frecuente en la población infantil. Se manifiesta por una perdida de diferenciación de progenitores linfoides produciendo un aumento de células inmaduras. La hipermetilación en la región promotora de genes supresores de tumores (GST) puede producir un silenciamiento génico que le proporciona a la célula leucémica una ventaja proliferativa o la previene de la apoptosis. Se estudia el estado de hipermetilación de 4 GST involucrados en la apoptosis: APAF1, ASPP1, p73 y FHIT y su asociación con la sobrevida de pacientes menores de 15 años con diagnóstico de LLA. Se analizaron 38 muestras de médula ósea mediante modificación con bisulfito del ADN y reacción en cadena de la polimerasa especifica de metilación (MSP). El rango de edad al diagnóstico fue de 10 meses a 13,8 años. La sobrevida global fue de 69 por ciento a los 5 años. El 81,5 por ciento de los pacientes tuvo al menos un gen hipermetilado. La frecuencia de metilación observada fue: APAF1 68,4 por ciento, FHIT 56,4 por ciento, p73 42 por ciento y ASPP1 18,4 por ciento. La asociación entre hipermetilación y grupo <5 años y 5 años fue: Global p=0,20, APAF1 p=0,03, FHIT p=0,51, p73 p=0,51 y ASPP1 p=0.67. Las curvas de sobrevida se calcularon según frecuencia de hipermetilación de cada gen: APAF1 p=0,05, FHIT p=0,31, p73 p=0,98 y ASPP1 p=0,82. La alta frecuencia de hipermetilación obtenida reafirma la participación de la metilación en la región promotora de GST en la patogénesis de la LLA. La hipermetilación del gen APAF1 fue muy frecuente y se asoció significativamente a la sobrevida del grupo de estudio, mostrando a este gen como un factor predictivo de mal pronostico en pacientes con LLA.

Acute lymphoblastic leukemia (ALL) is the most common malignancy in children. It is manifested by a loss of differentiation of lymphoid progenitors, producing an increase of immature cells. Hypermethylation in promoter region of tumor suppressor genes (GST) may produce a gene silencing that provides a leukemic cell a proliferative advantage or prevent apoptosis. We studied the hypermethylation status of 4 GST involved in apoptosis: APAF1, ASPP1, p73 and FHIT and its association with survival of patients <15 years diagnosed with ALL. We analyzed 38 samples of bone marrow by DNA bisulfite modification and chain reaction methylation-specific polymerase (MSP). The mean age at diagnosis was 10 months to 13.8 years. Overall survival was 69 percent at 5 years. 81.5 percent of patients had at least one hypermethylated gene. The frequency observed was: APAF1 68.4 percent, 56.4 percent FHIT, p73 ASPP1 42 percent and 18.4 percent. The association between hypermethylation and group <5 years and 5 years was: Global p = 0.20, APAF1 p = 0.03, FHIT p = 0.51, p73 p = 0.51, ASPP1 p = 0.67. Survival curves were calculated by frequency of hypermethylation of each gene: APAF1 p = 0.05, p = 0.31 FHIT, p73 p = 0.98 and ASPP1 p = 0.82. The high frequency of hypermethylation obtained confirms enrollment of methylation in the promoter region of GST in the pathogenesis of ALL. APAF1 gene hypermethylation was very frequent and was significantly associated with survival in the study group, showing this gene as a predictor of poor prognosis in patients with ALL.

Analysis of crucial molecules involved in herniated discs and degenerative disc disease

OBJECTIVES: Herniated discs and degenerative disc disease are major health problems worldwide. However, their pathogenesis remains obscure. This study aimed to explore the molecular mechanisms of these ailments and to identify underlying therapeutic targets. MATERIAL AND METHODS: Using the GSE23130 microarray datasets downloaded from the Gene Expression Omnibus database, differentially co-expressed genes and links were identified using the differentially co-expressed gene and link method with a false discovery rate ,0.25 as a significant threshold. Subsequently, the underlying molecular mechanisms of the differential co-expression of these genes were investigated using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. In addition, the transcriptional regulatory relationship was also investigated. RESULTS: Through the analysis of the gene expression profiles of different specimens from patients with these diseases, 539 differentially co-expressed genes were identified for these ailments. The ten most significant signaling pathways involving the differentially co-expressed genes were identified by enrichment analysis. Among these pathways, apoptosis and extracellular matrix-receptor interaction pathways have been reported to be related to these diseases. A total of 62 pairs of regulatory relationships between transcription factors and their target genes were identified as critical for the pathogenesis of these diseases. CONCLUSION: The results of our study will help to identify the mechanisms responsible for herniated discs and degenerative disc disease and provides a theoretical basis for further therapeutic study.