Metformin and lipopolysaccharide regulate transcription of NFATc2 gene via the transcription factor RUNX2 / 南方医科大学学报

OBJECTIVE@#To construct a luciferase reporter gene vector carrying human nuclear factor of activated T cells 2 (NFATc2) gene promoter and examine the effects of metformin and lipopolysaccharide (LPS) on the transcriptional activity of NFATc2 gene.@*METHODS@#The promoter sequence of human NFATc2 gene was acquired from UCSC website for PCR amplification. NFATc2 promoter fragment was inserted into pGL3-basic plasmid double cleaved with Kpn Ⅰ and Hind Ⅲ. The resultant recombinant plasmid pGL3-NFATC2-promoter was co-transfected with the internal reference plasmid pRL-TK in 293F cells, and luciferase activity in the cells was detected. Reporter gene vectors of human NFATc2 gene promoter with different fragment lengths were also constructed and assayed for luciferase activity. The changes in transcription activity of NFATc2 gene were assessed after treatment with different concentrations of metformin and LPS for 24 h. We also examined the effect of mutation in RUNX2-binding site in NFATC2 gene promoter on the regulatory effects of metformin and LPS on NFATc2 transcription.@*RESULTS@#We successfully constructed pGL3-NFATc2-promoter plasmids carrying different lengths (2170 bp, 2077 bp, 1802 bp, 1651 bp, 1083 bp, 323 bp) of NFATc2 promoter sequences as verified by enzymatic digestion and sequencing. Transfection of 293F cells with the plasmid carrying a 1651 bp NFATc2 promoter (pGL3-1651 bp) resulted in the highest transcriptional activity of NFATc2 gene, and the luciferase activity was approximately 3.3 times that of pGL3-2170 bp (1.843 ± 0.146 vs 0.547 ± 0.085). Moderate (5 mmol/L) and high (10 mmol/L) concentrations of metformin significantly upregulated the transcriptional activity of pGL3-1651 bp by up to 2.5 and 3 folds, respectively. LPS at different doses also upregulated the transcriptional activity of pGL3-1651 bp by at least 1.6 folds. The mutation in the RUNX2 binding site on pGL3-1651 bp obviously reduced metformin- and LPS-induced enhancement of pGL3-1651bp transcription by 1.7 and 2 folds, respectively.@*CONCLUSION@#pGL3-NFATc2-promoter can be transcribed and activated in 293F cells, and LPS and metformin can activate the transcription of pGL3- NFATc2-promoter in a RUNX2-dependent manner.

Pioneer of prostate cancer: past, present and the future of FOXA1

Prostate cancer is the most commonly diagnosed non-cutaneous cancers in North American men. While androgen deprivation has remained as the cornerstone of prostate cancer treatment, resistance ensues leading to lethal disease. Forkhead box A1 (FOXA1) encodes a pioneer factor that induces open chromatin conformation to allow the binding of other transcription factors. Through direct interactions with the Androgen Receptor (AR), FOXA1 helps to shape AR signaling that drives the growth and survival of normal prostate and prostate cancer cells. FOXA1 also possesses an AR-independent role of regulating epithelial-to-mesenchymal transition (EMT). In prostate cancer, mutations converge onto the coding sequence and cis-regulatory elements (CREs) of FOXA1, leading to functional alterations. In addition, FOXA1 activity in prostate cancer can be modulated post-translationally through various mechanisms such as LSD1-mediated protein demethylation. In this review, we describe the latest discoveries related to the function and regulation of FOXA1 in prostate cancer, pointing to their relevance to guide future clinical interventions.

Effects of density on growth and gene transcription characteristics of Rehmannia glutinosa / 中国中药杂志

The present study analyzed the effects of planting density on the development, quality, and gene transcription characte-ristics of Rehmannia glutinosa using 85-5 and J9 as materials with three planting densities of 5 000, 25 000, and 50 000 plants/Mu(1 Mu≈667 m~2). The agronomic characteristics of leaves and tuberous roots, the content of catalpol and acteoside, and the changes of gene expression were determined. The results showed that the leaf size, the diameter of tuberous root, leaf biomass, tuberous root number, and tuberous root biomass per plant at low density were significantly higher than those of medium and high densities. The content of catalpol and acteoside in leaves was higher at high density. The content of catalpol in tuberous roots was higher at low density, and the change trend was similar to that in leaves, while the content of acteoside in tuberous roots was higher at high density. Transcriptome analysis found that about 1/2 of the expansin genes could change regularly in response to density treatment, which was rela-ted to the development of tuberous roots. The change trend of the gene expression of multiple catalytic enzymes involved in the biosynthesis of catalpol and acteoside was consistent with that of their content, which was presumedly involved in the accumulation and regulation of density-responsive medicinal components. Based on the analysis of the development, medicinal components, and gene expression characteristics of R. glutinosa at different densities, this study is expected to provide an important basis for regulating the quality and yield of medicinal materials of R. glutinosa by managing the planting density.

The luciferase reporter system of the MMP12 endogenous promoter for investigating transcriptional regulation of the human MMP12 gene

Background: Matrix metalloproteinase 12 (MMP12), a member of MMPs, can take lots of roles including extracellular matrix component degradation, viral infection, inflammation, tissue remodeling and tumorigenesis. To explore the transcriptional regulation of MMP12 gene, a sensitive luciferase reporter HEK293 cell line for endogenous MMP12 promoter was generated by CRISPR/Cas9 technology. Results: The HEK293-MMP12-T2A-luciferase-KI cell line was successfully established by CRISPR/Cas9 technology. The sequencing results indicated that one allele of the genome was proven to have a site-directed insertion of luciferase gene and another allele of the genome was confirmed to have additional 48 bp insertion in this cell line. The cell line was further demonstrated to be a sensitive reporter of the endogenous MMP12 promoter by applying transcription factors STAT3, AP-1 and SP-1 to the cell line. The reporter cell line was then screened with bioactive small molecule library, and a small molecule Tanshinone I was found to significantly inhibit the transcriptional activity of MMP12 gene in HEK293-MMP12-T2A-luciferase-KI cell line by luciferase activity assay, which was further confirmed to inhibit the expression of MMP12 mRNA in wild-type HEK293 cells. Conclusions: This novel luciferase knock-in reporter system will be helpful for investigating the transcriptional regulation of MMP12 gene and screening the drugs targeting MMP12 gene.

Expression of microRNA-495-5p in preterm infants with bronchopulmonary dysplasia: a bioinformatics analysis / 中国当代儿科杂志

OBJECTIVE@#To study the expression of microRNA-495-5p (miRNA-495-5p) in the serum of preterm infants with bronchopulmonary dysplasia (BPD) based on a bioinformatics analysis, and to provide a theoretical basis for further research on the association between miRNA-495-5p and BPD.@*METHODS@#A total of 40 preterm infants who were admitted to the neonatal intensive care unit from January 2015 to December 2016 were enrolled. Among these infants, 20 with early clinical manifestations of BPD were enrolled as the BPD group, and 20 without such manifestations were enrolled as the control group. Peripheral blood samples were collected. The miRNA microarray technique was used to screen out differentially expressed miRNAs in serum between the two groups. RT-PCR was used for validation of results. TargetScan, miRDB, and miRWalk databases were used to predict the target genes of miRNA-495-5p. The DAVID database was used to perform gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the target genes.@*RESULTS@#Compared with the control group, the BPD group had a significant increase in the expression of miRNA-495-5p in serum (P<0.05). A total of 117 target genes of miRNA-495-5p were predicted by the above three databases and they were involved in several molecular functions (including transcriptional regulatory activity, transcriptional activation activity, and transcription cofactor activity), biological processes (such as metabolic regulation, DNA-dependent transcriptional regulation, and vascular pattern), and cell components (including nucleoplasm, membrane components, and insoluble components) (P<0.05). As for signaling pathways, these genes were significantly enriched in the mTOR signaling pathway (P<0.05).@*CONCLUSIONS@#MiRNA-495-5p may be involved in the development and progression of BPD by regulating angiogenesis, stem cell differentiation, apoptosis, and autophagy, which provides clues for further research on the role and functional mechanism of miRNA-495-5p in BPD.

Global Quantitative Mapping of Enhancers in Rice by STARR-seq / 基因组蛋白质组与生物信息学报·英文版

Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5' untranslated regions (5'UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis of the epigenetic features of enhancers at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and lack the enhancer mark of histone modification H3K4me1. Clustering analysis of enhancers according to their epigenetic marks revealed that about 40% of identified enhancers carried one or more epigenetic marks. Repressive H3K27me3 was frequently enriched with positive marks, H3K4me3 and/or H3K27ac, which together label enhancers. Intergenic enhancers were also predicted based on the location of DHS regions relative to genes, which overlap poorly with STARR-seq enhancers. In summary, we quantitatively identified enhancers by functional analysis in the genome of rice, an important model plant. This work provides a valuable resource for further mechanistic studies in different biological contexts.

Single-cell Analysis of CAR-T Cell Activation Reveals A Mixed T1/T2 Response Independent of Differentiation / 基因组蛋白质组与生物信息学报·英文版

The activation mechanism of chimeric antigen receptor (CAR)-engineered T cells may differ substantially from T cells carrying native T cell receptor, but this difference remains poorly understood. We present the first comprehensive portrait of single-cell level transcriptional and cytokine signatures of anti-CD19/4-1BB/CD28/CD3ζ CAR-T cells upon antigen-specific stimulation. Both CD4 helper T (T) cells and CD8 cytotoxic CAR-T cells are equally effective in directly killing target tumor cells and their cytotoxic activity is associated with the elevation of a range of T1 and T2 signature cytokines, e.g., interferon γ, tumor necrotic factor α, interleukin 5 (IL5), and IL13, as confirmed by the expression of master transcription factor genes TBX21 and GATA3. However, rather than conforming to stringent T1 or T2 subtypes, single-cell analysis reveals that the predominant response is a highly mixed T1/T2 function in the same cell. The regulatory T cell activity, although observed in a small fraction of activated cells, emerges from this hybrid T1/T2 population. Granulocyte-macrophage colony stimulating factor (GM-CSF) is produced from the majority of cells regardless of the polarization states, further contrasting CAR-T to classic T cells. Surprisingly, the cytokine response is minimally associated with differentiation status, although all major differentiation subsets such as naïve, central memory, effector memory, and effector are detected. All these suggest that the activation of CAR-engineered T cells is a canonical process that leads to a highly mixed response combining both type 1 and type 2 cytokines together with GM-CSF, supporting the notion that polyfunctional CAR-T cells correlate with objective response of patients in clinical trials. This work provides new insights into the mechanism of CAR activation and implies the necessity for cellular function assays to characterize the quality of CAR-T infusion products and monitor therapeutic responses in patients.

Ubiquitin specific peptidase 22 regulates the transcription activity of mitogen-activated protein kinase kinase 6 gene / 中南大学学报(医学版)

To clone human mitogen-activated protein kinase kinase 6 (MKK6) gene promoter and explore its transcription activity by ubiquitin specific peptidase 22 (USP22).
 Methods: MKK6 gene promoter was amplified by PCR and two bases mutation within USP22 binding site was subsequently introduced. The wild type and mutant MKK6 promoter were inserted into the luciferase report vector pGL3-Basic, respectively. Recombinant plasmids were co-transfected with plasmid pRL-TK into HeLa cells, and the luciferase activities were measured by dual luciferase reporter system. Furthermore, the direct interaction between USP22 and MKK6 promoter was detected by chromatin immunoprecipitation (ChIP) assay. Finally, the MKK6 transcription activity was measured after knockdown of USP22.
 Results: The recombinant luciferase report vectors containing wild or mutant type of MKK6 promoter were successfully constructed. Mutation of USP22 binding site resulted in decrease of MKK6 promoter-driven luciferase activity in HeLa cells (P<0.05). USP22 could interact directly with MKK6 promoter. Down-regulation of USP22 led to the decreased MKK6 mRNA expression (P<0.05).
 Conclusion: USP22 could regulate the transcription activity of MKK6 gene in HeLa cells.

Effects of Transcription Factor MZF-1 on Transcriptive Regulation of Acute Monocytic Leukemia-related Gene MLAA-34 / 中国实验血液学杂志

OBJECTIVE@#To investigate the transcriptional regulation of transcription factor MZF-1 on acute monocytic leukemia-related gene MLAA-34.@*METHODS@#The effect of MZF-1 on the transcriptional activity of MLAA-34 gene promoter was analyzed by luciferase reporter gene detection system and site-directed mutation technique. The EMSA and ChIP assay were used to verify whether MZF-1 directly and specifically binds to the core region of MLAA-34 promoter. The over-expression vector and interference vector of MZF-1 were constructed to transfect U937 cells, and RT-PCR and Western blot were used to detect the transcription and expression changes of MLAA-34 gene.@*RESULTS@#The transcription factor MZF-1 had a regulatory effect on MLAA-34 gene expression, and the relative luciferase activity was decreased after MZF-1 binding point mutation (P<0.01). EMSA and ChIP experiments demonstrated that MZF-1 could directly bind to MLAA-34 promoter and play a regulatory role. In the over-expression test, the increase of MZF-1 could up-regulate the expression of MLAA-34 (P<0.05). In the interference test, the decrease of MZF-1 could down-regulate the expression of MLAA-34 (P<0.05).@*CONCLUSION@#Transcription factor MZF-1 can bind to the transcriptional regulatory region on the promoter of MLAA-34 gene and promote the transcription of MLAA-34 gene in acute monocytic leukemia.

Estudo de marcadores transcricionais relacionados à agressividade tumoral em tumores HER2+ / Study of transcriptional markers related to tumor aggressiveness in HER2+ tumors

ERBB2/HER2 é um gene frequentemente amplificado em cânceres de mama, estômago e ovário e está diretamente associado ao mal prognóstico de pacientes portadores desta alteração genética. A proteína HER2, super-expressa nestes tumores, é um importante alvo de terapias dirigidas e tem um papel relevante no tratamento de tumores com esta característica molecular. Entretanto, o surgimento de resistência aos tratamentos ainda é um desafio a ser superado. Em 2011, foi identificado o miR-4728-3p dentro de uma região intrônica de ERBB2/HER2, cuja super-expressão acompanhava a amplificação do oncogene. Pouco ainda se sabe sobre a função e possíveis alvos deste microRNA, o que motivou os estudos desta tese, onde usamos técnicas como RNA-Seq e proteômica buscando a identificação de alvos, seguidos de comparação com bancos de dados, além de ensaios in vitro e in vivo. Genes como RNASEH1, PSMC3, TUFM e GNA11 mostraram-se fortes candidatos-alvo do miR-4728-3p, sendo regulados após super-expressão e knockdown do microRNA em diferentes linhagens celulares. O bloqueio de miR-4728-3p em tumores gástricos HER2+ levou à diminuição do volume e peso tumoral, sugerindo um importante papel terapêutico no controle de tumores com amplificação de ERBB2/HER2. Os resultados obtidos indicam uma possível participação do miR-4728-3p na carcinogênese de tumores gástricos HER2+ e ampliam o conhecimento sobre a biologia de ERBB2/HER2. A identificação de alvos deste microRNA pode adicionalmente elucidar os mecanismos pelo qual o bloqueio do miR-4728-3p interfere no crescimento tumoral, levantando informações importantes sobre o controle da expressão gênica mediada por RNAs não- codificantes no câncer

The ERBB2/HER2 gene is frequently amplified in breast, stomach and ovarian cancers and is directly associated with poor prognosis. The HER2 protein, overexpressed in these tumors, is an important therapeutic target and plays relevant roles in tumor biology and prognosis. However, the emergence of resistance to anti-HER2 treatment is still a challenge to be overcomed. In 2011, miR-4728-3p was identified within an intronic region of the ERBB2/HER2 gene; when this region is amplified, both transcripts are also amplified and overexpressed. Little is known about the function and possible targets of this microRNA, which motivated the studies of this thesis, where techniques such as RNA-Seq and proteomics were employed to identify targets, followed by database analyses, in vitro and in vivo assays. Genes such as RNASEH1, PSMC3, TUFM and GNA11 were found to be strong target-candidates of miR-4728-3p and were regulated after the overexpression or knockdown of this miRNA in different cell lines. miR-4728-3p blockade in HER2+ gastric tumors of mouse xenografts led to decreased tumor volume and weight, suggesting its important therapeutic potential in the control of ERBB2/HER2 amplified tumors. The results obtained here indicate a possible participation of miR-4728-3p in the carcinogenesis of HER2+ gastric tumors and expand the knowledge of ERBB2/HER2 biology. The identification of targets of this microRNA may further elucidate the mechanisms by which miR-4728-3p blockade interferes with tumor growth, raising important information about the control of gene expression mediated by noncoding RNAs in cancer

Comparação entre os perfis de expressão de microRNAs em Linfomas de Hodgkin Clássico / Comparison between microRNA expression profiles in Classic Hodgkin Lymphoma

Introdução: Linfoma de Hodgkin (LH) é um dos linfomas mais frequentes no mundo ocidental, com cerca de 3 a 4 novos casos a cada 100 mil pessoas. Os microRNAs são pequenas moléculas que regulam a transcrição gênica e estão associadas ao desenvolvimento e progressão das neoplasias. Em LH clássico (LHC), alguns microRNAs já foram identificados a partir de células infectadas pelo EBV. Além destes, outros microRNAs já foram descritos em LHC, tanto em estudos onde foram realizadas esta avaliação em culturas celulares como utilizando a massa tumoral total de linfonodos, mas com pouca correlação com o comportamento biológico. Objetivo: O presente estudo tem como objetivo principal avaliar o perfil de expressão de microRNA em LHC, comparando casos livres de doença após a terapia com casos que exibiram recidivas. Material e métodos: Foram avaliados 106 pacientes com o diagnóstico de LHC, sendo coletados dados clínicos e avaliados os marcadores imuno-histoquímicos CD30, CD15, CD20 e CD15 destes casos, além da presença de EBV por CISH. Vinte casos foram selecionados para a avaliação da expressão de 377 microRNAs, 10 casos com recidiva e 10 casos sem evidência de doença. Como grupos comparadores, foram selecionadas 8 amostras de linfonodos reativos, 4 com hiperplasia folicular e 4 com hiperplasia paracortical. Os resultados do perfil de expressão foram submetidos ao método de agrupamento hierárquico não supervisionado. Resultados e discussão: Os parâmetros clínico-patológicos desta coorte não diferiram daqueles encontrados na literatura. A sobrevida global e a sobrevida livre de progressão foram de 92,1% e 83,6% em 5 anos, respectivamente. Os fatores associados ao prognóstico em análise multivariada foram idade, níveis séricos de albumina e DHL e estadiamento. O perfil de expressão dos microRNAs de todos os casos de LHC possibilitaram a separação completa dos mesmos em relação aos linfonodos reativos, independentemente do tipo de hiperplasia. Na comparação entre os casos de LHC, foram identificados 3 microRNAs diferencialmente expressos: miR-502-3p e miR-363, ambos hipoexpressos no grupo que continha todos os casos com recidivas e miR-886-5p, hiperexpresso neste grupo. Os dois primeiros microRNAs estão associados a supressão tumoral, através da inibição da proliferação e migração celular. O miR-886-5p é associado ao aumento da proliferação celular e inibição da apoptose. Em linfomas, este já foi descrito como estando hiperexpresso em linfomas T, incluindo linfoma anaplásico de grandes células. Conclusão: Os LHC possuem um perfil distinto de expressão de microRNAs, com muitos deles envolvendo mecanismos fundamentais na oncogênese, como ciclo celular e apoptose. Os microRNAs encontrados diferencialmente expressos nos casos recidivados no presente estudo podem estar associados ao comportamento menos indolente destas neoplasias, podendo ser alvo de futuras investigações, incluindo seu uso como potenciais alvos de terapia

Introduction: Hodgkin lymphoma (HL) is one of the most common lymphomas in the western world, with about 3 to 4 new cases per 100,000 people. MicroRNAs are small molecules that regulate gene transcription and are associated with the development and progression of neoplasms. In classic HL (CHL), some microRNAs have already been identified from EBV-infected cells. In addition, other microRNAs have already been described in CHL, both in studies where this evaluation was performed in cell cultures and using whole lymph node tumor tissue, but with little correlation with biological behavior. Objective: The present study aims to evaluate the microRNA expression profile in CHL, comparing disease-free cases after therapy with cases that showed recurrences. A total of 106 patients diagnosed with CHL were evaluated. Clinical data were collected and the immunohistochemical markers CD30, CD15, CD20 and CD15 of these cases were evaluated, as well as the presence of EBV by CISH. Twenty cases were selected for the analysis of the expression of 377 microRNAs, 10 cases with recurrences and 10 cases without evidence of disease. For comparison, 8 samples of reactive lymph nodes were selected, 4 with follicular hyperplasia and 4 with paracortical hyperplasia. The expression profile results were submitted to the unsupervised hierarchical clustering method. Results and discussion: The clinico-pathological parameters of this cohort did not differ from those found in the literature. Overall survival and progression-free survival were 92.1% and 83.6% at 5 years, respectively. Factors associated with prognosis in multivariate analysis were age, serum albumin and DHL levels, and staging. The microRNA expression profile of all CHL cases allowed their complete separation from reactive lymph nodes, regardless of the type of hyperplasia. When comparing the cases of CHL, 3 differentially expressed microRNAs were identified: miR-502-3p and miR-363, both hypoexpressed in the group containing all relapsed cases and miR-886-5p, hyperexpressed in this group. The first two microRNAs are associated with tumor suppression through inhibition of cell proliferation and migration. The miR-886-5p is associated with increased cell proliferation and inhibition of apoptosis. In lymphomas, it has been described as being overexpressed in T-cell lymphomas, including anaplastic large cell lymphoma. Conclusion: CHLs have a distinct microRNA expression profile, with many involving key mechanisms in oncogenesis, such as cell cycle and apoptosis. The differentially expressed microRNAs found in the relapsed cases in the present study may be associated with the less indolent behavior of these neoplasms and may be the subject of future investigations, including their use as potential therapeutic targets

Ammonia determines transcriptional profile of microorganisms in anaerobic digestion

ABSTRACT Anaerobic digestion is important for the management of livestock manure with high ammonia level. Although ammonia effects on anaerobic digestion have been comprehensively studied, the molecular mechanism underlying ammonia inhibition still remains elusive. In this study, based on metatranscriptomic analysis, the transcriptional profile of microbial community in anaerobic digestion under low (1500 mg L-1) and high NH4 + (5000 mg L-1) concentrations, respectively, were revealed. The results showed that high NH4 + concentrations significantly inhibited methane production but facilitated the accumulations of volatile fatty acids. The expression of methanogenic pathway was significantly inhibited by high NH4 + concentration but most of the other pathways were not significantly affected. Furthermore, the expressions of methanogenic genes which encode acetyl-CoA decarbonylase and methyl-coenzyme M reductase were significantly inhibited by high NH4 + concentration. The inhibition of the co-expressions of the genes which encode acetyl-CoA decarbonylase was observed. Some genes involved in the pathways of aminoacyl-tRNA biosynthesis and ribosome were highly expressed under high NH4 + concentration. Consequently, the ammonia inhibition on anaerobic digestion mainly focused on methanogenic process by suppressing the expressions of genes which encode acetyl-CoA decarbonylase and methyl-coenzyme M reductase. This study improved the accuracy and depth of understanding ammonia inhibition on anaerobic digestion.

Corticoterapia / Corticotherapy

Glicocorticosteroides são fármacos efetivos no tratamento de doenças inflamatórias e imunes. Agem em praticamente todas as células do corpo, antagonizando os efeitos patogênicos de inúmeras doenças. A maior parte de seus efeitos parece ser produto de sua ligação a receptores específicos armazenados no interior das células. Suas ações moduladoras da transcrição genética iniciam-se com a ligação ao seu receptor e posterior conexão aos genes alvo, num processo que conta com a participação de outros fatores e envolve múltiplos mecanismos (ação genômica). Os genes alvo incluem aqueles responsáveis por mediadores inflamatórios, como quimiocinas, citocinas, fatores de crescimento e seus receptores. Além de seus efeitos sobre o DNA, estimulando a produção de produtos anti-inflamatórios ou inibindo a transcrição de genes pró-inflamatórios, via acetilação ou deacetilação das histonas, respectivamente, os glicocorticosteroides possuem outros mecanismos de ação que não envolvem regulação genética (ação não genômica). Aparentemente, por mecanismos ainda não esclarecidos, os efeitos da corticoterapia são produto da associação das ações genômicas com as não genômicas. Os glicocorticosteroides representam o grande pilar terapêutico da asma, com efeitos sobre as células estruturais e funcionais do trato respiratório. Nessa situação particular, na qual costumam ser empregados continuadamente por períodos prolongados, com risco potencial de efeitos indesejáveis relevantes, é fundamental desvendar os processos envolvidos em seus mecanismos de ação para tentar desenvolver meios de reduzir os riscos associados e potencializar os efeitos desejados.

Glucocorticosteroids are effective drugs in the treatment of inflammatory and immune diseases. They act on virtually every cell in the body by antagonizing the pathogenic effects of numerous diseases. Most of its effects appear to be the product of its binding to specific receptors stored within cells. Its modulatory actions on genetic transcription begin with a linkage to its receptor and later connection to target genes, in a process that counts on the participation of other factors and involves multiple mechanisms (genomic action). Target genes include those responsible for inflammatory mediators, such as chemokines, cytokines, growth factors, and their receptors. In addition to its effects on DNA, stimulating the production of anti-inflammatory products or inhibiting the transcription of pro-inflammatory genes, via acetylation or deacetylation of histones, respectively, glucocorticosteroids have other mechanisms of action that do not involve genetic regulation (non-genomic effect). Apparently, by mechanisms not yet clarified, the effects of corticotherapy are the product of the association of genomic and non-genomic actions. Glucocorticosteroids represent the great therapeutic pillar of asthma, with effects on structural and functional cells of the respiratory tract. In this particular situation, where they are often used for prolonged periods, with a potential risk of relevant undesirable effects, it is essential to uncover the processes involved in their mechanisms of action in order to develop ways to reduce the associated risks and potentiate the desired effects.

Ecdysis-related pleiotropic neuropeptides expression during Anopheles albimanus development / Expresión de neuropéptidos pleiotrópicos asociados con ecdisis durante el desarrollo del mosquito Anopheles albimanus

Abstract: Objective: To analyze the transcription pattern of neuropeptides in the ontogeny of a malaria vector, the mosquito Anopheles albimanus. Materials and methods: The transcription pattern of Crustacean CardioActive peptide (CCAP), corazonin, Ecdysis Triggering Hormone (ETH), allatostatin-A, orcokinin, Insulin Like Peptide 2 (ILP2), Insulin Like Peptide 5 (ILP5) and bursicon was evaluated using qPCR on larvae (1st - 4th instar), pupae and adult mosquitoes. Results: Unlike in other insects, transcripts of CCAP (70.8%), ETH (60.2%) and corazonin (76.5%) were expressed in 4th instar larvae, probably because these three neuropeptides are associated with the beginning of ecdysis. The neuropeptide ILP2 showed higher transcription levels in other stages and orcokinin decreased during the development of the mosquito. Conclusion: The CCAP, corazonin and ETH neuropeptides are potential targets for the design of control strategies aimed at disrupting An. albiamnus larval development.

Resumen: Objetivo: Describir la expresión de neuropéptidos durante la ontogenia del mosquito vector de la malaria Anopheles albimanus. Material y métodos: Se midió la expresión de CCAP, corazonina, ETH, allatostatina, orcokinina, ILP2, ILP5 y bursicon en larvas de primer (2mm), segundo (4mm), tercer (5mm) y cuarto (6mm) estadio, pupas y mosquitos adultos, mediante qPCR. Resultados. A diferencia de otros insectos en donde, CCAP, corazonina y ETH se expresan principalmente en estadios pupales, en An. albimanus se expresaron mayoritariamente en larvas de cuarto estadio, CCAP tuvo 70.8% de expresión relativa, corazonina 76.5% y ETH 60.2%. ILP2 fue el neuropéptido que más se expresó en el primer, segundo y tercer estadio y orcokinina disminuyó durante el desarrollo del mosquito. Conclusión. Los péptidos estudiados se expresaron en todos los estadios de desarrollo del mosquito. Sin embargo, su expresión varió en cada uno de ellos. Los neuropéptidos CCAP, corazonina y ETH, que son esenciales para la transformación de lavas a pupas, pueden ser blancos potenciales para el diseño de estrategias de control dirigidas a interrumpir el desarrollo larvario de An. albimanus.

Non-invasive messenger RNA transcriptional evaluation in human kidney allograft dysfunction

The aim of the present study was to evaluate messenger RNA expression in kidney allograft recipients. Forty-four kidney transplant recipients were evaluated up to three months after grafting. After transplantation, peripheral blood samples were drawn sequentially for real-time polymerase chain reaction analyses of perforin and TIM-3 genes. Biopsies were obtained to evaluate acute graft dysfunction and interpreted according to the Banff classification. Eight patients presented episodes of acute rejection. Recipients with rejection had significantly higher levels of TIM-3 mRNA transcripts compared to those without rejection (median gene expression 191.2 and 36.9 mRNA relative units, respectively; P<0.0001). Also, perforin gene expression was higher in patients with rejection (median gene expression 362.0 and 52.8 mRNA relative units; P<0.001). Receiver operating characteristic curves showed that the area under the curve (AUC) for the TIM-3 gene was 0.749 (95%CI: 0.670-0.827). Perforin gene mRNA expression provided an AUC of 0.699 (95%CI: 0.599 to 0.799). Overall accuracy of gene expression was 67.9% for the TIM-3 gene and 63.6% for the perforin gene. Combined accuracy was 76.8%. Negative predictive values were 95.3% for the TIM-3 gene, 95.5% for the perforin gene, and 95.4% in the combined analyses. Gene expression was significantly modulated by rejection treatment decreasing 64.1% (TIM-3) and 90.9% (perforin) compared to the median of pre-rejection samples. In conclusion, the longitudinal approach showed that gene profiling evaluation might be useful in ruling out the diagnosis of acute rejection and perhaps evaluating the efficacy of treatment.

TICA: Transcriptional Interaction and Coregulation Analyzer / 基因组蛋白质组与生物信息学报·英文版

Transcriptional regulation is critical to cellular processes of all organisms. Regulatory mechanisms often involve more than one transcription factor (TF) from different families, binding together and attaching to the DNA as a single complex. However, only a fraction of the regulatory partners of each TF is currently known. In this paper, we present the Transcriptional Interaction and Coregulation Analyzer (TICA), a novel methodology for predicting heterotypic physical interaction of TFs. TICA employs a data-driven approach to infer interaction phenomena from chromatin immunoprecipitation and sequencing (ChIP-seq) data. Its prediction rules are based on the distribution of minimal distance couples of paired binding sites belonging to different TFs which are located closest to each other in promoter regions. Notably, TICA uses only binding site information from input ChIP-seq experiments, bypassing the need to do motif calling on sequencing data. We present our method and test it on ENCODE ChIP-seq datasets, using three cell lines as reference including HepG2, GM12878, and K562. TICA positive predictions on ENCODE ChIP-seq data are strongly enriched when compared to protein complex (CORUM) and functional interaction (BioGRID) databases. We also compare TICA against both motif/ChIP-seq based methods for physical TF-TF interaction prediction and published literature. Based on our results, TICA offers significant specificity (average 0.902) while maintaining a good recall (average 0.284) with respect to CORUM, providing a novel technique for fast analysis of regulatory effect in cell lines. Furthermore, predictions by TICA are complementary to other methods for TF-TF interaction prediction (in particular, TACO and CENTDIST). Thus, combined application of these prediction tools results in much improved sensitivity in detecting TF-TF interactions compared to TICA alone (sensitivity of 0.526 when combining TICA with TACO and 0.585 when combining with CENTDIST) with little compromise in specificity (specificity 0.760 when combining with TACO and 0.643 with CENTDIST). TICA is publicly available at http://geco.deib.polimi.it/tica/.

TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers / 基因组蛋白质组与生物信息学报·英文版

In mammalian cells, transcribed enhancers (TrEns) play important roles in the initiation of gene expression and maintenance of gene expression levels in a spatiotemporal manner. One of the most challenging questions is how the genomic characteristics of enhancers relate to enhancer activities. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers' DNA code in a more systematic way. To address this problem, we developed a novel computational framework, Transcribed Enhancer Landscape Search (TELS), aimed at identifying predictive cell type/tissue-specific motif signatures of TrEns. As a case study, we used TELS to compile a comprehensive catalog of motif signatures for all known TrEns identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that combinations of different short motifs characterize in an optimized manner cell type/tissue-specific TrEns. Our study is the first to report combinations of motifs that maximize classification performance of TrEns exclusively transcribed in one cell type/tissue from TrEns exclusively transcribed in different cell types/tissues. Moreover, we also report 31 motif signatures predictive of enhancers' broad activity. TELS codes and material are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

Ilexgenin A enhances the effects of simvastatin on non-alcoholic fatty liver disease without changes in simvastatin pharmacokinetics / 中国天然药物

Cardiovascular disease (CVD) is the most common cause of death in patients with non-alcoholic fatty liver disease (NAFLD). New therapeutic strategies which have the potential for slowing down the evolution of NAFLD and reducing CVD-related mortality are urgently needed. Statins are well recognized in the treatment of dyslipidemia, but their use in the treatment of NAFLD is limited due to the safety concerns. Ilexgenin A (IA) is one of the main bioactive compounds in 'Shan-lv-cha', an herbal tea commonly used in China. In the present study, we investigated the possible synergistic therapeutic effects of IA and simvastatin (SV) on NAFLD. IA or SV showed beneficial effects on the rats with NAFLD by lowering the liver weight, liver index and plasma levels of alanine aminotransferase and aspartate aminotransferase, regulating abnormal metabolism of lipids and ameliorating steatosis in liver. IA significantly enhanced the hypolipidemic and anti-inflammation effects of SV. Furthermore, a sensitive, accurate, convenient and reproducible LC-MS method was developed to investigate the effects of IA on the pharmacokinetics of SV. No significant changes were observed in pharmacokinetic parameters of SV and simvastatin hydroxy acid in the IA plus SV co-treated group in comparison with those in the group treated with SV alone. The mRNA levels and activity of CYP3A1 were not altered by IA. In conclusion, the results obtained from the present study should be helpful for further clinical application of SV and IA alone or in combination.

Ilexgenin A enhances the effects of simvastatin on non-alcoholic fatty liver disease without changes in simvastatin pharmacokinetics / 中国天然药物

Cardiovascular disease (CVD) is the most common cause of death in patients with non-alcoholic fatty liver disease (NAFLD). New therapeutic strategies which have the potential for slowing down the evolution of NAFLD and reducing CVD-related mortality are urgently needed. Statins are well recognized in the treatment of dyslipidemia, but their use in the treatment of NAFLD is limited due to the safety concerns. Ilexgenin A (IA) is one of the main bioactive compounds in 'Shan-lv-cha', an herbal tea commonly used in China. In the present study, we investigated the possible synergistic therapeutic effects of IA and simvastatin (SV) on NAFLD. IA or SV showed beneficial effects on the rats with NAFLD by lowering the liver weight, liver index and plasma levels of alanine aminotransferase and aspartate aminotransferase, regulating abnormal metabolism of lipids and ameliorating steatosis in liver. IA significantly enhanced the hypolipidemic and anti-inflammation effects of SV. Furthermore, a sensitive, accurate, convenient and reproducible LC-MS method was developed to investigate the effects of IA on the pharmacokinetics of SV. No significant changes were observed in pharmacokinetic parameters of SV and simvastatin hydroxy acid in the IA plus SV co-treated group in comparison with those in the group treated with SV alone. The mRNA levels and activity of CYP3A1 were not altered by IA. In conclusion, the results obtained from the present study should be helpful for further clinical application of SV and IA alone or in combination.