Advances in the role of natural products in human gene expression / 中国天然药物

Natural products (NPs), especially those from traditional herbal medicines, can evidently modulate human gene expression at multiple levels, leading to a wide diversity of bioactivities. Although numerous bio-functions of NPs for human body have been found, there is little understanding about how NPs achieve it, as less attention was drawn to the definite mechnism by which NPs regulate gene expression. Furthermore, based on the rapidly advancing knowledge of mechanisms for gene regulation in recent years, newly-understood mechanisms, such as post-transcriptional regulation, are found to be involved in NP-elicited bio-effects, providing a new perspective on understanding the role of NPs in gene expression. Therefore, in the current review, we summarize the function of NPs in gene expression from the perspectives of transcriptional, post-transcriptional, and post-translational regulation, which will reinforce the understanding of NP-induced effects in gene expression and facilitate the exploration of more NPs with potential therapeutic effects.

Post-transcriptional gene silencing: Basic concepts and applications

Post-transcriptional gene silencing (PTGS)-mediated gene silencing exploits the cellular mechanism whereintranscripts having sequence similarity to the double-stranded RNA (dsRNA) molecules present in the cell will besubjected to degradation. PTGS is closely related to natural processes such as RNA-mediated virus resistance andcross-protection in plants. Gene silencing and the cellular machinery for affecting this phenomenon might haveevolved as a natural protective measure against viral infection in plants. In PTGS, small interfering RNA (siRNA)molecules of 21–23 nucleotides length act as homology guides for triggering the systemic degradation of transcriptshomologous to the siRNA molecules. PTGS phenomenon, first discovered in transgenic petunia plants harbouringchalcone synthase gene and termed co-suppression, has been subsequently exploited to target specific gene transcripts for degradation leading to manifestation of desirable traits in crop plants. Targeted gene silencing has beenachieved either through the introduction of DNA constructs encoding dsRNA or antisense RNA or by deploying cosuppression constructs producing siRNAs against the transcript of interest. Understanding the mechanism of genesilencing has led to the development of several alternative strategies for inducing gene silencing in a precise andcontrolled way. This has paved the way for using PTGS as one ofthe chief functional genomicstools in plants and hashelped in unraveling the mechanism of many cellular processes and identifying the focal points in pathways, besides,opening new vistas in genetic engineering of plants for human benefits. PTGS has shown great potential in silencingthe deleterious genes efficiently so that value-added plant products could be obtained. Thus, PTGS has ushered in anew era in the genetic manipulation of plants for both applied and basic studies. In this review, we have outlined thebasics of RNAi-mediated gene silencing and summarized the work carried out at our institute using this approach, ascase studies. In particular, adopting RNAi-mediated gene silencing (a) as a method to restore fertility in transgenicmale sterile lines developed based on orfH522 gene from sunflower PET1-CMS source, (b) as a tool to suppress theproduction of toxic proteins, ricin and RCA, in castor, and (c) as an approach to induce bud necrosis virus resistancein sunflower has been discussed. Examples from other plant systems also have been mentioned to exemplify theconcept and utility of gene silencing in crop plants.

LncRNA-599554 sponges miR-15a-5p to contribute inductive ability of dermal papilla cells through positive regulation of the expression of Wnt3a in cashmere goat

BACKGROUND: Long non-coding RNAs (lncRNAs), as post-transcriptional regulators, were thought to function in the inductive property of dermal papilla cells (DPCs) in cashmere goat. Previously, lncRNA-599554 was identified in secondary hair follicle (SHF) of cashmere goat, but its functional significance is unknown. RESULTS: In the present investigation, we verified that lncRNA-599554 had significantly higher expression at the anagen dermal papilla of cashmere goat SHF than that at telogen. Based on overexpression and knockdown techniques, we found that lncRNA-599554 contributes the inductive property of DPCs of cashmere goat, which was assessed by detecting the changes in the expression of several typical indictor genes in DPCs including ET-1, SCF, Versican, ALP, Lef1 and Ptc-1. Based on RNA pull-down assay, we verified that lncRNA-599554 directly interacted with chi-miR-15a-5p. Also, we showed that lncRNA-599554 positively regulated the Wnt3a expression in DPCs but which did not appear to involve its modulating of promoter methylation. Based on the use of Dual-luciferase reporter assays, our data indicated that lncRNA-599554 regulated the Wnt3a expression through chi-miR-15a-5p-mediated post-transcriptional level. CONCLUSIONS: We showed that lncRNA-599554 contributes the inductive property of DPCs in cashmere goat which might be achieved through sponging chi-miR-15b-5p to promote the Wnt3a expression. The results from the present investigation provided a novel insight into the functional mechanism of lncRNA-599554 in the SHF regeneration of cashmere goat along with the formation and growth of cashmere fiber.

Advances in molecular biology research on human parvovirus B19 / 生物工程学报

Human parvovirus B19 (B19 virus) is one of the two parvoviruses that cause human diseases. As an important pathogen to humans, it causes infectious erythema in children, acute aplastic anemia, fetal edema and death. In this review, we focus on the recent advances in the molecular virology of B19V, such as viral genotypes, viral receptor, genomic features and viral replication, viral transcription and post-transcription regulation, viral nonstructural and structural protein features and functions, viral diagnosis and antiviral agents, to provide reference for further study of B19 pathogenesis mechanisms, treatment and diagnostic strategies.

Virus-induced gene silencing (VIGS) in cape gooseberry (Physalis peruviana L., Solanaceae) / Silenciamento de genes induzidos por vírus (VIGS) em physalis (Physalis peruviana L., Solanaceae) / Silenciamiento génico inducido por virus (VIGS) en uchuva (Physalis peruviana L., Solanaceae)

Abstract Cape gooseberry (Physalis peruviana, L.) is a herbaceous plant belonging to the Solanaceae family that produces an edible berry appreciated for its nutraceutical and pharmaceutical properties. Its production is often limited by diseases and reproducible fruit quality. Recent studies have reported genes associated with fruit quality and resistance response to the root-infecting fungus Fusarium oxysporum f. sp. physali (Foph,) which causes vascular wilt. In order to standardize a method to validate the biological function of candidate genes in the non-model species P. peruviana, we tested the robust approach in reverse genetics, virus-induced gene silencing (VIGS). In this study, we validated and optimized VIGS using an insert of the phytoene desaturase (PDS) gene in a silencing viral vector generated from tobacco rattle virus (TRV). Leaves infiltrated with Agrobacterium (GV3101 strain) showed photo-bleached segments, which were distinctive for PDS suppression at 7 days post-infection (dpi). More than half of the treated plants showed photo-bleaching, indicating an efficiency rate of 50 % of the VIGS protocol. The results of this study showed that VIGS can be used for future functional gene characterization implicated in the immune response, disease resistance and fruit quality in capegooseberry.

Resumo A physalis (Physalis peruviana, L.) é uma planta herbácea pertencente à família Solanaceae, que produz uma baga comestível apreciada por suas propriedades nutracêuticas e farmacêuticas. Sua produção com frequência se vê limitada devido a enfermidades e baixa reprodutibilidade na qualidade do fruto. Estudos recentes reportaram genes associados com a qualidade do fruto e com a resposta de resistência ao fungo radicular Fusarium oxysporum f. sp. physali (Foph.), que causa esmorecimento vascular. Com a finalidade de padronizar um método para validar a função biológica de genes candidatos na espécie não-modelo P. p ruviana, avaliamos uma aproximação robusta em genética invertida, o sil nciamento de genes induzidos por vírus (VIGS). Neste estudo, validamos e otimizamos o VIGS usando um inserto da fitoeno desaturase (PDS) em um vetor viral de silenciamento produzido a partir do vírus do chocalho do tabaco (TRV). As folhas infiltradas com Agrobacterium (cepa GV3101) mostraram segmentos fotobranqueados, que foram distintivos para a supressão de PDS a 7 dias pós-infecção (dpi). Mais da metade das plantas tratadas mostraram fotobranqueamento, o que indica uma taxa de eficiência de 50 % do procotolo VIGS. Os resultados de este estudo mostraram que o VIGS pode ser usado em caracterizações futuras de genes funcionais implicados na resposta imune, na resistência a enfermidades e na qualidade do fruto de physalis.

Resumen La uchuva (Physalis peruviana, L.) es una planta herbácea perteneciente a la familia de las solanáceas, que produce una baya comestible apreciada por sus propiedades nutracéuticas y farmacéuticas. Su producción con frecuencia se ve limitada debido a enfermedades y a falta de reproducibilidad en la calidad del fruto. Estudios recientes han reportado genes asociados con la calidad del fruto y con la respuesta de resistencia al hongo radicular Fusarium oxysporum f. sp. physali (Foph,), que causa marchitamiento vascular. Con el fin de estandarizar un método para validar la función biológica de genes candidatos en la especie no-modelo P. peruviana, evaluamos la aproximación robusta en genética inversa, el silenciamiento génico inducido por virus (VIGS). En este estudio, validamos y optimizamos el VIGS usando un inserto de la fitoeno desaturasa (PDS) en un vector viral de silenciamiento producido a partir del virus del cascabeleo del tabaco (TRV). Las hojas infiltradas con Agrobacterium (cepa GV3101) mostraron segmentos fotoblanqueados, que fueron distintivos para la supresión de PDS a 7 días pos-infeccion (dpi). Más de la mitad de las plantas tratadas mostraron fotoblanqueo, lo cual indica una tasa de eficiencia del 50 % del protocolo VIGS. Los resultados de este estudio mostraron que el VIGS se puede usar en futuras caracterizaciones de genes funcionales implicados en la respuesta inmune, la resistencia a enfermedad y la calidad del fruto en la uchuva.

MicroRNA-383-5p inhibits the progression of gastric carcinoma via targeting HDAC9 expression

MicroRNAs (miRNAs), as post-transcriptional regulators, have been reported to be involved in the initiation and progression of various types of cancer, including gastric cancer (GC). The present study aimed to investigate the role of miR-383-5p in gastric carcinogenesis. Cell viability was analyzed using CCK-8 kit. Annexin V-fluorescein isothiocyanate/propidium iodide double staining was used to evaluate cell apoptosis. The expression levels of miR-383-5p and histone deacetylase 9 (HDAC9) mRNA in GC tissues and cell lines were analyzed using RT-qPCR. The protein expression of HDAC9 was detected by western blotting. We found that HDAC9 was up-regulated and miR-383-5p was down-regulated in GC tissues and cell lines. High HDAC9 expression or low miR-383-5p expression was closely related to poor prognosis and metastasis in GC patients. HDAC9 knockout or miR-383-5p mimics led to growth inhibition and increased apoptosis in AGS and SGC-7901 cells. More importantly, we validated that miR-383-5p as a post-transcriptional regulator inhibited HDAC9 expression and was inversely correlated with HDAC9 expression in GC tissues. miR-383-5p had the opposite effects to HDAC9 in gastric carcinogenesis. miR-383-5p played an important role in gastric carcinogenesis, and it is one of the important mechanisms to regulate oncogenic HDAC9 in GC, which might be helpful in the development of novel therapeutic strategies for the treatment of GC.

FGFR1 is an independent prognostic factor and can be regulated by miR-497 in gastric cancer progression

Fibroblast growth factor receptor 1 (FGFR1) has been reported in gastric cancer to be a prognostic factor. However, miR-497-targeted FGFR1 has not been explored in the carcinogenesis of gastric cancer. The present study intended to revalidate the prognostic significance of FGFR1 in patients with gastric cancer, and the mechanism of miR-497-regulated FGFR1 was investigated in gastric cancer cell proliferation and apoptosis. The messenger RNA (mRNA) and protein levels were assayed by RT-qPCR and western blotting, respectively. The targeted genes were predicted by a bioinformatics algorithm and confirmed by a dual luciferase reporter assay. Cell proliferation was analyzed by CCK-8 assay. Annexin V-FITC/PI staining was used to evaluate the apoptosis in AGS and SGC-7901 cells. FGFR1 was frequently up-regulated in gastric cancer tissues and associated with poor overall survival in patients with gastric cancer. Interestingly, FGFR1 loss-of-function resulted in a significant growth inhibition and apoptosis in AGS and SGC-7901 cells. In addition, we found that miR-497 was inhibited in gastric cancer tissues and cell lines, while overexpression of miR-497 could suppress proliferation and induce apoptosis in AGS and SGC-7901 cells. Importantly, bioinformatics analysis and experimental data suggested that FGFR1 was a direct target of miR-497, which could inhibit FGFR1 expression when transfected with miR-497 mimics. Furthermore, we found that overexpression of FGFR1 reversed the growth inhibition and apoptosis of miR-497 mimics in AGS and SGC-7901 cells. These findings suggested that overexpression of miR-497 inhibited proliferation and induced apoptosis in gastric cancer through the suppression of FGFR1.

Nicotinamide mononucleotide adenylyltransferase of Trypanosoma cruzi (TcNMNAT): a cytosol protein target for serine kinases

Nicotinamide/nicotinate adenine dinucleotide (NAD+/NaAD) performs essential functions in cell metabolism and energy production due to its redox properties. The nicotinamide/nicotinate mononucleotide adenylyltransferase (NMNAT, EC 2.7.7.1/18) enzyme catalyses the key step in the biosynthesis of NAD+. Previously, the enzyme NMNAT was identified in Trypanosoma cruzi (TcNMNAT), a pathogenic agent with epidemiological importance in Latin America. To continue with the functional characterisation of this enzyme, its subcellular location and its possible post-translational modifications were examined in this study. For this, polyclonal antibodies were generated in mice, with soluble and denatured recombinant protein being used to detect the parasite’s NMNAT. Immunodetection assays were performed on whole extracts of T. cruzi, and an approximation of its intracellular location was determined using confocal microscopy on wild and transgenic parasites, which revealed the cytosol distribution patterns. This localisation occurs according to the needs of the dinucleotides that exist in this compartment. Additionally, a bioinformatics study was performed as a first approach to establish the post-translational modifications of the enzyme. Possible phosphorylation events were experimentally analysed by western blot, highlighting TcNMNAT as a potential target for serine kinases.

Effect and mechanism of miR-206/miR-613 on expression of OATP1B1 / 药学学报

This study was designed to explore the effect and mechanism of miR-206/miR-613 on the expression of OATP1B1 gene. Bioinformatic analysis was used to predict the potential miRNAs target sites in 3'-untranslated region (3'-UTR) of OATP1B1 mRNA. The expression level of miR-206/miR-613 and OATP1B1 mRNA and protein was determined with RT-qPCR and Western blot, respectively. Luciferase assay was used to explore the exact mechanism of the effect of miR-206/miR-613 on the expression of OATP1B1 mRNA and protein. The results showed that the seed sequences of miR-206/miR-613 has perfect complementary with 3'-UTR of OATP1B1 mRNA in terms of sequence specificity. The secondary structure between miR-206/miR-613 and 3'-UTR of OATP1B1 mRNA was rather stable. The OATP1B1 protein level was down-regulated by 24.7%, 38.8% by overexpression of miR-206/miR-613. The expression was up-regulated by 25%, 38.2% by inhibition of miR-206/miR-613. However, overexpression or inhibition of miR-206/miR-613 had no effect on the expression of OATP1B1 mRNA. The luciferase activity of pMIR/OATP1B1-WT luciferase reporter gene was decreased by 35% and 30% through overexpression of miR-206/miR-613. The expression was increased by 33.1% and 32.5% through inhibition of miR-206/miR-613. When the binding sites in the 3'-UTR of OATP1B1 mRNA complementary with miR-206/miR-613 was mutated, overexpression or inhibition of miR-206/miR-613 had no effect on the luciferase activity. Collectively, miR-206/miR-613 post-transcriptionally regulates the expression of OATP1B1 protein by directly targeting the 3'-UTR of OATP1B1 mRNA.

Differential Expression of Transcriptional Variants of XAF1 in Colorectal Neoplasms / 胃肠病学

Background:The tumor suppressor,X-linked inhibitor of apoptosis(XIAP)-associated factor 1(XAF1)is a XIAP-binding protein that antagonizes the anti-caspase activity of XIAP,thereby enhancing apoptosis. Transcriptional variants of XAF1 have been detected in various tumor cells,however,the expression profile of these transcriptional variants in colorectal neoplasms remains unclear. Aims:To investigate the expressions of XAF1 and its transcriptional variants in different colorectal tissues and their roles in tumorigenesis and development of colorectal neoplasms. Methods:Samples of colorectal cancer and paired adjacent tissue,hyperplastic polyp,adenomatous polyp,and normal colorectal mucosa were collected from surgical operation or endoscopic biopsies. XAF1 protein expression was detected by immunohistochemistry and Western blotting,and the transcriptional variants of XAF1 were detected by RT-PCR. Results:Compared with normal colorectal mucosa,the expression level of XAF1 protein in nucleus was significantly reduced( P 0. 05)in hyperplastic polyp,adenomatous polyp,and cancerous tissue,and the overall expression level of XAF1 protein was decreased(P <0. 05). XAF1A protein expression in cancerous tissue was significantly reduced when compared with the paired adjacent tissue(P < 0. 05). mRNA expressions of three transcriptional variants of XAF1,XAF1A,XAF1B and XAF1C were all significantly lower in neoplastic tissues than in normal mucosa(P < 0. 05). Conclusions:XAF1 and its transcriptional variants are differentially expressed in colorectal neoplasms and normal colorectal mucosa. These changes occurred initially in adenomatous polyp accompanied by a redistribution of XAF1 from nucleus to cytoplasm. Post-transcriptional modification may affect XAF1 gene function.

Role of small noncoding RNA in the regulation of bacterial virulence / 华西口腔医学杂志

In the long-term interaction between pathogens and host, the pathogens regulate the expression of related viru-lence genes to fit the host environment in response to the changes in the host microenvironment. Gene expression was believed to be controlled mainly at the level of transcription initiation by repressors or activators. Recent studies have revealed that small noncoding RNAs (sRNAs) are key regulators in bacterial pathogenesis. sRNA in bacteria is a noncoding RNA with length ranging from 50 to 500 nucleotides. Pathogens can sense the changes in the host environment and consequently regulate the expression of virulence genes by sRNAs. This condition promotes the ability of pathogens to survive within the host, which is beneficial to the invasion and pathogenicity of pathogens. In contrast to transcriptional factors, sRNA-mediated gene regu-lation makes rapid and sensitive responses to environmental cues. Many sRNAs involved in bacterial virulence and pathogenesis have been identified. These sRNAs are key components of coordinated regulation networks, playing important roles in regulating the expression of virulence genes at post-transcriptional level. This review aims to provide an overview on the molecular mechanisms and roles of sRNAs in the regulation of bacterial virulence.

RNA-binding protein PTB in spermatogenesis: Progress in studies / 中华男科学杂志

RNA binding proteins (RBPs) regulate the function of cells by interacting with nascent transcripts and therefore are receiving increasing attention from researchers for their roles in tissue development and homeostasis. The polypyrimidine tract binding (PTB) protein family of RBPs are important posttranscriptional regulators of gene expression. Further investigations on the post-transcriptional regulation mechanisms and isoforms of PTB proteins in the spermatogenesis show that PTB protein 1 (Ptbp1) is a predominant isoform in mitotic cells (spermatogonia), while Ptbp2 predominates in meiotic spermatocytes and postmeiotic spermatids and binds to the specific 3' untranslated region (3' UTR) of the phosphoglycerate kinase 2 (Pgk-2) mRNA, which helps to stabilize Pgk-2 mRNA in male mouse germ cells. In case of Ptbp2 inactivation in the testis, the differentiation of germ cells arrests in the stage of round spermatids, with proliferation of multinucleated cells in the seminiferous tubule, increased apoptosis of spermatocytes, atrophy of seminiferous tubules, and lack of elongating spermatids, which consequently affects male fertility. This article presents an overview on the structure of the PTB protein and its role in regulating mammalian spermatogenesis.

Advances in research of microRNA and B-cell lymphoma / 肿瘤研究与临床

MicroRNAs (miRNAs) are a class of small single-stranded and non-coding RNAs that negatively regulate gene expression at the post-transcriptional level by degradation of target mRNA or inhibition of protein translation.Recent studies have shown that miRNAs play important roles in human diseases.It is of great importance to explore the role of miRNAs in the pathogenesis,early diagnosis and new therapeutic strategies of a variety of malignant tumors,including B-cell lymphoma.This review described the biosynthesis of miRNAs,the mechanisms of miRNAs target regulation and the involvement of miRNAs in the initiation and progression of human cancers,and summarized the role of miRNAs in B-cell lymphoma.

Construction of pGL3-TNF-α3′UTR luciferase reporter gene and tanshinone compounds screening / 中国药理学通报

Aim To screen the potential inhibitors of post-transcriptional activity of pro-inflammatory media-tor TNF-α from the lipophilic constituents in Chinese Medicine Salvia miltiorrhiza Bunge ( Danshen) , we es-tablished dual luciferase reporter gene system pGL3-TNF-α3′UTR ( 3′untranslated region ) co-transfected with Renilla control gene. Methods Complementary DNA ( cDNA) template was obtained from human um-bilical vein endothelial cells ( HUVECs ) . The full length DNA of TNF-α 3′-UTR was amplified through PCR, and then connected the luciferase reporter vector pGL3-control after enzyme digestion. pGL3-TNF-α 3′UTR constructs were co-transfected with pSVRenilla into the mononuclear macrophages RAW264. 7 cells. The relative activity of reporter genes was measured by dual luciferase reporter ( DLR ) assay system after the stimulus of lipopolysaccharide ( LPS ) in presence or absence of tanshinones compounds. Results The pGL3-TNF-α3′UTR luciferase reporter gene was suc-cessfully constructed. The cloning DNA fragment and sequence were both consistent with the GENBANK da-tabase. LPS significantly induced the relative reporter activityof RAW264 . 7 cells transfected with pGL3-TNF-α 3′UTR. Among four tanshinones compounds, we found only cryptotanshinone could significantly de-crease LPS-induced relative reporter activity. Conclu-sion The pGL3-TNF-α 3′UTR construct combined with DLR assay system was successfully established, which can be used to discover the agents such as cryp-totanshinone that regulate the post-transcription of TNF-α in treatment of inflammatory and malignant dis-eases.

Control of Inflammatory Responses: a New Paradigm for the Treatment of Chronic Neuronal Diseases

The term 'inflammation' was first introduced by Celsus almost 2000 years ago. Biological and medical researchers have shown increasing interest in inflammation over the past few decades, in part due to the emerging burden of chronic and degenerative diseases resulting from the increased longevity that has arisen thanks to modern medicine. Inflammation is believed to play critical roles in the pathogenesis of degenerative brain diseases, including Alzheimer's disease and Parkinson's disease. Accordingly, researchers have sought to combat such diseases by controlling inflammatory responses. In this review, we describe the endogenous inflammatory stimulators and signaling pathways in the brain. In particular, our group has focused on the JAK-STAT pathway, identifying anti-inflammatory targets and testing the effects of various anti-inflammatory drugs. This work has shown that the JAK-STAT pathway and its downstream are negatively regulated by phosphatases (SHP2 and MKP-1), inhibitory proteins (SOCS1 and SOCS3) and a nuclear receptor (LXR). These negative regulators are controlled at various levels (e.g. transcriptional, post-transcriptional and post-translational). Future study of these proteins could facilitate the manipulation of the inflammatory response, which plays ubiquitous, diverse and ambivalent roles under physiological and pathological conditions.

Regulation of luteinizing hormone receptor expression by an RNA binding protein: Role of ERK signaling.

A specific luteinizing hormone receptor (LHR) mRNA binding protein (LRBP) has been identified and purified. This LH receptor mRNA binding protein selectively binds to the polypyrimidine rich bipartite sequence in the coding region of the LHR mRNA and accelerates its degradation. In response to preovulatory LH surge, the LH receptor expression in the ovary undergoes downregulation by accelerated degradation of LH receptor mRNA through the involvement of this RNA binding protein. Here we describe the intracellular mechanism triggered by LH/hCG (human chorionic gonadotropin) that leads to the regulated degradation of LH receptor mRNA. Downregulation of LH receptor mRNA was induced by treatment of cultured human granulosa cells with 10 IU of hCG. Activation of downstream target, extracellular signal-regulated protein kinase 1 and 2 (ERK 1/2) showed an increase within five min and sustained up to 1 h. Confocal analysis showed that ERK1/2 translocates to the nucleus after 15 min of hCG treatment. This leads to an increase in LRBP expression which then causes downregulation of LH receptor mRNA by accelerating its degradation. Treatment with UO126 or transfection with ERK specific siRNA (small interfering RNA) resulted in the abolishment of ERK activation as well as LHR mRNA downregulation. RNA electrophoretic mobility gel shift assay of the cytosolic fractions showed that hCG-induced increase in the LH receptor mRNA binding activity was also abrogated by these treatments. These results show that LH/hCG-induced LH receptor mRNA downregulation is initiated by the activation of ERK1/2 pathway by regulating the expression and activity of LH receptor mRNA binding activity.

From Faulty Biochemical Assumptions to Poor Diagnostic Performance: Reflections on the Failure of DNA Microarrays to Become a Reliable Clinical Diagnostic Tool.

Since their inception about two decades ago, DNA microarrays have been considered as a great hope in translational research and personalized medicine. Although DNA microarrays for gene expression profiling proved to be an indispensable tool in the laboratory settings, their applications as an instrument for clinical diagnostics have not yet produced tangible results. In this paper, we convey the idea that, apart from notoriously poor reproducibility and complexities of experimental validations, there exist other reasons hindering clinical application of DNA microarrays. These reasons are rooted in the very core of the DNA microarrays methodology, that is, in faulty biochemical assumptions underlying microarray measurements. A key premise the microarray measurements are based on is that mRNA abundances harvested from the eukaryotic cytoplasm are indicative of the activity levels of corresponding genes. There are at least two reasons why this premise is questionable. First, each transcription is supported by a number of transcription factors expressed by many genes. Due to this reason, relations between the transcription rates of genes and the mRNA abundances are the 'many-to-one', not the 'one-to-one'; therefore, abnormality in a certain mRNA abundance does not unequivocally indicate abnormality of the gene bearing its complimentary code. Second, mRNA copy numbers in cytoplasm are regulated by a number of epigenetic factors among which the post-transcriptional mRNA stability is of primary importance. Abnormal concentration of certain mRNA may result from deviant Opinion Article British Journal of Medicine & Medical Research, 4(27): 4511-4522, 2014 4512 mRNA stability, thus mimicking, but having nothing to do with, presumed abnormality in transcription rates of corresponding genes. An instrument built upon so poorly understood biochemical basis can hardly serve as a reliable tool in the delicate task of diagnosis of human disease in clinical settings.

Rol biológico y aplicaciones de los miRNAs en cáncer de seno / Biological role and applications of miRNAs in breast cancer

Los miRNAs son pequeños RNAs que participan en diversos procesos de regulación génica, mediante ribointerferencia y juegan un papel clave en diversos procesos biológicos, tales como proliferación celular, diferenciación y apoptosis. En consecuencia, la expresión alterada de miRNAs contribuye a la enfermedad humana, incluyendo cáncer. En esta revisión, nos centraremos en los recientes hallazgos de miRNAs que inciden en el desarrollo de cáncer y particularmente en cáncer de seno, simultáneamente evaluaremos sus mecanismos de regulación, su clasificación, su uso como marcadores de invasión tumoral, de sensibilidad a fármacos y adicionalmente exploraremos la utilidad de los miRNAs en el diagnóstico, seguimiento y tratamiento individualizo. Finalmente encontramos que los miRNAs representan una gran alternativa para entender las bases moleculares de los procesos tumorales implícitos en cáncer de seno y una vez se conozcan todas sus dianas, será posible dilucidar al menos en parte este proceso complejo y multigénico, ayudado mediante herramientas como la generación de bases de datos, para reportan la expresión diferencial de miRNAs, elementos que nos permitirá realizar medicina preventiva y mejorar la calidad de vida de los pacientes y sus familias.

MiRNAs are small RNAs that are involved in various processes of gene regulation by RNAi and play a key role in various biological, such as cell proliferation, differentiation and apoptosis processes. Consequently, the altered expression of miRNAs contribute to human disease, including cancer. In this review, we will focus on the recent findings of miRNAs that affect the development of cancer, particularly breast cancer, simultaneously evaluate their regulatory mechanisms , their classification , their use as markers of tumor invasion, drug susceptibility and further explore the utility of miRNAs in the diagnosis, monitoring and individualize treatment. Finally found that miRNAs represent a great alternative for understanding the molecular basis of implicit tumor processes in breast cancer and once all targets are known, it will be possible to elucidate at least in part this complex and multigenic process, aided by tools such as generation of databases, to report the differential expression of miRNAs, elements that allow us to preventive medicine and improve the quality of life of patients and their families.

Research advances in the miRNA regulation of autophagy / 中国肿瘤临床

MicroRNAs are endogenously expressed non-coding RNAs, which are composed of approximately 18 nucleotides to 25 nucleotides. Mature microRNAs regulate gene expression by base pairing with the 3'-untranslated region of target mRNAs. These mature microRNAs can degrade target mRNAs or inhibit translation. This process is a type of post-transcriptional regulation of gene ex-pression. Studies have shown that microRNAs are important in physiological and pathological processes, such as cell proliferation, cell differentiation, and cell death. This article provides an overview of the function of microRNAs in the regulation of macrophages.

Ribosome Profiling for Biomarker Discovery / 日本補完代替医療学会誌

It has been well known that protein level is estimated by the expression level of its mRNA. However, it is also argued that correlation between mRNA abundance and protein levels is weaker than previously thought. Recently a newly developed technique called ribosome profiling has drawn attention as a drastic countermeasure to improve the weak correlation. Here it is discussed that weak association of protein and mRNA levels seen in genome-wide analysis of gene expression such as microarray is attributable to post-transcriptional regulation including translational inhibition. This review further discusses how these issues are resolved by ribosome profiling and also addresses a possibility of biomarker discovery derived from this technique.<br>