Bioinformatics analysis of the association between long non-coding RNA ubiquitin-specific peptidase 30 antisense RNA 1 (lncRNA USP30-AS1) and immune cell infiltration in ovarian serous cystadenocarcinoma / 细胞与分子免疫学杂志

Objective To investigate the expression of long non-coding RNA ubiquitin-specific peptidase 30 antisense RNA 1 (lncRNA USP30-AS1) and its relationship with immune infiltration in ovarian serous cystadenocarcinoma (OSC), and to determine its prognostic role in OSC. Methods The Cancer Genome Atlas (TCGA) database was utilized to retrieve the expression of USP30-AS1 and clinical information of 384 OSC patients. Wilcoxon rank-sum test was employed to compare the expression of USP30-AS1 between OSC and normal ovarian tissues. Logistic regression analysis was conducted to assess the relationship between clinical pathological features and USP30-AS1. Gene set enrichment analysis (GSEA) and single-sample gene set enrichment analysis (ssGSEA) were performed to investigate enrichment pathways and functions and quantify the degree of immune cell infiltration in USP30-AS1. Based on the expression level of long non-coding RNA (lncRNA) USP30-AS1, the samples were divided into high and low expression groups according to the expression mean. Log-rank tests, univariate and multivariate proportional hazards model (Cox) were used to compare prognostic differences between different USP30-AS1 expression groups. The impact of lncRNA USP30-AS1 expression on other genomic analyses was also analyzed. Results High expression of USP30-AS1 was significantly associated with the International Federation of Gynecology and Obstetrics (FIGO) stage of the tumor. Multivariate survival analysis indicated that USP30-AS1 expression level served as an independent prognostic marker for OSC. GSEA data showed that high expression of USP30-AS1 might activate programmed death 1 (PD-1) signaling pathway, cytotoxic T lymphocyte-associated protein 4 (CTLA4) pathway, B-cell receptor signaling pathway, cell apoptosis, fibroblast growth factor receptor (FGFR) signaling pathway, and Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway. The expression of USP30-AS1 was negatively correlated with immune cell infiltration, including B cells, CD4+ T cells, dendritic cells, CD8+ T cells, and neutrophils. Conclusion USP30-AS1 may be used as a prognostic molecular marker for OSC.

Evaluation of serum microRNA-30e-5p expression in systemic lupus erythematosus and its association with clinical manifestations: A cross-sectional study / Evaluación de la expresión del microARN-30e-5p sérico en el lupus eritematoso sistémico y su asociación con las manifestaciones clínicas: un estudio transversal

ABSTRACT Background: MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression post-transcriptionally. Accumulating evidence indicates that the miR-30 family takes part in the development of multiple tissues and organs, and is a potential contributor to various dis eases, including autoimmune disorders such as systemic lupus erythematosus (SLE). The aim of this study was to evaluate the expression of miR-30e-5p, a member of the miR-30 fam ily, and investigate its potential relationship to clinical characteristics and possible disease activity in an Egyptian SLE cohort. Methods: Serum samples from 40 SLE patients and 37 age and gender matched healthy sub jects were tested for miR-30e-5p expression level using the Taqman quantitative reverse transcription-polymerase chain reaction. Analysis was performed using the 2 - AACT method. Results: The mean age of the patients was 28.7 ± 7.9 years, with a mean disease duration of 6.4 ±5.3 years. The median fold change in serum miR-30e-5p among our SLE cohort was significantly higher 1.748 (0.223-20.485) compared to the control group 0.877 (0.058-3.522) (P = 0.02). Receiver operating characteristic curve analysis revealed that miR-30e-5p expres sion level can discriminate SLE patients from controls at a cut-off value >1.06 with the area under the curve (AUC) = 0.676 (95% CI: 0.559-0.794, P = 0.02), with 64.3% sensitivity and 61.5% specificity. There was no correlation between any of the demographic features, clinical manifestations (apart from serositis, P = 0.013) or disease activity and miR-30e-5p levels. Conclusion: Our study demonstrated elevated miR-30e-5p expression levels in serum sam ples of SLE patients. Apart from serositis, it was not associated with any other disease characteristics.

RESUMEN Antecedentes: Los microARN (miRNA) son ARN no codificantes que regulan la expresión de los genes después de la transcripción. Las pruebas acumuladas indican que la familia de miR-30 participa en el desarrollo de múltiples tejidos y órganos, y es un posible contribuyente a diversas enfermedades, incluidos los trastornos autoinmunes como el lupus eritematoso sistémico (LES). El objetivo de este estudio fue evaluar la expresión del miR-30e-5p, un miembro de la familia miR-30, e investigar su posible relación con las características clínicas y la posible actividad de la enfermedad en una cohorte egipcia de LES. Métodos: Se analizaron muestras de suero de 40 pacientes con LES y 37 sujetos sanos de edad y sexo similares para determinar el nivel de expresión de miR-30e-5p, utilizando la reacción en cadena de la polimerasa de transcripción inversa cuantitativa Taqman. El análisis se llevó a cabo empleando el método 2-AACT. Los resultados: La edad media de los pacientes fue de 28,7 ± 7,9 años, mientras que la duración media de la enfermedad fue de 6,4 ± 5,3 años. La mediana del cambio de pliegue del suero miR-30e-5p entre nuestra cohorte de LES fue significativamente mayor, 1,748 (0,223-20,485), en comparación con el grupo de control, 0,877 (0,058-3,522) (p = 0,02). El análisis de la curva característica de funcionamiento del receptor reveló que el nivel de expresión del miR-30e-5p puede discriminar a los pacientes con LES de los controles en un valor de corte > 1,06, con el área bajo la curva (AUC) = 0,676 (IC del 95%: 0,559-0,794; p = 0,02), una sensibilidad del 64,3% y una especificidad del 61,5%. No hubo asociación entre ninguna de las características demográficas, manifestaciones clínicas (aparte de la serositis, p = 0,013) o actividad de la enfermedad y los niveles de miR-30e-5p. Conclusión: Nuestro estudio demostró niveles elevados de expresión de miR-30e-5p en mues tras de suero de pacientes con LES. Aparte de la serositis, no se asoció con ninguna otra característica de la enfermedad.

Antisense noncoding mitochondrial RNA-2 gives rise to miR-4485-3p by Dicer processing in vitro

BACKGROUND: The antisense noncoding mitochondrial RNAs (ASncmtRNAs) derive from the mitochondrial 16S gene. Knockdown of these transcripts with chemically-modified antisense oligonucleotides induces proliferative arrest, apoptosis and invasiveness reduction in tumor but not normal cells. One of these transcripts, ASncmtRNA-2, contains the complete and identical sequence of hsa-miR-4485-3p and, upon knockdown of this transcript, there is a strong increase in levels of this miRNA, suggesting ASncmtRNA-2 as a source for miR-4485-3p, which is supported by several evidences from our group and others, in the ex vivo setting. RESULTS: Here we show that incubation of in vitro-transcribed ASncmtRNA-2 with recombinant Dicer produces RNA fragments corresponding to hsa-miR-4485-3p, showing that Dicer binds to and processes ASncmtRNA-2, strongly supporting the hypothesis that ASncmtRNA-2 acts as a precursor for miR-4485-3p. CONCLUSION: The in vitro results presented here strengthen the hypothesis that miR-4485-3p is derived from ASncmtRNA-2 by Dicer processing. Since miR-4485-3p is classified as a tumor suppressor miRNA, this evidence strengthens the application of ASncmtRNA knockdown for cancer therapy.

Anotação e caracterização de novos transcritos expressos no adenocarcinoma de pâncreas: RNAS não-codificadores longos associados a fenótipos tumorais e clínicos e formas alternativas de splicing associados a fenótipos tumorais e clínicos / Determination of relevant transcripts in ductal adenocarcinoma of pancreas: the transcriptional landscape of the long non-coding RNAs and protein-encoding RNAs revealed by the total RNAseq analysis of pancreatic adenocarcinoma

O câncer de pâncreas (PC) é uma das doenças mais devastadoras com o pior resultado de sobrevivência quando comparada com outros tipos de câncer. É apontado como o décimo câncer mais comum e a quarta causamortis por câncer, projetando-se para ser a segunda até 2030 nos Estados Unidos e na Alemanha. O PC constitui um conjunto heterogêneo de tumores, o adenocarcinoma ductal (PDAC) constitui o tipo mais frequente da neoplasia (80%). A prevenção, detecção precoce e tratamento enfrentam sérios problemas e é urgente a identificação de novos marcadores para diagnóstico, prognóstico e estratégias terapêuticas da doença. O objetivo desse trabalho foi realizar uma análise com alta-resolução do transcriptoma do PDAC) para identificar novos RNAs não codificadores, variantes de splicing e alterações transcricionais associados à malignidade. A metodologia empregada constituiu-se de gerar bibliotecas de RNA total a partir de 14 amostras cirúrgicas pareadas de tecido tumoral (PDAC) e tecido não-tumoral adjacente para sequenciamento NGS. A partir dos dados de RNAseq foi realizada a montagem do transcriptoma utilizando-se a referência do catálogo GENCODE para classificar os transcritos. Seguiram-se análises subsequentes de avaliação de características dos transcritos: estruturais, marcas regulatórias, potencial codificador, detecção em banco de dados independente (miTrascriptome, miT). Em segundo lugar foram realizadas análises de expressão diferencial, análise de sobrevida (utilizando banco de dados públicos) para seleção de transcritos potencialmente relevantes no PDAC. Foram geradas redes de co-expressão gênicas com enriquecimento de funções biológicas. Uma série de validações foram realizadas por RT-PCR de transcritos novos intergênicos e novas formas de splicing reconstruídas e selecionadas. RT-qPCR foi utilizada para validação da expressão aberrante de lncRNAs em PDAC, silenciamentos por siRNA e subsequentes ensaios de proliferação, migração e invasão. Foi avaliada in vivo o envolvimento com crescimento tumoral por ensaio xenográfico, e avaliação da implicação em funções biológicas mais específicas, como envolvimento em reparo de DNA por ensaio cometa alcalino e avaliação de enriquecimento em tumoresferas. A montagem reconstruiu 90.522 transcritos, dos quais 41.341 são anotados no GENCODE e 6.710 transcritos são novos não anotados no GENCODE (classificado como splicingvariant, intergenic RNA, antisense RNA). Desses foram validados 6 novos lincRNAs com expressão aumentada em PDAC, dois deles (TCONS00085964 e TCONS00036574) tem a expressão correlacionada com alterações na sobrevida. Foram validadas também novas formas de splicing de MMP14, CAPN8, LIF e OCT3 com expressão aumentada em PDAC. 7 lncRNAs, anotados no GENCODE, com expressão aumentada em PDAC, desses foram implicados com fenótipo tumoral de migração, invasão e proliferação: LINC01559; LINC01133, CCAT1 e UCA1. Desses LINC01559 e CCAT1 demonstraram regular a expressão de enzimas de O-glicosilação (GALNT3 e B3GNT3) envolvidas na manutenção de células tronco-tumorais em PDAC. O lncRNA UCA1 está envolvido com reparo de DNA e envolvido com a progressão tumoral invivo. Conclui-se que a abordagem por amostras pareadas a partir de RNAseq de bibliotecas de RNA total gerou um catálogo de transcritos mais completo no PDCA e revelou IncRNAs funcionalmente implicadas na doença como LINC01559 e UCA1, ampliando o conhecimento sobre os mecanismos moleculares que sustentam fenótipos malignos no câncer de pâncreas e revelando novos biomarcadores para prognóstico

Tese de DoutoradoDOIhttps://doi.org/10.11606/T.46.2019.tde-09032020-085211DocumentoTese de DoutoradoAutorPaixão, Vinicius Ferreira da (Catálogo USP)Nome completoVinicius Ferreira da PaixãoE-mailE-mailUnidade da USPInstituto de QuímicaÁrea do ConhecimentoBioquímicaData de Defesa2019-12-04ImprentaSão Paulo, 2019OrientadorReis, Eduardo Moraes (Catálogo USP) Banca examinadoraReis, Eduardo Moraes (Presidente) Hajj, Glaucia Noeli Maroso Malnic, Bettina Panepucci, Rodrigo Alexandre Título em portuguêsAnotação e caracterização de novos transcritos expressos no adenocarcinoma de pâncreas: RNAS não-codificadores longos associados a fenótipos tumorais e clínicos e formas alternativas de splicingPalavras-chave em portuguêsAlternative splicing lncRNA PDAC Transcriptoma UCA1 Xenotumor Resumo em portuguêsO câncer de pâncreas (PC) é uma das doenças mais devastadoras com o pior resultado de sobrevivência quando comparada com outros tipos de câncer. É apontado como o décimo câncer mais comum e a quarta causamortis por câncer, projetando-se para ser a segunda até 2030 nos Estados Unidos e na Alemanha. O PC constitui um conjunto heterogêneo de tumores, o adenocarcinoma ductal (PDAC) constitui o tipo mais frequente da neoplasia (80%). A prevenção, detecção precoce e tratamento enfrentam sérios problemas e é urgente a identificação de novos marcadores para diagnóstico, prognóstico e estratégias terapêuticas da doença. O objetivo desse trabalho foi realizar uma análise com alta-resolução do transcriptoma do PDAC) para identificar novos RNAs não codificadores, variantes de splicing e alterações transcricionais associados à malignidade. A metodologia empregada constituiu-se de gerar bibliotecas de RNA total a partir de 14 amostras cirúrgicas pareadas de tecido tumoral (PDAC) e tecido não-tumoral adjacente para sequenciamento NGS. A partir dos dados de RNAseq foi realizada a montagem do transcriptoma utilizando-se a referência do catálogo GENCODE para classificar os transcritos. Seguiram-se análises subsequentes de avaliação de características dos transcritos: estruturais, marcas regulatórias, potencial codificador, detecção em banco de dados independente (miTrascriptome, miT). Em segundo lugar foram realizadas análises de expressão diferencial, análise de sobrevida (utilizando banco de dados públicos) para seleção de transcritos potencialmente relevantes no PDAC. Foram geradas redes de co-expressão gênicas com enriquecimento de funções biológicas. Uma série de validações foram realizadas por RT-PCR de transcritos novos intergênicos e novas formas de splicing reconstruídas e selecionadas. RT-qPCR foi utilizada para validação da expressão aberrante de lncRNAs em PDAC, silenciamentos por siRNA e subsequentes ensaios de proliferação, migração e invasão. Foi avaliada in vivo o envolvimento com crescimento tumoral por ensaio xenográfico, e avaliação da implicação em funções biológicas mais específicas, como envolvimento em reparo de DNA por ensaio cometa alcalino e avaliação de enriquecimento em tumoresferas. A montagem reconstruiu 90.522 transcritos, dos quais 41.341 são anotados no GENCODE e 6.710 transcritos são novos não anotados no GENCODE (classificado como splicingvariant, intergenic RNA, antisense RNA). Desses foram validados 6 novos lincRNAs com expressão aumentada em PDAC, dois deles (TCONS00085964 e TCONS00036574) tem a expressão correlacionada com alterações na sobrevida. Foram validadas também novas formas de splicing de MMP14, CAPN8, LIF e OCT3 com expressão aumentada em PDAC. 7 lncRNAs, anotados no GENCODE, com expressão aumentada em PDAC, desses foram implicados com fenótipo tumoral de migração, invasão e proliferação: LINC01559; LINC01133, CCAT1 e UCA1. Desses LINC01559 e CCAT1 demonstraram regular a expressão de enzimas de O-glicosilação (GALNT3 e B3GNT3) envolvidas na manutenção de células tronco-tumorais em PDAC. O lncRNA UCA1 está envolvido com reparo de DNA e envolvido com a progressão tumoral invivo. Conclui-se que a abordagem por amostras pareadas a partir de RNAseq de bibliotecas de RNA total gerou um catálogo de transcritos mais completo no PDCA e revelou IncRNAs funcionalmente implicadas na doença como LINC01559 e UCA1, ampliando o conhecimento sobre os mecanismos moleculares que sustentam fenótipos malignos no câncer de pâncreas e revelando novos biomarcadores para prognóstico.Título em inglêsDetermination of relevant transcripts in ductal adenocarcinoma of pancreas: the transcriptional landscape of the long non-coding RNAs and protein-encoding RNAs revealed by the total RNAseq analysis of pancreatic adenocarcinomaPalavras-chave em inglêsAlternative splicing lncRNA PDAC Transcriptome UCA1 Xenotumor Resumo em inglêsPancreatic cancer (PC) is the deadliest malignancy, one of the most devastating diseases with the worst survival outcome compared to any cancer. It is touted as the tenth most common cancer and the fourth leading cause of cancer in the United States and Germany. It is projected to be the second leading cause of cancer death in a decade. PC is a heterogeneous set of tumors with high aggressiveness and mortality. Of these tumors, ductal adenocarcinoma (PDAC) is the most frequent type of cancer (80%). Prevention, early detection and treatment face serious problems, and the identification of new markers for diagnosis, prognosis and therapeutic strategies of the disease is urgent. The aim of this study was to perform a high-resolution analysis of pancreatic adenocarcinoma (PDAC) transcriptome to identify new noncoding RNAs, splicing variants, and transcriptional changes associated with malignancy in pancreatic ductal adenocarcinoma. The methodology employed consisted of generating total RNA libraries from 14 paired surgical samples of tumor tissue (PDAC) and adjacent non-tumor tissue for NGS sequencing. From the RNAseq data, the transcriptome assembly was performed using the GENCODE catalog reference to classify the transcripts. Subsequent analyzes of evaluation of transcript characteristics were followed: structural, regulatory markers, potential encoder, independent database detection (miTrascriptome, miT). Secondly, differential expression analysis, survival analysis (using public database) were performed to select potentially relevant transcripts in the PDAC. Genic co-expression networks with biological function enrichment were generated. A series of validations were performed by RT-PCR of new intergenic transcripts and new forms of reconstructed and selected splicing. RT-qPCR was used for validation of aberrant expression of lncRNAs in PDAC, siRNA silencing and subsequent proliferation, migration and invasion assays. Involvement with tumor growth was evaluated by in vivo xenograph assay. Biological function tests to determine an involvement in DNA repair was evaluated by alkaline comet assay and was performed an evaluation of tumorsphere expression enrichment. The assembly reconstructed a total of 90,522 transcripts, of which 41,341 are noted in GENCODE. 6,710 transcripts are new (splicing variant, intergenic RNA, antisense RNA) not noted in the GENCODE reference. Of these 6 new PDAC-enhanced lincRNAs were validated, two of them (TCONS00085964 and TCONS00036574) correlated with changes in survival. New forms of splicing of MMP14, CAPN8, LIF and OCT3 with increased expression in PDAC were also validated. 7 lncRNAs noted with increased expression in PDAC were implicated with tumor migration, invasion and proliferation phenotype: LINC01559; LINC01133, LINC01614; CCAT1; LINC02577; LINC00920 and UCA1. Of these LINC01559 has been shown to regulate the expression of O-glycosylation enzymes (GALNT3 and B3GNT3) involved in maintaining CSCs in PDAC. It has been identified that UCA1 is involved with DNA repair and involved with tumor progression in vivo. It is concluded that the approach of sampling RNAseq from total RNA libraries generated a more accurate transcript catalog of PDAC and revealed IncRNAs functionally implicated in the disease, such as LINC01559 and UCA1, expanding the knowledge about the molecular mechanisms that underlie malignant phenotypes in pancreatic cancer and revealing novel prognostic biomarke

Antisense RNA: the new favorite in genetic research / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Antisense RNA molecule represents a unique type of DNA transcript that comprises 19-23 nucleotides and is complementary to mRNA. Antisense RNAs play the crucial role in regulating gene expression at multiple levels, such as at replication, transcription, and translation. In addition, artificial antisense RNAs can effectively regulate the expression of related genes in host cells. With the development of antisense RNA, investigating the functions of antisense RNAs has emerged as a hot research field. This review summarizes our current understanding of antisense RNAs, particularly of the formation of antisense RNAs and their mechanism of regulating the expression of their target genes. In addition, we detail the effects and applications of antisense RNAs in antivirus and anticancer treatments and in regulating the expression of related genes in plants and microorganisms. This review is intended to highlight the key role of antisense RNA in genetic research and guide new investigators to the study of antisense RNAs.

Antisense transcription regulates the expression of sense gene via alternative polyadenylation

Natural antisense transcripts (NAT) and alternative polyadenylation (APA) of messenger RNA (mRNA) are important contributors of transcriptome complexity, each playing a critical role in multiple biological processes. However, whether they have crosstalk and function collaboratively is unclear. We discovered that APA enriched in human sense-antisense (S-AS) gene pairs, and finally focused on RNASEH2C-KAT5 S-AS pair for further study. In cis but not in trans over-expression of the antisense KAT5 gene promoted the usage of distal polyA (pA) site in sense gene RNASEH2C, which generated longer 3' untranslated region (3'UTR) and produced less protein, accompanying with slowed cell growth. Mechanistically, elevated Pol II occupancy coupled with SRSF3 could explain the higher usage of distal pA site. Finally, NAT-mediated downregulation of sense gene's protein level in RNASEH2C-KAT5 pair was specific for human rather than mouse, which lacks the distal pA site of RNASEH2C. We provided the first evidence to support that certain gene affected phenotype may not by the protein of its own, but by affecting the expression of its overlapped gene through APA, implying an unexpected view for understanding the link between genotype and phenotype.

Association of CDKN2B-AS1 Polymorphisms with Premature Triple-vessel Coronary Disease and Their Sex Specificity in the Chinese Population / 生物医学与环境科学（英文）

OBJECTIVE@#The aim of this study is to establish whether cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1) gene polymorphisms are associated with premature triple-vessel disease (PTVD).@*METHODS@#Nine single-nucleotide polymorphisms (rs1063192, rs10757274, rs1333042, rs1333049, rs2285327, rs3217986, rs3217992, rs4977574, and rs9632884) were genotyped in 884 PTVD patients and 907 control subjects (males ⪕ 50 years old and females ⪕ 60 years old) using the improved multiplex ligase detection reaction method.@*RESULTS@#The allele frequencies of rs10757274 G, rs1333049 C, rs4977574 G (all P < 0.001), and rs3217986 G (P = 0.040) were significantly higher in the PTVD group than in the control group, but those of rs1063192 A, rs1333042 G, and rs9632884 C (all P < 0.001) were significantly lower in the former than in the latter. Logistic regression analysis revealed that homozygote AA of rs1333042 is associated with decreased risk for PTVD (OR = 0.42, 95% CI: 0.22-0.82, P = 0.011). In addition, the allele frequencies observed differed between genders. The G allele of rs3217986 was associated with increased risk for PTVD in male patients only (OR = 2.94, 95% CI: 1.27-6.80, P = 0.012) in the dominant model, and no positively mutated allele was found in female patients.@*CONCLUSION@#Polymorphisms of the CDKN2B-AS1 gene are associated with the incidence of PTVD in the Chinese population. Furthermore, the frequencies of mutated alleles differed between genders.

Development of a novel vector for cloning and expressing extremely toxic genes in Escherichia coli

Background: Escherichia coli has been widely used as a host to clone and express heterologous genes. However, there are few vectors available for cloning and expressing extremely toxic genes, which limits further basic and applied research on extremely toxic proteins. Results: In this study, a novel vector pAU10 was constructed in E. coli. pAU10 utilizes the combination of the efficient but highly repressible T7-lacO promoter/operator and the strong rrnBT2 transcriptional terminator upstream of the T7 promoter to strictly control unwanted transcription of the extremely toxic gene; in addition, the trp promoter/operator is oriented opposite to the T7 promoter to control the production of the antisense RNA that may block the translation of leaky mRNA. Without the supplementation of IPTG and L-tryptophan in the culture medium, transcription of the extremely toxic gene by the T7 promoter is highly repressed, and the trp promoter produces the antisense RNA, which strictly prevents unwanted expression of the extremely toxic protein in E. coli. With the supplementation of IPTG and L-tryptophan, the T7 promoter efficiently transcribes the extremely toxic gene, and the trp promoter does not produce the antisense RNA, ensuring efficient expression of the extremely toxic protein in E. coli. Tight regulation and efficiency of expression of an extremely toxic gene cloned in the vector pAU10 were confirmed by cloning and expressing the restriction endonuclease-encoding gene bamHI without its corresponding methylase gene in E. coli JM109(DE3). Conclusion: pAU10 is a good vector used for cloning and expressing extremely toxic genes in E. coli.

High expression of p15 antisense RNA is a frequent event in acute myeloid leukemia / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To detect the presence of p15 antisense RNA(p15AS) in acute myeloid leukemia(AML).</p><p><b>METHODS</b>p15AS and p15 mRNA in two leukemia cell lines was detected with strand-specific primer RT-qPCR. To explore the connection between p15AS and AML, 43 patients with newly diagnosed AML and 21 patients with benign diseases (Iron deficiency anemia) as controls were enrolled. The expression level of p15AS in bone marrow cells derived from the patients and the controls were determined by strand-specific primer RT-qPCR, and its relationship with clinical features was analyzed.</p><p><b>RESULTS</b>The two AML lines displayed high p15AS and low p15 expression. Samples derived from the AML patients showed relatively increased expression of p15AS and down-regulated p15 expression in their bone cells. In contrast, the 21 controls showed high expression of p15 but relatively low expression of the p15AS. Compared with the normal controls, the expression levels of p15 protein were significantly lower among the AML patients (P<0.01). No relationships were detected between the level of p15AS and the patient's age, gender, FAB subtype, total white blood cell count, platelet count, proliferative degree of bone marrow cell and karyotype classification (P>0.05 for all comparisons).</p><p><b>CONCLUSION</b>High expression of p15 antisense RNA was frequently found among AML patients, and may play an important role in epigenetic silencing of p15.</p>

Downregulation of lanosterol synthase gene expression by antisense RNA technology in Saccharomyces cerevisiae / 药学学报

The cyclization of 2,3-oxidosqualene is the key branch point of ergosterol and triterpenoid biosynthesis. Downregulation of 2,3-oxidosqualene metabolic flux to ergosterol in Saccharomyces cerevisiae may redirect the metabolic flux toward the triterpenoid synthetic pathway. In our study, primers were designed according to erg7 gene sequence of S. cerevisiae. Three fragments including 5' long fragment, 5' short fragment and erg7 coding region fragment were amplified by PCR. 5' long fragment consists of the promoter and a part of erg7 coding region sequence. 5' short fragment consists of a part of promoter and a part of erg7 coding region sequence. These fragments were inserted reversely into pESC-URA to construct antisense expression plasmids. The recombinant plasmids were transformed into S. cerevisiae INVSc1 and recombinant strains were screened on the nutritional deficient medium SD-URA. The erg7 expression level of recombinant strains, which harbored antisense expression plasmid of erg7 coding region, was similar to that of INVScl by semi-quantitative PCR detection. But erg7 expression level of recombinant strains, which harbored 5' long antisense fragment and 5' short antisense fragment, was significantly lower than that of the control. The results of TLC and HPLC showed that the ergosterol content of recombinant strains, which harbored 5' long antisense fragment, decreased obviously. The ergosterol contents of the others were almost equal to that of INVSc1. Lanosterol synthase gene expression was downregulated by antisense RNA technology in S. cerevisiae, which lays a foundation for reconstructing triterpenoid metabolic pathway in S. cerevisiae by synthetic biology technology.

Microvesicle-delivery miR-150 promotes tumorigenesis by up-regulating VEGF, and the neutralization of miR-150 attenuate tumor development

Tumor-associated macrophages (TAMs) mostly exhibit M2-like (alternatively activated) properties and play positive roles in angiogenesis and tumorigenesis. Vascular endothelial growth factor (VEGF) is a key angiogenic factor. During tumor development, TAMs secrete VEGF and other factors to promote angiogenesis; thus, anti-treatment against TAMs and VEGF can repress cancer development, which has been demonstrated in clinical trials and on an experimental level. In the present work, we show that miR-150 is an oncomir because of its promotional effect on VEGF. MiR-150 targets TAMs to up-regulate their secretion of VEGF in vitro. With the utilization of cell-derived vesicles, named microvesicles (MVs), we transferred antisense RNA targeted to miR-150 into mice and found that the neutralization of miR-150 down-regulates miR-150 and VEGF levels in vivo and attenuates angiogenesis. Therefore, we proposed the therapeutic potential of neutralizing miR-150 to treat cancer and demonstrated a novel, natural, microvesicle-based method for the transfer of nucleic acids.

Characteristics of antisense non-coding RNA in the INK4 locus and its roles in disease / 中国医学科学杂志(英文版)

With the development of genome-wide sequencing technology, 195 types of functional long non-coding RNAs (lncRNAs) have so far been found, and their cellular roles are gradually being revealed. Now lncRNAs have become a hotspot in the life science. These small molecules exist in almost all higher eukaryotes, and have very important regulatory roles in these organisms. This review briefly summarizes recent progress in researches on antisense non-coding RNA in the INK4 locus.

Current Challenges in Bacterial Transcriptomics

Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.

Phospholamban antisense RNA improves SR Ca2+-ATPase activity and left ventricular function in STZ-induced diabetic rats / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>To study the effect of phospholamban antisense RNA (asPLB) on sarcoplasmic reticulum Ca2+-ATPase activity and cardiac function in rats with diabetes mellitus (DM) mediated by recombinant adeno-associated virus (rAAV) vector.</p><p><b>METHODS</b>Six weeks after the induction of DM by streptozotocin injected intraperitoneally, the rats were divided into three groups, namely: DM-rAAV-asPLB group, DM-saline group and DM group (control group). The rats in the DM-rAAV-asPLB group were intramyocardially injected with rAAV-asPLB, the rats in the DM-saline group were injected with saline, and those in the control group did not receive any treatment. Six weeks after gene transfer, the expressions of PLB protein and PLB phosphorylation were detected by Western-blot, while the activity of sarcoplasmic reticulum (SR) Ca2+-ATPase and left ventricular function were measured.</p><p><b>RESULTS</b>The PLB protein expression level was significantly higher whereas the PLB phosphorylation, SR Ca2+-ATPase activity and left ventricular function were significantly lower in the DM-saline group than in the control group. No significant difference was found in PLB protein expression level, PLB phosphorylation or SR Ca2+-ATPase activity between the DM-rAAV-asPLB group and the control group. The left ventricular function in the DM-rAAV-asPLB group was poorer than in the control group and was better than in the DM-saline group.</p><p><b>CONCLUSION</b>rAAV-asPLB can down-regulate PLB protein expression and up-regulate PLB phosphorylation and SR Ca2+-ATPase activity, thus contributing to the improvement of in vivo left ventricular function.</p>

Inhibition of allergic airway inflammation by antisense-induced blockade of STAT6 expression / 中华医学杂志(英文版)

<p><b>BACKGROUND</b>The signal transducer and activator of transcription 6 (STAT6) expression in lung epithelial cells plays a pivotal role in asthma pathogenesis. Activation of STAT6 expression results in T helper cell type 2 (Th2) cell differentiation leading to Th2-mediated IgE production, development of allergic airway inflammation and hyperreactivity. Therefore, antagonizing the expression and/or the function of STAT6 could be used as a mode of therapy for allergic airway inflammation.</p><p><b>METHODS</b>In this study, we synthesized a 20-mer phosphorothioate antisense oligonucleotide (ASODN) overlapping the translation starting site of STAT6 and constructed STAT6 antisense RNA (pANTI-STAT6), then transfected them into murine spleen lymphocytes and analyzed the effects of antagonizing STAT6 function in vitro and in a murine model of asthma.</p><p><b>RESULTS</b>In vitro, we showed suppression of STAT6 expression and interleukin (IL)-4 production of lymphocytes by STAT6 ASODN. This effect was more prominent when cells were cultured with pANTI-STAT6. In a murine model of asthma associated with allergic pulmonary inflammation in ovalbumin (OVA)-sensitized mice, local intranasal administration of fluorescein isothiocyanate (FITC)-labeled STAT6 ASODN to DNA uptake in lung cells was accompanied by a reduction of intracellular STAT6 expression. Such intrapulmonary blockade of STAT6 expression abrogated signs of lung inflammation, infiltration of eosinophils and Th2 cytokine production.</p><p><b>CONCLUSION</b>These data suggest a critical role of STAT6 in the pathogenesis of asthma and the use of local delivery of STAT6 ASODN as a novel approach for the treatment of allergic airway inflammation such as in asthma.</p>

Screening and identification of natural antisense transcript in mouse cerebral cortex / 中国医学科学院学报

<p><b>OBJECTIVE</b>To screen and identify the possible existence of natural antisense transcript (NAT) within the mouse neocortex.</p><p><b>METHODS</b>Sixty-three cerebral cortex layer-specific genes were screened by bioinformatics prediction in mice, among which 31 mice with potential NATs were screened. NAT was identified using reverse transcription polymerase chain reaction (RT-PCR) and then cloned in pGEM-T Vector System for sequencing.</p><p><b>RESULTS</b>Among 31 genes predicted using bioinformatics, 8 were proved to be NAT positive by RT-PCR.</p><p><b>CONCLUSIONS</b>NATs exist in the mouse neocortex tissue during the development of cerebral cortex. NATs may influence mouse cortical development by regulating the related coding genes.</p>

Effects of survivin antisense RNA and HSP70 double gene transfection on MCF-7 cells in vitro / 南方医科大学学报

<p><b>OBJECTIVE</b>To explore the effects of survivin antisense RNA and HSP70 double gene transfection on breast cancer cell line MCF-7.</p><p><b>METHODS</b>MCF-7 cells was transfected with the double-gene vector pIRES2-EGFP-survivin antisense RNA/HSP70 via liposome. After a 72-h transfection, the cells were collected for observation under inverted fluorescent microscope. The changes of survivin mRNA and HSP70 protein expressions in the cells were detected with real-time PCR and Western-blot before and after the cell transfection, and the apoptotic rate of the transfected MCF-7 cells was detected by flow cytometry analysis with Annexin-V-cy5/7AAD double staining.</p><p><b>RESULTS</b>Green fluorescence was detected in MCF-7 cells transfected with the double-gene expression vector and the empty vector under inverted fluorescent microscope. The expression level of survivin mRNA in the cells was reduced effectively after the transfection with the double-gene expression vector, which also induced obvious cell apoptosis and enhanced the expression level of HSP70 protein as compared with those in MCF-7 cells transfected with the empty vector and the untransfected MCF-7 cells.</p><p><b>CONCLUSION</b>Survivin antisense RNA can interfere with the expression of endogenous survivin and induce apoptosis of MCF-7 cells. HSP70 can increase the expression of HSP70 protein in MCF-7 cells.</p>

Identificação de perfis de expressão de RNAs codificadores e não codificadores de proteína como preditores de recorrência de câncer de próstata / Identification of protein-coding and non-coding RNA expression profiles as prognostic marker of prostate cancer biochemical recurrence

O câncer de próstata é o quinto tipo mais comum de câncer no mundo e o mais comum em homens. Fatores clínicos e anatomopatológicos atualmente usados na clínica não são capazes de distinguir entre a doença indolente e a agressiva. Existe uma grande necessidade de novos marcadores de prognóstico, a fim de melhorar o gerenciamento clínico de pacientes de câncer de próstata. Além das anormalidades em genes codificadores de proteínas, alterações em RNAs não codificadores (ncRNAs) contribuem para a patogênese do câncer e, portanto, representam outra fonte potencial de biomarcadores de câncer de próstata. Entretanto, até o momento, poucos estudos de perfis de expressão de ncRNAs foram publicados. Este projeto teve como principal objetivo identificar perfis de expressão de genes codificadores e não codificadores de proteína correlacionados com recorrência de tumor de próstata, a fim de gerar um perfil prognóstico com potencial uso como biomarcadores e elucidar o possível papel de ncRNAs no desenvolvimento do câncer. Para isso, foram analisados os perfis de expressão de genes codificadores e não codificadores de proteína de um conjunto de 42 amostras de tecido tumoral de câncer de próstata de pacientes de amostras de pacientes submetidos à prostatectomia radical, com longo acompanhamento clínico (cinco anos) e conhecida evolução da doença Nós utilizamos microarranjos por nós desenhados e fabricados pela Agilent sob encomenda, interrogando aproximadamente 18.709 transcritos não codificadores longos (>500 nt), sem evidência de splicing, que mapeiam em regiões intrônicas dentro de 5.660 loci genômicos. Os dados de expressão foram extraídos de cada arranjo, normalizados entre todas as 42 amostras de pacientes. Usando uma estratégia de múltipla amostragem, foi identificado um perfil de expressão de mau prognóstico, contendo 51 transcritos intrônicos não codificadores de proteína. O perfil prognóstico de ncRNAs foi aplicado a um conjunto teste independente de 22 pacientes...

Prostate cancer is the fifth most common type of cancer in the world, and the most common in men. Clinical and anatomo-pathological factors currently used in clinic are not able to distinguish between the indolent and the aggressive disease. There is a major need of new prognostic makers in order to improve the clinical management of prostate cancer patients. Apart from abnormalities in protein-coding genes, changes in non-coding RNAs (ncRNAs) contribute to the pathogenesis of cancer and thus represent another potential source of prostate cancer biomarkers. However, few studies of expression profiles of ncRNAs have been published. This project aimed to identify expression profiles of protein-coding and non-coding genes correlated to prostate cancer biochemical recurrence. For this, we analyzed the expression profile of 42 prostate cancer samples from patients undergoing radical prostatectomy, with long follow-up (five years), and know disease outcome. We used a custom microarray designed by us and printed by Agilent, that probes 18,709 long (>500 nt) ncRNAs mapping to intronic regions within 5,660 genomic loci. The expression data were extracted from each array and normalized across all 42 samples. Using a multiple random sampling validation strategy, we identified an expression profile of poor prognosis, comprising 51 ncRNAs. The prognostic profile of ncRNAs was applied to an independent test set of 22 patients, correctly classifying 82% of the samples. A Kaplan-Meier analysis of the test set of patients indicated that the survival curves of high and low risk groups were significantly different (Log-rank test p = 0.0009, Hazard ratio = 23.4, 95% CI = 3.62 to 151.2) thus confirming that this classifier is useful for identifying patients at high risk of recurrence. Furthermore, these findings indicate a potential role of these intronic non-coding RNAs in the progression of prostate tumors and points to the intronic ncRNAs as potential new markers of câncer.

[Inhibition of ackA and pta genes using two specific antisense RNAs reduced acetate accumulation in batch fermentation of E. coli BL21 [DE3]]

Expression of foreign proteins in E. coli is normally inhibited by exogenous production of acetate. To overcome this problem, various strategies have been proposed and tested to reduce the extent of acetate accumulation. Although these strategies can improve the outcome, the implementation of their proposed techniques is not practical. Because to achieve optimal results, it requires extremely tight control conditions and the actual cost is very high. Furthermore, a simple knockout mutation of the target metabolic pathway would not be appropriate because the acetate pathway plays an important physiological role in E. coli. In this study, we employed an antisense RNA strategy as an elaborated metabolic engineering tool to partially block biosynthesis of two major acetate pathway enzymes, acetate kinase [ACK] and phosphotransacetylase [PTA]. The fragments of antisense cassette were cloned sequentially in pBluescriptsk+ and completed cassette subcloned in pLT10T3. The function of this cassette was evaluated with RT-PCR and ACK and PTA assay. The effect of cassette on cell physiology was monitored by determination of optical density, glucose consumption and acetate production. We found that the antisense method partially reduced mRNA levels of the target genes, lowered the concentration of acetate in culture media and increased growth rate and final cell density in antisense-regulated strain. This strategy could provide us with a useful, inexpensive and practical tool to achieve a large-scale protein production system

Reversal of multidrug resistance in hepatocellular cell line HepG2R by mdr1-antisense RNA / 中华肝脏病杂志

<p><b>OBJECTIVE</b>To investigate whether multidrug resistance gene 1(mdr1) could reverse multidrug resistance (MDR) in HepG2R cells.</p><p><b>METHODS</b>An adenovirus vector, Adeno-asmdr, containing the antisense RNA driven by AFP promoter, was construct. Adeno-EGFP was transfected into HepG2, an AFP producing cell line, L02, a normal human liver cell line, and HeLa, a human cervical cancer cell line, the EGFP transcription level was detected by RT-PCR. Adeno-asmdr was transfected into HepG2R cells, the expression of P-gp170 was detected by western blotting, apoptosis was detected using TUNEL and flow cytometry, cell cycle was analyzed by flow cytometry.</p><p><b>RESULTS</b>EGFP was highly expressed in HepG2 cells, however, its expression in L02 or HeLa cells was very weak. Western blot showed that the P-gp170 was marked down-regulated 48h after transfection with Adeno-asmdr, and the expression of P-gp170 was detectable at least 7d post-transfection. Compared with control cells, Adeno-asmdr transfected HepG2R cells were more sensitive to different chemicals, as indicated by TUNEL staining and flow cytometry. Chemical treatment arrested the cells in S and G0/M phase.</p><p><b>CONCLUSION</b>The recombinant adenoviral vector, Adeno-asmdr, can block the expression of mdr1, and reverse MDR in HepG2R cells.</p>