The possibility of early diagnosis of colorectal cancer through expression of Lncrna UCA1, Lncrna LINC00970, and Wnt genes; an in-vitro study

Colorectal cancer is the 4thcause of cancer death; with considering the growth process of this cancer and the necessity of early diagnosis, the purpose of the research is to state the LncRNA 00970, LncRNA UCAI,and the Wntgene before and after the treatment by 5-Azacytidine epigenetic medicine, to reach the biomarker in the very first steps of colorectal cancer. In this experiment, the human colon cancer cell line (HT29) treated with different concentrations of 5-aza-2'-deoxycytidine (5-aza-dC) was utilized to induce DNA demethylation; Quantitative PCR (qPCR) was used to measure LncRNA UCA1and LncRNA LINC00970 and Wntexpression. There was a significant relationship between the expression of LncRNA 00970, LncRNA UCAI,and the Wntgene and its effects on colorectal (p < 0.05). The Wntgene was treated by 1 and 10 of 5-Azacytidine epigenetic medicine, which then experienced decreases. In LncRNA UCAI and LncRNA00970 in dose 1 micromolar of 5-Azacytidine had decrement and increment of expressionrespectively that explains their efficiency but in treatment by dose 10 mM of this medicine, no significant LncRNA expression difference was detected, 5-azacitidine has a direct impact on its target genes and LncRNAs.Therefore, it can be used in the early diagnosis of colorectal cancer.

Silencing lncRNA UCA1 affects radiosensitivity of glioma cells by up-regulating miR-873-5p expression / 中华放射肿瘤学杂志

Objective:To investigate the effect of lncRNA UCA1 on the radiosensitivity of in vitro cultured glioma cell lines SHG-44, U87 and U251 by regulating the miR-873-5p expression. Methods:The survival of glioma cells SHG-44, U87 and U251 treated with different radiation intensities (0, 2, 4, 6 and 8 Gy) was detected by colony formation assay. The expression levels of UCA1 in glioma cells SHG-44, U87 and U251 were measured by qRT-PCR. The radiation-resistant glioma cells U87 and U251 were selected for subsequent study. After silencing UCA1 expression and/or over-expressing miR-873-5p, the cell survival rate was detected by colony formation assay, and the cell apoptosis rate was determined by flow cytometry. The dual luciferase reporter gene assay and qRT-PCR were employed to verify the targeting relationship between UCA1 and miR-873-5p.Results:UCA1 was up-regulated in the radiation-resistant U87 and U251 cells. Silencing UCA1 or over-expressing miR-873-5p inhibited the survival of U87 and U251 cells, and promoted the cell apoptosis induced by radiation exposure. miR-873-5p was a target gene of UCA1, and UCA1 negatively regulated the expression of miR-873-5p. The inhibition of miR-873-5p could reverse the effect of silencing UCA1 on the radiosensitivity of glioma cells. Silencing UCA1 increased the inhibitory effect of radiation on the glioma cell U251 xenografts.Conclusion:Silencing UCA1 inhibits the survival of glioma cells and promotes the cell apoptosis by up-regulating the expression of miR-873-5p, thereby increasing the radiosensitivity of glioma cells.

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

The expression of lncRNA UCA1 and its role on the proliferation and invasion in hepatic cancer and HepG2 cells / 天津医药

@# Objective Toinvestigatetheeffectsoflongnon-codingRNAurothelialcarcinoma-associated1(lncRNA UCA1) silencing on cell proliferation and invasion of human hepatic cancer HepG2 cells, and its mechanism thereof. Methods TheexpressionoflncRNAUCA1wasanalyzedbyreal-timePCRin20tumortissueand20adjacentnon-tumor tissuesamplesofhepaticcancer.HepG2cellswasculturedin vitro,andlncRNAUCA1specificshorthairpinRNA(shRNA1 andshRNA2)wastransfected.CCK-8assay,TranswellassayandWound-healingassaywereusedtodetecttheeffectof lncRNAUCA1silencingoncellproliferation,invasionandmigrationofHepG2cells.TheeffectoflncRNAUCA1silencing onproteinandmRNAexpressionofCyclinD1,vascularendothelialgrowthfactor(VEGF),matrixmetalloproteinase(MMP)9,focaladhesionkinase(FAK)andIntegrinβ3onlncRNAUCA1silencingwasmeasuredbyreal-timePCRandWestern blotassay.Results TheexpressionofLncRNAUCA1washigherinhepaticcancertissues.ThesilencingoflncRNAUCA1 significantly inhibited the growth of HepG2 cells, and the abilities of cell invasion and migration were downregulated. Westernblotassayandreal-timePCRshowedthatexpressionsofCyclinD1,VEGF,MMP-9,FAKandIntegrinβ3were significantlyinhibited.Conclusion TheresultssuggestthattheabnormalexpressionoflncRNAUCA1isassociatedwith thedevelopmentofhumanhepaticcancer.ThesilencingoflncRNAUCA1couldsuppressthecellproliferation,invasionand migrationofhepaticcarcinomacells.

Study on effects and mechanisms of long non-coding RNA UCA1 on cell survival and migration of bladder cell UM-UC-3 via targeting miR-582-5p / 中国免疫学杂志

Objective:To investigate the effects and mechanisms of long non-coding RNA UCA1 on cell survival and migration of bladder cancer cell UM-UC-3 by targeting miR-582-5p.Methods:Cells were transferred with UCA1 shRNA(sh-UCA1)and(or)miR-582-5p,the transfection efficiency and level of miR-582-5p were detected by RT-PCR.The luciferase report assay was performed for validate the relationship of UCA1 and miR-582-5p.The cell viability was measured by CCK8 assay.Apoptosis was detected by flow cy-tometry.The metastatic ability was calculated by wound healing and Transwell assay.And the protein levels of proliferation-,apoptosis-and migration-related were determined by Western blot.Results:sh-UCA1 inhibited the expression of UCA1 and induced the expression of miR-582-5p(P<0.05),and miR-582-5p inhibitor alleviated the effect of UCA1 on miR-582-5p(P<0.05).The luciferase reporter assay indicated that there was miR-582-5p binding site on UCA1.Silencing of UCA1 inhibited proliferation of bladder cancer cells and the expression of Ki67,induced apoptosis and expression of cleaved caspase-3(P<0.05).Meanwhile,sh-UCA1 inhibited migration and invasion of bladder cancer cells coupled with decreasing VEGF(P<0.05).In addition,miR-582-5p inhibitor attenuated the effects of UCA1 on proliferation,apoptosis and migration(P<0.05).Conclusion:UCA1 promotes survival and migration of bladder cancer cells through targeting miR-582-5p.

Effect and mechanism of lncRNA UCA1 target regulating miR-185-5p on non-small cell lung cancerA549 cell / 中国肿瘤生物治疗杂志

@# Objective: To investigate the effect and underlying mechanism of Long non-coding RNAurothelial carcinoma associated 1 (lncRNA UCA1) on proliferation, invasion and migration of non-small cell lung cancer (NSCLC) A549 cells. Methods: NSCLS A549 cells were cultured and transfected with lentivirus; RT-PCR was employed to detect the levels of UCA1 in A549 cells. The relationship between UCA1 and miR-185-5p was validated by luciferase reporter assays. Cell viability ofA549 cells was measured by MTT. Cell invasion and migration were determined by Transwell and Wound healing assay, respectively; and western blotting was performed for measuring the levels of Wnt1/β-catenin pathway-related proteins. Results: sh-UCA1 significantly decreased UCA1 expression and increased miR-185-5p expression in A549 cells (all P<0.05). miR-185 inhibitor attenuated the promotion effect of sh-UCA1 on miR-1855p (P<0.05). UCA1 could significantly down-regulate miR-185-5p expression in A549 cells (P<0.05), which was reversed by miR-185 mimic (P<0.05). Luciferase reporter assay validated the binding site on UCA1 to link miR-185-5p. sh-UCA1 significantly inhibited cell proliferation, invasion and migration ofA549 cells (all P<0.05), and also decreased the protein levels of Wnt1, β-catenin and TCF-4 notably (all P<0.05); however, miR-185 inhibitor attenuated such inhibitory effects of sh-UCA1 (P<0.05). Conclusion: UCA1 could promote proliferation, invasion and migration of A549 cells through targeting miR-185-5p, and the mechanisms might be related with activation of Wnt1/β-catenin pathway.

Urothelial carcinoma-associated 1 enhances tamoxifen resistance in breast cancer cells through competitively inhibiting miR-18a / 北京大学学报(医学版)

Objective:To investigate how urothelial carcinoma-associated 1 (UCA1) and miR-18a modulates acquired tamoxifen resistance and the relevant mechanisms in estrogen receptor (ER) positive cancer cells.Methods: qRT-PCR was performed to detect UCA1 and miR-18a expression in breast cancer cells.Dual luciferase assay was performed to detect the binding between miR-18a and UCA1 3′UTR.Tamoxifen sensitive MCF-7 cells were transfected with UCA1 expression vector or miR-18a inhi-bitors.Tamoxifen resistant LCC9 and BT474 cells were transfected with UCA1 siRNA or miR-18a mi-mics.CCK-8 assay was performed to detect cell viability.Soft agar assay was performed to assess cell colony formation.Flow cytometric analysis was performed to check cell cycle distribution.Results: UCA1 was significantly upregulated in tamoxifen resistant LCC2,LCC9,and BT474 cells than in tamoxifen sensitive MCF-7 cells.UCA1 expression was significantly upregulated in MCF-7 cells after treatment with 0.1 μmol/L tamoxifen.UCA1 overexpression enhanced cell viability of MCF-7 cells after tamoxifen treatment,while UCA1 siRNA significantly suppressed viability of LCC9 and BT474 cells after tamoxifen treatment.In MCF-7 cells,compared with vector control+tamoxifen group,the average cell colony number and colony size of the UCA1+tamoxifen group was 19.0％ more and 29.0％ larger respectively,while the proportions of the cells in G1 phase and in S phase were 7.3％ lower and 6.7％ higher respectively.In BT474 cells,compared with siRNA control+tamoxifen group,the average cell colony number and colony size of the si-UCA1+tamoxifen group were 54.0％ less and 42.0％ smaller respectively,while the proportions of the cells in G1 phase and in S phase were 9.0％ higher and 6.2％ lower respectively.UCA1 directly interacted with miR-18a and reduced its expression in ER positive breast cancer cells.Knockdown of miR-18a increased viability of MCF-7 cells after tamoxifen treatment,while miR-18a overexpression significantly reduced viability of BT474 cells after tamoxifen treatment.In MCF-7 cells,compared with miRNA inhibitor control+tamoxifen group,the average cell colony number and colony size of the miR-18a inhibitor+tamoxifen group were 15.0％ more and 33.0％ larger respectively,while the proportions of the cells in G1 phase and in S phase were 8.8％ lower and 5.3％ higher respectively.In BT474 cells,compared with miRNA control+tamoxifen group,the average cell colony number and colony size of the miR-18a mimics+tamoxifen group were 47.0％ less and 25.0％ smaller respectively,while the proportions of the cells in G1 phase and in S phase were 13.3％ higher and 7.9％ lower respectively.Conclusion: UCA1 can increase tamoxifen resistance of ER positive breast cancer cells via competitively inhibiting of miR-18a.

Construction of eukaryotic expression vector of UCA1 a(CUDR) gene and its expression in bladder cancer UM-UC-2 cells / 吉林大学学报(医学版)

Objective To construct an eukaryotic expression vector pcDNA-UCA1a(CUDR)and to observe its expression in bladder cancer UM-UC-2 cells, and to provide experimental basis for study on the relationship between UCA1a(CUDR)gene and bladder cancer.Methods Human total length of UCA1a(CUDR)gene was obtained from the 5′-RACE-Ready cDNA of bladder cancer BLZ-2 1 1 cells by PCR and was inserted into pcDNA3.1 (+)vector.pcDNA-UCA1a(CUDR)was identified by digestion with EcoRⅠ and BamHⅠ.The bladder cancer UM-UC-2 cells were transfected stably with the constructed eukaryotic expression vector pcDNA-UCA1a(CUDR). The expressions of UCA1a(CUDR)gene in the UM-UC-2 cells transfected with pcDNA-UCA1a(CUDR)and the UM-UC-2 cells transfected with pcDNA3.1(+)(control vector)were detected by RT-PCR.Results The inserted fragment with 2 200 bp was successfully amplified, which was in accordance with the expected results. The eukaryotic expression vector pcDNA-UCA1a(CUDR)was constructed successfully after identified by double enzyme digestion and sequencing.The RT-PCR results showed that the expression of UCA1a(CUDR)gene in the cells transfected with pcDNA-UCA1 a (CUDR ) was significantly increased compared with the cells transfected with pcDNA3.1 (+). Conclusion The eukaryotic expression vector pcDNA-UCA1a (CUDR ) is successfully constructed.The UCA1a(CUDR)gene highly expresses in the UM-UC-2 cells transfected with the expression vector.