scholarly journals Aberrant Long Noncoding RNAs Expression Profiles Affect Cisplatin Resistance in Lung Adenocarcinoma

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Lijuan Hu ◽  
Jian Chen ◽  
Fan Zhang ◽  
Junjun Wang ◽  
Jingye Pan ◽  
...  

Background. Long noncoding RNAs (lncRNAs) have been shown to be involved in the mechanism of cisplatin resistance in lung adenocarcinoma (LAD). However, the roles of lncRNAs in cisplatin resistance in LAD are not well understood. Methods. We used a high-throughput microarray to compare the lncRNA and mRNA expression profiles in cisplatin resistance cell A549/DDP and cisplatin sensitive cell A549. Several candidate cisplatin resistance-associated lncRNAs were verified by real-time quantitative reverse transcription polymerase chain reaction (PCR) analysis. Results. We found that 1,543 lncRNAs and 1,713 mRNAs were differentially expressed in A549/DDP cell and A549 cell, hinting that many lncRNAs were irregular from cisplatin resistance in LAD. We also obtain the fact that 12 lncRNAs were aberrantly expressed in A549/DDP cell compared with A549 cell by quantitative PCR. Among these, UCA1 was the aberrantly expressed lncRNA and can significantly reduce the IC50 of cisplatin in A549/DDP cell after knockdown, while it can increase the IC50 of cisplatin after UCA1 was overexpressed in NCI-H1299. Conclusions. We obtained patterns of irregular lncRNAs and they may play a key role in cisplatin resistance of LAD.

2020 ◽  
Vol 2020 ◽  
pp. 1-22
Author(s):  
Abulaihaiti Maitiseyiti ◽  
Hongbo Ci ◽  
Qingbo Fang ◽  
Sheng Guan ◽  
Alimujiang Shawuti ◽  
...  

Objective. Long noncoding RNAs (lncRNAs) have emerged as critical molecular regulators in various diseases. However, the potential regulatory role of lncRNAs in the pathogenesis of abdominal aortic aneurysm (AAA) remains elusive. The aim of this study was to identify crucial lncRNAs associated with human AAA by comparing the lncRNA and mRNA expression profiles of patients with AAA with those of control individuals. Materials and Methods. The expression profiles of lncRNAs and mRNAs were analyzed in five dilated aortic samples from AAA patients and three normal aortic samples from control individuals using microarray technology. Functional annotation of the screened lncRNAs based on the differentially expressed genes was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Results. Microarray results revealed 2046 lncRNAs and 1363 mRNAs. Functional enrichment analysis showed that the mRNAs significantly associated with AAA were enriched in the NOD-like receptor (NLR) and nuclear factor kappa-B (NF-κB) signaling pathways and in cell adhesion molecules (CAMs), which are closely associated with pathophysiological changes in AAA. The lncRNAs identified using microarray analysis were further validated using quantitative real-time polymerase chain reaction (qRT-PCR) analysis with 12 versus 11 aortic samples. Finally, three key lncRNAs (ENST00000566954, ENST00000580897, and T181556) were confirmed using strict validation. A coding-noncoding coexpression (CNC) network and a competing endogenous RNA (ceRNA) network were constructed to determine the interaction among the lncRNAs, microRNAs, and mRNAs based on the confirmed lncRNAs. Conclusions. Our microarray profiling analysis and validation of significantly expressed lncRNAs between patients with AAA and control group individuals may provide new diagnostic biomarkers for AAA. The underlying regulatory mechanisms of the confirmed lncRNAs in AAA pathogenesis need to be determined using in vitro and in vivo experiments.


2018 ◽  
Vol Volume 11 ◽  
pp. 5383-5390 ◽  
Author(s):  
Bing Zhao ◽  
Hang Xu ◽  
Xiaoye Ai ◽  
Yasheng Adalat ◽  
Ying Tong ◽  
...  

2020 ◽  
Vol 34 (4) ◽  
pp. 508-518
Author(s):  
Yanyan Yang ◽  
Yu Zhang ◽  
Yujuan Yang ◽  
Jing Guo ◽  
Liping Yang ◽  
...  

Background The mechanism of long noncoding RNAs (lncRNAs) involved in the development of allergic rhinitis (AR) remains unclear. Objective We investigated the mechanism by which differentially expressed lncRNAs contribute to pathogenesis of AR. Methods Expression profiles of lncRNAs and mRNAs were analyzed by microarray detection from the blood samples of 3 AR patients and 3 control subjects, and the main lncRNAs were verified by quantitative real-time polymerase chain reaction (qRT-PCR) in the peripheral blood of 16 AR patients and 18 control subjects. GO (Gene_Ontology), Pathway, and Disease analysis of differentially expressed lncRNAs and mRNAs, and transcription factor prediction analysis were performed to explore synergistic effect of differentially expressed lncRNAs and their function-related mRNAs on AR pathogenesis. Results Thirty-one lncRNAs were differentially expressed in the peripheral blood from AR patients, and 4 of the 5 most differentially expressed lncRNAs had significantly higher levels in AR patients than in control subjects by qRT-PCR analysis. A lncRNA-mRNA coexpression network analysis identified 16 pairs of positive correlations between the 4 lncRNAs and coexpressed mRNAs. GO, Pathway, and Disease analyses indicated that the 4 lncRNAs were correlated with 7 mRNAs enriched in terms of inflammation, immune response, and allergic diseases. Transcription factor prediction results suggested that Oct-1, AP-1, NF-kappaB, and c-Rel play key roles in the pathogenesis of AR mediated by lncRNAs. Conclusion Our results provide new insights into how lncRNAs and their function-related mRNAs might contribute to AR.


2020 ◽  
Vol 19 ◽  
pp. 153303382093011
Author(s):  
Ke-kang Sun ◽  
Xiao-jun Shen ◽  
Dong Yang ◽  
Yang Jiao ◽  
Xiao-yang Wu

Gastric cancer is one of the most commonly occurring cancers worldwide. Investigation of long noncoding RNAs is of increasing interest, particularly in relation to their contribution to progression and prognosis of gastric cancers; however, insufficient studies been performed investigating the part of long noncoding RNAs play in gastric cancer carcinogenesis. Patterns of dysregulated long noncoding RNA and messenger RNA between mucosa gastric cancer and adjacent normal tissues were identified using long noncoding RNAs microarray analysis. Quantitative real-time polymerase chain reaction was conducted as a means to verify the obtained data. Both Gene Ontology and Kyoto Encyclopedia of Genes and Genomes  (KEGG) pathway analyses were subsequently used to investigate the function of dysregulated long noncoding RNAs and messenger RNAs. Cis and trans action was used to predict the possible targets of long noncoding RNAs, and a coexpression network was created to simulate the complex intergenic interactions. Ninety-five dysregulated long noncoding RNAs and 123 messenger RNAs were identified, and quantitative real-time polymerase chain reaction was used to validate 6 filtered long noncoding RNAs. Gene Ontology and KEGG pathway analyses identified several remarkably biological processes and signaling pathways, including spliceosome, RNA transport, and ubiquitin-mediated proteolysis. The transcriptional factors MYC, GABPA, and E2F1 were found to play a central function in the long noncoding RNAs process, as indicated by the coexpression network. This study revealed the dysregulated long noncoding RNA profiles of mucosal gastric cancer. The results shed light on the biological function of long noncoding RNAs in gastric cancer pathogenesis. This provides useful information for exploring potential early screening biomarkers in gastric cancer.


BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.


LWT ◽  
2015 ◽  
Vol 63 (1) ◽  
pp. 714-719 ◽  
Author(s):  
Sahilah Abd Mutalib ◽  
Nursheila Mustafa Muin ◽  
Aminah Abdullah ◽  
Osman Hassan ◽  
Wan Aida Wan Mustapha ◽  
...  

Author(s):  
Jun-Hyung Lim ◽  
Sang Hwan Nam ◽  
Jongwoo Kim ◽  
Nam Hoon Kim ◽  
Gun-Soo Park ◽  
...  

Abstract In this study, a three-stage bioaerosol sampler with a sampling flow rate of 170 L/min was designed and fabricated for sampling the bioaerosols released during human breathing and coughing, and its performance was evaluated. The sampler was constructed using a cyclone separator with a cutoff size of 2.5 µm as a preseparator, a multi-nozzle virtual impactor with a cutoff size of 0.34 µm as an aerosol concentrator, and a BioSampler, which is a commercial product, for collecting bioaerosols in a collection fluid. The collection efficiency of the sampler was evaluated through simulations and experiments. Only particles with sizes of 0.1-4 µm were selectively collected in the collection fluid. Bacteriophage bioaerosols were sampled using the developed sampler and ACD-200 Bobcat sampler, which is a commercial product. The amounts of collected bacteriophages were compared using the polymerase chain reaction (PCR) technique. The sampling performance of the developed sampler was similar to that of the ACD-200 Bobcat sampler. Moreover, the developed sampler showed its ability to sample bioaerosols of a specific size-range and collect them directly in a collection fluid for the PCR analysis. Therefore, the developed sampler is expected to be useful for indoor environmental monitoring by effectively sampling the bioaerosols released indoors during human breathing and coughing.


2013 ◽  
Author(s):  
Γεωργία Κόκκαλη

IntroductionOne of the most difficult aspects in assisted reproductive technology (ART) is the selection of asuitable embryo for transfer to the patient’s uterus, in order to achieve implantation anddevelopment to term. This study was based on the hypothesis that preimplantation embryosmay have different gene expression profiles that characterize their ability to implant in theuterus and develop to a healthy baby at term.The main aim of this study was to investigate molecular markers associated with developmentalcompetence and successful implantation in ART. The primary aim of the study was to developand optimize a blastocyst biopsy method, suitable for application in clinical practice. Thesecondary aim of the study was to investigate the gene expression of beta Human ChorionicGonadotropin (CGβ) in blastocysts and correlate it with their morphology. Previously to thecurrent study, blastocyst biopsy was not implemented in clinical practice and no prior researchon the existence, quantification and standardization of transcripts of CGβ has been performedin blastocysts.MethodologyThe methodology for trophectoderm cell biopsy from blastocysts was developed and optimizedprimary to be a safe technique for the embryo and secondary to ensure biopsy of a sufficientnumber of cells, in order to allow the application of multiple molecular analyses. The blastocystbiopsy method involved three steps: A., opening of a hole in the zona pellucida using lowfrequency laser, B., blastocyst culture to allow trophectoderm cells to herniate from the holeand C., trophectoderm cell dissection of the blastocyst mass by laser ablation.The methodology for the investigation of CGβ gene expression in blastocysts, included RNAisolation, cDNA synthesis, amplification and quantification of CGβ transcripts. Because CGβ isencoded by a cluster of homologous genes (CGβ1, CGβ2, CGβ3, CGβ5, CGβ7, CGβ8),methodology was designed considering the homology between them into groups (A: CGβ1,CGβ2 and B: CGβ3, CGβ5, CGβ7, CGβ8). For group A, real time polymerase chain reaction (RealTime PCR, RT-PCR) was applied and then transcripts were identified using restriction enzymedigestion. For group B, nested polymerase chain reaction (Nested-PCR) was used incombination with polymerase chain reaction temperature decreasing hybridization (Touch-downPCR). Following amplification, the products were sequenced (DNA sequencing) for theiridentification.ResultsThe biopsy technique did not appear to impact on the blastocyst’s ability to reform a blastocoelecavity and continue to grow and hatch from the zona pellucida, as it was shown followingfurther in vitro culture. No blastocyst showed signs of morphological damage at the lightmicroscopic level. Blastocyst biopsy was applied in clinical practice in two steps: A., 49 couples undergoing IVF had a biopsy in 153 blastocysts. The implantation rate per blastocysttransferred was 34.3% and lead to 23 full-term pregnancies (46.9%) with 37 babies born. B.,24 couples undergoing IVF for PGD of monogenic diseases had biopsy in 144 blastocysts. Thediagnosis success rate was 93%, the implantation rate per blastocyst transferred was 40% andlead to 11 full-term pregnancies (50%) with 15 term newborns. Then, a randomized pilot studywas conducted with the aim to evaluate and compare the diagnosis and implantation successrates between patients undergoing blastomere biopsy and blastocyst transfer and those havingtrophectoderm biopsy and blastocyst transfer for the diagnosis of monogenic diseases. Theresults showed that the diagnosis success rate was superior in the blastocyst biopsy group,while implantation and pregnancy rates were not statistically significant between the twogroups.For the study of CGβ expression profiles 45 blastocysts were donated to research, of which 39generated trophectoderm cells cDNA libraries. RT-PCR revealed the presence of CGB3, CGB5,CGB7, CGB8 transcripts in 5 blastocysts. The transcripts CGB5, CGB7, CGB8 were expressed inone hatched and one hatching blastocysts (fair morphology on day 7 post insemination) and thetranscript CGβ3 was expressed in three hatched blastocysts (excellent morphology on day 5/6post insemination). The transcript CGβ1 was identified in one only blastocyst. Four blastocystswere biopsied in order to investigate whether CGβ expression can be detected at the minimallevel of few trophectoderm cells. No transcript was found in trophectoderm cell samples orbiopsied blastocyst proper.DiscussionIn recent years, many new technologies have been introduced in clinical practice of ART.Blastocyst biopsy since its first announcement in 2005, until today, has been adopted andintegrated into the application of preimplantation genetic diagnosis (Kokkali et al., 2005). Asblastocyst biopsy has the advantage of providing adequate number of cells for multipleanalyses, it has been lately used for the PGD for monogenic diseases in combination withhistocompatibility screening (HLA matching) or PGD for monogenic diseases screening forstructural or numerical chromosomal abnormalities. Besides its clinical application, blastocystbiopsy offers great opportunities for research, such as the study for the expression ofpreimplantation genetic profiles for the identification of the single most viable blastocyst amongthe cohort developing in vitro that will enable single blastocyst transfers without a concomitantreduction in pregnancy rates.In this study, we investigated whether the β HCG may be used as a predictive marker ofdevelopmental competence for human embryos. This study showed that CGβ gene expressionwas diverse and heterogeneous between blastocysts. Further studies need to be accomplishedto investigate this further.ConclusionsBlastocyst biopsy was developed and optimized to serve as powerful tool for diagnostics ofhuman diseases or to identify diagnostic markers of competence to develop to term for humanembryos.


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