scholarly journals LncRNA LEF1-AS1 promotes metastasis of prostatic carcinoma via the Wnt/β-catenin pathway

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Weiyuan Li ◽  
Ganggang Yang ◽  
Dengke Yang ◽  
Dong Li ◽  
Qian Sun
Keyword(s):  
Next Generation Sequencing ◽  
Rna Binding ◽  
Next Generation ◽  
Next Generation Sequencing Technology ◽  
Normal Tissues ◽  
Factor C ◽  
Generation Sequencing

Abstract Background Long noncoding RNAs (lncRNAs) are important functional regulators of many biological processes of cancers. However, the mechanisms by which lncRNAs modulate androgen-independent prostate cancer (AIPC) development remain largely unknown. Methods Next-generation sequencing technology and RT-qPCR were used to assess LEF1-AS1 expression level in AIPC tissues and adjacent normal tissues. Functional in vitro experiments, including colony formation, EDU and transwell assays were performed to assess the role of LEF1-AS1 in AIPC. Xenograft assays were conducted to assess the effect of LEF1-AS1 on cell proliferation in vivo. Chromatin immunoprecipitation (ChIP) and RNA binding protein immunoprecipitation (RIP) assays were performed to elucidate the regulatory network of LEF1-AS1. Results The next-generation sequencing results showed that LEF1-AS1 is significantly overexpressed in AIPC. Furthermore, our RT-qPCR assay data showed that LEF1-AS1 is overexpressed in AIPC tissues. Functional experiments showed that LEF1-AS1 promotes the proliferation, migration, invasion and angiogenic ability of AIPC cells in vitro and tumour growth in vivo by recruiting the transcription factor C-myb to the promoter of FZD2, inducing its transcription. Furthermore, LEF1-AS1 was shown to function as a competing endogenous RNA (ceRNA) that sponges miR-328 to activate CD44. Conclusion In summary, the results of our present study revealed that LEF1-AS1 acts as a tumour promoter in the progression of AIPC. Furthermore, the results revealed that LEF1-AS1 functions as a ceRNA and regulates Wnt/β-catenin pathway activity via FZD2 and CD44. Our results provide new insights into the mechanism that links the function of LEF1-AS1 with AIPC and suggests that LEF1-AS1 may serve as a novel potential target for the improvement of AIPC therapy.

scholarly journals LncRNA LEF1-AS1 promotes metastasis of prostatic carcinoma via the Wnt/β-catenin pathway

2020 ◽  
Author(s):  
Weiyuan Li ◽  
Ganggang Yang ◽  
Dengke Yang ◽  
Dong Li ◽  
Qian Sun
Keyword(s):  
Next Generation Sequencing ◽  
Rna Binding ◽  
Next Generation ◽  
Next Generation Sequencing Technology ◽  
Normal Tissues ◽  
Factor C ◽  
Generation Sequencing

Abstract Background: Long noncoding RNAs (lncRNAs) are important functional regulators of many biological processes of cancers. However, the mechanisms by which lncRNAs modulate androgen-independent prostate cancer (AIPC) development remain largely unknown.Methods: Next-generation sequencing technology and RT-qPCR were used to assess LEF1-AS1 expression level in AIPC tissues and adjacent normal tissues. Functional in vitro experiments, including colony formation, EDU and transwell assays were performed to assess the role of LEF1-AS1 in AIPC. Xenograft assays were conducted to assess the effect of LEF1-AS1 on cell proliferation in vivo. Chromatin immunoprecipitation (ChIP) and RNA binding protein immunoprecipitation (RIP) assays were performed to elucidate the regulatory network of LEF1-AS1.Results: The next-generation sequencing results showed that LEF1-AS1 is significantly overexpressed in AIPC. Furthermore, our RT-qPCR assay data showed that LEF1-AS1 is overexpressed in AIPC tissues. Functional experiments showed that LEF1-AS1 promotes the proliferation, migration, invasion and angiogenic ability of AIPC cells in vitro and tumour growth in vivo by recruiting the transcription factor C-myb to the promoter of FZD2, inducing its transcription. Furthermore, LEF1-AS1 was shown to function as a competing endogenous RNA (ceRNA) that sponges miR-328 to activate CD44.Conclusion: In summary, the results of our present study revealed that LEF1-AS1 acts as a tumour promoter in the progression of AIPC. Furthermore, the results revealed that LEF1-AS1 functions as a ceRNA and regulates Wnt/β-catenin pathway activity via FZD2 and CD44. Our results provide new insights into the mechanism that links the function of LEF1-AS1 with AIPC and suggests that LEF1-AS1 may serve as a novel potential target for the improvement of AIPC therapy.

scholarly journals LncRNA LEF1-AS1 promotes metastasis of prostatic carcinoma via the Wnt/β-catenin pathway

2020 ◽  
Author(s):  
Weiyuan Li ◽  
Ganggang Yang ◽  
Dengke Yang ◽  
Dong Li ◽  
Qian Sun
Keyword(s):  
Cell Proliferation ◽  
Migration And Invasion ◽  
Biological Processes ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Normal Tissues ◽  
Factor C ◽  
Generation Sequencing

Abstract Background Long noncoding RNAs (lncRNAs), which are important functional regulators in cancer, have emerged as critical molecular regulators in various biological processes. However, the mechanisms by which LEF1-AS1 modulates Androgen-Independent Prostate Cancer (AIPC) development remain largely unknown. Methods The LEF1-AS1 expression level was detected in tumour tissues and adjacent normal tissues of AIPC patients by using next-generation sequencing technology and qRT-PCR. Cell proliferation, migration and invasion were assessed by colony formation, EDU assays and transwell assays, respectively. Xenograft assay was conducted to determine the effect of LEF1-AS1 on cell proliferation in vivo. Results LEF1-AS1 promoted the proliferation, migration, invasion and angiogenic ability of AIPC cells in vitro and in vivo. In this mechanism, LEF1-AS1 recruited the transcription factor C-myb to the promoter region of FZD2, which activated FZD2 transcription. Moreover, LEF1-AS1 functioned as a competing endogenous RNA (ceRNA) acting as a sponge for miR-328, which activated CD44. Conclusion Collectively, these data indicate that LEF1-AS1 is a tumour promoter in the development of AIPC and that it may contribute to the improvement of AIPC diagnosis and therapy.

scholarly journals LncRNA LEF1-AS1 promotes metastasis of prostatic carcinoma via the Wnt/β-catenin pathway

2020 ◽  
Author(s):  
Weiyuan Li ◽  
Ganggang Yang ◽  
Dengke Yang ◽  
Dong Li ◽  
Qian Sun
Keyword(s):  
Cell Proliferation ◽  
Migration And Invasion ◽  
Biological Processes ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Normal Tissues ◽  
Factor C ◽  
Generation Sequencing

Abstract Background: Long noncoding RNAs (lncRNAs), which are important functional regulators in cancer, have emerged as critical molecular regulators in various biological processes. However, the mechanisms by which LEF1-AS1 modulates Androgen-Independent Prostate Cancer (AIPC) development remain largely unknown.Methods: The LEF1-AS1 expression level was detected in tumour tissues and adjacent normal tissues of AIPC patients by using next-generation sequencing technology and qRT-PCR. Cell proliferation, migration and invasion were assessed by colony formation, EDU assays and transwell assays, respectively. Xenograft assay was conducted to determine the effect of LEF1-AS1 on cell proliferation in vivo.Results: LEF1-AS1 promoted the proliferation, migration, invasion and angiogenic ability of AIPC cells in vitro and in vivo. In this mechanism, LEF1-AS1 recruited the transcription factor C-myb to the promoter region of FZD2, which activated FZD2 transcription. Moreover, LEF1-AS1 functioned as a competing endogenous RNA (ceRNA) acting as a sponge for miR-328, which activated CD44.Conclusion: Collectively, these data indicate that LEF1-AS1 is a tumour promoter in the development of AIPC and that it may contribute to the improvement of AIPC diagnosis and therapy.

scholarly journals LncRNA LEF1-AS1 Promotes Metastasis of Prostatic Carcinoma via the Wnt/β-Catenin Pathway

2020 ◽  
Author(s):  
Weiyuan Li ◽  
Ganggang Yang ◽  
Dengke Yang ◽  
Dong Li ◽  
Qian Sun
Keyword(s):  
Cell Proliferation ◽  
Migration And Invasion ◽  
Biological Processes ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Normal Tissues ◽  
Factor C ◽  
Generation Sequencing

Abstract Background: Long noncoding RNAs (lncRNAs), which are important functional regulators in cancer, have emerged as critical molecular regulators in various biological processes. However, the mechanisms by which LEF1-AS1 modulates Androgen-Independent Prostate Cancer (AIPC) development remain largely unknown.Methods: The LEF1-AS1 expression level was detected in tumour tissues and adjacent normal tissues of AIPC patients by using next-generation sequencing technology and qRT-PCR. Cell proliferation, migration and invasion were assessed by colony formation, EDU assays and transwell assays, respectively. Xenograft assay was conducted to determine the effect of LEF1-AS1 on cell proliferation in vivo.Results: LEF1-AS1 promoted the proliferation, migration, invasion and angiogenic ability of AIPC cells in vitro and in vivo. In this mechanism, LEF1-AS1 recruited the transcription factor C-myb to the promoter region of FZD2, which activated FZD2 transcription. Moreover, LEF1-AS1 functioned as a competing endogenous RNA (ceRNA) acting as a sponge for miR-328, which activated CD44.Conclusion: Collectively, these data indicate that LEF1-AS1 is a tumour promoter in the development of AIPC and that it may contribute to the improvement of AIPC diagnosis and therapy.

Multicenter validation study for the certification of a CFTR gene scanning method using next generation sequencing technology

2018 ◽  
Vol 56 (7) ◽  
pp. 1046-1053 ◽  
Author(s):  
Anne Bergougnoux ◽  
Valeria D’Argenio ◽  
Stefanie Sollfrank ◽  
Fanny Verneau ◽  
Antonella Telese ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Genetic Analysis ◽  
Analytical Sensitivity ◽  
Next Generation ◽  
Sequencing Data ◽  
Scanning Method ◽  
Next Generation Sequencing Technology ◽  
Wide Range ◽  
Generation Sequencing

Abstract Background: Many European laboratories offer molecular genetic analysis of the CFTR gene using a wide range of methods to identify mutations causative of cystic fibrosis (CF) and CFTR-related disorders (CFTR-RDs). Next-generation sequencing (NGS) strategies are widely used in diagnostic practice, and CE marking is now required for most in vitro diagnostic (IVD) tests in Europe. The aim of this multicenter study, which involved three European laboratories specialized in CF molecular analysis, was to evaluate the performance of Multiplicom’s CFTR MASTR Dx kit to obtain CE-IVD certification. Methods: A total of 164 samples, previously analyzed with well-established “reference” methods for the molecular diagnosis of the CFTR gene, were selected and re-sequenced using the Illumina MiSeq benchtop NGS platform. Sequencing data were analyzed using two different bioinformatic pipelines. Annotated variants were then compared to the previously obtained reference data. Results and conclusions: The analytical sensitivity, specificity and accuracy rates of the Multiplicom CFTR MASTR assay exceeded 99%. Because different types of CFTR mutations can be detected in a single workflow, the CFTR MASTR assay simplifies the overall process and is consequently well suited for routine diagnostics.

scholarly journals Next-Generation Sequencing in a Direct Model of HIV Infection Reveals Important Parallels to and Differences from In Vivo Reservoir Dynamics

2020 ◽  
Vol 94 (9) ◽  
Author(s):  
Marilia Rita Pinzone ◽  
Maria Paola Bertuccio ◽  
D. Jake VanBelzen ◽  
Ryan Zurakowski ◽  
Una O’Doherty
Keyword(s):  
T Cells ◽  
Next Generation Sequencing ◽  
Cd4 T Cells ◽  
Next Generation ◽  
Activated T Cells ◽  
Selection Pressures ◽  
Hiv Dna ◽  
Generation Sequencing

ABSTRACT Next-generation sequencing (NGS) represents a powerful tool to unravel the genetic make-up of the HIV reservoir, but limited data exist on its use in vitro. Moreover, most NGS studies do not separate integrated from unintegrated DNA, even though selection pressures on these two forms should be distinct. We reasoned we could use NGS to compare the infection of resting and activated CD4 T cells in vitro to address how the metabolic state affects reservoir formation and dynamics. To address these questions, we obtained HIV sequences 2, 4, and 8 days after NL4-3 infection of metabolically activated and quiescent CD4 T cells (cultured with 2 ng/ml interleukin-7). We compared the composition of integrated and total HIV DNA by isolating integrated HIV DNA using pulsed-field electrophoresis before performing sequencing. After a single-round infection, the majority of integrated HIV DNA was intact in both resting and activated T cells. The decay of integrated intact proviruses was rapid and similar in both quiescent and activated T cells. Defective forms accumulated relative to intact ones analogously to what is observed in vivo. Massively deleted viral sequences formed more frequently in resting cells, likely due to lower deoxynucleoside triphosphate (dNTP) levels and the presence of multiple restriction factors. To our surprise, the majority of these deleted sequences did not integrate into the human genome. The use of NGS to study reservoir dynamics in vitro provides a model that recapitulates important aspects of reservoir dynamics. Moreover, separating integrated from unintegrated HIV DNA is important in some clinical settings to properly study selection pressures. IMPORTANCE The major implication of our work is that the decay of intact proviruses in vitro is extremely rapid, perhaps as a result of enhanced expression. Gaining a better understanding of why intact proviruses decay faster in vitro might help the field identify strategies to purge the reservoir in vivo. When used wisely, in vitro models are a powerful tool to study the selective pressures shaping the viral landscape. Our finding that massively deleted sequences rarely succeed in integrating has several ramifications. It demonstrates that the total HIV DNA can differ substantially in character from the integrated HIV DNA under certain circumstances. The presence of unintegrated HIV DNA has the potential to obscure selection pressures and confound the interpretation of clinical studies, especially in the case of trials involving treatment interruptions.

Genome study of PDGFRA D842V mutant GIST using next generation sequencing approach.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 10540-10540
Author(s):  
Maria A. Pantaleo ◽  
Annalisa Astolfi ◽  
Milena Urbini ◽  
Valentina Indio ◽  
Margherita Nannini ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Tyrosine Kinases ◽  
Therapeutic Targets ◽  
Mapk Signaling ◽  
Gastric Gist ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Generation Sequencing

10540 Background: Mutations of the receptors KIT and PDGFRA in GIST are the oncogenetic events of disease as well as the targets of molecular therapies. Within the PDGFRA mutations, the D842V mutation in exon 18 confers in vitro and in vivo resistance to imatinib. Next generation sequencing techniques may completely dissect all the possible somatic mutations and genomic rearrangements in order to identify novel therapeutic targets in this patients population. Methods: Five patients with gastric GIST were analyased (3 M, 2 F; mean age 65,5 years, range 51-77). The tumor dimension ranged between 3 and 15 cm, MI < 2 and 8 /50 HPF. No metastases were present in all cases. The KIT and PDGFRA anlysis showed a D842V mutation in exon 18 of PDGFRA in all cases. Whole transcriptome sequencing was performed with Illumina HiScanSQ platform with a paired-end strategy (75x2). After performing quality controls, the short reads were mapped with Tophat-Botie pipeline against the human reference genome (HG19). The variations, such as Single nucleotide variants (SNVs) and InDels, were called by SNVMix2 (a software suited for SNVs discovery in tumor samples) implementing an accurate filtering procedures developed in our laboratory. Two predictors of mutations effect at protein level (SNPs&GO and Provean) were employed in order to prioritize the emerging variation. Results: An average of 206 coding non-synonymous variants were highlighted in the five GIST samples, of which ~ 30% were predicted as deleterious with at least one predictor. In addition to PDGFRA D842V mutation, in all five patients were found mutations on different receptor tyrosine kinases, such as FGFR4 and DDR2. Moreover three out of five patients harboured mutations on members of the MDR/TAP subfamily that are involved in multidrug resistance, in particular on ABCB1, ABCB4 and on ABCB6 genes. Other mutations were found on the hedgehog and MAPK signaling pathway and on SNF/SWI chromatin remodeling complex. Conclusions: New molecular events have been identified in PDGFRA D842V mutant GIST. These data should be validated in larger series and the role of these mutations as therapeutic targets should be further investigated.

scholarly journals Potentially Actionable Targets: Evidence Standards for Credible Next Generation Sequencing Technology Assessment Claims

2017 ◽  
Vol 8 (3) ◽  
pp. 9
Author(s):  
Paul C Langley
Keyword(s):  
Next Generation Sequencing ◽  
Technology Assessment ◽  
Critical Issue ◽  
Evidence Base ◽  
Cost Of Care ◽  
Next Generation ◽  
Next Generation Sequencing Technology ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Despite considerable resources devoted to developing databases to support competitive credible claims for next generation sequencing (NGS) claims, we have yet to meet the standards required in health technology assessment to support such claims. The purpose of this commentary is to consider options open in establishing claims for NGS recommendations. Although NGS platforms offer potential promise in improving clinical outcomes, supporting cost-effectiveness and reducing the overall cost of care in target populations, this has yet to be demonstrated on a scale that is likely to satisfy reimbursers and health care decision makers. Issues addressed include (i) the importance of credible, evaluable and replicable claims from individual NGS platforms; (ii) the difficulties in moving beyond broad-brush claims for improved survival; (iii) the standards required for an NGS evidence base; (iv) protocol designs in establishing the independent contribution of NGS actionable therapy recommendations to outcomes claims; (v) the role of NGS registries; and (vi) protocols to support ongoing credible, evaluable and replicable claims in target patient populations. The critical issue is not analytical and clinical validity but clinical utility. This has yet to be demonstrated.   Type: Commentary

scholarly journals Insertion Specificity of the hATx-6 Transposase of Hydra magnipapillata

2021 ◽  
Vol 8 ◽  
Author(s):  
Paul Riggs ◽  
George Blundell-Hunter ◽  
Joanna Hagelberger ◽  
Guoping Ren ◽  
Laurence Ettwiller ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bioinformatic Analysis ◽  
Next Generation ◽  
Hydra Vulgaris ◽  
Domains Of Life ◽  
Hydra Magnipapillata ◽  
Sequence Bias ◽  
Generation Sequencing

Transposable elements (TE) are mobile genetic elements, present in all domains of life. They commonly encode a single transposase enzyme, that performs the excision and reintegration reactions, and these enzymes have been used in mutagenesis and creation of next-generation sequencing libraries. All transposases have some bias in the DNA sequence they bind to when reintegrating the TE DNA. We sought to identify a transposase that showed minimal sequence bias and could be produced recombinantly, using information from the literature and a novel bioinformatic analysis, resulting in the selection of the hATx-6 transposase from Hydra vulgaris (aka Hydra magnipapillata) for further study. This transposase was tested and shown to be active both in vitro and in vivo, and we were able to demonstrate very low sequence bias in its integration preference. This transposase could be an excellent candidate for use in biotechnology, such as the creation of next-generation sequencing libraries.

scholarly journals Functional validation of genetic variants identified by next generation sequencing in malformations of cortical development

2021 ◽  
Author(s):  
Dalila De Vita
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Variants ◽  
Cortical Development ◽  
Next Generation ◽  
Malformations Of Cortical Development ◽  
Functional Studies ◽  
Generation Sequencing ◽  
In Vitro Treatment

Malformations of cortical development (MCDs) result from a disruption in the process of the human brain cortex formation: currently, there are no pharmacological treatments for diffuse MCDs. Next-generation sequencing has accelerated the identification of MCDs causing genes: in some cases, functional studies are needed to clarify the role of genetic variants. The aim of this PhD project has been to apply a multidisciplinary approach to identify causative mutations in patients with MCDs, validate the pathogenic role of the identified mutations, and assess the effectiveness of novel in vitro treatment for mTOR pathway related MCDs.

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