scholarly journals MicroRNA profiling of plasma exosomes from patients with ovarian cancer using high‑throughput sequencing

2019 ◽  
Author(s):  
Honghong Zhang ◽  
Sijuan Xu ◽  
Xiaoli Liu
Keyword(s):  
Ovarian Cancer ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Microrna Profiling

scholarly journals High-throughput sequencing of T-cell receptors reveals a homogeneous repertoire of tumour-infiltrating lymphocytes in ovarian cancer

2013 ◽  
Vol 231 (4) ◽  
pp. 433-440 ◽  
Author(s):  
Ryan O Emerson ◽  
Anna M Sherwood ◽  
Mark J Rieder ◽  
Jamie Guenthoer ◽  
David W Williamson ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
T Cell ◽  
High Throughput ◽  
T Cell Receptors ◽  
High Throughput Sequencing ◽  
Cell Receptors ◽  
Tumour Infiltrating Lymphocytes ◽  
Infiltrating Lymphocytes

scholarly journals Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Delia J. Scoville ◽  
Tae Kyu Brian Uhm ◽  
Jamie A. Shallcross ◽  
Rebecca J. Whelan
Keyword(s):  
Ovarian Cancer ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Selection Process ◽  
Response To Therapy ◽  
Diagnostic Tools ◽  
Dna Aptamers ◽  
One Pot ◽  
Protein Target ◽  
Target Binding

CA125 is a mucin glycoprotein whose concentration in serum correlates with a woman’s risk of developing ovarian cancer and also indicates response to therapy in diagnosed patients. Accurate detection of this large, complex protein in patient samples is of great clinical relevance. We suggest that powerful new diagnostic tools may be enabled by the development of nucleic acid aptamers with affinity for CA125. Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides. This data-rich approach, combined with bioinformatics tools, enabled the entire selection process to be characterized. Using fluorescence anisotropy and affinity probe capillary electrophoresis, the binding affinities of four aptamer candidates were evaluated. Two aptamers, CA125_1 and CA125_12, both without primers, were found to bind to clinically relevant concentrations of the protein target. Binding was differently influenced by the presence of Mg2+ions, being required for binding of CA125_1 and abrogating binding of CA125_12. In conclusion, One-Pot SELEX was found to be a promising selection method that yielded DNA aptamers to a clinically important protein target.

scholarly journals Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing

2015 ◽  
Vol 407 (23) ◽  
pp. 6965-6973 ◽  
Author(s):  
Rachel M. Eaton ◽  
Jamie A. Shallcross ◽  
Liora E. Mael ◽  
Kepler S. Mears ◽  
Lisa Minkoff ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Cancer Biomarker ◽  
Dna Aptamers ◽  
Selection Of

scholarly journals Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM

2016 ◽  
Vol 113 (9) ◽  
pp. 2544-2549 ◽  
Author(s):  
Alan S. L. Wong ◽  
Gigi C. G. Choi ◽  
Cheryl H. Cui ◽  
Gabriela Pregernig ◽  
Pamela Milani ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Drug Combinations ◽  
Human Cells ◽  
Ovarian Cancer Cells ◽  
Specific Gene ◽  
Cancer Cell Growth ◽  
Guide Rna ◽  
Systematic Identification

The orchestrated action of genes controls complex biological phenotypes, yet the systematic discovery of gene and drug combinations that modulate these phenotypes in human cells is labor intensive and challenging to scale. Here, we created a platform for the massively parallel screening of barcoded combinatorial gene perturbations in human cells and translated these hits into effective drug combinations. This technology leverages the simplicity of the CRISPR-Cas9 system for multiplexed targeting of specific genomic loci and the versatility of combinatorial genetics en masse (CombiGEM) to rapidly assemble barcoded combinatorial genetic libraries that can be tracked with high-throughput sequencing. We applied CombiGEM-CRISPR to create a library of 23,409 barcoded dual guide-RNA (gRNA) combinations and then perform a high-throughput pooled screen to identify gene pairs that inhibited ovarian cancer cell growth when they were targeted. We validated the growth-inhibiting effects of specific gene sets, including epigenetic regulators KDM4C/BRD4 and KDM6B/BRD4, via individual assays with CRISPR-Cas–based knockouts and RNA-interference–based knockdowns. We also tested small-molecule drug pairs directed against our pairwise hits and showed that they exerted synergistic antiproliferative effects against ovarian cancer cells. We envision that the CombiGEM-CRISPR platform will be applicable to a broad range of biological settings and will accelerate the systematic identification of genetic combinations and their translation into novel drug combinations that modulate complex human disease phenotypes.

scholarly journals N2-neutrophils Promote Invasion and Metastasis of Ovarian Cancer by Upregulating MAPK Signaling

2020 ◽  
Author(s):  
caixia li ◽  
Chuandi Men ◽  
Weihong Yang ◽  
Qi Liu ◽  
Shupeng Liu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Molecular Biology ◽  
Signaling Pathway ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Invasion And Metastasis ◽  
Relationship Of ◽  
The Relationship

Abstract Background: Metastasis is an important factor of high mortality in ovarian cancer. Neutrophils are involved in multiple pathologic mechanisms of cancer,including invasion and metastasis. However, the relationship of neutrophils and invasion and metastasis in ovarian cancer is unclear,as well as the exact mechanism.Methods:To verify the relationship of neutrophils and invasion and metastasis in ovarian cancer,we tested the expression of CD11b in 24 groups of benign and malignant ovarian tumor tissues.And then,we tested the expression of CD11b,CXCL8,and CXCR1 in 16 cases of ovarian cancer,including primary lesions, metastatic lesions and adjacent carcinoma tissues.We successfully build tumor associated neutrophils research model (N1 and N2) and prove that N2-neutrophils can promote the invasion and metastasis of ovarian cancer. Next,we screened the significantly changed MAPK signaling pathway by high-throughput sequencing. And then confirmed this conclusion by molecular biology experiments. Results:The expression of CD11b was significantly higher in malignant tumor than benign tumor tissues tested by western blot and Immunohistochemistry.The expression of CD11b,CXCL8 and CXCR1 is highest in ovarian cancermetastases ,followed by the primary lessions, and then the adjacent carcinoma tissues tested by PCR and WB methods.We proved that N2-neutrophils can promote the invasion and metastasis of ovarian cancer by transwell assay.Forthermore,we detected the related indicators of metastasis including MMP-2,MMP-9,E-Cadherin,N-cadherin and Vimentin by PCR and WB methods.Next,we screened the significantly changed MAPK signaling pathway by High-throughput sequencing through comparing ovarian cancer cells before and after co-cultured with N2-neutrophils. At last,we found the key gene P38 of MAPK signaling pathway by molecular biology experiments. Conclusions: N2-neutrophils promote the invasion and metastasis of ovarian cancer by Upregulating MAPK signaling pathway, find a key gene P38.

scholarly journals mirTools: microRNA profiling and discovery based on high-throughput sequencing

2010 ◽  
Vol 38 (suppl_2) ◽  
pp. W392-W397 ◽  
Author(s):  
Erle Zhu ◽  
Fangqing Zhao ◽  
Gang Xu ◽  
Huabin Hou ◽  
LingLin Zhou ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Microrna Profiling
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