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

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.

2015 ◽  
Vol 407 (23) ◽  
pp. 6965-6973 ◽  
Author(s):  
Rachel M. Eaton ◽  
Jamie A. Shallcross ◽  
Liora E. Mael ◽  
Kepler S. Mears ◽  
Lisa Minkoff ◽  
...  

2014 ◽  
Vol 42 (22) ◽  
pp. e169-e169 ◽  
Author(s):  
Inmaculada Rentero Rebollo ◽  
Michal Sabisz ◽  
Vanessa Baeriswyl ◽  
Christian Heinis

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3114-3114
Author(s):  
Wen-Kai Weng ◽  
Randy Armstrong ◽  
Sally Arai ◽  
Katherine Sutherland ◽  
Richard T. Hoppe ◽  
...  

Abstract Abstract 3114 Mycosis fungoides (MF) is a mature T-cell lymphoma arising primarily from the skin. Patients with advanced stage disease either with skin tumor lesions or its leukemic form, Sezary syndrome (SS), consistently require therapy for disease control and symptom relief. Currently, there is no curative therapy and none of the available therapies provides a long-term remission. We have performed non-myeloablative allogeneic transplant in 11 MF/SS patients using total skin electron beam therapy (TSEBT), total lymphoid irradiation (TLI) and anti-thymocyte globulin (ATG) preparative regimen in an attempt to provide prolonged disease control. The median age was 63 years (range 20–73). All but one patient had stage IV disease at the time of preparative regimen. The median number of prior systemic therapies was 5 (range 2–8). Eight patients achieved complete response after transplant and 3 patients had partial response (ORR 100%). However, 4 patients experienced disease progression post transplant, requiring additional therapy. Patients tolerated the transplant extremely well. Only one patient developed grade 2 acute GVHD (skin), and another patient developed extensive chronic GVHD (skin, oral, GI). All patients were alive at the last evaluation (median follow-up, 10.6 months). The current method for monitoring residual disease in MF/SS uses flow cytometry to detect circulating Sezary cells and pathological evaluation of skin biopsy samples. However, there are no MF/SS specific tumor markers that can easily and consistently differentiate malignant clones from normal T cells and these standard diagnostic tools lack sensitivity in detecting minimal residual disease (MRD). Here, we tested whether high-throughput sequencing of T cell receptor (TCR) provides a new tool for monitoring MRD after allogeneic transplant. Genomic DNA was extracted from either peripheral blood mononuclear cells or selected skin biopsy samples. The rearranged VDJ of TCR ß was amplified using V ß-specific forward and J ß-specific reverse primers. The Illumina GA2 system generated up to 1, 000, 000 reads of 54 base pairs, covering the entire CDR3 lengths. Raw sequence data were processed to remove PCR/sequencing errors, and a nearest neighbor algorithm was used to collapse the data into unique sequences (Blood 2009, 114 :4099). Of blood samples from six SS patients, malignant clone was identified in all 6 cases by a dominant unique TCR ß CDR3 sequence. At the time of preparative regimen, 3 patients had measurable circulating Sezary cells by standard flow cytometry and pathological evaluation of peripheral blood smear. TCR ß sequencing data showed that malignant clones contributed to 69%, 81% and 68% of circulating T cells in these 3 patients, respectively. The other 3 patients did not have detectable circulating Sezary cells by standard diagnostic tools. However, 8.47%, 0.38% and 0.22% of the TCR ß sequences were from the malignant clones in these 3 cases at the time of preparative regimen. The percentage of malignant T cell clones decreased in all cases immediately after transplant. Three patients eventually achieved molecular remission. Two of them cleared the malignant clone at day+30 and the third cleared the MRD at day+270. The follow-up is still short to determine whether achieving molecular remission correlate with better clinical outcome. We have also started to perform TCR ß sequencing of skin biopsy samples to assess the MRD status in the skin of MF patients. In addition to providing highly sensitive and specific MRD quantification, deep sequencing of TCR also revealed vital information on the T cell repertoire reconstitution after allogeneic transplant. Based on our preliminary data, adaptive transfer of donor TCR repertoire clearly occurred immediately after allogeneic transplant and the TCR diversification slowly appeared months later. In summary, we have shown a safe and effective unique preparatory regimen for non-myeloablative allogeneic transplant in patients with advanced stage MF and SS. We also demonstrated the utility of high throughput sequencing of CDR3 of TCR ß in assessing MRD status after therapy with utmost sensitivity and specificity, and for the first time, showed a therapy resulting in molecular remission in this patient population. Disclosures: No relevant conflicts of interest to declare.


2021 ◽  
Vol 22 (17) ◽  
pp. 9202
Author(s):  
Alissa Drees ◽  
Markus Fischer

Aptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. ‘High-throughput sequencing fluorescent ligand interaction profiling’ (HiTS–FLIP) significantly increases the selection efficiency and is consequently a very powerful and versatile technology for the selection of high-performance aptamers. It is the first experiment to allow the direct and quantitative measurement of the affinity and specificity of millions of aptamers simultaneously by harnessing the potential of optical next-generation sequencing platforms to perform fluorescence-based binding assays on the clusters displayed on the flow cells and determining their sequence and position in regular high-throughput sequencing. Many variants of the experiment have been developed that allow automation and in situ conversion of DNA clusters into base-modified DNA, RNA, peptides, and even proteins. In addition, the information from mutational assays, performed with HiTS–FLIP, provides deep insights into the relationship between the sequence, structure, and function of aptamers. This enables a detailed understanding of the sequence-specific rules that determine affinity, and thus, supports the evolution of aptamers. Current variants of the HiTS–FLIP experiment and its application in the field of aptamer selection, characterisation, and optimisation are presented in this review.


2016 ◽  
Vol 18 (6) ◽  
pp. 302-313 ◽  
Author(s):  
Stefania Valenzano ◽  
Annalisa De Girolamo ◽  
Maria C. DeRosa ◽  
Maureen McKeague ◽  
Roberto Schena ◽  
...  

2013 ◽  
Vol 231 (4) ◽  
pp. 433-440 ◽  
Author(s):  
Ryan O Emerson ◽  
Anna M Sherwood ◽  
Mark J Rieder ◽  
Jamie Guenthoer ◽  
David W Williamson ◽  
...  

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