| Title |
A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts
|
|---|---|
| Published in |
Oncotarget, September 2016
|
| DOI | 10.18632/oncotarget.11809 |
| Pubmed ID | |
| Authors |
Malachia Hoover, Yvess Adamian, Mark Brown, Ali Maawy, Alexander Chang, Jacqueline Lee, Armen Gharibi, Matthew H. Katz, Jason Fleming, Robert M. Hoffman, Michael Bouvet, Robert Doebler, Jonathan A. Kelber |
| Abstract |
Next-generation sequencing (NGS) can identify and validate new biomarkers of cancer onset, progression and therapy resistance. Substantial archives of formalin-fixed, paraffin-embedded (FFPE) cancer samples from patients represent a rich resource for linking molecular signatures to clinical data. However, performing NGS on FFPE samples is limited by poor RNA purification methods. To address this hurdle, we developed an improved methodology for extracting high-quality RNA from FFPE samples. By briefly integrating a newly-designed micro-homogenizing (mH) tool with commercially available FFPE RNA extraction protocols, RNA recovery is increased by approximately 3-fold while maintaining standard A260/A280 ratios and RNA quality index (RQI) values. Furthermore, we demonstrate that the mH-purified FFPE RNAs are longer and of higher integrity. Previous studies have suggested that pancreatic ductal adenocarcinoma (PDAC) gene expression signatures vary significantly under in vitro versus in vivo and in vivo subcutaneous versus orthotopic conditions. By using our improved mH-based method, we were able to preserve established expression patterns of KRas-dependency genes within these three unique microenvironments. Finally, expression analysis of novel biomarkers in KRas mutant PDAC samples revealed that PEAK1 decreases and MST1R increases by over 100-fold in orthotopic versus subcutaneous microenvironments. Interestingly, however, only PEAK1 levels remain elevated in orthotopically grown KRas wild-type PDAC cells. These results demonstrate the critical nature of the orthotopic tumor microenvironment when evaluating the clinical relevance of new biomarkers in cells or patient-derived samples. Furthermore, this new mH-based FFPE RNA extraction method has the potential to enhance and expand future FFPE-RNA-NGS cancer biomarker studies. |
X Demographics
The data shown below were collected from the profiles of 13 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Italy | 3 | 23% |
| United States | 3 | 23% |
| Mexico | 2 | 15% |
| Unknown | 5 | 38% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 10 | 77% |
| Practitioners (doctors, other healthcare professionals) | 1 | 8% |
| Science communicators (journalists, bloggers, editors) | 1 | 8% |
| Scientists | 1 | 8% |
Mendeley readers
The data shown below were compiled from readership statistics for 48 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Denmark | 1 | 2% |
| Unknown | 47 | 98% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 9 | 19% |
| Student > Master | 8 | 17% |
| Student > Ph. D. Student | 8 | 17% |
| Student > Bachelor | 4 | 8% |
| Student > Postgraduate | 3 | 6% |
| Other | 8 | 17% |
| Unknown | 8 | 17% |
| Readers by discipline | Count | As % |
|---|---|---|
| Medicine and Dentistry | 9 | 19% |
| Agricultural and Biological Sciences | 8 | 17% |
| Biochemistry, Genetics and Molecular Biology | 7 | 15% |
| Engineering | 2 | 4% |
| Chemistry | 2 | 4% |
| Other | 6 | 13% |
| Unknown | 14 | 29% |
Attention Score in Context
This research output has an Altmetric Attention Score of 11. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 24 May 2019.
All research outputs
#2,873,525
of 22,901,818 outputs
Outputs from Oncotarget
#1,167
of 14,331 outputs
Outputs of similar age
#51,412
of 337,441 outputs
Outputs of similar age from Oncotarget
#69
of 1,214 outputs
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