Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer
Joint Authors
Source
Issue
Vol. 2019, Issue 2019 (31 Dec. 2019), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2019-03-17
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
The dysfunction of the DNA mismatch repair system results in microsatellite instability (MSI).
MSI plays a central role in the development of multiple human cancers.
In colon cancer, despite being associated with resistance to 5-fluorouracil treatment, MSI is a favourable prognostic marker.
In gastric and endometrial cancers, its prognostic value is not so well established.
Nevertheless, recognising the MSI tumours may be important for predicting the therapeutic effect of immune checkpoint inhibitors.
Several gene expression signatures were trained on microarray data sets to understand the regulatory mechanisms underlying microsatellite instability in colorectal cancer.
A wealth of expression data already exists in the form of microarray data sets.
However, the RNA-seq has become a routine for transcriptome analysis.
A new MSI gene expression signature presented here is the first to be valid across two different platforms, microarrays and RNA-seq.
In the case of colon cancer, its estimated performance was (i) AUC = 0.94, 95% CI = (0.90 – 0.97) on RNA-seq and (ii) AUC = 0.95, 95% CI = (0.92 – 0.97) on microarray.
The 25-gene expression signature was also validated in two independent microarray colon cancer data sets.
Despite being derived from colorectal cancer, the signature maintained good performance on RNA-seq and microarray gastric cancer data sets (AUC = 0.90, 95% CI = (0.85 – 0.94) and AUC = 0.83, 95% CI = (0.69 – 0.97), respectively).
Furthermore, this classifier retained high concordance even when classifying RNA-seq endometrial cancers (AUC = 0.71, 95% CI = (0.62 – 0.81).
These results indicate that the new signature was able to remove the platform-specific differences while preserving the underlying biological differences between MSI/MSS phenotypes in colon cancer samples.
American Psychological Association (APA)
Pačínková, Anna& Popovici, Vlad. 2019. Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer. BioMed Research International،Vol. 2019, no. 2019, pp.1-9.
https://search.emarefa.net/detail/BIM-1126923
Modern Language Association (MLA)
Pačínková, Anna& Popovici, Vlad. Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer. BioMed Research International No. 2019 (2019), pp.1-9.
https://search.emarefa.net/detail/BIM-1126923
American Medical Association (AMA)
Pačínková, Anna& Popovici, Vlad. Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer. BioMed Research International. 2019. Vol. 2019, no. 2019, pp.1-9.
https://search.emarefa.net/detail/BIM-1126923
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1126923