Process for the identification of patients at risk for OSCC
The present disclosure involves a process to identify a patient likely to have OSCC by taking a sample containing miRNA from epithelial cells from the patient's oral cavity and determining the relative level of expression of miRNA sequences which have different levels of expression in epithelial cell OSCC tissue than in benign tissue. The epithelial cells are those that form the mucosal epithelium that consists mainly of keratinocytes with some immune cells. It involves determining the relative level of expression of at least miRNA sequences hsa-miR-130-3p, hsa-miR-7-5p, hsa-miR-101-3p and hsa-miR-146b-5p. It also involves discriminating between benign oral lesions and OSCC using a sample of epithelial cells of the lesion and determining the relative level of expression of miRNA sequences which have different levels of expression in epithelial cell OSCC tissue than in benign tissue. It uses the relative level of expression of at least miRNA sequences hsa-miR-196a-5p and hsa-miR-873-5p.
1. A process comprising;
a. obtaining a sample taken by brush cytology containing miRNA from essentially epithelial cells from a patient's oral cavity;
b. selecting a plurality of miRNA sequences from a set of miRNA sequences dawn from the human transcriptome that have previously been determined to have levels of expression of one half or less and/or double or more in human epithelial cells afflicted with OSCC compared to those of cells not so afflicted by obtaining samples by brush cytology from two populations of human subjects, one afflicted with OSCC and one not so afflicted; and
c. measuring the levels of expression of the selected plurality of miRNA sequences.
2. The process of claim 1 wherein the levels of expression of a panel of miRNA sequences including at least all of hsa-miR-130-3p, hsa-miR-7-5p, hsa-miR-101-3p and hsa-miR-146b-5p are determined.
3. The process of claim 2 wherein the levels of expression of the miRNA sequences hsa-miR-365a-3p and hsa-miR-21-5p are also determined.
4. The process of claim 3 wherein the levels of expression of the miRNA sequences hsa-miRNA-486-5p, hsa-miR-18b-5p, hsa-miRNA-126-3p, hsa-miR-20b-5p, hsa-miR-100-5p, hsa-miR-19a-3p, hsa-miR-190a and hsa-miRNA-10b-5 are also determined.
5. The process of claim 1 wherein the levels of expression of a panel of miRNA sequences including at least all of hsa-miR-101-3p, has-miR-186-5p, hsa-miR-18a-5p and hsa-miR-423-5p or all of hsa-miR-101-3p, hsa-miR-142-3p and hsa-miR-146b-5p or all of hsa-miR-186-5p, hsa-miR-146b-5p, hsa-miR-101-3p and hsa-miR-142-3p or all of hsa-miR-873-5p are determined.
6. A process to discriminate between benign oral lesions and OSCC comprising;
a. obtaining a sample taken by brush cytology of essentially the epithelial cells of the lesion;
b. selecting a plurality of miRNA sequences from a set of miRNA sequences dawn from the human transcriptome that have previously been determined to have levels of expression of one half or less and/or double or more in human epithelial cells afflicted with OSCC compared to those of cells not so afflicted by obtaining samples by brush cytology from two populations of human subjects, one afflicted with OSCC and one not so afflicted; and
c. measuring the levels of expression of the selected plurality of miRNA sequences.
7. The process of claim 6 wherein the levels of expression of a panel including both of the miRNA sequences hsa-miR-196a-5p and hsa-miR-873-5p are determined.
8. The process of claim 6 wherein the levels of expression of the sample are examined by a classifier developed by applying a statistical tool to the expression levels of a panel of miRNA sequences of samples of normal and OSCC cells.
9. The process of claim 1 wherein the selected plurality comprises at least six miRNA sequences.
10. The process of claim 6 wherein the selected plurality comprises at least six miRNA sequences.
11. The process of claim 1 wherein the set of miRNA sequences is within the 372 miRNA sequences covered by the Exiqon Human panel 1.
12. The process of claim 1 wherein the set of miRNA sequences is drawn from hsa-miRNA sequences 210, 375, 100-5p, 101-3p, 10a-5p, 10b-5p, 126-3p, 126-5p, 127-3p, 130b-3p, 135a-5p, 135b-5p, 142-3p, 146a-5p, 146b-5p, 150-5p, 155-5p, 185-3p, 187-3p, 18a-5p, 18b-5p, 190a-5p, 194-5p, 196a-5p, 199a-5p, 20b-5p, 21-5p, 214-3p, 218-5p, 296-5p, 301a-3p, 30b-3p, 31-3p, 31-5p, 328-3p, 339-5p, 340-5p, 345-5p, 34a-5p, 3605-3p, 363-3p, 423-5p, 424-5p, 454-3p, 486-5p, 597-5p, 671-5p, 7-5p, 766-3p, 7d-3p, 873-5p, 885-5p, and 99b-3p.
13. A process comprising;
a. obtaining a sample from saliva containing miRNA from essentially epithelial cells from a patient's oral cavity:
b. selecting hsa-miRNA sequences 130-3p, 7-5p, 101-3p and 146b-5p; and
c. measuring the level of expression of the selected miRNA sequences.
14. The process of claim 6 wherein the level of expression of the miRNA sequences is subjected to a statistically derived classifier which has a prediction accuracy of at least 80% in distinguishing between OSCC tissue and benign tissue.
15. The process of claim 6 wherein the set of miRNA sequences is drawn from hsa-miRNA sequences 210, 375, 100-5p, 101-3p, 10a-5p, 10b-5p, 126-3p, 126-5p, 127-3p, 130b-3p, 135a-5p, 135b-5p, 142-3p, 146a-5p, 146b-5p, 150-5p, 155-5p, 185-3p, 187-3p, 18a-5p, 18b-5p, 190a-5p, 194-5p, 196a-5p, 199a-5p, 20b-5p, 21-5p, 214-3p, 218-5p, 296-5p, 301a-3p, 30b-3p, 31-3p, 31-5p, 328-3p, 339-5p, 340-5p, 345-5p, 34a-5p, 3605-3p, 363-3p, 423-5p, 424-5p, 454-3p, 486-5p, 597-5p, 671-5p, 7-5p, 766-3p, 7d-3p, 873-5p, 885-5p, and 99b-3p.
16. The process of claim 1 wherein the results of the measurement are subjected to a statistically derived classifier which has a prediction accuracy of at least 80% in distinguishing between OSCC tissue and benign tissue.
17. The process of claim 8 wherein the statistical tool is selected from the group consisting of compound covariate predictor, diagonal linear discriminant analysis, 1-nearest neighbor, 3-nearest neighbors, nearest centroid, support vector machines and bayesian compound covariate predictor.
18. The process of claim 8 wherein the probability that the discrimination is correct is at least about 80%.
19. The process of claim 13 wherein the epithelial cell miRNA is obtained from saliva supernatant.
20. The process of claim 13 wherein the epithelial cell miRNA is obtained from cells isolated from saliva.