COMPOSITIONS AND METHODS FOR DETECTING SESSILE SERRATED ADENOMAS/POLYPS

• US 20200131583A1
• Filed: 03/01/2018
• Published: 04/30/2020
• Est. Priority Date: 03/01/2017
• Status: Active Grant

• Current Assignee: Bioventures, LLC, US Department of Veterans Affairs (Government of the United States of America)
• Original Assignee: Bioventures, LLC
• Inventors: GLAZKO, Galina, HAGEDORN, Curt H., RAHMATALLAH, Yasir
• Granted Patent: US 11,236,398 B2
• Time in Patent Office: Days
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G01N 2800/7028 Cancer
• CPC Class Codes: G01N 33/57446 of stomach or intestine

Abstract

The disclosure provides a method to detect sessile serrated adenomas/polyps (SSA/Ps) and to differentiate SSA/Ps from hyperplastic polyps (HPs). The method uses a molecular signature that is platform-independent and could be used with multiple platforms such as microarray, RNA-seq or real-time quantitative platforms.

Claims

1. A method of detecting sessile serrated adenomas/polyps (SSA/Ps) in a subject, the method comprising:

a. determining the level of expression of the nucleic acids in the molecular signature in a biological sample obtained from the subject, wherein the molecular signature is selected from the group consisting of CHFR, CHGA, CLDN1, KIZ, MEGF6, NTRK2, PLA2G16, PTAFR, SBSPON, SEMG1, SLC7A9, SPIRE1, TACSTD2, FOXD1, PIK3R3, PRUNE2, TPD52L1, TRIB2, C4BPA, CPE, DPP10, GRAMD1B, GRIN2D, KLK7, MYCN, and TM4SF4;

b. comparing the level of expression of each nucleic acid in the molecular signature to a reference value; and

c. detecting SSA/Ps in the subject based on the level of expression of each nucleic acid in the molecular signature relative to the reference value.

5. The method of claim 1, wherein the molecular signature further comprises one or more nucleic acids to be used as a normalization control.

6. The method of claim 5, wherein the one or more nucleic acids used as a normalization control are selected from the group consisting of GAPDH, ACTB, B2M, TUBA, G6PD, LDHA, HPRT, ALDOA, PFKP, PGK1, PGAM1, VIM and UBC.

9. The method of claim 1, wherein step (c) comprises detecting SSA/Ps in the subject when CHFR, CHGA, and NTRK2 are decreased relative to the reference value and when CLDN1, KIZ, MEGF6, PLA2G16, PTAFR, SBSPON, SEMG1, SLC7A9, SPIRE1, and TACSTD2 are increased relative to the reference value, wherein the reference value is the level of expression of each nucleic acid in the molecular signature in a non-diseased or HP sample.

10. The method of claim 1, wherein step (c) comprises detecting SSA/Ps in the subject when NTRK2 is decreased relative to the reference value and when CLDN1, FOXD1, KIZ, MEGF6, PIK3R3, PLA2G16, PRUNE2, PTAFR, SBSPON, SEMG1, SLC7A9, SPIRE1, TACSTD2, TPD52L1, and TRIB2 are increased relative to the reference value, wherein the reference value is the level of expression of each nucleic acid in the molecular signature in a non-diseased or HP sample.

11. The method of claim 1, wherein step (c) comprises detecting SSA/Ps in the subject when CHGA, CPE, DPP10, and NTRK2 are decreased relative to the reference value and when C4BPA, CLDN1, GRAMD1B, GRIN2D, KIZ, KLK7, MEGF6, MYCN, PLA2G16, SBSPON, SEMG1, SLC7A9, SPIRE1, and TM4SF4 are increased relative to the reference value, wherein the reference value is the level of expression of each nucleic acid in the molecular signature in a non-diseased or HP sample.

12. The method of claim 1, wherein the method to determine the level of expression of the nucleic acids in the molecular signature is microarray, RNA-seq or real-time qPCR.

13. The method of claim 1, wherein the biological sample is a tissue biopsy.

2-4. -4. (canceled)

7-8. -8. (canceled)

14-17. -17. (canceled)

18. A method of differentiating sessile serrated adenomas/polyps (SSA/Ps) from hyperplastic polyps (HPs) in a subject, the method comprising:

a. determining the level of expression of the nucleic acids in the molecular signature in a biological sample obtained from the subject, wherein the molecular signature is selected from the group consisting of CHFR, CHGA, CLDN1, KIZ, MEGF6, NTRK2, PLA2G16, PTAFR, SBSPON, SEMG1, SLC7A9, SPIRE1, TACSTD2, FOXD1, PIK3R3, PRUNE2, TPD52L1, TRIB2, C4BPA, CPE, DPP10, GRAMD1B, GRIN2D, KLK7, MYCN, and TM4SF4;

b. comparing the level of expression of each nucleic acid in the molecular signature to a reference value; and

c. detecting SSA/Ps or HPs in the subject based on the level of expression of each nucleic acid in the molecular signature relative to the reference value.

19. The method of claim 18, wherein the molecular signature further comprises one or more nucleic acids to be used as a normalization control.

20. The method of claim 18, wherein step (c) comprises detecting SSA/Ps in the subject when CHFR, CHGA, and NTRK2 are decreased relative to the reference value and when CLDN1, KIZ, MEGF6, PLA2G16, PTAFR, SBSPON, SEMG1, SLC7A9, SPIRE1, and TACSTD2 are increased relative to the reference value, wherein the reference value is the level of expression of each nucleic acid in the molecular signature in a non-diseased or HP sample.

21. The method of claim 18, wherein step (c) comprises detecting SSA/Ps in the subject when NTRK2 is decreased relative to the reference value and when CLDN1, FOXD1, KIZ, MEGF6, PIK3R3, PLA2G16, PRUNE2, PTAFR, SBSPON, SEMG1, SLC7A9, SPIRE1, TACSTD2, TPD52L1, and TRIB2 are increased relative to the reference value, wherein the reference value is the level of expression of each nucleic acid in the molecular signature in a non-diseased or HP sample.

22. The method of claim 18, wherein step (c) comprises detecting SSA/Ps in the subject when CHGA, CPE, DPP10, and NTRK2 are decreased relative to the reference value and when C4BPA, CLDN1, GRAMD1B, GRIN2D, KIZ, KLK7, MEGF6, MYCN, PLA2G16, SBSPON, SEMG1, SLC7A9, SPIRE1, and TM4SF4 are increased relative to the reference value, wherein the reference value is the level of expression of each nucleic acid in the molecular signature in a non-diseased or HP sample.

23. The method of claim 18, wherein the method to determine the level of expression of the nucleic acids in the molecular signature is microarray, RNA-seq or real-time qPCR.

24. The method of claim 18, wherein the biological sample is a tissue biopsy.

25. A method of determining treatment of a subject diagnosed with serrated polyps or suspected of having serrated polyps, the method comprising:

a. determining the level of expression of the nucleic acids in the molecular signature in a biological sample obtained from the subject, wherein the molecular signature is selected from the group consisting of CHFR, CHGA, CLDN1, KIZ, MEGF6, NTRK2, PLA2G16, PTAFR, SBSPON, SEMG1, SLC7A9, SPIRE1, TACSTD2, FOXD1, PIK3R3, PRUNE2, TPD52L1, TRIB2, C4BPA, CPE, DPP10, GRAMD1B, GRIN2D, KLK7, MYCN, and TM4SF4;

b. comparing the level of expression of each nucleic acid in the molecular signature to a reference value;

c. detecting SSA/Ps in the subject based on the level of expression of each nucleic acid in the molecular signature relative to the reference value; and

d. treating the subject more aggressively if SSA/Ps are detected.

26. The method of claim 25, wherein step (c) comprises detecting SSA/Ps in the subject when CHFR, CHGA, and NTRK2 are decreased relative to the reference value and when CLDN1, KIZ, MEGF6, PLA2G16, PTAFR, SBSPON, SEMG1, SLC7A9, SPIRE1, and TACSTD2 are increased relative to the reference value, wherein the reference value is the level of expression of each nucleic acid in the molecular signature in a non-diseased or HP sample.

27. The method of claim 25, wherein step (c) comprises detecting SSA/Ps in the subject when NTRK2 is decreased relative to the reference value and when CLDN1, FOXD1, KIZ, MEGF6, PIK3R3, PLA2G16, PRUNE2, PTAFR, SBSPON, SEMG1, SLC7A9, SPIRE1, TACSTD2, TPD52L1, and TRIB2 are increased relative to the reference value, wherein the reference value is the level of expression of each nucleic acid in the molecular signature in a non-diseased or HP sample.

28. The method of claim 25, wherein step (c) comprises detecting SSA/Ps in the subject when CHGA, CPE, DPP10, and NTRK2 are decreased relative to the reference value and when C4BPA, CLDN1, GRAMD1B, GRIN2D, KIZ, KLK7, MEGF6, MYCN, PLA2G16, SBSPON, SEMG1, SLC7A9, SPIRE1, and TM4SF4 are increased relative to the reference value, wherein the reference value is the level of expression of each nucleic acid in the molecular signature in a non-diseased or HP sample.

29. The method of claim 25, wherein the treatment includes one or more of the following:

increased surveillance, polypectomy, endoscopic resection, and surgical resection.