IP Library › Granted Patent US 12,497,660
Granted Patent B2
US 12,497,660 · App. 16/636,320 · Granted Dec 16, 2025

Use of immune cell-specific gene expression for prognosis of prostate cancer and prediction of responsiveness to radiation therapy

Inventors: Elai Davicioni (La Jolla, CA); Nicholas George Erho (Vancouver, CA); Jonathan Lehrer (Vancouver, CA); Felix Y. Feng (Hillsborough, CA); Shuang G. Zhao (Ann Arbor, MI)
Assignee: Veracyte SD, Inc.
C12Q1/6886G16H20/40G16H50/20C12Q2600/106C12Q2600/118
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Quick Facts
Patent No.
US 12,497,660
App. No.
16/636,320
Granted
Dec 16, 2025
Kind
B2
Abstract

Methods, systems, and kits for the diagnosis, prognosis and the determination of cancer progression of prostate cancer in a subject are disclosed. In particular, the disclosure relates to the use of immune cell-specific gene expression in determining prognosis and identifying individuals in need of treatment for prostate cancer who will be responsive to radiation therapy.

Claims (24)

1 . A method for treating a subject for prostate cancer, the method comprising:

a) obtaining a prognosis of the subject for distant metastasis-free survival (DMFS) based at least on levels of a plurality of immune cell types in a biological sample comprising prostate cancer cells from the subject, wherein the levels of the plurality of immune cell types comprise the ratio of the levels of M1 and M2 macrophages to M0 macrophages, wherein a higher ratio of the level of M1 and M2 macrophages to M0 macrophages compared to a reference value indicates that the subject will have a shorter DMFS; and

b) administering a treatment to the subject based on the prognosis, wherein the prognosis of the subject indicates that the subject will have a shorter DMFS, and wherein the treatment comprises a treatment selected from the group consisting of surgery, chemotherapy, radiation therapy, immunotherapy/biological therapy, hormonal therapy, and photodynamic therapy.

2 . The method of claim 1 , wherein the method further comprises measuring or having measured levels of immune cell-specific gene expression of PD-L2, and wherein the administering the treatment to the subject in b) is based on the prognosis that is further based on immune cell-specific gene expression of PD-L2 in the sample, wherein the higher ratio of the level of M1 and M2 macrophages to M0 macrophages compared to the reference value and higher levels of immune cell-specific gene expression of PD-L2 in the sample compared to a reference value indicates that the subject will have shorter DMFS.

3 . The method of claim 2 , wherein the treatment comprises radiation therapy.

4 . The method of claim 1 , wherein the plurality of immune cells comprises activated and resting mast cells, and wherein administering the treatment to the subject in b) is based on the prognosis that is further based on the ratio of the level of activated and resting mast cells in the sample, wherein the higher ratio of the level of M1 and M2 macrophages to M0 macrophages compared to the reference value and a lower ratio of activated mast cells to resting mast cells compared to a reference value indicates that the subject will have shorter DMFS.

5 . The method of claim 4 , wherein the treatment comprises radiation therapy.

6 . The method of claim 1 , wherein the plurality of immune cells comprises activated and resting NK cells, and wherein administering the treatment to the subject in b) is based on the prognosis that is further based on the ratio of the level of activated and resting NK cells in the sample wherein the higher ratio of the level of M1 and M2 macrophages to M0 macrophages compared to the reference value and a lower ratio of activated NK cells to resting NK cells compared to a reference value indicates that the subject will have shorter DMFS.

7 . The method of claim 6 , wherein the treatment comprises radiation therapy.

8 . The method of claim 1 , wherein the plurality of immune cells comprises activated and resting dendritic cells, and wherein administering the treatment to the subject in b) is based on the prognosis that is further based on the ratio of the level of activated and resting dendritic cells in the sample, wherein the higher ratio of the level of M1 and M2 macrophages to M0 macrophages compared to the reference value and a lower ratio of activated dendritic cells to resting dendritic cells compared to a reference value indicates that the subject will have longer shorter DMFS.

9 . The method of claim 8 , wherein the treatment comprises radiation therapy.

10 . The method of claim 1 , wherein the levels of the plurality of immune cell types in the biological sample were calculated based on levels of immune cell-specific gene expression in the biological sample.

11 . The method of claim 10 , wherein the levels of immune cell-specific gene expression are determined by using a method selected from the group consisting of in situ hybridization, a PCR-based method, an array-based method, an immunohistochemical method, an RNA assay method and an immunoassay method.

12 . The method of claim 10 , wherein the levels of immune cell-specific gene expression are determined using one or more reagents selected from the group consisting of nucleic acid probes, nucleic acid primers, and antibodies.

13 . The method of claim 10 , wherein the levels of the plurality of immune cell types calculated based on levels of immune cell-specific gene expression in the biological sample further comprises the levels of at least one of the following pairs of immune cell types:

i) activated mast cells and resting mast cells,

ii) activated natural killer (NK) cells and resting NK cells, or

iii) activated dendritic cells and resting dendritic cells.

14 . The method of claim 10 , wherein the levels of the plurality of immune cell types calculated based on levels of immune cell-specific gene expression in the biological sample further comprises the levels of at least activated mast cells and resting mast cells.

15 . The method of claim 10 , wherein the levels of the plurality of immune cell types calculated based on levels of immune cell-specific gene expression in the biological sample further comprises the levels of at least activated natural killer (NK) cells and resting NK cells.

16 . The method of claim 10 , wherein the levels of the plurality of immune cell types calculated based on levels of immune cell-specific gene expression in the biological sample further comprises the levels of at least activated dendritic cells and resting dendritic cells.

17 . The method of claim 1 , wherein the method is performed after the subject undergoes radical prostatectomy.

18 . The method of claim 1 , wherein the biological sample is a biopsy or a tumor sample.

19 . The method of claim 1 , wherein the treatment comprises radiation therapy.

Assignments (3)
CHANGE OF NAME Recorded Nov 18, 2023
From: DECIPHER BIOSCIENCES, INC.
To: VERACYTE SD, INC.
Reel/Frame 065627/0138 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Sep 8, 2021
From: FENG, FELIX Y.; ZHAO, SHUANG G.
To: THE REGENTS OF THE UNIVERSITY OF MICHIGAN
Reel/Frame 057417/0811 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 15, 2021
From: DAVICIONI, ELAI; ERHO, NICHOLAS GEORGE; LEHRER, JONATHAN
To: DECIPHER BIOSCIENCES, INC.
Reel/Frame 055592/0622 →
Continuity (2)
Provisional Application 62541566 · Aug 4, 2017
Related Publication 20210317531A1 · Oct 14, 2021
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