Methods and kits for monitoring response to radiation therapies in cancer

1. A method of treating a patient receiving a cancer treatment regimen comprising radiation, the method comprising:

a. obtaining isolated RNA of a cancer cell sample from a patient who has received one or more doses of radiation for cancer treatment; the isolated RNA comprising radiation induced degraded RNA and intact RNA;

b. separating the isolated RNA through a separation channel of a RNA chip using an analytic microcapillary electrophoresis system where intercalating fluorescent dye binds the RNA and detecting the isolated RNA by detecting the fluorescent dye; wherein the detecting is recorded in an electropherogram dataset;

c. measuring the amount of degraded RNA and intact RNA, the measuring comprising:

locating a dye-only peak, an 18S peak, and a 28S peak, and determining an intermediate region and a low C banding region, where the dye-only peak is at about 22.5 seconds, the intermediate region is the region of the electropherogram between the located 18S and 28S peaks, and the low C banding region is the region between 35 seconds and a start of the 18S peak; and

determining values for the 18S peak area, the 28S peak area, and at least one of the intermediate region area and the low C banding region area;

d. determining an RNA Disruption assay (RDA) score for the cancer cell sample, the RDA score comprising: (1) a ratio of the intermediate area to a sum of the 28S peak area and the 18S peak area; (2) a ratio of the low C banding region area to the sum of the 28S peak area and the 18S peak area; or (3) a ratio of the sum of the low C banding region area and the intermediate area to the sum of the 28S peak area and the 18S peak area;

e. comparing the RDA score determined for the cancer cell sample to at least one RDA score threshold determined from a plurality of samples from responders to the cancer treatment regimen comprising radiation or non-responders to the cancer treatment regimen comprising radiation, and;

f. detecting that the RDA score determined for the cancer cell sample is at least as high as the RDA score threshold determined from a plurality of responders, and continuing the cancer treatment regimen comprising radiation; or

detecting that the RDA score determined for the cancer cell sample is lower than the RDA score threshold determined from a plurality of responders, or lower than the RDA score threshold determined from a plurality of non-responders, and changing the cancer treatment regimen comprising radiation, the changing selected from increasing the dosage level and/or schedule of the radiation, adding a chemotherapeutic agent, biologic or radiosensitizing agent to the treatment, or changing to an alternate cancer drug therapy or surgery.

2. The method of claim 1 , further comprising measuring RNA concentration.

3. The method of claim 1 , wherein the cancer cells have received 1, 2, 3, 4, 5, 6 or more doses of radiation.

4. The method of claim 1 , wherein cells of the cancer cell sample are treated with a dose of a chemotherapeutic agent, prior to, concurrently and/or subsequent to the radiation treatment, optionally wherein the chemotherapeutic agent is selected from anthracyclines, taxanes and combinations thereof, preferably wherein the chemotherapeutic agent comprises epirubicin, docetaxel or combinations thereof; optionally wherein the taxane is selected from paclitaxel, docetaxel, larotaxel, Abraxane, docoxahexaenoic acid-linked paclitaxel, paclitaxel polyglumex, Ortataxel, Genexol, liposomal-encapsulated paclitaxel, and paclitaxel in a Vitamin E emulsion.

5. The method of claim 1 , wherein the cells are treated with a test agent prior to the radiation treatment to determine if the test agent is a radiosensitizer or a radio protector.

6. The method of claim 1 , wherein the RDA score threshold, is more than one RDA score thresholds defining multiple zones, the RDA score thresholds derived from a plurality of unresponsive samples and responsive samples.

7. The method of claim 1 , wherein the cancer cell sample is a breast cancer cell sample obtained from a breast cancer patient, or an ovarian cancer cell sample obtained from an ovarian cancer patient, optionally wherein the breast cancer is Her2+, basal subtype or luminal B subtype and/or wherein the breast cancer patient has locally advanced breast cancer (LABC).

8. The method of claim 6 , wherein the RDA score thresholds define 3 zones stratified for risk.

9. The method of claim 6 , wherein the cancer cell sample is a breast cancer cell sample obtained from a breast cancer patient, or an ovarian cancer cell sample obtained from an ovarian cancer patient, optionally wherein the breast cancer is Her2+, basal subtype or luminal B subtype and/or wherein the breast cancer patient has locally advanced breast cancer (LABC).

10. The method of claim 7 , wherein the RDA score threshold is more than one RDA score thresholds defining multiple zones, the RDA score thresholds derived from a plurality of unresponsive samples and responsive samples.

11. The method of claim 1 , wherein the changed treatment comprises treating the patient with a chemotherapeutic agent, selected from taxane chemotherapeutics, anthracyclines and combinations thereof, optionally wherein the taxane is selected from paclitaxel, docetaxel, larotaxel, Abraxane, docoxahexaenoic acid-linked paclitaxel, paclitaxel polyglumex, Ortataxel, Genexol, liposomal-encapsulated paclitaxel, and paclitaxel in a Vitamin E emulsion.

12. The method of claim 1 , wherein two or more cancer cell samples are obtained from the subject and assayed and an average or maximum RDA score is determined.

13. The method of claim 1 , wherein the method further comprises:

a) exposing the patient with cancer to a radiation dose;

b) obtaining a cancer cell sample after administration of the radiation dose, wherein said cancer cell sample is processed for obtaining the isolated RNA.

14. The method of claim 1 , wherein the changed treatment comprises treating the patient with an increased radiation treatment dose and/or schedule.

15. The method of claim 1 , comprising:

obtaining the cancer cell from the patient who has received one or more doses of radiation for cancer treatment, and wherein the RDA score determined for the cancer cell sample is lower than the RDA score threshold determined from a plurality of responders, or lower than the RDA score threshold determined from a plurality of non-responders, and changing the cancer treatment regimen comprises administration of a chemotherapeutic agent, alternate cancer drug therapy or surgery.

16. The method of claim 13 , wherein the cancer cell sample is a breast cancer cell sample or an ovarian cancer cell sample.