Methods of stratifying patients for treatment with retinoic acid receptor-α agonists
Described herein are methods that define cellular populations that are sensitive to RARA agonists and identify patient populations that will benefit from treatment with RARA agonists. The methods may comprise administering RARA agonists to patient populations.
1. A method of treating non-acute promyelocytic leukemia acute myelogenous leukemia (non-APL AML) or myelodysplastic syndrome (MDS), the method comprising a step of administering a combination of tamibarotene and a second therapeutic agent to a subject having non-APL AML or MDS, wherein a biological sample obtained from the subject has been determined to have an IRF8 biomarker and/or a RARA biomarker, wherein:
(I) the IRF8 biomarker is or comprises
(a) an elevated IRF8 RNA transcript level relative to a threshold level that defines a dividing line between subjects who respond to tamibarotene and subjects who do not respond to tamibarotene and is pre-determined by analysis of IRF8 RNA transcript levels in a population of samples comprising a cell line representing non-APL AML, a cell line representing MDS, a xenograft representing non-APL AML, a xenograft representing MDS, a biological sample from a patient suffering from non-APL AML, or a biological sample from a patient suffering from MDS, wherein
the number of samples in the population is sufficient to reasonably reflect the distribution of IRF8 RNA transcript levels in a group of non-APL AML or MDS patients that is larger than the population of samples;
the analysis of IRF8 RNA transcript levels in the population comprises testing at least some of the samples for responsiveness to tamibarotene and establishing (i) the lowest IRF8 RNA transcript level of a sample in the population that responds to tamibarotene and (ii) the highest IRF8 RNA transcript level of a sample in the population that does not respond to tamibarotene, thereby defining the lowest IRF8 RNA transcript responder and the highest IRF8 RNA transcript non-responder, respectively; and
the threshold level is set (i) at a level equal to or up to 5% above the IRF8 RNA transcript level in the lowest IRF8 RNA transcript responder, (ii) equal to or up to 5% above the IRF8 RNA transcript level in the highest IRF8 RNA transcript non-responder, or (iii) to a value in between the IRF8 RNA transcript level of the lowest IRF8 RNA transcript responder and the IRF8 RNA transcript level of the highest IRF8 RNA transcript non-responder or
(b) a super enhancer associated with an IRF8 gene;
(II) the RARA biomarker is or comprises
(a) an elevated RARA RNA transcript level relative to a threshold level that defines a dividing line between subjects who respond to tamibarotene and subjects who do not respond to tamibarotene and is pre-determined by analysis of RARA RNA transcript levels in a population of samples comprising a cell line representing non-APL AML, a cell line representing MDS, a xenograft representing non-APL AML, a xenograft representing MDS, a biological sample from a patient suffering from non-APL AML, or a biological sample from a patient suffering from MDS, wherein
the number of samples in the population is sufficient to reasonably reflect the distribution of RARA RNA transcript levels in a group of non-APL AML or MDS patients that is larger than the population of samples;
the analysis of RARA RNA transcript levels in the population comprises testing at least some of the samples for responsiveness to tamibarotene and establishing (i) the lowest RARA RNA transcript level of a sample in the population that responds to tamibarotene and (ii) the highest RARA RNA transcript level of a sample in the population that does not respond to tamibarotene, thereby defining the lowest RARA RNA transcript responder and the highest RARA RNA transcript non-responder, respectively; and
the threshold level is set (i) at a level equal to or up to 5% above the RARA RNA transcript level in the lowest RARA RNA transcript responder, (ii) equal to or up to 5% above the RARA RNA transcript level in the highest RARA RNA transcript non-responder, or (iii) to a value in between the RARA RNA transcript level of the lowest RARA RNA transcript responder and the RARA RNA transcript level of the highest RARA RNA transcript non-responder or
(b) a super enhancer associated with a RARA gene; and
the second therapeutic agent is a BCL2 inhibitor, a DNA methyltransferase inhibitor, a DNA synthase inhibitor, a topoisomerase inhibitor, a FLT3 inhibitor, a folate inhibitor, a BRD4 inhibitor, a Zn finger transcription factor inhibitor, a GCR inhibitor, a CDK7 inhibitor, an HDAC inhibitor, a JMJD3/JARID1B inhibitor, an EZH2 inhibitor, a LSD1 inhibitor, a proteasome inhibitor, a DNA damage repair inhibitor, a PARP inhibitor, a mTOR inhibitor, a DOT1L inhibitor, a tubulin inhibitor, a PLK inhibitor, or an Aurora kinase inhibitor.
2. The method of claim 1 , wherein the tamibarotene and the second therapeutic agent are administered concurrently.
3. The method of claim 1 , wherein the tamibarotene and the second therapeutic agent are administered sequentially.
4. The method of claim 1 , wherein the elevated RARA RNA transcript level and/or the elevated IRF8 RNA transcript level have been independently determined using fluorescent hybridization, PCR, qPCR, qRT-PCR, RNA sequencing, RNA hybridization and signal amplification or northern blot.
5. The method of claim 1 , wherein the subject is suffering from non-APL AML.
6. The method of claim 1 , wherein the subject is suffering from MIDS.
7. The method of claim 1 , wherein the biological sample obtained from the subject is a bone marrow aspirate or whole blood.
8. The method of claim 7 , wherein the bone marrow aspirate or whole blood is processed to remove one or more components therefrom.
9. The method of claim 8 , wherein the whole blood is processed to yield a peripheral blood mononuclear cell (PBMC) sample or an enriched PBMC sample.
10. The method of claim 1 , wherein the biological sample obtained from the subject has been determined to have the IRF8 biomarker.
11. The method of claim 10 , wherein the IRF8 RNA transcript is transcribed from a genomic DNA sequence that encodes an interferon consensus sequence-binding protein or splice variant thereof and specifically excludes gene fusions that comprise all or a portion of the IRF8 gene, and the IRF8 gene is located at chr16:85862582-85990086 in genome build hg19.
12. The method of claim 1 , wherein the biological sample obtained from the subject has been determined to have the RARA biomarker.
13. The method of claim 12 , wherein the RARA RNA transcript is transcribed from a genomic DNA sequence that encodes a functional retinoic acid receptor-α gene and specifically excludes gene fusions that comprise all or a portion of the RARA gene, and the RARA gene is located at chr17:38458152-38516681.
14. The method of claim 1 , wherein the IRF8 RNA transcript is an IRF8 mRNA.
15. The method of claim 1 , wherein the RARA RNA transcript is a RARA mRNA.
16. The method of claim 1 , wherein the second therapeutic agent is a DNA synthase inhibitor.
17. The method of claim 16 , wherein the DNA synthase inhibitor is ara-C.
18. The method of claim 1 , wherein the second therapeutic agent is a DNA methyltransferase inhibitor.
19. The method of claim 16 , wherein the DNA methyltransferase inhibitor is decitabine or azacitidine.
20. The method of claim 1 , wherein the second therapeutic agent is a CDK7 inhibitor.
21. The method of claim 1 , wherein the second therapeutic agent is a BCL2 inhibitor.
22. The method of claim 21 , wherein the BCL2 inhibitor is ABT199.