阅读说明：本技术 克莱拉尼的新用途 (New application of Claranib ) 是由 维奈·K·柴恩 于 2020-01-10 设计创作，主要内容包括：本发明包括监测患有增殖性疾患的患者中可测量的残余疾病,确定哪些患者可从克莱拉尼或盐的治疗或干预中在减少残余疾病和维持缓解方面受益,以及将治疗有效量的克莱拉尼作为单一药物或与另一种治疗剂相继或同时给药的方法。(The invention includes methods of monitoring measurable residual disease in patients with a proliferative disorder, determining which patients would benefit from treatment or intervention with clariant or salt in reducing residual disease and maintaining remission, and administering a therapeutically effective amount of clariant as a single agent or sequentially or simultaneously with another therapeutic agent.)

1. A method of treating a subject with or without a mutation in FLT3 tyrosine kinase that causes a proliferative disorder, comprising administering to the subject a therapeutically effective amount of klebside or a pharmaceutically acceptable salt thereof in combination with at least one of an alkylating agent, an antimetabolite agent, a natural product, or a combination thereof.

2. The method of claim 1, wherein the minimal residual disease of the proliferative disorder is detected by:

a. obtaining a sample from the subject comprising tumor cells;

b. sequencing single cells from a sample, wherein the sequencing comprises at least 1000000 reads per sample;

c. only samples with allele dropout of 10% or less were analyzed for mutations.

3. The method of claim 1, wherein the presence or absence of one or more mutations is used to make a patient-specific single-cell mutation profile associated with the proliferative disorder.

4. The method of claim 1, wherein the one or more co-occurring mutations is at least one of: NPM1, DNMT3A, NRAS, KRAS, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP1, ZRSR2, GRB7, SRSF 7, MLL, NUP 7, ETV 7, TCL 17, TUSC 7, BRP 7, CD 7, TYK 7, TP 7, EZH 7, GATA 7, KIT, PHF 7, MYC, ERG, MYD 7, RAD 7, STAT 7, NF 7, KDF, KDM6 BRA3672, SETBP 7, CALR, CBL, MPL 27, PHF 7, PHCSF, MUAS 7, MUEKAS 7, SMC 7.

5. The method of claim 1, wherein the FLT3 mutation is: at least one of FLT3-ITD, FLT3-TKD, or other FLT3 mutant variants.

6. The method of claim 5, wherein the FLT3-TKD mutation is an alteration, deletion or point mutation of at least one of F612, L616, M664, M665, N676, A680, F691, D835, I836, D839, N841, Y842 or A848.

7. The method of claim 5, wherein the FLT3 mutation comprises a point mutation that results in an alteration or deletion of at least one of L20, D324, L442, E444, S451, V491, Y572, E573, L576, Y572, Q580, V591, T582, D586, Y589, V592, F594, E596, E598, Y599, D600, R607, or A848.

8. The method of claim 2, further comprising the steps of:

repeating steps (a) to (c) from one or more longitudinally consecutive samples of the subject;

combining one or more longitudinal single cell genome mutation profiles to determine the presence or absence of one or more co-occurring mutations that are altered in response to administration of a therapeutically effective dose of crilagonil or a pharmaceutically acceptable salt thereof; and

determining a measurable residual disease state of the proliferative disorder as measured by an increase or decrease in percentage of the patient-specific single-cell mutation profile after treatment associated with the proliferative disorder.

9. The method of claim 2, wherein the sample obtained is at least one of bone marrow, peripheral blood, or tumor tissue.

10. The method of claim 2, wherein the single cell sequencing comprises preparing genomic DNA with one or more markers per cell and sequencing the prepared DNA.

11. The method of claim 2, wherein the single cell sequencing uses a MiSeq, HiSeq, or NovaSeq platform.

12. The method of claim 1, wherein the alkylating agent is selected from at least one of carmustine, chlorambucil, cyclophosphamide, ifosfamide, lomustine, streptozotocin, temozolomide, cisplatin, carboplatin, nedaplatin, or oxaliplatin.

13. The method of claim 1, wherein the antimetabolite agent is selected from at least one of the following: methotrexate, pemetrexed, raltitrexed, cytarabine, fludarabine, fluorouracil, floxuridine, capecitabine or gemcitabine.

14. The method of claim 1, wherein the natural product is selected from at least one of: vinblastine, vinorelbine, vincristine, vindesine, vinflunine, paclitaxel, docetaxel, cabazitaxel, etoposide, teniposide, topotecan, irinotecan, daunorubicin, doxorubicin, idarubicin, epirubicin, valrubicin, mitoxantrone, bleomycin, estramustine, and/or mitomycin.

15. The method of claim 1, wherein the subject is a pediatric patient.

16. A method of treating a subject suffering from a proliferative disorder comprising wild-type FLT3 having one or more co-occurring RAS mutations, comprising administering to the subject a therapeutically effective amount of klebside or a pharmaceutically acceptable salt thereof in combination with at least one of an alkylating agent, an antimetabolite agent, a natural product, or a combination thereof.

17. The method of claim 16, wherein the minimal residual disease of the proliferative disorder is detected by:

a. obtaining a sample from the subject comprising tumor cells;

b. sequencing the sample for single cells, wherein the sequencing comprises at least 1,000,000 reads per sample; and

c. mutations were analyzed only from samples with allele dropout of 10% or less.

18. The method of claim 16, wherein the presence or absence of one or more mutations is used to make a patient-specific single-cell mutation profile associated with the proliferative disorder.

19. The method of claim 16, wherein the RAS mutation is at least one of an NRAS or KRAS mutation.

20. The method of claim 16, wherein the one or more co-occurring mutations is at least one of FLT3, NPM1, DNMT3A, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP 2, ZRSR2, GRB 2, SRSF2, MLL, NUP 2, ETV 2, TCL 12, TUSC 2, BRP 2, CD 2, TYK2, TP 2, EZH2, GATA2, KIT, PHF 2, MYC, ERG, MYD 2, tyrd 2, STAT 2, NF 2, brakdf, KDM6, setf 2, setp 2, PHF 2, kmas 2, PHF 2, SMC 36.

21. The method of claim 17, further comprising the steps of:

repeating steps (a) to (c) from one or more longitudinally consecutive samples of the subject;

combining one or more vertical single cell genome mutation profiles to determine the presence or absence of one or more mutations that change in response to administration of a therapeutically effective amount of cremaster or a pharmaceutically acceptable salt thereof; and

determining a measurable residual disease state of the proliferative disorder as measured by an increase or decrease in percentage of the patient-specific single-cell mutation profile after treatment associated with the proliferative disorder.

22. The method of claim 17, wherein the sample obtained is at least one of bone marrow, peripheral blood, or tumor tissue.

23. The method of claim 17, wherein the single cell sequencing comprises preparing genomic DNA with one or more markers per cell and sequencing the prepared DNA.

24. The method of claim 17, wherein the single cell sequencing uses the aMiSeq, HiSeq, or NovaSeq platforms.

25. The method of claim 17, wherein the alkylating agent is selected from at least one of: carmustine, chlorambucil, cyclophosphamide, ifosfamide, lomustine, streptozotocin, temozolomide, cisplatin, carboplatin, nedaplatin, or oxaliplatin.

26. The method of claim 17, wherein the antimetabolite agent is selected from at least one of the following: methotrexate, pemetrexed, raltitrexed, cytarabine, fludarabine, fluorouracil, floxuridine, capecitabine or gemcitabine.

27. The method of claim 17, wherein the natural product is selected from at least one of: vinblastine, vinorelbine, vincristine, vindesine, vinflunine, paclitaxel, docetaxel, cabazitaxel, etoposide, teniposide, topotecan, irinotecan, daunorubicin, doxorubicin, idarubicin, epirubicin, valrubicin, mitoxantrone, bleomycin, estramustine, and/or mitomycin.

28. The method of claim 17, wherein the subject further mutates FLT3 tyrosine kinase.

29. The method of claim 17, wherein the subject is a pediatric patient.

30. A method of preventing recurrence of a proliferative disorder in a subject previously treated to have no proliferative disorder, comprising administering to said subject a therapeutically effective amount of crealanib, or a pharmaceutically acceptable salt thereof, following response to induction of chemotherapy, consolidation, or following hematopoietic stem cell transplantation for a period of time sufficient to prevent recurrence of said proliferative disorder.

31. The method of claim 30, wherein the proliferative disorder is characterized by comprising one or more functional alteration mutations and at least one recurrent gene mutation.

32. The method of claim 30, wherein the proliferative disorder is characterized by comprising wild-type FLT3 with or without one or more co-occurring mutations.

33. The method of claim 30, wherein the prior treatment of the subject is with:

an alkylating agent selected from at least one of: carmustine, chlorambucil, cyclophosphamide, ifosfamide, lomustine, streptozotocin, temozolomide, cisplatin, carboplatin, nedaplatin, or oxaliplatin;

an antimetabolite agent selected from at least one of: methotrexate, pemetrexed, raltitrexed, cytarabine, fludarabine, fluorouracil, floxuridine, capecitabine, or gemcitabine;

or a natural product selected from at least one of: vinblastine, vinorelbine, vincristine, vindesine, vinflunine, paclitaxel, docetaxel, cabazitaxel, etoposide, teniposide, topotecan, irinotecan, daunorubicin, doxorubicin, idarubicin, epirubicin, valrubicin, mitoxantrone, bleomycin, estramustine, and/or mitomycin.

34. The method of claim 30, wherein the one or more co-occurring mutations are at least one of: NPM1, DNMT3A, NRAS, KRAS, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP1, ZRSR2, GRB7, SRSF 7, MLL, NUP 7, ETV 7, TCL 17, TUSC 7, BRP 7, CD 7, TYK 7, TP 7, EZH 7, GATA 7, KIT, PHF 7, MYC, ERG, MYD 7, RAD 7, STAT 7, NF 7, KDF, KDM6 BRA3672, SETBP 7, CALR, CBL, MPL 27, PHF 7, PHCSF, MUAS 7, MUEKAS 7, SMC 7.

35. The method of claim 30, wherein the subject is a pediatric patient.

Technical Field

The present invention relates to methods of reducing or inhibiting normal and mutant FLT3 kinase activity in a cell or subject by first detecting clonal heterogeneity and then using clainib to prevent or treat one or more cell proliferative disorders associated with FLT 3.

Statement of federally sponsored research

Not applicable.

Incorporation of optical disc archive materials

Not applicable.

Background

Without limiting the scope of the invention, the background of the invention relates to a novel use of cancer therapy and genetic analysis to monitor measurable residual disease throughout the course of therapy, determine the presence or absence of recurrent genetic mutations, and administer kleinian or a pharmaceutically acceptable salt thereof to patients carrying appropriate recurrent genetic mutations to remove measurable residual disease and/or maintain disease remission.

Different proliferative diseases, such as leukemia, are often associated with specific patterns of recurrent gene mutations or variations. Acute Myeloid Leukemia (AML) is particularly associated with recurrent mutations in a series of genes FLT3, DNMT3A, NPM1, etc. (Tyner et al, 2018). AML is polyclonal and heterogeneous based on the pathogenic nature of leukemia, with different cell subsets expressing different combinations of genetic mutations. After treatment with chemotherapy or targeted agents or a combination of these drugs, the patient can obtain a morphologically complete remission, but still have a small fraction of cells with persistent leukemia-associated mutations. This is referred to as measurable residual disease or MRD (Ding et al, 2012). MRD patients, while morphologically remitting, may still benefit from long-term treatment to prevent disease recurrence. This method of treatment is commonly referred to as maintenance therapy.

Mutations in the receptor tyrosine kinase FLT3 are associated with a high risk of relapse and a poor prognosis. It is also one of the most common genetic mutations in AML, with an incidence of about 20-30% (Daver, Schlenk, Russell, & Levis, 2019). Mutations in FLT3 have also been associated with other proliferative disorders. The frequency and prognostic value of this gene mutation makes FLT3 an attractive drug target in proliferative disorders, particularly hematologic malignancies such as AML. Drugs targeting this protein have recently been approved or are under development. One such drug currently under development is crelazide, a tyrosine kinase inhibitor with significant activity against the FLT3 mutation.

The impact of FLT3 mutations on patient prognosis makes FLT3 persistent mutations particularly interesting in MRD. Traditional methods of monitoring measurable residual disease are somewhat limiting in that they fail to detect mutations in very small numbers of cells, or rely on changes in cellular marker expression patterns, which over time or between mechanisms may make the detection unreliable (Ommen, 2016). Thus, there is a need for a more sensitive method to detect recurrent genetic mutations associated with increased risk of recurrence, allowing the physician to select a more appropriate method or treatment, and eliminate or reduce measurable residual disease, thereby maintaining disease remission.

Disclosure of Invention

The invention includes a method of treating a subject suffering from a proliferative disorder including wild-type FLT3 with or without one or more co-occurring FLT3 mutations, the method comprising administering to the subject a therapeutically effective amount of klebside, or a pharmaceutically acceptable salt thereof, in combination with at least one of an alkylating agent, an antimetabolite agent, a natural product, or a combination thereof. In another aspect, a method of treating a subject suffering from a proliferative disorder comprising wild-type FLT3 having one or more co-occurring RAS mutations, comprising administering to the subject a therapeutically effective dose of creylanib, or a pharmaceutically acceptable salt thereof, and at least one of an alkylating agent, an antimetabolite agent, a natural product, or a combination thereof. In yet another aspect, is a method of preventing recurrence of a proliferative disorder; comprising administering a therapeutically effective amount of clainib, or a pharmaceutically acceptable salt thereof, alone or in combination with another agent. In one aspect, the proliferative disorder is characterized by comprising one or more functional alteration mutations and at least one recurrent gene mutation. In one aspect, minimal residual disease can be detected by: obtaining a sample from a subject; performing single cell sequencing of the genetic code of the above gene, wherein the sequencing comprises at least 1,000,000 reads per sample; and analyzing only samples having an allele dropout rate of 10% or less. In another aspect, the presence or absence of one or more mutations in the above genes that produce a patient-specific single-cell mutation profile associated with a proliferative disorder is found. In another aspect, the recurrent gene mutation is found in at least one of: FLT3, NPM1, DNMT3A, NRAS, KRAS, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP 2, ZRSR2, GRB 2, SRSF2, MLL, NUP 2, ETV 2, TCL 12, TUSC 2, BRP 2, CD 2, RSTYK 2, TP 2, EZH2, GATA2, KIT, PHF 2, MYC, ERG, MYD 2, RAD2, STAT 2, NF 2, BRAF, RSRM 6 2, SETBP 2, CSF, CBL, KMT2, KMT2, MUAS 2, SMC 2, or at least one other. In another aspect, the FLT3 mutations found include at least one of FLT3-ITD, FLT3-TKD, or other FLT3 mutant variants. In another aspect, the FLT3-TKD mutations include point mutations that result in at least one alteration or deletion in F612, L616, K663, M664, M665, N676, a680, F691, a833, R834, D835, I836, D839, N841, Y842 or a 848. In another aspect, FLT3 variant mutations include point mutations that result in an alteration or deletion of at least one of L20, D324, K429, L442, E444, S451, V491, Y572, E573, L576, Y572, Q580, V591, T582, D586, Y589, V592, F594, E596, E598, Y599, D600, R607, a848, or others. In another aspect, the subject is a pediatric subject.

In another aspect, the method further comprises the steps of: repeating steps (a) to (c) from one or more longitudinally consecutive samples of the subject, combining one or more longitudinal single cell genomic mutation profiles to determine a Klelara dose in response to administration of a therapeutically effective amount of the Klelara doseThe presence or absence of one or more mutations altered by ni, or a pharmaceutically acceptable salt thereof, and the measurable residual disease state of the proliferative disorder is determined by an increase or decrease in the percentage of the patient-specific single-cell mutation profile after treatment associated with the proliferative disorder. In another aspect, the obtained sample is at least one of bone marrow, peripheral blood, or tumor tissue. In another aspect, single cell sequencing includes the use of single cell multicomponent analysis such as tapesti for simultaneous detection of single nucleotide variations, copy number variations and protein changes from the same cell^TMA platform to prepare genomic DNA of the above gene with a label and sequencing the prepared DNA with at least one of MiSeq, HiSeq or NovaSeq sequencing platforms. In another aspect, the subject is a pediatric subject.

In another embodiment, a method of treating a subject suffering from a proliferative disorder comprising wild-type FLT3 having one or more co-occurring RAS mutations, comprising administering to the subject a therapeutically effective amount of creiranib, or a pharmaceutically acceptable salt thereof, in combination with at least one of an alkylating agent, an antimetabolite agent, a natural product, or a combination thereof. In one aspect, the minimal residual disease of the proliferative disorder is detected by: : (a) obtaining a sample from a subject comprising tumor cells; (b) sequencing single cells from a sample, wherein the sequencing comprises at least 1,000,000 reads per sample; (c) samples with allele dropout of 10% or less were analyzed for mutations. In another aspect, the presence or absence of one or more mutations is used to make a patient-specific single-cell mutation profile associated with a proliferative disorder. In another aspect, the RAS mutation is at least one of an NRAS or KRAS mutation. In another aspect, the one or more co-occurring mutations is at least one of FLT3, NPM1, DNMT3A, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP 2, ZRSR2, GRB 2, SRSF2, MLL, NUP 2, ETV 2, TCL 12, TUSC 2, BRP 2, CD 2, TYK2, TP 2, EZH2, GATA2, KIT, PHF 2, MYC, ERG, MYD 2, NF 2, BRAF, KDM6 2, setp CSF, kml 2, pht 2, MYC 2, SMC 36. In another aspect, the method further comprises the steps of: repeating steps (a) to (c) from one or more longitudinally consecutive samples of the subject, combining one or more longitudinal single cell genomic mutation profiles to determine the presence or absence of one or more mutations that are altered in response to administration of a therapeutically effective amount of crelazanib or a pharmaceutically acceptable salt thereof, and determining a measurable residual disease state of the proliferative disorder as measured by an increase or decrease in the percentage of the patient-specific single cell mutation profile after treatment associated with the proliferative disorder. In another aspect, the obtained sample is at least one of bone marrow, peripheral blood, or tumor tissue. In another aspect, single cell sequencing comprises preparing genomic DNA with one or more markers per cell, and sequencing the prepared DNA. In another aspect, single cell sequencing uses the aMiSeq, HiSeq or NovaSeq platforms. In another aspect, the alkylating agent is selected from at least one of the following: carmustine, chlorambucil, cyclophosphamide, ifosfamide, lomustine, streptozotocin, temozolomide, cisplatin, carboplatin, nedaplatin, or oxaliplatin. In another aspect, the antimetabolite agent is selected from at least one of the following: methotrexate, pemetrexed, raltitrexed, cytarabine, fludarabine, fluorouracil, floxuridine, capecitabine or gemcitabine. In another aspect, the natural product is selected from at least one of the following: vinblastine, vinorelbine, vincristine, vindesine, vinflunine, paclitaxel, docetaxel, cabazitaxel, etoposide, teniposide, topotecan, irinotecan, daunorubicin, doxorubicin, idarubicin, epirubicin, valrubicin, mitoxantrone, bleomycin, estramustine, and/or mitomycin. In another aspect, the subject further comprises a mutant FLT3 tyrosine kinase. In another aspect, the subject is a pediatric patient.

In another embodiment, the invention includes a method of preventing recurrence of a proliferative disorder in a subject previously treated to be free of the proliferative disorder, comprising administering to the subject a therapeutically effective amount of crealanib, or a pharmaceutically acceptable salt thereof, following response to induction of chemotherapy, consolidation, or following hematopoietic stem cell transplantation for a period of time sufficient to prevent recurrence of the proliferative disorder. In another aspect, the proliferative disorder is characterized by comprising one or more functional alteration mutations and at least one recurrent gene mutation. In another aspect, the proliferative disorder is characterized by comprising wild-type FLT3 with or without one or more co-occurring mutations. In another aspect, prior treatment of the subject can be performed with: the alkylating agent is selected from at least one of the following: carmustine, chlorambucil, cyclophosphamide, ifosfamide, lomustine, streptozotocin, temozolomide, cisplatin, carboplatin, nedaplatin, or oxaliplatin; the antimetabolite is selected from at least one of: methotrexate, pemetrexed, raltitrexed, cytarabine, fludarabine, fluorouracil, floxuridine, capecitabine, or gemcitabine; or the natural product is selected from at least one of the following: vinblastine, vinorelbine, vincristine, vindesine, vinflunine, paclitaxel, docetaxel, cabazitaxel, etoposide, teniposide, topotecan, irinotecan, daunorubicin, doxorubicin, idarubicin, epirubicin, valrubicin, mitoxantrone, bleomycin, estramustine, and/or mitomycin. In another aspect, the one or more co-occurring mutations are at least one of: NPM1, DNMT3A, NRAS, KRAS, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP1, ZRSR2, GRB7, SRSF 7, MLL, NUP 7, ETV 7, TCL 17, TUSC 7, BRP 7, CD 7, TYK 7, TP 7, EZH 7, GATA 7, KIT, PHF 7, MYC, ERG, MYD 7, RAD 7, STAT 7, NF 7, KDF, KDM6 BRA3672, SETBP 7, CALR, CBL, MPL 27, PHF 7, PHCSF, MUAS 7, MUEKAS 7, SMC 7. In another aspect, the subject is a pediatric patient.

The invention provides methods of reducing measurable residual disease in a subject having a proliferative disorder. Other features and advantages of the invention will be apparent from the following detailed description of the invention and from the claims.

Drawings

For a more complete understanding of the features and advantages of the present invention, reference is now made to the detailed description of the invention along with the accompanying figures in which:

FIG. 1 is a diagrammatic representation of a patient longitudinal bone marrow specimen. Normal Wild Type (WT) cells appear grey. The total subclone population within the sample at diagnosis, 35 days after initiation of induction chemotherapy and three time points during maintenance is shown. The samples show that the variation FLT3 and FLT3 activating mutations can be eliminated with combination therapy of intensive induction chemotherapy with clarianib, consolidation of high dose cytarabine (HiDAC) with clarianib, and maintenance of clarianib as a single drug for mutation elimination.

FIGS. 2A and 2B are scatter plots showing individual cells expressing mutant KRAS (y-axis) in a bone marrow sample of a patient at diagnosis (FIG. 2A) and 35 days after initiation of induction (FIG. 2B). Figure 2A shows that the cell population comprises the following mutations from left to right; DNMT3A/NPM1/FLT3-A680V/FLT3-ITD, DNMT3A/NPM1/FLT3-N841K, wild type, DNMT3A/NPM1/FLT3-A680V, DNMT3A/NPM1/FLT3-D839G and finally small subcloned cells with various mutations. Fig. 2B shows the cell populations as follows: wild type, DNMT3A/NPM1, DNMT3A and DNMT3A/NPM1/FLT 3-ITD. Clainib treatment abrogated the vast majority of cancer cell populations containing mutations.

FIGS. 3A and 3B are scatter plots showing individual cells expressing mutant DNMT3 (y-axis) in bone marrow samples from patients at diagnosis (FIG. 3A) and 35 days after induction began (FIG. 3B). Figure 3A shows that the cell population comprises the following mutations from left to right; DNMT3A/NPM1/FLT3-A680V/FLT3-ITD, DNMT3A/NPM1/FLT3-N841K, wild type, DNMT3A/NPM1/FLT3-A680V and DNMT3A/NPM1/FLT 3-D839G. Fig. 3B shows the cell populations as follows: wild type, DNMT3A/NPM1, DNMT3A, DNMT3A/NPM1/FLT3-ITD and FLT 3-D835E. Clainib treatment abrogated the vast majority of cancer cell populations containing mutations.

FIGS. 4A and 4B are scatter plots showing individual cells expressing mutant NPM1 (y-axis) in bone marrow samples from patients at diagnosis (FIG. 4A) and 35 days after induction began (FIG. 4B). Figure 4A shows that the cell population comprises the following mutations from left to right; DNMT3A/NPM1/FLT3-A680V/FLT3-ITD, DNMT3A/NPM1/FLT3-N841K, wild type, DNMT3A/NPM1/FLT3-A680V and DNMT3A/NPM1/FLT3-D839G, and finally small subcloned cells with various mutations. Fig. 4B shows the cell populations as follows: wild type, DNMT3A/NPM1, DNMT3A, DNMT3A/NPM1/FLT3-ITD and FLT 3-D835E. Clainib treatment abolished the vast majority of mutants containing cancer cells.

Fig. 5 shows various views of a longitudinal bone marrow specimen of a patient. Normal Wild Type (WT) cells appear grey. The total subclone population within the sample at diagnosis, 35 days after induction initiation and three time points during maintenance is shown. The samples show that the variation FLT3 and FLT3 activating mutations can be eliminated with combination therapy of intensive induction chemotherapy with clarianib, consolidation of high dose cytarabine (HiDAC) with clarianib, and maintenance of clarianib as a single drug for mutation elimination.

Detailed Description

While the making and using of various embodiments of the present invention are discussed in detail below, it should be appreciated that the present invention provides many applicable inventive concepts that can be embodied in a wide variety of specific contexts. The specific embodiments discussed herein are merely illustrative of specific ways to make and use the invention, and do not delimit the scope of the present invention.

To facilitate an understanding of the present invention, certain terms are defined below. Terms defined herein have meanings as commonly understood by one of ordinary skill in the art to which this invention pertains. Terms such as "a," "an," and "the" are not intended to refer to only a singular entity, but include the general class of which a specific example may be used for illustration. The terms used herein are used to describe specific embodiments of the invention, but their use does not limit the invention, except as defined in the claims.

Definition of

As used herein, the terms "measurable residual disease", "minimal residual disease" and "MRD" refer to a condition or condition in which no evidence of cancer is detectable in a subject by traditional methods (including but not limited to cytogenetics, histology). Although tumor cells may remain in vivo, the number of these tumor cells was found to be below the detection limit of conventional methods. However, these residual tumor cells are fully capable of recapitulating proliferative disorders. MRD usually occurs after a complete response or complete remission following chemotherapy, radiation therapy and/or allogeneic stem cell transplantation. MRD detection methods known in the art include flow cytometry-based methods and molecule-based methods that monitor the presence of a predetermined cell expression marker. Molecular-based MRD detection methods include PCR-based assays for the presence or absence of mutations, such as NPM1, DNMT3A, NRAS, KRAS, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP1, ZRSR2, GRB7, SRSF 7, MLL, NUP 7, ETV 7, TCL 17, rsscs 7, BRP 7, CD 7, TYK 7, 36tp 72, EZH 7, GATA 7, KIT, PHF 7, MYC, ERG, MYD 7, MPL 7, STAT 7, NF 7, BRAF, tbm 67, SETBP 7, mut 7, PHF 7, SMC 7. PCR-based methods can be used for patients with one or more of these genetic abnormalities.

As used herein, the term "subject" refers to an animal, such as a mammal or a human, that has been the subject of treatment, observation or experiment. In certain examples, the mammal or human is pediatric.

As used herein, the terms "proliferative disorder(s)" and "cell proliferative disorder(s)" refer to excessive cell proliferation of one or more subsets of cells in a multicellular organism, causing damage (i.e., discomfort or decreased life expectancy) to the multicellular organism. Cell proliferative disorders can occur in different types of animals and humans. As used herein, "cell proliferative disorder" includes neoplastic disorders.

As used herein, the term "neoplastic disorder" refers to a tumor caused by abnormal or uncontrolled cell growth. Examples of neoplastic disorders include, but are not limited to, the following disorders, for example: cancer, lymphoma, blastoma, sarcoma, and leukemia. Non-limiting examples of proliferative disorders treated by the invention include bladder cancer, breast cancer, cervical cancer, CNS cancer, colon cancer, esophageal cancer, head and neck cancer, liver cancer, lung cancer, nasopharyngeal cancer, neuroendocrine cancer, ovarian cancer, pancreatic cancer, prostate cancer, kidney cancer, salivary gland cancer, small cell lung cancer, squamous cell cancer, skin cancer, gastric cancer, testicular cancer, thyroid cancer, uterine cancer, glioma cancer, and gastric cancer. As used herein, the term "neoplastic disorder" refers to a tumor caused by abnormal or uncontrolled cell growth. Examples of neoplastic disorders include, but are not limited to, the following disorders, for example: cancer, lymphoma, blastoma, sarcoma, and leukemia. Non-limiting examples of proliferative disorders treated by the invention include bladder cancer, breast cancer, cervical cancer, CNS cancer, colon cancer, esophageal cancer, head and neck cancer, liver cancer, lung cancer, nasopharyngeal cancer, neuroendocrine cancer, ovarian cancer, pancreatic cancer, prostate cancer, kidney cancer, salivary gland cancer, small cell lung cancer, squamous cell cancer, skin cancer, gastric cancer, testicular cancer, thyroid cancer, uterine cancer, glioma cancer, and gastric cancer.

The term "recurrent genetic mutation" as used herein refers to one or more genetic mutations often found in proliferative disorders, many of which are considered highly heterogeneous diseases. A number of recurrent mutations have been shown to affect the prognosis of the disease. Examples of recurrent gene mutations include, but are not limited to, the following mutations: NPM1, DNMT3A, NRAS, KRAS, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP1, ZRSR2, GRB7, SRSF 7, MLL, NUP 7, ETV 7, TCL 17, TUSC 7, BRP 7, CD 7, TYK 7, TP 7, EZH 7, GATA 7, KIT, PHF 7, MYC, ERG, MYD 7, RAD 7, STAT 7, NF 7, KDF, KDM6 BRA3672, SETBP 7, CALR, CBL, MPL 2, PHF 7, PHCSF, MUAS 7, MUEKAS 7, SMC 7, and particularly those genes causing proliferation or PTEP/HREK/7.

The term "functionally modifying mutation" as used herein refers to one or more genetic mutations that result in a mutant protein having an activity different from that of the wild-type protein. This includes mutations which result in loss of function (mutants no longer having the function of the wild type) and gain of function (mutants which have an additional function not possessed by the wild type). Also included are activating mutations, wherein the mutations have the same activity as the wild type; however, this mutant lacks negative regulation controlling wild-type signaling.

As used herein, the term "therapeutically effective amount" refers to a dose of clarithrob, or a pharmaceutically acceptable salt thereof, administered to a subject as a single agent or in combination with another agent (e.g., a chemotherapeutic agent) that elicits the biological or medical response in the subject that is being sought by a researcher, veterinarian, medical doctor or other clinician, including alleviation of the symptoms of the disease or disorder being treated. Methods for determining therapeutically effective dosages of pharmaceutical compositions comprising the compounds of the present invention are well known in the art. Techniques and compositions for preparing useful dosage forms using the present invention are described in a number of references, including: anderson, j.e.knoben and w.g.troutman, Handbook of clinical drug data,10th ed.new York; toronto McGraw-Hill Medical pub.division,2002, pp.xvii,1148p (Anderson, Knoben, & Troutman, 2002); goldstein, W.B.Pratt and P.Taylor, Principles of drug action the basis of pharmacology,3rd ed.New York Churchill Livingstone,1990, pp.xiii,836p. (Goldstein, Pratt, & Taylor, 1990); katzung, Basic & clinical pharmacology,9th ed. (Lange Medical book), New York: Lange Medical Books/McGraw Hill,2004, pp.xiv,1202p. (Katzung, 2004); goodman, J.G.Hardman, L.E.Limbird and A.G.Gilman, Goodman and Gilman's the pharmaceutical basic of therapeutics,10th ed.New York: McGraw-Hill,2001, pp.xxvii,2148p. (Goodman, Hardman, Limbird, & Gilman, 2001); remington, the science and practice of pharmacy,20th ed. baltimore, Md. Lippincott Williams & Wilkins,2000, pp.xv,2077 p; martindale, J.E.F.Reynolds, and Royal Pharmaceutical Society of Great Britain.Council, The extra Pharmaceutical Society, 31st ed.London, Royal Pharmaceutical Society,1996, pp.xxi, 2739; and g.m.wilkes, Oncology nuclear Drug Handbook 2016,20ed.sudbury: Jones & Bartlett Publishers,2016, p.1500p. (Wilkes,2016), relevant portions of each of which are incorporated herein by reference.

As used herein, "in combination with … …" means that clarithrob or a pharmaceutically acceptable salt thereof and one or more agents are administered simultaneously or sequentially in any order, e.g., such that one agent may be administered before, simultaneously or after another agent or any combination thereof, e.g., during standard treatment procedures, such as in one cycle or more than one cycle.

As used herein, the term "chemotherapeutic agent" refers to anti-cell proliferation therapeutic agents, such as alkylating agents, antimetabolites, and natural products. Chemotherapy is known to those skilled in the art, and suitable dosages and schedules for chemotherapy should be similar to those already employed in clinical therapy, which has been administered in combination with other therapies or used alone. A variety of chemotherapeutic agents may be used in conjunction with the present invention. By way of example only, taxane compounds (e.g., docetaxel) are present at 75mg per square meter (mg/m)²) The dosage of the body surface area is safe to administer in combination with the compounds of the present invention. The skilled artisan will recognize that the dosage of the chemotherapeutic agent selected will depend on a variety of factors, such as body weight, age, sex, extent of disease, and the like, which will vary the dosage for the intended treatment in best medical practice.

As used herein, the term "alkylating agent" refers to a group of chemotherapeutic agents that typically add an alkyl group to DNA, and is now used to refer to any chemotherapeutic agent that adds a small chemical moiety to DNA. Examples of alkylating agents include, but are not limited to, carmustine, chlorambucil, cyclophosphamide, ifosfamide, lomustine, streptozotocin, temozolomide, cisplatin, carboplatin, nedaplatin, and/or oxaliplatin.

As used herein, the term "antimetabolite agent" refers to a group of chemotherapeutic agents that are structurally similar to naturally occurring chemicals in the body, which can bind to enzymes or proteins in place of the chemical, but differ therefrom in that they are sufficient to prevent termination of the normal action of the chemical in the body. Examples of antimetabolites include, but are not limited to, methotrexate, pemetrexed, raltitrexed, cytarabine, fludarabine, fluorouracil, floxuridine, capecitabine, and/or gemcitabine.

As used herein, the term "natural product" refers to a group of chemotherapeutic and/or chemotherapeutic agents that are produced by secondary metabolic pathways, purified organic compounds originally isolated from a living organism. Examples of 20 natural products include, but are not limited to, vinblastine, vinorelbine, vincristine, vindesine, vinflunine, paclitaxel, docetaxel, cabazitaxel, etoposide, teniposide, topotecan, irinotecan, daunorubicin, doxorubicin, idarubicin, epirubicin, valrubicin, mitoxantrone, bleomycin, estramustine, and/or mitomycin.

As used herein, the term "composition" refers to a product comprising the specified ingredients in the specified amounts, as well as any product which results, directly or indirectly, from combination of the specified ingredients in the specified amounts.

Single cell DNA sequencing can analyze recurrent gene mutations at the single cell level. This can eliminate early obstacles to monitoring measurable residual disease (Eastburn et al, 2017) due to the relatively high detection limits and other disadvantages of conventional methods. To date, such methods have been used primarily in academic laboratory settings to discover genetic mutations associated with particular diseases, new potentially recurrent mutations, or genetic mutations or alterations that may confer resistance to a therapeutic agent. But these methods have potentially powerful uses: residual disease measurable in a patient is monitored to determine whether the patient may benefit from a particular therapeutic or intervention to achieve or maintain disease remission.

The present invention is based, at least in part, on the following findings: administration of klebside or a separate treatment of klebside sequentially after standard chemotherapy reduces or eliminates MRD, as well as cells isolated from blood or bone marrow of subjects with proliferative disorders, during treatment of the subject. The invention includes the use of a compound of the invention together with standard chemotherapy to reduce or eliminate MRD in a subject having at least one recurrent genetic mutation as measured by single cell genome sequencing.

Claranib (4-piperidinamine, 1- [2- [5- [ (3-methyl-3-oxetanyl) methoxy ] -1H-benzimidazol-1-yl ] -8-quinolinyl ] and pharmaceutically acceptable salts thereof, including but not limited to kraanib besylate, kraanib phosphate, kraanib lactate, kraanib hydrochloride, kraanib citrate, kraanib acetate, kraanib tosylate, and kraanib succinate, but may also be free of salts. Inc.), U.S. patent application publication No. US 2005/0124599(Pfizer, Inc. ) And U.S. patent No.7,183,414(Pfizer, Inc. ) The relevant portions are incorporated herein by reference. Krelanide is a protein tyrosine kinase inhibitor that selectively inhibits the FLT3 mutation, including the FLT3 ITD and FLT3 TKD mutations. Unlike previous FLT3 inhibitors of the prior art, there is evidence that the besylate form of kramerin is very effective in eliminating the percentage of circulating peripheral blood blasts and the percentage of myeloid blasts in heavily preconditioned FLT3 mutant AML. Clinanib is currently being investigated in combination with standardized therapy for use in combination with newly diagnosed FLT3 mutant AML, relapsed or refractory constitutively activated FLT3 mutant primary AML, or AML secondary to myelodysplasia.

In one embodiment, the compounds of the invention have formula I:

or a pharmaceutically acceptable salt or solvate thereof, is an amount effective for the treatment or prevention of a proliferative disease selected from at least one of: leukemia, myeloma, myeloproliferative disease, myelodysplastic syndrome, idiopathic hypereosinophilic syndrome (HES), bladder cancer, breast cancer, cervical cancer, CNS cancer, colon cancer, esophageal cancer, head and neck cancer, liver cancer, lung cancer, neuroendocrine cancer, ovarian cancer, pancreatic cancer, prostate cancer, kidney cancer, salivary gland cancer, small cell lung cancer, skin cancer, stomach cancer, testicular cancer, thyroid cancer, uterine cancer, and hematologic malignancies. As known to those skilled in the art, pharmaceutically acceptable salts, including hydrochloride, phosphate and lactate salts, are prepared in a manner similar to besylate.

The compounds of the invention may be administered systemically (e.g., orally, intravenously, subcutaneously, intramuscularly, intradermally, or parenterally). The compounds of the invention may also be administered topically to a subject.

The compounds of the invention may be formulated in slow release or fast release formulations for the purpose of allowing the compounds of the invention to contact the target tissue for a desired time period.

Ingredients suitable for oral administration include solid forms (e.g., pills, tablets, caplets, capsules, granules, and powders), and liquid forms (e.g., solutions, emulsions, and suspensions). Forms for parenteral administration include sterile solutions, emulsions and suspensions.

The daily dosage of the compounds of the invention may vary within a wide range from 15 to 500, 25 to 450, 50 to 400, 100 to 350, 150 to 300, 200 to 250, 15, 25, 50, 75, 100, 150, 200, 250, 300, 400, 450 or 500 mg/day. The compounds of the present invention may be administered once, twice, three times or more daily. Optimal dosages to be administered may be determined by those skilled in the art and will vary with the study compound employed, the mode of administration, the time of administration, the strength of the preparation, the particulars of the disease condition. One or more factors related to the subject's characteristics, such as age, weight, and diet, require adjustment of the dosage. Techniques and compositions for preparing useful dosage forms using clariant are described in one or more of the following references: anderson, Philip o.; knoben, James e.; troutman, William G, eds., "handbook of clinical drug data", tenth edition, McGraw Hill, 2002; pratt and Taylor, eds., (principles of drug action), third edition, churchil Livingston, new york, 1990; katzeng, editors, "basic and clinical pharmacology", ninth edition, McGraw Hill, 20037 ybg; goodman and Gilman, editors, "pharmacological basis for therapeutic agents", tenth edition, McGraw Hill, 2001; remington pharmaceutical sciences, twentieth edition, Lippincott Williams & Wilkins, 2000; martindale, Extra Pharmacopoeia, thirty-second edition (pharmaceutical press, london, 1999); relevant portions are incorporated herein by reference.

The dosage unit for clarithrob may be a single compound or a combination thereof with other compounds, such as enhancers. These compounds may be mixed together to form ionic or even covalent bonds. The compounds of the invention may be administered orally, intravenously (by injection or infusion), intraperitoneally, subcutaneously, or intramuscularly, all using dosage forms well known to those of ordinary skill in the pharmaceutical arts. Depending on the particular site or method of delivery, the compounds of the present invention may be provided to a patient in need of treatment, including the compounds of formula I, using various dosage forms, such as tablets, capsules, pills, powders, granules, elixirs, tinctures, suspensions, syrups, and emulsions.

The administration of clarithromycin is generally carried out in admixture with suitable pharmaceutical salts, buffers, diluents, extenders, excipients, and/or carriers (collectively referred to herein as pharmaceutically acceptable carriers or carrier materials) selected based on the intended form and mode of administration. Depending on the optimal site of administration, the clarithrob may be formulated for a particular form of, e.g., maximum and/or consistent dosage for oral, rectal, topical, intravenous injection, or parenteral administration. Although the clarithrob may be administered alone, it is generally provided in a stable salt form in admixture with a pharmaceutically acceptable carrier. The carrier may be a solid or a liquid, depending on the type and/or location of administration selected.

Preparation of the compounds of the invention. A general synthetic method useful for preparing compounds of formula I is provided below: U.S. patent No.5,426,300, 5990146 (published 1999 11/23) (Warner-Lambert Co.), and PCT published application No. WO 99/16755 (published 1999 4/8) (Merck & Co.) WO 01/40217 (published 2001/7) (Pfizer, Inc.), U.S. patent application publication No. US 2005/0124599(Pfizer, Inc.), and U.S. patent 7,183,414(Pfizer, Inc.), relevant portions of which are incorporated herein by reference.

Pharmaceutically acceptable salts such as hydrochloride, phosphate and lactate are prepared in a manner similar to besylate and are well known to those skilled in the art. The following representative compounds of the invention are for illustrative purposes only and are in no way meant to limit the invention, including crilanib, such as crilanib tosylate, crilanib phosphate, crilanib lactate, crilanib hydrochloride, crilanib citrate, crilanib acetate, crilanib tosylate, and crilanib sulfonate.

The invention also provides prophylactic and therapeutic methods for treating a subject at risk of or susceptible to developing a cell proliferative disorder driven by abnormal kinase activity of FLT3 receptor tyrosine kinase. In one example, the present invention provides a method for preventing a cell proliferative disorder associated with FLT3, comprising administering to a subject a prophylactically effective amount of a pharmaceutical composition comprising a compound of the present invention. Administration of the prophylactic agent may occur prior to the onset of symptoms characteristic of FLT 3-driven cell proliferative disorders, thereby preventing or alternatively delaying the progression of the disease or disorder.

As used herein, the terms "mutant FLT 3", "disorder associated with FLT 3" or "disorder associated with FLT3 receptor" or "disorder associated with FLT3 receptor tyrosine kinase" or "FLT 3 driven cell proliferative disorder" refer to diseases involving or associated with FLT3 activity, such as mutations that result in constitutive activation of FLT 3. Examples of "disorders associated with FLT 3" include disorders due to overstimulation of mutant FLT3 in FLT3, or disorders due to abnormally high amounts of FLT3 activity due to abnormally high amounts of mutations in FLT 3. The overactivity of FLT3 is known to be involved in the pathogenesis of a number of diseases, including cell proliferative disorders, neoplastic disorders, and cancer, as listed below.

In mutant FLT3 tumors, altered presence or expression of one or more gene mutations or deletions within the coding region or intron-exon boundary regions may lead to a decreased prognosis. In addition to the preexisting FLT3 mutation, the additional gene mutations disclosed herein significantly reduce the prognosis of the patient. Poor prognosis can refer to any negative clinical outcome, such as, but not limited to, decreased likelihood of survival (e.g., overall survival, recurrence-free survival, or metastasis-free survival), decreased survival time (e.g., less than 5 years or less than 1 year), presence of malignancy, increased disease severity, decreased response to therapy, increased recurrence of tumor, increased metastasis, and the like. In particular examples, poor prognosis decreases the chance of survival (e.g., survival equal to or less than 60 months, e.g., 50 months, 40 months, 30 months, 20 months, 12 months, 6 months, or 3 months, from diagnosis or first treatment).

One aspect of the invention relates to the use of TAPESTRI^TMSingle cell sequencing analysis of recurrent AML gene mutations by platform. To use the platform, a cell suspension was introduced using microfluidics, and then each cell was encapsulated in an oil droplet together with a protease to aid in the isolation of DNA. The cells were then lysed and returned to TAPESTRI^TMOn the platform, each mononuclear was encapsulated with a unique DNA-based barcode linked in oil droplets to a master mix of acrylamide-based beads and PCR and a primer set for recurrent AML mutant genes. These droplets were deposited directly into the PCR tube and exposed to UV light to release the barcode. Subsequently, the barcode genomic DNA within the droplets can be amplified according to standard PCR amplification techniques. In the same regard, PCR products were subsequently isolated using standard molecular biology techniques, and libraries were prepared for next generation sequencing compatible with the Illumina platform (including MiSeq, HiSeq and NovaSeq) and then sequenced on one of the validated Illumina platforms (including MiSeq, HiSeq and NovaSeq). In the same aspect, sequencing comprises at least 1,000,000 reads per sample with an allele dropout rate of at most 10%. The next generation sequencing data can be analyzed for at least one, but is not limited to, genetic variant calls generated using the tapperi pipeline, followed by a final analysis of the tapperi Insight, including determining co-occurring genetic mutations, or standard Next Generation Sequencing (NGS) analysis methods well known to those skilled in the art.

In one embodiment, the presence or absence of one or more mutations in the relapsed AML mutant gene give rise to a patient-specific single-cell mutation profile associated with a proliferative disorder.

In one aspect, the above steps are repeated for at least one additional longitudinal serial sample from the subject, and then the presence or absence of one or more mutations that change over time with the combination of chemotherapy and FLT3-TKI is determined in conjunction with the longitudinal single cell genomic mutation profile, thereby giving a method for determining MRD status from an increase or decrease in the percentage of patient-specific single cell mutation profile after treatment.

In another embodiment, the sample to be tested in the method of the invention comprises bone marrow or peripheral blood.

In one embodiment, the method of the invention comprises the use of tapesti^TMThe platform prepares genomic DNA for recurrent AML gene mutations of single cells, which is then sequenced on Illumina sequencing platforms including but not limited to MiSeq, HiSeq and NovaSeq.

The invention also includes a method of removing measurable residual disease in a subject with a proliferative disorder, comprising administering to said patient a therapeutically effective amount of clainib, or a pharmaceutically acceptable salt thereof, and standard chemotherapy, against a proliferative disorder characterized by dysregulated FLT3 activity and at least one recurrent AML gene mutation, selected from one of the following: leukemia, myeloma, myeloproliferative disease, myelodysplastic syndrome, Hodgkin's disease, myeloma, Acute Lymphocytic Leukemia (ALL), Acute Myeloid Leukemia (AML), Acute Promyelocytic Leukemia (APL), Chronic Lymphocytic Leukemia (CLL), Chronic Myeloid Leukemia (CML), Chronic Neutrophilic Leukemia (CNL), Acute Undifferentiated Leukemia (AUL), Anaplastic Large Cell Lymphoma (ALCL), prolymphocytic leukemia (PML), juvenile myelomonocytic leukemia (JMML), adult T-cell ALL, and myelodysplasia with trilineage (AMLI)^TMDS), Mixed Lineage Leukemia (MLL), myelodysplastic syndromes (MDSs), myeloproliferative disorders (MPD), or Multiple Myeloma (MM).

The present invention includes the following method of preparing single cell DNA sequencing. One example is a single cell multigroup assay for assaying from the same cell (e.g., TAPESTRI)^TM) And simultaneously detecting single nucleotide variation, copy number variation and protein variation. Via aThe gradient separated mononuclear cells from the bone marrow sample, resuspended in 10% DMSO solution, and incubatedFreezing at-20 ℃ until required. Single cell suspensions were prepared from thawed monocyte samples to final concentrations as indicated by the manufacturer's instructions and then loaded into TAPESTRI^TMOn the instrument. According to the manufacturer, TAPESTRI^TMThe platform uses microfluidic technology to separate individual cells, encapsulate each cell within a lipid droplet, and add proteases to each droplet to aid in DNA separation. According to TAPESTRI^TMInstructions for platform manufacturer, Using TAPESTRI^TMThe platform and Thermo Fisher simplex thermocycler (catalog No. a24811, or equivalent) were used for cell encapsulation, targeted PCR, and next generation library preparation. The prepared single cell DNA pools were sequenced using the MiSeq instrument from Illumina according to the manufacturer's instructions. Analysis of these next generation sequencing data was performed by first processing the sequencing data using a tapesti pipeline (available on the Mission Bio website) to ultimately generate variant calls. Then leading the generated loom file into TAPESTRI^TMBioinformatics software, Insight, can be used to identify relevant mutations, including co-occurring and rare mutations.

Example 1

In 2016, a 54 year old female was diagnosed with AML with monocyte differentiation. The patient exhibited 63% of myeloid blasts. At diagnosis, molecular testing of batch (bulk) DNA sequencing showed that the patient had FLT3-ITD, FLT3-N814K, FLT3-A680V, DNMT3A and NPM1 mutations. This is a particularly high risk patient with multiple FLT3 mutations associated with poor prognosis, with the emergence of NPM1-FLT3^ITDThe DNMT3A mutation is also associated with a poor prognosis (Papaemmanuil et al, 2016). Furthermore, monocyte differentiation is associated with CD163 overexpression, which has been observed retrospectively in diagnostic bone marrow samples of this patient, and also with poor prognosis (van Galen et al, 2019). To treat the patient's disease and overcome the FLT3 mutation, the patient was given oral kleanib besylate in combination with standard chemotherapy in a clinical trial against a newly diagnosed AML patient with an activating FLT3 mutation. With induction chemotherapy (including 7 days cytarabine and 3 days daunorubicin), and oral administration of Claranib besylate (3 times daily) started on day 10 of treatment100mg each time) to treat the patient.

Bone marrow biopsy on day 35 of treatment showed a reduction in medulloblasts to less than 5% and confirmed patients achieved morphologically complete remission of AML in response to klearnib combination chemotherapy. To maintain remission, the patient subsequently received four cycles of high dose cytarabine consolidation chemotherapy. During each cycle, the patient received a standard dose of cytarabine chemotherapy, then oral administration of 100mg of klebside besylate three times a day starting 48 hours after the last chemotherapy and continuing until 72 hours before the start of the next chemotherapy cycle. Bone marrow specimens after completion of consolidation chemotherapy (day 237 of treatment) confirmed that the patient was still in morphologically remission. Due to the aggressiveness of AML mutated in FLT3, patients continued to receive a single-agent klearnib besylate maintenance therapy for a period of 12 months, three times daily, 100mg each. To monitor the patient's condition, bone marrow samples are taken periodically throughout the maintenance treatment period, confirming that the patient is still in remission. The last bone marrow sample at the completion of maintenance treatment (day 406 of treatment) confirmed that the patient was still in morphologically remission.

Single cell sequencing was used to analyze longitudinal bone marrow samples obtained throughout the course of treatment. These samples included a baseline sample (induction D1), a sample obtained at the completion of induction combination therapy (induction D35), a sample obtained at the completion of consolidation combination therapy (consolidation D237), a sample obtained at approximately one quarter of the time of cremains maintenance therapy with a single dose of benzenesulfonic acid (maintenance D294), and a final sample obtained at the completion of cremains maintenance therapy with a single dose of toluenesulfonic acid (maintenance D406). Table 1 summarizes the samples obtained, the number of cell sequencing, the number of reads per sample and the allele dropout rate per sample.

Table 1 is a summary of sequencing runs using single cell dna (scdna) analysis via the tapesti platform (Mission Bio, USA). Bone marrow samples of newly diagnosed FLT3-AML patients were collected longitudinally and analyzed retrospectively by cytogenomic sequencing. The total labeled cells for all bone marrow analytes was 12699 cells, each individual cell analyzed by single cell DNA library and sequencing methods. Average read for all samples was 17.6M, eachAmplicons averaged 99 reads. The number of reads that allowed high pool (panel) uniformity [ 92-94%](ii) a And on average, the allele shedding rate is low. Cell encapsulation, targeted PCR and next generation library preparation were performed using a tapesti instrument and a Thermo Fisher simplex thermocycler (catalog No. a24811, or equivalent) according to the manufacturer's instructions. The single cell DNA pool prepared was sequenced using the MiSeq instrument from Illumina according to the manufacturer's instructions. Analysis of the next generation sequencing data is performed by first processing the sequencing data using the tapesti pipeline to ultimately generate variant calls. Then, the generated room file is imported into the TAPESTRI^TMBioinformatics software, Insight, was used to identify relevant variants of FLT3-AML, including co-occurring and rare mutations.

TABLE 1 Single cell sequencing summary data of bone marrow samples from newly diagnosed FLT3-AML patients.

ADO, allele dropout rate

Single cell sequencing revealed many genetic mutations not visible using bulk sequencing techniques, including FLT3-D835E, FLT3-D839G, KRAS-G12D, NRAS-G13V, and two separate DNMT3A mutations R882C and R882H (only DNMT3A-R882C mutations can be seen using bulk sequencing Single cell sequencing also confirmed the presence of FLT3-ITD, FLT3-A680V, FLT3-N814K, and NPM1 mutations Table 2 details the mutations found in the diagnosed (induced D1) samples.

Table 2 is a summary of single cell sequencing of FLT3 variants, FLT3 activating mutations and co-occurring mutations in patients with newly diagnosed FLT3-AML variant calls using tapesti pipelines (pipeline) for next generation (Miseq) sequencing of single cell DNA libraries. Analysis shows the variant gene family, nucleotide changes observed, mutated encoded proteins within the gene family, and the effect on the transcriptional coding of the proteins. In addition, deleterious annotation of genetic variants using the neural network (DANN) indicates the likelihood of being truly positive, with a maximum score of 1[ range: 0-1]. Although limited by scope, the MissionBio Insight software does not provide a6580V and FLT3-ITD encoding for clinical significance, the clinical significance of each mutation is pathogenic. Each variant subclone also had the percent of genotyping from the total cells analyzed, [ range: 66% to 99% ] depends on the variant.

Table 2 summary of single cell sequencing of FLT3 variants, FLT3 activating mutations and co-occurring mutations detected in newly diagnosed FLT3-AML patients.

The longitudinal bone marrow sample obtained allows tracing the above identified mutations during the course of treatment of the patient. Table 3 below shows some of these mutations lost following induction and consolidation chemotherapy. After consolidation, FLT3-A680V, FLT3-D839G, KRAS-G12D, DNMT3A-R882C and DNMT3A-R882H mutations still exist. The DNMT3A mutation was age-related and did not necessarily indicate evidence of potential recurrence under the low mutation load seen here. These mutations are known to persist after treatment. The persistent presence of FLT3 and KRAS mutations puts patients at risk of relapse, and their presence is of concern after four cycles of consolidation chemotherapy are induced and completed. However, after approximately two months of single dose klearnib tosylate maintenance therapy, the remaining FLT3 and KRAS mutations were cleared. These mutations were still absent at the completion of maintenance therapy, confirming the benefit of the benzosulfonate klearnib single agent maintenance therapy in suppressing the variant FLT3 mutation that may lead to relapse.

Table 3 is a single cell DNA analysis that revealed 4 different FLT3 subclones at diagnosis, including FLT3-ITD and three FLT3 activating mutations (D839G, a680V, N841K), with a co-occurrence of NPM1 and two DNMT3A mutations (R882C, R882H). Leukemic clones with NRAS or KRAS activating mutations, excluding FLT3 mutant clones. After the first induction cycle, single cell sequencing showed low levels of detection of FLT3-ITD (3%), FLT3-D839G (3%) and FLT3-D835E (1%). Analysis of single cell DNA after consolidation showed clearance of NPM1 and FLT3-ITD, but showed low levels of detected variant FLT3-D839G (1%) and FLT3-a680V (1%) clones. The patient received a one-year maintenance therapy with clainib and by day 79 of maintenance therapy all variant FLT3 clones were cleared.

Table 3 single cell sequencing data of variant allele frequencies of FLT3 variant, FLT3 activating mutation and co-occurring mutations in longitudinal bone marrow samples of newly diagnosed FLT3-AML patients.

The results are graphically represented in the following figure 1 in tabular form. The co-occurrence of identified mutations within the cells is also shown. Each vertical bar represents the entire population of bone marrow cells tested in the sample identified at the bottom of the bar. As shown in the right legend, each bone marrow cell population with some sets of 10 mutations was assigned a color. The relative size of each color within the bar is the relative proportion of each different population or clone. The samples obtained at diagnosis showed the greatest clonal heterogeneity. After induction of chemotherapy, many clonal populations have cleared. Finally, only wild-type cells (grey) and only clones carrying the DNMT3A-R882C mutation (green) were retained after maintenance treatment. It is important to note that in this data representation, due to format limitations, the small clonal populations corresponding to persistent FLT3-A680V, FL3-D839G, KRAS-G12D and DNMT3A-R882H in 1% cells are not shown.

FIG. 1 shows a graphical interpretation of single cell sequencing data for variant allele frequencies of FLT3 variant, FLT3 activating mutation and co-occurring mutations in longitudinal bone marrow samples of newly diagnosed FLT3-AML patients.

Fig. 2A and 2B are scatter plots showing individual cells expressing mutant KRAS (y-axis) in bone marrow samples of patients at diagnosis (fig. 2A) and 35 days after induction began (fig. 2B). Figure 2A shows that the cell population comprises the following mutations from left to right; DNMT3A/NPM1/FLT3-A680V/FLT3-ITD, DNMT3A/NPM1/FLT3-N841K, wild type, DNMT3A/NPM1/FLT3-A680V, DNMT3A/NPM1/FLT3-D839G, and finally small subcloned cells with various mutations. Fig. 2B shows the cell populations as follows: wild type, DNMT3A/NPM1, DNMT3A and DNMT3A/NPM1/FLT 3-ITD. Treatment with clainib abolished the vast majority of mutants containing cancer cells.

Fig. 3A and 3B are scatter plots showing individual cells expressing mutant DNMT3 (y-axis) in bone marrow samples of patients at diagnosis (fig. 3A) and 35 days after induction began (fig. 3B). Figure 3A shows that the cell population comprises the following mutations from left to right; DNMT3A/NPM1/FLT3-A680V/FLT3-ITD, DNMT3A/NPM1/FLT3-N841K, wild type, DNMT3A/NPM1/FLT3-A680V and DNMT3A/NPM1/FLT 3-D839G. Fig. 3B shows the cell populations as follows: wild type, DNMT3A/NPM1, DNMT3A, DNMT3A/NPM1/FLT3-ITD and FLT 3-D835E. Treatment with clainib abolished the vast majority of mutants containing cancer cells.

FIGS. 4A and 4B are scatter plots showing individual cells expressing mutant NPM1 (y-axis) in a bone marrow sample of a patient at diagnosis (FIG. 4A) and 35 days after induction began (FIG. 4B). Figure 4A shows that the cell population comprises the following mutations from left to right; DNMT3A/NPM1/FLT3-A680V/FLT3-ITD, DNMT3A/NPM1/FLT3-N841K, wild type, DNMT3A/NPM1/FLT3-A680V and DNMT3A/NPM1/FLT3-D839G, and finally small subcloned cells with various mutations. Fig. 4B shows the cell populations as follows: wild type, DNMT3A/NPM1, DNMT3A, DNMT3A/NPM1/FLT3-ITD and FLT 3-D835E. Treatment with clainib abolished the vast majority of mutants containing cancer cells.

Fig. 5 shows various views of a longitudinal bone marrow specimen of a patient. Normal Wild Type (WT) cells are shown. The graph represents the total subclone population in the sample at diagnosis, 35 days after induction initiation, and at three time points during maintenance. The samples show that the variation FLT3 and FLT3 activating mutations can be eliminated with combination therapy of intensive induction chemotherapy with clarianib, consolidation of high dose cytarabine (HiDAC) with clarianib, and maintenance of clarianib as a single drug for mutation elimination.

Example 2

One 68 year old male diagnosed AML in 2016. At the time of diagnosis, molecular testing using a bulk DNA sequencing method showed that this patient had wild-type FLT3 and carried mutations in the BCOR, NRAS and U2AF1 genes, which were considered pathological changes. Initially, patients received standard cytarabine/anthracycline-based chemotherapy regimens. The patient did not respond to the initial treatment and was considered refractory AML. To treat the patient's disease and overcome the elevation of FLT3 ligand (which has been reported to occur after several consecutive rounds of chemotherapy, even in FLT3 wild-type patients), the relapsed/refractory patient is provided with oral klearnib besylate in combination with rescue chemotherapy. At baseline, the patient had a 17% proportion of myeloid blasts. The patient received rescue chemotherapy including fludarabine for 5 days, cytarabine for 5 days, idarubicin for 3 days and G-CSF, and then starting on day 7 of treatment the benzosulfonic acid klearnib was administered 3 times daily at 100mg each time.

Bone marrow biopsy on day 32 of treatment showed that the patient had less than 5% reduction in myeloid blasts, confirming that the patient achieved complete morphological remission following the claimanib combination chemotherapy. At this time, no BCOR, NRAS and U2AF1 mutations present at diagnosis and study enrollment were detected using the batch DNA sequencing method.

This study was aimed at determining the safety of criollanib in combination with standard rescue chemotherapy in relapsed/refractory AML patients, with patients continuing only 1-2 cycles of the induced criollanib combination therapy study. Since the patient achieved a morphological remission after one cycle, the patient completed the study treatment as per the protocol and remained alive and in remission during the last follow-up. This example demonstrates the ability of klearnib combination therapy to eliminate malignant leukemia cells in FLT3 wild-type relapsed/refractory AML patients.

Example 3

One 36 year old male diagnosed AML in 2016. At the time of diagnosis, molecular testing by batch DNA sequencing methods showed that the patient had FLT3-ITD, NRAS and NPM1 mutations. To treat the patient's disease and overcome the FLT3 mutation, the patient was provided with an oral kleanib besylate in combination with a standard chemotherapy regimen in a clinical trial directed to a newly diagnosed AML patient carrying the FLT3 mutation. At baseline, the proportion of myeloid blasts was 8%. An induction chemotherapy comprising 7 days of cytarabine and 3 days of daunorubicin was administered to the patient, and the patient started to take oral administration of klebside besylate 3 times a day, 100mg each time, from day 10 of the treatment.

Bone marrow biopsy on day 24 of treatment showed a reduction in the proportion of medulloblasts to 5%, confirming that the patient achieved complete morphological remission in response to the kliranine combination therapy. At this point, the FLT3-ITD mutation at the time of diagnosis (other mutations that appeared at the time of non-test diagnosis) was no longer detected using PCR-based assays. To maintain remission, patients underwent a cycle of high-dose cytarabine consolidation chemotherapy beginning with oral administration of 100mg of klearnib besylate three times a day 48 hours after the last dose of chemotherapy. One cycle after completion of consolidation therapy, bone marrow samples taken on day 98 of treatment confirmed that the patient was still in remission and that the at-diagnosis FLT3-ITD mutation was still not detected by standard PCR testing. This example illustrates the ability of the clainib combination to eliminate malignant leukemia cells and the FLT3-ITD mutation in newly diagnosed AML patients.

Example 4

A 59 year old male diagnosed AML in 2017. Molecular testing of the bulk DNA sequencing method at the time of initial diagnosis showed that the patient had FLT3-D835V, FLT3-D835E, DNMT3A, NRAS, RUNX1, BCOR and U2AF1 mutations. To treat the patient's disease and overcome the FLT3 mutation, the patient was provided with an oral kleanib besylate in combination with a standard chemotherapy regimen in a clinical trial directed to a newly diagnosed AML patient carrying the FLT3 mutation. At baseline, the proportion of myeloid blasts was 70%. The patients received two cycles of induction chemotherapy, including 7 days of cytarabine and 3 days of idarubicin, orally administered with kraelanib besylate three times a day, 100mg each, starting on day 10 of treatment.

Bone marrow biopsy on day 50 of treatment showed that the patient had decreased medulloblasts to less than 5%, confirming that the patient achieved complete morphologic remission in response to the klearnib combination therapy. At this time, the FLT3 mutation present at the time of initial diagnosis was not detected using the batch NGS method (D835V and D835E). This example demonstrates the ability of the clainib combination to eliminate malignant leukemia cells and multiple FLT3 mutations in newly diagnosed AML patients.

Example 5

One 36 year old female was diagnosed with AML in 2012. At the time of diagnosis, molecular testing indicated that the patient had the FLT3-D835 mutation. Initially, the patient received standard induction chemotherapy and bone marrow transplant therapy. Unfortunately, the patient subsequently relapsed and received rescue chemotherapy, achieving a transient remission, and then relapsed again. At the second recurrence, the patient was found to still carry the FLT3-D835 mutation, as well as mutations in the NPM1, NOTCH1, CEBPA and WT1 genes. To treat the patient's disease and overcome the FLT3-D835 mutation, the patient was provided with an oral kleanib besylate regimen in a clinical trial of AML patients with an activating FLT3 mutation for relapse/refractory. At baseline, the patient showed 90% myeloid blasts. The patient was treated with a single dose of klearnib besylate at a dose of 200mg/m²Three times daily.

Bone marrow biopsy on day 53 of treatment showed that the patient had decreased medulloblasts to less than 5% and the patient was determined to achieve complete morphological remission (incomplete hematological recovery) in response to kleylanib monotherapy. At this time, the FLT3-D835 mutation present at diagnosis was not detected using PCR-based detection. This example illustrates the ability of single drug claimanic therapy to clear malignant leukemic blast cells and FLT3-D835 mutations in relapsed/refractory AML patients receiving severe pretreatment.

Example 6

An 87 year old female had confirmed diagnosis of AML in 2014. At the time of diagnosis, molecular testing indicated that the patient had the FLT3-ITD mutation. Initially, the patient received a low dose standard induction chemotherapy treatment followed by sorafenib maintenance treatment; but did not achieve complete morphological remission and the patient developed disease within 5 months. Molecular testing performed after sorafenib treatment showed that this patient had acquired the FLT3-D835 mutation and a second FLT3-ITD mutation. In addition, bulk DNA sequencing revealed mutations in the NRAS and RUNX1 genes. To treat the patient's disease and overcome FLT3-ITD and FLT3-D835 mutations, AML patients with activating FLT3 mutations for relapse/refractoryIn a clinical trial of (a), the patient is provided with oral klearnib besylate. At baseline, the patient showed 68% myeloid blast. The patient received a single dose of 200mg/m of kleanib besylate²Three times daily.

Bone marrow biopsy on day 27 of treatment showed a reduction of 7% in patient medulloblasts, confirming that the patient achieved a morphological partial remission in response to klearnib monotherapy. At this time, the allele ratio of one of the FLT3-ITD mutations was reduced by 75%, and no second ITD mutation was detected. This example illustrates the ability of a single drug, crealanib, to significantly reduce malignant leukemic blast cells and reduce the mutational burden of multiple FLT3 mutations in relapsed/refractory patients.

Example 7

A 54 year old female was diagnosed with AML in 2016. Which diagnoses that bone marrow aspirate is sent for NGS of cancer-associated genes. She was found to have FLT3-ITD, FLT3-I836del, FLT3-N841I, FLT3-V491L, FLT3-V592A, IDH2, NMP1 and SRSF2 mutations. To treat the patient's disease and overcome the FLT3-D835 mutation, the patient was provided with oral kleanib besylate in combination with standard chemotherapy in a clinical trial of newly diagnosed AML patients with activating FLT3 mutation. At baseline, the patient showed 95% myeloid blasts. The patient received an induction chemotherapy treatment comprising 7 days of cytarabine and 3 days of idarubicin, followed by 100mg of klebside besylate three times a day starting on day 10 of the treatment.

Bone marrow biopsy on day 27 of treatment showed a decrease of 2% in patient medulloblasts, confirming that the patient achieved complete remission in response to the kliranine combination chemotherapy. At this time, no FLT3-ITD and FLT3-I836del were found by molecular detection; no other mutations were detected. To maintain remission, the patient was then given a four cycle bolus dose of cytarabine consolidation chemotherapy. During each cycle, patients received standard doses of cytarabine chemotherapy, followed by oral administration of klebside besylate 48 hours after the last chemotherapy, three times a day, 100mg each, for up to 72 hours before the start of the next chemotherapy cycle. Due to the aggressiveness of AML mutated in FLT3, the patient then continues to receive 100mg of the single drug klearnib besylate three times a day for 21 months, also called maintenance therapy.

Example 8

One boy was diagnosed with t (9; 11) + AML at 2016, month 4. He received two cycles of cytarabine, daunorubicin, etoposide (ADE) treatment followed by one cycle of each of cytarabine etoposide (AE) and mitoxantrone cytarabine (MA), respectively, with remission obtained within two years. By the end of 2018, patients had relapsed leukemia and confirmed extramedullary disease in the sinuses, orbit and sphenoids. Subsequently, the patient received one cycle of fludarabine, cytarabine and G-CSF (FLAG), but did not respond to the treatment. The patient again received FLAG and added gemtuzumab ozogamicin (gemtuzumab ozogamicin) and azacytidine, obtaining flow cytometry-negative relief of measurable residual disease, and then allogeneic stem cell transplantation of umbilical cord stem cells. The patient then relapsed a second time in 2019, when the patient was found to have the FLT3-a848P mutation by bulk DNA sequencing. The patient was then enrolled in a clinical trial and received a cycle of high doses of cytarabine and idarubicin with venetocks (venetocalax), but the patient did not respond to the treatment. The patient then received three doses of liposomal chemotherapy (daunorubicin and cytarabine)And gemtuzumab ozogamicin); the oral administration is started after five days, and 66.7mg/m²Kralonib besylate. After one month, complete morphological remission was found with no recovery of counts. The patient adhered to klearnib before receiving another allogeneic stem cell transplant. Currently, the patient is still in remission for more than 100 days after transplantation.

The invention includes a method of treating a subject having a proliferative disorder comprising wild-type FLT3 with or without one or more co-occurring FLT3 mutations, the method comprising, consisting essentially of, or consisting of: administering to the subject a therapeutically effective amount of clainib, or a pharmaceutically acceptable salt thereof, in combination with at least one of an alkylating agent, an antimetabolite agent, a natural product, or a combination thereof. In another aspect, a method of treating a subject suffering from a proliferative disorder comprising wild-type FLT3 having one or more co-occurring RAS mutations, comprising administering to the subject a therapeutically effective amount of creylanib, or a pharmaceutically acceptable salt thereof, and at least one of an alkylating agent, an antimetabolite agent, a natural product, or a combination thereof. In another aspect, is a method of preventing recurrence of a proliferative disorder; comprising administering a therapeutically effective amount of clainib, or a pharmaceutically acceptable salt thereof, in a single agent or in combination with another agent. In one aspect, the proliferative disorder is characterized by comprising one or more function-altering mutations and at least one recurrent genetic mutation. In one aspect, minimal residual disease is detected by: obtaining a sample from a subject; performing single cell sequencing of the genetic code of the above gene, wherein the sequencing comprises at least 1,000,000 reads per sample; and analyzing only samples having an allele dropout rate of 10% or less. In another aspect, the presence or absence of one or more mutations in the above genes that produce a patient-specific single-cell mutation profile associated with a proliferative disorder is found. In another aspect, the recurrent gene mutation is present in at least one of: FLT3, NPM1, DNMT3A, NRAS, KRAS, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP 2, ZRSR2, GRB 2, SRSF2, MLL, NUP 2, ETV 2, TCL 12, TUSC 2, BRP 2, CD 2, RSTYK 2, TP 2, EZH2, GATA2, KIT, PHF 2, MYC, ERG, MYD 2, RAD2, STAT 2, NF 2, BRAF, RSRM 6 2, SETBP 2, CSF, CBL, KMT2, KMT2, MUAS 2, SMC 36. In another aspect, the FLT3 mutations found include at least one of: FLT3-ITD, FLT3-TKD, or other FLT3 mutant variants. In another aspect, the FLT3-TKD mutations include point mutations that result in at least one alteration or deletion in F612, L616, K663, M664, M665, N676, a680, F691, a833, R834, D835, I836, D839, N841, Y842 or a 848. In another aspect, FLT3 variant mutations include point mutations that result in an alteration or deletion of at least one of: l20, D324, K429, L442, E444, S451, V491, Y572, E573, L576, Y572, Q580, V591, T582, D586, Y589, V592, F594, E596, E598, Y599, D600, R607, a848, or others. In another aspect, the subject is a pediatric subject.

In another aspect, further comprising the steps of: repeating steps (a) to (c) from one or more longitudinally consecutive samples of the subject, combining one or more longitudinal single cell genomic mutation profiles to determine one or more mutations that change in response to administration of a therapeutically effective amount of clainib, or a pharmaceutically acceptable salt thereof, and determining a residual disease state for a measurable proliferative disorder that is increased or decreased by a percentage of the post-treatment patient-specific single cell mutation profile associated with the proliferative disorder. In another aspect, the obtained sample is at least one of: bone marrow, peripheral blood or tumor tissue. In another aspect, single cell sequencing comprises the use of tapesti^TMPlatform to prepare genomic DNA of the above genes with markers associated with each cell, and sequencing the prepared DNA with at least one of MiSeq, HiSeq, or NovaSeq sequencing platforms. In another aspect, the subject is a pediatric subject.

In another embodiment, the invention includes a method of treating a subject suffering from a proliferative disorder comprising wild-type FLT3 having one or more co-occurring RAS mutations, comprising, consisting essentially of, or consisting of: administering to the subject a therapeutically effective amount of clainib, or a pharmaceutically acceptable salt thereof, in combination with at least one of an alkylating agent, an antimetabolite agent, a natural product, or a combination thereof. In one aspect, minimal residual disease of the proliferative disorder is detected by: (a) obtaining a sample from a subject comprising tumor cells; (b) sequencing the sample for single cells, wherein sequencing comprises at least 1000000 reads per sample; and (c) analyzing only the mutation in the sample having the allele dropout rate of 10% or less. In another aspect, the presence or absence of one or more mutations is used to generate a patient-specific single-cell mutation profile associated with a proliferative disorder. In another aspect, the RAS mutation is at least one of an NRAS and KRAS mutation. In another aspect, the one or more co-occurring mutations is at least one of FLT3, NPM1, DNMT3A, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP 2, ZRSR2, GRB 2, SRSF2, MLL, NUP 2, ETV 2, TCL 12, TUSC 2, BRP 2, CD 2, TYK2, TP 2, EZH2, GATA2, KIT, PHF 2, MYC, ERG, MYD 2, NF 2, BRAF, KDM6 2, setp CSF, kml 2, pht 2, MYC 2, SMC 36. In another aspect, the method further comprises the steps of: repeating steps (a) to (c) from one or more longitudinally consecutive samples of the subject; combining one or more vertical single cell genome mutation profiles to determine the presence or absence of one or more mutations that are altered in response to administration of a therapeutically effective amount of clainib, or a pharmaceutically acceptable salt thereof; and determining a measurable residual disease state of the proliferative disorder as measured by an increase or decrease in the percentage of the patient-specific single-cell mutation profile after treatment associated with the proliferative disorder. In another aspect, the sample obtained is at least one of bone marrow, peripheral blood, or tumor tissue. In another aspect, single cell sequencing comprises preparing genomic DNA with one or more markers per cell and sequencing the prepared DNA. In another aspect, single cell sequencing uses the aMiSeq, HiSeq, or NovaSeq platforms. In another aspect, the alkylating agent is selected from at least one of carmustine, chlorambucil, cyclophosphamide, ifosfamide, lomustine, streptozotocin, temozolomide, cisplatin, carboplatin, nedaplatin, or oxaliplatin. In another aspect, the antimetabolite agent is selected from at least one of: methotrexate, pemetrexed, raltitrexed, cytarabine, fludarabine, fluorouracil, floxuridine, capecitabine or gemcitabine. In another aspect, the natural product is at least one of: vinblastine, vinorelbine, vincristine, vindesine, vinflunine, paclitaxel, docetaxel, cabazitaxel, etoposide, teniposide, topotecan, irinotecan, daunorubicin, doxorubicin, idarubicin, epirubicin, valrubicin, mitoxantrone, bleomycin, estramustine, and/or mitomycin. In another aspect, the subject further comprises a mutant FLT3 tyrosine kinase. In another aspect, the subject is a pediatric patient.

In another embodiment, the invention includes a method of preventing recurrence of a proliferative disorder in a subject previously treated to be free of the proliferative disorder, comprising, consisting essentially of, or consisting of: administering to said subject a therapeutically effective amount of clainib, or a pharmaceutically acceptable salt thereof, following response to induction of chemotherapy, consolidation or following hematopoietic stem cell transplantation for a period of time sufficient to prevent recurrence of said proliferative disorder. In another aspect, the proliferative disorder is characterized by comprising one or more functional alteration mutations and at least one recurrent gene mutation. In another aspect, the proliferative disorder is characterized by comprising wild-type FLT3 with or without one or more co-occurring mutations. In another aspect, prior treatment of the subject can be performed with: the alkylating agent is selected from at least one of the following: carmustine, chlorambucil, cyclophosphamide, ifosfamide, lomustine, streptozotocin, temozolomide, cisplatin, carboplatin, nedaplatin, or oxaliplatin; the antimetabolite is selected from at least one of: methotrexate, pemetrexed, raltitrexed, cytarabine, fludarabine, fluorouracil, floxuridine, capecitabine, or gemcitabine; or the natural product is selected from at least one of the following: vinblastine, vinorelbine, vincristine, vindesine, vinflunine, paclitaxel, docetaxel, cabazitaxel, etoposide, teniposide, topotecan, irinotecan, daunorubicin, doxorubicin, idarubicin, epirubicin, valrubicin, mitoxantrone, bleomycin, estramustine, and/or mitomycin. In another aspect, the one or more co-occurring mutations are at least one of: NPM1, DNMT3A, NRAS, KRAS, JAK2, PTPN11, TET2, IDH1, IDH2, WT1, RUNX1, CEBPA, ASXL1, BCOR, SF3B1, U2AF1, STAG2, SETBP1, ZRSR2, GRB7, SRSF 7, MLL, NUP 7, ETV 7, TCL 17, TUSC 7, BRP 7, CD 7, TYK 7, TP 7, EZH 7, GATA 7, KIT, PHF 7, MYC, ERG, MYD 7, RAD 7, STAT 7, NF 7, KDF, KDM6 BRA3672, SETBP 7, CALR, CBL, MPL 27, PHF 7, PHCSF, MUAS 7, MUEKAS 7, SMC 7. In another aspect, the subject is a pediatric patient.

It is to be understood that any embodiment discussed in the present specification may be implemented with respect to any method, kit, reagent or composition of the present invention and vice versa. Furthermore, the compositions of the invention can be used to carry out the methods of the invention.

It is to be understood that the specific embodiments described herein are shown by way of illustration and not as limitations of the invention. The main features of the present invention can be applied to various embodiments without departing from the scope of the present invention. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of the invention and are covered by the claims.

All publications and patent applications mentioned in this specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

In the claims and/or the specification, the words "a" or "an" when used with the term "comprising" may mean "one," but it is also consistent with the meaning of "one or more," at least one, "and" one or more than one. The use of the term "or" in the claims is intended to mean "and/or" unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports only alternatives and the definition of "and/or". Throughout this application, the term "about" is used to indicate that a value includes variations in the error inherent in the device, the method used to determine the value or variations that exist between study subjects.

As used in this specification and one or more claims, the terms "comprises" (and any form of comprising, such as "comprises" and "comprising"), "having" (and any form of having, such as "has" and "has"), "including" (and any form of including, such as "includes" and "includes") or "containing" (and any form of containing, such as "includes" and "contains") are inclusive or open-ended and do not exclude the presence of additional, unrecited features, elements, components, groups, integers, and/or steps, but do not exclude the presence of other unrecited features, elements, components, groups, integers and/or steps. In any of the compositional and methodological embodiments provided herein, "comprising" may alternatively "consist essentially of … or" consist of …. As used herein, the term "consisting of …" is used to indicate that only the stated integer(s) (e.g., feature, element, characteristic, attribute, method/process step or limitation) or group of integers (e.g., feature(s), element(s), feature(s), attribute(s), method/process step(s) or limitation (s)) is/are present. As used herein, the phrase "consisting essentially of …" requires the presence of stated features, elements, components, groups, integers, and/or steps, but does not preclude the presence or addition of other unclaimed features, elements, components, groups, integers, and/or steps, as well as those that do not materially affect one or more of the basic and novel characteristics and/or functions of the claimed invention.

The term "or combinations thereof" as used herein refers to all permutations and combinations of the listed terms and terms. For example, "A, B, C or a combination thereof" is intended to include at least one of: A. b, C, AB, AC, BC, or ABC, and if the order is important in a particular context, BA, CA, CB, CBA, BCA, ACB, BAC, or CAB. Continuing with the present example, explicitly included are combinations containing one or more subject or item repetitions, such as BB, AAA, AB, BBC, AAABCCCC, CBBAAA, CABABB, and the like. The skilled artisan will appreciate that in general, no limitation to the number of items or terms is intended in any combination, unless otherwise apparent from the context.

As used herein, approximating language, such as, but not limited to, "about," "substantially," or "substantially," means that the modification is not necessarily absolute or perfect, but will be recognized as being sufficiently close to those of skill in the art to warrant the existence of the stated condition. The degree of variation described will depend on how much variation can be made and still allow one of ordinary skill in the art to recognize that the modified features still have the desired characteristics and capabilities of the unmodified features. In general, but given the preceding discussion, a numerical value modified herein by an approximating language, such as "about," may differ from the stated value by at least ± 1, 2, 3,4, 5, 6, 7, 10, 12, or 15%.

All of the compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the methods described herein without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

To assist the patent office and any reader of any patent issued in this application in interpreting claims appended hereto, applicants wish to note that they are not intended that the appended claims recite 35u.s.c. § 112, clause 6, u.s.c. § 112, clause (f) or equivalents thereof, as they exist on the date of filing this application, unless "means for …" or "step for …" are explicitly used in the specific claims.

For each claim, each dependent claim may depend on both the independent claim and each preceding dependent claim of each or all claims, provided that the preceding claims provide appropriate basis for claim terms or elements.

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