WO2019023263A1 - Methods and compositions for treating tumors comprising a bcr-abl1 gene fusion - Google Patents

Abstract

Some embodiments of the methods and compositions provided herein relate to the treatment and amelioration of tumors comprising a BCR-ABL1 fusion gene. In some embodiments, a tumor comprising BCR-ABL1 fusion gene, such as a chronic myeloid leukemia tumor (CML), can be treated by reducing the activity of NOX2 in a cell of a subject. In some embodiments, the activity of NOX2 can be reduced by administering a NOX2 inhibitor, such as histamine dihydrochloride (HDC).

Description

METHODS AND COMPOSITIONS FOR TREATING TUMORS COMPRISING A

BCR-ABL1 GENE FUSION

RELATED APPLICATIONS

[0001] This application claims priority to U.S. Prov. App. No. 62/536,936 filed July 25, 2017 entitled "COMPOUNDS AND METHODS FOR TREATING CANCER", and U.S. Prov. App. No. 62/536,944 filed July 25, 2017 entitled "COMPOUNDS AND METHODS FOR TREATING CANCER" the contents of which are incorporated herein by reference in their entirety.

REFERENCE TO SEQUENCE LISTING

[0002] The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled IMMUN231 WOSEQLIST, created July 19, 2018, which is approximately 6 Kb in size. The information in the electronic format of the Sequence Listing is incorporated herein by reference in its entirety.

FIELD

[0003] Some embodiments of the methods and compositions provided herein relate to the treatment and amelioration of tumors comprising a BCR-ABL1 fusion gene. In some embodiments, a tumor comprising BCR-ABL1 fusion gene, such as a chronic myeloid leukemia tumor, can be treated by reducing the activity of NOX2 in a cell of a subject. In some embodiments, the activity of NOX2 can be reduced by administering a NOX2 inhibitor, such as histamine dihydrochloride (HDC).

BACKGROUND

[0004] Chronic myeloid leukemia (CML) is caused by a (9;22) translocation that yields a fusion oncogene, BCR-ABL1 , which in turn encodes a tyrosine kinase that supports the accumulation and survival of BCR-ABL1^"1" leukemic cells in blood and bone marrow (Faderl et al., N Engl J Med 341 : 164-72, 1999). Transformation of haematopoietic cells by BCRDABLl yields a constitutive activation of the ABL1 tyrosine kinase that promotes proliferation and survival of granulocytes with ensuing CML (Sattler, M., et ah, (2000) Journal of Biological Chemistry, 275, 24273-24278).

[0005] A specific inhibitor of the BCR-ABLl -derived kinase, imatinib is available for the treatment of patients with CML. Treatment with imatinib, or more recent compounds that target the BCR-ABLl -derived tyrosine kinase, results in a dramatic reduction of the burden of leukemic cells and has strongly improved the long-term survival of patients diagnosed with CML (Kantarijan et al. (2012) Blood 119, 1981-7). However, in most cases a minimal clone of BCR-ABLl^"1" leukemic cells persists in patients treated with imatinib and other tyrosine kinase inhibitors, and the treatment therefore is life-long with significant medication costs and toxicity. A method to further reduce or eliminate the burden of leukemic cells is therefore needed for patients with CML.

SUMMARY

[0006] Some embodiments of the methods and compositions provided herein include a method for treating or ameliorating a disorder in a subject comprising a BCR- ABLl gene fusion, the method comprising: reducing the activity of nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2), or reducing the expression level of a nucleic acid encoding NOX2, or reducing the expression level of NOX2 protein in a cell of the subject.

[0007] Some embodiments also include identifying the presence of the BCR- ABLl gene fusion in the subject. In some embodiments, the presence of the BCR-ALB 1 gene fusion is identified from an analytical assay selected from the group consisting of: nucleic acid sequencing polypeptide sequencing, restriction digestion, capillary electrophoresis, nucleic acid amplification-based assays, nucleic acid hybridization assay, comparative genomic hybridization, real-time PCR, quantitative reverse transcription PCR (qRT-PCR), PCR-RFLP assay, HPLC, mass-spectrometric genotyping, fluorescent in-situ hybridization (FISH), next generation sequencing (NGS), a kinase activity assay, and any combination thereof.

[0008] In some embodiments, reducing the activity of NOX2 comprises administering an effective amount of a NOX2 inhibitor to the subject. In some embodiments, the NOX2 inhibitor is selected from the group consisting of histamine, a histamine salt, histamine dihydrochloride (HDC), histamine diphosphate, a histamine structural analog having H2-receptor activities, an endogenous histamine releasing preparation, a non- histamine derivative H2-receptor agonist, GSK2795039, apocynin, diphenylene iodonium, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD084, NSC23766, CAS 1 177865-17- 6, CAS 1090893-12-1, and shionogi. In some embodiments, the NOX2 inhibitor is HDC.

[0009] In some embodiments, reducing the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein comprises contacting the cell with an isolated nucleic acid selected from the group consisting of a guide RNA (gRNA), a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, a locked nucleic acid, and a ribozyme. In some embodiments, the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof. In some embodiments, the isolated nucleic acid comprises a gRNA comprising a sequence complementary to the sequence of a target gene selected from the group consisting of NOX2, CYBA, NCF1, NCF2, NCF4, RAC1, and RAC2. In some embodiments, the target gene is NOX2.

[0010] Some embodiments also include administering at least one chemotherapeutic agent in combination with the NOX2 inhibitor or the isolated nucleic acid. In some embodiments, the at least one chemotherapeutic agent comprises a tyrosine kinase inhibitor. In some embodiments, the tyrosine kinase inhibitor is selected from the group consisting of: imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, and rebastinib. In some embodiments, the at least one chemotherapeutic agent is selected from the group consisting of: actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vemurafenib, vinblastine, vincristine, vindesine, and vinorelbine. In some embodiments, the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered concurrently. In some embodiments, the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered sequentially

[0011] In some embodiments, the disorder is a leukemia. In some embodiments, the disorder is selected from the group consisting of chronic myeloid leukemia, acute myeloid leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, gastrointenstinal stromal tumors (GIST), and a combination thereof. In some embodiments, the disorder comprising a BCR-ABLl gene fusion is a chronic myeloid leukemia selected from the group consisting of a de novo chronic myeloid leukemia, a secondary chronic myeloid leukemia, a refractory chronic myeloid leukemia, a recurrent chronic myeloid leukemia, and a relapsing chronic myeloid leukemia.

[0012] In some embodiments, the cell is a hematopoietic cell. In some embodiments, the cell is a myeloid cell.

[0013] In some embodiments, the subject is mammalian. In some embodiments, the subject is human.

[0014] Some embodiments of the methods and compositions provided herein include a method for increasing a survival rate of a subject having a disorder, wherein the subject comprises a BCR-ABLl gene fusion, the method comprising: reducing the activity of nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2), or reducing the expression level of a nucleic acid encoding NOX2, or reducing the expression level of NOX2 protein in a cell of the subject, wherein the survival rate of the subject is increased compared to the survival rate of an untreated subject in which the activity of NOX2, or the expression level of a nucleic acid encoding NOX2, or the expression level of NOX2 protein in a cell of the untreated subject has not been reduced.

[0015] Some embodiments also include identifying the presence of the BCR- ABLl gene fusion in the subject. In some embodiments, the presence of the BCR-ALB 1 gene fusion is identified from an analytical assay selected from the group consisting of: nucleic acid sequencing polypeptide sequencing, restriction digestion, capillary electrophoresis, nucleic acid amplification-based assays, nucleic acid hybridization assay, comparative genomic hybridization, real-time PCR, quantitative reverse transcription PCR (qRT-PCR), PCR-RFLP assay, HPLC, mass-spectrometric genotyping, fluorescent in-situ hybridization (FISH), next generation sequencing (NGS), a kinase activity assay, and any combination thereof.

[0016] In some embodiments, the survival rate of the subject is increased by at least 10% compared to the survival rate of the untreated subject. In some embodiments, the survival rate of the subject is increased by at least 50% compared to the survival rate of the untreated subject. In some embodiments, the survival rate of the subject is increased by 20% - 80% compared to the survival rate of the untreated subject. In some embodiments, the survival rate of the subject is increased by 30% - 50%. In some embodiments, the survival rate is leukemia-free survival rate. In some embodiments, the survival rate is overall survival rate.

[0017] In some embodiments, reducing the activity of NOX2 comprises administering an effective amount of a NOX2 inhibitor to the subject. In some embodiments, the NOX2 inhibitor is selected from the group consisting of histamine, a histamine salt, histamine dihydrochloride (HDC), histamine diphosphate, a histamine structural analog having H2-receptor activities, an endogenous histamine releasing preparation, a non- histamine derivative H2-receptor agonist, GSK2795039, apocynin, diphenylene iodonium, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD084, NSC23766, CAS 1177865-17- 6, CAS 1090893-12-1, and shionogi. In some embodiments, the NOX2 inhibitor is HDC.

[0018] In some embodiments, reducing the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein comprises contacting the cell with an isolated nucleic acid selected from the group consisting of a guide RNA (gRNA), a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, a locked nucleic acid, and a ribozyme. In some embodiments, the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof. In some embodiments, the isolated nucleic acid comprises a gRNA comprising a sequence complementary to the sequence of a target gene selected from the group consisting of NOX2, CYBA, NCF1, NCF2, NCF4, RAC1, and RAC2. In some embodiments, the target gene is NOX2. [0019] Some embodiments also include administering an additional chemotherapeutic agent in combination with the NOX2 inhibitor or the isolated nucleic acid. In some embodiments, the chemotherapeutic agent comprises a tyrosine kinase inhibitor. In some embodiments, the tyrosine kinase inhibitor is selected from the group consisting of: imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, and rebastinib. In some embodiments, the chemotherapeutic agent is selected from the group consisting of: actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vemurafenib, vinblastine, vincristine, vindesine, and vinorelbine. In some embodiments, the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered concurrently. In some embodiments, the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered sequentially.

[0020] In some embodiments, the disorder comprising a BCR-ABL1 gene fusion is a leukemia. In some embodiments, the disorder comprising a BCR-ABL1 gene fusion is selected from the group consisting of chronic myeloid leukemia, acute myeloid leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, and gastrointenstinal stromal tumors (GIST). In some embodiments, the disorder comprising a BCR-ABL1 gene fusion is a chronic myeloid leukemia selected from the group consisting of a de novo chronic myeloid leukemia, a secondary chronic myeloid leukemia, a refractory chronic myeloid leukemia, a recurrent chronic myeloid leukemia, and a relapsing chronic myeloid leukemia.

[0021] In some embodiments, the cell is a hematopoietic cell. In some embodiments, the cell is a myeloid cell.

[0022] In some embodiments, the subject is mammalian. In some embodiments, the subject is human.

[0023] Some embodiments of the methods and compositions provided herein include a method for inhibiting growth of a tumor in a subject, the tumor comprising a BCR- ABL1 gene fusion, the method comprising: reducing the activity of nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2), reducing the expression level of a nucleic acid encoding NOX2, or reducing the expression level of NOX2 protein in a cell of the subject.

[0024] Some embodiments also include identifying the presence of the BCR- ABL1 gene fusion in the subject. In some embodiments, the presence of the BCR-ALB 1 gene fusion is identified from an analytical assay selected from the group consisting of: nucleic acid sequencing polypeptide sequencing, restriction digestion, capillary electrophoresis, nucleic acid amplification-based assays, nucleic acid hybridization assay, comparative genomic hybridization, real-time PCR, quantitative reverse transcription PCR (qRT-PCR), PCR-RFLP assay, HPLC, mass-spectrometric genotyping, fluorescent in-situ hybridization (FISH), next generation sequencing (NGS), a kinase activity assay, and any combination thereof.

[0025] In some embodiments, growth of the tumor is inhibited by at least about 20%. In some embodiments, growth of the tumor is inhibited by at least about 50%. In some embodiments, growth of the tumor is inhibited by at least about 70%.

[0026] In some embodiments, reducing the activity of NOX2 comprises administering an effective amount of a NOX2 inhibitor to the subject. In some embodiments, the NOX2 inhibitor is selected from the group consisting of histamine, a histamine salt, histamine dihydrochloride (HDC), histamine diphosphate, a histamine structural analog having H2-receptor activities, an endogenous histamine releasing preparation, a non- histamine derivative H2-receptor agonist, GSK2795039, apocynin, diphenylene iodonium, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD084, NSC23766, CAS 1 177865-17- 6, CAS 1090893-12-1, and shionogi. In some embodiments, the NOX2 inhibitor is HDC.

[0027] In some embodiments, reducing the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein comprises contacting the cell with an isolated nucleic acid selected from the group consisting of a guide RNA (gRNA), a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, a locked nucleic acid, and a ribozyme. In some embodiments, the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof. In some embodiments, the isolated nucleic acid comprises a gRNA comprising a sequence complementary to the sequence of a target gene selected from the group consisting of NOX2, CYBA, NCF1, NCF2, NCF4, RAC1, and RAC2. In some embodiments, the target gene is NOX2.

[0028] Some embodiments also include administering an additional chemotherapeutic agent in combination with the NOX2 inhibitor or the isolated nucleic acid. In some embodiments, the chemotherapeutic agent comprises a tyrosine kinase inhibitor. In some embodiments, the tyrosine kinase inhibitor is selected from the group consisting of: imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, and rebastinib. In some embodiments, the chemotherapeutic agent is selected from the group consisting of: actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vemurafenib, vinblastine, vincristine, vindesine, and vinorelbine. In some embodiments, the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered concurrently. In some embodiments, the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered sequentially.

[0029] In some embodiments, the tumor comprising a BCR-ABL1+ cell is a leukemia. In some embodiments, the tumor comprising a BCR-ABL1+ cell is selected from the group consisting of chronic myeloid leukemia, acute myeloid leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, and gastrointenstinal stromal tumors (GIST). In some embodiments, the tumor comprising a BCR-ABL1+ cell is a chronic myeloid leukemia selected from the group consisting of a de novo chronic myeloid leukemia, a secondary chronic myeloid leukemia, a refractory chronic myeloid leukemia, a recurrent chronic myeloid leukemia, and a relapsing chronic myeloid leukemia.

[0030] In some embodiments, the cell is a hematopoietic cell. In some embodiments, the cell is a myeloid cell.

[0031] In some embodiments, the subject is mammalian. In some embodiments, the subject is human. [0032] Some embodiments of the methods and compositions provided herein include use of a nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) inhibitor or an isolated nucleic acid to treat or ameliorate a tumor in a subject, the subject comprising a BCR-ABL1 gene fusion, wherein the isolated nucleic acid reduces the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein in a cell of the subject.

[0033] Some embodiments of the methods and compositions provided herein include use of a nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) inhibitor or an isolated nucleic acid to increase a survival rate of a subject having a disorder comprising BCR-ABL1 gene fusion, wherein the isolated nucleic acid reduces the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein in a cell of the subject, wherein the survival rate of the subject is increased compared to the survival rate of an untreated subject in which the activity of NOX2, or the expression level of a nucleic acid encoding NOX2, or the expression level of NOX2 protein in a cell of the untreated subject has not been reduced.

[0034] Some embodiments of the methods and compositions provided herein include use of a nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) inhibitor or an isolated nucleic acid to inhibit growth of a tumor comprising a cell comprising a BCR- ABL1 gene fusion in a subject, wherein the isolated nucleic acid reduces the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein in a cell of the subject.

[0035] In some embodiments, the NOX2 inhibitor is selected from the group consisting of histamine, a histamine salt, histamine dihydrochloride (HDC), histamine diphosphate, a histamine structural analog having H2-receptor activities, an endogenous histamine releasing preparation, a non-histamine derivative H2-receptor agonist, GSK2795039, apocynin, diphenylene iodonium, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD084, NSC23766, CAS 1 177865-17-6, CAS 1090893- 12- 1, and shionogi. In some embodiments, the NOX2 inhibitor is HDC.

[0036] In some embodiments, the isolated nucleic acid selected from the group consisting of a guide RNA (gRNA), a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, a locked nucleic acid, and a ribozyme. In some embodiments, the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof. In some embodiments, the isolated nucleic acid comprises a gRNA comprising a sequence complementary to the sequence of a target gene selected from the group consisting of NOX2, CYBA, NCFl , NCF2, NCF4, RACl, and RAC2. In some embodiments, the target gene is NOX2.

[0037] In some embodiments, the use is in combination with an additional chemotherapeutic agent. In some embodiments, the chemotherapeutic agent comprises a tyrosine kinase inhibitor. In some embodiments, the tyrosine kinase inhibitor is selected from the group consisting of: imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, and rebastinib. In some embodiments, the chemotherapeutic agent is selected from the group consisting of: actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vemurafenib, vinblastine, vincristine, vindesine, and vinorelbine.

[0038] In some embodiments, the disorder comprising a BCR-ABL1 gene fusion is a leukemia. In some embodiments, the disorder comprising a BCR-ABL1 gene fusion is selected from the group consisting of chronic myeloid leukemia, acute myeloid leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, and gastrointenstinal stromal tumors (GIST). In some embodiments, the disorder comprising a BCR-ABL1 gene fusion is a chronic myeloid leukemia selected from the group consisting of a de novo chronic myeloid leukemia, a secondary chronic myeloid leukemia, a refractory chronic myeloid leukemia, a recurrent chronic myeloid leukemia, and a relapsing chronic myeloid leukemia.

[0039] In some embodiments, the cell is a hematopoietic cell. In some embodiments, the cell is a myeloid cell.

[0040] In some embodiments, the subject is mammalian. In some embodiments, the subject is human. BRIEF DESCRIPTION OF THE DRAWINGS

[0041] FIG.s 1A-1D relate to the impact of genetic and pharmacologic inhibition of NOX2 on wild type (WT) and NOX2-knock-out BCR-ABL1⁺ cells. FIG. 1A is a graph depicting the colony formation capacity of WT cells and NOX2-knock-out BCR-ABLl ⁺ cells, during serial plating. * P < 0-05. The bars show mean ± SEM. FIG. IB is a graph depicting the percentage of BCR-ABLl^"1" cells in blood at different time points after transplantation into mice. FIG. 1C is a FACS plot showing BCR-ABLl^"1" cells in blood from mice at 3 weeks post-transplantation with WT BCR-ABL1⁺ cells. FIG. ID is a FACS plot showing BCR-ABLl^"1" cells in blood in mice at 3 weeks post-transplantation with NOX2-KO BCR-ABLl ⁺ cells.

[0042] FIG.s 2A-2D relate to the induction of a more aggressive leukemia by WT BCR-ABLl ⁺ cells compared to NOX2-KO BCR-ABL1⁺ cells. FIG. 2A is a graph depicting the survival of mice transplanted with wild type (WT; solid line, n = 6) or NOX2-KO; (dashed line, n = 6) BCR-ABLl^"1" cells. FIG. 2B is a series of FACS plots depicting the gating strategy used and representative bone marrow (BM) samples from a mouse transplanted with WT BCR-ABL1⁺ cells (top row) and a mouse transplanted with NOX2-KO BCR-ABL1⁺ cells (bottom row). FIG. 2C is a graph depicting the results of flow cytometry analyses of BM samples from mice transplanted with WT or NOX2-KO BCR-ABLl ⁺ cells, at the time of sacrifice. FIG. 2D is a graph depicting ROS production by cells isolated from BM with ROS production shown as area under the curve in the absence of stimulation (Ctrl) and in response to D-peptide for BM cells isolated from mice transplanted with WT cells or NOX2- KO BCR-ABL1⁺ cells. * P < 005. The bars indicate the SEM.

[0043] FIG. 3A is a graph of ex vivo ROS production in FACS-sorted BCR- ABLl^"1" WT cells stimulated by D-peptide, and treated or not with HDC. FIG. 3B is a graph of ex vivo ROS production in FACS-sorted BCR-ABLl ⁺ NOX2-KO cells stimulated by ROS, and treated or not with HDC.

[0044] FIG. 4A is a graph showing the fraction of BCR-ABL1⁺ cells among all hematopoietic cells in blood from mice at different time points after transplantation with BCR-ABLl^"1" WT cells. The mice were treated with HDC (dashed line) or untreated (control: Ctl, black line). FIG. 4B is a graph of the survival rate of mice transplanted with BCR- ABL1⁺ WT cells, and either treated with HDC (dashed line), or left untreated (Ctl, black line).

DETAILED DESCRIPTION

[0045] Some embodiments of the methods and compositions provided herein relate to the treatment and amelioration of a cancer comprising a BCR-ALB 1 gene fusion in a subject. In some embodiments, a disorder comprising a BCR-ALB 1 gene fusion may be treated by reducing the activity of NOX2 in a cell of a subject. In some embodiments, the activity of NOX2 can be reduced by administering a NOX2 inhibitor, such as histamine dihydrochloride (HDC). In some embodiments, the activity of NOX2 can be reduced by administering an isolated nucleic acid which reduces the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein in a cell of the subject.

[0046] The NADPH oxidase of myeloid cells, NOX2, generates reactive oxygen species (ROS) to eliminate pathogens and malignant cells. The NOX2 protein is encoded by the CYBB gene and forms a holoenzyme that can include other proteins such as cytochrome b alpha encoded by a CYBA gene, and can include regulatory subunits p67phox, p47phox, p40phox, Racl, and Rac2. Expression of the BCR-ABLl oncoprotein in chronic myeloid leukemia (CML) cells is associated with elevated production of ROS, which has been implicated in the genetic instability and mutagenesis that is characteristic of leukemic BCR- ABLl^"1" cells. While human and murine leukemic cells express a functional NOX2 (Aurelius, J., et ah, (2013) Journal of Leukocyte Biology, 93, 155-160), little is known about the role of NOX2 for the progression of leukemia, especially in CML. Further studies will elucidate the precise role of ROS in leukemogenesis and clarify whether interference with ROS levels or targeting of the ROS-forming NOX2 enzyme affect the growth and survival of leukemic cells and thus alter the course of CML. Embodiments described herein include the use of genetically modified BCR-ABLl cells to elucidate the role of NOX2 for the progression of leukemia. After intravenous inoculation of WT BCR-ABL1⁺ or NOX2-KO BCR-ABL1⁺ cells, the inoculated mice were monitored for evidence of in vivo expansion of BCR-ABLl^"1" cells. WT BCR-ABLl^"1" cells expand more readily, and induce a more aggressive leukemia compared with NOX2-KO BCR-ABLl^"1" cells. Moreover, systematic treatment with the NOX2-inhibitor, HDC, inhibited expansion of BCR-ABLl^"1" cells, and improved the survival rate for the inoculated mice. Administration of HDC inhibits ROS production in WT BCR-ABL1⁺ cells.

[0047] Presence of the BCRDABL1 oncoprotein is associated with augmented formation of ROS (Sattler, M., et al, (2000) Journal of Biological Chemistry, 275, 24273- 24278; and Reddy, M.M., et al, (201 1) Leukemia, 25, 281-289). ROS (e.g., reactive oxygen intermediates, reactive oxygen metabolites or "oxygen radicals") are short-lived, toxic derivatives of oxygen that arise from the transfer of electrons over biological membranes where the electron acceptor is molecular oxygen and the initial product is superoxide anion (0₂ ^~). ROS refer to oxygen radicals such as 0₂ ^~ and the hydroxyl radical (OH.) along with nonradicals, including hydrogen peroxide, that share the oxidizing capacity of oxygen radicals and may be converted into radicals. ROS are produced as a by-product of energy metabolism and mitochondrial respiration, and are also produced in a regulated fashion by transmembrane NADPH oxidases (NOX1-5) and by the dual oxidases (DUOX1-2). NOX2 is the NADPH oxidase of myeloid cells, and its only known function is to produce ROS. Although NOX2-derived ROS produced by myeloid cells are essential for the efficient elimination of bacteria and other microbes, an imbalance between the production and detoxification of ROS may be harmful to adjacent cells and cellular components, including DNA.

[0048] The NOX proteins are structurally similar and utilize a similar principal mechanism of ROS generation but vary in cellular and subcellular distribution. NOX2 is expressed almost exclusively in cells of the myeloid lineage such as monocyte/macrophages and neutrophilic granulocytes. These cells utilize NOX2-derived ROS to eliminate intra- and extracellular microorganisms. NOX2 has also been linked to immunosuppression in cancer: when released from myeloid cells into the extracellular space, ROS generated by NOX2 may trigger dysfunction and apoptosis of adjacent antineoplastic lymphocytes, including natural killer (NK) cells. The strategy to target ROS formation by myeloid cells has been proposed to improve the efficiency of cancer immunotherapy.

[0049] The role of ROS and NOX2 for the growth and metastatic spread of cancer cells is, however, complex and controversial. Thus, although the genetic disruption of NOX2 reduces the subcutaneous growth of murine leukemic cells, it does not affect sarcoma growth or prostate cancer growth in mice. Also, the in vivo administration of scavengers of ROS such as N-acetyl-cysteine reduces the tumorigenicity of murine melanoma cells but enhances lymph node metastasis in other melanoma models, accelerates tumor progression in mouse models of B-RAF- and K-RAS-induced lung cancer and accelerates the metastasis of xenografted human melanoma cells in immunodeficient mice.

[0050] In addition to BCR□ ABL1 translocations, hematopoietic cancers with other genetic abnormalities entailing enhanced tyrosine kinase activity such as FLT3□ ITD and JAK2 mutations are associated with high intracellular ROS levels suggesting that several tyrosine kinases may promote ROS formation. ROS is thought to augment tyrosine kinase activity. Earlier studies show that the enhanced ROS formation in BCRDABL1 D transformed cells is blocked by the ABL1□ specific tyrosine kinase inhibitor (TKI) imatinib, but also that intracellular ROS levels remain elevated in CML stem cells despite exposure to imatinib. In addition, high levels of intracellular ROS in CML cells at diagnosis reportedly predict reduced efficacy of TKI therapy in CML (Bolton□ Gillespie, E., et ah, (2013) Blood, 121, 4175-4183). These results, along with those presented herein, support the important role of NOX2 in the BCR DABL1/ROS circuit and the effectiveness of therapies targeting NOX2D derived ROS in CML.

[0051] Some embodiments described herein include determining the impact of genetic and pharmacologic inhibition of NOX2 in a murine model of leukemic cell expansion. Disclosed herein are results supporting that genetic ablation of NOX2 reduces the in vivo expansion of murine BCRD ABL1⁺ hematopoietic cells.

Methods of treatment

[0052] Some embodiments of the methods and compositions provided herein include treating or ameliorating a subject having a disorder, such as a cell of a subject comprising a BCR-ABL1 gene fusion. As used herein, "subject" can include a human or a non-human mammal, e.g., a dog, a cat, a mouse, a rat, a cow, a sheep, a pig, a goat, a non- human primate or a bird, e.g., a chicken, as well as any other vertebrate or invertebrate. The terms, "patient" and "subject" are used interchangeably herein. In some embodiments, the term "subject" refer to a human harboring a BCR-ABL1 fusion gene or suspected of harboring a BCR-ABL1 fusion gene. As used herein, "treat," "treatment," or "treating," can include administering a pharmaceutical composition to a subject for therapeutic purposes, and can include reducing the symptoms of a disorder, such as reducing the number of leukemic cells, reducing the number of BCR-ABL1^"1" cells, and inhibiting the growth or expansion thereof. As used herein, "treat," "treatment," or "treating," can include curing a disorder, such as eliminating the symptoms of a disorder, such as the elimination of BCR-ABL1 cells of a metastatic tumor in a subject. As used herein, "ameliorate", or "ameliorating" can include a therapeutic effect which relieves, to some extent, one or more of the symptoms of a disorder. As used herein, an "effective amount" can include an amount, such as a dose, of a therapeutic compound sufficient to treat a disorder. As used herein, "prevent," "preventing" and "prevention" can include an action that occurs before a subject begins to suffer from the regrowth of the cancer and/or which inhibits or reduces the severity of the cancer. As used herein, reducing the activity of NOX2 can include reducing the activity of NADPH oxidase 2, and/or reducing the activity of a NADPH oxidase holoenzyme which includes the NOX2 protein.

[0053] Some embodiments include reducing the activity of NOX2 in a cell by contacting the cell with a NOX2 inhibitor. In some embodiments, the cell is a hematopoietic cell. In some embodiments, the cell is a myeloid cell. Examples of myeloid cells include monocytes, macrophages, neutrophils, basophils, eosinophils, erythrocytes, and megakaryocytes to platelets. In some embodiments, the cell is a CDl lb⁺ myeloid cell. In some embodiments, the cell is a cell comprising a BCR-ABL1 fusion oncogene. In some embodiments, an effective amount of a NOX2 inhibitor can be administered to a subject in need thereof. Examples of NOX2 inhibitors include histamine dihydrochloride (HDC), GSK2795039, apocynin, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD 084, and shionogi. Altenhofer, S. et ah, "Evolution of NADPH Oxidase Inhibitors: Selectivity and Mechanisms for Target Engagement", Antioxid Redox Signal. 2015 23: 406-427; Hirano, K. et al, "Discovery of GSK2795039, a Novel Small Molecule NADPH Oxidase 2 Inhibitor", Antioxid Redox Signal. 2015 23: 358-374, which are each incorporated by reference in its entirety. More examples of NOX2 inhibitors include histamine, histamine salts, N-methyl- histamine, 4-methyl-histamine, histamine phosphate, histamine diphosphate, and a histamine structural analog having H₂-receptor activities, an endogenous histamine releasing preparation, a non-histamine derivative H₂-receptor agonist. In some embodiments, the NOX2 inhibitor is HDC.

[0054] In some embodiments, a NOX2 inhibitor can include RAC1 inhibitors and RAC2 inhibitor, such as NSC23766, CAS 1177865-17-6, and CAS 1090893-12-1. RAC1 and RAC2 can each be associated with NOX2 holoenzyme, and inhibition of RAC1 or RAC 2 can inhibit NOX2. See e.g., Veluthakal R., et al, (2016) "NSC23766, a Known Inhibitor of Tiaml-Racl Signaling Module, Prevents the Onset of Type 1 Diabetes in the NOD Mouse Model" Cell Physiol Biochem 39:760-767; and Cifuentes-Pagano, E., et al, (2014) "The Quest for Selective Nox Inhibitors and Therapeutics: Challenges, Triumphs and Pitfalls" Antioxid Redox Signal. 20: 2741-2754, which are each incorporated by reference in its entirety. More examples of RAC1 inhibitors are disclosed in Arnst, J.L. et al, (2017) "Discovery and characterization of small molecule Racl inhibitors", Oncotarget. 8: 34586- 34600.

Reducing expression levels of NOX2

[0055] Some embodiments of the methods and compositions provided herein include reducing the activity of NOX2 in a cell by reducing the expression level of a nucleic acid encoding NOX2, or the expression level of a NOX2 protein in the cell. In some embodiments, the cell is a hematopoietic cell. In some embodiments, the cell is a myeloid cell. In some embodiments, the cell is a lymphoid cell. Some embodiments include reducing the expression level of a nucleic acid encoding NOX2, or the expression level of a NOX2 protein in a cell by RNA interference and/or antisense technologies, or using a CRISPR based system, such as a CRISPR/C s9 system.

[0056] Some embodiments include reducing the expression level of a nucleic acid encoding NOX2, or the expression level of a NOX2 protein in a cell using a CRISPR based system, such as a CRISPR/C s9 system. In some embodiments, a CRISPR (clustered regularly interspaced short palindromic repeats) system can be used to modify a cell to reduce the expression level of a nucleic acid encoding NOX2, or the expression level of a NOX2 protein in the cell. For example, a cell can be modified such that a target gene, such as NOX2 gene, can be functionally knocked-out. In some embodiments, a cell can be obtained from a subject. In some embodiments, the cell can be modified by a CRISPR system ex vivo. In some embodiments, the modified cell can be delivered to a subject. Examples of CRISPR systems useful with the methods and compositions provided herein are disclosed in U.S. Pat. App. Pub. 20180201951, U.S. Pat. App. Pub. 20180177893, and U.S. Pat. App. Pub. 20180105834 which are each incorporated by reference in its entirety.

[0057] A CRISPR system includes a microbial nuclease system involved in defense against invading phages and plasmids that provides a form of acquired immunity. CRISPR loci in microbial hosts contain a combination of CRISPR-associated (Cas) genes as well as non-coding RNA elements capable of programming the specificity of the CRISPR- mediated nucleic acid cleavage. Short segments of foreign DNA, called spacers, are incorporated into the genome between CRISPR repeats, and serve as a memory of past exposures. Cas9 forms a complex with the 3' end of the sgRNA, and the protein-RNA pair recognizes its genomic target by complementary base pairing between the 5' end of the sgRNA sequence and a predefined 20 bp DNA sequence, known as the protospacer. This complex is directed to homologous loci of pathogen DNA via regions encoded within the crRNA, i.e., the protospacers, and protospacer-adjacent motifs (PAMs) within the pathogen genome. The non-coding CRISPR array is transcribed and cleaved within direct repeats into short crRNAs containing individual spacer sequences, which direct Cas nucleases to the target site (protospacer). By simply exchanging the 20 bp recognition sequence of the expressed sgRNA, the Cas9 nuclease can be directed to new genomic targets. CRISPR spacers are used to recognize and silence exogenous genetic elements in a manner analogous to RNAi in eukaryotic organisms.

[0058] Three classes of CRISPR systems (Types I, II and III effector systems) are known. The Type II effector system carries out targeted DNA double-strand break in four sequential steps, using a single effector enzyme, Cas9, to cleave dsDNA. Compared to the Type I and Type III effector systems, which require multiple distinct effectors acting as a complex, the Type II effector system may function in alternative contexts such as eukaryotic cells. The Type II effector system consists of a long pre-crRNA, which is transcribed from the spacer-containing CRISPR locus, the Cas9 protein, and a tracrRNA, which is involved in pre-crRNA processing. The tracrRNAs hybridize to the repeat regions separating the spacers of the pre-crRNA, thus initiating dsRNA cleavage by endogenous RNase III. This cleavage is followed by a second cleavage event within each spacer by Cas9, producing mature crRNAs that remain associated with the tracrRNA and Cas9, forming a Cas9:crRNA-tracrRNA complex.

[0059] The Cas9:crRNA-tracrRNA complex unwinds the DNA duplex and searches for sequences matching the crRNA to cleave. Target recognition occurs upon detection of complementarity between a "protospacer" sequence in the target DNA and the remaining spacer sequence in the crRNA. Cas9 mediates cleavage of target DNA if a correct protospacer-adjacent motif (PAM) is also present at the 3' end of the protospacer. For protospacer targeting, the sequence must be immediately followed by the protospacer- adjacent motif (PAM), a short sequence recognized by the Cas9 nuclease that is required for DNA cleavage. Different Type II systems have differing PAM requirements. The Streptococcus pyogenes CRISPR system may have the PAM sequence for this Cas9 (SpCas9) as 5' -NRG-3', where R is either A or G, and characterized the specificity of this system in human cells. A unique capability of the CRISPR/Cas9 system is the straightforward ability to simultaneously target multiple distinct genomic loci by co- expressing a single Cas9 protein with two or more sgRNAs. For example, the S. pyogenes Type II system naturally prefers to use an "NGG" sequence, where "N" can be any nucleotide, but also accepts other PAM sequences, such as "NAG" in engineered systems (Hsu et al., Nature Biotechnology (2013) doi: 10.1038/nbt.2647). Similarly, the Cas9 derived from Neisseria meningitidis (NmCas9) normally has a native PAM of NNNNGATT, but has activity across a variety of PAMs, including a highly degenerate NNNNGNNN PAM (Esvelt et al. Nature Methods (2013) doi: 10.1038/nmeth.2681).

[0060] An engineered form of the Type II effector system of Streptococcus pyogenes was shown to function in human cells for genome engineering. In this system, the Cas9 protein was directed to genomic target sites by a synthetically reconstituted "guide RNA" ("gRNA", also used interchangeably herein as a chimeric single guide RNA ("sgRNA")), which is a crRNA-tracrRNA fusion that obviates the need for RNase III and crRNA processing in general. Provided herein are CRISPR/Cas9-based engineered systems for use in genome editing. The CRISPR/Cas9-based engineered systems may be designed to target any gene, such as a gene encoding NOX2. The CRISPR/Cas9-based systems may include a Cas9 protein or Cas9 fusion protein and at least one gRNA. The Cas9 fusion protein may, for example, include a domain that has a different activity that what is endogenous to Cas9, such as a transactivation domain.

[0061] The CRISPR/Cas9-based system may include a Cas9 protein or a Cas9 fusion protein. Cas9 protein is an endonuclease that cleaves nucleic acid and is encoded by the CRISPR loci and is involved in the Type II CRISPR system. The Cas9 protein may be from any bacterial or archaea species, such as Streptococcus pyogenes. The Cas9 protein may be mutated so that the nuclease activity is inactivated. An inactivated Cas9 protein from Streptococcus pyogenes (iCas9, also referred to as "dCas9") with no endonuclease activity has been recently targeted to genes in bacteria, yeast, and human cells by gRNAs to silence gene expression through steric hindrance. As used herein, "iCas9" and "dCas9" can include a Cas9 protein that has the amino acid substitutions D10A and H840A and has its nuclease activity inactivated.

[0062] The CRISPR/Cas9-based system may include a fusion protein. The fusion protein may comprise two heterologous polypeptide domains, wherein the first polypeptide domain comprises a Cas protein and the second polypeptide domain has nuclease activity that is different from the nuclease activity of the Cas9 protein. The fusion protein may include a Cas9 protein or a mutated Cas9 protein, as described above, fused to a second polypeptide domain that has nuclease activity. A nuclease, or a protein having nuclease activity, is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Nucleases are usually further divided into endonucleases and exonucleases, although some of the enzymes may fall in both categories. Well known nucleases are deoxyribonuclease and ribonuclease.

[0063] In some embodiments, a gRNA provides the targeting of the CRISPR/Cas9-based system. The gRNA is a fusion of two noncoding RNAs: a crRNA and a tracrRNA. The gRNA may target any desired DNA sequence, such as a DNA sequence encoding a NOX2 protein, by exchanging the sequence encoding a 20 bp protospacer which confers targeting specificity through complementary base pairing with the desired DNA target. gRNA mimics the naturally occurring crRNA: tracrRNA duplex involved in the Type II Effector system. This duplex, which may include, for example, a 42-nucleotide crRNA and a 75-nucleotide tracrRNA, acts as a guide for the Cas9 to cleave the target nucleic acid. The "target region", "target sequence" or "protospacer" as used interchangeably herein refers to the region of the target gene to which the CRISPR/Cas9-based system targets. The CRISPR/Cas9-based system may include at least one gRNA, wherein the gRNAs target different DNA sequences. The target DNA sequences may be overlapping. The target sequence or protospacer is followed by a PAM sequence at the 3' end of the protospacer. Different Type II systems have differing PAM requirements. For example, the Streptococcus pyogenes Type II system uses an "NGG" sequence, where "N" can be any nucleotide.

[0064] The gRNA may target any nucleic acid sequence such as an endogenous gene, such as a NOX2 gene. The CRISPR/Cas9-based system may use gRNA of varying sequences and lengths. The gRNA may comprise a complementary polynucleotide sequence of the target DNA sequence followed by a PAM sequence. The gRNA may comprise a "G" at the 5 ' end of the complementary polynucleotide sequence. The gRNA may comprise at least a 10 base pair, at least a l l base pair, at least a 12 base pair, at least a 13 base pair, at least a 14 base pair, at least a 15 base pair, at least a 16 base pair, at least a 17 base pair, at least a 18 base pair, at least a 19 base pair, at least a 20 base pair, at least a 21 base pair, at least a 22 base pair, at least a 23 base pair, at least a 24 base pair, at least a 25 base pair, at least a 30 base pair, or at least a 35 base pair complementary polynucleotide sequence of the target DNA sequence followed by a PAM sequence. The PAM sequence may be "NGG", where "N" can be any nucleotide. The gRNA may target at least one of the promoter region, the enhancer region or the transcribed region of the target gene.

[0065] In some embodiments, a target gene can include the NOX2 gene also known as the CYBB gene which encodes a NOX2 protein, also known as cytochrome b-245 beta chain protein. In some embodiments, a target gene can encode a polypeptide that binds to or is associated with the NOX2 protein in vivo. Examples of such target genes include the CYBA gene which encodes a p22phox protein, the NCF1 gene which encodes neutrophil cytosolic factor 1 protein, the NCF2 gene which encodes a neutrophil cytosolic factor 2 protein, the NCF4 gene which encodes a neutrophil cytosolic factor 4 protein, the RAC1 gene which encodes a Racl protein, and the RAC2 gene which encodes a Rac2 protein. Accession numbers for example human genomic DNA sequences that contain certain target genes and are useful to generate targeted nucleic acids for use in a CRISPR system to reduce activity of a NOX2 protein in a cell are listed in TABLE 1. TABLE 1

[0066] Adeno-associated virus (AAV) vectors may be used to deliver CRISPRs to the cell using various construct configurations. For example, AAV may deliver Cas9 and gRNA expression cassettes on separate vectors. Alternatively, if the small Cas9 proteins, derived from species such as Staphylococcus aureus or Neisseria meningitidis, are used then both the Cas9 and up to two gRNA expression cassettes may be combined in a single AAV vector within the 4.7 kb packaging limit.

[0067] In some embodiments, the delivery of the CRISPR/Cas9-based system may be the transfection or electroporation of the CRISPR/Cas9-based system as a nucleic acid molecule that is expressed in the cell and delivered to the surface of the cell. The nucleic acid molecules may be electroporated using BioRad Gene Pulser Xcell or Amaxa Nucleofector lib devices. Several different buffers may be used, including BioRad electroporation solution, Sigma phosphate -buffered saline product #D8537 (PBS), Invitrogen OptiMEM I (OM), or Amaxa Nucleofector solution V (N.V.). Transfections may include a transfection reagent, such as Lipofectamine 2000. Upon delivery of the CRISPR/Cas9 system to the tissue, and thereupon the vector into the cells of the mammal, the transfected cells will express the CRISPR/Cas9-based system and/or a site-specific nuclease. In some embodiments, a modified AAV vector can be capable of delivering and expressing the site- specific nuclease in the cell of a subject. For example, the modified AAV vector may be an AAV-SASTG vector (Piacentino et al. (2012) Human Gene Therapy 23:635-646). The modified AAV vector may be based on one or more of several capsid types, including AAVl, AAV2, AAV5, AAV6, AAV8, and AAV9. The modified AAV vector may be based on AAV2 pseudotype with alternative muscle-tropic AAV capsids, such as AAV2/1 , AAV2/6, AAV2/7, AAV2/8, AAV2/9, AAV2.5 and AAV/SASTG vectors that efficiently transduce skeletal muscle or cardiac muscle by systemic and local delivery (Seto et al. Current Gene Therapy (2012) 12: 139-151). In some embodiments, a cell can be modified ex vivo, and the modified cell can be delivered to a subject. In some embodiments, a modified cells may be injected or implanted into a subject, used exogenously, or developed into tissue engineered constructs.

[0068] Some embodiments include reducing the expression level of a nucleic acid encoding NOX2, or the expression level of a NOX2 protein in a cell by RNA interference and/or antisense technologies. RNA interference is an efficient process whereby double- stranded RNA (dsRNA), also referred to as siRNAs (small interfering RNAs) or ds siRNAs (double-stranded small interfering RNAs), induces the sequence-specific degradation of targeted mRNA in animal or plant cells (Hutvagner, G. et al. (2002) Curr. Opin. Genet. Dev. 12:225-232); Sharp, P. A. (2001) Genes Dev. 15:485-490). RNA interference can be triggered by various molecules, including 21 -nucleotide duplexes of siRNA (Chiu, Y.-L. et al. (2002) Mol. Cell. 10:549-561. Clackson, T. et al. (1991) Nature 352:624-628.; Elbashir, S. M. et al. (2001) Nature 411 :494-498), or by micro-RNAs (miRNA), functional small- hairpin RNA (shRNA), or other dsRNAs which can be expressed in vivo using DNA templates with RNA polymerase III promoters (Zheng, B. J. (2004) Antivir. Ther. 9:365-374; Paddison, P. J. et al. (2002) Genes Dev. 16:948-958; Lee, N. S. et al. (2002) Nature Biotechnol. 20:500-505; Paul, C. P. et al. (2002) Nature Biotechnol. 20:505-508; Tuschl, T. (2002) Nature Biotechnol. 20:446-448; Yu, J.-Y. et al. (2002) Proc. Natl. Acad. Sci. USA 99(9):6047-6052; McManus, M. T. et al. (2002) RNA 8:842-850; Sui, G. et al. (2002) Proc. Natl. Acad. Sci. USA 99(6):5515-5520, each of which are incorporated herein by reference in their entirety).

[0069] In some embodiments, reducing the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein in a cell can include contacting the cell with an isolated nucleic acid selected from the group consisting of a guide RNA (gRNA), small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, and a ribozyme. In some embodiments, the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof.

[0070] A fragment of a polynucleotide sequence can include any nucleotide fragment having, for example, at least about 5 successive nucleotides, at least about 12 successive nucleotides, at least about 15 successive nucleotides, at least about 18 successive nucleotides, or at least about 20 successive nucleotides of the sequence from which it is derived. An upper limit for a fragment can include, for example, the total number of nucleotides in a full-length sequence encoding a particular polypeptide. A fragment of a polypeptide sequence can include any polypeptide fragment having, for example, at least about 5 successive residues, at least about 12 successive residues, at least about 15 successive residues, at least about 18 successive residues, or at least about 20 successive residues of the sequence from which it is derived. An upper limit for a fragment can include, for example, the total number of residues in a full-length sequence of a particular polypeptide.

[0071] Some embodiments include reducing the expression level of a nucleic acid encoding NOX2, or the expression level of a NOX2 protein in a cell by at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any percentage within a range of any two of the foregoing percentages.

[0072] As used herein, "antisense polynucleotide" can include a nucleic acid that binds to a target nucleic acid, such as a RNA or DNA. An antisense polynucleotide can upregulate or downregulate expression and/or function of a target nucleic acid. An antisense polynucleotide can include any exogenous nucleic acid useful in therapeutic and/or diagnostic methods. Antisense polynucleotides can include antisense RNA or DNA molecules, micro RNA, decoy RNA molecules, siRNA, enzymatic RNA, therapeutic editing RNA and agonist and antagonist RNA, antisense oligomeric compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, primers, probes, and other oligomeric compounds that hybridize to at least a portion of the target nucleic acid. As such, these compounds may be introduced in the form of single-stranded, double-stranded, partially single-stranded, or circular oligomeric compounds.

[0073] As used herein, "short hairpin RNA" ("shRNA"), also known as "small hairpin RNAs", refers to an RNA (or RNA analog) including a first portion and a second portion, having sufficient complementarity to anneal or hybridize to form a duplex or double - stranded stem portion. The two portions need not be fully or perfectly complementary. The first and second "stem" portions are connected by a portion having a sequence that has insufficient sequence complementarity to anneal or hybridize to other portions of the shRNA. This latter portion is referred to as a "loop" portion in the shRNA molecule. shRNA molecules are processed to generate siRNAs. shRNAs can also include one or more bulges, such as extra nucleotides that create a small nucleotide "loop" in a portion of the stem, for example a one-, two- or three-nucleotide loop. The stem portions can be the same length, or one portion can include an overhang of, for example, 1-5 nucleotides. The overhanging nucleotides can include, for example, uracils (Us), e.g., all Us. Such Us are notably encoded by thymidines (Ts) in the shRNA-encoding DNA which signal the termination of transcription.

[0074] In some embodiments, a shRNA can include a portion of the duplex stem is a nucleic acid sequence that is complementary (e.g., perfectly complementary or substantially complementary, e.g., anti-sense) to the NOX2 target sequence. In some embodiments, one strand of the stem portion of the shRNA is sufficiently complementary (e.g., antisense) to a target RNA (e.g., a NOX2 mRNA sequence) to mediate degradation or cleavage of said target RNA via RNA interference (RNAi). Alternatively, one strand of the stem portion of the shRNA is sufficiently complementary (e.g., antisense) to a target RNA (e.g., a NOX2 mRNA sequence) to inhibit translation of said target RNA via RNA interference (RNAi). Thus, engineered RNA precursors include a duplex stem with two portions and a loop connecting the two stem portions. The antisense portion can be on the 5' or 3' end of the stem. The stem portions of a shRNA are preferably about 15 to about 50 nucleotides in length. Preferably the two stem portions are about 18 or 19 to about 21 , 22, 23, 24, 25, 30, 35, 37, 38, 39, or 40 or more nucleotides in length. In some embodiments, the length of the stem portions should be 21 nucleotides or greater. When used in mammalian cells, the length of the stem portions should be less than about 30 nucleotides to avoid provoking non-specific responses like the interferon pathway.

[0075] As used herein, the term "small interfering RNA" ("siRNA"), also referred to in the art as "short interfering RNAs", refers to an RNA or RNA analog comprising between about 10-50 nucleotides or nucleotide analogs which is capable of directing or mediating RNA interference. Preferably, an siRNA comprises between about 15-30 nucleotides or nucleotide analogs, between about 16-25 nucleotides or nucleotide analogs, between about 18-23 nucleotides or nucleotide analogs, or between about 19-22 nucleotides or nucleotide analogs, such as 19, 20, 21 or 22 nucleotides or nucleotide analogs. The term "short" siRNA can refer to a siRNA comprising about 21 nucleotides or nucleotide analogs, for example, 19, 20, 21 or 22 nucleotides. The term "long" siRNA can refer to a siRNA comprising about 24-25 nucleotides, for example, 23, 24, 25 or 26 nucleotides. Short siRNAs may, in some instances, include fewer than 19 nucleotides, e.g., 16, 17 or 18 nucleotides, provided that the shorter siRNA retains the ability to mediate RNAi. Likewise, long siRNAs may, in some instances, include more than 26 nucleotides, provided that the longer siRNA retains the ability to mediate RNAi absent further processing, such as enzymatic processing to a short siRNA.

[0076] As used herein, "microRNA" ("miRNA"), also referred to in the art as "small temporal RNAs" ("stRNAs"), can refer to a small (10-50 nucleotide) RNA or nucleotide analogs which can be genetically encoded, such as by viral, mammalian, or plant genomes, or synthetically produced and is capable of directing or mediating RNA silencing. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into an RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA.

[0077] In some embodiments, an siRNA is a duplex consisting of a sense strand and complementary antisense strand, the antisense strand having sufficient complementary to a NOX2 sequence to mediate RNAi. In some embodiments, an miRNA is optionally a duplex consisting of a 3' strand and complementary 5' strand, the 5' strand having sufficient complementary to a NOX2 sequence to mediate RNAi. In some embodiments, the siRNA or miRNA molecule has a length from about 10-50 or more nucleotides, i.e., each strand comprises 10-50 nucleotides (or nucleotide analogs). In some embodiments, the siRNA or miRNA molecule has a length from about 16-30, e.g., 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in each strand, wherein one of the strands is sufficiently complementary to a target region. In some embodiments, the strands are aligned such that there are at least 1 , 2, or 3 bases at the end of the strands which do not align (i.e., for which no complementary bases occur in the opposing strand) such that an overhang of 1, 2 or 3 residues occurs at one or both ends of the duplex when strands are annealed. In some embodiments, the siRNA molecule has a length from about 10-50 or more nucleotides, i.e., each strand comprises 10-50 nucleotides (or nucleotide analogs). In some embodiments, the siRNA or miRNA molecule has a length from about 16-30, e.g., 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in each strand, wherein one of the strands is substantially complementary to a target sequence, and the other strand is identical or substantially identical to the first strand. siRNAs or miRNAs can be designed by using any method known in the art. The siRNAs or miRNAs provided herein can be chemically synthesized, or can be transcribed in vitro from a DNA template, or in vivo from, e.g., shRNA. The dsRNA molecules can be designed using any method known in the art.

[0078] In some embodiments, miRNAs can regulate gene expression at the post transcriptional or translational level. One common feature of miRNAs is that they are all excised from an approximately 70 nucleotide precursor RNA stem-loop, probably by Dicer, an RNase Ill-type enzyme, or a homolog thereof. By substituting the stem sequences of the miRNA precursor with miRNA sequence complementary to the target mRNA, a vector construct that expresses the novel miRNA can be used to produce siRNAs to initiate RNAi against specific mRNA targets in mammalian cells {See e.g., Zheng, B. J. (2004) Antivir. Ther. 9:365-374). When expressed by DNA vectors containing polymerase III promoters, micro-RNA designed hairpins can silence gene expression, such as NOX2 expression.

[0079] An example method for designing dsRNA molecules is provided in the pSUPER RNAi SYSTEM™ (OligoEngine, Seattle, WA). The system provides inducible expression of a siRNA in a transfected cell. To effect silencing of a specific gene, a pSUPERIOR vector is used in concert with a pair of custom oligonucleotides that include a unique 19-nt sequence derived from the mRNA transcript of the gene targeted for suppression (the "N-19 target sequence"). The N- 19 target sequence corresponds to the sense strand of the pSUPER-generated siRNA, which in turn corresponds to a 19-nt sequence within the mRNA. In the mechanism of RNAi, the antisense strand of the siRNA duplex hybridizes to this region of the mRNA to mediate cleavage of the molecule. These forward and reverse oligonucleotides are annealed and cloned into the vector so that the desired siRNA duplex can be generated. The sequence of the forward oligonucleotide includes the unique N-19 target in both sense and antisense orientation, separated by a 9-nt spacer sequence. The resulting transcript of the recombinant vector is predicted to fold back on itself to form a 19-base pair stem-loop structure. The stem-loop precursor transcript is quickly cleaved in the cell to produce a functional siRNA (T.R. Brummelkamp, et al, Science 296, 550 (2002)). More example methods are provided in Taxman DJ. et al. (2006) BMC Biotechnol. 6:7; and Mclntyre G. J. et al. (2006) BMC Biotechnol. 6: 1, each of which is incorporated by reference in its entirety.

[0080] As used herein, "ribozyme" can include a catalytic RNA molecule that cleaves RNA in a sequence specific manner. Ribozymes that cleave themselves are known as czs-acting ribozymes, while ribozymes that cleave other RNA molecules are known as transacting ribozymes. The term "czs-acting ribozyme sequence" as used herein refers to the sequence of an RNA molecule that has the ability to cleave the RNA molecule containing the czs-acting ribozyme sequence. A c/s-acting ribozyme sequence can contain any sequence provided it has the ability to cleave the RNA molecule containing the c/s-acting ribozyme sequence. For example, a c/s-acting ribozyme sequence can have a sequence from a hammerhead, axhead, or hairpin ribozyme. In addition, a c/s-acting ribozyme sequence can have a sequence from a hammerhead, axhead, or hairpin ribozyme that is modified to have either slow cleavage activity or enhanced cleavage activity. For example, nucleotide substitutions can be made to modify cleavage activity (Doudna and Cech, Nature, 418:222- 228 (2002)). Examples of ribozyme sequences that can be used with the methods and compositions described herein include those described in U.S. Patent No. 6,271 ,359, and U.S. Patent No. 5,824,519, incorporated by reference in their entireties. One example method for preparing a ribozyme is to synthesize chemically an oligodeoxynbonucleotide with a ribozyme catalytic domain (approximately 20 nucleotides) flanked by sequences that hybridize to the target mRNA. The oligodeoxynbonucleotide is amplified by using the substrate binding sequences as primers. The amplified product is cloned into a eukaryotic expression vector. A ribozyme can be expressed in eukaryotic cells from the appropriate DNA vector. If desired, the activity of the ribozyme may be augmented by its release from the primary transcript by a second ribozyme (Ohkawa et al, Nucleic Acids Symp. Ser., 27: 15-6 ( 1992); Taira et al, Nucleic Acids Res., 19: 5125-30 ( 1991); Ventura et al, Nucleic Acids Res., 21 , 3249-55 ( 1993).

[0081] In some embodiments, an isolated nucleic acid can include an antisense nucleic acid sequence selected such that it is complementary to the entirety of NOX2 or to a portion of NOX2. In some embodiments, a portion can refer to at least about 1 %, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, and at least about 80%, at least about 85%, at least about 90%, at least about 95%, or any portion within a range of any two of the foregoing percentages. In some embodiments, a portion can refer up to 100%. An example mRNA sequence (SEQ ID NO:01 ) of human NOX2 is shown in TABLE 2.

TABLE 2

1 attggaagaa gaagcatagt atagaagaaa ggcaaacaca acacattcaa cctctgccac 61 catggggaac tgggctgtga atgaggggct ctccattttt gtcattctgg tttggctggg 121 gttgaacgtc ttcctctttg tctggtatta ccgggtttat gatattccac ctaagttctt 181 ttacacaaga aaacttcttg ggtcagcact ggcactggcc agggcccctg cagcctgcct 241 gaatttcaac tgcatgctga ttctcttgcc agtctgtcga aatctgctgt ccttcctcag 301 gggttccagt gcgtgctgct caacaagagt tcgaagacaa ctggacagga atctcacctt 361 tcataaaatg gtggcatgga tgattgcact tcactctgcg attcacacca ttgcacatct 421 atttaatgtg gaatggtgtg tgaatgcccg agtcaataat tctgatcctt attcagtagc 481 actctctgaa cttggagaca ggcaaaatga aagttatctc aattttgctc gaaagagaat 541 aaagaaccct gaaggaggcc tgtacctggc tgtgaccctg ttggcaggca tcactggagt 601 tgtcatcacg ctgtgcctca tattaattat cacttcctcc accaaaacca tccggaggtc 661 ttactttgaa gtcttttggt acacacatca tctctttgtg atcttcttca ttggccttgc 721 catccatgga gctgaacgaa ttgtacgtgg gcagaccgca gagagtttgg ctgtgcataa 781 tataacagtt tgtgaacaaa aaatctcaga atggggaaaa ataaaggaat gcccaatccc 841 tcagtttgct ggaaaccctc ctatgacttg gaaatggata gtgggtccca tgtttctgta 901 tctctgtgag aggttggtgc ggttttggcg atctcaacag aaggtggtca tcaccaaggt 961 ggtcactcac cctttcaaaa ccatcgagct acagatgaag aagaaggggt tcaaaatgga 1021 agtgggacaa tacatttttg tcaagtgccc aaaggtgtcc aagctggagt ggcacccttt 1081 tacactgaca tccgcccctg aggaagactt ctttagtatc catatccgca tcgttgggga 1141 ctggacagag gggctgttca atgcttgtgg ctgtgataag caggagtttc aagatgcgtg 1201 gaaactacct aagatagcgg ttgatgggcc ctttggcact gccagtgaag atgtgttcag 1261 ctatgaggtg gtgatgttag tgggagcagg gattggggtc acacccttcg catccattct 1321 caagtcagtc tggtacaaat attgcaataa cgccaccaat ctgaagctca aaaagatcta 1381 cttctactgg ctgtgccggg acacacatgc ctttgagtgg tttgcagatc tgctgcaact 1441 gctggagagc cagatgcagg aaaggaacaa tgccggcttc ctcagctaca acatctacct 1501 cactggctgg gatgagtctc aggccaatca ctttgctgtg caccatgatg aggagaaaga 1561 tgtgatcaca ggcctgaaac aaaagacttt gtatggacgg cccaactggg ataatgaatt 1621 caagacaatt gcaagtcaac accctaatac cagaatagga gttttcctct gtggacctga 1681 agccttggct gaaaccctga gtaaacaaag catctccaac tctgagtctg gccctcgggg 1741 agtgcatttc attttcaaca aggaaaactt ctaacttgtc tcttccatga ggaaataaat 1801 gtgggttgtg ctgccaaatg ctcaaataat gctaattgat aatataaata ccccctgctt 1861 aaaaatggac aaaaagaaac tataatgtaa tggttttccc ttaaaggaat gtcaaagatt 1921 gtttgatagt gataagttac atttatgtgg agctctatgg ttttgagagc acttttacaa 1981 acattatttc atttttttcc tctcagtaat gtcagtggaa gttagggaaa agattcttgg 2041 actcaatttt agaatcaaaa gggaaaggat caaaaggttc agtaacttcc ctaagattat 2101 gaaactgtga ccagatctag cccatcttac tccaggtttg atactctttc cacaatactg 2161 agctgcctca gaatcctcaa aatcagtttt tatattcccc aaaagaagaa ggaaaccaag 2221 gagtagctat atatttctac tttgtgtcat ttttgccatc attattatca tactgaagga 2281 aattttccag atcattagga cataatacat gttgagagtg tctcaacact tattagtgac 2341 agtattgaca tctgagcata ctccagttta ctaatacagc agggtaactg ggccagatgt 2401 tctttctaca gaagaatatt ggattgattg gagttaatgt aatactcatc atttaccact 2461 gtgcttggca gagagcggat actcaagtaa gttttgttaa atgaatgaat gaatttagaa 2521 ccacacaatg ccaagataga attaatttaa agccttaaac aaaatttatc taaagaaata 2581 acttctatta ctgtcataga ccaaaggaat ctgattctcc ctagggtcaa gaacaggcta 2641 aggatactaa ccaataggat tgcctgaagg gttctgcaca ttcttatttg aagcatgaaa 2701 aaagagggtt ggaggtggag aattaacctc ctgccatgac tctggctcat ctagtcctgc 2761 tccttgtgct ataaaataaa tgcagactaa tttcctgccc aaagtggtct tctccagcta 2821 gcccttatga atattgaact taggaattgt gacaaatatg tatctgatat ggtcatttgt 2881 tttaaataac acccacccct tattttccgt aaatacacac acaaaatgga tcgcatctgt 2941 gtgactaatg gtttatttgt attatatcat catcatcatc ctaaaattaa caacccagaa 3001 acaaaaatct ctatacagag atcaaattca cactcaatag tatgttctga atatatgttc 3061 aagagagagt ctctaaatca ctgttagtgt ggccaagagc agggttttct ttttgttctt 3121 agaactgctc ccatttctgg gaactaaaac cagttttatt tgccccaccc cttggagcca 3181 caaatgttta gaactcttca acttcggtaa tgaggaagaa ggagaaagag ctgggggaag 3241 ggcagaagac tggtttagga ggaaaaggaa ataaggagaa aagagaatgg gagagtgaga 3301 gaaaataaaa aaggcaaaag ggagagagag gggaaggggg tctcatattg gtcattccct 3361 gccccagatt tcttaaagtt tgatatgtat agaatataat tgaaggaggt atacacatat 3421 tgatgttgtt ttgattatct atggtattga atcttttaaa atctggtcac aaattttgat 3481 gctgaggggg attattcaag ggactaggat gaactaaata agaactcagt tgttctttgt 3541 catactacta ttcctttcgt ctcccagaat cctcagggca ctgagggtag gtctgacaaa 3601 taaggcctgc tgtgcgaata tagcctttct gaaatgtacc aggatggttt ctgcttagag 3661 acacttaggt ccagcctgtt cacactgcac ctcaggtatc aattcatcta ttcaacagat 3721 atttattgtg ttattactat gagtcaggct ctgtttattg tttcaattct ttacaccaaa 3781 gtatgaactg gagagggtac ctcagttata aggagtctga gaatattggc cctttctaac 3841 ctatgtgcat aattaaaacc agcttcattt gttgctccga gagtgtttct ccaaggtttt 3901 ctatcttcaa aaccaactaa gttatgaaag tagagagatc tgccctgtgt tatccagtta 3961 tgagataaaa aatgaatata agagtgcttg tcattataaa agtttccttt tttattctct 4021 caagccacca gctgccagcc accagcagcc agctgccagc ctagcttttt tttttttttt 4081 ttttttttag cacttagtat ttagcattta ttaacaggta ctctaagaat gatgaagcat 4141 tgtttttaat cttaagacta tgaaggtttt tcttagttct tctgcttttg caattgtgtt 4201 tgtgaaattt gaatacttgc aggctttgta tgtgaataat tctagcgggg gacctgggag 4261 ataattccta cggggaattc ttaaaactgt gctcaactat taaaatgaat gagctttcaa 4321 aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaa

(SEQ ID NO: 01)

DEFINITION: Homo sapiens cytochrome b-245 beta chain (CYBB),

ACCESSION: NM_000397

VERSION: NM_000397.3

[0082] In some embodiments, an antisense oligonucleotide can have a length of at least about 5 nucleotides, at least about 7 nucleotides, at least about 10 nucleotides, at least about 15 nucleotides, at least about 20 nucleotides, at least about 25 nucleotides, at least about 30 nucleotides, at least about 35 nucleotides, at least about 40 nucleotides, at least about 45 nucleotides, at least about 50 nucleotides, at least about 55 nucleotides, at least about 60 nucleotides, at least about 65 nucleotides, at least about 70 nucleotides, at least about 75 nucleotides, at least about 80 nucleotides, at least about 85 nucleotides, at least about 90 nucleotides, at least about 95 nucleotides, or at least about 100 nucleotides. An antisense nucleic acid disclosed herein can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, such as phosphorothioate derivatives and acridine substituted nucleotides can be used. The antisense nucleic acid also can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation, namely, RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest. The antisense nucleic acid molecules can be administered to a subject, such as systemically or locally by direct injection at a tissue site, or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding NOX2 to thereby inhibit its expression. Alternatively, antisense nucleic acid molecules can be modified to target particular cells and then administered systemically. For systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies that bind to particular cell surface receptors or antigens. The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter can be used.

[0083] In some embodiments, antisense oligonucleotide include a-anomeric nucleic acid molecules. An α-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual beta-units, the strands run parallel to each other (Gaultier, C. et al. (1987) Nucleic Acids. Res. 15:6625-6641). The antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide, or a chimeric RNA-DNA analogue (Inoue, H. et al. (1987) Nucleic Acids Res. 15:6131-6148; Inoue, H. et al. (1987a) FEBS Lett. 215:327-330).

[0084] In some embodiments, an isolated nucleic acid can be unconjugated or can be conjugated to another moiety, such as a nanoparticle, to enhance a property of the compositions, e.g., a pharmacokinetic parameter such as absorption, efficacy, bioavailability, and/or half-life. The conjugation can be accomplished by methods known in the art, such as the methods of Lambert, G. et al. (2001) Drug Deliv. Rev. 47(1): 99-1 12 (describes nucleic acids loaded to polyalkylcyanoacrylate (PACA) nanoparticles); Fattal et al. ( 1998) J. Control Release 53(1-3): 137-43 (describes nucleic acids bound to nanoparticles); Schwab et al. (1994) Ann. Oncol. 5 Suppl. 4:55-58 (describes nucleic acids linked to intercalating agents, hydrophobic groups, polycations or PACA nanoparticles); and Godard, G. et al. (1995) Eur. J. Biochem. 232(2):404- 10 (describes nucleic acids linked to nanoparticles). Because RNAi is believed to progress via at least one single stranded RNA intermediate, the skilled artisan will appreciate that ss-siRNAs (e.g., the antisense strand of a ds-siRNA) can also be designed as described herein and utilized according to the claimed methodologies.

[0085] Some embodiments reducing the expression level of a nucleic acid encoding NOX2, or the expression level of a NOX2 protein in a cell can include delivering an isolated nucleic acid, such as an siRNA to a cell by methods known in the art, including cationic liposome transfection and electroporation. In some embodiments, an siRNA can show short term persistence of a silencing effect which may be beneficial in certain embodiments. To obtain longer term suppression of expression for targeted genes, such as NOX2, and to facilitate delivery under certain circumstances, one or more siRNA duplexes, such as a ds siRNA, can be expressed within cells from recombinant DNA constructs. Such methods for expressing siRNA duplexes within cells from recombinant DNA constructs to allow longer-term target gene suppression in cells are known in the art, including mammalian Pol III promoter systems (e.g., HI or U6/snRNA promoter systems (Tuschl, T. (2002) Nature Biotechnol. 20:446-448) capable of expressing functional double-stranded siRNAs; (Lee, N. S. et al. (2002) Nature Biotechnol. 20:500-505; Miyagishi, M. and Taira, K. (2002) Nature Biotechnol. 20:497-500; Paul, C. P. et al. (2002) Nature Biotechnol. 20:505-508; Yu, J.-Y. et al. (2002) Proc. Natl. Acad. Sci. USA 99(9):6047-6052; Sui, G. et al. (2002) Proc. Natl. Acad. Sci. USA 99(6):5515-5520). Transcriptional termination by RNA Pol III occurs at runs of four consecutive T residues in the DNA template, providing a mechanism to end the siRNA transcript at a specific sequence. The siRNA is complementary to the sequence of the target gene in 5'-3' and 3'-5' orientations, and the two strands of the siRNA can be expressed in the same construct or in separate constructs. Hairpin siRNAs, driven by an HI or U6 snRNA promoter can be expressed in cells, and can inhibit target gene expression. Constructs containing siRNA sequence(s) under the control of a T7 promoter also make functional siRNAs when co-transfected into the cells with a vector expressing T7 RNA polymerase (Jacque J.-M. et al. (2002) Nature 418:435-438). A single construct may contain multiple sequences coding for siRNAs, such as multiple regions of the NOX2 gene, such as a nucleic acid encoding the NOX2 mRNA, and can be driven, for example, by separate Pol III promoter sites.

[0086] Some embodiments reducing the expression level of a nucleic acid encoding NOX2, or the expression level of a NOX2 protein in a cell can include viral- mediated delivery of certain isolated nucleic acids to a cell. In some such embodiments, specific silencing of targeted genes through expression of certain nucleic acids, such as an siRNA by generating recombinant adenoviruses harboring siRNA under RNA Pol II promoter transcription control (Xia et al. (2002) Nature Biotechnol. 20(10): 1006-10). Injection of recombinant adenovirus vectors into transgenic mice expressing the target genes of the siRNA results in in vivo reduction of target gene expression. In adult mice, efficient delivery of siRNA can be accomplished by the "high-pressure" delivery technique, a rapid injection (within 5 seconds) of a large volume of siRNA containing solution into animal via the tail vein (Lewis, D. L. (2002) Nature Genetics 32: 107-108). Nanoparticles, liposomes and other cationic lipid molecules can also be used to deliver siRNA into animals. A gel-based agarose/liposome/siRNA formulation is also available (Jiamg, M. et al. (2004) Oligonucleotides 14(4):239-48).

Methods of reducing levels of ROS

[0087] Some embodiments of the methods and compositions provided herein include decreasing the level of ROS production in a population of cells, such as a population comprising leukemic cells. In some such embodiments, decreasing the level of ROS production in the population of cells can include reducing the activity of NOX2 in a cell of the population. In some configurations, a leukemic cell comprises a BCR-ABL1 gene fusion. In some embodiments, the level of ROS production may be reduced in a tumor. In some embodiments, a tumor may comprise the leukemic cells. In some embodiments, the cell is a myeloid cell. In some such embodiments, the level of ROS production in the population of cells in which the activity of NOX2 in a cell of the population has been reduced is decreased compared to the level of ROS production in a population of cells in which the activity of NOX2 in a cell has not been reduced. In some embodiments, the level of production of ROS in the population of cells can be decreased by at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any percentage in a range between any two of the foregoing percentages.

Combination therapies

[0088] Some embodiments of the methods and compositions provided herein include contacting a cell and/or administering to a subject a NOX2 inhibitor or isolated nucleic acid in combination with an additional therapeutic agent. As used herein, administering in combination can include administering two or more agents to a subject, such as a NOX2 inhibitor or isolated nucleic acid and an additional therapeutic agent, such that the two or more agents may be found in the subject's bloodstream at the same time, regardless of when or how they are actually administered. In some embodiments, the agents are administered simultaneously. In some such embodiments, administration in combination is accomplished by combining the agents in a single dosage form. When combining the agents in a single dosage form, they may be physically mixed, such as by co-dissolution or dry mixing, or may form an adduct or be covalently linked such that they split into the two or more active ingredients upon administration to the subject. In some embodiments, the agents are administered sequentially. In some embodiments, the agents are administered through the same route, such as orally. In some embodiments, the agents are administered through different routes, such as one being administered orally and another being administered i.v.

[0089] In some embodiments, the additional therapeutic agent can include a tyrosine kinase inhibitor. Examples of such tyrosine kinase inhibitors include imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, rebastinib, and 1 ,3,4 thiadiazole derivatives. In some embodiments, the additional therapeutic agent can include a chemotherapeutic agent. The chemotherapeutic agent may be a tyrosine kinase inhibitor, or another cell cycle inhibitor. As used herein, "cell cycle inhibitor" can include a chemotherapeutic agent that inhibits or prevents the division and/or replication of cells. In some embodiments, "cell cycle inhibitor" can include a chemotherapeutic agent such as Doxorubicin, Melphlan, Roscovitine, Mitomycin C, Hydroxyurea, 50Fluorouracil, Cisplatin, Ara-C, Etoposide, Gemcitabine, Bortezomib, Sunitinib, Sorafenib, Sodium Valproate, a HDAC Inhibitors, or Dacarbazine. More examples of additional chemotherapeutic agents include HDAC inhibitors such as FR01228, Trichostatin A, SAHA and PDX101. In some embodiments, the cell cycle inhibitor is a DNA synthesis inhibitor. As used herein, "DNA synthesis inhibitor" can include a chemotherapeutic agent that inhibits or prevents the synthesis of DNA by a cancer cell. Examples of DNA synthesis inhibitors include AraC (cytarabine), 6-mercaptopurine, 6-thioguanine, 5-fluorouracil, capecitabine, floxuridine, gemcitabine, decitabine, vidaza, fludarabine, nelarabine, cladribine, clofarabine, pentostatin, thiarabine, troxacitabine, sapacitabine or forodesine. More examples of additional chemotherapeutic agents include FLT3 inhibitors such as Semexanib (SU5416), Sunitinib (SU11248), Midostaurin (PKC412), Lestautinib (CEP-701), Tandutinib (MLN518), CHIR- 258, Sorafenib (BAY-43-9006) and KW-2449. More examples of additional chemotherapeutic agents include farnesyltransferase inhibitors such as tipifarnib (Rl 15777, Zarnestra), lonafarnib (SCH66336, Sarasar™) and BMS-214662. More examples of additional chemotherapeutic agents include topoisomerase II inhibitors such as the epipodophyllotoxins etoposide and teniposide, and the anthracyclines doxorubicin and 4-epi- doxorubicin. More examples of additional chemotherapeutic agents include P-glycoprotein modulators such as zosuquidar trihydrochloride (Z.3HCL), vanadate, and/or verapamil. More examples of additional chemotherapeutic agents include hypomethylating agents such as 5- aza-cytidine and/or 2' deoxyazacitidine. In some configurations, the chemotherapeutic agent may be actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vemurafenib, vinblastine, vincristine, and vindesine, vinorelbine.

Pharmaceutical compositions and formulations

[0090] Some embodiments of the methods and compositions provided herein include pharmaceutical compositions, and administration of such compositions. In some embodiments, a pharmaceutical composition can include a NOX2 inhibitor, such as a therapeutically effective amount of a NOX2 inhibitor. In some embodiments, a pharmaceutical composition can include a NOX2 inhibitor and a pharmaceutically acceptable excipient. As used herein, a "pharmaceutically acceptable" can include a carrier, diluent or excipient that does not abrogate the biological activity and properties of a NOX2 inhibitor. In some embodiments, pharmaceutical composition can include a NOX2 inhibitor and an additional therapeutic agent. Standard pharmaceutical formulation techniques can be used, such as those disclosed in Remington's The Science and Practice of Pharmacy, 21st Ed., Lippincott Williams & Wilkins (2005), incorporated by reference in its entirety.

[0091] In some embodiments, a pharmaceutical composition can be administered to a subject by any of the accepted modes of administration for agents that serve similar utilities including, but not limited to, orally, subcutaneously, intravenously, intranasally, topically, transdermally, intraperitoneally, intramuscularly, intrapulmonary, vaginally, rectally, or intraocularly.

[0092] In some embodiments, a pharmaceutical composition comprising a NOX2 inhibitor can be administered at a therapeutically effective dosage, such as a dosage sufficient to provide treatment for a disorder. The amount of active compound administered can be dependent on the subject and disease state being treated, the severity of the disorder, the manner and schedule of administration and the judgment of the prescribing physician. The actual dose of the active compounds, such as NOX2 inhibitors depends on the specific compound, and on the condition to be treated; the selection of the appropriate dose is well within the knowledge of the skilled artisan.

[0093] In some embodiments, the pharmaceutical composition is administered subcutaneously. Solutions of an active compound, such as a NOX2 inhibitor, as a free acid or a pharmaceutically-acceptable salt may be administered in water with or without a surfactant such as hydroxypropyl cellulose. Dispersions are also contemplated such as those utilizing glycerol, liquid polyethylene glycols and mixtures thereof and oils. Antimicrobial compounds may also be added to the preparations. Injectable preparations may include sterile aqueous solutions or dispersions and powders which may be diluted or suspended in a sterile environment prior to use. Carriers such as solvents dispersion media containing, e.g., water, ethanol polyols, vegetable oils and the like, may also be added. Coatings such as lecithin and surfactants may be utilized to maintain the proper fluidity of the composition. Isotonic agents such as sugars or sodium chloride may also be added as well as products intended for the delay of absorption of the active compounds such as aluminum monostearate and gelatin. Sterile injectable solutions are prepared as is known in the art and filtered prior to storage and/or administration. Sterile powders may be vacuum dried freeze dried from a solution or suspension containing them. In some embodiments, the pharmaceutical compositions are administered by intravenous, intra-arterial, or intra-muscular injection of a liquid preparation. Suitable liquid formulations include solutions, suspensions, dispersions, emulsions, oils and the like. In some embodiments, the pharmaceutical compositions are administered intravenously and are thus formulated in a form suitable for intravenous administration. In some embodiments, the pharmaceutical compositions are administered intra- arterially and are thus formulated in a form suitable for intra-arterial administration. In some embodiments, the pharmaceutical compositions are administered intra-muscularly and are thus formulated in a form suitable for intra-muscular administration.

[0094] Proper formulation is dependent upon the route of administration selected. For injection, the agents of the compounds may be formulated into aqueous solutions, preferably in physiologically compatible buffers such as Hanks solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.

[0095] For oral administration, the compounds can be formulated by combining the active compounds with pharmaceutically acceptable carriers known in the art. Such carriers enable the compounds of the disclosure to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a subject to be treated. Pharmaceutical preparations for oral use can be obtained using a solid excipient in admixture with the active ingredient (agent), optionally grinding the resulting mixture, and processing the mixture of granules after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients include: fillers such as sugars, comprising lactose, sucrose, mannitol, or sorbitol; and cellulose preparations, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum, methyl cellulose, hydroxypropylmethyl- cellulose, sodium carboxymethylcellulose, or polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as crosslinked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.

[0096] Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, polyvinyl pyrrolidone, Carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active agents.

[0097] Pharmaceutical preparations that can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with fillers such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate, and, optionally, stabilizers. In soft capsules, the active agents may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for such administration. For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.

[0098] For administration intranasally or by inhalation, the compounds, such as NOX2 inhibitors, for use according to the present disclosure may be conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, such as carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of gelatin for use in an inhaler or insufflator and the like may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

[0099] The compounds, such as NOX2 inhibitors, may be formulated for parenteral administration by injection, e.g. , by bolus injection or continuous infusion. Formulations for injection may be presented in unit-dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.

[0100] Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds, such as NOX2 inhibitors, in water-soluble form. Additionally, suspensions of the active agents may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents that increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.

[0101] In addition to the formulations described herein, the compounds, such as NOX2 inhibitors, may also be formulated as a depot preparation. Such long-acting formulations may be administered by implantation, such as subcutaneously or intramuscularly, or by intramuscular injection. Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example, as an emulsion in an acceptable oil) or ion-exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt. A pharmaceutical carrier for hydrophobic compounds is a co-solvent system comprising benzyl alcohol, a non-polar surfactant, a water-miscible organic polymer, and an aqueous phase. The co-solvent system may be a VPD co-solvent system. VPD is a solution of 3% w/v benzyl alcohol, 8% w/v of the non-polar surfactant polysorbate 80, and 65% w/v polyethylene glycol 300, made up to volume in absolute ethanol. The VPD co- solvent system (VPD: 5 W) contains VPD diluted 1 : 1 with a 5% dextrose in water solution. This co-solvent system dissolves hydrophobic compounds well, and itself produces low toxicity upon systemic administration. The proportions of a co-solvent system may be suitably varied without destroying its solubility and toxicity characteristics. Furthermore, the identity of the co-solvent components may be varied: for example, other low-toxicity non- polar surfactants may be used instead of polysorbate 80; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g. polyvinyl pyrrolidone; and other sugars or polysaccharides may be substituted for dextrose.

[0102] In some embodiments, delivery systems for hydrophobic pharmaceutical compounds may be employed. Liposomes and emulsions are known examples of delivery vehicles or carriers for hydrophobic drugs. Certain organic solvents such as dimethylsulfoxide also may be employed, although usually at the cost of greater toxicity due to the toxic nature of DMSO. Additionally, the compounds, such as NOX2 inhibitors, may be delivered using a sustained-release system, such as semipermeable matrices of solid hydrophobic polymers containing the therapeutic agent. Various sustained-release materials have been established and are known by those skilled in the art. Sustained-release capsules may, depending on their chemical nature, release the compounds for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the therapeutic reagent, additional strategies for protein stabilization may be employed.

[0103] The pharmaceutically acceptable formulations can contain a compound, or a salt or solvate thereof, in an amount of about 50 mg, about 100 mg, about 150 mg, about 200 mg, about 250 mg, about 300 mg, about 350 mg, about 400 mg, about 450 mg, or about 500 mg. Additionally, the pharmaceutically acceptable formulations may contain a compound such as NOX2 inhibitor, or a salt or solvate thereof, in an amount from about 0.5 w/w % to about 95 w/w %, or from about 1 w/w % to about 95 w/w %, or from about 1 w/w % to about 75 w/w %, or from about 5 w/w % to about 75 w/w %, or from about 10 w/w % to about 75 w/w %, or from about 10 w/w % to about 50 w/w %.

Kits

[0104] Some embodiments of the methods and compositions provided herein include kits comprising a NOX2 inhibitor and/or an isolated nucleic acid, wherein the isolated nucleic acid reduces the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein in a cell. In some embodiments, the NOX2 inhibitor can include HDC (CEPLENE), GSK2795039, apocynin, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD 084, and shionogi. More examples of NOX2 inhibitors include histamine, histamine salts, N-methyl-histamine, 4-methyl-histamine, histamine phosphate, histamine diphosphate, and a histamine structural analog having H₂-receptor activities, an endogenous histamine releasing preparation, a non-histamine derivative H₂-receptor agonist. In some embodiments, the NOX2 inhibitor is HDC. In some embodiments, the NOX2 inhibitor is HDC. In some embodiments, the isolated nucleic acid can include a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, and a ribozyme. In some embodiments, the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof.

[0105] In some embodiments, a kit can include an additional therapeutic agent. In some embodiments, the additional therapeutic agent is a cell cycle inhibitor. For example, in some embodiments, the additional therapeutic agent is a chemotherapeutic agent such as a tyrosine kinase inhibitor. In some embodiments, the tyrosine kinase inhibitor is, or comprises, one or more of imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, and rebastinib.

[0106] In some embodiments, a kit can include reagents to generate the modified cell. In some such embodiments, a kit can include reagents useful for use with a CRISPR system. In some embodiments, reagents can include a modified AAV vector and a nucleotide sequence encoding a site-specific nuclease. The site-specific nuclease may include a ZFN, a TALEN, or CRISPR/Cas9-based system that specifically binds and cleaves a modified target gene, such as a modified NOX2 gene. The site-specific nuclease may be included in the kit to specifically bind and target a particular region in the endogenous target gene, such as a NOX2 target gene. The kit may further include donor DNA, a gRNA, or a transgene. In some embodiments, a kit can include a Cas9 protein or Cas9 fusion protein, a nucleotide sequence encoding a Cas9 protein or Cas9 fusion protein, and/or at least one gRNA. The CRISPR/Cas9-based system may be included in the kit to specifically bind and target a particular target region upstream, within or downstream of the coding region of the target gene, such as a NOX2 gene. For example, a CRISPR/Cas9-based system may be specific for a promoter region of a target gene or a CRISPR/Cas9-based system may be specific for the coding region.

Indications

[0107] Some embodiments of the methods and compositions provided herein include treating or ameliorating a subject having a disorder, such as a disorder comprising a cell having a BCR-ABLl gene fusion. In some embodiments, the disorder may be a leukemia, such as chronic myeloid leukemia (CML), acute myeloid leukemia, acute lymphocytic leukemia, and chronic lymphocytic leukemia. In some embodiments, the disorder may comprise a gastrointenstinal stromal tumor (GIST). In certain embodiments, the leukemia may comprise one or more BCR-ABLl^"1" cells, such as BCR-ABLl^"1" myeloid cells.

[0108] In some embodiments, a subject treated by the methods disclosed herein has or is suffering from a leukemia, such as CML. In some embodiments, a subject treated by the methods disclosed herein is in remission from CML. In some embodiments, the subject has a de novo CML. In some embodiments, the subject has a secondary CML. In some embodiments, a subject treated by the methods disclosed herein is in complete remission (CR) of CML. In some embodiments, complete remission can include one or more of the following criteria: (i) normal values for absolute neutrophil count and platelet count, and independence from red cell transfusion; (ii) a bone marrow biopsy that reveals no clusters or collections of blast cells and extramedullary leukemia is absent; (iii) a bone marrow aspiration reveals normal maturation of all cellular components (i.e., erythrocytic, granulocytic, and megakaryocyte); (iv) less than 5% blast cells are present in the bone marrow, and none have a leukemic phenotype; (v) absence of previously detected clonal cytogenetic abnormality confirms the morphologic diagnosis of complete remission. In some embodiments, complete remission (CR) is defined as less than 5% blast cells in normocellular bone marrow, without evidence of extramedullary leukemia. In some embodiments, the subject is one that has complete remission with insufficient hematological recovery.

[0109] In some embodiments, a subject treated by the methods disclosed herein is suffering from refractory or relapsed myeloid leukemia. As used herein, "relapsed myeloid leukemia" is defined as reappearance of leukemic blasts in the blood or greater than 5% blasts in the bone marrow after complete remission not attributable to any other cause. For subjects presenting with relapsed myeloid leukemia, more than 5% blasts on baseline bone marrow assessment is required in some embodiments. As used herein, "refractory myeloid leukemia" is defined as a failure to achieve a complete remission or complete remission with incomplete blood recovery after previous therapy. Any number of prior anti- leukemia schedules is allowed. In some embodiments, "complete remission" is defined as morphologically leukemia free state (i.e. bone marrow with less than 5% blasts by morphologic criteria and no Auer rods, no evidence of extramedullary leukemia) and absolute neutrophil count greater than or equal to 1,000/μ1, and platelets greater than 100,000/μ1. As used herein, "complete remission with incomplete blood recovery" is defined as morphologically leukemia free state (i.e., bone marrow with less than 5% blasts by morphologic criteria and no Auer rods, no evidence of extramedullary leukaemia) and neutrophil count less than 1 ,000/μ1, or platelets less than 100,000/μ1 in the blood.

[0110] In some embodiments, a subject treated by the methods disclosed herein has been treated with surgery, chemotherapy, radiation therapy, a targeted therapy, including therapies that are intended to boost immune system responses against cancer, or a combination thereof. In some embodiments, the leukemia is resistant to treatment with chemotherapy. For example, in some embodiments the cancer is chemotherapy-resistant leukemia. In some embodiments, the methods described herein are for the treatment of a subject with recurring or relapsing leukemia. In some embodiments, relapsing leukemia caused by minimal residual disease (MRD) and/or leukemic stem cells. In some embodiments, the subject is not in complete remission. For example, in some embodiments the subject has one or more detectable leukemic cells. In some embodiments, the subject has previously undergone chemotherapeutic treatment for cancer but the cancer cells do not respond to the chemotherapy treatment (i.e. refractory cancer). In some embodiments, the subject has previously underdone chemotherapeutic treatment for cancer and has one or more detectable cancer cells. In some embodiments, the subject has not previously undergone chemotherapeutic treatment for cancer.

[0111] In some embodiments, a subject treated by the methods disclosed herein has failed a prior therapy for the treatment of leukemia such as chemotherapy or radiation and is now in remission. In some embodiments, a subject treated by the methods disclosed herein is in first complete remission (CRl). In some embodiments, a subject treated by the methods disclosed herein is in second complete remission (CR2). In some embodiments, a subject treated by the methods disclosed herein is in third complete remission (CR3). In some embodiments, a subject treated by the methods disclosed herein is in fourth complete remission (CR4).

[0112] In some embodiments, the survival rate is leukemia-free survival rate. In some embodiments, the survival rate is overall survival rate. Durations of leukemia-free survival (LFS) are measured as the time from random assignment of the subjects to the date of relapse or death from any cause, whichever occurred first. Durations of overall survival (OS) are measured as the time from the date of random assignment to death from any cause. In some embodiments, the Kaplan-Meier procedure is used to estimate the survival distributions and survival rate for a population of subjects.

[0113] In some embodiments, the subject comprises a BCR-ABLl fusion gene caused by a (9;22) translocation. In some embodiments, the presence of a BCR-ABLl fusion gene is determined by identifying the presence of a BCR-ABLl oncoprotein in a subject's cells. For example, in some embodiments, the BCR-ABLl oncoprotein is identified in the cells by identifying the BCR-ABLl oncoprotein in cytoplasm of the cells. In some such embodiments, the BCR-ABLl oncoprotein is identified in cytoplasm of the cells immunohistochemically.

[0114] In some embodiments disclosed herein, the presence of a BCR-ABLl fusion gene in a subject is determined by identifying a nucleic acid comprising the BCR- ABLl fusion gene in the subject, for example a biological sample or a derivative thereof from the subject. In some embodiments, the nucleic acid is genomic DNA and/or mRNA. In some embodiments, the nucleic acid is obtained from an acellular body fluid (e.g., serum and/or plasma) of said subject. In some embodiments, identifying a nucleic acid comprising the BCR-ABLl fusion gene comprises amplification of at least a portion of the BCR-ABLl fusion gene. In some embodiments, the amplification comprises polymerase chain reaction (PCR), such as, for example, real-time PCR (RT-PCR). In some embodiments, identifying a nucleic acid comprising the BCR-ABLl fusion gene comprises using an oligonucleotide probe complimentary to a portion of the BCR-ABL1 fusion gene. In some such embodiments, the oligonucleotide probe comprises a label (e.g., a fluorescent label).

[0115] Also disclosed herein include methods of identifying the presence of one or more molecular alterations in a biological sample from a subject having leukemia. As used herein, the term "one or more molecular alterations" shall be given its ordinary meaning and shall also refer to any variation in the genetic or protein sequence in or more cells of a subject as compared to the corresponding wild-type genes or proteins. One or more molecular alterations include, but are not limited to, genetic mutations, gene amplifications, splice variants, deletions, insertions/deletions, gene rearrangements, single-nucleotide variations (SNVs), insertions, and aberrant RNA/protein expression. In some embodiments, said one or more molecular alterations comprises the presence of mutant NPM1. In some embodiments, knowledge of the presence of the BCR-ABL1 fusion gene is acquired from an analytical assay, such as, for example, nucleic acid sequencing, polypeptide sequencing, restriction digestion, capillary electrophoresis, nucleic acid amplification-based assays, nucleic acid hybridization assay, comparative genomic hybridization, real-time PCR, quantitative reverse transcription PCR (qRT-PCR), PCR-RFLP assay, HPLC, mass-spectrometric genotyping, fluorescent in-situ hybridization (FISH), next generation sequencing (NGS), a kinase activity assay, and any combination thereof.

[0116] In some embodiments, the analytical assay used to acquire the knowledge of the one or more molecular alterations in the biological sample involves polymerase chain reactions (PCR) or nucleic acid amplification-based assays. A number of PCR-based analytical assays known in the art are suitable for the methods disclosed herein, comprising but not limited to real-time PCR, quantitative reverse transcription PCR (qRT-PCR), and PCR-RFLP assay.

[0117] In some embodiments, the analytical assay used to identify the presence of the one or more molecular alterations in the biological sample involves determining a nucleic acid sequence and/or an amino acid sequence comprising the one or more molecular alterations. In some embodiments, the nucleic acid sequence comprising the one or more molecular alterations from a subject having cancer is sequenced. In some embodiments, the sequence is determined by a next generation sequencing procedure. As used herein "next- generation sequencing" refers to oligonucleotide sequencing technologies that have the capacity to sequence oligonucleotides at speeds above those possible with conventional sequencing methods (e.g. Sanger sequencing), due to performing and reading out thousands to millions of sequencing reactions in parallel. Non-limiting examples of next-generation sequencing methods/platforms include Massively Parallel Signature Sequencing (Lynx Therapeutics); solid-phase, reversible dye-terminator sequencing (Solexa/Illumina); DNA nanoball sequencing (Complete Genomics); SOLiD technology (Applied Biosystems); 454 pyro-sequencing (454 Life Sciences/Roche Diagnostics); ion semiconductor sequencing (ION Torrent); and technologies available from Pacific Biosciences, Intelligen Bio-systems, Oxford Nanopore Technologies, and Helicos Biosciences. Accordingly, in some embodiments, the NGS procedure used in the methods disclosed herein can comprise pyrosequencing, sequencing by synthesis, sequencing by ligation, or a combination of any thereof. In some embodiments, the NGS procedure is performed by an NGS platform selected from Illumina, Ion Torrent, Qiagen, Invitrogen, Applied Biosystem, Helicos, Oxford Nanopore, Pacific Biosciences, and Complete Genomics.

[0118] In some embodiments, the analytical assay used to acquire the knowledge of the one or more molecular alterations in the biological sample involves a nucleic acid hybridization assay that includes contacting nucleic acids derived from the biological sample with a nucleic acid probe comprising ( 1 ) a nucleic acid sequence complementary to a nucleic acid sequence encoding the BCR-ABL1 fusion gene and further comprising (2) a detectable label. As used herein, the term "detectable label" shall be given its ordinary meaning and shall also refer to a molecule or a compound or a group of molecules (e.g., a detection system) used to identify a target molecule of interest. Typically, detectable labels represent a component of a detection system and are attached to another molecule that specifically binds to the target molecule. In some cases, the detectable label may be detected directly. In other cases, the detectable label may be a part of a binding pair, which can then be subsequently detected. Signals from the detectable label may be detected by various means and will depend on the nature of the detectable label. Examples of means to detect detectable label include but are not limited to spectroscopic, photochemical, biochemical, immunochemical, electromagnetic, radiochemical, or chemical means, such as fluorescence, chemifluorescence, chemiluminescence, or any other appropriate means. [0119] In some embodiments, the biological sample comprises sputum, bronchoalveolar lavage, pleural effusion, tissue, whole blood, serum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, circulating tumor cells, circulating nucleic acids, bone marrow, or any combination thereof. In some embodiments, the biological sample includes whole blood and blood components. In some embodiments, the blood component comprises plasma.

EXAMPLES

Example 1— Role of NOX2 on the colony□ forming properties of BCRDABL1⁺ cells

[0120] A role for NOX2 in the colony-forming and disease-initiating properties of BCR-ABL1^"1" cells was investigated. Hematopoietic cells containing an exogenous BCR- ABL1 transgene were developed from wild type (WT) cells, and NOX2 knock out (NOX2- KO) cells. The NOX2-KO cells were incapable of producing NOX2 D derived ROS.

[0121] Briefly, a BCRDABL1 p210 transgene was cloned into a MSCVD GFP⁺ vector. The vector was transduced into bone marrow (BM) cells from C57BL/6 (WT) mice (Charles River Laboratories, Sulzfeld, Germany) or B6.129S6DCybb^tmlDin (NOX2D KO) mice (Jackson Laboratories, Bar Harbor, ME, USA), as described (Palmqvist, L., et ah, (2006) Blood, 108, 1030-1036). Specifically, BM cells from the C57BL/6 (WT) mice or the B6.129S6 DCybb^tmlDin (NOX2 DKO) mice were treated with 5 Dfluorouracil, and then cultured with irradiated GP+E86 BCRUABL1□ virus□ producing cells. Two days later, nonD adherent BM cells were separated from adherent GP+E86 BCR UABL1 cells and expanded for 5 days. Transduced BM cells were selected by sorting BCRDABL1⁺ cells for the presence of GFP using a three□ laser BD FACSAria (405, 488 and 633 nm from BD Biosciences, San Diego, CA, USA) to a purity of >98 %.

[0122] 500 or 5,000 BCRDABL1⁺ WT (n = 2) or BCRDABL1⁺ NOX2D KO cells were seeded in methylcellulose medium (Methocult GF M3434, StemCell Technologies, Vancouver, Canada) for 7 days before colonies were counted. Cells were re□ plated for three consecutive weeks. Statistical analysis was performed using Student's tDtest.

[0123] BCRDABL1⁺ WT cells demonstrated enhanced serial colony□ formation (CFC) compared with control cells transduced only with the selection marker GFP (data not shown). Interestingly, there was a pronounced reduction of the serial CFC of cells expressing BCRDABL1 in a NOX2 D KO background (FIG. 1A). This difference was not due to variable expression of BCRDABL1 because BCRDABL1 mRNA levels were equal in WT and NOX2□ KO cells as determined by real□ time quantitative reverse transcriptase polymerase chain reaction (RTDqPCR) (2-9 for both WT and NOX2 D KO cells with values representing 2 after normalization to the expression of the reference gene Hprt). BCRD ABL1 RTDqPCR was performed using primers as described (Gabert, J., et ah, (2003) Leukemia, 17, 2318-2357) and Hpri was measured by TaqMan Gene Expression Assay Mm01545399_ml (Applied Biosystems, Life Technologies Europe BV, Stockholm, Sweden) according to manufacturer's instructions, both analyzed on an ABI PRISM®7900HT instrument (Applied Biosystems).

Example 2— Role of NOX2 in the disease-initiating properties of BCRDABL1⁺ cells

[0124] To investigate a role of NOX2 in the disease-initiating properties of BCRDABLr cells, 100,000 BCRDABL1⁺ WT or BCRDABL1⁺ NOX2 D KO cells were injected into the tail vein of lethally irradiated C57BL6/J mice together with 2 x 10⁶ lifeD sparing naive WT BM cells. Blood was drawn from transplanted mice every second week and analyzed by flow cytometry for the presence of BCRDABL1⁺ cells. The blood was examined using a four D laser BD LSRFortessa (405, 488, 532 and 640 nm) to estimate the percentage of BCRDABLl⁺cells (reflected by GFP expression).

[0125] The first blood draw at 3 weeks post D transplantation demonstrated successful engraftment in all animals (FIG. IB). Also at three weeks, mice transplanted with WT BCRDABL cells demonstrated a significantly higher fraction of BCRD ABL1⁺ cells in blood compared with mice transplanted with BCRDABL1^"1" NOX2D KO cells (n = 6 in each group, P = 0-038, Student's tU test; FIG. IB and FIG. 1C). By comparison, in mice receiving BCRD ABL1⁺ NOX2D KO transplants, the rise in BCRDABL1⁺ cells occurred at later time D points, or not at all, during the observation period (FIG. IB and FIG. ID). The percentage of BCRDABL1+ cells in blood of mice at 3 weeks post D transplantation with BCRDABLr WT or BCRDABL1⁺ NOX2D KO cells was 68.5% and 3.5%, respectively. Example 3— BCR-ABL1^"1" WT cells induce a more aggressive leukemia compared with BCR-ABL1⁺ NOX2-KO cells

[0126] The survival rates of mice transplanted with BCRDABL1⁺ WT (n = 6) or BCRDABL1⁺ NOX2 D KO were measured. A significantly prolonged survival was observed in mice transplanted with BCRDABL1⁺ NOX2 D KO cells, compared with BCRD ABL1⁺ WT cells (FIG. 2A). Five out of six mice transplanted with BCRD ABL1⁺ WT cells died within the study period (80 days). By comparison, only two out of six mice transplanted with BCRDABL1⁺ NOX2 D KO cells died within the study period. Survival of mice transplanted with BCRDABL1⁺ WT (n = 6) or BCRDABL1⁺ NOX2D KO; (n = 6) BCRD ABL1⁺ cells was compared using the log rank test. These results indicate that BCRD ABL1⁺ WT cells induce a more aggressive leukemia compared with BCRD ABL1⁺ NOX2D KO cells. Mice that did not become moribund within the study period were not further analyzed.

[0127] A gating strategy was used on representative bone marrow (BM) samples from a mouse transplanted with BCRDABL1⁺ WT cells and a mouse transplanted with BCRDABL1⁺ NOX2 D KO cells (FIG. 2B). BM cells were stained with the following panel of antibodies: GR1 DPE clone RB6D 8C5, CDl lbDBWl l clone Ml/70, and CD34 DAPC clone RAM34. The percentage of BCRDABL1⁺ cells among viable cells was first determined. Among the population of BCRDABL1⁺ cells the percentage of GRl⁺CDl lb⁺ and GRFCD1 lb^" cells was determined, and the GR1XD1 lb^" cells were further gated for CD34 positivity. FIG. 2C depicts the results of flow cytometry analyses of BM samples from mice transplanted with WT and BCRDABL1⁺ NOX2D KO cells at the time of sacrifice.

[0128] At the time of death the diseased mice showed pronounced splenomegaly (spleen weight 0- 5 g ± 0-07 (mean ± SEM), n = 5 for mice transplanted with BCRDABL1⁺ WT cells and 0-2 g ± 0-02, n = 2 for mice transplanted with BCRDABL1⁺ NOX2D KO cells) along with infiltration of BCRD ABL1⁺ cells in BM (FIG. 2B and FIG. 2C), spleen and liver (not shown). Fluorometric analysis revealed that the majority of BCRDABL1^"1" cells in BM were granulocytes that coDexpressed CDl lb and GR1, consistent with a mature phenotype. A minor fraction of the BCRDABL1^"1" cells displayed a blast D like phenotype (CDl lb^"GRl^"CD34⁺) (FIG. 2B and FIG. 2C). The BCR D ABL 1 ⁺ NOX2 D KO cells tended to express a more mature phenotype with an increased proportion of cells carrying GR1⁺ and CDl lb⁺ and fewer GRl^"CDl lb^"CD34⁺ cells. These results support the concept that NOX2 is involved in myeloid differentiation (Corzo, C.A., et al., (2009) Journal of Immunology, 182, 5693-5701).

Example 4— BCR-ABL1⁺ NOX2-KO cells exhibit reduced ROS production ex vivo

[0129] BM cells were isolated from mice that had been transplanted with BCRD ABL1⁺ WT cells and BCR□ ABL 1 ⁺ NOX2□ KO cells. E v vo ROS formation was measured for the isolated cells. Cells were stimulated with 1 x 10 mol/1 D Dpeptide (R&D Systems, Minneapolis, MN, USA) "TypDLys D TyrDMetDVal DdDMet" (SEQ ID NO:02), or not stimulated (Ctrl). ROS production was continuously monitored using an isoluminol D chemoluminescence technique (Dahlgren, C. et al., Journal of Immunological Methods, 232, 3-14). Briefly, ROS production was measured using isoluminol in a FLUOstar Omega plate reader (BMG, Ortenberg, Germany), for 8- 5 min and an area under the curve was determined. Results were obtained for isolated cells from mice transplanted with BCRD ABL1⁺ WT cells (n = 5) or with BCRDABL1⁺ NOX2D KO cells (n = 2), respectively. The difference in radical production between un D stimulated and D peptide D stimulated cells was analyzed using Student's paired tDtest.

[0130] BM cells isolated from mice transplanted with BCRD ABL1⁺ NOX2D KO cells produced minute amounts of spontaneous and D peptide D induced ROS (FIG. 2D). In comparison, BM cells isolated from mice transplanted with BCRDABL1⁺ WT cells generated ROS spontaneously and in significantly higher amounts in response to D Dpeptide.

Example 5— Ex vivo effects of HDC on ROS production with BCR- ABL1⁺ cells

[0131] Ex vivo effects of HDC on ROS formation were investigated with cells from mice transplanted with BCRD ABL1⁺ WT cells or BCR-ABL1⁺ NOS-KO cells. FACS- sorted BCRD ABL1⁺ WT cells and FACS-sorted BCR-ABL1⁺ NOS-KO were stimulated with the formyl peptide receptor agonist D Dpeptide (Typ DLys DTyrDMetDVal DdDMet) (SEQ ID NO:02). Cells were treated with 100 μΜ HDC. ROS production was measured as described above. [0132] Treatment with HDC reduced ROS formation in FACS-sorted BCR- ABLl^"1" WT cells, compared to untreated cells (FIG. 3A). No significant ROS formation was detected in treated and untreated FACS-sorted BCR-ABL1⁺ NOX2-KO cells (FIG. 3B). Thus, HDC inhibits ROS formation in stimulated BCRDABL1⁺ WT cells.

Example 6— HDC inhibits in vivo expansion of transplanted BCR-ABLl ⁺ hematopoietic cells

[0133] The effects of a NOX2 inhibitor, HDC, were measured in mice transplanted with BCR-ABLl^"1" WT cells. As described above in Example 1, BM cells were transduced to express a GFP-labeled human BCR-ABLl from a p210 construct cloned into a MSCV vector. Irradiated C57BL/6J mice received transplants of the transduced hematopoietic cells.

[0134] The transplanted mice were treated with HDC at 1.5 mg/mouse three times per week for 4 weeks via i.p. injections, beginning 5 days after transplantation. Treated and untreated control mice were monitored for the presence of leukemic cells in blood and survival, for 15 weeks after transplantation. Peripheral blood was drawn biweekly from the mice for fluorimetric quantification of BCR-ABLl^"1" cells.

[0135] Three out of five mice treated with HDC showed no significant expansion of BCR-ABLl^"1" cells (FIG. 4A). In stark contrast, six out of seven untreated control mice demonstrated a significant increase in BCR-ABLl^"1" cells in blood during the study period. Survival rate of the mice mirrored the growth and inhibition of the transplanted BCR-ABLl^"1" cells. Only two out of five of the HDC treated mice showed an expansion BCR-ABLl^"1" cells in blood and died during the study period (FIG. 4B). In contrast, the six out of seven untreated control mice that demonstrated a significant increase in BCR-ABLl^"1" cells also did not survive during the study period. These results demonstrate the efficacy of the NOX2 inhibitor HDC, to inhibit the in vivo expansion of BCR-ABLl^"1" hematopoietic cells, and concomitant survival of subjects.

[0136] The term "comprising" as used herein is synonymous with "including," "containing," or "characterized by," and is inclusive or open-ended and does not exclude additional, unrecited elements or method steps. [0137] The above description discloses several methods and materials of the present invention. This invention is susceptible to modifications in the methods and materials, as well as alterations in the fabrication methods and equipment. Such modifications will become apparent to those skilled in the art from a consideration of this disclosure or practice of the invention disclosed herein. Consequently, it is not intended that this invention be limited to the specific embodiments disclosed herein, but that it cover all modifications and alternatives coming within the true scope and spirit of the invention.

[0138] All references cited herein, including but not limited to published and unpublished applications, patents, and literature references, are incorporated herein by reference in their entirety and are hereby made a part of this specification. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and/or take precedence over any such contradictory material.

Claims

WHAT IS CLAIMED IS:

1. A method for treating or ameliorating a disorder in a subject comprising a BCR-ABL1 gene fusion, the method comprising: reducing the activity of nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2), or reducing the expression level of a nucleic acid encoding NOX2, or reducing the expression level of NOX2 protein in a cell of the subject.

2. The method of claim 1, further comprising identifying the presence of the BCR-ABL1 gene fusion in the subject.

3. The method of claim 2, wherein the presence of the BCR-ALB1 gene fusion is identified from an analytical assay selected from the group consisting of: nucleic acid sequencing polypeptide sequencing, restriction digestion, capillary electrophoresis, nucleic acid amplification-based assays, nucleic acid hybridization assay, comparative genomic hybridization, real-time PCR, quantitative reverse transcription PCR (qRT-PCR), PCR-RFLP assay, HPLC, mass-spectrometric genotyping, fluorescent in-situ hybridization (FISH), next generation sequencing (NGS), a kinase activity assay, and any combination thereof.

4. The method of any one of claims 1-3, wherein reducing the activity of NOX2 comprises administering an effective amount of a NOX2 inhibitor to the subject.

5. The method of claim 4, wherein the NOX2 inhibitor is selected from the group consisting of histamine, a histamine salt, histamine dihydrochloride (HDC), histamine diphosphate, a histamine structural analog having H₂-receptor activities, an endogenous histamine releasing preparation, a non-histamine derivative H₂-receptor agonist, GSK2795039, apocynin, diphenylene iodonium, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD084, NSC23766, CAS 1177865-17-6, CAS 1090893-12-1, and shionogi.

6. The method of claim 5, wherein the NOX2 inhibitor is HDC.

7. The method of any one of claims 1-6, wherein reducing the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein comprises contacting the cell with an isolated nucleic acid selected from the group consisting of a guide RNA (gRNA), a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, a locked nucleic acid, and a ribozyme.

8. The method of claim 7, wherein the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof.

9. The method of claim 7 or 8, wherein the isolated nucleic acid comprises a gRNA comprising a sequence complementary to the sequence of a target gene selected from the group consisting of NOX2, CYBA, NCF1, NCF2, NCF4, RAC1, and RAC2.

10. The method of claim 9, wherein the target gene is NOX2.

11. The method of any one of claims 1-10, further comprising administering at least one chemotherapeutic agent in combination with the NOX2 inhibitor or the isolated nucleic acid.

12. The method of claim 11, wherein the at least one chemotherapeutic agent comprises a tyrosine kinase inhibitor.

13. The method of claim 12, wherein the tyrosine kinase inhibitor is selected from the group consisting of: imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, and rebastinib.

14. The method of claim 11, wherein the at least one chemotherapeutic agent is selected from the group consisting of: actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vemurafenib, vinblastine, vincristine, vindesine, and vinorelbine.

15. The method of any one of claims 4-14, wherein the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered concurrently.

16. The method of any one of claims 4-14, wherein the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered sequentially.

17. The method of any one of claims 1-16, wherein the disorder is a leukemia.

18. The method of any one of claims 1-16, wherein the disorder is selected from the group consisting of chronic myeloid leukemia, acute myeloid leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, gastrointenstinal stromal tumors (GIST), and a combination thereof.

19. The method of any one of claims 1-16, wherein the disorder comprising a BCR-ABLl gene fusion is a chronic myeloid leukemia selected from the group consisting of a de novo chronic myeloid leukemia, a secondary chronic myeloid leukemia, a refractory chronic myeloid leukemia, a recurrent chronic myeloid leukemia, and a relapsing chronic myeloid leukemia.

20. The method of any one of claims 1-19, wherein the cell is a hematopoietic cell.

21. The method of any one of claims 1-20, wherein the cell is a myeloid cell.

22. The method of any one of claims 1-21, wherein the subject is mammalian.

23. The method of any one of claims 1-22, wherein the subject is human.

24. A method for increasing a survival rate of a subject having a disorder, wherein the subject comprises a BCR-ABLl gene fusion, the method comprising: reducing the activity of nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2), or reducing the expression level of a nucleic acid encoding NOX2, or reducing the expression level of NOX2 protein in a cell of the subject, wherein the survival rate of the subject is increased compared to the survival rate of an untreated subject in which the activity of NOX2, or the expression level of a nucleic acid encoding NOX2, or the expression level of NOX2 protein in a cell of the untreated subject has not been reduced.

25. The method of claim 24, further comprising: identifying the presence of the BCR-ABLl gene fusion in the subject.

26. The method of claim 25, wherein the presence of the BCR-ALB1 gene fusion is identified from an analytical assay selected from the group consisting of: nucleic acid sequencing polypeptide sequencing, restriction digestion, capillary electrophoresis, nucleic acid amplification-based assays, nucleic acid hybridization assay, comparative genomic hybridization, real-time PCR, quantitative reverse transcription PCR (qRT-PCR), PCR-RFLP assay, HPLC, mass-spectrometric genotyping, fluorescent in-situ hybridization (FISH), next generation sequencing (NGS), a kinase activity assay, and any combination thereof.

27. The method of any one of claims 24-26, wherein the survival rate of the subject is increased by at least 10% compared to the survival rate of the untreated subject.

28. The method of any one of claims 24-27, wherein survival rate of the subject is increased by at least 50% compared to the survival rate of the untreated subject.

29. The method of any one of claims 24-26, wherein survival rate of the subject is increased by 20% - 80% compared to the survival rate of the untreated subject.

30. The method of any one of claims 24-26, wherein survival rate of the subject is increased by 30% to 50%.

31. The method of any one of claims 24-30, wherein survival rate is leukemia-free survival rate.

32. The method of any one of claims 24-31, wherein survival rate is overall survival rate.

33. The method of any one of claims 24-32, wherein reducing the activity of NOX2 comprises administering an effective amount of a NOX2 inhibitor to the subject.

34. The method of claim 33, wherein the NOX2 inhibitor is selected from the group consisting of histamine, a histamine salt, histamine dihydrochloride (HDC), histamine diphosphate, a histamine structural analog having H₂-receptor activities, an endogenous histamine releasing preparation, a non-histamine derivative H₂-receptor agonist, GSK2795039, apocynin, diphenylene iodonium, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD084, NSC23766, CAS 1177865-17-6, CAS 1090893-12-1, and shionogi.

35. The method of claim 34, wherein the NOX2 inhibitor is HDC.

36. The method of any one of claims 24-35, wherein reducing the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein comprises contacting the cell with an isolated nucleic acid selected from the group consisting of a guide RNA (gRNA), a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, a locked nucleic acid, and a ribozyme.

37. The method of claim 36, wherein the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof.

38. The method of claim 36 or 37, wherein the isolated nucleic acid comprises a gRNA comprising a sequence complementary to the sequence of a target gene selected from the group consisting of NOX2, CYBA, NCF1, NCF2, NCF4, RAC1, and RAC2.

39. The method of claim 38, wherein the target gene is NOX2.

40. The method of any one of claims 24-39, further comprising administering an additional chemotherapeutic agent in combination with the NOX2 inhibitor or the isolated nucleic acid.

41. The method of claim 40, wherein the chemotherapeutic agent comprises a tyrosine kinase inhibitor.

42. The method of claim 41, wherein the tyrosine kinase inhibitor is selected from the group consisting of: imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, and rebastinib.

43. The method of claim 40, wherein the chemotherapeutic agent is selected from the group consisting of: actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vemurafenib, vinblastine, vincristine, vindesine, and vinorelbine.

44. The method of any one of claims 40-43, wherein the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered concurrently.

45. The method of any one of claims 40-43, wherein the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered sequentially.

46. The method of any one of claims 24-45, wherein the disorder comprising a BCR-ABL1 gene fusion is a leukemia.

47. The method of any one of claims 24-45, wherein the disorder comprising a BCR-ABL1 gene fusion is selected from the group consisting of chronic myeloid leukemia, acute myeloid leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, and gastrointenstinal stromal tumors (GIST).

48. The method of any one of claims 24-45, wherein the disorder comprising a BCR-ABLl gene fusion is a chronic myeloid leukemia selected from the group consisting of a de novo chronic myeloid leukemia, a secondary chronic myeloid leukemia, a refractory chronic myeloid leukemia, a recurrent chronic myeloid leukemia, and a relapsing chronic myeloid leukemia.

49. The method of any one of claims 24-48, wherein the cell is a hematopoietic cell.

50. The method of any one of claims 24-48, wherein the cell is a myeloid cell.

51. The method of any one of claims 24-48, wherein the subject is mammalian.

52. The method of any one of claims 24-48, wherein the subject is human.

53. A method for inhibiting growth of a tumor in a subject, the tumor comprising a BCR-ABLl gene fusion, the method comprising: reducing the activity of nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2), reducing the expression level of a nucleic acid encoding NOX2, or reducing the expression level of NOX2 protein in a cell of the subject.

54. The method of claim 53, further comprising: identifying the presence of the BCR-ABLl gene fusion in the subject.

55. The method of claim 54, wherein the presence of the BCR-ALB1 gene fusion is identified from an analytical assay selected from the group consisting of: nucleic acid sequencing polypeptide sequencing, restriction digestion, capillary electrophoresis, nucleic acid amplification-based assays, nucleic acid hybridization assay, comparative genomic hybridization, real-time PCR, quantitative reverse transcription PCR (qRT-PCR), PCR-RFLP assay, HPLC, mass-spectrometric genotyping, fluorescent in-situ hybridization (FISH), next generation sequencing (NGS), a kinase activity assay, and any combination thereof.

56. The method of any one of claims 53-55, wherein growth of the tumor is inhibited by at least about 20%.

57. The method of any one of claims 53-56, wherein growth of the tumor is inhibited by at least about 50%.

58. The method of any one of claims 53-57, wherein growth of the tumor is inhibited by at least about 70%.

59. The method of any one of claims 53-58, wherein reducing the activity of NOX2 comprises administering an effective amount of a NOX2 inhibitor to the subject.

60. The method of claim 59, wherein the NOX2 inhibitor is selected from the group consisting of histamine, a histamine salt, histamine dihydrochloride (HDC), histamine diphosphate, a histamine structural analog having H₂-receptor activities, an endogenous histamine releasing preparation, a non-histamine derivative H₂-receptor agonist, GSK2795039, apocynin, diphenylene iodonium, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD084, NSC23766, CAS 1177865-17-6, CAS 1090893-12-1, and shionogi.

61. The method of claim 60, wherein the NOX2 inhibitor is HDC.

62. The method of any one of claims 53-61, wherein reducing the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein comprises contacting the cell with an isolated nucleic acid selected from the group consisting of a guide RNA (gRNA), a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, a locked nucleic acid, and a ribozyme.

63. The method of claim 62, wherein the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof.

64. The method of claim 62 or 63, wherein the isolated nucleic acid comprises a gRNA comprising a sequence complementary to the sequence of a target gene selected from the group consisting of NOX2, CYBA, NCF1, NCF2, NCF4, RAC1, and RAC2.

65. The method of claim 64, wherein the target gene is NOX2.

66. The method of any one of claims 53-65, further comprising administering an additional chemotherapeutic agent in combination with the NOX2 inhibitor or the isolated nucleic acid.

67. The method of claim 66, wherein the chemotherapeutic agent comprises a tyrosine kinase inhibitor.

68. The method of claim 67, wherein the tyrosine kinase inhibitor is selected from the group consisting of: imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, and rebastinib.

69. The method of claim 66, wherein the chemotherapeutic agent is selected from the group consisting of: actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vemurafenib, vinblastine, vincristine, vindesine, and vinorelbine.

70. The method of any one of claims 66-69, wherein the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered concurrently.

71. The method of any one of claims 66-69, wherein the NOX2 inhibitor or the isolated nucleic acid and the additional chemotherapeutic agent are administered sequentially.

72. The method of any one of claims 53-71, wherein the tumor comprising a BCR-ABL1⁺ cell is a leukemia.

73. The method of any one of claims 53-71, wherein the tumor comprising a BCR-ABL1^"1" cell is selected from the group consisting of chronic myeloid leukemia, acute myeloid leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, and gastrointenstinal stromal tumors (GIST).

74. The method of any one of claims 53-71, wherein the tumor comprising a BCR-ABL1^"1" cell is a chronic myeloid leukemia selected from the group consisting of a de novo chronic myeloid leukemia, a secondary chronic myeloid leukemia, a refractory chronic myeloid leukemia, a recurrent chronic myeloid leukemia, and a relapsing chronic myeloid leukemia.

75. The method of any one of claims 53-74, wherein the cell is a hematopoietic cell.

76. The method of any one of claims 53-75, wherein the cell is a myeloid cell.

77. The method of any one of claims 53-76, wherein the subject is mammalian.

78. The method of any one of claims 53-77, wherein the subject is human.

79. Use of a nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) inhibitor or an isolated nucleic acid to treat or ameliorate a tumor in a subject, the subject comprising a BCR-ABL1 gene fusion, wherein the isolated nucleic acid reduces the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein in a cell of the subject.

80. Use of a nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) inhibitor or an isolated nucleic acid to increase a survival rate of a subject having a disorder comprising BCR-ABL1 gene fusion, wherein the isolated nucleic acid reduces the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein in a cell of the subject, wherein the survival rate of the subject is increased compared to the survival rate of an untreated subject in which the activity of NOX2, or the expression level of a nucleic acid encoding NOX2, or the expression level of NOX2 protein in a cell of the untreated subject has not been reduced.

81. Use of a nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) inhibitor or an isolated nucleic acid to inhibit growth of a tumor comprising a cell comprising a BCR-ABL1 gene fusion in a subject, wherein the isolated nucleic acid reduces the expression level of a nucleic acid encoding NOX2 or the expression level of NOX2 protein in a cell of the subject.

82. The use of any one of claims 79-81, wherein the NOX2 inhibitor is selected from the group consisting of histamine, a histamine salt, histamine dihydrochloride (HDC), histamine diphosphate, a histamine structural analog having H2-receptor activities, an endogenous histamine releasing preparation, a non-histamine derivative H2-receptor agonist, GSK2795039, apocynin, diphenylene iodonium, GKT136901, GKT137831, ML171, VAS2870, VAS3947, celastrol, ebselen, perhexiline, grindelic acid, NOX2ds-tat, NOXAlds, fulvene-5, ACD084, NSC23766, CAS 1177865-17-6, CAS 1090893-12-1, and shionogi.

83. The use of claim 82, wherein the NOX2 inhibitor is HDC.

84. The use of any one of claims 79-83, wherein the isolated nucleic acid selected from the group consisting of a guide RNA (gRNA), a small hairpin RNA (shRNA), a small interfering RNA (siRNA), a micro RNA (miRNA), an antisense polynucleotide, a locked nucleic acid, and a ribozyme.

85. The use of claim 84, wherein the isolated nucleic acid comprises a sequence encoding NOX2 or a fragment thereof, a sequence encoding antisense NOX2 or a fragment thereof, or an antisense nucleic acid complementary to a sequence encoding NOX2 or a fragment thereof.

86. The use of claim 84 or 85, wherein the isolated nucleic acid comprises a gRNA comprising a sequence complementary to the sequence of a target gene selected from the group consisting of NOX2, CYBA, NCF1, NCF2, NCF4, RAC1, and RAC2.

87. The use of claim 86, wherein the target gene is NOX2.

88. The use of any one of claims 79-87, in combination with an additional chemotherapeutic agent.

89. The use of claim 88, wherein the additional chemotherapeutic agent comprises a tyrosine kinase inhibitor.

90. The use of claim 89, wherein the tyrosine kinase inhibitor is selected from the group consisting of: imatinib, nilotinib, dasatinib, bosutinib, ponatinib, bafetinib, and rebastinib.

91. The use of claim 88, wherein the additional chemotherapeutic agent is selected from the group consisting of: actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vemurafenib, vinblastine, vincristine, vindesine, and vinorelbine.

92. The use of any one of claims 79-91, wherein the disorder comprising a BCR- ABL1 gene fusion is a leukemia.

93. The use of any one of claims 79-91, wherein the disorder comprising a BCR-ABL1 gene fusion is selected from the group consisting of chronic myeloid leukemia, acute myeloid leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, and gastrointenstinal stromal tumors (GIST).

94. The use of any one of claims 79-91, wherein the disorder comprising a BCR-ABLl gene fusion is a chronic myeloid leukemia selected from the group consisting of a de novo chronic myeloid leukemia, a secondary chronic myeloid leukemia, a refractory chronic myeloid leukemia, a recurrent chronic myeloid leukemia, and a relapsing chronic myeloid leukemia.

95. The use of any one of claims 79-94, wherein the cell is a hematopoietic cell.

96. The use of any one of claims 79-95, wherein the cell is a myeloid cell.

97. The use of any one of claims 79-96, wherein the subject is mammalian.

98. The use of any one of claims 79-97, wherein the subject is human.