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• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
  • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
  • A61P35/02—Antineoplastic agents specific for leukemia

Definitions

• follicular lymphoma FL
• gene mutations that can be used to predict a subject’s nonresponsiveness to treatment of follicular lymphoma with ibrutinib.
• follicular lymphoma FL
• methods of treating follicular lymphoma (FL) in a subject comprising administering to the subject a therapeutically effective amount of ibrutinib to thereby treat the FL, wherein the subject does not have one or more mutations as defined in Table 2 in one or more genes selected from AHNAK.
• Also provided are methods of predicting a likelihood of nonresponsiveness to ibrutinib in a subject having follicular lymphoma comprising analyzing a sample from the subject for one or more of the mutations as defined in Table 2 in one or more genes selected from AHNAK, ARID 1A, ATP6AP1, BCL9L, CLTC, CNOT1, EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1, wherein one or more of the mutations in the one or more genes is indicative of
• FIG. 2 illustrates a heatmap of genes mutated in > 10% of samples (75 genes) from the DAWN study.
• FIG. 3 illustrates a heatmap of ranked nonresponder gene mutations from the DAWN study.
• FIG. 4 illustrates the mean ORR of predicted responders based on cross- validation studies.
• FIG. 5 is an exemplary plot of somatic mutations in the ATP6AP1 gene in DAWN patients.
• FIG. 6 is an exemplary plot of somatic mutations in the EP400 gene in DAWN patients.
• FIG. 7 is an exemplary plot of somatic mutations in the ARID 1 A gene in DAWN patients.
• FIG. 8 is an exemplary plot of somatic mutations in the SOCS1 gene in DAWN patients.
• FIG. 9 is an exemplary plot of somatic mutations in the TBL1XR1 gene in DAWN patients.
• range includes the endpoints thereof and all the individual integers and fractions within the range, and also includes each of the narrower ranges therein formed by all the various possible combinations of those endpoints and internal integers and fractions to form subgroups of the larger group of values within the stated range to the same extent as if each of those narrower ranges was explicitly recited. It is not intended that the scope of the methods be limited to the specific values recited when defining a range. All ranges are inclusive and combinable.
• the term“comprising” is intended to include examples encompassed by the terms“consisting essentially of’ and“consisting of’; similarly, the term“consisting essentially of’ is intended to include examples encompassed by the term“consisting of.”
• Ibrutinib a first-in-class, oral, covalent inhibitor of Bruton’s tyrosine kinase (BTK), approved for several B-cell malignancies in the United States and other countries, disrupts signaling pathways essential for the adhesion, proliferation, homing, and survival of malignant B cells.
• Treatment includes reducing the severity and/or frequency of symptoms, eliminating symptoms and/or the underlying cause of the symptoms, reducing the frequency or likelihood of symptoms and/or their underlying cause, and improving or remediating damage caused, directly or indirectly, by the follicular lymphoma.
• Treatment includes complete response and partial response to the administered agent (ibrutinib).
• Treatment also includes prolonging survival as compared to the expected survival of a subject not receiving treatment.
• the phrase“therapeutically effective amount” refers to an amount of the ibrutinib, as described herein, effective to achieve a particular biological or therapeutic result such as, but not limited to, biological or therapeutic results disclosed, described, or exemplified herein.
• the therapeutically effective amount may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the composition to cause a desired response in a subject.
• Exemplary indicators of a therapeutically effective amount include, for example, improved well-being of the patient, reduction of a tumor burden, arrested or slowed growth of the follicular lymphoma, and/or absence of metastasis of follicular lymphoma cells to other locations in the body.
• BTK tyrosine kinase
• R/R relapsed or refractory
• ORR overall response rate
• OS overall survival
• FL follicular lymphoma
• FL complete response
• PR partial response
• follicular lymphoma FL
• methods of treating follicular lymphoma (FL) in a subject comprising:
• ibrutinib administered to the subject a therapeutically effective amount of ibrutinib to thereby treat the FL, wherein the subject does not have one or more mutations as defined in Table 2 in one or more genes selected from A NAK. ARID1A, ATP6AP1, BCL9L, CLTC, CNOT1, EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16,
• the methods comprise administering to the subject a therapeutically effective amount of ibrutinib to thereby treat the FL, wherein the subject does not have one or more mutations as defined in Table 2 in one or more genes selected from AHNAK, ARID1A, ATP6AP1, BCL9L, CLTC , ( 'NOTE EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1.
• the methods can be performed on subjects not having one or more mutations as defined in Table 2 in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or all 17 o ⁇ AHNAK, ARID 1 A, ATP6AP1, BCL9L, CLTC, CNOT1, EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1 as provided in Table 2 and various combinations thereof.
• the therapeutically effective amount of ibrutinib can comprise from about 420 mg to about 840 mg.
• the therapeutically effective amount of ibrutinib can comprise about 420 mg, 440 mg, 460 mg, 480 mg, 500 mg, 520 mg, 540 mg, 560 mg, 580 mg, 600 mg, 620 mg, 640 mg, 660 mg, 680 mg, 700 mg, 720 mg, 740 mg, 760 mg, 780 mg, 800 mg, 820 mg, or 840 mg.
• the therapeutically effective amount of ibrutinib is 560 mg.
• the FL is relapsed/refractory (R/R) FL.
• Suitable subjects for treatment include those who, prior to the administering: • had a diagnosis of grade 1, 2, or 3 a nontransformed FL;
• the subject can have a partial response. In some embodiments, the subject can have a complete response.
• ibrutinib in the manufacture of a medicament for the treatment of follicular lymphoma (FL) in a subject not having one or more mutations as defined in Table 2 in one or more genes selected from AHNAK, ARID1A, ATP6AP1, BCL9L, CLTC , CNOT1, EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1.
• ibrutinib for use in the treatment of follicular lymphoma (FL) in a subject not having one or more mutations as defined in Table 2 in one or more genes selected from AHNAK.
• ARID 1 A A ⁇ R6ARI. BCL9L, CLTC , CNOT1, EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1.
• the mutations provided in Table 2 in one or more of AHNAK, ARID 1 A, ATP6AP1, BCL9L, CLTC, CNOT1, EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1 are indicative of nonresponsiveness to ibrutinib treatment, as disclosed herein.
• the methods comprise analyzing a sample from the subject for one or more mutations as defined in Table 2 in one or more genes selected from AHNAK, ARID1A, ATP6AP1, BCL9L, CLTC, CNOT1, EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1, wherein a lack of the one or more mutations in the one or more genes is indicative of responsiveness to the ibrutinib.
• nonresponsiveness to ibrutinib in a subject having follicular lymphoma is combined with a subsequent treatment of the follicular lymphoma.
• FL follicular lymphoma
• Suitable samples from the subject include any biological sample that contains the gene of interest including, but not limited to, whole blood samples and tumor biopsy samples.
• the DAWN study evaluated the efficacy and safety of ibrutinib monotherapy in patients with relapsed/refractory (R/R) follicular lymphoma (FL).
• the overall response rate (ORR) for ibrutinib was 20.9% (95% confidence interval [Cl], 13.7-29.7), not meeting the primary end point. However, responders experienced a long duration of response (median 19.4 months).
• a genetic investigation was performed on samples from the DAWN study to determine whether somatic mutations could be used to identify FL patients who will respond, or not respond, to ibrutinib.
• Classifiers were built with variable numbers of genes ranked with a greedy algorithm that selected genes that would, at each iteration, allow the removal of the greatest number of nonresponders from the patient pool, while severely penalizing the removal of responders. Classification results were first assessed with 10-fold cross-validation within the DAWN dataset, subsequently (See Bartlett NL, et al. Blood. 2018;131: 182-190).
• Exome data were generated from FFPE samples of 88 subjects with FL, each from a different subject. Eighty -three of these subjects were indicated as either“responder” (CR + PR) or“nonresponder” (SD + PD) after ibrutinib treatment. Exome Sequencing
• VAF variant allele frequency
• Variants were marked as (a)“deleterious” based on MetaSVM annotations in dbNSFP and/or (b)“Personalis gene” variants based on whether they were in genes found in the Personalis Cancer Panel used in the Bartlett CTEP study.
• Exome data were generated from the paraffin-embedded tumor samples from 88 patients. 974,686 total nonsynonymous variants were identified. After filtering out potential errors and likely germline mutations, the number of variants was reduced to 13,554. Response data were available on 83 patients, comprising 17 responders and 66
• VAF histogram for filtered variants showed a significant reduction in the peaks at 0.5 and 1.0 seen in the original set of variants return by LabCorp, indicating a much higher ratio of somatic to germline variants.
• the variants in the dbSNP non-COSMIC set largely fell in the zones near 0.5 and 1.0, indicating that many of them are likely germline mutations.
• the VAF distribution of the COSMIC (“known somatic”) variants found within the dataset was examined and found to have a similar distribution (note, however, that there are known contaminating variants in COSMIC that are likely to be nearly exclusively germline, accounting for the small peak around 0.5).
• the number of mutated genes in each sample varied from under 100 to over 500, and variance was greater across non-responder NR subjects, likely due to a larger sample size.
• FIG. 2 The overall pattern of variant frequencies identified from the whole exome sequencing is provided in FIG. 2. There were 75 genes with putative mutations in > 10% of the patients, including many of those previously implicated in FL (e.g., CREBBP, BCL2, and KMT2D). The left panel of FIG. 2 shows the percentage of individuals with a mutation in each gene, while the right panel shows the distribution of mutations in those genes in the 83 patients for which responder data were available.
• the mean ORR of predicted responders shown by the solid line (“mean ORR of predicted responders”) in FIG. 4 is based on 10-fold cross-validation for 17 different responder/nonresponder classification models, showing an increase in predicted ORR as more genes were added. Each model was defined by the number of genes used to build it, with genes being added in order of decreasing new information content, as shown in FIG. 3.
• the dotted line in FIG. 4 (“ORR”) represents the ORR of the entire patient cohort regardless of classification.
• ATP6AP1 The majority of the mutations seen in the ATP6API gene were found in the ATP-synthase SI region (FIG. 5).
• EP400 - 7 nonresponder patients had somatic mutations in the EP400 gene, and 5 of these patients had mutations marked as“deleterious” by metaSVM (FIG. 6).
• EP400 encodes a histone acetylase complex component.
• TBL1XR1 - 4 of the 5 putative somatic mutations in the TBLXR1 gene were predicted as deleterious by metaSVM; the remaining variant represents the gain of a premature stop codon (FIG.9).
• CARD 11 - CARD 11 contained 8 variants found in 6 patients. Each of the CARD11 variants were identified individually, even though CARD11 was not a top ranked gene in this analysis. A total of 4 variants from 2 patients were left after the filtering applied here (T117P, D230N, C351S, and S352P), and could be deleterious, though they were not identified as deleterious by metaSVM.
• VAF variant allele frequency
• Embodiment 1 Use of ibrutinib in the manufacture of a medicament for the treatment of follicular lymphoma (FL) in a subject not having one or more mutations as defined in Table 2 in one or more genes selected from AHNAK, ARID1A, ATP6AP1, BCL9L, CLTC , CNOT1, EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1.
• Embodiment 2 Ibrutinib for use in the treatment of follicular lymphoma (FL) in a subject not having one or more mutations as defined in Table 2 in one or more genes selected from AHNAK, ARID1A, ATP6AP1, BCL9L, CLTC , CNOT1, EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1.
• Embodiment 3 A method of treating follicular lymphoma (FL) in a subject, the
• Embodiment 5 The use or method of any one of embodiments 2-4, wherein the
• therapeutically effective amount of ibrutinib comprises from about 420 mg to about 840 mg.
• Embodiment 6 The use or method of embodiment 5, wherein the therapeutically
• ibrutinib comprises 560 mg.
• Embodiment 7 The use or method of any one of the previous embodiments, wherein the FL is relapsed/refractory (R/R) FL.
• Embodiment 8 The use or method of any one of the previous embodiments, wherein, prior to the administering, the subject had a diagnosis of grade 1, 2, or 3a
• Embodiment 9 The use or method of embodiment 8, wherein, prior to the
• Embodiment 10 The use or method of embodiment 9, wherein, prior to the
• the subject was R/R to a last prior line of therapy with an anti-CD20 monoclonal antibody-containing chemoimmunotherapy regimen.
• Embodiment 11 The use or method of any one of the previous embodiments, wherein the subject has a partial response or a complete response.
• Embodiment 12 A method of predicting a likelihood of nonresponsiveness to ibrutinib in a subject having follicular lymphoma, the method comprising analyzing a sample from the subject for one or more mutations as defined in Table 2 in one or more genes selected from AHNAK, ARID1A, ATP6AP1, BCL9L, CLTC , ( 'NOTE EP400, KDM2B, MYBBP1A, NACA, NBPF1, NBPF10, NCOA4, NEDD4L, PRDM16, SOCS1, and TBL1XR1, wherein the one or more mutations in the one or more genes is indicative of nonresponsiveness to ibrutinib.
• Embodiment 13 The method of embodiment 12, further comprising administering a therapeutically effective amount of ibrutinib to thereby treat the FL if the subject does not have the one or more mutations in the one or more genes.

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