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Wo2018/200489 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/200489 Al 01 November 2018 (01.11.2018) W !P O PCT (51) International Patent Classification: [US/US]; 415 Main Street, Cambridge, Massachusetts C12Q 1/6883 (2018.01) 02142 (US). (21) International Application Number: (74) Agent: MCNEILL, Rebecca M. et al; McNeill Baur PCT/US20 18/029098 PLLC, 125 Cambridge Park Drive, Suite 301, Cambridge, Massachusetts 02140 (US). (22) International Filing Date: 24 April 2018 (24.04.2018) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (25) Filing Language: English AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, (26) Publication Language: English CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, (30) Priority Data: HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, 62/489,823 25 April 2017 (25.04.2017) KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, 62/567,735 03 October 2017 (03.10.2017) MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (71) Applicants: THE BRIGHAM AND WOMEN'S HOSPI¬ OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, TAL, INC. [US/US]; 75 Francis Street, Boston, Massachu SC, SD, SE, SG, SK, SL, SM, ST, SV, SY,TH, TJ, TM, TN, setts 021 15 (US). THE GENERAL HOSPITAL CORP. TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. [US/US]; 55 Fruit Street, Boston, Massachusetts 02144 (84) Designated States (unless otherwise indicated, for every (US). kind of regional protection available): ARIPO (BW, GH, (72) Inventors; and GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (71) Applicants: SIDDHARTHA, Jaiswal [US/US]; 415 UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, Main Street, Cambridge, Massachusetts 02142 (US). TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, KATHIRESAN, Sekar [US/US]; 415 Main Street, Cam EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, bridge, Massachusetts 02142 (US). EBERT, Benjamin MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (54) Title: IL-8, IL-6, IL-1B AND TET2 AND DNMT3A IN ATHEROSCLEROSIS (57) Abstract: The application presently discloses a method of treating atherosclerosis in a hu man subject comprising administering an effective amount of an IL-8 inhibitor, an IL-6 inhibitor, and/or an IL- Ι inhibitor, wherein the subject has a TET2 and/or DNMT3A mutation thereby treating atherosclerosis. It also discloses a method for treating atherosclerosis in a human subject comprising sequencing at least a part of a genome comprising TET2 and/or DNMT3A of one or more cells in a blood sample of the subject; determining from the sequencing whether the subject has one or more mutations in TET2 and/or DNMT3A, if it is determined that the subject has at least one TET2 and/or DNMT3A mutation, administering an IL-8 inhibitor, an IL-6 inhibitor, and/ or an IL- Ι inhibitor to a subject to the subject thereby treating atherosclerosis. Gene Fig. 1A 00 o 00 o Fig. 1B o [Continued on next page] WO 2018/200489 Al llll II II 11III II I 11II II III 111III II I II TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: — with international search report (Art. 21(3)) — before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) — with sequence listing part of description (Rule 5.2(a)) IL-8, IL-6, IL-Ι β AND TET2 AND DNMT3A IN ATHEROSCLEROSIS FIELD [001] Methods of treating atherosclerosis and methods for diagnosing atherosclerosis in subjects having a TET2 and/or DNMT3A mutation PRIORITY CLAIM [002] This application claims priority to U.S. Provisional Appln. No. 62/489,823, filed on April 25, 2017, and to U.S. Provisional Appln. No. 62/567,735, filed on October 3, 2017, both of which are incorporated by reference herein in their entirety. SEQUENCE LISTING [003] This application is filed with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled "2018-04-20_01 179-0001- 00PCT_Seq_List_ST25" created on April 20, 2018, which is 910 bytes in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety. BACKGROUND [004] Aging is associated with an increased incidence of both cancer and cardiovascular disease, including atherosclerosis and elevated cholesterol. Whole exome sequencing data has been used to identify a common, age-related disorder marked by an expansion of hematopoietic clones carrying recurrent somatic mutations, most commonly loss- of-function alleles in the genes DNMT3A, TET2, and ASXL1 (1-3). These mutations, which are also common in the myelodysplastic syndrome and acute myeloid leukemia, provide a selective advantage to the hematopoietic stem cells in which they occur, and are detectable as clones in peripheral blood samples because the mutated stem cells maintain the ability to differentiate into circulating granulocytes, monocytes, and lymphocytes. Individuals under the age of 40 rarely accumulate these clones, but they become common in aging, with over 10% of those over age 70 harboring such a mutation. Carriers of these mutations have a ~10-fold increased risk of developing a hematologic malignancy. [005] Clonal hematopoiesis of indeterminate potential (CHIP), defined by the presence of an expanded somatic blood cell clone in those without other hematologic abnormalities, is common in older individuals and associates with an increased risk of developing hematologic cancer. Some evidence of a connection between somatic TET2 and/or DNMT3A mutations in blood cells and atherosclerosis has also been demonstrated. However, the nature of this association was unclear and these mutations were not previously known to be associated with increased IL-8, IL-6, IL- Ι β levels or a need to inhibit IL-8 activity. Thus, anew method of treating and diagnosing atherosclerosis is now warranted, relying on the presence of both at least one TET2 and/or DNMT3A mutation and elevated IL-8 levels. SUMMARY [006] The present inventors have found that individuals with CHIP are at increased risk for all-cause mortality and, surprisingly, for developing coronary heart disease. While traditional risk factors such as hypercholesterolemia, type 2 diabetes, hypertension, and smoking account for a large proportion of the risk for coronary heart disease, some individuals who develop coronary heart disease lack known risk factors, suggesting that unknown factors may also contribute to atherosclerotic complications. [007] As described in detail herein, carriers of clonal hematopoiesis of indeterminate potential (CHIP) had a 1.9-fold (95% confidence interval 1.4-2.7) increased risk of coronary heart disease compared to non-carriers in two prospective case-control cohorts. In two case- control cohorts for early-onset myocardial infarction, those with CHIP had a 4.0-fold greater risk (95% confidence interval 2.4-6.7) of having myocardial infarction. Those without clinical coronary heart disease but with clonal hematopoiesis also had increased coronary artery calcification, a marker of atherosclerotic burden and risk. Mutations in DNMT3A, TET2, ASXL1, and JAK2 individually associated with coronary heart disease in at least one set of cohorts. Hyperlipidemic mice engrafted with Tet2-I- or Tet2+I- bone marrow developed larger atherosclerotic lesions in the aortic root and aorta than mice receiving control marrow. Accordingly, clonal hematopoiesis associates with coronary heart disease in humans and causes accelerated atherosclerosis in a mouse model. [008] It was found that TET2 mutations, as well as those in DNMT3A, ASXL1, and JAK2, individually associate with risk of coronary heart disease in at least one set of human cohorts. [009] In some embodiments, a method of treating atherosclerosis in a human subject comprises administering an effective amount of at least one IL-8 inhibitor, IL-6 inhibitor, and/or IL- Ι β inhibitor, wherein the subject has a TET2 and/or DNMT3A mutation, thereby treating atherosclerosis. [0010] In some embodiments, a method for treating atherosclerosis in a human subject comprises (a) sequencing at least a part of a genome comprising TET2 and/or DNMT3A of one or more cells in a blood sample of the subject; (b) determining from the sequencing whether the subject has one or more mutations in TET2 and/or DNMT3A, and (c) if it is determined that the subject has at least one TET2 and/or DNMT3A mutation, administering at least one IL-8 inhibitor to the subject thereby treating atherosclerosis. [001 1] In some embodiments, a method of treating atherosclerosis in a human subject comprises administering an effective amount of at least one IL-8 inhibitor, IL-6 inhibitor, and/or IL- Ι β inhibitor, wherein the subject's plasma IL-8 level is at least 20 ng/mL thereby treating atherosclerosis. [0012] In some embodiments, a method for treating atherosclerosis in a human subject comprises (a) determining from a plasma sample whether the subject has an increased level of plasma IL-8 and (b) if it is determined that the subject has an IL-8 level of at least 20 ng/mL, administering an effective amount of at least one IL-8 inhibitor to a subject to the subject thereby treating atherosclerosis. [0013] In some embodiments, the method further comprises administering an effective amount of at least one cholesterol-lowering medication to the subject.
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