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WO 2017/190020 Al 02 November 2017 (02.11.2017) W !P O PCT

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WO 2017/190020 Al 02 November 2017 (02.11.2017) W !P O PCT (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 2017/190020 Al 02 November 2017 (02.11.2017) W !P O PCT (51) International Patent Classification: SCHORK, Nicholas Joseph [US/US]; 567 South Sierra C12Q 1/68 (2006.01) G01N 33/53 (2006.01) #87, Solana Beach, California 92075 (US). (21) International Application Number: (72) Inventors: CAYER, Devon Michael; 1019 Loring Street, PCT/US20 17/030 146 Unit A, San Diego, California 92 109 (US). GHADIRI, Mo¬ hammad Reza; 5133 Seagrove Court, San Diego, Califor (22) International Filing Date: nia 92130 (US). 28 April 2017 (28.04.2017) (74) Agent: MCNAMARA, Laurie et al; WILSON SONSINI (25) Filing Language: English GOODRICH & ROSATI, 650 Page Mill Road, Palo Alto, (26) Publication Language: English California 94304 (US). (30) Priority Data: (81) Designated States (unless otherwise indicated, for every 62/329,138 28 April 2016 (28.04.2016) US kind of national protection available): AE, AG, AL, AM, 62/329,143 28 April 2016 (28.04.2016) US AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, (71) Applicant: THE SCRIPPS RESEARCH INSTITUTE DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, [US/US]; 10550 North Torrey Pines Road, La Jolla, Cali HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, KP, KR, fornia 92037 (US). KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, (72) Inventors; and MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (71) Applicants: NAZOR, Kristopher Lancaster [US/US]; PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 10607 Porto Court, San Diego, California 92124 (US). (54) Title: OLIGONUCLEOTIDE CONJUGATES AND USES THEREOF universal s universal s 2 (reverse GS primer] (forward NGS primer} FIG. 12A © o o (57) Abstract: Oligonucleotide conjugates and uses thereof are provided. Aspects of the subject oligonucleotide conjugates include a targeting component, a linker component, a cleavage component, and an oligonucleotide component. The oligonucleotide comprises an identifier sequence or a first and second identifier sequence, allowing for detection and quantification of a target using methods such as next generation sequence and quantitative PCR. Methods of making and using the oligonucleotide conjugates in the diagnosis, © prevention and/or treatment of cancer and other diseases are also provided. o [Continued on nextpage] WO 2017/190020 Al llll II II 11III I II I II I II II 11II III II I II SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, 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)) OLIGONUCLEOTIDE CONJUGATES AND USES THEREOF CROSS-REFERENCE [0001] This application claims the benefit of U.S. Provisional Application No. 62/329,138, filed April 28, 2016, and U.S. Provisional Application No. 62/329,143, filed April 28, 2016, both of which are incorporated herein by reference. REFERENCE TO A SEQUENCE LISTING [0002] The instant application contains a Sequence Listing which has been filed electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on April 27, 2017, is named 52184-702_601_SL.txt and is 68,942 bytes in size. STATEMENT AS TO FEDERALLY SPONSORED RESEARCH [0003] This invention was made with the support of the United States government under Contract number GM067170 by the National Institute of General Medical Sciences. BACKGROUND [0004] Malignant tumors (cancers) are the second leading cause of death in the United States, after heart disease (Boring et al., CA Cancel J. Clin. 43:7 (1993)). Cancer is characterized by the increase in the number of abnormal, or neoplastic, cells derived from a normal tissue that proliferate to form a tumor mass, the invasion of adjacent tissues by these neoplastic tumor cells, and the generation of malignant cells which eventually spread via the blood or lymphatic system to regional lymph nodes and to distant sites via a process called metastasis. In a cancerous state, a cell proliferates under conditions in which normal cells would not grow. Cancer manifests itself in a wide variety of forms, characterized by different degrees of invasiveness and aggressiveness. [0005] In attempts to discover effective cellular targets for cancer therapy, researchers have sought to identify transmembrane or otherwise membrane-associated polypeptides that are specifically expressed on the surface of one or more particular types of cancer cells as compared to normal, non-cancerous cells. Often, such membrane-associated polypeptides are more abundantly expressed on the surface of the cancer cells as compared to non-cancerous cells, and thus provide a mechanism for identifying and distinguishing cancer cells from non-cancerous cells. The identification of such tumor-associated cell surface antigen polypeptides has given rise to the ability to specifically target cancer cells for destruction. [0006] Every cancer is unique, with a subset of mutations that give rise to a tumorigenic phenotype. As such, the cell surfaces of cancerous cells are highly variable, making treatment of cancer highly dependent on the ability of targeted therapeutic agents to bind tumorigenic tissue. The ability to probe cancerous cells with all currently available targeted therapies (antibody- drug-conjugates, CAR T-cells, or bispecific antibodies) and to quickly determine which treatment comprising these targeted therapies is able to bind cancerous cells would be highly desirable. In addition, the ability to quickly and cost-effectively track and adjust therapy depending on how cancerous cells mutate and gain resistance to particular therapies would allow for maximal treatment efficacy with minimal side effects. In addition, the ability to determine whether circulating cancerous cells are present in a patient prior to manifestation of cancer with metastatic potential would enable early-treatment of cancer that is isolated in select tissues. The present disclosure addresses these and other needs. SUMMARY [0007] Oligonucleotide conjugates and uses thereof are provided. An aspect of the subject oligonucleotide conjugates includes a targeting component, a linker component, a cleavage component, and an oligonucleotide component. Methods of making and using the subject oligonucleotide conjugates in the diagnosis, prevention and/or treatment of cancer and other diseases are also provided. [0008] An aspect of the disclosure includes an oligonucleotide conjugate, comprising: a) a targeting component, b) a linker component, c) a cleavage component, and d) an oligonucleotide component. In one aspect, the targeting component comprises a polymer. In one aspect, the polymer comprises an amino acid, a nucleic acid, or a polysaccharide. In one aspect, the nucleic acid is selected from the group consisting of: a morpholino, a peptide nucleic acid (PNA), a thioester peptide nucleic acid (tPNA), a locked nucleic acid (LNA), a phosphorothioate, a phosphonoacetate (PACE) phosphoramidite, a ribonucleic acid (RNA), and a deoxyribonucleic acid (DNA). In one aspect, the targeting component is selected from the group consisting of: an antibody, an antibody fragment, an enzyme, a small molecule, a lectin, and a carbohydrate. In one aspect, the linker component comprises a polypeptide. In one aspect, the linker component does not comprise a polypeptide. In one aspect, the linker component is selected from the group consisting of: a tetrazine ligation linker, a strain-promoted-azide-alkylene (SPAAC) linker, a maleimide linker, a succinimide linker, a tyrosine linker, a chemoenzymatic linker, a hydrazone linker, and a hydrazine linker. In one aspect, the cleavage component comprises a light- cleavable cleavage component. In one aspect, the cleavage component comprises a chemically- cleavable cleavage component. In one aspect, the cleavage component comprises an oligonucleotide. In one aspect, the oligonucleotide of the cleavable component comprises a restriction site. In one aspect, the restriction site comprises a number of nucleic acid residues ranging from about 6 to about 12. In one aspect, the length of the oligonucleotide component comprises a number of nucleic acid residues ranging from about 16 to about 120. [0009] In one aspect, the oligonucleotide component comprises a first universal sequence, a second universal sequence, and an identifier sequence, and wherein the identifier sequence identifies a binding target of the targeting component. In one aspect, the targeting component binds to a protein, a lipid, a carbohydrate, or a small molecule. In one aspect, the small molecule is a folate molecule. In one aspect, the targeting component binds to a protein. In one aspect, the protein is a lectin or a cytokine. In one aspect, the protein is an intracellular protein, an extracellular protein, or a cell surface protein. In one aspect, the protein is a cell surface protein. In one aspect, the cell surface protein is HER2, FOLR1, NCAM1 (CD56), CD274 (PD-L2), CD278 (ICOS), CD9, CD 104 or CD1 19. In one aspect, the first and the second universal sequences are different.
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