Agents for decreasing psts-SATB1 expression for treatment of metastatic cancer

Abstract

The present disclosure provides agents for inhibiting expression and / or activity of pSTS-SATB1 in a cancer cell; methods of treating or preventing metastatic cancer by using the agents; and methods of identifying a subject as having metastatic cancer or at risk of developing metastasis.

Description

Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252AGENTS FOR DECREASING pSTS-SATBl EXPRESSION FOR TREATMENT OF METASTATIC CANCERCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Provisional Patent Application No.63 / 748,255, filed January 22, 2025, which application is incorporated herein by reference in its entirety.INCORPORATION-BY-REFERENCE OF MATERIAL ELECTRONICALLY SUBMITTED

[0002] A Sequence Listing is provided herewith as a Sequence Listing XML,“UCSF-659WO_SEQLIST” created on January 20, 2026 and having a size of 39,217 bytes. The contents of the Sequence Listing XML are incorporated by reference herein in their entirety.TECHNICAL FIELD

[0003] The present disclosure relates to agents comprising polypeptides or nucleic acids that decrease expression and / or activity of pSTS-Special AT-rich Sequence Binding Protein 1 (pSTS-SATB 1) in metastatic cancer cells and methods for using the agents to treat or prevent metastatic cancer including triple-negative breast cancer (TNBC) and for detecting metastatic cancer cells.INTRODUCTION

[0004] The main cause of death of patients with cancer, such as breast cancer, is metastasis. Methods for preventing metastasis and treating metastatic cancer require identifying the key molecular mechanisms essential for promoting metastasis.

[0005] Examining about 1000 patients with breast cancer of various types, SATB 1 is found expressed in tumor cell nuclei of a subset of tumors, and its high expression indicates poor prognosis independent of the lymph node status (PcO.OOl)1,2. SATB1 is expressed specifically in highly metastatic breast cancers, and many of them are triple-negative breast cancer (TNBC). TNBC accounts for -15% of all breast cancer cases, corresponding to almost 200,000 new cases worldwide and over 35,000 in the United States3. Clinical features of TNBC include high metastatic potential, proneness to relapse, and poor prognosis. Unlike other breast cancer subtypes, there are no targeted treatments for TNBC4'6. Systemic and cytotoxic chemotherapy remains the main treatment for TNBC. Residual tumor lesions resistant to chemotherapy eventually lead to tumor recurrence and high mortality rates (75% within 3 months)3. To date, this activity of SATB 1 and its high prognostic significance have been verified in about 20 different types of epithelial cancers1,7 16.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0006] SATB 1 was previously identified by virtue of its binding specificity to specialized DNA sequences that readily adopt non-B DNA structure17,18, 19. SATBI is a nuclear protein with a unique mesh-like distribution in nuclei20. Subsequently, it was found that SATBI has genome organizing functions and regulates 3D chromatin architecture21,22. Novel genome organization mediated by SATBI has been reported recently23. SATBI reprograms gene expression by folding chromatin into loops and recruiting transcription factors, chromatin remodeling and epigenetic factors onto its target gene loci and promotes changes in cellular phenotypic21,24-29. SATB 1 protein is expressed in a subset of adult progenitor cells (e.g., ameloblasts and thymocytes), activated T cells and cortical neurons, having pivotal roles in these normal cells29-35. However, once it becomes expressed in tumor cells, it globally regulates about 1000 genes known to function in tumor progression, cell morphology, cell cycle / growth, apoptosis, chemoresistance, etc. Being a master regulator of these genes, results using human breast cancer cell lines in mouse models revealed that SATBI promotes tumor growth and metastasis of breast tumors, and knockdown of SATBI greatly reduces malignant phenotypes1-2-15-24. $ATB1 expression promotes drug resistance in breast cancer, and SATBI downregulation reverses resistance36. While these results suggest that SATB 1 could be a good therapeutic target for metastatic cancer, SATB 1 has pivotal roles in specific normal cell function (e.g., T cell activation, specific cell lineage development, neuronal connectivity)21,26’28-35’37’38.SUMMARY

[0007] Agents that bind to pSTS-SATBl protein or SATBI exon Id variant mRNA are disclosed. An agent that binds to pSTS-SATBl may be a polypeptide. An example of a polypepride agent that binds to pSTS-SATB 1 protein is an antibody that specifically binds to pSTS-SATB 1 protein. An agent that binds to SATB1 exon Id variant mRNA may be a nucleic acid.

[0008] These agents may be used for detecting pSTS-SATB 1 or SATB1 exon Id variant mRNA. These agents may be used for decreasing expression and / or activity of pSTS-SATB 1. An agent for detecting pSTS-SATB 1 may be an antibody specific for pSTS-SATB 1. An antibody specific for pSTS-SATB 1 may be an antibody as provided herein. SATBI exon Id mRNA variant is associated with expression of pSTS-SATB 1 protein. An agent that decreases the expression of pSTS-SATB 1 may be a nucleic acid that binds to the SATB1 exon Id mRNA variant, thereby reducing translation of the SATB1 exon Id mRNA variant. The nucleic acid may be an interfering RNA (e.g., siRNA), an antisense oligonucleotide (ASO) or a morpholino oligonucleotide (PMO). The nucleic acid may decrease translation of SATBI exon Id mRNA variant by binding to SATBI exon Id mRNA variant and either degrading this mRNA (e.g., siRNA and ASO) or by acting as a steric blocker of translation (e.g., a PMO). The interfering RNA or the antisense RNA may include modification. For example, the ASO may comprise a locked nucleic acid (LNA). The ASO may comprise a phosphorothioate (PS) linkage. TheAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 ASO may be an LNA-PS-ASO comprising the LNA and the PS linkage. The ASO may be a gapmer. The gapmer may comprise a central single stranded DNA sequence (which forms a gap) flanked by RNA sequences which may comprise LNA. The nucleic acid, e.g., siRNA or ASO may comprise a nucleotide sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 98% identity, or a 100% identity to the sequence of any of SEQ ID NO: 1-6. A composition for reducing expression of pSTS-S ATB 1 may comprise two or more nucleic acids having different sequences and / or a combination of a siRNA or an ASO. For example, a nucleic acid comprising a nucleotide sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 98% identity, or a 100% identity to the sequence of SEQ ID NO:36 (RED 1) and a nucleic acid comprising a nucleotide sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 98% identity, or a 100% identity to SEQ ID NO:37 (RED 2). A morpholino oligonucleotide (PMO) is a synthetic nucleic acid analog with a morpholine ring backbone and phosphorodiamidate linkages. The PMO may a nucleotide sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 98% identity, or a 100% identity to the sequence of any of SEQ ID NO: 1-6.

[0009] An agent for detecting and / or for decreasing activity of pSTS-SATBl may be a polypeptide. The polypeptide may be an anti-pSTS-SATBl antibody. For example, the anti-pSTS-S ATB 1 antibody may comprise a variable heavy ( VH) chain and a variable light (VL) chain comprising the CDRs of the VH and VL chains, respectively, of an anti -pSTS-S ATB 1 antibody, 4F, 6B, or 1 ID, disclosed herein.

[0010] Aspects of the present disclosure also include a pharmaceutical composition comprising an agent that decreases expression and / or activity of pSTS-S ATB 1 in a cancer cell and a pharmaceutically acceptable excipient.

[0011] Aspects of the present disclosure further include methods for treating or preventing metastatic cancers in a subject in need thereof comprising administering an effective amount of an agent of the present disclosure or a pharmaceutical composition of the present disclosure. In other embodiments, the method further comprises administering one or more additional therapeutic treatments, such as cancer chemotherapy, radiation therapy or surgery.

[0012] Aspects of the present disclosure further include methods of identifying a subject as having metastatic cancer or at risk of developing metastasis. In some embodiments, the method comprises determining the presence or absence of pSTS-SATBl in a cancer sample from the subject, wherein the presence of pSTS-S ATB 1 indicates that the subject has metastatic cancer or is at risk of developing metastasis. In some embodiments, determining the presence or absence of pSTS-SATB 1 in a cancer sample comprises contacting the sample with an antibody that specifically binds to pSTS-SATB 1. In other embodiments, the presence of pSTS-SASTBl in the sample identifies the subject as a candidateAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 for treatment with an agent of the present disclosure or a pharmaceutical composition of the present disclosure.BRIEF DESCRIPTION OF THE FIGURES

[0013] FIGS. 1A to ID show aggressive cancer-specific expression of pSTS-SATBl. FIG.1A shows that anti-SATBl antibody (anti-whole SATB1) detects SATB1 levels in both MDA-MB-231 (metastatic) and T47D (non-metastatic) cells but anti-pSTS-S ATB 1 antibody only detects SATB 1 in metastatic MDA-MB-231 cells. FIG. IB shows that anti-pSTS-SATBl immunostaining selectively detects pSTS-SATB 1 in aggressive cancer cells lines. FIG. 1C shows Western blot data from 5 TNBC patient derived xenografts (PDXs) (lane 1-5), 1 ER+PR+-PDX (lane 6) and MDA-MB-231 cells (lane 7) for total SATB1 (top panel) and pSTS-SATB 1 (middle panel). FIG. ID shows that pSTS-SATB 1 is not detected in normal cells.

[0014] FIGS. 2A to 2C show that SATB 1 exon 1 variants are transcribed from multiple promoters. FIG. 2A shows that SATB 1 translation starts from Exon 2. Exon Id starts 20kb upstream of ATG start and is aggressive cancer-specific. Two antisense ASO oligonucleotides (LNA-PS-gapmers, RED1 (SEQ ID NO:36) and RED2 (SEQ ID NO:37) were designed to hybridize and degrade the exon Id mRNA variant. FIG.2B shows treatment of a human oral squamous cell carcinoma ceil line with a high metastatic potential, HOC313 cells, with MO-ld (Vivo-Morpholino modified antisense oligo (SEQ ID NO:3), another exon Id ASO that greatly reduces pSTS-SATB 1 without affecting total SATB1 levels. Control MO-lc does not reduce pSTS-SATB 1 level. FIG. 2C show's that RED2 also effectively reduces pSTS-SATB 1 in MDA-MB-231 cells. Many of these cells undergo apoptosis (data not shown). While RED2 preferentially targets pSTS-SATB 1, total SATB1 was mildly reduced as well.

[0015] FIGS. 3A to 3D show that SATB1 far distal Id promoter is active specifically in aggressive cancer. FIG. 3A. RT-PCR data are shown for 1. SATB I exon la variant mRNA, 2. SATB1 exon Id variant mRNAs, and 3. SATB1 internal exon 10 in TNBC PDXs, an ER+PR+BC PDX, two TNBC cell lines (MDA-MB-231 and B549) and an immortalized epithelial MCF10A relative to SATB1 internal exon 10 transcript level in BT549 cells. Results agree with protein expression levels (FIG. 1C top). FIG.3B shows transcript levels of exon Id variant relative to Hs578T. FIGS. 3C and 3D depict that RT-PCR data for transcripts (1. SATB1 exon la variant mRNA, 2. SATB1 exon Id valiant mRNAs, and 3. SATB1 internal exon 10) are shown after exposure of MDA-MB-231 (TNBC cell line) or PC 3 (prostate cancer line) to RED1, RED2, or control ASO. Exon Id mRNA variant was selectively and greatly reduced by RED1 and RED2 in both cell lines. While a more complete elimination of exon Id mRNA could be achieved with MDA-MB-231, RED2 also reduced exon la to 40%.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0016] FIG.4 shows that SATB1 ASO (RED1 and RED2) effectively kills multiple types of aggressive epithelial cancer cells in culture. (A) Cell viability (MTT assay) of breast cancer cells (MDA-MB-231, BT549, and T47D), HNSCCs (SCC4, HOC313) and prostate cancer (PC3) cells was greatly reduced with either RED1 or RED2 at 50nM with LTX (lipid nanoparticle) in culture. RED1 greatly reduced viability of most cells at 25 nM by Day 3. Exception was non-aggressive T47D cells, which are less sensitive to both RED1 and RED2 compared to aggressive cancers. (B) Control (non-specific) ASO is non-toxic. (C) RED1 and RED2 greatly reduced viability of MIA PaCa-2 (aggressive pancreatic cancer cells). Though RED1 / RED2 are effective without delivery agent (top), increased effects seen at earlier times with LTX (bottom). (D) Cell death monitored by Celltox green cytotoxic assay in MDA-MB-231 cells. Majority of cells are apoptotic with RED1 or RED2 (plateaued by RED2 at 31-48hrs), while most survived with control (cont.) ASO.

[0017] FIG.5 shows RED1 effects tested on tumor growth of breast cancer MDA-MB-31 cells in nude mice. RED1 mixed with in vzvo-jetPEI® (in vivo delivery) was injected distal to tumor sites (mammary fat pads). ASO administration was initiated once tumor reached a 100mm3volume. After day 21, ASO injected into the peri-tumor area (n=6). RED1 20pg / injection: Img / kg / week; RED2 and Control ASO, 40pg / injeclion: 2mg / kg / week.

[0018] FIG.6 shows that RED1 inhibits experimental lung metastasis of MDA-MB-231 cells. Cells (IxlO6cells) were injected through tail vein. After 3 days, the RED1 or control-ASO treatment (lOOug / injection) was performed intravenously through tail vein twice per week. Lungs were isolated from mice after 49 days. The levels of human house-keeping gene (B2M) derived from MDA-MB-231 cells were determined by normalization with mouse B2M gene. The human B2M gene levels for lungs of individual RED 1 -treated mice compared against average levels of human B2M gene of control-ASO-treated mice is shown. Two-tailed t-test comparing human B2M levels of RED 1 -treated and untreated mice showed P=0.005 (n=6, each).

[0019] FIG.7 shows that pSTS-SATB 1 is highly expressed in mitotic cells. Two mitotic cells showing pSTS-SATB 1 painting metaphase chromosomes of tumor cells.

[0020] FIG.8 shows that patients’ survival information stratified by the level of total SATB1 mRNA. Initial analysis of the patient survival data from the 34 TNBC PDX’s shows some concordance between high expression of SATB 1 (total SATB 1 transcript) and decreased survival. It is known that normal breast tissue does uniformly express varying levels of total SATB1 transcripts (based on The Genotype-Tissue Expression project, GTEx), even though it does not express SATB1 protein1.Therefore, total SATB1 transcripts are not necessarily informative for predicting patients’ survival.

[0021] FIG.9. Intravenous injection of ASOs mixed with in vzvo-jetPEI® inhibited the growth of xenografted tumor cells in the mammary fat pads of mice.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0022] FIGS. 10A-10B. RED1 and RED2 promote cell death in TNBC patient-derived xenografts (TNBC-PDXs), HCI-041 and HCI-010, in organoid culture. FIG. 10A. TNBC-PDX: HCI-041 in organoid culture. FIG. 10B. TNBC-PDX: HCI-010 in organoid culture.

[0023] FIG. 11. RNA-seq analysis to assess off-targets of RED1 and RED2. Panel A.Summary of sample preparation. Panel B. Summary of differential gene expression.DETAILED DESCRIPTION

[0024] The inventors have discovered a phosphorylated version of SATB1 (pSTS-SATBl, phosphorylated S465, T466, S469 (pSTS)) that is specifically expressed in aggressive, metastasis-prone cancers. In contrast, SATB1 is not tumor specific. This tumor-specific SATB1 can be targeted for treatment of metastatic cancer, such as metastatic breast cancer, while sparing normal cells. pSTS-SATB1 is required for invasive phenotype of cancer cells. Mutating all three adjacent serine / threonine (S465, T466, S469; STS) to alanine completely abolishes its ability to induce the invasive phenotypes. pSTS-SATBlactivity can be targeted to induce cell death in aggressive, metastasis-prone cancers. The presence of pSTS-SATB 1 is associated with expression of SATBJ exon Id mRNA variant. Expression of SATB1 exon Id mRNA variant can be targeted to reduce its amount in cancer cells and / or prevent its translation in cancer cells.

[0025] Aspects of the present disclosure include agents and compositions for decreasing expression and / or activity of pSTS-SATBl in a cancer cell. Agents can include a polypeptide that reduces activity of pSTS-SATB 1 in a cancer cell or a nucleic acid that decreases expression of pSTS-SATB1 in a cancer cell.

[0026] Pharmaceutical compositions can comprise an agent comprising a polypeptide or a nucleic acid that reduces expression and / or activity of pSTS-SATB 1 in a cancer cell as disclosed herein and a pharmaceutically acceptable excipient.

[0027] Aspects of the present disclosure further include methods for treating or preventing metastatic cancers in a subject in need thereof comprising administering an effective amount of an agent or a pharmaceutical composition disclosed herein. Aspects of the present disclosure further include methods of identifying a subject as having metastatic cancer or at risk of developing metastasis.

[0028] Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0029] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

[0030] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and / or materials in connection with which the publications arc cited.

[0031] It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an antisense oligonucleotide” includes a plurality of such oligonucleotides and reference to “the nucleic acid modification” includes reference to one or more nucleic acid modifications and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.

[0032] As will be apparent to those of skill in the art upon reading this disclosure, each of the individual aspects described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several aspects without departing from the scope or spirit of the present methods. Any recited method can be carried out in the order of events recited or in any other order that is logically possible.1. Definitions

[0033] As used herein, the term “antibody” refers to an immunoglobulin molecule that recognizes and binds a target through at least one antigen-binding site. The term “antibody” is used in the broadest sense and encompasses various antibody structures, including but not limited to, polyclonal antibodies, recombinant antibodies, monoclonal antibodies, chimeric antibodies (e.g., chimera of antibody sequences from two or more different species, such as, human, bovine, ovine, caprine, camelid, etc.), humanized antibodies, human antibodies, bovinized antibodies, ovinized antibodies, caprinizedAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 antibodies, camelidized antibodies, bispecific antibodies, multispecific antibodies, diabodies, tribodies, tetrabodies, single chain Fv (scFv) antibodies, single domain antibodies, and antibody fragments.

[0034] The term “monoclonal antibody” as used herein refers to a substantially homogenous antibody population involved in the highly specific recognition and binding of a single antigenic determinant or epitope. The individual antibodies comprising the population are identical, except for possible naturally occurring mutations that may be present in minor amounts. The term “monoclonal antibody” encompasses intact and full-length monoclonal antibodies as well as antibody fragments (e.g., Fab, Fab', F(ab')2, Fv), single chain (scFv) antibodies, fusion proteins comprising an antibody fragment, and any other modified immunoglobulin molecule comprising an antigen-binding site. Furthermore, “monoclonal antibody” refers to such antibodies made by any number of techniques, including but not limited to, hybridoma production, phage library display, recombinant expression, and transgenic animals.

[0035] As used herein, an “antisense oligonucleotide” or “ASO” refers to a short nucleic acid sequence that is complementary to a RNA sequence, such as that of a mRNA. An ASO may be an RNA, DNA, or a combination of RNA and DNA. An ASO may be a gapmer.

[0036] As used herein "an interfering RNA" refers to any double stranded or single stranded RNA sequence, capable, either directly or indirectly (i.e., upon conversion), of inhibiting or down regulating gene expression by mediating RNA interference. Interfering RNA includes, but is not limited to, interfering RNA ("siRNA") and small hairpin RNA ("shRNA"). "RNA interference" refers to the selective degradation of a sequence -compatible messenger RNA transcript.

[0037] As used herein "an shRNA" (small hairpin RNA) refers to an RNA molecule comprising an antisense region, a loop portion and a sense region, wherein the sense, region has complementary nucleotides that base pair with the antisense region to form a duplex stem. Following post-transcriptional processing, the small hairpin RNA is converted into a small interfering RNA by a cleavage event mediated by the enzyme Dicer, which is a member of the RNase III family.

[0038] A "small interfering RNA" or "siRNA" as used herein refers to any small RNA molecule capable of inhibiting or down regulating gene expression by mediating RNA interference in a sequence specific manner. The small RNA can be for example, about 18 to 21 nucleotides long.

[0039] As used herein, a "microRNA" (miRNA) is a single-stranded RNA molecule of about 21-23 nts in length. In general, ntiRNAs regulate gene expression. miRNAs are encoded by genes from whose DNA they are transcribed, but miRNAs are not translated into protein. Each primary miRNA transcript is processed into a short stem-loop structure before undergoing further processing into a functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to down-regulate gene expression.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0040] As used herein, the term "cancer" or "tumor" are used interchangeably and refer to a cell or population of cells whose growth, proliferation or survival is greater than growth, proliferation or survival of a normal counterpart cell, e.g., a cell proliferative, hyperproliferative or differentiative disorder. Typically, the growth is uncontrolled. The term "malignancy" refers to invasion of nearby tissue. Cancers include benign, malignant, metastatic, and non-metastatic types, and include any stage (I, II, III, IV or V) or grade (Gl, G2, G3, etc.). In particular, the term "cancer" includes carcinomas, such as squamous cell carcinoma, adenocarcinoma, adenosquamous carcinoma, anaplastic carcinoma, large cell carcinoma, and small cell carcinoma.

[0041] As used herein, the term “metastatic cancer” or a secondary, recurring, or recurrent tumor or cancer are used interchangeably and refers to cancer that spreads from where it started to a distant part of the body. For many types of cancer, it is also called stage IV (4) cancer. When observed under a microscope and tested in other ways, metastatic cancer cells can have features like that of the primary cancer and not like the cells in the place where the metastatic cancer is found. Metastatic cancer is referred by the same name as the primary cancer. For example, breast cancer that spreads to the lung is called metastatic breast cancer, not lung cancer.

[0042] As used herein, the term “metastasis” refers to the spread of cancer cells from the place where they first formed to another part of the body. In metastasis, cancer cells break away from the original (primary) tumor, travel through the blood or lymph system, and form a new tumor in other organs or tissues of the body.

[0043] As used herein, the term “breast cancer” refers to a disease in which cells in the breast grow out of control. Breast cancer can begin in different parts of the breast. A breast is made up of three main parts: lobules, ducts, and connective tissue. Most breast cancers begin in the ducts or lobules. Breast cancer can spread outside the breast through blood vessels and lymph vessels. When breast cancer spreads to other parts of the body, it is said to have metastasized. The term “metastatic breast cancer” refers to stage 4 breast cancer and advanced breast cancer. The most common kinds of breast cancer are invasive ductal carcinoma and invasive lobular carcinoma. Invasive carcinoma refers to cancer cells beginning in the ducts and then growing outside the ducts into other parts of the breast tissue. Invasive lobular carcinoma refers to cancer cells beginning in the lobules and then spreading from the lobules to the breast tissues that are close by. Invasive cancer cells can also spread, or metastasize, to other parts of the body.

[0044] As used herein, the term “triple-negative breast cancer (TNBC)” refers to a subtype of breast cancer that does not have any of the receptors that are commonly found in breast cancer. TNBC represents around 15% of all breast cancer patients and the mortality rate is 40% within the first 5 years after diagnosis. A diagnosis of TNBC means that the three most common types of receptors known toAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 fuel most breast cancer growth-estrogen, progesterone, and the HER-2 / neu gene- are not present in the cancer tumor. This means that the breast cancer cells have tested negative for hormone epidermal growth factor receptor 2 (IIER-2), estrogen receptors (ER), and progesterone receptors (PR).

[0045] As used herein, the phrase “post-translational modification (PTM)” refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. PTMs are important components in cell signaling, as for example when prohormones are converted to hormones. Post-translational modifications can occur on the amino acid side chains or at the protein's C- or N- termini. They can extend the chemical repertoire of the 22 proteinogenic amino acids by modifying an existing functional group or introducing a new one, such as, phosphate.

[0046] By "an effective amount" is meant the amount of a required agent (e.g., an agent of the present disclosure) or a pharmaceutical composition of the present disclosure, comprising the agent to ameliorate the symptoms of a disease relative, to an untreated patient. The effective amount of an agent or a composition used to practice a therapeutic treatment of a disease or disorder varies depending upon the manner of administration, the age, body weight, and general health of the subject. Ultimately, the attending, physician or veterinarian will decide the appropriate amount and dosage regimen. Such amount is referred to as an "effective amount."

[0047] As used herein, the term "therapeutically effective dose or amount" of a pharmaceutical compound identified by screening, as described in this disclosure, is intended an amount that, when administered as described herein, brings about a positive therapeutic response in treatment of mitochondrial diseases. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the condition being treated, the particular drug or drugs employed, mode of administration, and the like. An appropriate "effective" amount in any individual case may be determined by one of ordinary skill in the art using routine experimentation, based upon the information provided herein. For example, a therapeutically effective amount can be determined based on an observed effectiveness of the composition. A therapeutically effective amount can be determined using assays that measure the level of pSTS-SATBl and the desired effect.

[0048] As used herein, the term "pharmaceutically acceptable excipient or carrier" refers to an excipient that may optionally be included in the compositions of the invention and that causes no significant adverse toxicological effects to the patient.

[0049] As used herein, the term "pharmaceutically acceptable salt" includes, but is not limited to, amino acid salts, salts prepared with inorganic acids, such as chloride, sulfate, phosphate, diphosphate,Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 bromide, and nitrate salts, or salts prepared from the corresponding inorganic acid form of any of the preceding, e.g., hydrochloride, etc., or salts prepared with an organic acid, such as malate, maleate, fumarate, tartrate, succinate, ethylsuccinate, citrate, acetate, lactate, methanesulfonate, benzoate, ascorbate, para-toluenesulfonate, palmoate, salicylate and stearate, as well as estolate, gluceptate and lactobionate salts. Similarly, salts containing pharmaceutically acceptable cations include, but are not limited to, sodium, potassium, calcium, aluminum, lithium, and ammonium (including substituted ammonium).

[0050] As used herein, the terms “treatment,” “treating,” and the like, refer to obtaining a desired pharmacologic and / or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and / or may be therapeutic in terms of a partial or complete cure for a disease and / or adverse effect attributable to the disease. “Treatment,” as used herein, covers any treatment of a disease in a mammal, e.g., in a human, and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease.

[0051] The terms “prevent”, “preventing”, “prevention” and the like refer to a course of action (such as administering a polypeptide or a nucleic acid encoding the polypeptide or a cell comprising the nucleic acid encoding the polypeptide or expressing the polypeptide) initiated in a manner (e.g., prior to the onset of a disease, disorder, condition or symptom thereof) so as to prevent, suppress, inhibit or reduce, either temporarily or permanently, a subject’s risk of developing a disease, disorder, condition or the like (as determined by, for example, the absence of clinical symptoms) or delaying the onset thereof, generally in the context of a subject predisposed to having a particular disease, disorder or condition. In certain instances, the terms also refer to slowing the progression of the disease, disorder or condition or inhibiting progression thereof to a harmful or otherwise undesired state.

[0052] As used herein, the term "administering" a nucleic acid, such as an inhibitory or regulatory nucleic acid (e.g., microRNA, siRNA, or antisense nucleic acid) to a cell comprises transducing, transfecting, electroporating, translocating, fusing, phagocytosing, shooting or ballistic methods, etc., i.e., any means by which a nucleic acid can be transported across a cell membrane.

[0053] As used herein, the term "liposome" means a vesicle composed of amphiphilic lipids arranged in a bilayer or bilayers. Liposomes are unilamellar or multilamellar vesicles that have a membrane formed from a lipophilic material and an aqueous interior that contains the composition to be delivered. Cationic liposomes are positively charged liposomes that are believed to interact with negatively charged DNA molecules to form a stable complex. Liposomes that are pH-sensitive or negatively charged are believed to entrap DNA rather than complex with it. Both cationic and noncationic liposomes have been used to deliver DNA to cells.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0054] As used herein, the term “combination” or “combining” refers to including therapies that can be administered separately, for example, formulated separately for separate administration (e.g., as may be provided in a kit), and therapies that can be administered together in a single formulation (i.e., a "co-formulation").

[0055] The terms “individual,” “subject,” “host,” and “patient,” used interchangeably herein, refer to an individual organism, e.g., a mammal, including, but not limited to, murines, simians, humans, non-human primates, ungulates, felines, canines, bovines, ovines, mammalian farm animals, mammalian sport animals, and mammalian pets. In some cases, an “individual” is a human.

[0056] The use of the terms “a,” “an,” and “the,” and similar referents in the context of describing the disclosure (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context.

[0057] The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to,”) unless otherwise noted.

[0058] Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if the range 10-15 is disclosed, then 11, 12, 13, and 14 arc also disclosed.

[0059] All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context.

[0060] The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the embodiments of the disclosure and does not pose a limitation on the scope of the disclosure unless otherwise claimed.

[0061] No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the embodiments of the disclosure.

[0062] As used herein, the term “about” used in connection with an amount indicates that the amount can vary by 10% of the stated amount. For example, “about 100” means an amount of from 90-110. Where about is used in the context of a range, the “about” used in reference to the lower amount of the range means that the lower amount includes an amount that is 10% lower than the lower amount of the range, and “about” used in reference to the higher amount of the range means that the higher amount includes an amount 10% higher than the higher amount of the range. For example, from about 100 to about 1000 means that the range extends from 90 to 1100.

[0063] The term “and / or” as used herein a phrase such as “A and / or B” is intended to include both A and B; A or B; A (alone); and B (alone). Likewise, the term “and / or” as used herein a phrase suchAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 as “A, B, and / or C” is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

[0064] It is understood that aspects and embodiments of the present disclosure described herein include “comprising,” “consisting,” and “consisting essentially of’ aspects and embodiments.

[0065] It is appreciated that certain features of the present disclosure, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of this disclosure, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments pertaining to this disclosure are specifically embraced by the present disclosure and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub-combinations of the various embodiments and elements thereof are also specifically embraced by the present disclosure and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.

[0066] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.2. Agents for Decreasing Expression and / or Activity of pSTS-SATBl

[0067] The present disclosure provides agents for inhibiting expression and / or activity of pSTS-SATBl in a cancer cell. pSTS-SATBl is SATB1 that is phosphorylated at S465, T466, and 8459. The numbering of the amino acid residues is based on the human SATB 1 amino acid sequence set forth in UniProt Q01826-1 and reproduced below.

[0068] MDHLNEATQGKEHSEMSNNVSDPKGPPAKIARLEQNGSPLGRGRLGSTGAKM QGVPLKHSGHLMKTNLRKGTMLPVFCVVEHYENAIEYDCKEEHAEFVLVRKDMLFNQLIEMAL LSLGYSHSSAAQAKGLIQVGKWNPVPLSYVTDAPDATVADMLQDVYHVVTLKIQLHSCPKLED LPPEQWSHTTVRNALKDLLKDMNQSSLAKECPLSQSMISSIVNSTYYANVSAAKCQEFGRWYK HFKKTKDMMVEMDSLSELSQQGANHVNFGQQPVPGNTAEQPPSPAQLSHGSQPSVRTPLPNLH PGLVSTPISPQLVNQQLVMAQLLNQQYAVNRLLAQQSLNQQYLNHPPPVSRSMNKPLEQQVST NTEVSSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQN FLQLPEAERDRIYQDERERSLNAASAMGPAPLISTPPSRPPQVKTATIATERNGKPENNTMNINAS IYDEIQQEMKRAKVSQALFAKVAATKSQGWLCELLRWKEDPSPENRTLWENLSMIRRFLSLPQP ERDAIYEQESNAVHHHGDRPPHIIHVPAEQIQQQQQQQQQQQQQQQAPPPPQPQQQPQTGPRLPAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 PRQPTVASPAESDEENRQKTRPRTKISVEALGILQSFIQDVGLYPDEEAIQTLSAQLDLPKYTIIKFF QNQRYYLKHHGKLKDNSGLEVDVAEYKEEELLKDLEESVQDKNTNTLFSVKLEEELSVEGNTD INTDLKD (SEQ ID NO: 7).

[0069] As described in the Examples section, pSTS-SATBl is expressed in aggressive cancer cells and in metastasis-prone cancer and is not detectable in normal cells. In contrast, SATB1 is also expressed by normal cells. All three adjacent serine / threonine (S465, T466, S469; STS) sites in SATB1 have a critical function for promoting aggressive cancer characteristics and mutating all three adjacent serine / threonine (S465, T466, S469; STS) to alanine completely abolishes its ability to induce the invasive phenotypes.

[0070] pSTS-SATB 1 is uniquely expressed in metastatic cancers and is not expressed in non-aggressive cancers and in normal cells. SATB1 is expressed in cancer cells and in normal cells, such as thymocytes, T cells, and cortical neurons. pSTS-SATB 1 correlates with cancer severity. For example, the presence of pSTS-SATB 1 in a cancer cell indicates that the cell is an aggressive cancer cell or a metastatic cancer cell. The absence of pSTS-SATB 1 in a cell indicates that the cell is a non-aggressive cancer cell, a non-metastatic cancer cell or a normal cell.

[0071] Metastatic cancer includes, but is not limited to, metastatic breast cancer (e.g., metastatic triple-negative breast cancer (TNBC)), metastatic brain cancer, metastatic liver cancer, metastatic colorectal cancer, metastatic bone cancer, metastatic ovarian cancer, metastatic pancreatic cancer, metastatic prostate cancer or metastatic lung cancer.

[0072] SATB 1 protein is translated from exon 2 of SATB 1 gene. SATB 1 is a nuclear protein with a unique mesh-like distribution in nuclei20. SATB1 has genome organizing functions and regulates 3D chromatin architecture21-22. SATB1 reprograms gene expression by folding chromatin into loops and recruiting transcription factors, chromatin remodeling and epigenetic factors onto its target gene loci and promotes changes in cellular phenotypic21 2429. SATB 1 protein is expressed in a subset of adult progenitor cells (e.g., ameloblasts and thymocytes), activated T cells and cortical neurons, having pivotal roles in these normal cells29’35. SATB 1 has been shown to induce breast cancer tumor growth and metastasis through the altered expression of large numbers of genes.

[0073] SATB1 gene encodes multiple untranslated exon 1 variants transcribed from different promoters. See FIG. 2A. The generation of pSTS-SATB 1 protein specifically depends on a far distal promoter (Id) of the SATB1 gene that transcribes the SATB1 exon Id variant niRNA. Expression of pSTS-SATB 1 protein is correlated with the expression of SATB1 exon Id variant mRNA. In other words, phosphorylation of SATB 1 protein at S465, T466, and S469 (STS) resulting in the protein pSTS-SATB 1 is correlated with the presence of SATB1 exon Id variant mRNA. SATB1 exon Id mRNA variant is specific to cancer cells highly capable of metastasis.Atty. Dkt: UCSF-659WO Client Ref: SF-2021-252

[0074] As demonstrated in the Examples section, inhibiting translation of SATB1 exon Id variant mRNA and / or degradation of SATBI exon Id variant mRNA results in decrease in amount of pSTS-S ATB 1 which results in death of cancer cells.Inhibitory Nucleic Acid

[0075] An agent of the present disclosure may decrease the amount of SATBI exon Id variant mRNA or block translation of SATB1 exon Id variant mRNA, resulting in reduced expression of pSTS-SATB1. Such an agent may be a nucleic acid, e.g., an oligonucleotide. An agent of the present disclosure may decrease activity of pSTS-S ATB 1 protein. Such an agent may be a polypeptide (e.g., an antibody) that binds specifically to pSTS-SATB 1 and does not show significant binding to SATB 1. Reduced expression and / or activity of pSTS-SATB 1 results in death of cancer cells, such as, metastatic cancer cells.

[0076] As shown in FIG. 2A, SATBI exon Id variant mRNA includes Exon Id which is absent from SATBI Exonla, lb, and 1c mRNA variants. Thus, a nucleic acid, such as, a siRNA, ASO, or miRNA that binds to a sequence in exon Id region of SATBI exon Id variant mRNA will specifically reduce the amount of SATB J exon Id variant mRNA without affecting the amount of the other SATBI mRNA. Similarly, a nucleic acid, e.g., a morpholino that binds to a sequence in exon Id region of SATBI exon Id variant mRNA will specifically reduce translation of SATBI exon Id variant mRNA. A nucleic acid of the present disclosure may bind to a sequence in exon Id region of SATBI exon Id variant mRNA, wherein the sequence of the SATBI exon Id is:

[0077] UCCUUCCCUUGGCCCCGCGCGCUCGCUCGCUCGCUCCUCGCCUCGCUCUC CCCUUUAAACGCCCACUUCGUAUGGGGAAAGAGGACAACUUGAAGUCAAGUUGCAAUUA ACUUCCGCGGCAGCCGCAGCUCCGGCGGCGGCGGCGGCGGCAGGAGAGGCAGAAGCCGCC GCCUCGGAAGUCCGACGCCGGCGCGCCCGCCCGGGGAGCCGUUCUUGGUUUCAGGCCCGC ACUCGACAGCCACCGCCGCCCCCAACGUCCAUGCCUGA (SEQ ID NO: 11).

[0078] Any region of exon Id variant mRNA may be targeted by the nucleic acid. The Examples section demonstrate that a morpholino that binds to the sequence CGGGGAGCCGUUCUUGGUUUCAGGC (SEQ ID NO:8) in exon Id, results in reduced levels of pSTS-SATB 1. The Examples section also demonstrate that the ASO, RED1, that binds to the sequence CCGUUCUUGGUUUCAG (SEQ ID NO:9) in exon Id, results in reduced levels of SATBI exon Id variant mRNA and pSTS-SATB 1. The Examples section also demonstrate that the ASO, RED2, that binds to the sequence GGAGCCGUUCUUGGUU (SEQ ID NO: 10) in exon Id, results in reduced levels of SATBI exon Id variant mRNA and pSTS-SATB 1.

[0079] An agent for decreasing the amount of SATBI exon Id variant mRNA or blocking translation of SATBI exon Id variant mRNA, resulting in reduced expression of pSTS-SATB 1, may be aAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 nucleic acid, e.g., a siRNA, miRNA, shRNA, morpholino, or ASO. The nucleic acid may bind to a region in exon Id of SATB1 exon Id variant mRNA. The nucleic acid may include a nucleotide sequence that binds to the sequence: CGGGGAGCCGUUCUUGGUUUCAGGC (SEQ ID NO: 8), CCGUUCUUGGUUUCAG (SEQ ID NO:9), or GGAGCCGUUCUUGGUU (SEQ ID NO: 10). The nucleic acid that binds specifically to SATB1 exon Id variant mRNA may comprise nucleotide sequence having at least 85%, at least 90%, at least 95%, at least 99%, or 100% identity to a nucleotide sequence selected from CTGAAACCAAGAACGG (SEQ ID NO:1), AACCAAGAACGGCTCC (SEQ ID NO:2), GCCTGAAACCAAGAACGGCTCCCCG (SEQ ID NO:3), ACCAAGAACGG (SEQ ID NO:4), GCCTGAAACCAAGAACGG (SEQ ID NO:5), or ACCAAGAACGGCTCC (SEQ ID NO:6). The nucleic acid may have a length of 8 to 30 nucleotides, e.g., 8 to 25 nucleotides, 8 to 20 nucleotides, 10 to 25 nucleotides, 11 to 25 nucleotides, 12 to 25 nucleotides, 14 to 25 nucleotides, 16 to 25 nucleotides, or 11 to 20 nucleotides. The nucleic acid may have a length of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides, or any range therewith.

[0080] A nucleic acid that inhibits expression of pSTS-SATBl in a cancer cell may be antisense oligonucleotides (ASO), ribozymes, external guide sequence (EGS) oligonucleotides, single- or double-stranded RNA interference (RNAi) compounds such as siRNA compounds, modified bases / locked nucleic acids (LNAs), antagomirs, peptide nucleic acids (PNAs), and other oligomeric compounds or oligonucleotide mimetics which hybridize to at least a portion of the target nucleic acid (i.e., exon Id region of SATB1 exon Id mRNA variant) and blocks its translation and / or induces its degradation. The nucleic acids include antisense RNA, antisense DNA, chimeric antisense oligonucleotides, antisense oligonucleotides comprising modified linkages, interference RNA (RNAi), short interfering RNA (siRNA); a micro, interfering RNA (miRNA); a small, temporal RNA (stRNA); or a short, hairpin RNA (shRNA); small RNA-induced gene activation (RNAa); small activating RNAs (saRNAs), or combinations thereof.

[0081] In some aspects, the nucleic acid of the present disclosure is an ASO that reduces expression of pSTS-SATB 1 in a cancer cell. In some embodiments, the ASO of the present disclosure binds to exon Id region of SATB1 exon Id variant mRNA and inhibits expression of pSTS-SATB 1 in a cancer cell. The SATB1 exon Id variant mRNA is associated with the pSTS-SATB 1 production.

[0082] In some embodiments, an ASO that decreases expression of pSTS-SATB 1 in a cancer cell is an oligonucleotide that has a length of 8 to 30 nucleotides, e.g., 8 to 25 nucleotides, 8 to 20 nucleotides, 10 to 25 nucleotides, 12 to 25 nucleotides, 14 to 25 nucleotides, 16 to 25 nucleotides, or 14 to 20 nucleotides. In yet other embodiments, the ASO has a length of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides, or any range therewith. In certain embodiments, the ASO has a length of about 16 nucleotides.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0083] In some embodiments, nucleic acids that inhibit expression of pSTS-SATBl in a cancer cell arc chimeric oligonucleotides that contain two or more chemically distinct regions, each made up of at least one nucleotide. These oligonucleotides typically contain at least one region of modified nucleotides that confers one or more beneficial properties (such as, for example, increased nuclease resistance, increased uptake into cells, increased binding affinity for the target) and a region that is a substrate for enzymes capable of cleaving RNA:DNA hybrids. Chimeric inhibitory nucleic acids of the present disclosure may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonucleosides and / or oligonucleotide mimetics. Examples of chimeric oligonucleotides include gapmers.

[0084] The term “gapmer” refers to short antisense oligonucleotide comprising a single stranded DNA sequence and two RNA-like segments on both sides of the DNA sequence. This oligonucleotide is designed to hybridize to a target RNA and silence the gene encoding the target RNA through the induction of RNase H mediated cleavage of the DNA / targct RNA hybrid structure. A gapmer is more resistance to degradation by nucleases than an anti-sense RNA. Gapmers are currently being developed as therapeutics for a variety of cancers, viruses, and other chronic genetic disorders. The two RNA-like segments are RNA mimics composed of chemical analogs of natural RNA nucleic acids such as locked nucleic acids (LNA), 2'-0Me, or 2’-F modified bases. LNA sequences are RNA analogues "locked" into an ideal Watson-Crick base pairing conformation. Gapmers may also have reduced immunogenicity and / or decreased toxicity as compared to anti-sense RNA.

[0085] An ASO of the present disclosure may include chemically modified locked nucleic acid (LNA) monomers. Such ASOs are referred to as LNAs. In some embodiments, the LNAs include 2’-OMe, or 2’-F modified bases. In some embodiments, the ASO designed in the form of LNA (ASO-LNA) decreases amount of SATB1 exon Id variant resulting in death of aggressive cancer cellsand / or reduced cancer growth. In some embodiments, the ASO designed in the form of LNA (ASO-LNA) decreases expression of pSTS-SATBl effectively killing aggressive cancer cells of multiple types and / or reducing cancer growth. In some embodiments, the ASO-LNA inhibits colonization and growth of a metastatic cancer. LNA ribose modification significantly prolongs the ASO’ s half-life through increasing resistance against nucleases. In some embodiments, the LNA-ASO can be redesigned to make small changes, such as having slightly shortening the length of ASO if any toxicity, such as liver, kidney, or immune response, is detected. In certain embodiments, the LNA-ASO comprises the nucleotide sequences of the nucleic acids disclosed herein.

[0086] In other embodiments, the ASO comprises nucleotides modified with phosphorothioates (PS) groups (PS-ASO). The PS linkage increases ASO affinity to the plasma proteins and thus increases their uptake into systemic tissues. In certain embodiments, PS-ASO comprises the nucleotide sequences of the nucleic acids disclosed herein.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0087] In some embodiments, an ASO of the present disclosure comprises LNA and PS linkage thereby comprising LNA-PS-ASO structure. The LNA-PS-ASO of the present disclosure may be a gapmer. The gapmer may have increased resistance to nuclease degradation and enhanced stability in vivo. The gapmer may have a high binding affinity to the target SATB1 exon Id mRNA variant. Binding of the gapmer to the target has a higher affinity due to the modified RNA flanking regions, as well as resistance to degradation by nucleases. This high binding affinity reduces off-target effects, non-specific binding, and unwanted gene silencing. These modifications allow for an increase in nuclease resistance, reduced immunogenicity, and a decrease in toxicity.

[0088] In some embodiments, LNA-PS-ASO gapmer of the present disclosure comprises a central single stranded DNA-based gap flanked by RNA-based regions. The RNA-based regions may include RNA mimics, e.g., LNA. In some embodiments, the mimics are composed of LNAs, such as 2’-OMe, or 2’-F modified bases. In certain embodiments, the LNA comprises 2’ -0,4’ -C-methylene -bridged nucleic acid.

[0089] The LNA-PS-ASO gapmer of the present disclosure may bind to exon Id of SATB1 exon Id mRNA variant. This binding has a higher affinity due to the RNA-based LNA modified flanking regions, as well as resistance to degradation by nucleases. The LNA-PS-ASO of the present disclosure may hybridize to the target SATB1 exon Id mRNA variant and silence the SATB1 exon Id mRNA variant through the induction of RNase H mediated cleavage. Upon hybridization of LNA-PS-ASO gapmers to its target SATB1 exon Id mRNA variant, the resulting RNA-DNA duplex acts as a substrate for RNase Hl, leading to the degradation of the target transcript without inducing overt inflammatory response. The LNA-PS-ASO of the present disclosure may inhibit colonization and growth of metastatic cancer cell by degrading SATB1 exon Id mRNA variant.

[0090] In some embodiments, an LNA-PS-ASO that targets SATB1 exon Id mRNA variant with minimum predicted off-targeting comprises a nucleotide sequence at least 85%, 86 %, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to a nucleotide sequence: +C*+T*+G*A*A*A*C!i:C*A!i:A*G!i;A*A*+C*-i-G*-i-G (SEQ ID NO:36, hereinafter “RED 1”). In other embodiments, an LNA-PS-ASO that targets SATB1 exon Id mRNA variant with minimum predicted off-targeting comprises a nucleotide sequence identical to the nucleotide sequence of RED 1. The nucleotide sequences RED 1 have a length of 16 nucleotides. indicates the PS linkage, and wherein “+” immediately preceding a nucleotide indicates that the nucleotide is an LNA.

[0091] In some embodiments, an LNA-PS-ASO that targets SATB] exon Id mRNA variant with minimum predicted off-targeting comprises a nucleotide sequence at least 85%, 86 %, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to a nucleotide sequence:+A*+A*+C*C*A*A*G*A*A*C*G*G*C*+T*-I-C*-I-C (SEQ ID NO:37, hereinafter “RED 2”). In otherAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 embodiments, an LNA-PS-ASO that targets SATB1 exon Id mRNA variant with minimum predicted off-targeting comprises a nucleotide sequence identical to the nucleotide sequence of RED 2. The nucleotide sequences RED 2 have a length of 16 nucleotides. indicates the PS linkage, and wherein “+” immediately preceding a nucleotide indicates that the nucleotide is an LNA.

[0092] In some embodiments, an ASO targeting SATB 1 mRNA exon 1 variant includes a modification with phosphorodiamidate morpholino (PMO) (also called Vivo-morpholino). In other embodiments, PMO-ASO of the present disclosure blocks translation of the exon Id mRNA variant by steric hindrance. The PMO-ASO reduces the pSTS-SATBl levels without affecting bulk SATB1 proteins (FIG.2B, left), with accompanying loss of invasive activity of cancer cells. In certain embodiments, PMO-ASO that inhibits SATB 1 mRNA exon 1 variant comprises a nucleotide sequence:5’-GCCTGAAACCAAGAACGGCTCCCCG-3’ (SEQ ID NO:3; Morpholino modified by Gene Tools, LLC)

[0093] In certain aspects, an agent that inhibits expression of pSTS-SATBl as described herein is an RNAi compound that binds to exon Id region of SATB1 exon Id mRNA variant and inhibits or decreases expression of pSTS-SATBl. In some embodiments, the RNAi compound may be a short interfering RNA (siRNA). In other embodiments, the siRNA is a short hairpin RNA (shRNA). In certain embodiments, siRNA that binds to exon Id region of SATB1 exon Id mRNA variant is capable of inhibiting or downregulating expression of pSTS-S ATB 1 in a metastatic cancer, thereby leading to loss of metastatic activity. In some embodiments, siRNA that inhibits expression of pSTS-SATBl in a cancer cell is 15 to 25 nucleotides in length. In some embodiments, the RNAi compound is a miRNA. In certain embodiments, miRNA that binds to exon Id region of SATB1 exon Id mRNA variant is capable of inhibiting or downregulating expression of pSTS-SATB 1 in a metastatic cancer, thereby leading to loss of metastatic activity. In some embodiments, miRNA that inhibits expression of pSTS-SATB 1 in a cancer cell is 15 to 25 nucleotides in length. Methods for making RNAi compounds to inhibit expression of any known gene sequence are known to those of skill in the art. In some embodiments, the siRNA for decreasing expression of pSTS-SATB 1 includes nucleic acid sequence complementary to exon Id mRNA.

[0094] In some embodiments, two or more agents of the present disclosure may be used in a mixture or sequentially to decrease expression of pSTS-SATB 1 in a cancer cell. In some embodiments, a mixture of any nucleic acids that reduce expression of pSTS-SATB 1 in a cancer cell and any polypeptides that inhibit activity of pSTS-SATB 1 in a cancer cell may be used. In other embodiments, an agent of the present disclosure comprises a mixture of any kind of anti-pSTS-SATB 1 antibodies. In other embodiments, an agent of the present disclosure comprises a mixture of anti-pSTS-SATB 1 antibody and RNAi compounds that inhibits expression of pSTS-SATBl. In still other embodiments, an agent of the present disclosure comprises a mixture of anti-pSTS-SATB 1 antibody and siRNA thatAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 inhibits expression of pSTS-S ATB 1. In yet further embodiments, an agent of the present disclosure comprises a mixture of any kind of RNAi compounds that inhibit expression of pSTS-S ATB 1. In further embodiments, an agent of the present disclosure comprises a mixture of siRNA and shRNA that inhibit expression of pSTS-SATBl.

[0095] In some embodiments, an agent of the present disclosure comprises a mixture of any nucleotide sequence at least 85%, 86 %, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to RED1. In other embodiments, an agent of the present disclosure comprises a mixture of any nucleotide sequence at least 85%, 86 %, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to RED2. In other embodiments, an agent of the present disclosure comprises a mixture of nucleotide sequence at least 85%, 86 %, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to RED1 and nucleotide sequence at least 85%, 86 %, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to RED2. In some embodiments, an agent of the present disclosure comprises a mixture of RED1 and RED2. In still other embodiments, an agent of the present disclosure comprises a mixture of any kinds of PMO-ASOs that decreases amount of or translation of SATB 1 mRNA exon 1 variant. In yet other embodiments, an agent of the present disclosure comprises a mixture of PMO-ASOs.Polypeptide that inhibits activity of pSTS-SATBl in a cancer cell

[0096] In some embodiments, an agent is a polypeptide that binds to pSTS-S ATB 1 and inhibits activity of pSTS-SATBl. In some embodiments, the polypeptide is an anti-pSTS-SATBl antibody that binds to pSTS-S ATB 1 and inhibits activity of pSTS-SATB 1. In some embodiments, the agent is an anti- an anti-pSTS-SATB 1 antibody bound to a nucleic acid disclosed herein for targeting the nucleic acid to cells expressing pSTS-.S'.477i / exon Id variant mRNA.

[0097] As used herein, the term antibody encompasses antigen-binding fragment thereof unless the context clearly dictates otherwise. In some embodiments, the antibody that binds to pSTS-SATB1 may be a plurality of polyclonal antibodies that bind to different epitopes on the antigen, a monoclonal antibody, a chimeric antibody, a humanized antibody, a human antibody, a bovinized antibody, a bovine antibody, an ovinized antibody, an ovine antibody, a caprinized antibody, a caprine antibody, a camelized antibody, or a camelid antibody. In some embodiments, the antibody that binds to pSTS-SATB 1 is an IgA, IgD, IgE, IgG, or IgM antibody. In still other embodiments, the antibody that binds to pSTS-SATBl is an IgGl, IgG2, IgG3, or IgG4 antibody. In some embodiments, the antibody that binds to pSTS-SATB 1 is an antibody fragment comprising at least one antigen-binding site. In some embodiments, the antibody that binds to pSTS-SATB 1 is a scFv. In still other embodiments, the antibody that binds to pSTS-SATB 1 is a Fab. In yet other embodiments, the antibody that binds to pSTS-SATB l is a bispecific antibody or a multispecific antibody.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0098] The above-described antibodies that bind to pSTS-SATBl can be prepared by any method known to those of skill in the art. In some embodiments, monoclonal antibodies arc also made using recombinant DNA techniques as known to one skilled in the art. In some embodiments, a monoclonal antibody is modified by using recombinant DNA technology to generate alternative antibodies. Once antibodies are identified, affinity maturation strategies known in the art, including but not limited to, chain shuffling and site-directed mutagenesis, may be employed to generate higher affinity human antibodies.

[0099] In some embodiments, an anti-pSTS-SATBl antibody comprises an antibody in which at least one or more of the constant regions has been modified or deleted. In some embodiments, the antibodies may comprise modifications to one or more of the three heavy chain constant regions (CHI, CH2 or CH3) and / or to the light chain constant region (CL). In some embodiments, the heavy chain constant region of the modified antibodies comprises at least one human constant region. In some embodiments, the heavy chain constant region of the modified antibodies comprises more than one human constant region. In some embodiments, modifications to the constant region comprise additions, deletions, or substitutions of one or more amino acids in one or more regions. In some embodiments, one or more regions are partially or entirely deleted from the constant regions of the modified antibodies. In some embodiments, the entire CH2 domain has been removed from an antibody (ACH2 constructs). In some embodiments, a deleted constant region is replaced by a short amino acid spacer that provides some of the molecular flexibility typically imparted by the absent constant region. In some embodiments, a modified antibody comprises a CH3 domain directly fused to tire hinge region of the antibody. In some embodiments, a modified antibody comprises a peptide spacer inserted between the hinge region and modified CH2 and / or CH3 domains.

[0100] It is known in the art that the constant region(s) of an antibody mediates several effector functions, and these effector functions can vary depending on the isotype of the antibody. For example, binding of the Cl component of complement to the Fc region of IgG or IgM antibodies (bound to antigen) activates the complement system. Activation of complement is important in the opsonization and lysis of cell pathogens. The activation of complement also stimulates the inflammatory response and can be involved in autoimmune hypersensitivity. In addition, the Fc region of an antibody can bind a cell expressing a Fc receptor (FcR). There are a number of Fc receptors that are specific for different classes of antibody, including IgG (gamma receptors), IgE (epsilon receptors), IgA (alpha receptors) and IgM (mu receptors). Binding of antibody to Fc receptors on cell surfaces triggers a number of important and diverse biological responses including engulfment and destruction of antibody-coated particles, clearance of immune complexes, lysis of antibody-coated target cells by killer cells (called antibody-dependent cell cytotoxicity or ADCC), release of inflammatory mediators, placental transfer, and control of immunoglobulin production.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0101] In some embodiments, an anti-pSTS-SATBl antibody comprises a variant Fc region. The amino acid sequences of the Fc region of human IgGl, IgG2, IgG3, and IgG4 arc known to those of ordinary skill in the art. In some embodiments, the variant Fc region provides altered effector functions that, in turn, affect the biological profile of the antibody. For example, in some embodiments, the deletion or inactivation (through point mutations or other means) of a constant region reduces or eliminates Fc receptor binding of the modified antibody as it circulates. In some embodiments, the constant region modifications increase the serum half-life of the antibody. In some embodiments, the constant region modifications reduce the serum half-life of the antibody. In some embodiments, the constant region modifications decrease, reduce, or remove ADCC and / or complement dependent cytotoxicity (CDC) of the antibody. In some embodiments, specific amino acid substitutions in a human IgGl Fc region with corresponding IgG2 or IgG4 residues may reduce effector functions (e.g., ADCC and CDC) in the modified antibody. In some embodiments, an antibody does not have one or more effector functions. In some embodiments, the antibody has no ADCC activity and / or no CDC activity. In some embodiments, the antibody does not bind an Fc receptor and / or complement factors. In some embodiments, the antibody has no effector function(s) (e.g., “effectorless” antibodies). In some embodiments, the constant region modifications increase or enhance effector functions of the antibody. In some embodiments, the constant region modifications increase or enhance ADCC and / or CDC of the antibody. In some embodiments, the constant region is modified to eliminate disulfide linkages or oligosaccharide moieties. In some embodiments, the constant region is modified to add / substitute one or more amino acids to provide one or more cytotoxin, oligosaccharide, or carbohydrate attachment sites.

[0102] Modifications to the constant region of antibodies described herein may be made using well-known biochemical or molecular engineering techniques. In some embodiments, antibody variants are prepared by introducing appropriate nucleotide changes into the encoding DNA, and / or by synthesis of the desired antibody or polypeptide. Using this technique, it may be possible to disrupt the activity or effector function provided by a specific sequence or region while substantially maintaining the structure, binding activity, and other desired characteristics of the modified antibody.

[0103] The present disclosure further embraces additional variants and equivalents that are substantially homologous to the recombinant, monoclonal, chimeric, humanized, and human antibodies, or antibody fragments thereof, described herein. In some embodiments, it is desirable to improve the binding affinity of the antibody. In some embodiments, it is desirable to modulate biological properties of the antibody, including but not limited to, specificity, thermostability, expression level, effector function / s), glycosylation, immunogenicity, and / or solubility. Those skilled in the art will appreciate that amino acid changes may alter post-translational processes of an antibody, such as changing the number or position of glycosylation sites or altering membrane anchoring characteristics. Variations may be a substitution, deletion, or insertion of one or more nucleotides encoding the antibody or polypeptide thatAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 results in a change in the amino acid sequence as compared with the native antibody or polypeptide sequence. In some embodiments, amino acid substitutions are the result of replacing one amino acid with another amino acid having similar structural and / or chemical properties, such as the replacement of a leucine with a serine, e.g., conservative amino acid replacements. The variant antibodies or polypeptides described herein may be generated using methods known in the art, including but not limited to, site-directed mutagenesis, alanine scanning mutagenesis, and PCR mutagenesis.

[0104] In some embodiments, anti-pSTS-S ATB 1 antibody is chemically modified by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by known protecting / blocking groups, proteolytic cleavage, and / or linkage to a cellular ligand or other protein. Any of numerous chemical modifications may be carried out by known techniques.

[0105] In certain embodiments, anti-pSTS-S ATB 1 antibody that binds to pSTS-S ATB 1 and inhibits or decreases expression and / or activity of pSTS-SATBl comprises the VH and VL CDRs of an and -pSTS-S ATB 1 antibody disclosed herein.3. Pharmaceutical composition

[0106] In some aspects of the invention, a pharmaceutical composition comprises one or two or more of the agents described in the above section 2 of the present disclosure. In some embodiments, the pharmaceutical composition further comprises additional components, such as a pharmaceutically acceptable excipient, carrier, adjuvant, buffers, etc. In general, those of skill in the art and the U.S. FDA consider a pharmaceutically acceptable excipient, carrier, or adjuvant to be an inactive ingredient of any formulation.

[0107] In some embodiments, the agent described in the above section 2 can be admixed with nontoxic pharmaceutically acceptable excipients which are suitable for manufacture. In other embodiments, the pharmaceutical acceptable excipient can be prepared according to any method known to the art for the manufacture of pharmaceuticals. In some embodiments, the pharmacculical composition may contain one or more diluents, emulsifiers, preservatives, buffers, excipients, etc. and may be provided in such forms as liquids, powders, emulsions, lyophilized powders, sprays, creams, lotions, controlled release formulations, tablets, pills, gels, on patches, in implants, etc.

[0108] In some embodiments, the agent described in the above section 2 can be admixed with pharmaceutically acceptable salt. For example, the pharmaceutically acceptable salt includes, but is not limited to, amino acid salts, salts prepared with inorganic acids, such as chloride, sulfate, phosphate, diphosphate, bromide, and nitrate salts, or salts prepared from the corresponding inorganic acid form of any of the preceding.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0109] The pharmaceutical compositions of the present disclosure can be formulated to be compatible with the intended method or route of administration. In some embodiments, suitable routes of administration include an intravenous, an intracardial, an intramuscular, an intratumoral, a peritumoral, a subcutaneous, intrathecal, or epidural route of administration. In certain embodiments, the route of administration is intravenous. In certain embodiments, the route of administration is intratumoral. In certain embodiments, the route of administration is intramuscular. Suitable pharmaceutically acceptable or physiologically acceptable diluents, carriers or excipients include, but are not limited to, nuclease inhibitors, protease inhibitors, a suitable vehicle such as physiological saline soludon or citrate buffered saline.

[0110] The pharmaceutical composition of the present disclosure may comprise a gene therapy vector. In some embodiments, the pharmaceutical composition comprising a gene therapy vector include an acceptable diluent. In other embodiments, the pharmaceutical composition comprising a gene therapy vector comprise a slow-rclcasc matrix in which the gene delivery vehicle is imbedded.Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral or lentiviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system.

[0111] The pharmaceutical composition may comprise in vzvo-jetPEI® or a similar molecule. For example, the pharmaceutical composition may comprise a cationic polymer reagent. The cationic polymer agent may be the cationic polymer polyethylenimine. A cationic polymer agent, such as, polyethylenimine may be used for administering an agent for reducing translation of or for degradation of SATB1 exon Id mRNA. The agent may be as discussed above, such as, a nucleic acid (e.g., siRNA, shRNA, ASO, and other oligonucleotides) that specifically binds to SATB1 exon Id mRNA.4. Methods for treating metastatic cancer or preventing metastasis

[0112] The present disclosure provides a method using an agent of the present disclosure or a pharmaceutical composition of the present disclosure for treating metastatic cancer or preventing metastasis in a subject in need thereof.

[0113] In some aspects of the invention, the method of the present disclosure comprises administering to a subject in need thereof an effective amount of an agent of the present disclosure or a pharmaceutical composition of the present disclosure. In some embodiments, the method comprises administering to a subject in need thereof an effective amount of antibody that binds to pSTS-S ATB 1 and inhibits or decreases expression and / or activity of pSTS-SATB 1 in metastatic cancer. In other embodiments, the method comprises administering to a subject in need thereof an effective amount of RNAi compound that binds to SATB1 exon Id mRNA variant and inhibits or decreases expression ofAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 pSTS-SATBl in metastatic cancer. In still other embodiments, the method comprises administering to a subject in need thereof an effective amount of siRNA that binds to SATB1 exon Id mRNA variant and inhibits or decreases expression of pSTS-SATB 1 in metastatic cancer. In further embodiments, the method comprises administering to a subject in need thereof an effective amount of ASO that binds to SATB1 exon Id mRNA variant and inhibits or decreases expression of pSTS-SATB 1 in metastatic cancer. In further embodiments, the method comprises administering to a subject in need thereof an effective amount of LNA-ASO that binds to a SATB1 exon Id variant mRNA and inhibits or decreases expression of pSTS-SATB 1 in metastatic cancer. In yet further embodiments, the method comprises administering to a subject in need thereof an effective amount of LNA-ASO-PS that binds to a SATB1 exon Id variant mRNA and inhibits or decreases expression of pSTS-SATB 1 in metastatic cancer. In certain embodiments, the method comprises administering to a subject in need thereof an effective amount of RED 1. In certain embodiments, the method comprises administering to a subject in need thereof an effective amount of RED 2. In certain embodiments, the method comprises administering to a subject in need thereof an effective amount of RED 1 and RED 2.

[0114] In some embodiments, an agent of the present disclosure or a pharmaceutical composition of the present disclosure is administered in a lipid nanoparticle. In other embodiments, an agent of the present disclosure or a pharmaceutical composition of the present disclosure can be delivered by the use of liposomes. By using liposomes, particularly where the liposome surface carries ligands specific for target cells, or are otherwise preferentially directed to a specific organ, one can focus the delivery of the active agent of the present disclosure into target cells w vivo. See, e.g., U.S. Pat. Nos. 6,063,400; 6,007,839; Al-Muhammed (1996) J. Microencapsul. 13:293-306; Chonn (1995) Curr. Opin. Biotechnol. 6:698-708; Ostro (1989) Am. J. Hosp. Pharm. 46:1576-1587.

[0115] In some embodiments, suitable routes of administration include an intravenous, an intracardial, an intramuscular, an intratumoral, a peritumoral, a subcutaneous, intrathecal, or epidural route of administration. In certain embodiments, the route of administration is intravenous. In certain embodiments, the route of administration is intratumoral. In certain embodiments, the route of administration is intramuscular.

[0116] In some embodiments, an agent of the present disclosure or a pharmaceutical composition of the present disclosure is administered with any delivery agents. In other embodiments, an agent of the present disclosure or a pharmaceutical composition of the present disclosure is administered without any delivery agents.

[0117] In some embodiments, an agent comprising a nucleic acid that inhibits expression and / or activity of pSTS-SATB 1 in a cancer cell may be inserted into vectors which can be used as gene therapy vectors. In general, gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration, or by stereotactic injection.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0118] Subjects suitable for treatment with a method of the present disclosure include individuals having an aggressive cancer. Subjects suitable for treatment with a method of the present disclosure include metastatic cancer. Subjects suitable for treatment with a method of the present disclosure include individuals having metastatic breast cancer. Subjects suitable for treatment with a method of the present disclosure include individuals having metastatic triple-negative breast cancer (TNBC). Subjects suitable for treatment with a method of the present disclosure include individuals at risk of developing metastasis.

[0119] In some embodiments, the metastatic cancer is, but not limited to, metastatic breast cancer, metastatic brain cancer, metastatic liver cancer, metastatic colorectal cancer, metastatic ovarian cancer, metastatic pancreatic cancer, metastatic prostate cancer or metastatic lung cancer. In certain embodiments, the metastatic breast cancer is metastatic triple-negative breast cancer (TNBC). In some embodiments, the metastasis is, but not limited to, bone metastasis, multi-organ metastasis, lung metastasis, liver metastasis, brain metastasis, heart metastasis or spleen metastasis.

[0120] In some embodiments, a therapeutically effective amount of an agents of the present disclosure is an amount that, when administered in one or more doses, is sufficient to reduce or decrease any level (e.g., a baseline level) of pSTS-SATBl. In some embodiments, a therapeutically effective amount of an agent of the present disclosure is an amount that, when administered in one or more doses, is sufficient to reduce or decrease pSTS-SATBl levels by more than about 40% to 50%, by more than about 50% to 60%, by more than about 60% to 70%, by more than about 70% to 80%, by more than 80 to 90 % and so on. In some embodiments, a therapeutically effective amount of an inhibitory nucleic acid of the present disclosure is an amount is an amount sufficient to reduce or decrease pSTS-SATBl levels by about 45%, 50%, 55%, 60%, 63%, 65%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, or more. For example, the effective amount of an agent of the present disclosure is about between 1 to 5000 mg / kg / week, such as 1, 2, 5, 10, 15, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 200, 240, 300, 350, 400, 450, 500, 550, 600, 700, 800, 900, 1000, 2000, or 5000 mg / kg / week which is sufficient to reduce a pSTS-SATBl level by more than about 40% to 50%, by more than about 50% to 60%, by more than about 60% to 70%, by more than about 70% to 80%, by more than 80 to 90 %. The dosage schedule and amounts effective for this use. i.e., the dosing regimen, will depend upon a variety of factors, including the stage of the disease or condition, the severity of the disease or condition, the general state of the patient's health, the patient's physical status, age and the like. In calculating the dosage regimen for a patient, the mode of administration also is taken into consideration. In some examples, the dose may be the human equivalent for a dose of 2mg / kg / week in mice.

[0121] The present disclosure contemplates the use of an agent of the present disclosure or a pharmaceutical composition of the present disclosure in combination with one or more additional agentsAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 (e.g., one or more additional active therapeutic agents) or other prophylactic or therapeutic modalities. In some embodiments, the additional therapeutic treatments comprise cancer chemotherapy, radiation therapy, surgery or combination thereof. In such combination therapy, the various active agents frequently have different mechanisms of action. Such combination therapy may be especially advantageous by allowing a dose reduction of one or more of the agents, thereby reducing or eliminating the adverse effects associated with one or more of the agents; furthermore, such combination therapy may have a synergislic therapeutic or prophylactic effect on the underlying disease, disorder, or condition. In certain embodiments, combining the use an agent of the present disclosure or a pharmaceutical composition of the present disclosure in combination with chemotherapy may improve the efficacy of the treatment and inhibit future recurrence.5. Methods for identifying a subject as having metastatic cancer or at risk of developing metastasis

[0122] A method of identifying a subject as having metastatic cancer or at risk of developing metastasis is disclosed. The method may comprise determining the presence or absence of pSTS-S ATB 1 in a cancer sample from the subject, wherein the presence of pSTS-SATB 1 indicates that the subject has metastatic cancer or at risk of developing metastasis.

[0123] pSTS-SATB 1 may be idenli lied by any suitable method. For example, pSTS-SATB 1 expressed in metastatic cancers is identified by performing an assay for measuring binding of anti-pSTS-SATB1 antibody to pSTS-SATB 1. An anti -pSTS-SATB 1 antibody may be a monoclonal antibody.

[0124] An anti -pSTS-S ATB 1 antibody may be antibody comprising:A VH-4F:METGLRWLLLVAVLKGVQCQSLEESGGDLVKPGASLTLTCTASGFSFSSGYDMCWVR QAPGKGLELIACIYVGSSVTTWYASWAKGRFTISKTSSTTVTLQMTSLTAADTATYFC ARYPYGSSNGGGYFNL (SEQ ID NO: 12); and■=> VL-4F:MDTRAPTQLLGLLLLWLPGARCADIVMTQTPASVEAAVGGTVTINCQASENIYSNLA WYQQKPGQRPKLLIYTASTLASGVPSRFKGSGSGTQFTLTISGVQCDDAATYYCQQGI SRTNADNV (SEQ ID NO: 13); orVH-6B:METGLRWLLLVAVLKGVQCQSLEESGGDLVKPGASLTLTCTASGFSFSSGYDMCWVR QAPGKGLEEIACIYAGSSVTTWYASWAKGRFTISKTSSTTVTLQMTSLTAADTATYFC ARYPYGSSNGGGYFNL (SEQ ID NO: 14); andA VL-6B:MDTRAPTQLLGLLLLWLPGARCADIVMTQTPASVEAAVGGTVTIKCQASQNISSYLSW YQQKPGQRPKLLIYTASTLASGVPSRFKGSGSGTQFTLTISGVQCDDAATYYCQQGISR TNADNV (SEQ ID NO: 15); orA VII-11D:METGLRWLLLVAVLKGVQCQSLEESGGDLVKPGASLTLTCTASGFSFSSTYWICWVRAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 QAPGKGLEWIACIYGGSSGSIYYASWAKGRFTISKTSSTTVTLQMTSLTVADTATYFCA DSTASTYGYAFNL (SEQ ID NO: 16); andVL-11D:MDTRAPTQLLGLLLLWLPGATFAQVLTQTPSPVSAAVGGTVTISCQSSKNVYNNNYLS WFQQKPGQPPKLLIYRASNLASGVPSRFKGSGSGTQFTLTISEVQCDDAATYYCQGYY SGYIWA (SEQ ID NO: 17).

[0125] The anti-pSTS-SATBl antibody may be an antibody comprising a heavy chain variable region (VH) comprising the heavy chain CDRsl-3 and a light chain variable region (VL) comprising the light chain CDRs 1-3 of the 4F, 6B, or 1 ID antibody.

[0126] The CDRs of an anti-pSTS-S ATB 1 antibody according to IMGT definition may be as follows:VH-4F CDR1: GFSFSSGYD (SEQ ID NO: 18);VH-4F CDR2: IYVGSSVTT (SEQ ID NO: 19);VH-4F CDR3: ARY (SEQ ID NO:20);VL-4F CDR1: ENIYSN (SEQ ID NO:21);VL-4F CDR2: TAS (SEQ ID NO:22); andVL-4F CDR3: QQGI (SEQ ID NO:23); orVH-6B CDR1: GFSFSSGYD (SEQ ID NO:24);VH-6B CDR2: IYAGSSVTT (SEQ ID NO:25);VH-6B CDR3: ARY (SEQ ID NO:26);VL-6B CDR1: QNISSY (SEQ ID NO:27);VL-6B CDR2: TAS (SEQ ID NO:28); andVL-6B CDR3: QQGI (SEQ ID NO:29); orVH-11 CDR1: GFSFSSTYW (SEQ ID NO:30);VH-11 CDR2: IYGGSSGSI (SEQ ID NO:31);VH-11 CDR3: ADSTA (SEQ ID NO:32);VL-11 CDR1: KNVYNNNY (SEQ ID NO:33);VL-11 CDR2: RAS (SEQ ID NO:34); andVL-11 CDR3: QGYYSG (SEQ ID NO:35).

[0127] Representative examples of metastatic cancer include, but are not limited to, metastatic breast cancer, metastatic brain cancer, metastatic liver cancer, metastatic colorectal cancer, metastaticAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 ovarian cancer, metastatic pancreatic cancer, metastatic prostate cancer or metastatic lung cancer. In certain embodiment, the metastatic cancer is TNBC.

[0128] The method of identifying a subject as having metastatic cancer or at risk of developing metastasis comprises determining the presence or absence of pSTS-SATBl in a cancer sample from the subject. In some embodiments, the presence of pSTS-SATBl indicates that the subject has metastatic cancer. In other embodiments, the presence of pSTS-SATBl indicates that the subject is at risk of developing metastasis. In still other embodiments, the presence of pSTS-SASTB 1 in the sample identifies the subject as a candidate for treatment with an agent of the present disclosure or a pharmaceutical composition of the present disclosure. In some embodiments, the absence of pSTS-SATB 1 indicates that the subject does not have aggressive cancer such as metastatic cancer. In other embodiments, the absence of pSTS-SATB 1 indicates that the subject is not identified as a candidate for treatment with an agent of the present disclosure or a pharmaceutical composition of the present disclosure.

[0129] In some embodiments, a subject is mammal suffering from a tumor or cancer. In certain embodiments, a subject is human suffering from a tumor or cancer. In certain embodiments, a subject is mammal having an unknown lump tissue. In certain embodiments, a subject is human having an unknown lump tissue.

[0130] In some embodiments, the cancer sample is obtained from a subject having a tumor or cancer. For example, the cancer sample is, but not limited to, breast cancer, brain cancer, liver cancer, colorectal cancer, ovarian cancer, pancreatic cancer, prostate cancer or lung cancer. In certain embodiments, the cancer sample is obtained from an unknown lump tissue in a subject. In some embodiments, the cancer sample is a primary cancer.

[0131] In another aspect of the invention, the present disclosure provides a method of evaluating a subject to determine whether to have aggressive cancer such as metastatic cancer. The method comprises measuring the level of pSTS-SATB 1 in a cancer sample obtained from the subject. In some embodiments, the level of pSTS-SATB 1 in cancer sample correlates with disease severity. In some embodiments, the higher level of pSTS-SATB 1 in cancer sample relative to the reference level indicates the subject has an aggressive cancer, such as metastatic cancer. The reference level is a transcript level of pSTS-SATB 1 in a control sample. In some embodiments, the control sample is a non-aggressive cancer cell. In other embodiments, the control sample is a normal cell. In some embodiments, the reference level is extremely / very low level compared to levels of pSTS-SATB 1 in metastatic cancer samples. In other embodiments, the reference level is zero. In some embodiments, the absence of pSTS-SATB 1 in a sample from a subject indicates that the subject does not have aggressive cancer. In some embodiments, the absence of pSTS-SATB 1 in a sample from a subject indicates that the subject does not have metastatic cancer. In other embodiments, the absence of pSTS-SATB 1 in a sample from a subjectAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 indicates that the sample is a normal cell. In still other embodiments, the absence of pSTS-SATBl in a sample from a subject indicates that the sample is not an aggressive cancer cell. In still other embodiments, the absence of pSTS-SATBl in a sample from a subject indicates that the sample is not a metastatic cancer cell. In some embodiments, the extremely low level of pSTS-SATB 1 in a sample from a subject compared to levels of pSTS-SATB 1 indicates that the subject does not have aggressive cancer. In other embodiments, the extremely low level of pSTS-SATB 1 in a sample from a subject compared to levels of pSTS-SATB 1 indicates that the subject does not have metastatic cancer. In some embodiments, the extremely low level of pSTS-SATB 1 in a sample from a subject compared to levels of pSTS-SATB 1 indicates that the sample is not an aggressive cancer cell. In some embodiments, the extremely low level of pSTS-SATB 1 in a sample from a subject compared to levels of pSTS-SATB 1 indicates that the sample is not a metastatic cancer cell.

[0132] In some embodiments, high expression of SATB1 exon Id variant mRNA is correlated to poor prognosis of metastatic cancer. The level of SATB1 exon Id variant mRNA is correlated to prognosis of metastatic cancer.

[0133] In some embodiments, the metastatic cancer is, but not limited to, metastatic breast cancer, metastatic brain cancer, metastatic liver cancer, metastatic colorectal cancer, metastatic ovarian cancer, metastatic pancreatic cancer, metastatic prostate cancer or metastatic lung cancer. In certain embodiments, the metastatic breast cancer is metastatic triple-negative breast cancer (TNBC). In some embodiments, the metastasis is, but not limited to, bone metastasis, multi-organ metastasis, lung metastasis, liver metastasis, brain metastasis, heart metastasis or spleen metastasis.

[0134] In some embodiments, the method of determining the presence or absence of pSTS-SATB 1 in a cancer sample from the subject comprises contacting the sample with an antibody that specifically binds to pSTS-SATB 1. In other embodiments, the method of measuring the level of pSTS-SATB 1 in the cancer sample comprises contacting the sample with an antibody that specifically binds to pSTS-SATB 1. As used herein, the term “antibody” encompasses antigen-binding fragment thereof unless the context clearly dictates otherwise. In some embodiments, the antibody that binds to pSTS-SATB 1 comprises a plurality of polyclonal antibodies that bind to different epitopes on the antigen. In other embodiments, the antibody that binds to pSTS-SATB 1 is a recombinant antibody. In still other embodiments, the antibody that binds to pSTS-SATB 1 is a monoclonal antibody. In further embodiments, the antibody that binds to pSTS-SATB 1 is a chimeric antibody. In still further embodiments, the antibody that binds to pSTS-SATB 1 is a humanized antibody. In yet further embodiments, the antibody that binds to pSTS-SATB 1 is a human antibody. In further embodiments, the antibody that binds to pSTS-SATB 1 is a camelid antibody. In some embodiments, the antibody that binds to pSTS-SATB 1 is an IgA, IgD, IgE, IgG, or IgM antibody. In still other embodiments, the antibody that binds to pSTS-SATB 1 is an IgGl, IgG2, IgG3, or IgG4 antibody. In some embodiments,Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 the antibody that binds to pSTS-SATBl is an antibody fragment comprising at least one antigen-binding site. In some embodiments, the antibody that binds to pSTS-SATB 1 is a scFv. In still other embodiments, the antibody that binds to pSTS-SATB 1 is a Fab. In yet other embodiments, the antibody that binds to pSTS-SATB 1 is a bispecific antibody or a multispecific antibody. In some embodiments, any antibodies that bind to pSTS-SATB 1 can be prepared by any method known to those of skill in the art.

[0135] The antibody that binds to pSTS-SATB 1 is anti-pSTS-SATB 1 antibody. In some embodiments, the anti-pSTS-SATB 1 antibody selectively detects anti-pSTS-SATB 1 in highly aggressive cancer cells such as TNBC (FIG. 1A, IB and 1C). In other embodiments, the anti-pSTS-SATB 1 anubody does not detect anti-pSTS-SATB 1 in normal cells (FIG. ID). In further embodiments, pSTS-SATB 1 is distinct from bulk S ATB 1. In yet other embodiments, the level of pSTS-SATB 1 in cancer cells correlates with disease severity. The higher level of pSTS-SATB 1 indicates a more aggressive cancer such as metastatic cancer.

[0136] In some embodiments, anti-pSTS-SATB 1 antibody is used to monitor the efficacy of the antisense oligo-based therapy of the present disclosure. In other embodiments, the anti-pSTS-SATB 1 antibody can serve as a diagnostic tool to identify patients who need treatments for metastatic cancer.Examples of Non-Limiting Aspects of the Disclosure

[0137] Aspects, including embodiments, of the present subject matter described above may be beneficial alone or in combination, with one or more other aspects or embodiments. Without limiting the foregoing description, certain non-limiting aspects of the disclosure numbered as aspects are provided below. As will be apparent to those of skill in the art upon reading this disclosure, each of the individually numbered aspects may be used or combined with any of the preceding or following individually numbered aspects. This is intended to provide support for all such combinations of aspects and is not limited to combinations of aspects explicitly provided below:1. An agent that binds to pSTS-SATB 1 or an agent that binds to SATB 1 exon Id variant mRNA in a cancer cell.2. The agent of aspect 1 , wherein the agent that binds to pSTS-SATB 1 is a polypeptide and the agent that binds to SATB1 exon Id variant mRNA is a nucleic acid.3. The agent of aspect 2, wherein the nucleic acid binds to exon Id region of the SATB 1 exon Id variant mRNA and is an antisense oligonucleotide (ASO), a short interfering (siRNA) or a microRNA (miRNA).4. The agent of aspect 3, wherein the nucleic acid is a locked nucleic acid (LNA) comprising one or more LNA monomers.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 5. The agent of aspect 3 or 4, wherein the nucleic acid comprises one or more phosphorothioate (PS) linkages.6. The agent of aspect 4 or 5, wherein the nucleic acid comprises one or more LNA monomers and one or more phosphorothioate (PS) linkages.7. The agent of any one of aspects 3-6, wherein the nucleic acid is a gapmer comprising a central single stranded DNA sequence flanked by RNA sequences.8. The agent of aspect 7, wherein the RNA sequences comprise one or more LNA monomers.9. The agent of aspect 8, wherein the LNA comprises 2’-O,4’-C-methylene -bridged LNA monomers.10. The agent of aspect 3, wherein the nucleic acid is a morpholino oligonucleotide.11. The agent of any one of aspects 3-10, wherein the nucleic acid comprises a nucleotide sequence at least 85%, at least 90%, at least 95%, at least 99% identical, or 100% identical to a nucleotide sequence selected from SEQ ID NO: 1-6, 36, and 37.12. The agent of any one of aspects 1-11, wherein the nucleic has a length of from about 8 nucleotides to about 30 nucleotides.13. The agent of aspect 12, wherein nucleic acid comprises the nucleotide sequence of SEQ ID NO:1, 2, 3, 4, 5, 6, 36, or 37 and has a length of up to 30 nucleotides.14. I’he agent of aspect 13, wherein the nucleic acid has a length of about 11-26 or 15-26 nucleotides.15. A composition comprising two or more nucleic acids having different sequences that each bind to exon Id region of a SATB1 exon Id variant mRNA.16. The composition of aspect 15, wherein the two or more nucleic acids are selected from an antisense oligonucleotide (ASO), a short interfering (siRNA) or a microRNA (miRNA).17. The composition of aspect 15 or 16, wherein at least one nucleic acid is a locked nucleic acid (LNA) comprising one or more LNA monomers.18. The composition of any one of aspects 15-17, wherein at least one nucleic acid comprises one or more phosphorothioate (PS) linkages.19. The composition of any one of aspects 15-18, wherein at least one nucleic acid comprises one or more LNA monomers and one or more phosphorothioate (PS) linkages.20. The composition of any one of aspects 15-19, wherein at least one nucleic acid is a gapmer comprising a central single stranded DNA sequence flanked by RNA sequences.21. The composition of aspect 20, wherein the RNA sequences comprise one or more LNA monomers.22. The composition of aspect 21 , wherein the LNA comprises 2’ -0,4’ -C-methylene-bridged LNA monomers.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 23. The composition of any one of aspects 15-20, wherein at least one nucleic acid is a morpholino oligonucleotide.24. The composition of any one of aspects 15-23, wherein the two or more nucleic acids have a length of from about 8 nucleotides to about 30 nucleotides.25. The composition of any one of aspects 15-23, wherein the two or more nucleic acids have a length of from about 15-26 nucleotides.26. The composition of any one of aspects 15-25, wherein a first nucleic acid comprises a nucleotide sequence at least 85%, at least 90%, at least 95%, at least 99% identical, or 100% identical to the nucleotide sequence of SEQ ID NO:36 and a second nucleic acid comprises a nucleotide sequence at least 85%, at least 90%, at least 95%, at least 99% identical, or 100% identical to the nucleotide sequence of SEQ ID NO:37.27. The composition of any one of aspects 15-26, further comprising a pharmaceutically acceptable excipient.28. The agent of aspect 2, wherein the polypeptide is an anti-pSTS-S ATB 1 antibody.29. The agent of aspect 28, wherein the anti-pSTS-SATB 1 antibody comprises a variable heavy (VH) chain comprising heavy chain complementarity determining regions (HCDRs) and a variable light (VL) chain comprising light chain complementarity determining regions (LCDRs) from the VH and VL chains, respectively, of an anti-pSTS-SATB 1 antibody comprising one of the following pairs of VH and VL chains:VH-4F:METGLRWLLLVAVLKGVQCQSLEESGGDLVKPGASLTLTCTASGFSFSSGYDMCWVRQAPGK GLELIACIYVGSSVTTWYASWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARYPYGSSNGG GYFNL (SEQ ID NO: 12); andVL-4F:MDTRAPTQLLGLLLLWLPGARCADIVMTQTPASVEAAVGGTVTINCQASENIYSNLAWYQQKP GQRPKLLIYTASTLASGVPSRFKGSGSGTQFTLTISGVQCDDAATYYCQQGISRTNADNV (SEQ ID NO: 13); orVH-6B:METGLRWLLLVAVLKGVQCQSLEESGGDLVKPGASLTLTCTASGFSFSSGYDMCWVRQAPGK GLELIACIYAGSSVTTWYASWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARYPYGSSNGG GYFNL (SEQ ID NO: 14); andVL-6B:MDTRAPTQLLGLLLLWLPGARCADIVMTQTPASVEAAVGGTVTIKCQASQNISSYLSWYQQKP GQRPKLLIYTASTLASGVPSRFKGSGSGTQFTLTISGVQCDDAATYYCQQGLSRTNADNV (SEQ ID NO: 15); orAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 VH-11D:METGLRWLLLVAVLKGVQCQSLEESGGDLVKPGASLTLTCTASGFSFSSTYWICWVRQAPGKG LEWIACIYGGSSGSIYYASWAKGRFTISKTSSTTVTLQMTSLTVADTATYFCADSTASTYGYAFNL(SEQ ID NO: 16); andVL-11D:MDTRAPTQLLGLLLLWLPGATFAQVLTQTPSPVSAAVGGTVTLSCQSSKNVYNNNYLSWFQQK PGQPPKLLIYRASNLASGVPSRFKGSGSGTQFTLTISEVQCDDAATYYCQGYYSGYIWA (SEQ ID NO:17),optionally, the anti-pSTS-SATBl antibody further comprising a VH and a VL chain each having at least 90%, at least 95%, or at least 99% amino acid sequence identity to the VH and VL chain, respectively, of one of the above-listed antibodies.30. A pharmaceutical composition comprising:a) the agent of any one of aspects 1-14 and 28-29 or the composition of any one of aspects 15-27; and b) a pharmaceutically acceptable excipient.31. A method for treating metastatic cancer or pre ve nli ng metastasis in a subject in need thereof, comprising:administering an effective amount of the agent of any one of aspects 1-14 and 28-29, the composition of any one of aspects 15-27, or a pharmaceutical composition of aspect 30 to the subject.32. The method of aspect 31 , wherein the metastatic cancer is metastatic breast cancer, metastatic brain cancer, metastatic liver cancer, metastatic colorectal cancer, melaslalic ovarian cancer, metastatic pancreatic cancer, metastatic prostate cancer or metastatic lung cancer.33. The method of aspect 32, wherein the metastatic breast cancer is metastatic triple-negative breast cancer (TNBC).34. The method of aspect 31 , wherein the metastasis is bone metastasis, multi-organ metastasis, lung metastasis, liver metastasis, brain metastasis, heart metastasis or spleen metastasis.35. The method of any one of aspects 31-34, wherein said administering comprises an intravenous, an intracardial, an intramuscular, an intratumoral, or a peritumoral route of administration.36. The method of any one of aspects 31-35, further comprising administering one or more additional therapeutic treatments.37. The method of aspect 36, wherein the additional therapeutic treatments comprise cancer chemotherapy, radialion therapy, surgery or combination thereof.38. A method of identifying a subject as having metastatic cancer or at risk of developing metastasis, the method comprising:determining the presence or absence of pSTS-SATB 1 in a cancer sample from the subject,Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 wherein the presence of pSTS-SATBl indicates that the subject has metastatic cancer or at risk of developing metastasis.39. The method of aspect 38, wherein the determining the presence or absence of pSTS-SATBl in a cancer sample comprises contacting the sample with an antibody that specifically binds to pSTS-SATB1; optionally, wherein the antibody is the antibody of aspect 29.40. The method of aspect 38 or 39, wherein the metastatic cancer is metastatic breast cancer, metastatic brain cancer, metastatic liver cancer, metastatic colorectal cancer, metastatic ovarian cancer, metastatic pancreatic cancer, metastatic prostate cancer or metastatic lung cancer.41. The method of aspect 40, wherein the metastatic breast cancer is metastatic triple-negative breast cancer (TNBC).42. rhe method of aspect 38, wherein the metastasis is bone metastasis, multi-organ metastasis, lung metastasis, liver metastasis, brain metastasis, kidney metastasis or spleen metastasis.43. The method of any one of aspects 38-42, wherein the presence of pSTS-SATB 1 in a sample identifies the subject as a candidate for treatment with any one of aspects 1-14 and 28-29, the composition of any one of aspects 15-27, or a pharmaceutical composition of aspect 30.44. The method of any one of aspects 38-42, further comprising treating the subject identified as having metastatic cancer or at risk of developing metastasis by administering the agent any one of aspects 1-14 and 28-29, the composition of any one of aspects 15-27, or a pharmaceutical composition of aspect 30.EXAMPLES

[0138] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric.

[0139] All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

[0140] The present invention has been described in terms of particular embodiments found or proposed by the present inventor to comprise preferred modes for the practice of the invention. It will be appreciated by those of skill in the art that, in light of the present disclosure, numerous modifications andAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 changes can be made in the particular embodiments exemplified without departing from the intended scope of the invention. For example, due to codon redundancy, changes can be made in the underlying DNA sequence without affecting the protein sequence. Moreover, due to biological functional equivalency considerations, changes can be made in protein structure without affecting the biological action in kind or amount. All such modifications are intended to be included within the scope of the appended claims.1. Introduction

[0141] Among the total SATB 1 protein population, the aggressive tumor-specific SATB 1 subpopulation, pSTS-SATBl, is the crucial determinant for cancer metastasis and this form of SATB1 needs to be targeted to abrogate metastasis. In this experiment, pSTS-SATBl is targeted with the specific antisense oligonucleotides to degrade the SATB1 exon Id variant mRNA to effectively eliminate the generation of pSTS-SATBl to inhibit breast cancer metastasis and tumor growth using mouse models with human breast cancer cell lines and human TNBC PDXs.2. Identification of pSTS-SATBl critical for breast cancer invasion.

[0142] We found that a specific isoform of SATB1 (pSTS-SATBl) is essential for promoting metastasis in cancer. pSTS-S ATB 1 is biochemically distinct from the bulk of SATB 1 proteins expressed in restricted normal cells (c.g. thymocytes, T cells, and cortical neurons). By analyzing SATB1 protein purified from aggressive MDA-MB-231 cells by Mass Spectroscopy, at least 22 different post-translational modifications (PTMs) were identified. We performed site-directed mutagenesis of each PTM site to alanine and constructed mammalian expression plasmids expressing mutant SATB1 harboring 1~3 of these mutations. We studied their effects on non-malignant immortalized breast epithelial cell line MCF10A cells, which normally does not express SATB1. When transduced with wild-type SATB1, these cells acquire highly invasive, metastatic cancer phenotypes1,2. However, we found that SATB1 mutated at all three adjacent serine / threonine (S465, T466, S469; STS) to alanine completely abolished its ability to induce the invasive phenotypes, indicating the critical function of these sites for promoting aggressive cancer characteristics. By raising rabbit monoclonal antibodies against pSTS-SATBl, we found that pSTS-S ATB 1 antibody specifically detects SATB1 in highly aggressive tumor cell lines of multiple epithelial cancers as well as TNBC PDXs (representative cases are shown, FIG. 1A, IB and 1C). In contrast, this pSTS-SATBl antibody does not detect SATB1 in normal cells, such as mouse thymocytes, human leukocytes and brain where SATB1 protein is normally expressed (FIG. ID). By including T47D, an exceptional case of a non-aggressive, ER+breast cancer line that happens to highly express SATB1 (FIG. IB), pSTS-SATBl is absent. This showed that pSTS-SATBl is distinct from bulk SATB1 and correlates with disease severity.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0143] The pSTS-SATBl monoclonal antibody, 4F, was used to generate the data for FIG.l. Similar data was obtained using pSTS-SATB 1 monoclonal antibody, 1 ID and 6B.

[0144] The pSTS-SATB 1 monoclonal antibody is used to monitor the efficacy of the antisense oligo-based therapy. It serves as a diagnostic tool to identify patients who can benefit from the therapy proposed herein.3. Identification of tumor-specific SATB1 exon Id mRNA variant and its link to pSTS-SATBl.

[0145] SATB1 is transcribed from multiple promoters, generating many exon 1 variants (FIG.2A), and active transcription of SATB1 exon Id variant reflects aggressive cancers. This is shown for TNBC cell lines and TNBC PDXs (FIG. 3A, PDX1-6 same as lane 1-6 in FIG. 1C). An ASO (MO-ld), which targets the S ATB 1 mRNA exon 1 variant, having a modification with phosphorodiamidate morpholino (PMO) (also called Vivo-morpholino) was prepared. MO-ld blocks translation of the exon Id mRNA variant by steric hindrance. We found a major reduction of pSTS-SATB 1 levels with MO-ld (24hr treatment), without affecting bulk SATB1 proteins (FIG. 2B, left), accompanied by loss of invasive activity of cancer cells in vitro. Thus, expression of the exon Id variant is linked to pSTS-SA TB1 production.4. Induction of cell death by SATB1 ASOs in vitro and reduction of tumor growth in vivo.

[0146] PMO-ASOs interact minimally with plasma proteins and they are rapidly cleared via urinary excretion39. Thus, we next prepared chemically-modified ASOs with phosphorothioate (PS) linkage and locked nucleic acid (LNA, 2’ -0,4’ -C-methylene -bridged nucleic acid)40,41. PS linkage increases ASO affinity to the plasma proteins and thus increases their uptake into systemic tissues. The LNA ribose modification significantly prolongs tissues’ half-lives through increasing resistance against nucleases42,43. We prepared the LNA-PS ASOs gapmer (LNA-PS gapmer) that consists of a central DNA-based ‘gap’ surrounded by RNA-based (LNA modified) flanking regions that promote target binding. Upon hybridization of LNA-PS gapmers to its target RNA, the resulting RNA-DNA duplex acts as a substrate for RNase Hl, leading to the degradation of the target transcript without inducing overt inflammatory response40. We designed two 16 nucleotide LNA- ASOs (RED1 and RED2 with partially overlap) to target SATB1 exon Id mRNA variant specifically with minimum predicted off-targeting.

[0147] +C*+ T*+G*A!|:A*A!|:C*C!|:A*A!|:G*A!|:A*+C!|:+G!|:+G (SEQ ID NO: 36, “RED1”)

[0148] A*+A*+C*C*A*A*G*A*A*C*G*G*C*+T*+C*+C (SEQ ID NO: 37, “RED2”)

[0149] [phosphorothioate bond (*), LNA-modified (+)]

[0150] These ASOs degrade SATB1 exon Id mRNA variant by the RNase H pathway, and the transcript level of SATB1 exon Id mRNA variant is selectively reduced (FIG.3B). Similar to MO-ld inAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 HOC313, RED2 also reduced pSTS-SATBl in MDA-MB-231 cells (FIG. 2B, right). Testing multiple human cancer types, it is observed that both RED 1 and RED2 individually are highly efficacious in killing these cancer cells in vitro, verified by CellTox™ assay (Promega) in addition to MTT assay (FIG.4).

[0151] We also tested the effect of RED1 on tumor growth at mammary fat pads in vivo by subcutaneously injecting RED1 (up to 2mg / kg / week) in MDA-MB-231 cell-xenografted mice. We used poly(ethyleneimine)-based in vzvo-jetPEI® nanoparticle (Polyplus-transfection®), non-toxic for tumor growth inhibition studies44’56, as a delivery agent, and we observed significant reduction of tumor growth (FIG.5). Mice treated with RED1 showed normal weight and behaviors during experiments, suggesting RED1 is non-toxic. We used RED1 at much lower doses of ASO with in vzvo-jetPEI® (FIG. 5) than others who used only ASO: e.g., ASO for STAT3 (240mg / kg / week) and ASO (KRAS) (500mg / kg / week), both found non-toxic in mice57,58. Thus, the use of in vz'vo-jetPEI® allows for lowering of the amount of ASO required for efficacy.

[0152] We also tested whether RED1 has any inhibitory effects on experimental lung metastasis using MDA-MB-231 cells when cancer cells were injected through tail vein. The RED1 treatment was performed intravenously through tail vein for this experiment. The effect assessed by RT-PCR was dramatic, and we detected very low levels of human-specific house-keeping gene in lungs after treatment compared to control ASO (FIG. 6). This indicated that the majority of tumor cells injected did not survive in lungs. Thus, targeting pSTS-SATBl likely offers a promising, safe and effective approach for treatment of patients with metastatic cancer, offering great advantages over chemotherapies.5. Test efficacy and safety of RED1 and RED2 for prevention and treatment of TNBC metastasis in vivo using mouse model

[0153] With these experimental models, a candidate therapeutic approach is addressed whether our LNA-ASOs can prevent metastasis and potentially treat metastatic cancer. Previously, with a TNBC cell line (MDA-MB-231), we showed that shRNA-mediated SATB 1 knockdown led to loss of metastatic activity and tumor growth activity in xenografted mice1. Here we show inhibition of tumor growth of xenografted MDA-MB-231 cells by subcutaneous injection of RED1 with in vzvo-jetPEI® (FIG. 5). We observed 72% reduction of tumor growth by RED1 with the delivery agent in vzvo-jetPEI®. Our experimental metastasis experiment showed even greater inhibitory effect: RED1 dramatically prevented (by -85%) intravenously injected MDA-MB-231 tumor cells from metastasizing into lungs (FIG.6).

[0154] We identified multiple Welm’s TNBC PDXs for this study based on Western blot (FIG. 1C), RT-PCR for exon 1 variants (FIG. 3A), and patients’ survival information (FIG. 8). Many Welm’s TNBC PDXs with high SATB1 levels are available from Certis Oncology (San Diego). WeAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 selected two representative TNBC PDXs for this study (HCI-001, and HCI-010, lane 2 and lane 1 of FIG. 1C, respectively). These PDXs show high SATBI exon Id transcript and pSTS-SATBl levels, and these PDXs are associated with short patient survival. IICI-001 was collected from primary tumor of a patient and HCI-010 was collected from pleural effusion from a patient who died four years postdiagnosis.

[0155] Our LNA-ASOs have minimal predicted off-targeting: RED1 has one (EPM2AIP1), and RED2 has none.6. Wide targeting applicability of RED-1 and RED-2 for TNBC treatment.

[0156] High SATB 1 protein expression in tumor nuclei tightly correlates with poor prognosis of many tumor types1 13 16,24. Normal breast tissue does not express SATBI protein1, but does uniformly express medium to high levels of SATBI transcription at gene level (as total SATBI transcripts).Normalized transcript counts from normal breast tissue (The Genotype-Tissue Expression project, GTEx) show a range of -2000-3000 reads [22.8 TPM (transcripts per million) mean from OncoDB] while in breast cancer tissues from TCGA, counts varied widely from -80-10,000 (10.6 TPM mean). For 192 TNBC samples from TCGA-BRCA, many TNBCs (169 out of 192) transcribe medium-high total SATBI (>500 counts), of which 122 TNBCs transcribe high total SATBI (>1000 counts).

[0157] The exon Id variant transcript level is tightly associated with high total SATBI transcription levels in TNBCs: 87% of 122 high SATBI (>1000) TNBC case express exon Id variant, whereas only 30.4% of 23 low SATB 1 (<500) TNBCs express this variant at very low levels. In 54 normal healthy tissues (breast, spleen, frontal cortex, whole blood, skin, etc), the SATB exon Id variant was essentially undetectable (from GTEx plot of all transcripts). Initial RNA-seq analysis for Welm’s TNBC samples was only able to identify and measure total SATBI transcripts (gene level)59, not individual transcripts, such as exon 1 variant transcripts. Our initial analysis of the patient survival data from the 34 TNBC PDX’s (Welm Lab) show some concordance between high expression of SATBI (total SATBI transcript) and decreased survival (FIG.8). To further elucidate isoform-specific differences in expression, raw sequencing data was re -processed and analyzed for some PDXs. We have now bioinformatically reanalyzed the data to identify each SATBI transcript variant in five of these TNBC PDXs, of which three retained high levels of total SATBI and the SATBI exon Id variant (FIG.3A). This is consistent with 105 PDXs derived from various other tumor types analyzed at Ccrtis.Importantly, these PDXs with high exon Id levels were preferentially derived from metastatic tumors.7. REDl / RED2-mediated reduction of pSTS-SATBl affects mitosis of aggressive tumor cells as a potential mechanism of tumor cell death.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0158] We found pSTS-SATBl expressed at the highest level in mitotic cells, painting mitotic chromosomes (FIG.7). This feature is similar to topoisomerase II and suggests that tumor cells might depend on pSTS-SATB 1 for mitosis. As a potential mechanism of ASO-induced cell death, pSTS-SATB1 knockdown by ASOs may impair mitosis, thereby inducing tumor cell death.8. REDl / RED2-mediated reduction of tumor growth.

[0159] We further examined the effects of ASOs (RED1 and RED2, compared to control ASO) on tumor cells both in vitro and in vivo. Specifically, we investigated their impact on 1) the growth of breast cancer cells xenografted into the mammary fat pads of mice following intravenous ASO injection, and 2) cell death in triple-negative breast cancer (TNBC) patient-derived xenografts cultured as organoids.

[0160] Our findings indicate that when ASOs mixed with in vzvo-jetPEI were injected via the tail vein (intravenous injection, i.v.), the growth of xenografted MDA-MB-231 cells was effectively blocked by either RED1 or RED2, in contrast to the control ASO under the conditions tested (FIG. 9). Furthermore, intravenous administration of ASOs proved to be more effective than peri-tumoral injection shown in FIG. 5. Also, during experiments, mice treated with RED1, RED2, or control ASO showed normal weight and behaviors.

[0161] The effects of ASOs on TNBC patient-derived xenografts (TNBC-PDX: HCI-010, and HCI-041) were examined using organoids cultured in the presence of Matrigel. These TNBC-PDXs were selected for their highly aggressive properties39. HCI-010 was obtained from pleural effusion from a patient who died four years post-diagnosis; and HCI-041 was collected from a biopsy of a primary tumor before treatment, with the patient dying less than one year after diagnosis. In these two cases, RED1 and RED2 promoted cell death compared to the control ASO (FIGS. 10A and 10B). RED2 had a stronger effect than REDl. IICI-010 was the more sensitive to both RED1 and RED2, with cell death evident at the lowest concentration (125 nM). The CellTox™ Green Cytotoxicity Assay (Promega) was used to measure cell death. The CellTox™ Green Dye binds to the DNA of cells with impaired membrane integrity, a consequence of cell death. Viable cells produce no significant increase in fluorescence, making the fluorescent signal generated by the dye binding to dead-cell DNA proportional to cytotoxicity. This assay continuously monitors cell death in culture for up to approximately 72 hours, but we optimized the technique to extend monitoring to 96 hours, as the doubling time of tumor cells in organoids varied: HCI-010 (4-7 days), and HCI-041 (7-10 days) (based on Star protocol59).

[0162] In general, these results indicate that cell death was induced in TNBC tumor cells in organoids by both RED 1 and RED 2. However, organoids of TNBC-PDXs were less sensitive to ASOs than triple-negative breast cancer cells (e.g. MDA-MB-231) cultured on plastic dishes (2D culture). It isAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 important to consider that ASOs may have limited access to tumor cells within organoids due to the cell morphology and presence of Matrigel. Similarly, CellTox™ Green Dye may not easily penetrate to bind DNA in dead cells for the same reason.

[0163] The potential off-target effects of RED1, RED2, and control ASO were studied using an RNA-seq experiment. In this case, we used parental MCF10A-1 cells, which were utilized for SATB 1 transduction to identify SATBl-target genes. The parental MCF10A-1 cells do not express SATB1 transcripts, making them useful for examining the ASO’s direct effects while avoiding any indirect effects from the knockdown of SATB1 transcripts. The samples tested included 1) PBS treated, 2) RED1, 3) RED2, and 4) control ASO. For each ASO, two concentrations were tested (3 nM and 10 nM). Paired-end sequencing was performed, and the sequencing data were processed and analyzed.

[0164] Raw sequencing data went through quality control steps, using HTStream (vl.0.0, https: / / github.com / s4hts / HTStream) to remove technical features such as Illumina adapters, polyAT sequences, PhiX contamination, and reads less than 21 bp in length. Reads were then aligned to GRCh37 reference genome using STAR aligner ’. Raw counts generated from STAR aligner were normalized using TMM method in edgeR;jl. Differential expression analysis was carried out using limma+voom6263. For differential expression testing, the genomic alignments were restricted to those that map uniquely to the set of known Ensembl IDs. STAR aggregates this subset of mappings on a per gene basis as raw input for the program limmat+voom. False Discovery Rate was controlled using Benjamini-Hochberg procedure Differential expression was analyzed for RED1 vs PBS, RED2 vs PB, and RED2 vs cASO. Genes were filtered based on fold changes (fc >2 or fc < 0.5) and adjusted p-values (<0.05). Either no genes or very few genes (1 to 6) were identified as upregulated by >2 or downregulated by < 0.5 following treatment with either 3 nM or lOnM ASO.These results for mildly affected genes were not consistently reproduced between the 3nM and 10 nM ASO treatments, indicating that no protein-coding genes were identified as off-targeted (FIG. 11). This supports the conclusion that both RED1 and RED2 are specific to SATB1 exon Id variant mRNA.

[0165] FIG. 9. Intravenously injected ASOs mixed with in vzvo-jetPEI inhibited the growth of xenografted tumor cells in the mammary fat pads of mice. This experiment was conducted similarly to that shown in FIG. 5, with the exception of the administration route for the ASOs. In this study, ASOs (RED1, RED2, and control ASO) were administered intravenously through the tail vein (i.v.). The ASOs (50 pg, 2.5 mg / kg / wcck) were mixed with in vzvo-jctPEI (an in vivo delivery agent) for injection following manufacturer’s protocol. On day 10, after MDA-MB-231 cells were injected into the mammary fat pads and when the tumor volume reached 100 mm3, ASO injections (i.v.) were performed on the indicated days. RED1 (n=5), RED2 (n=6), control ASO (n=3). P values were determined using Student's t-test.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252

[0166] FIG. 10. RED1 and RED2 promote cell death in TNBC patient-derived xenografts in organoid culture. TNBC patient-derived xenografts (TNBC-PDX: HCI-041, and HCI-010) were cultured as organoids in the presence of Matrigel, resulting in a "cauliflower-like" cell morphology. The effects of RED1, RED2, and control ASO (cASO) on cell death in TNBC tumor cells within the organoids were measured using the CellTox™ Green Cytotoxicity Assay (Promega). The results are shown for HCI-041 (FIG. 10A) and for HCI-010 (FIG. 10B). The fluorescence signal from the CellTox™ Green Dye, which is proportional to the number of dead cells, was obtained for organoids treated with either RED1 or RED2 and normalized against that of the control ASO. The experiments were conducted in triplicate, and statistical errors were calculated using Excel with Student's t-test (significant p values are indicated). Three concentrations of ASOs were tested (125nM, 250nM, and 500nM) and measurements were taken at 72-hour and 96-hour time points of treatment with each ASO (cASO, RED1 and RED2).

[0167] FIG. 11. RNA-seq analysis to assess off-targets of RED1 and RED2. MCF10A-1 cells were treated with PBS, RED1, RED2, and control ASO, using cither 3 nM or 10 nM for each ASO (Panel A). Each sample was prepared in triplicate, resulting in a total of 21 samples subjected to RNA-seq. Differential gene expression results for genes filtered by fold change (fc > 2 or fc < 0.5) and adjusted p-values (p< 0.05) are shown in FIG. 11, Panel B. The results indicate that no gene was consistently downregulated by either RED1 or RED2 compared to either PBS or control ASO at 3 nM or 10 nM ASO concentration.REFERENCES1. Han, H.J., Russo, J., Kohwi, Y. & Kohwi-Shigematsu, T. SATB 1 reprogrammes gene expression to promote breast tumour growth and metastasis. Nature 452, 187-193 (2008). 2. Ordinario, E., Han, H.J., Furuta, S., Heiser, L.M., Jakkula, L.R., Rodier, F., Spellman, P.T., Campisi, J., Gray, J.W., Bissell, M.J., Kohwi, Y. & Kohwi-Shigematsu, T. ATM suppresses SATB 1-induced malignant progression in breast epithelial cells. PLoS One 7, e51786 (2012).3. Sung, H., Ferlay, J., Siegel, R.L., Laversanne, M., Soerjomataram, I., Jemal, A. & Bray, F.Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. C’A Cancer J Clin 71, 209-249 (2021).4. Bianchini, G., Balko, J.M., Mayer, I. A., Sanders, M.E. & Gianni, L. Triple-negative breast cancer: challenges and opportunities of a heterogeneous disease. Nature reviews. Clinical oncology 13, 674-690 (2016).5. Al-Mahmood, S., Sapiezynski, J., Garbuzenko, O.B. & Minko, T. Metastatic and triplenegative breast cancer: challenges and treatment options. Drug Deliv Transl Res 8, 1483-1507 (2018).6. Yin, L., Duan, J.-.J., Bian, X.-W. & Yu, S.-C. Triple-negative breast cancer molecular subtyping and treatment progress. Breast cancer research : BCR 22, 61-61 (2020).7. 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[0168] While the present invenlion has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be subsliluied without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

Claims

Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 ClaimsWhat is claimed is:

1. An agent that binds to pSTS-S ATB 1 or an agent that binds to SATB1 exon Id variant mRNA in a cancer cell.

2. The agent of claim 1, wherein the agent that binds to pSTS-S ATB 1 is a polypeptide and the agent that binds to SATB1 exon Id variant mRNA is a nucleic acid.

3. The agent of claim 2, wherein the nucleic acid binds to exon Id region of the SATB1 exon Id variant mRNA and is an antisense oligonucleotide (ASO), a short interfering (siRNA) or a microRNA (miRNA).

4. The agent of claim 3, wherein the nucleic acid is a locked nucleic acid (LNA) comprising one or more LNA monomers.

5. The agent of claim 3 or 4, wherein the nucleic acid comprises one or more phosphorothioate (PS) linkages.

6. The agent of claim 4 or 5, wherein the nucleic acid comprises one or more LNA monomers and one or more phosphorothioate (PS) linkages.

7. The agent of any one of claims 3-6, wherein the nucleic acid is a gapmer comprising a central single stranded DNA sequence flanked by RNA sequences.

8. The agent of claim 7, wherein the RNA sequences comprise one or more LNA monomers.

9. The agent of claim 8, wherein the LNA comprises 2’ -0,4’ -C-methylene -bridged LNA monomers.

10. The agent of claim 3, wherein the nucleic acid is a morpholino oligonucleotide.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 11. The agent of any one of claims 3-10, wherein the nucleic acid comprises a nucleotide sequence at least 85%, at least 90%, at least 95%, at least 99% identical, or 100% identical to a nucleotide sequence selected from SEQ ID NO: 1-6, 36, and 37.

12. The agent of any one of claims 1-11, wherein the nucleic has a length of from about 8 nucleotides to about 30 nucleotides.

13. The agent of claim 12, wherein nucleic acid comprises the nucleotide sequence of SEQ ID NO:1, 2, 3, 4, 5, 6, 36, or 37 and has a length of up to 30 nucleotides.

14. The agent of claim 13, wherein the nucleic acid has a length of about 11-26 or 15-26 nucleotides.

15. A composition comprising two or more nucleic acids having different sequences that each bind to exon Id region of a SATB1 exon Id variant mRNA.

16. The composition of claim 15, wherein the two or more nucleic acids are selected from an antisense oligonucleotide (ASO), a short interfering (siRNA) or a microRNA (miRNA).

17. The composition of claim 15 or 16, wherein at least one nucleic acid is a locked nucleic acid (LNA) comprising one or more LNA monomers.

18. The composition of any one of claims 15-17, wherein at least one nucleic acid comprises one or more phosphorothioate (PS) linkages.

19. The composition of any one of claims 15-18, wherein at least one nucleic acid comprises one or more LNA monomers and one or more phosphorothioate (PS) linkages.

20. The composition of any one of claims 15-19, wherein at least one nucleic acid is a gapmer comprising a central single stranded DNA sequence flanked by RNA sequences.

21. The composition of claim 20, wherein the RNA sequences comprise one or more LNA monomers.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 22. The composition of claim 21, wherein the LNA comprises 2’-O,4’-C-methylene-bridged LNA monomers.

23. The composition of any one of claims 15-20, wherein at least one nucleic acid is a morpholino oligonucleotide.

24. The composition of any one of claims 15-23, wherein the two or more nucleic acids have a length of from about 8 nucleotides to about 30 nucleotides.

25. The composition of any one of claims 15-23, wherein the two or more nucleic acids have a length of from about 15 -26 nucleotides.

26. The composition of any one of claims 15-25, wherein a first nucleic acid comprises a nucleotide sequence at least 85%, at least 90%, at least 95%, at least 99% identical, or 100% identical to the nucleotide sequence of SEQ ID NO:36 and a second nucleic acid comprises a nucleotide sequence at least 85%, at least 90%, at least 95%, at least 99% identical, or 100% identical to the nucleotide sequence of SEQ ID NO:37.

27. The composition of any one of claims 15-26, further comprising a pharmaceutically acceptable excipient.

28. The agent of claim 2, wherein the polypeptide is an anti-pSTS-SATB 1 antibody.

29. The agent of claim 28, wherein the anti-pSTS-SATB 1 antibody comprises a variable heavy (VH) chain comprising heavy chain complementarity determining regions (HCDRs) and a variable light (VL) chain comprising light chain complementarity determining regions (LCDRs) from the VH and VL chains, respectively, of an anti-pSTS-SATB 1 antibody comprising one of the following pairs of VH and VL chains:=> VH-4F:METGLRWLLLVAVLKGVQCQSLEESGGDLVKPGASLTLTCTASGFSFSSGYDMCWVR QAPGKGLELIACIYVGSSVTTWYASWAKGRFTISKTSSTTVTLQMTSLTAADTATYFC ARYPYGSSNGGGYFNL (SEQ ID NO: 12); and-> VL-4F:MDTRAPTQLLGLLLLWLPGARCADIVMTQTPASVEAAVGGTVTINCQASENIYSNLA WYQQKPGQRPKLLIYTASTLASGVPSRFKGSGSGTQFTLTISGVQCDDAATYYCQQGI SRTNADNV (SEQ ID NO: 13); orAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 ■=> VH-6B:METGLRWLLLVAVLKGVQCQSLEESGGDLVKPGASLTLTCTASGFSFSSGYDMCWVR QAPGKGLELIACIYAGSSVTTWYASWAKGRFTISKTSSTTVTLQMTSLTAADTATYFC ARYPYGSSNGGGYFNL (SEQ ID NO: 14); andV VL-6B:MDTRAPTQLLGLLLLWLPGARCADIVMTQTPASVEAAVGGTVTIKCQASQNISSYLSW YQQKPGQRPKLLIYTASTLASGVPSRFKGSGSGTQFTLTISGVQCDDAATYYCQQGISR TNADNV (SEQ ID NO: 15); or= VH-11D:METGLRWLLLVAVLKGVQCQSLEESGGDLVKPGASLTLTCTASGFSFSSTYWICWVR QAPGKGLEWIACIYGGSSGSIYYASWAKGRFTISKTSSTTVTLQMTSLTVADTATYFCA DSTASTYGYAFNL(SEQ ID NO: 16); andA VL-11D:MDTRAPTQLLGLLLLWLPGATFAQVLTQTPSPVSAAVGGTVTISCQSSKNVYNNNYLS WFQQKPGQPPKLLIYRASNLASGVPSRFKGSGSGTQFTLTISEVQCDDAATYYCQGYY SGYIWA (SEQ ID NO: 17),optionally, the anti-pSTS-S ATB 1 antibody further comprising a VH and a VL chain each having at least 90%, at least 95%, or at least 99% amino acid sequence identity to the VH and VL chain, respectively, of one of the above-listed antibodies.

30. A pharmaceutical composition comprising:a) the agent of any one of claims 1-14 and 28-29 or the composition of any one of claims 15-27; andb) a pharmaceutically acceptable excipient.

31. A method for treating metastatic cancer or preventing metastasis in a subject in need thereof, comprising:administering an effective amount of the agent of any one of claims 1-14 and 28-29, the composition of any one of claims 15-27, or a pharmaceutical composition of claim 30 to the subject.

32. The method of claim 31 , wherein the metastatic cancer is metastatic breast cancer, metastatic brain cancer, metastatic liver cancer, metastatic colorectal cancer, metastatic ovarian cancer, metastatic pancreatic cancer, metastatic prostate cancer or metastatic lung cancer.

33. The method of claim 32, wherein the metastatic breast cancer is metastatic triplenegative breast cancer (TNBC).

34. The method of claim 31 , wherein the metastasis is bone metastasis, multi-organ metastasis, lung metastasis, liver metastasis, brain metastasis, heart metastasis or spleen metastasis.Atty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 35. The method of any one of claims 31-34, wherein said administering comprises an intravenous, an intracardial, an intramuscular, an intratumoral, or a peritumoral route of administration.

36. The method of any one of claims 31-35, further comprising administering one or more additional therapeutic treatments.

37. The method of claim 36, wherein the additional therapeutic treatments comprise cancer chemotherapy, radiation therapy, surgery or combination thereof.

38. A method of identifying a subject as having metastatic cancer or at risk of developing metastasis, the method comprising:determining the presence or absence of pSTS-SATBl in a cancer sample from the subject, wherein the presence of pSTS-SATB 1 indicates that the subject has metastatic cancer or at risk of developing metastasis.

39. The method of claim 38, wherein the determining the presence or absence of pSTS-SATB 1 in a cancer sample comprises contacting the sample with an antibody that specifically binds to pSTS-SATB 1 ; optionally, wherein the antibody is the antibody of claim 29.

40. The method of claim 38 or 39, wherein the metastatic cancer is metastatic breast cancer, metastatic brain cancer, metastatic liver cancer, metastatic colorectal cancer, metastatic ovarian cancer, metastatic pancreatic cancer, metastatic prostate cancer or metastatic lung cancer.

41. The method of claim 40, wherein the metastatic breast cancer is metastatic triplenegative breast cancer (TNBC).

42. The method of claim 38, wherein the metastasis is bone metastasis, multi-organ metastasis, lung metastasis, liver metastasis, brain metastasis, kidney metastasis or spleen metastasis.

43. The method of any one of claims 38-42, wherein the presence of pSTS-SATBl in a sample identifies the subject as a candidate for treatment with any one of claims 1-14 and 28-29, the composition of any one of claims 15-27, or a pharmaceutical composition of claim 30.

44. The method of any one of claims 38-42, further comprising treating the subject identified as having metastatic cancer or at risk of developing metastasis by administering the agentAtty. Dkt: UCSF-659WO Client Ref.: SF-2021-252 any one of claims 1-14 and 28-29, the composition of any one of claims 15-27, or a pharmaceutical composition of claim 30.

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