MicroRNAs 206 and 21 cooperate to promote RAS-extracellular signal-regulated kinase signaling by suppressing the translation of RASA1 and SPRED1

The present invention provides a method for inhibiting the RAS-ERK pathway by upregulation of RASA1 and SPRED1 mRNAs in tumor cells by anti-miR treatment. The method includes wherein an anti-miR-206 binds to a nucleotide comprising the sequence UAGCUUAUCAGACU (SEQ ID NO: 21), or to a nucleotide comprising the sequence UGGAAUGUAAGGAAGUGUGUGG (SEQ ID NO: 9). A method of re-expression of RAS-ERK pathway inhibitory proteins in triple negative cancer cells by administering to a patient having cancer an effective amount of an antagonist of KLF4-dependent microRNAs.

SEQUENCE LISTING

Following the Abstract Of The Disclosure is set forth a paper copy of the SEQUENCE LISTING in written form (.PDF format) having SEQ ID NO:1 through SEQ ID NO: 49. The paper copy of the SEQUENCE LISTING is incorporated by reference into this application. A SEQUENCE LISTING in computer-readable form (.txt file) also accompanies this application with A Statement Of Identity Of Computer Readable Form and Written Sequence Listing.

BACKGROUND OF THE INVENTION

1. Field of the Invention

In triple-negative breast cancer (TNBC) there is recurrent genetic alteration of pathway components. Using shRNA methods, we observed that the zinc finger transcription factor Kruppel-like factor 4 (KLF4) can promote RAS-ERK signaling in TNBC cells. Endogenous KLF4 bound to the promoter regions and promoted the expression of two microRNAs (miRs), miR-206 and miR-21 (miR-206/21). Antisense-mediated knockdown (anti-miR) revealed that miR-206/21 coordinately promote RAS-ERK signaling and the corresponding cell phenotypes by inhibiting translation of the pathway suppressors RASA1 and SPRED1. The present invention identifies RASA1 and SPRED1 mRNAs as latent RAS-ERK pathway suppressors that can be upregulated in tumor cells by anti-miR treatment. Consequently, KLF4-regulated miRs are important for the maintenance of RAS-ERK pathway activity in TNBC cells. The present invention provides a method of treating a patient having cancer comprising providing an upregulation of RASA1 and SPRED1 by anti-microRNA (anti-miR) treatment. The pronounced inhibitory effect of anti-miR-206/21 on the level of activated ERK 1/2 identifies the enhanced translation of RASA1 and SPRED1 as an attractive therapeutic modality. Further, this invention provides suppression of KLF4 or the anti-sense mediated silencing of miR-206 and/or miR-21 to be used in combination with MEK inhibitors or other pathway antagonists to attenuate drug resistance in cancer patients.

2. Background of the Invention

In comparison to simpler organisms, the evolution of metazoans required adaptations for the proper regulation of cell fate (1). One such adaptation is the mitogen-activated protein kinase (MAPK) pathway composed of RAS, RAF, MEK, and ERK, which regulates a variety of cell physiologic processes (2-9). Diverse stimuli including growth factors, interaction with extracellular components, and cell stress can signal through receptor tyrosine kinases (RTKs), integrins, or ion channels to regulate signaling through the RAS GTPases. GTP-bound RAS (RAS-GTP) can activate MAP3Ks (i.e., the RAF family of protein kinases), leading to sequential phosphorylation and activation of MAP2Ks (i.e., MEK 1/2) and the extracellular signal-regulated kinases (ERK 1/2).

Inhibitory proteins play important roles in RAS-ERK pathway regulation. These include the RAS p21 protein activator (GTPase activating protein [GAP]) 1 (RASA1), the GAP neurofibromin 1 (NF1), the sprouty homologs SPRY1 and SPRY2, and the sprouty-related, EVH1 domain containing (SPRED) proteins, SPRED1 and SPRED2 (10-12). SPRED1 associates with NF1 to mediate its membrane localization, implicating GAP activity as a shared molecular mechanism among pathway inhibitory proteins (13). Congenital disorders that deregulate this kinase cascade include Neurofibromatosis type I, Legius syndrome, Noonan syndrome, Costello syndrome, and cardiofaciocutaneous syndrome (8,9,14-16).

In addition, somatic alteration of this pathway is critical for the initiation and progression of a variety of cancers. Activating point mutation of RAS genes or BRAF occur in approximately 15-30% and 7% of all human cancers, respectively (3,17-20). In human breast cancer, point mutation of these genes is rare, but activated ERK 1/2 levels are frequently elevated and contribute to the aggressive behavior of cancer cells (21,22).

RAS-ERK pathway activity appears particularly critical in triple-negative breast cancers (TNBCs), tumors that are deficient in estrogen receptor (ER) a, HER2, and progesterone receptor (23,24). This group of clinically aggressive tumors overlaps extensively with the basal-like and claudin-low molecular subtypes (25). Genomic analysis of human basal-like breast tumors indicates frequent copy number gain of KRAS (32%) and BRAF (30%), and reduced gene copy number for pathway inhibitors such as RASA1 and DUSP4 (26-31). For RASA1, the correlation of mRNA levels, genomic copy number and clinical outcome supports a functional role in TNBC (29). Consistent with these results, basal-like breast tumors have a high RAS-ERK pathway activity signature (24,30). Despite this insight, therapeutic targeting of the pathway is hindered by cellular mechanisms of escape, including dynamic reprogramming of the kinome and PI 3-kinase activation, and improved strategies for inhibiting the pathway are needed (32,33).

The zinc-finger transcription factor Kruppel-like factor 4 (KLF4) is a pluripotency factor that functions in tumors in a context-dependent fashion, capable of exerting both pro-tumorigenic and anti-tumorigenic effects (34-36). Supporting a tumor suppressor role, its expression is reduced during development of tumors such as colorectal cancer, and endogenous Klf4 suppresses tumorigenesis in the ApcMinmouse model (37). In normal cells, KLF4 is often induced in response to cell stress or wounding, and protumorigenic influences may reflect its role in the stress response (38-46). Loss- or gain-of-function studies show that KLF4 can promote malignant properties, including epithelial transformation in vitro, escape from RAS-induced senescence, enhanced cell survival following γ-radiation-induced DNA damage, increased tumorigenicity of colorectal cancer stem cell-enriched spheroid cells, and skin tumor initiation in transgenic mice (43,47-50).

In human breast cancers, there is typically higher expression of KLF4 in tumor cells compared with the adjacent, uninvolved epithelium. This elevated protein level, or else demethylation of the KLF4 promoter, portends a poor prognosis (51-54). We previously identified microRNA (miR)-206 as a potential downstream effector of KLF4 that, in turn, directly regulates KLF4 translation, constituting a feedback loop (55). miRs associate with the RNA-induced silencing complex (RISC) to regulate the translation of cognate mRNAs. miR deregulation occurs in multiple cancer types and can promote or inhibit tumorigenesis (56-58).

SUMMARY OF THE INVENTION

The present invention provides a method of treating a patient having cancer comprising transfecting cancerous cells in vitro with either anti-miR-206, or anti-miR-21, or both said anti-miR-206 and said anti-miR-21, and injecting a therapeutically effective amount of the transfected cells into a tumor of the patient, and achieving an upregulation of RASA1 and SPRED1 for treating the cancer of the patient. Preferably, this method includes wherein the cancer is a triple negative breast cancer. In another embodiment of this method, as described herein, the injection is an orthotopic injection. Another embodiment of this method of this invention, as described herein, further includes administering a therapeutically effective amount of one or more of a MEK inhibitor or one or more of an antagonist of a RAS-ERK pathway.

Another embodiment of this invention provides a method of treating a patient having cancer comprising crippling the expression of micro RNA-206 and micro RNA-21.

Another embodiment of this invention provides a method of treating a patient having breast cancer by administering to the patient a therapeutically effective amount of an anti-microRNA 206 and a therapeutically effective amount of an anti-microRNA 21.

Another embodiment of this invention includes a compound comprising an antagonist of KLF4 dependent microRNAs.

Another embodiment of this invention includes a compound comprising transcripts of RASA1 and SPRED1.

Another embodiment of this invention includes a compound comprising anti-microRNA 206 knockdown and anti-microRNA 21 knockdown.

Another embodiment of this invention provides the method, as described herein, wherein the anti-miR-206 is capable of binding to (binds to) a nucleotide comprising the sequence

Another embodiment of this invention provides the method, as described herein, wherein the anti-miR-206 is capable of binding to (binds to) a nucleotide comprising the sequence

DETAILED DESCRIPTION OF THE INVENTION

As used herein, the term “patient” includes any member of the animal kingdom, including but not limited tohomo sapiens.

As used herein, the term “an effective amount” or “a therapeutically effective amount” refers to that amount of a substance that is needed to bring about a desired result, such as for example that amount of a substance that is needed to treat a patient having a disease.

The natural progression of breast cancer, HER2-enriched specifically, can be difficult to determine. Furthermore, drug resistance is nearly inevitable for the current selected therapies towards this disease. Gaining a better understanding of the intrinsic nature of a patient's tumor will help direct future treatments and inform, likely clinical outcome. Scientifically, characterizing what makes an aggressive tumor more lethal will also provide insight to tumor biology and potential drug targets. Molecular markers are attractive solutions to these problems, as they provide critical information towards the nature of the cancer, ultimately providing the physician and the patients with a more tailored approach to their disease.

The expression, of KLF4 and KLF5 in HER2-enriched breast cancer substantially stratifies the risk for distant metastasis. Patients with tumors that have lower than median expression of both KLF4 and KLF5 exhibit prolonged distant metastasis free survival (DMFS). In fact, in this cohort no deaths were seen after −5 years. This would suggest that patients with this expression profile may be essentially cured if they survived past the fives post diagnosis. Likewise, patients with tumors that exhibit higher than median expression of both KLF4 and KLF5 have dramatically reduced DMFS and poor clinical outcome.

Using KLF4 and KLF5 as predictive markers may aid in the treatment of individuals with HER2-enriched breast cancer. If a patient were to have elevated levels of both these genes, then a physician may opt for a more aggressive treatment course due to the increased likelihood of developing distant metastasis. On the other hand, if patients were to have tumors with less KLF4 and KLF5, doctors may opt for a more conservative treatment regime thus sparing the patient money and the potential burdens of medical intervention. Furthermore, if a patient lived 5 years past their initial diagnosis with this molecular profile, this assay would provide the information to them that they may be cured.

We have also characterized the relationship between KLF4 and microRNAs (miRs)-206 and -21, downstream effectors of KLF4's functions. MicroRNAs are short, non-coding RNAs which regulate gene expression by impacting RNA translation or stability. Inhibition of these microRNAs perturbs many of the pro-tumorigenic functions KLF4 exerts, thus improving a patients length of survival.

We have evidence that KLF4 can promote drug resistance, likely through its prosurvival signals mediated by miRs. The miRs target two pathways by which HER2 and related receptor tyrosine kinases (RTKs) promote tumorigenesis in breast cancer, for example, HER2-PI3K-AKT and EGFR-RAS-RAF-MEK-ERK.

Current technology focuses on traditional molecular markers such as HER2 amplification and ER status. While these genes certainly are useful for prognosis, many times two tumors which contain the same HER2 and ER profile can progress quite differently. Therefore, for clinical decision making (e.g., radiotherapy, aggressive chemotherapy) there is a need for additional markers to further describe these tumors, as well as their likely clinical progression. KLF4 and KLF5 have been shown to stratify' a patient's DMFS interval, with lower than median expression of both genes correlating with prolonged DMFS and positive patient outcome. Likewise, tumors with higher than median expression of KLF4 and KLF5 are associated with reduced DMFS and an aggressive clinical course. The expression of these two factors has several clinical applications: Oncotype Dx, a current test available clinically, only is applicable for HER2 negative, ER positive, node-negative patients. Another available molecular test, Mammoprint only has limited utility in the HER2-enriched group and is not clinically justified. KLF4 and KLF5 levels in HER2-enriched tumors provide prognostic information to the length of DMFS independent of ER status, thus informing the physician and patient on the likely progression of their disease where a current test could not. Furthermore, the expression of KLF4 and KLF5 may enhance the prognostic capabilities for the Mammoprint test, making said analysis clinically applicable. If a physician has better understanding of the likely progression of the disease, he/she would be better able to optimize a patient's treatment regimen (i.e a more aggressive treatment course for tumors likely to reoccur distally). If a patient has a better understanding of the likely progression of their disease, it will better able them to mentally prepare for the future. Furthermore, if a patient's tumor expresses low levels of KJLF4 and KLF5 and they survive 5 years post diagnosis, current data suggests that their risk for distal reoccurrence is negligible, providing rational to curtail excessive scans and check ups as well as peace of mind. This last factor, peace of mind, would factor greatly into future clinical application and commercial usefulness. It is possible therapeutic inhibition of KLF4 and KLF5 in tumors which highly express the two genes results in dramatically prolonged DMFS. This may be accomplished by inhibiting downstream targets of the KLFs (eg. microRNA-206, microRNA-21) thus abrogating many of KLF4's protumorigenic functions. The present invention provides the use of miR-206 antagonists to sensitize tumor cells to HER2 inhibitors such as Flerceptin or lapatinib, both of which are clinically approved already, but for which initial response rates appears similar to 30% and development of resistance is nearly inevitable.

If the expression of KLF4 and KLF5 can improve prognostic capabilities in prospective studies, the clinical application can almost be immediate. Therefore, the observation of KLF4, KLF5 and DMFS may be linked to initial response to these treatments, as well as the interval of time required for the development of resistance. Furthermore, it is possible that the downstream effectors of KLF4 (miR-206 and miR-21) contribute to acquired resistance given their importance in Ras-Erk signaling, one of the main pathways HER2 signaling goes through. Therefore, therapeutic inhibition of these miRs may disrupt Ras-Erk signaling and reduce the development of resistance.

In the short term, patients will want to know if they have the “safe” form of HER2+ cancers and clinicians would use the prognostic risk in deciding if more aggressive therapy is warranted.

Despite the low prevalence of activating point mutation of RAS or RAF genes, the RAS-ERK pathway is implicated in breast cancer pathogenesis. Indeed, in triple-negative breast cancer (TNBC) there is recurrent genetic alteration of pathway components. Using shRNA methods, we observed that the zinc finger transcription factor Kruppel-like factor 4 (KLF4) can promote RAS-ERK signaling in TNBC cells. Endogenous KLF4 bound to the promoter regions and promoted the expression of two microRNAs (miRs), miR-206 and miR-21 (miR-206/21). Antisense-mediated knockdown (anti-miR) revealed that miR-206/21 coordinately promote RAS-ERK signaling and the corresponding cell phenotypes by inhibiting translation of the pathway suppressors RASA1 and SPRED1. In TNBC cells, including cells with mutation of RAS, the suppression of either RASA1 or SPRED1 increased the levels of GTP-bound, wild-type RAS and activated ERK 1/2. Unlike the control cells, treatment of RASA1- or SPRED1-suppressed cells with anti-miR-206/21 had little or no impact on the level of activated ERK 1/2 or on cell proliferation, and failed to suppress tumor initiation. These results identify RASA1 and SPRED1 mRNAs as latent RAS-ERK pathway suppressors that can be upregulated in tumor cells by anti-miR treatment. Consequently, KLF4-regulated miRs are important for the maintenance of RAS-ERK pathway activity in TNBC cells.

In this invention, we suppressed KLF4 in TNBC cells and observed a decrease in miR-206 levels, attributed to the reduced association of KLF4 with a MIR206 promoter-proximal consensus site. Pathway analysis of putative miR-206 regulated genes identified this miR as a likely regulator of MAPK signaling, and in KLF4-deficient cells we observed marked downregulation of activated ERK 1/2 regardless of the RAS mutational status. As miRs can function in a combinatorial fashion, we sought additional miR effectors of KLF4 signaling to RAS-ERK. The protumorigenic miR-21 is upregulated in breast cancer and was previously validated to target RAS-ERK pathway inhibitory proteins (59-65). Furthermore, pathway enrichment identified MAPK signaling as likely to be co-targeted by miR-206 and miR-21 (miR-206/21). We subsequently observed reduced levels of miR-21 in KLF4-deficient cells, attributed to a direct interaction of KLF4 with the MIR21 promoter. These results identified a pathway by which a pluripotency factor can signal through two distinct miRs to impact RAS-ERK signaling.

The loss of activated ERK 1/2 upon KLF4 depletion corresponded to a decrease in the level of GTP-bound wild-type (WT) RAS, and we found that miR-206 and miR-21 co-target both RASA1 and SPRED1 to repress their translation. Although each miR alone had only modest effects on the level of activated ERK 1/2, simultaneous inhibition of both miRs led to marked downregulation of activated ERK 1/2, similarly as observed for KLF4-deficient cells. In RAS-WT and RAS-mutant cells alike, depletion of either RASA1 or SPRED1 promoted RAS-ERK pathway activity by modulating the levels of WT RAS-GTP. Knockdown of either RASA1 or SPRED1 conferred resistance to antisense miR (anti-miR) mediated inhibition of RAS-ERK signaling and promoted in vivo tumor initiation. These studies identify miR-206/21 as protumorigenic outputs of KLF4 signaling in TNBC cells, identify RASA1 and SPRED1 transcripts as latent RAS-ERK suppressors, and point to antagonists of KLF4-dependent miRs as potential agents for the therapeutic re-expression of RAS-ERK pathway inhibitory proteins.

The present invention provides a method of treating a patient having cancer comprising transfecting cancerous cells in vitro with either anti-miR-206, or anti-miR-21, or both said anti-miR-206 and said anti-miR-21, and injecting a therapeutically effective amount of the transfected cells into a tumor of the patient, and achieving an upregulation of RASA1 and SPRED1 for treating the cancer of the patient. Preferably, this method includes wherein the cancer is a triple negative breast cancer. In another embodiment of this method, as described herein, the injection is an orthotopic injection. Another embodiment of this method of this invention, as described herein, further includes administering a therapeutically effective amount of one or more of a MEK inhibitor or one or more of an antagonist of a RAS-ERK pathway. Another embodiment of this invention provides a method of treating a patient having cancer comprising crippling the expression of micro RNA-206 and micro RNA-21.

Another embodiment of this invention provides a method of treating a patient having breast cancer by administering to the patient a therapeutically effective amount of an anti-microRNA 206 and a therapeutically effective amount of an anti-microRNA 21.

Another embodiment of this invention includes a compound comprising an antagonist of KLF4 dependent microRNAs.

Another embodiment of this invention includes a compound comprising transcripts of RASA1 and SPRED1.

Another embodiment of this invention includes a compound comprising anti-microRNA 206 knockdown and anti-microRNA 21 knockdown.

Another embodiment of this invention provides a method for treating a patient having breast cancer comprising providing for the therapeutic re-expression of RAS-extracellular signal-regulated kinase signaling pathway inhibitory proteins.

Another embodiment of this invention provides the method, as described herein, wherein the anti-miR-206 is capable of binding to (binds to) a nucleotide comprising the sequence

Another embodiment of this invention provides the method, as described herein, wherein the anti-miR-206 is capable of binding to (binds to) a nucleotide comprising the sequence

Materials and Methods

Cell Lines, Cell Culture, and Drug Treatments.

MDA-MB-231, HCC1143, HCC1937, MDA-MB-468, and Hs578t breast cancer cell lines were obtained from ATCC. MCF10A and MCF10AT cells were provided by Steven M. Frisch (West Virginia University). SUM159PT cells were provided by Gary L. Johnson (University of North Carolina at Chapel Hill) and M6 cells were provided by Jeffrey E. Green (National Cancer Institute). MDA-MB-231 and M6 cells were cultured in DMEM supplemented with 10% (v/v) FBS. HCC1143 cells were cultured in RPMI-1640 supplemented with 10% FBS. Hs578t cells were cultured in DMEM supplemented with 5 μg/ml insulin and 10% FBS. HCC1937 and MDA-MB-468 cells were cultured in RPMI-1640 supplemented with 5 μg/ml insulin and 10% FBS. SUM159PT cells were cultured in 50:50 DMEM/F12 supplemented with 5 μg/ml insulin, 1 μg/ml hydrocortisone, and 5% horse serum. MCF10A and MCF10AT cells were cultured in 50:50 DMEM/F12 supplemented with 10 μg/ml insulin, 0.5 μg/ml hydrocortisone, 20 ng/ml EGF, 100 ng/ml cholera toxin, and 5% horse serum. Cell culture media was also supplemented with penicillin and streptomycin. 4-hydroxytamoxifen (4-OHT) was dissolved in ethanol and used at 0.3 μM. U0126 (Sigma) was dissolved in DMSO and used at 20 μM. 5-aza-2′-deoxycytidine/decitabine (AZA; Selleck Chemicals) and trichostatin A (TSA; Selleck Chemicals) were dissolved in DMSO and used at 10 μM and 400 nM respectively. Subconfluent cell cultures were treated with AZA for 96 hours or TSA for 12 hours. For the AZA treatment, the drug containing media was replenished every 24 hours.

pMIR-REPORT firefly luciferase (luc) vector was purchased from Ambion/Invitrogen. pRL-TKRenillaluc reporter was obtained from Promega (Madison, Wis.). cDNA clones containing full length RASA1 (clone ID BC033015) and a 1.2 kb fragment of the 3′ untranslated region (3′ UTR) of SPRED1 (clone ID BG167687) were purchased from Open Biosystems. To construct a WT RASA1 translational reporter, a 926 by fragment of the RASA1 3′ UTR region was generated by sequential treatment with BamHI, Klenow fragment, and XbaI. This fragment was inserted into pMIR-REPORT vector that was prepared by sequential treatment with HindIII, Klenow fragment, and SpeI. To construct a WT SPRED1 reporter containing the putative miR-206 binding site, the 1.2 kb SPRED1 3′ UTR from clone BG167687 was excised by treatment with MluI and inserted into the same site of pMIR-REPORT. Finally, a 744 by fragment of the SPRED1 3′ UTR containing two putative miR-21 binding sites was amplified by PCR from MDA-MB-231 cDNA using the oligonucleotides 5′-cccacgcgtTGAAAAACTGTTTAACTCATGT-3′ (SEQ ID NO: 27) and 5′-cccacgcgtTGAAAAACCTGTAAATAAGCAC-3′ (SEQ ID NO: 28) (SPRED1 sequence indicated in uppercase). Following MluI digestion, the product was cloned into the same site of pMIR-REPORT vector.

Transient Transfection and Translational Reporter Assays.

Anti-miR inhibitors (AM) and miR-mimics (PM) were obtained from Ambion/Invitrogen including, hsa-miR-206 (AM10409, PM10409), hsa-miR-21-5p (AM17000, PM17100), AM Negative Control #1 (AM17010), and PM Negative Control #1 (AM17110). Inhibitors and mimics were diluted to 20 μM in nuclease free water and where indicated, transfected either singly or in combination into cells at a final total concentration of 25 nM. Where two miR reagents were cotransfected, the final concentration was 12.5 nM each. For analysis of endogenous protein or miR levels, two sequential transfections were performed. Cells were subjected to reverse transfection and, 24 hours later, forward transfection was performed as described (55). At 24 hours after the start of the forward transfection, cell extracts were prepared for expression studies, or cells were used for phenotypic studies. Translational reporter assays were performed after only a single transfection, and extracts were prepared at 24 hours after the start of the reverse transfection. Inhibitors or mimics were cotransfected with reporter plasmids, including the pRL-TK control, and Dual-Luciferase® Reporter Assays (DLR Assay, Promega) were performed as described (55).

Cells were plated for the respective assay at 24 hours following the final transfection with AM or PM. To measure cell proliferation, 1×103cells/well were transferred to 96-well plates and cultured for the indicated interval. Cell proliferation was determined using the ATPlite Luminescence ATP Detection Assay System (PerkinElmer). Cell number was calculated by constructing a standard curve and correlating cell number with the luminescence signal. In parallel, 2D cell viability was measured by trypan blue exclusion.

For transwell migration assays, 1×104cells were plated in the top chamber using growth medium containing 0.5% FBS (24 well plates, pore size, 8 μm; BD Biosciences). Growth medium containing 10% FBS was used as chemoattractant in the lower chamber. After 24 hours, cells on the lower surface of the membrane were stained using the Diff-Quik™ Stain Set (Siemens) and counted.

To quantitate cell death (anoikis), 1×105cells/well in DMEM complete growth medium containing 1% (w/v) methylcellulose were added to a 6-well Ultra-Low Attachment Cluster Dish (Costar). After 24 hours in suspension, the cells were washed twice with PBS and suspended in 200 μL of AccuMax (Innovative Cell Tech). Cell death was measured by trypan blue exclusion. Alternatively, suspended cells were analyzed for cell death by flow cytometry.

Flow cytometric analysis of apoptosis was performed using Alexa Flour® 488 Annexin V/Dead Cell Apoptosis Kit (Invitrogen). Samples were analyzed on a BD Fortessa flow cytometer using BD FACSDiva 7.0 software (BD Biosciences). 10,000 events were collected per sample. Data analysis was performed using FCS Express 4 Research Edition software (De Novo Software).

Immunoblot Analysis and Antibodies.

Affinity precipitation of active RAS (RAS-GTP) utilized the RAS Assay Reagent, a GST-fusion protein corresponding to the RBD (residues 1-149) of Raf-1 (Millipore). For analysis of RAS-GTP levels, cells were fed with complete growth medium 18-24 hours prior to protein extraction. Cells were washed twice in PBS and then lysed in ice-cold magnesium-containing lysis buffer (MLB; 25 mM HEPES, pH 7.5, 150 mM NaCl, 1% Igepal CA-630, 0.25% sodium deoxycholate, 10% glycerol, 10 mM MgCl2, 1 mM EDTA, 25 mM NaF, 1 mM sodium orthovanadate, 10 μg/ml leupeptin, and 10 μg/ml aprotinin). Whole cell lysates (WCL) were centrifuged at 15,000×g for 15 minutes and the protein concentration was determined using the Bradford Assay (Bio-Rad). WCLs were diluted to 1 mg/ml and 1 ml of the lysate was precleared with glutathione agarose and used for affinity precipitation with 10 μg of the Raf-1 RBD agarose conjugate. The agarose beads were collected by centrifugation at 15,000×g and washed three times with MLB. Beads were resuspended in 2× Laemmli sample buffer and boiled at 95° C. for 5 minutes. Samples were diluted to 1× Laemmli buffer and subjected to SDS-PAGE and immunoblot analysis.

Reverse Transcription and Real-Time PCR Detection of miRs.

Total RNA was extracted using mirVana™ miRNA Isolation Kit (Ambion/Invitrogen). For mRNA analysis, total RNA was reverse transcribed using SuperScript II reverse transcriptase (Invitrogen). ESR1 transcripts were analyzed using the Brilliant II SYBR® Green QPCR Master Mix (Agilent) with the following primers: 5′-AGGTGGACCTGATCATGGAG-3′ (SEQ ID NO: 37), 5′-AAGCTTCGATGATGGGCTTA-3′ (SEQ ID NO: 38). Reactions were normalized to B2M: 5′-TCTCTGCTGGATGACGTGAG-3′ (SEQ ID NO: 39), 5′-TAGCTGTGCTCGCGCTACT-3′ (SEQ ID NO: 40). Individual miRs were analyzed by stem-loop reverse transcription followed by quantitative real-time PCR (qPCR) detection using TaqMan MicroRNA Assays (Applied Biosystems) and normalized to U6 snRNA: hsa-miR-206 (#000510), hsa-miR-21-5p (#000397), U6 snRNA (#001973). PCR reactions were performed on a Mx3005P™ Real-Time PCR System (Stratagene). mRNA and miR levels were determined by the ΔΔCTmethod. Three independent experiments were performed in duplicate fashion.

Potential KLF4 binding sites were identified using JASPAR (67). Chromatin from 4×107cells was prepared as described (68) and used as input for each immunoprecipitation (IP). Chromatin was sonicated in ice water using a Bioruptor (Diagenode) set at high energy, cycling on/off at 30 second intervals for 6 cycles of 10 minutes each. IP was performed using 1 μg of the indicated antibody. Following IP, elution, reversal of crosslinks, and proteinase K digestion, DNA was purified using Qiaquick spin columns (Qiagen) and then eluted in 50 μl of 10 mM Tris-HCl (pH 8.0). 2% of the ChIP yield was used as input for each PCR reaction. ChIP Intensity levels were determined by use of the ΔCTmethod to compare the yield obtained using anti-KLF4 or normal IgG. The sequences of oligonucleotides are: miR-21 site 1, 5′-CTTAGATTGAGAAAGACCGC-3′ (SEQ ID NO: 41) and 5′-ACTTATGCTTGTGTCATCCC-3′ (SEQ ID NO: 42); miR-21 site 2, 5′-GCAACCTCCACTTCCTGGGT-3′ (SEQ ID NO: 43) and 5′-CCAACACAGTGAAACCCTGT-3′ (SEQ ID NO: 44); miR-206 site 1, 5′-CATCAACAACACCCCAAGCG-3′ (SEQ ID NO: 45) and 5′-GGCACAGTTTTGGATCAACCC-3′ (SEQ ID NO: 46); miR-206 site 2, 5′-TGCAAAGCACAGAGAAACGTG-3′ (SEQ ID NO: 47) and 5′-ACCTTCTTCCCATTTTCCTGGAC-3′ (SEQ ID NO: 48).

Female Athymic Nude mice (Crl:NU(NCr)-Foxn1nn, Charles River) were obtained at 6-8 weeks of age. 2×106cells in in 100 μl of DMEM were injected into the 4th mammary fat pad. Caliper measurements were performed twice a week and tumor initiation was defined as >4 mm for both L1and L2(L1, long axis; L2, short axis). All animal procedures were performed under an approved protocol.

Data were analyzed using the unpaired t-test (two-tailed), or else one-way analysis of variance (ANOVA) followed by Tukey's multiple comparison ad hoc post-test. Growth curves were analyzed using non-linear regression curve fitting. Tumor initiation was analyzed using a 2×2 contingency table with Fisher's exact test. Statistical analyses were performed in GraphPad Prism 5 (GraphPad Software). Except where noted, assays were performed three times in duplicate fashion. Cell proliferation assays were performed in three independent experiments, each containing 5 replicates. Differences were considered significant when the analysis yielded P<0.05.

Results

Consistent with our previous study, miR-206 levels were markedly repressed in KLF4-depleted cells (FIG. 1A) (55). Similar results were obtained in the RAS-mutant (KRASG13D) and claudin-low tumor line MDA-MB-231, and the RAS-WT and basal-like HCC1143 cells. ChIP analysis of KLF4 at consensus sites in the MIR206 locus identified enrichment of site 1, located within the promoter-proximal region (FIG. 1B). Supporting specificity, this enrichment was reduced in KLF4-deficient cells and increased in cells with exogenous KLF4 (FIG. 1C).

As protumorigenic mechanisms of KLF4 signaling remain poorly understood, we sought potential effectors of miR-206. In silico enrichment analysis identified MAPK signaling as likely to be regulated by miR-206, which has the potential to target 17 genes in this pathway (p=1.24×10−2, Table 1). Because of its ability to regulate miR-206, we first determined whether endogenous KLF4 can regulate steady state RAS-ERK activity in TNBC cells by analyzing ERK 1/2 activation loop phosphorylation (i.e., activated ERK 1/2 or pERK 1/2). In KLF4-deficient cells the pERK 1/2 levels were suppressed (FIG. 2A). In these cell lines, the reduction of pERK 1/2 reflected lower levels of WT RAS-GTP, whereas mutant RAS-GTP levels were unaffected by KLF4 knockdown (FIG. 2B). In KLF4-deficient MDA-MB-231 cells, introduction of HA-tagged KLF4 rescued the levels of miR-206 and pERK 1/2 (FIG. 2C).

To temporally correlate the induction of miR-206 and pERK 1/2 by KLF4, we transduced KLF4-depleted MDA-MB-231 cells with KLF4-ER or empty vector (FIG. 2D). The KLF4-ER fusion protein is constitutively expressed but functionally inactive until treatment of cells with 4-hydroxytamoxifen (4-OHT) (48,69). As previously reported, addition of 4-OHT to KLF4-ER cells resulted in upregulation of miR-206 between 0.5 and 2 hours post-treatment (FIG. 2E, left panel) (55). In this experiment the induction of pERK 1/2 was apparent by 2 hours (FIG. 2E, right panel). KLF4-ER activity was supported by the induction of cyclin-dependent kinase inhibitor 1A (p21Cip1/Waf1) in these cells (70) (FIG. 2E, right panel). The modest induction of activated ERK 1/2 by exogenous KLF4 (FIGS. 2C and 2E) was in contrast to the larger fold effect of endogenous KLF4 (FIG. 2A), identifying a discordance between the two approaches.

miR-206 Suppresses the Translation of the RAS-ERK Pathway Inhibitors RASA1 and SPRED1.

Consistent with the mutual dependence of both miR-206 and RAS-ERK activity upon KLF4, we sought to identify specific components of the RAS-ERK pathway that are regulated by this miR. The two RAS-ERK pathway suppressors RASA1 and SPRED1 were consistently identified as likely miR-206 targets across multiple miR algorithms (Table 2). Consistent with regulation by miR-206, KLF4 depletion was associated with higher levels of RASA1 and SPRED1 (FIG. 3A). To examine a role for endogenous miR-206 we utilized antisense inhibitor specific to the mature miR (anti-miR). As compared to the control, anti-miR-206 depleted the miR levels in TNBC cells (FIG. 3B). This suppression of miR-206 activity was sufficient to increase the levels of the two pathway inhibitors (FIG. 3C, left panels). Conversely, transfection of exogenous miR-206 (miR-206-mimic) decreased the level of each protein (FIG. 3C, right panels). These results identified miR-206 as a potential link between KLF4 and RAS-ERK signaling.

To analyze the regulation of protein translation by miR-206, we utilized translational reporter assays. Fragments of the 3′ UTRs containing putative miR-206 binding sites were cloned downstream of the open reading frame of firefly luc (FIGS. 4A-4B). Relative to the control anti-miR, in MDA-MB-231 cells transfected with anti-miR-206, the luc activity was 3.9 fold induced for the WT RASA1 reporter and 2.4 fold induced for the WT SPRED1 reporter (FIGS. 4C-4D, upper and middle panels). Conversely, transfection of each reporter with miR-206-mimic decreased luc activity by 32% for the RASA1 reporter and by 64% for the SPRED1 reporter (FIGS. 4C-4D, lower panels). Reporter regulation by miR-206 was abolished by mutation of RASA1 or SPRED1 sequences important for miR-206 binding (FIGS. 4C-4D). These results identify miR-206 as a direct regulator of these transcripts, supporting a role for KLF4 in promotion of RAS-ERK signaling through miR-206 mediated suppression of RASA1 and SPRED1.

miR-21 is a KLF4-Dependent miR that Represses the Translation of Both RASA1 and SPRED1.

As modulation of miR-206 alone was not sufficient to recapitulate the effects of KLF4 on pERK 1/2 levels, we therefore sought additional downstream effectors. Similarly to miR-206, miR-21 is upregulated in breast cancer and is predicted by pathway enrichment analysis to regulate MAPK signaling (p=2.09×10−3; Table 3) (59). Furthermore, miR-21 has been validated to directly regulate the translation of several RAS-ERK-activator protein 1 (AP-1) inhibitory components, including RASA1, SPRY1, SPRY2, and PDCD4 (56-58). These common features suggested the possibility of shared signaling by these two miRs. Providing compelling support for this idea, MAPK signaling was ranked first among the pathways likely to be co-regulated by miR-206/21 (p=3.00×10−4; Table 4).

The ability of KLF4 to regulate RAS-ERK signaling, and the established role of miR-21 in regulation of this pathway identified KLF4 as a potential regulator of miR-21. To determine whether KLF4 might signal through miR-21, we assayed KLF4-deficient TNBC cells for miR-21 levels, observing marked suppression (FIG. 5A). ChIP analysis of KLF4 at consensus sites in the MIR21 locus of MDA-MB-231 cells identified enrichment of site 1, located within the promoter region (FIG. 5B). This enrichment was reduced in KLF4-deficient cells and increased in cells with exogenous KLF4 (FIG. 5C). In contrast to the enhanced ChIP intensity signal in cells with exogenous KLF4, miR-21 levels were not enhanced (FIG. 5D). Restoration of KLF4 in MDA-MB-231/shKLF4 cells was likewise insufficient to increase miR-21 (FIG. 5E). As a control, miR-206 levels were induced by exogenous KLF4 in these experiments (FIG. 5D), suggesting different modes of miR regulation by KLF4.

To address possible off-targeting by KLF4 shRNAs (shKLF4), we analyzed additional shKLF4 constructs. We observed only weak activity of shKLF4-3, but more efficient KLF4 suppression by shKLF4-4 and shKLF4-5 (FIG. 5F, left panels). Compared to shCtl and shKLF4-3, cells transduced with the active constructs had consistently reduced levels of miR-21 (FIG. 5F, right panels). Consequently, the regulation of miR-21 by endogenous KLF4 was supported by a total of four active shRNAs (FIGS. 5A and 5F).

The failure of exogenous KLF4 to restore miR-21 levels appeared consistent with a stable alteration of MIR21 chromatin in KLF4-deficient cells (71,72). To examine this possibility we treated shCtl cells or shKLF4-1 cells with the DNA methyltransferase inhibitor AZA or the histone deacetylase inhibitor TSA (FIG. 5G). Unlike TSA, AZA largely restored miR-21 levels (FIG. 5G, left panel). Neither AZA nor TSA significantly altered miR-206 levels, whereas ESR1 served as a positive control and was induced by both agents (FIG. 5G, middle and right panels respectively) (73,74). These results show that endogenous KLF4 is permissive for the expression of miR-21 in TNBC cells, and support a role for chromatin modification in the suppression of miR-21 following KLF4 depletion.

The regulation of RASA1 by miR-21 is well established (64). Our results above indicate that RASA1 is co-targeted by miR-206/21, suggesting a broader role for this pair as co-regulators of RAS-ERK pathway components (FIG. 4). Although miR-206 was predicted to regulate SPRED1 and this was subsequently validated, whether miR-21 can likewise regulate this factor was unknown. Nevertheless, transfection of anti-miR-21 into MDA-MB-231 cells increased the protein levels of both RASA1 and SPRED1, whereas exogenous miR-21 was suppressive (FIG. 6A). Unlike the well-conserved miR-21 sites in RASA1, analysis in TargetScan revealed that SPRED1 contains two candidate binding sites for miR-21 with only limited species conservation (FIGS. 6B-6C) (75). Translational reporter assays identified only one of these sites as functional, and supported the direct regulation of both RASA1 and SPRED1 transcripts by miR-21 (FIGS. 6D-6E). As a control, transfection of anti-miR-21 led to reduced miR-21 activity, as indicated by immunoblot analysis of PDCD4, a well-established target of this miR (FIG. 6A) (63). These results validate SPRED1 as a miR-21 targeted transcript. Therefore, the miR-206/21 pair can indeed co-target distinct RAS-ERK pathway components, validating the idea that MAPK signaling represents an important signaling intersection for these two miRs (Table 4).

Consistent KLF4 Regulation of miR-206/21 Levels and RAS-ERK Signaling in RAS-WT and RAS-Mutant Tumor Cells.

The results observed for MDA-MD-231 and HCC1143 cells suggested a functional relationship between the KLF4-miR-206/21 axis and the RAS-ERK pathway. We analyzed this signaling in a broader panel of mammary epithelial cells (MECs) and cancer cells (FIG. 7A). KLF4 depletion in nontumorigenic MCF10A cells, in HRAS-mutant MCF10AT cells, or in a variety of human or mouse TNBC lines led to consistently reduced levels of activated ERK 1/2 and to increased levels of RASA1 and/or SPRED1. In the KLF4-deficient TNBC cells, RASA1 and SPRED1 were concordantly upregulated. However, in MECs, the RASA1 levels were not appreciably altered, and reduced pERK 1/2 levels were associated with increased SPRED1 alone. KLF4 depletion was likewise associated with reduced miR-206/21 levels, except in MDA-MB-468 cells where miR-206 was undetected (FIG. 7B). In this miR-206-deficient cell line, the overall effect of KLF4 on pERK 1/2 appeared more modest. In summary, KLF4-miR-206/21 signaling appears to generally regulate the RAS-ERK pathway in TNBC cells, with similar effects in RAS-WT (HCC1143, HCC1937, and MDA-MB-468) and RAS-mutant cells (MDA-MB-231, Hs578t, and SUM159PT).

miR-206 and miR-21 Cooperate to Promote RAS-ERK Signaling and ERK 1/2 Dependent Phenotypes.

Transfection of anti-miR-206 or anti-miR-21 alone did not have prominent effects on pERK 1/2 levels (FIG. 8, lanes 2, 3, 6, and 7). To test for cooperativity, we inhibited both miRs in TNBC cells (i.e., anti-miR-206/21), and then assayed for RASA1 and SPRED1 levels (FIG. 8, lanes 4 and 8). Compared to the individual anti-miRs, SPRED1 was consistently induced to a greater extent by anti-miR-206/21. In contrast, RASA1 levels responded to each of the anti-miRs (FIG. 8, lanes 2 and 6), but anti-miR-206/21 cooperativity was only apparent in HCC1143 cells (FIG. 8, lanes 4 and 8). Nevertheless, anti-miR-206/21 transfection of TNBC cells reduced the levels of pMEK 1/2 and pERK 1/2 to a greater extent than did either anti-miR when used alone. These findings identify two KLF4-dependent miRs as maintenance factors for RAS-ERK signaling in TNBC cells, potentially through cooperativity for regulation of SPRED1 and/or other pathway regulators.

In breast cancer cells the RAS-ERK pathway promotes cell proliferation, migration, and resistance to cell death (21,22). TNBC cells transfected with both anti-miRs displayed slower growth over a three day time course than did control or single anti-miR transfected cells (FIG. 9A, upper panels). This marked attenuation of proliferation was not explained by changes in cell viability as measured by trypan blue exclusion (FIG. 9A, lower panels).

Similarly to cell proliferation, inhibition of both miRs abrogated TNBC cell migration in transwell chambers to a greater extent than the inhibition of either miR alone (FIG. 9B). Finally, anti-miR-206/21 rendered TNBC cells more susceptible to cell death in anoikis assays (FIG. 9C-9D). As a control, treatment of matrix-deprived MDA-MB-231 cells with the MEK 1/2 inhibitor U0126 yielded a higher rate of cell death (76). These results indicate that miR-206/21 can cooperate to promote RAS-ERK pathway signaling as well as pathway dependent phenotypes.

miR-206 and miR-21 Promote RAS-ERK Signaling by Repression of RASA1 and SPRED1.

To determine whether miR-206/21 impact RAS-ERK signaling through their co-regulation of RASA1 and/or SPRED1, we depleted either RASA1 (FIG. 10A) or SPRED1 (FIG. 10B). Knockdown of either factor had little effect upon the other protein. Regardless of the RAS mutational status, knockdown of RASA1 or SPRED1 led to increased steady-state levels of pERK 1/2 relative to control cells. This increase in pathway activity was associated with elevated levels of WT RAS-GTP (FIG. 10C). In contrast to the results obtained for WT RAS proteins, the KRAS-GTP levels in MDA-MB-231 cells (KRASG13D) were not appreciably altered by suppression of RASA1 or SPRED1. Similarly, the HRAS-GTP levels in SUM159PT cells (HRASG12D) were unchanged by suppression of either RASA1 or SPRED1, even though pERK 1/2 levels were increased (FIG. 10D). These results suggest that WT RAS proteins mediate the enhanced RAS-ERK pathway activity in RASA1- or SPRED1-deficient TNBC cells.

To test for a function of RASA1 and SPRED1 as mediators of miR-206/21 effects on RAS-ERK signaling, we delivered anti-miR-206/21 to control cells or cells deficient in either protein (FIG. 11A). As an indicator of successful miR suppression we assayed the protein levels of PDCD4, which is regulated by miR-21. As expected, combined miR-206/21 inhibition in control cells reduced the levels of pERK 1/2 (FIG. 11A; lanes 1-2 in each panel). Suppression of RASA1 rendered cells largely independent of miR-206/21, as pERK 1/2 showed little or no attenuation by anti-miR (lanes 3-4). In SPRED1-suppressed cells, RASA1 and/or some other miR-206/21-dependent component appeared to be limiting for pathway activity, as anti-miRs induced RASA1 and also suppressed the levels of pERK 1/2 (lanes 5-6). In TNBC cells depleted of RASA1 or SPRED1 and then treated with anti-miR-206/21, the residual activated ERK 1/2 was increased relative to control cells (FIG. 11A, lanes 2, 4, and 6). This anti-miR-resistant signaling supports functional roles for both RASA1 and SPRED1 as mediators of the KLF4-dependent miRs.

Phenotypic data consistent with these immunoblot results were obtained by analysis of cell proliferation (FIG. 11B). Compared to parental (untransduced and untransfected) TNBC cells or control (shCtl) cells, shRASA1 and shSPRED1 cells proliferated at a rate that was only slightly faster. For each cell line we next measured cell proliferation following treatment with either anti-miR-Ctl or anti-miR-206/21. Whereas shCtl cells transfected with anti-miR-206/21 proliferated much more slowly (p<0.001), shRASA1 cells displayed anti-miR-206/21-resistant cell proliferation (p>0.05;FIG. 11B). shSPRED1 cells had an intermediate phenotype, with a smaller size effect than observed for shCtl cells that were treated with anti-miR-206/21 (p<0.05;FIG. 11B). The effects of anti-miR-206/21 on cell proliferation appeared consistent with the residual levels of activated ERK 1/2 (seeFIG. 11A).

Consistent results were obtained when anti-miR-treated TNBC cells were orthotopically injected into the mammary gland of immunodeficient mice (FIG. 11C). Relative to anti-miR-Ctl, anti-miR-206/21 suppressed tumor initiation by the control cells (shCtl), attributed to their decreased proliferation and/or increased cell death following implantation into the mammary gland. In contrast, cells deficient in RASA1 or SPRED1 were competent for tumor initiation. These results support functional roles for both RASA1 and SPRED1 in miR-206/21 signaling.

Restoration of RAS-ERK Signaling by Exogenous miR-206/21 in KLF4-Depleted Cells Promotes Resistance to Cell Death.

To complement the anti-miR data, we delivered exogenous miRs into KLF4-deficient TNBC cells (FIG. 12A). As compared to the individual miR-mimics (FIG. 12A, lanes 2, 3, 6, and 7), more pronounced signaling effects were obtained using the miR-206/21-mimic (lanes 4 and 8). These effects included suppression of RASA1 and SPRED1 and the induction of activated MEK 1/2 and ERK 1/2.

Relative to the control, transfection of either miR-206- or miR-21-mimic into KLF4-depleted cells reduced the cell death following matrix deprivation (FIG. 12B, lanes 2, 3, 8, and 9). Consistent with the cooperative regulation of pERK 1/2 levels (FIG. 12A, lanes 4 and 8), a greater fold effect on cell death was observed for cells treated with both mimics (FIG. 12B, lanes 4 and 10). In these studies, exogenous KLF4 effects were similar to that of the miR-mimics, and suppressed cell death (FIG. 12B, left panel, lanes 5 and 6). These gain-of-function studies provide independent support for the cooperative regulation of RAS-ERK signaling by KLF4-dependent miRs-206/21. In the light of previous studies by others, our results support a model for miR-206/21 co-targeting and co-regulation of RAS-ERK signaling (FIG. 13).

Compared to other breast cancer subtypes, TNBCs express elevated levels of RTKs such as EGFR and FGFRs that represent major regulators of RAS-ERK signaling (30,77). Although genetic changes in these receptors or the mutational activation of RAS or RAF are rare, these tumors often harbor other genetic alterations that promote RAS-ERK pathway activity (26-31). Supporting the importance of this signaling, TNBC cells are particularly sensitive to drugs such as MEK or PI3K inhibitors, and combination therapies have been analyzed in clinical trials (23,24,78,79).

KLF4 is a major regulator of pluripotency with the potential to either promote or suppress malignant properties, and dissecting the relevant mechanisms has the potential to identify new therapeutic approaches. We previously implicated miR-206 as a potential downstream effector of KLF4 (55). Evidence from the current study supported a direct role of KLF4 in regulation of miR-206. Consistent with a role for this signaling in TNBCs, miR-206 is upregulated in breast cancer and ER-negative tumors express higher levels relative to ER-positive tumors (59,80).

miR-206 has been well characterized in muscle cells, where it promotes skeletal muscle regeneration in response to injury (81-83). An in silico search for cancer-relevant influences of miR-206 identified regulation of MAPK signaling as a likely effector pathway, with potential effects on RASA1 and SPRED1 (Tables 1-2). Subsequently, analysis of KLF4-deficient cells revealed upregulation of these two pathway inhibitors in conjunction with markedly reduced levels of pERK 1/2, and protein translation reporter studies identified direct roles for miR-206 in regulation of RASA1 and SPRED1.

As compared to the pronounced effect of endogenous KLF4 on pERK 1/2 levels, modulation of miR-206 alone revealed only modest effects (FIG. 12A), and we therefore sought additional effectors downstream of KLF4. We evaluated miR-21 as a candidate because of its upregulation in breast cancer and its known role in regulation of RAS-ERK pathway components, including RASA1 (Table 3) (58-65). Strikingly, an intersection approach identified MAPK signaling as the pathway most likely to be co-regulated by miR-206/21 (Table 4). We subsequently observed a critical role for endogenous KLF4 in maintenance of miR-21 levels, and found that both RASA1 and SPRED1 contain binding sites for miR-206/21. These results identified a recurrent regulatory strategy in which two KLF4-regulated miRs can impact the same transcript. As shown by suppression of KLF4 or by the introduction of anti-miR-206/21, this regulation results in pronounced alteration of RAS-ERK signaling in the multiple TNBC models examined.

The protumorigenic miR-21 is abundant in TNBC cells and inhibits the translation of multiple negative regulators of RAS-ERK-AP1 signaling (FIG. 13). Despite extensive interactions with the RAS-ERK pathway, we and others have observed that antisense-mediated inhibition of endogenous miR-21 gives relatively modest effects on overall pathway activity, as indicated by analysis of activated ERK 1/2 (FIG. 8). In the current study, we observed that miR-206/21 function as a pair to co-target RAS-ERK pathway inhibitory proteins, with profound consequences on RAS-ERK signaling. Such co-targeting is not without precedent. For example, miR-27a, miR-96, and miR-182 co-target the tumor suppressor FOXO1 in breast cancer cells (84).

Our analysis of KLF4-depleted TNBC cells indicated that endogenous KLF4 could influence the levels of both miR-206 and miR-21, a response obtained using each of four distinct KLF4 shRNAs (FIGS. 5A and 5F). We also characterized the temporal KLF4 regulation of miR levels using a 4OHT-conditional KLF4-ER fusion protein. In combination with ChIP data that strongly supported direct interaction of KLF4 with the promoter-proximal regions of MIR206 and MIR21, these studies implicated MIR206 and MIR21 as direct transcriptional targets of KLF4, but with distinct modes of regulation.

Unlike for the regulation of MIR206, we observed that endogenous and exogenous KLF4 function discordantly for regulation of MIR21. Previous studies have shown that MIR21 is transcribed as an independent unit located in the intron of the TMEM49 gene (85). Relative to the control cells, in KLF4-deficient cells we observed a decrease of TMEM49 of similar to 35% (not shown). Unlike for miR-206, exogenous KLF4 did not alter miR-21 levels in TNBC cells. Similarly, restoration of KLF4 activity in KLF4-depleted tumor cells induced miR-206 but did not significantly alter miR-21 levels. The insufficiency of exogenous KLF4 for induction of miR-21 suggests an “on-off” mode of regulation, and identifies KLF4 suppression as a potential hit-and-run strategy for the therapeutic silencing of miR-21 in tumors. Also, this lack of regulation of miR-21 by exogenous KLF4 is quite consistent with the more limited effect of exogenous KLF4 on activated ERK 1/2 levels relative to the endogenous transcription factor (FIGS. 2A and 2C).

These results suggested a working model in which endogenous KLF4 maintains an open chromatin structure at MIR21. Initial support for this model was obtained by analyzing a role for DNA methylation. In KLF4-deficient cells, but not in control cells, treatment with the DNA methyltransferase inhibitor AZA was sufficient to upregulate miR-21 levels. Kruppel-like factors such as Erythroid Kruppel-like factor (EKLF or KLF1) can regulate chromatin structure by interacting with chromatin modifying proteins or chromatin remodelers (86-88). The observed regulation of MIR21 by KLF4 is especially interesting given the relationship between open chromatin and pluripotency (89).

KLF4-miR-21 signaling highlights the potential for distinct effects of KLF4 in loss- and gain-of-function experimental settings. As the oncogenic miR-21 is expressed independently of exogenous KLF4, KLF4 gain-of-function phenotypic studies may potentially underestimate protumorigenic signaling by the endogenous transcription factor. It is currently unclear whether KLF4 can regulate other loci in a similar fashion as for MIR21, or whether its regulation of MIR21 extends to other cell types.

Importantly, shRNA studies revealed both RASA1 and SPRED1 to be limiting endogenous factors for steady state RAS-ERK signaling through modulation of WT RAS-GTP levels, identifying these components as potential mediators of miR-206/21 effects (FIG. 10). miR loss- and gain-of-function studies using single anti-miRs or miR-mimics indicated that either miR-21 or miR-206 could individually regulate the level of these pathway inhibitors, but with only subtle effects on pERK 1/2 levels. Indicating cooperativity, larger fold effects were observed when anti-miRs or miR-mimics were combined to modulate both miR-206 and -21. Cooperativity was observed for the expression level of SPRED1, for the levels of pERK 1/2, and for relevant phenotypic parameters including tumor cell proliferation, migration, and survival.

As observed for SPRED1, RASA1 protein levels were dependent upon both miR-206 and miR-21. However, RASA1 did not consistently show cooperative regulation. Strikingly, RASA1 expression was nevertheless critical for miR-206/21 signaling, as anti-miR-206/21 had little or no discernible effect on pERK 1/2 levels in RASA1-deficient cells (FIG. 11). Likewise, cell proliferation and tumor initiation were concordantly anti-miR resistant in RASA1-deficient cells.

Supporting a functional role for SPRED1 in KLF4-miR signaling to RAS-ERK, SPRED1-suppressed cells not only displayed elevated pERK 1/2 levels, but also had resistance to anti-miR-206/21 that was intermediate as compared to shCtl cells and shRASA1 cells. This was shown by analysis of pERK 1/2 and cell proliferation, and tumor initiation in mice was anti-miR-resistant. The failure of anti-miR-206/21 to regulate pERK 1/2 levels in RASA1-deficient cells, despite upregulation of SPRED1, suggests that SPRED1 activity may be somehow limited in this context (FIG. 11). For example, this data would appear consistent with a critical role for RASA1 in signaling by SPRED1 or SPRED1-NF1 (13). On the other hand, in the context of MDA-MB-231 cells where SPRED1 but not RASA1 was cooperatively induced by anti-miR-206/21, the cooperative suppression of pERK 1/2 levels may be largely attributed to SPRED1, with RASA1 serving a more permissive role (FIG. 8).

Of interest in the current study was the similar effect of anti-miR-206/21 on RAS-ERK signaling in RAS-WT and RAS-mutant breast cancer cells alike. In RAS-mutant cells that were analyzed for RAS-GTP levels, only the WT RAS GTP was increased following depletion of either RASA1 or SPRED1. Consistent with our results, previous studies support the potential for these pathway inhibitors to antagonize signaling in cells harboring activated RAS (90-92). The effects of RASA1 and SPRED1 that we observed appear consistent with an important role of WT RAS proteins (i.e., KRAS, NRAS, and/or HRAS) for pathway activation in RAS-mutant TNBC cells. This model is supported by several previous analyses in non-mammary contexts (93-96). For example, suppression of the guanine nucleotide exchange factor SOS1 in a RAS-mutant context results in attenuation of WT RAS-GTP levels and pERK 1/2 levels, and suppresses tumorigenesis (94). In addition to effects on WT RAS proteins, the possibility that RASA1 and/or SPRED1 could suppress signaling by impacting other steps in the pathway is not excluded. Although additional studies are needed, these results support the targeting of RASA1 and SPRED1 for therapy of RAS-mutant as well as RAS-WT cancers.

We have identified a facet of KLF4 signaling that promotes malignant properties in TNBC cells, through miR-mediated activation of RAS-ERK signaling. The results highlight RASA1 and SPRED1 transcripts as latent tumor suppressors in TNBC cells, held at bay through KLF4-dependent miRs. The pronounced inhibitory effect of anti-miR-206/21 on the level of activated ERK 1/2 identifies the enhanced translation of RASA1 and SPRED1 as an attractive therapeutic strategy. In TNBCs the use of MEK 1/2 inhibitors typically induces a rapid compensatory reprogramming of the kinome, leading to drug resistance (33). Suppression of KLF4 or the anti-sense mediated silencing of miR-206 and/or miR-21 might be used in combination with MEK inhibitors or other pathway antagonists to attenuate this drug resistance.

We thank Steven M. Frisch (West Virginia University), Gary L. Johnson (University of North Carolina at Chapel Hill) and Jeffrey E. Green (NIH) for providing cell lines. Flow cytometry experiments were performed in the West Virginia University Flow Cytometry Core Facility. Orthotopic tumor cell injections were performed in the West Virginia University Animal Models & Imaging Facility.

TABLE 2Putative miR-206 target genes related to the MAPK/ERK signaling pathway.TARGET GENEDIANAMIRANDAMIRBRIDGEPICTARPITARNA22TARGETSCANTOTAL HITRASA1VVVVVVV7SPRED1VVVVVV6RIT2VVVVVV6MAP4K3VVVVVV6BDNFVVVVVV6NGFRVVVVV5PDGFAVVVVV5PDCD4VVVV4MAPK1VVVV4CRKVVVV4MAP3K1VVVV4SRCVVV3RPS6KA5VVV3RAP1AVVV3RALAVVV3MAPK3VVV3KRASVVV3GNB1VVV3IKBKBVVV3RAPGEF2VVV3PRKACBVVV3Candidate miR-206 target genes relevant to MAPK/ERK signaling were identified using KEGG, BIOCARTA, or REACTOME pathway analysis tools. Ranking (Total Hit) was performed using miRSystem (98).

TABLE 4Intersection of the pathways targeted by miR-206 and miR-21.KEGG pathwayp-valuePredicted targets inMAPK signaling pathway3.00E−0426Neurotrophin signaling pathway6.59E−0414Regulation of actin cytoskeleton3.19E−0319Analysis was performed using DIANA miRPath (97).

REFERENCES