# Patent

## Title
Means and methods for diagnosing and/or treating a subject at risk of developing heart failure

## Abstract

The present invention relates to a method for identifying a subject at risk of developing heart failure, comprising: (a) determining the level of one or more biological markers in a biological sample of said subject; (b) comparing the level of said biological marker to a standard level of the same biological marker; and (C) determining whether the level of the marker is indicative of a risk for developing heart failure, wherein the biological marker is Krüppel Like Factor 15 (KLF-15) and/or lysosomal integral membrane protein-2 (LIMP-2) and/or fragments and/or variants thereof, and/or wherein the biological marker is a gene coding for KLF15 and/or LIMP-2, and/or fragments and/or variants thereof. The invention further relates to use of the KLF15 and/or LIMP-2 protein, and/or the gene coding for KLF15 and/or LIMP2, and/or fragments, and/or variants of said genes and/or proteins, for the preparation of a medicament for a prophylactic and/or a therapeutic medicament for prevention and/or treatment of heart failure.

## Background
The present invention in general relates to the field of medicine, more specifically the field of cardiology. The invention in particular relates to means and methods for diagnosing and/or treating subjects at risk of developing heart failure.
It is generally known that chronic cardiac loading, as occurs during long-standing hypertension, valvular disease or other chronic disorders like diabetes, induces cardiac hypertrophy, which is one of the most important risk factors for heart failure. Congestive heart failure (HF) is a common but severe and complex clinical syndrome, especially among elderly people, characterized by a diminished cardiac contractile function and decreased exercise tolerance. Symptoms of heart failure include, amongst others, pulmonary and peripheral edema, fatigue and/or dyspnea. Severe heart failure may also lead to reduced function in other organs because these are not receiving enough blood.
Not all hypertrophied hearts, however, will ultimately fail. Thus, while an important number of patients progress to developing life-threatening complications, others may remain stable for prolonged periods. Until now, the molecular changes that precede and herald this transition from hypertrophy towards heart failure are incompletely understood.
As early identification of patients at risk for developing hypertensive end organ damage, such as heart failure, may prevent rapid progression, it would be preferable to be able to identify (diagnose) those patients in which heart failure is likely to occur before it actually does so. Early diagnosed patients may thus be treated in order to prevent the onset of heart failure. In addition, it would be preferable to be able to identify those patients suffering from heart failure who are at risk for developing severe complications.
Current methods can reliably exclude the actual presence of heart failure, but cannot reliably prove the existence of heart failure, nor can these methods predict the outcome of established heart failure, or predict the occurrence of heart failure.
A need therefore exists for simple and reliable methods for predicting the likelihood of onset of heart failure and/or for predicting the outcome of already established heart failure. In addition, the development of means and methods for treating patients who are at risk of developing heart failure, before heart failure and/or its complications occur, would be of great clinical importance.
The object of the present invention is to provide diagnostic methods by which patients can be identified who are at particular risk of developing heart failure, and/or who are at particular risk to develop complications of heart failure. It is a further object of the present invention to provide means and methods for treating patients who are at risk of developing heart failure, and/or who are at risk for developing complications of heart failure.
This objective is achieved by the invention by providing a method for diagnosing a subject at risk of developing heart failure, comprising the steps of:

    
    
        (a) determining the level of one or more biological markers in a biological sample of said subject;
        (b) comparing the level of said biological marker(s) to a standard level of the same biological marker(s), and
        (c) determining whether the level of the biological marker(s) is indicative of a risk for developing heart failure,
        
            wherein the biological marker is lysosomal integral membrane protein-2 (LIMP-2) and/or Krüppel-like transcription factor 15 (KLF15).
        
        
    
    


In the research that led to the present invention, a number of genes have been identified that are involved in the development of heart failure. The identified genes have been listed in Table 2. It has furthermore been demonstrated that specific polypeptides encoded by said genes are indeed mechanistically linked to heart failure. It has in particular been demonstrated that specific proteins encoded by the genes from table 2 are involved in the molecular mechanisms that are responsible for the transition from cardiac hypertrophy towards heart failure, and thus can be used as a biological marker for identifying patients at risk of developing heart failure. In addition, these proteins, and/or the genes encoding said proteins, and/or polypeptide and/or polynucleotide fragments or variants of said proteins and/or genes can be used as a target for treating those patients at risk.
According to the present invention, it has in particular been demonstrated that specific intercalated disc components, in particular lysosomal integral membrane protein-2 (LIMP-2) and Krüppel-like transcription factor 15 (KLF15) are involved in the molecular mechanisms that predict the transition from cardiac hypertrophy towards heart failure, and can suitably be used as biological markers (biomarkers) for the identification of individuals who are at risk of developing heart failure.
According to the present invention, it has thus been found that subjects at risk for developing heart failure, can be identified by determining the level of one or more of the identified biological markers in a biological sample of said subject and comparing the level of said marker to a standard level. Said standard level is derived from healthy subjects, i.e. the standard level is the level of said biological marker in said biological sample of healthy persons, i.e. persons free from cardiac disease. If the level of the biological marker tested is altered, e.g. elevated or reduced (depending on the specific biological-marker concerned) compared to said standard level, the subject is at risk for developing HF and/or for developing severe complications of heart failure.
An early diagnosis of heart failure, preferably before clinical symptoms occur, is essential for e.g. successfully addressing underlying diseases, and/or preventing further myocardial dysfunction and clinical deterioration by for example treatment of the diagnosed patients.
In the research that led to the present invention, the gene expression profile of a large number of genes from hearts that were hypertrophied due to high blood pressure, but appeared well functional and compensated by traditional techniques (echocardiography), however, later proved to develop heart failure, was investigated. This expression profile was compared to the gene expression profile obtained from hearts that that were also hypertrophied due to high blood pressure and appeared equally well functional and compensated by traditional techniques (echocardiography), but later proved NOT to develop heart failure and remained stable. This way, genes were identified that predicted the occurrence of later developing heart failure, which, according to the present invention, have been shown to be novel and crucial modulators of hypertrophy and the transition towards heart failure. These genes have been listed in Table 2. Subsequently, specific preferred biological markers, in particular specific intercalated disc related biological markers were identified. The intercalated disc (ID) forms the connection between cardiac myocytes making up the cardiac fibers in the heart. The intercalated disc thus is a specialized cell-cell junction providing mechanical and electrical coupling between the cells and supporting synchronized contraction of cardiac tissue.
According to the present invention it has thus been demonstrated that increased cardiac expression of LIMP-2, as compared to standard levels of expression, identifies those hypertrophied hearts that are prone to progress to overt heart failure. Thus, while cardiac development is normal in LIMP-2 null mice (Gamp et al., 2003), hypertension induced dilated cardiomyopathy in these mice. It was shown that LIMP-2 binds to the vital cardiac adherens junction protein N-cadherin and is essential to secure proper interactions between N-cadherin and β-catenin. It has further been found that expression of LIMP-2 is increased in hypertrophied rat hearts that are on the brink to progress to heart failure, thus suggesting that increased LIMP-2 expression by cardiac myocytes heralds their inability to normalize mechanical forces. As such, increased LIMP-2 expression may be seen as a desperate attempt of the myocyte to respond to worsening loading and be indicative of imminent failure. It has moreover been shown that LIMP-2 expression is significantly increased in patients with clinically severe pressure loading. By determining the level of LIMP-2 protein and/or the level of expression of the gene coding for LIMP-2 in hypertensive subjects, and comparing said level(s) with a standard level, and subsequently determining whether the level is indicative of a risk for developing heart failure, it thus is possible to identify in a very early stage the myocardium that is about to succumb to the pressure. In particular, an increased level of LIMP-2 protein and/or an increased level of LIMP-2 gene expression as compared to a standard level is indicative of a risk for developing heart failure and/or heart-failure relates complications.
In the research that led to the present invention it has further been shown that the gene coding for Krüppel Like Factor 15 (KLF15) characterised hypertrophied hearts that quickly progressed to heart failure. This was confirmed by real-time PCR, which showed that KLF15 was down-regulated in compensated LVH, but that KLF-15 was significantly further suppressed in the hypertrophied hearts that quickly progressed to failure. It was further shown that KLF15 has a role in cardiac myocytes as a suppressor of cardiac hypertrophy. Determining the level of the KLF15 protein and/or the level of expression of the gene coding for KLF15 in hypertensive subjects, and comparing said levels to standard levels thus also is useful for identifying in a very early stage those patients that are likely to develop heart failure. In the case of KLF15, a decreased level of KLF15 protein and/or decreased KLF15 gene expression in a biological sample, as compared to standard levels, is indicative for the development of heart failure.
The present invention relates both to in vivo methods, i.e. methods wherein the level of the biological marker is determined in a biological sample in vivo and to in vitro methods.
In a preferred embodiment of the invention, the level of the biological marker is determined in vitro in a biological sample obtained from an individual. For in vitro determining the level of the biological markers of the present invention, any suitable biological sample of any bodily fluid that may comprise a biological marker identified by this research may be used. Preferably, the biological sample is selected from the group consisting of blood, plasma, serum, cardiac tissue. More preferably, the biological sample is a peripheral blood sample, or a plasma or serum sample derived from peripheral blood. Peripheral blood samples can e.g. easily be taken from the patients and do not need complex invasive procedures such as catheterization. The biological sample may be processed according to well-known techniques to prepare the sample for testing.
For measuring the level of the biological markers of the invention use can be made of conventional methods known in the art.
When the biological marker is a protein and/or a fragment and/or a variant thereof, several conventional methods for determining the level of a specific protein, and/or fragments and/or variants thereof, which are well-known to the skilled person, may be used. The level of the marker may for example be measured by using immunological assays, such as enzyme-linked immunosorbent assays (ELISA), thus providing a simple, reproducible and reliable method. Antibodies for use in such assays are available, and additional (polyclonal and monoclonal) antibodies may be developed using well-known standard techniques for developing antibodies. Other methods for measuring the level of the biological protein markers may furthermore include (immuno)histochemistry, Western blotting, flow-cytometry, RIA, competition assays, etc. and any combinations thereof. In vivo, the level of for example non-secreted proteins can be determined by labeling and tagging specific antibodies against one of the proteins of interest. This allows visualization of the amount of protein in the heart by so called ‘molecular imaging’ techniques.
When the biological marker is a gene, and/or a polynucleotide fragment and/or variant thereof, e.g. DNA, cDNA, RNA, mRNA etc., such as a gene coding for a specific protein, or mRNA that is transcribed, the biological marker can be measured in e.g. cardiac biopsies, by e.g. well-known molecular biological assays, such as in situ hybridization techniques using probes directed to the specific polynucleotides. Other nucleic-acid based assays which may be used according to the invention include RT-PCR, nucleic acid based ELISA, Northern blotting etc, and any combinations thereof.
In order to enhance the specificity and/or sensitivity of the diagnostic method, the method of the invention may include the detection of the level of one or more other (biological) markers, i.e. the detection of the biological markers of the present invention may suitably be combined with the detection of other markers which are indicative for the development of heart failure.
The present invention further relates to kits for performing the diagnostic methods as described above. The invention in particular relates to such diagnostic kits for identifying a subject at risk of developing heart failure, comprising means for receiving one or more biological samples of said subject, and means for determining the level of the biological marker(s) in said biological sample of said subject. Thus a kit is provided which can be used as a reliable and easy diagnostic tool. The means for receiving the biological sample may for example comprise a well of a standard microtiter plate. The means for determining the level of an intercalated disc related biological marker in said biological sample of said subject may for example comprise one or more specific antibodies, polynucleotide probes, primers etc. suitable for detecting the biological marker(s), identified according to the present invention. The kits may further also comprise calibration means and instruction for use.
The invention also relates to the use of the biological markers of the present invention and/or fragments and/or functional variants thereof in a screening method for identifying compounds for the prevention and/or treatment of heart failure. In a particular embodiment, the method for identifying a compound for prevention and/or treatment of heart failure comprises:
(a) contacting one or more compounds with a polypeptide encoded by a polynucleotide listed in table 2, preferably KLF15 and/or LIMP-2, and/or fragments, and/or variants thereof;
(b) determining the binding affinity of the compound to said polypeptide;
(c) contacting a population of mammalian cells with the compound that exhibits a binding affinity of at least 10 micromolar; and
(d) identifying the compound that is capable of prevention and/or treatment of heart failure.
The polypeptides to be tested in the screening method of the present invention may be tested in vitro, e.g. free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly, or in vivo.
To perform the methods it is feasible to immobilize either the polypeptide of the present invention or the compound to facilitate separation of complexes from uncomplexed forms of the polypeptide, as well as to accommodate automation of the assay. Interaction (e.g., binding of) of the polypeptide of the present invention with a compound can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and microcentrifuge tubes.
The binding affinity of the compound with the polypeptide can e.g. be measured by methods known in the art, such as using surface plasma resonance biosensors (Biacore), by saturation binding analysis with a labeled compound (e.g. Scatchard and Lindmo analysis), via displacement reactions, by differential UV spectrophotometer, fluorescence polarisation assay, Fluorometric Imaging Plate Reader (FLIPR®) system, Fluorescence resonance energy transfer, and Bioluminescence resonance energy transfer. The binding affinity of compounds can also be expressed in a dissociation constant (Kd) or as IC50 or EC50. The IC50 represents the concentration of a compound that is required for 50% inhibition of binding of another ligand to the polypeptide. The EC50 represents the concentration required for obtaining 50% of the maximum effect in vitro. The dissociation constant, Kd, is a measure of how well a ligand binds to the polypeptide, it is equivalent to the ligand concentration required to saturate exactly half of the binding-sites on the polypeptide. Compounds with a high affinity binding have low Kd, IC50 and EC50 values, i.e. in the range of 100 nM to 1 pM; a moderate to low affinity binding relates to a high Kd, IC50 and EC50 values, i.e. in the micromolar range.
The present invention also relates to the use of the genes and/or proteins listed in table 2, preferably of the KLF15 and/or LIMP-2 gene and/or protein, for the preparation of a medicament for a prophylactic and/or therapeutic medicament for the prevention and/or treatment of heart failure.
Preferably, the present invention relates to the use of a modulator of the genes and/or proteins listed in table 2, preferably of the KLF15 and/or LIMP-2 gene and/or protein, for the preparation of a prophylactic and/or therapeutic medicament for the prevention and/or treatment of heart failure.
In the present application a modulator may be any compound that stimulates the expression of and/or increases the level of one or more of the biological markers which are found to be reduced according to the invention (e.g. an agonist), or any compound that suppresses the expression and/or reduces the level of one or more of the biological markers which are found to be increased according to the invention (e.g. an antagonist).
The medicament may be a protein-based molecule, such as for example an antibody directed against the protein marker, and/or fragments and/or variants thereof. The present invention also includes chimeric, single chain and humanized antibodies, as well as Fab fragments and the products of a Fab expression library and Fv fragments and the products of a Fv expression library.
Alternatively, the medicament may be a nucleic-acid based molecule. The down-regulation of a gene can for example be achieved at the translational or transcriptional level using e.g. antisense nucleic acids. Antisense nucleic acids are nucleic acids capable of specifically hybridizing with all or a part of a nucleic acid encoding a protein and/or the corresponding mRNA. The preparation of antisense nucleic acids, DNA encoding antisense RNAs is known in the art. The medicament may also comprise small interfering (hairpin) RNA (siRNA). SiRNAs mediate the post-translational process of gene silencing by double stranded DNA (dsDNA) that is homologous in sequence to the silenced RNA. The preparation of siRNAs is known in the art. Similarly, the up-regulation of a gene (or over-expression) may be achieved by several methods that are known in the art.
In a preferred embodiment of the present invention, the modulator is an inhibitor of TGFβ. According to the present invention, it has been shown that suppression of KLF-15 is a crucial step in the development of failure prone forms of hypertrophy and that TGFβ strongly suppresses KLF-15. Inhibitors of TGFβ, which are currently being developed in different fields, thus may suitably be used for the development of a prophylactic and/or therapeutic medicament for the prevention and/or treatment of heart failure. Examples of suitable inhibitors of TGFβ which can be used according to the invention are TGFβ receptor inhibitors as made by Scios Inc., Los Angeles, U.S.A., who indicate on their website (http://www.sciosinc.com/scios/tgf): “Scios has developed novel and potent small molecule inhibitors designed to inhibit the action of TGF-beta at its receptor. These small molecules have been shown to be effective in reducing scar formation (fibrosis) when given orally to animals. Scios expects to advance two lead molecules, representing different chemical classes, into preclinical development that could potentially be used to treat disease conditions in patients with significant unmet medical needs.”
The present invention further relates to the use of the proteins identified according to the invention for generating diagnostic means for use in (molecular) imaging of one or more of the identified proteins to assess the level of the protein and thus identify a subject at risk of developing heart failure. The diagnostic means may for example comprise labeled antibodies directed against the biological protein markers.
The present invention is further illustrated by the following Figures and Examples.



FIGURES
FIG. 1: Increased expression of LIMP-2 in Ren-2 rats. (a) A left ventricular cardiac biopsy was taken at age 10 weeks, when Ren-2 rats exhibit comparable cardiac hypertrophy and fractional shortening cannot distinguish rats that will progress to heart failure or stay compensated. Between 15 and 18 weeks of age, part of the Ren-2 rats developed heart failure and the remainder stayed compensated until sacrifice at 21 weeks of age. *, P<5e−6. (b) LIMP-2 mRNA was found by microarray analysis in 10 weeks-old hypertrophic Ren-2 rats to be specifically overexpressed in failure-prone rats (HF-prone LVH, n=4), as compared to the hypertrophied LVs that remained compensated (comp LVH, n=6) and to controls (n=4). (c) LIMP-2 protein was up-regulated in end-stage failing Ren-2 rats (HF, n=9), as compared to compensated Ren-2 rats (comp, n=6). Both failing and compensated Ren-2 rats had significantly-elevated levels of LIMP-2 protein as compared to control rats (n=6). *, P<0.05 versus control; **, P<0.01 versus control; $, P<0.05 versus comp; Mwm, molecular weight marker; au, arbitrary units.
FIG. 2 AngII-treated LIMP-2 KO (KO Ang) mice have dilated cardiomyopathy. (a) WT Ang mice (n=14) significantly increased their LV weight, while KO Ang (n=14) mice did not (*, P<0.0 versus WT (n=8) and KO Ang). In KO Ang mice, individual myocytes failed to increase their volume (WT and KO, n=4; WT Ang and KO Ang, n=5; myocyte area (au): 264±42, versus 308±14 in WT Ang; *, P<0.01). Bars represent 50 μm. (b) LIMP-2 KO (n=3) and WT (n=4) mice showed comparable blood pressure responses to AngII. (c) AngII-treated WTs (n=8) and KOs (n=8) showed comparable increases in BNP and ANF mRNA expression (*, P<0.05 versus baseline (n=4)), while aska mRNA expression was induced to a significantly lesser extend in KO Ang mice, consistent with their reduced myocyte volume (*, P<0.05 versus KO (n=4); $, P<0.05 versus WT Ang). (d) Baseline echocardiographic parameters were similar for WT (n=10) and KO (n=11) mice (day 0). After 14 and 28 days of AngII, wild-type LV walls were significantly hypertrophied, while knockouts did not show hypertrophy and were even dilated (*, P<0.005 versus baseline and versus KO Ang; $, P<0.005 versus baseline and vs WT Ang). (e) Beta-adrenergic response to dobutamin was decreased in KO Ang mice (WT and KO, n=4; WT Ang, n=14; KO Ang, n=9; *, P<0.005). LVW/BW, LV weight corrected for body weight.
FIG. 3 AngII-treated LIMP-2 KO mice have massive interstitial fibrosis. Sirius red staining of LVs of AngII-treated LIMP-2 knockout (n=4) and wild-type (n=5) mice shows marked interstitial fibrosis in knockout mice (*, P<0.02 versus WT Ang and KO baseline), while both knockout and wild-type mice treated with AngII show similar degree of perivascular fibrosis. Bars represent 250 μm.
FIG. 4 AngII-treated LIMP-2 KO mice show myocyte disarray. Desmin-stained cardiac myocytes of AngII-treated LIMP-2 KO mice show disarray and have a disturbed internal structure, as shown by the higher and more capricious desmin-expression in these mice. Bars represent 250 μm.
FIG. 5 LIMP-2 expression is up-regulated in other forms of cardiac stress. (a) In neonatal rat cardiac myocytes, 6 hours stretch elevated LIMP-2 mRNA expression (n=4 per group). LIMP-2 mRNA was also up-regulated in hypertrophic myocardium (b) from rats that had undergone exercise training for 10 weeks (5 days per week, n=6) as compared to non-hypertrophic control rats (n=7) and (c) from patients suffering from aortic stenosis (LVH, n=20) as compared to non-hypertrophic control patients (n=7). *, P<0.05 versus control; **, P<0.01 versus control; LVH; LV hypertrophy.
FIG. 6 LIMP-2 is present at the plasma membrane of cardiac myocytes and is important for intercalated disc function. (a) Paraffin-embedded tissue section of pressure-overloaded mouse LV immunostained with anti-LIMP-2 shows positive staining not only in intracellular compartments (*) but also on plasma membranes of cardiac myocytes (). Scale bar represents 250 μm. (b) Immuno-electron microscopy with anti-LIMP-2 in pressure-overloaded rat LV tissue sections also shows the presence of LIMP-2 at the plasma membrane (). Scale bar represents 1 μm. (c) Electron microscopy shows normal intercalated discs in AngII-treated wild-type mice, while in AngII-treated LIMP-2 KO mice the intercalated discs have a higher degree of convolution and a higher concentration of adherens junctions (appreciate the dark black spots in the right panel), which is paralleled by the dilated cardiomyopathy in these mice. Bars represent 2 μm. M, mitochondrion; ID, intercalated disc; a, adherens junction; d, desmosome.
FIG. 7 LIMP-2 regulates cadherin distribution. (a) LIMP-2 binds to cadherin in neonatal rat ventricular myocytes. LIMP-2 was immunoprecipitated (IP), and cadherin was immunoblotted (IB) in the total cell lysate (input), the supernatant (sup) and the precipitated protein lysate (IP). Part of the cadherin protein content of cardiac myocytes is bound by LIMP-2. (b) Tissue sections of control subject and 2 heart failure patients were immunofluorescently stained with anti-pan-cadherin (red) and anti-LIMP-2 (green). Arrows () show co-localisation of LIMP-2 and cadherin at the ID of cardiac myocytes. Bars represent 50 μm. (c) Tissue sections of AngII-treated LIMP-2 knockout and wild-type LVs were immunostained with anti-pan-cadherin. In wild-type mice the cadherin distribution is confined to the intercalated discs yielding a regular appearance of cadherin, while in LIMP-2 KO mice the localisation of cadherin has lost the typical pattern produced by a strict location at the intercalated disc. Bars represent 250 μm.
FIG. 8 LIMP-2 regulates intercalated disc integrity by regulating the binding of phosphorylated beta-catenin to cadherin. (a) Immunoblot (IB) of lysates of neonatal rat cardiac myocytes that were treated either with shRNA against LIMP-2 (shLIMP-2) or with control shRNA. After 10 days of culture cardiac myocytes show a 92% knockdown of LIMP-2 protein. Equal protein loading was confirmed by GAPDH. (b) Immunoblot (IB) shows diminished levels of P-beta-catenin after immunoprecipitation (IP) with anti-pan-cadherin in shLIMP-2 lysates as compared to control lysates. Cadherin loading was comparable in control and shLIMP-2 IP-lysates. Phosphorylation of beta-catenin in total shLIMP-2 and control protein lysates was comparable. *, P=0.0006. (c) Immunoblot showing the specificity of the immunoprecipitation with anti-pan-cadherin. When adding IgG instead of pan-cadherin antibody to the protein lysates, no P-beta-catenin is bound.
FIG. 9 a. KLF15 expression assessed by real-time CR in left ventricular biopsies from Ren-2 rats at the age of 10 weeks. After biopsy, rats were allowed to recover and followed to determine whether they would progress to failure or remain compensated. Expression of KLF15 is significantly down-regulated in hypertrophied hearts that remained compensated, but significantly further suppressed in the hypertrophied hearts that quickly progressed to overt failure, indicating that the level of KLF15 suppression identifies failure prone forms of cardiac hypertrophy; b. In situ hybridisation for KLF15 in a normotensive control heart compared to hypertrophic myocardium. The widespread nuclear staining in the normal heart is lost in a large number of myocytes, while there is residual staining in non-myocyte nuclei, indicating that KLF15 expression occurs specifically in cardiac myocytes; c. Stable knock-down of KLF15 by lentiviral introduction of short hairpin RNA, induced expression of BNP in cultured NRVM.
FIG. 10 a. Addition of TGFβ (10 ng/ml) to cultured cardiac myocytes almost completely suppressed KLF15 mRNA expression. Stable knock-down of the TGFβ type I receptor by lentiviral introduction of short hairpin RNA abolished this effect, demonstrating that TGFβ via its TGFβ type I receptor is capable of suppressing KLF15 expression; b. Whole heart homogenate immunoblotted against the Tgfβ type I receptor shows a substantial and significant reduction in expression of Tgfβ type I receptor, but no compete loss of the receptor; c. Immunohistochemistry demonstrates that the myocyte specific activation of cre resulted in a clear and robust loss of TGFβ type I receptors from cardiac myocytes when comparing WT hearts to the MerCreMer-TGFβ type I mice; d. Angiotensin II infusion induced a significant hypertrophic response in Wt mice, which was blunted in MerCreMer-TGFβ type I mice; e. Angiotensin II infusion induced a significant loss in fractional shortening as an indicator of loss of cardiac function, which was blunted in MerCreMer-TGFβ receptor mice; f. Angiotensin II infusion and subsequent hypertrophy induced a down-regulation of KLF15, which was blunted in the MerCreMer-TGFβ receptor mice.
FIG. 11 The upper panel shows significantly upregulated KLF15 mRNA in the mouse heart after AAV9-KLF15 injection, compared to green fluorescent protein (AAV9-GFP) injection. **: p<0.05 camp to GFP group. *: p<0.05 compared to GFP group. #: p<0.05 compared to GFP+AngII group. The lower panel shows significantly less hypertrophy in the AAV9-KLF15 group after AngII stimulation compared to the AAV9-GFP group with AngII (#: p<0.05). Statistical analysis with student's t-test, n=3-5 animals/group.



EXAMPLES
Example 1
Lysosomal Integral Membrane Protein-2 is a Novel Component of Intercalated Discs and Prevents Cardiomyopathy
Materials and Methods
Ren-2 Rats, Microarray Analysis and Immunoblotting
From 10-weeks old Ren-2 and Sprague-Dawley (SD) rats (Möllegard, Lille Skensveld, Denmark), a biopsy of the LV was taken as described previously (Van Haaften et al., 2006). Rats were followed by serial echocardiography at 10, 12, 15, 16, 18, 19 and 21 weeks of age and sacrificed at 15-18 weeks upon clinical signs of heart failure (heart failure-prone/HF-prone rats) or at 21 weeks when clinical signs of failure had not appeared (compensated/comp rats). Total RNA was isolated from LV biopsies and amplified as previously described (Schroen et al., 2004; Heymans et al., 2005), hybridized to Affymetrix rat 230 2.0 GeneChips and analyzed with Microarray Analysis Suite Software 5.0. LV protein extracts (50 μg) were immunoblotted with polyclonal rabbit anti-LIMP-2 (Novus Biologicals, Littleton, Colo., 1:500) and polyclonal rabbit anti-GAPDH (Abcam, Leusden, Netherlands; 1:10,000).
LIMP-2 Knockout Mice, RNA Isolation and Quantitative PCR Analysis
Ten to twelve weeks-old male LIMP-2 KO and WT C57/B16 mice weighing 20-25 grams were used. To study blood pressure effects of AngII, arterial pressures were monitored during intravenous infusions at doses of 0.5, 1.5, 5, 15, and 50 ng per minute. To study development of LV hypertrophy, AngII (1.5 μg/g/day) was infused subcutaneously by osmotic minipump 2004 (Alzet osmotic pumps, Cupertino, Calif.) for 28 days.
Echocardiography was performed at day 0, day 14 and day 28. At day 28 mice were hemodynamically monitored (dP/dt) using Millar® under basal and dobutamin stimulated conditions, where after LVs were removed. RNA was isolated with RNeasy mini kit (Qiagen, Valencia, Calif.) and SYBR Green quantitative PCR analysis was performed on a BioRad iCycler to determine BNP, ANF and alpha-skeletal actin (aska) expression (Table 1). LV sections were stained with hematoxylin-eosin (HE) and Picro serious red (SR) as described before (Junqueira et al., 1979), or were immunohistochemically stained with monoclonal mouse anti-pan-cadherin (Sigma, Saint Louis, USA; 1:500) and monoclonal mouse anti-human desmin (Dako Cytomation, Denmark, 1:50). Ultrastructural-analysis was performed by transmission electron microscopy as described previously (Schroen et al., 2004).
LIMP-2 in Aortic Stenosis and Heart Failure Patients
RNA was isolated from transmural biopsies obtained from 20 aortic stenosis patients and 7 non-hypertrophic control patients as described before (Heymans et al., 2005), and SYBR Green quantitative PCR analysis was performed to determine LIMP-2 expression (Table 1).
Double immunofluorescent stainings with rabbit anti-LIMP-2 (1:250, Cy2) and mouse anti-pan-cadherin (1:500, Cy3) were done on sections of 1 control subject and 2 patients that died of overt heart failure, as defined by an ejection fraction of less than 35%. Nuclear counterparts were stained with Topro-3 (Invitrogen, Breda, The Netherlands). Sections were imaged with a laser scanning confocal system (Leica, Rijswijk, The Netherlands), digitized at a final magnification of ×126 and analyzed with Leica Confocal Software. The ethics committees of the Academic Hospital Maastricht and of University Hospital Leuven approved the study, and all patients gave informed consent.
Cell Culture and Lentiviral Vector
A rat-LIMP-2 shRNA expressing lentiviral vector was generated by annealing complementary shLIMP-2 oligonucleotides (Table 1) and ligating them into HpaI XhoI digested pLL3.7 puro vector DNA (modified from a kind donation by Luk van Parijs, Massachusetts Institute of Technology, Cambridge, USA). Lentiviral production was performed by co-transfection of 3 μg shLIMP-2/pLL3.7 puro or empty pLL3.7puro and packaging vectors into 293FT cells by Lipofectamine 2000 (Invitrogen) and virus-containing supernatant was harvested after 48 hours.
Rat ventricular cardiac myocytes (RCMs) were isolated by enzymatic disassociation of 1- to 2-day-old neonatal rats as described previously (De Windt et al., 1997). For lentiviral infection, RCMs were plated on gelatinized 6-wells plates with 5*105 cells per well, cultured overnight in DMEM/M199 (4:1) media supplemented with 10% horse serum, 5% newborn calf serum, glucose, gentamycin and AraC, and next day infected with shLIMP-2 or empty lentivirus, facilitated by Polybrene (Sigma). After puromycin selection (3 μg/ml), infection efficiencies were above 80%. After 10 culture days, cellular protein was isolated for immunoprecipitation (IP) with anti-LIMP-2 (1:100), monoclonal mouse anti-pan-cadherin (Sigma, 1:100) or IgG. IP lysates were immunoblotted with monoclonal anti-pan-cadherin (1:5000), polyclonal anti-phospho-beta-catenin (Ser33/37/Thr41; Cell Signaling Technology, Danvers, Mass., USA, 1:1000) and monoclonal anti-beta-catenin (BD Transduction Laboratories, Franklin Lakes, USA, 1:1000).
For stretch experiments, RCMs were cultured on a collagen type I-coated silastic membrane (Specialty Manufacturing, Inc, USA) and subjected to static, equibiaxial stretch during 6 hours. RNA was isolated with RNeasy mini kit (Qiagen) for LIMP-2 SYBR Green quantitative RT-PCR (Table 1). All study protocols involving animal experiments were approved by the Animal Care and Use Committee of the Universiteit Maastricht, and were performed according to the official rules formulated in the Dutch law on care and use of experimental animals, highly similar to those of the NIH.
Statistical Analyses
Data are presented as average±SEM. The data for each study group were compared using Mann Whitney or student's t-test where appropriate. P<0.05 was considered to be statistically significant.
Results
In Table 2, a list is presented of genes differentially expressed in failure-prone as compared to compensated Ren-2 rats. The differential expression of these genes precedes the development of heart failure in Ren-2 rats, because it is derived from cardiac biopsies taken at 10 weeks of age, when all rats still have compensatory hypertrophy.
In Table 3, elaborate echocardiographic data are presented of LIMP-2 WT and KO mice at baseline, and after 14 and 28 days of AngII treatment.
Gene Expression Profile of Failure-Prone LV Hypertrophy
Cardiac biopsies in 10 homozygous Ren-2 rats were obtained at a stage of compensated LV hypertrophy at 10 weeks of age. Four rats rapidly progressed towards heart failure within five weeks after the biopsy was taken, while the remaining 6 rats remained compensated for 11 weeks after biopsy (FIG. 1a). After linear T7 based amplification and subsequent Affymetrix 230 2.0 gene expression analysis in these biopsies (GEO number GSE4286), 143 differentially expressed genes that were up- or downregulated only in the hypertrophied hearts that progressed towards heart failure were identified (Table 2). LIMP-2, a lysosomal membrane protein, was one of the up-regulated mRNAs in heart failure-prone rats (FIG. 1b), and of particular interest given its ability to interact with thrombospondins (TSP) 1 (Crombie et al., 1998) and 2 (data not shown), the latter has been shown earlier to be crucial in the transition from hypertrophy towards heart failure. FIG. 1c shows that LIMP-2 protein also has a role in end-stage heart failure in Ren-2 rats.
Angiotensin II Induces Dilated Cardiomyopathy in LIMP-2 Knockout Mice
Since loss-of-function mutations in lysosomal proteins have been linked to heart failure (Eskelinen et al., 2003; Nishino et al., 2000; Stypmann et al., 2002), the role of LIMP-2 in a mouse model of angiotensin II (AngII) induced hypertension was further investigated. AngII was given subcutaneously for 4 weeks to LIMP-2 knockout and control mice. AngII treatment resulted in a 30% increase in LV mass index in wild-type mice, but the hypertrophic response was attenuated in the AngII-treated LIMP-2 knockout mice (14% increase in LV mass index; P<0.01) (FIG. 2a). This was confirmed by measurement of individual cardiac myocyte area. LV myocyte area was significantly smaller in AngII-treated knockout mice than in AngII-treated WT controls (myocyte area in arbitrary units: 264±42 in AngII-treated knockout mice, versus 308±14 in AngII-treated wild-types; P<0.01). In addition, while AngII induced comparable increases in perivascular fibrosis in LIMP-2 knockout and wild-type mice (data not shown), AngII induced a massive interstitial fibrotic response in the LV of LIMP-2 knockout mice as opposed to wild-type control littermates (interstitial fibrosis: 15.0±6.0% in AngII-treated knockout mice versus 1.8±0.1% in AngII-treated controls; P<0.002) (FIG. 3).
Immunohostochemical staining for desmin showed myocyte disarray in AngII-treated LIMP-2 null mice (FIG. 4).
It was confirmed that AngII induced a similar blood pressure response in both wild-type and knockout mice (FIG. 2b). Despite decreased LV hypertrophy, LIMP-2 null mice demonstrated a normal response of the classical markers for hypertrophy Brain Natriuretic Peptide (BNP) and Atrial Natriuretic Factor (ANF) (FIG. 2c), suggesting that the hypertrophic gene expression program was normally initiated upon AngII-treatment. In contrast, the structural cellular hypertrophy marker alpha-skeletal actin was induced to a significantly lesser extent in AngII-treated LIMP-2 knockouts as compared to AngII-treated wild-types (FIG. 2c), reflecting the reduced hypertrophic response of cardiac myocytes (Stilli et al., 2006). Serial echocardiography revealed that AngII induced significant cardiac dilatation in Ang-II treated LIMP-2 null mice, whereas AngII-treated wild-types showed concentric LV hypertrophy without dilatation (FIG. 2d and Table 3). In addition, AngII induced loss of contractile reserve in LIMP-2 null mice as demonstrated by a reduced contractile response to dobutamine infusion (+dP/dt 79.8/second±5.1 in AngII-treated knockout mice versus 100.0/second±4.0 in AngII-treated controls; P<0.005) (FIG. 2e).
Taken together, in LIMP-2 null mice hypertension did not induce the normal hypertrophic response but rather dilated cardiomyopathy with reactive interstitial fibrosis and loss of cardiac function.
LIMP-2 Expression is Regulated by Cardiac Stress
The finding that AngII-treated LIMP-2 null mice failed to mount a hypertrophic response, yet normally induced expression of BNP and ANF suggested that LIMP-2 is a crucial part of the normal response to mechanical loading. Indeed it was also shown that LIMP-2 expression increased significantly after cardiac myocyte stretch in vitro (P=0.02) and also increased in exercise-induced physiological hypertrophy (P=0.04) (FIGS. 5a and b). To ascertain that LIMP-2 is also involved in the human adaptation to cardiac pressure loading, the expression of LIMP-2 was analyzed by quantitative RT-PCR in cardiac biopsies of 20 aortic stenosis patients with overt cardiac hypertrophy and 7 controls. This experiment showed a significant LIMP-2 upregulation in the hypertrophic hearts of aortic stenosis patients as compared to controls by Mann-Whitney test (1.23-fold; P=2.3e−4).
LIMP-2 is Present at the Cardiac Intercalated Disc
Next the expression pattern of LIMP-2 in pressure overloaded murine myocardium was analysed by immunohistochemistry. The protein is expressed, as expected, in intracellular vacuole-shaped compartments of cardiac myocytes and endothelial cells, but was also found to be atypically distributed on the plasma membrane of cardiac myocytes (FIG. 6a). Immuno-electron microscopy confirmed this finding (FIG. 6b). Strikingly, electron-microscopy of AngII-treated LIMP-2 knockout and control left ventricular sections revealed abnormal morphology of the ID in LIMP-2 null mice, suggesting that LIMP-2 may be involved in normal ID biology. At cell-cell contacts, the membrane at the AngII-treated KO-ID showed a higher degree of convolution with a higher concentration of adherens junction proteins (FIG. 6c), indicative of disturbed ID architecture (Perriard et al., 2003). Since alterations in the ID have been shown to cause dilated cardiomyopathy (Periard et al., 2003), it was surmised that LIMP-2 may be crucial for proper functioning of the ID.
Immunoprecipitation of neonatal rat cardiac myocytes protein showed that LIMP-2 physically interacts with N-cadherin, a vital constituent of adherens junctions (FIG. 7a). This finding was translated to the human situation as confocal microscopy of control as well as failing human myocardium confirmed the interaction between cadherin and LIMP-2 and showed that this interaction takes place at the site of the ID, where cadherin and LIMP-2 co-localize (FIG. 7b). This suggested that LIMP-2 may be important for proper ID function by mediating the role of cadherin. Indeed, histochemical analysis of cadherin in hearts of LIMP-2 null mice showed aberrant cadherin distribution (FIG. 7c), but normal distribution in AngII-treated wild-types. AngII-treated wild-type mice show cadherin expression at the contact sites between two longitudinal cardiac myocytes, while this expression is less organized and more diffuse in cardiac myocytes of AngII-treated LIMP-2 knockout mice. These data establish that LIMP-2 is crucial for the proper structural organization of the intercalated disc.
LIMP-2 Regulates Intercalated Disc Integrity
To identify which regulatory mechanism depends on LIMP-2, lentivirally introduced short-hairpin RNA against LIMP-2 (shLIMP-2) was used to obtain a separate model of LIMP-2 inactivation in neonatal rat cardiac myocytes. After 10 days of culture, LIMP-2 protein expression was diminished by 92% in shLIMP-2 treated cardiac myocytes as compared to control treated cardiac myocytes (FIG. 8a). It has been reported that the functional integrity of the intercalated disc depends on the proper interaction between P(Ser37)-β-catenin and cadherin. Therefore, it was investigated whether the absence of LIMP-2 affected the binding of P-β-catenin to cadherin.
Immunoprecipitation of cadherin in lysates of cardiac myocytes showed that knock-down of LIMP-2 indeed diminished the interaction between P-β-catenin and cadherin (FIG. 8b). Immunoprecipitation was specific for cadherin (FIG. 8c).
It was demonstrated in this study that the lysosomal protein LIMP-2 is an, important and novel component of the cardiac myocyte intercalated disc, in particular adherens junctions. According to the present invention, it has been shown that LIMP-2 binds to N-cadherin, and that LIMP-2 null mice develop dilated cardiomyopathy upon AngII-induced hypertension, accompanied by disturbed localisation of N-cadherin in the heart. Confirming this in-vitro it was shown that knock-down of LIMP-2 in cultured myocytes disturbs interactions between N-cadherin and β-catenin. This suggests that LIMP-2, which was initially known as a lysosomal protein, is an important part of the intercalated disc.
LIMP-2 has a Role in the Heart During Pressure Overload
LIMP-2 stands out among ID proteins. Complete loss of other major constituents of the ID (cadherin, β-catenin, plakoglobin) results in lethal developmental cardiac derangements, suggesting that these components of the ID are essential for normal cardiac development. In contrast, according to the invention it was found that LIMP-2 null mice have normal cardiac development, but that its loss only affects postnatal cardiac remodeling. This suggests that LIMP-2 represents a different type of ID protein, whose role is essential mainly under increased loading conditions. This specific role for LIMP-2 is underlined by the finding that expression of LIMP-2 further rises in hypertrophied rat hearts that are on the brink to progress to failure, which suggests that LIMP-2 expression particularly increases in cardiac myocytes which seem unable to normalize loading conditions. Taken together, it was suggested that LIMP-2 is a novel mediator of ID function, and represents a hitherto unidentified class of mediators that are essential for the ID and the myocyte to respond to increased loading conditions.
LIMP-2 Null Mice Respond Abnormally to Increased Loading
LIMP-2 increased particularly in those hypertrophied hearts that would later progress to failure, in comparison to the hypertrophied hearts that remained compensated. This indicates that cardiac LIMP-2 expression may be an early molecular sign of excessive loading. That LIMP-2 constitutes a defensive mechanism against excessive loading is suggested by the finding that when LIMP-2 null mice were subjected to pressure loading by chronic angiotensin II infusion, they developed cardiac dilatation and fibrosis, yet very little cardiac myocyte hypertrophy. Natriuretic peptides were normally induced, which suggests that the cardiac myocytes of LIMP-2 null mice do sense increased loading conditions, yet fail to mount an adequate hypertrophic response, as evidenced by the attenuated expression of alpha-skeletal actin. This suggests that LIMP-2 is essential for a normal response to cardiac loading, and that LIMP-2 expression is strongly increased when loading conditions exceed compensatory mechanisms. These findings were translated to the human situation, which showed that LIMP-2 is also robustly increased in patients with clinically severe pressure loading. Taken together, LIMP-2 is a novel constituent of the ID and seems to represent a novel type of ID protein, essential for the response to loading rather than for normal cardiac function.
Mechanisms of LIMP-2 Response to Loading
Intercalated disc abnormalities were documented in pressure-loaded LIMP-2 null mice, characteristic of a disturbed cardiac intercalated disc, which normally acts to organise adjoining myocytes. Remodelling of the intercalated disc has been shown previously during the transition from compensated LV hypertrophy towards heart failure, while structural perturbations of the intercalated disc have been linked to dilated cardiomyopathy in humans, hamsters and pigs. It was shown that LIMP-2 binds N-cadherin, suggesting a role for LIMP-2 via this ID constituent. Indeed, pressure overloaded LIMP-2 KO mice show abnormal intercalated discs on electron microscopy and their N-cadherin distribution is disturbed, suggesting a defect in the adherens junctions. The strength of adherens junctions is determined by the binding affinity between N-cadherin and β-catenin (Gumbiner et al., 2000), which is regulated by phosphorylation of the latter. It was shown in-vitro, by knock-down of LIMP-2 in cultured myocytes, that loss of LIMP-2 disturbs this N-cadherin/β-catenin complex. Given the linkage of adherens junctions to myofibrils, a loss of LIMP-2 is expected to lead to less efficient force transduction across the plasma membrane (Ferreira et al., 2002).
It has been suggested that LIMP-2 is essential for the proper binding of N-cadherin to β-catenin, and that this role is particularly important under loading conditions. However, the precise way by which LIMP-2 assures binding of N-cadherin to β-catenin remains to be elucidated. LIMP-2 contains two transmembrane domains, a cytoplasmic loop and two luminal glycosylated domains. It is known that lysosomal membrane proteins can shuttle between lysosomal and plasma membranes, where LIMP-2 can bind to TSP1 and -2 (data not shown). This latter is intriguing, as it has been documented earlier that TSP2 is also essential for the response to cardiac pressure loading and increases in failure prone forms of LV hypertrophy (Schroen et al., 20040. This suggests that both LIMP-2 and TSP2 may be part of a complex that is needed for the cardiac myocyte to mount an adaptive response to loading.
Implications
According to the present invention, a novel role for LIMP2 has been uncovered as an important mediator of the ID when the myocardium faces increased loading conditions. Apart from this novel biological insight, the finding that expression of LIMP-2 rises in hypertrophied rat hearts that are on the brink to progress to failure, makes it tempting to speculate that increased LIMP-2 expression by cardiac myocytes demonstrates their inability to normalize loading conditions. As such, increased LIMP-2 expression may signify imminent failure. Since it has been shown that LIMP-2 expression is also robustly increased in patients with clinically severe pressure loading, and is located at the plasma membrane, LIMP-2 may be an attractive target for molecular imaging to identify already in a very early stage, the myocardium that is about to succumb to the pressure.
Example 2
TGF-Beta Promotes Cardiac Hypertrophy by Suppressing Krüppel Like Factor 15, a Novel Inhibitor of Cardiac Hypertrophy
Materials and Methods
Transgenic Rats, Left Ventricular Biopsies and Hemodynamic Studies
Eighteen male homozygous Ren-2 rats and 5 age-matched Sprague-Dawley (SD) (Möllegard Breeding Center, Lille Skensveld, Denmark) were studied. Three Ren-2 rats were sacrificed at 10 to 12 weeks of age upon clinical signs of heart failure and excluded from the study. From the remaining healthy 15 Ren-2 rats and 5 SD controls a biopsy of the left ventricle was taken at 10 weeks of age, as described previously. Rats were followed by serial echocardiography at 10, 12, 15, 16, 18, 19 and 21 weeks of age as described above. Nine Ren-2 rats were sacrificed at 15 to 18 weeks of age upon clinical signs of heart failure and designated ‘heart failure-prone’ rats. The remaining 6 Ren-2 rats were monitored and sacrificed at 21 weeks when clinical signs of failure had not appeared, and they were designated ‘compensated’ rats.
Microarray Analysis
Total RNA was isolated and amplified as previously described from LV biopsies taken at 10 weeks of age of 4 SD controls, of 6 rats that remained compensated and of 4 heart failure-prone rats. Amplified cRNA was then hybridized to Affymetrix rat 230 2.0 GeneChips. Gene transcript levels of SD controls, compensated and HF rats were determined with Microarray Analysis Suite Software version 5.0 (MAS5.0).
Lentiviral shKLF15 Production
Lentiviral vectors were generated by annealing complementary shKLF-15 oligonucleotides (sense 5′-GATGTACACCAAGAGCAGC-3′ (SEQ ID NO:1) and antisense 5′-GCTGCTCTTGGTGTACAT-3′ (SEQ ID NO:2)) and cloning them into digested pLL3.7 puro vector DNA (kindly donated by Luk van Parijs, Department of Biology, Massachusetts Institute of Technology, Cambridge, USA) using E. Coli DH5a competent cells. Constructs were purified using Qiagen Plasmid Midi kit. 293 FT cells were cultured in DMEM with 10% FCS, 2 mM L-Glut, 10 mM non essential amino acids, 1 mM sodium pyruvate and pen/strep antibiotics. Lentiviral production was performed by co-transfection of 3 μg shKLFl5 or shTgfbr1/pLL3.7 puro or empty pLL3.7 puro and packaging vectors into 293FT cells by Lipofectamine 2000 (Invitrogen Life Technology, Breda, The Netherlands) and virus containing supernatant was harvested, filtrated and snap-frozen after 48 hours.
Neonatal Rat Ventricular Myocyte Experiments
Neonatal rat ventricular myocytes (NRVM) were isolated by enzymatic disassociation of 1-3-day-old neonatal rat hearts as previously described (Schroen et al., 2004). NRVMs were cultured in DMEM/M199 (4:1) media supplemented with 10% horse serum (HS), 5% new born calf serum (NBCS), glucose, gentamycin and 2% antibiotic/antimycotic on a gelatinized 6-well plate with 5*105 cells per well. For shKLF15 infection, NRVM were cultured overnight and the next day infected with shKLF15 and an empty lentiviral control vector, facilitated by polybrene (Sigma). After 48 hours cells were washed free of vector and placed under puromycin selection for another 48 hours. Then, cells were kept under quiescent conditions overnight in DMEM/M199 (4:1), glucose, gentamycin and 10% antibiotic/antimycotic. The next day, medium was replaced by medium containing DMEM/M199, glucose, gentamycin, 5% antibiotic/antimycotic, insulin, L-carnitin and BSA. After 1 hour TGF-b (10 ng/ml medium) was added for 1 hour and whereafter RNA was isolated using the RNeasy mini protocol (Qiagen) for SYBR Green quantitative PCR with KLF15 or BNP primers (F 5′-GCT GCT TTG GGC AGA AGA TAG A-3′ (SEQ ID NO:3), R 5′-GCC AGG AGG TCT TCC TAA AAC A-3′ (SEQ ID NO: 4)). Knock-down efficiency of shKLF15 is about 80% compared to levels in NRVM infected with an empty lentiviral vector.
MEF2 Luciferase Promotor Assay
NRVM were isolated as described above. Cells were cultured in DMEM/M199 (4:1) media supplemented with 10% horse serum (HS), 5% new born calf serum (NBCS), glucose, gentamycin and 2% antibiotic/antimycotic on a gelatinized 6-well plate with 5*105 cells per well. For shKLF15 infection, NRVM were cultured overnight and the next day infected with shKLF15 and an empty lentiviral control vector, facilitated by polybrene (Sigma). After 48 hours cells were washed free of vector and placed under puromycin selection for another 48 hours. A Mef2 reporter plasmid (pGL2-3xMEF2-luciferase) containing three Mef2 binding sites cloned upstream of the Tata-box and luciferase in the cells via transient transfection. Cells were washed and per well, 1.6 μg of the MEF2 construct was added together with Opti-MEM I media (Invitrogen) and lipofectamine 2000, and antibiotics free media. The next morning, cells were washed and placed under normal culture media for another two days. Cells were kept overnight under low serum conditions (see above) and the next morning AngII (x grams/ml) was added for 4 hours. The luciferase assay was performed using the Luciferase Assay Protocol (Promega).
Generation of Double Transgenic Mice
TGFβRIf/f mice (C57Bl/6 background) generated by flanking exon 3 of TGFβRI with lox-P site (Sohal et al., 2001) were crossed with mice (C57Bl/6 FVB background) containing cre-recombinase under the control of α-MHC promoter (MerCreMercre/wt (Larsson et al.) to generate heterozygous double transgenic mice that contained TGFβRIf1/wtcre genes. These mice were then back-crossed with TGFβRlf/f mice resulting in a colony with TGFβRIf/cre and TGFβRlf/wcre in a mixed background of C57Bl/6 FVB, and C57BL/6.
DNA Isolation and Genotyping
DNA was isolated from the mouse tail using genomic DNA Purification kit (Promega) according to the manufacturer's instruction. We used PCR to assess the genotype of TβRI flox mice, using the 3 primers, 5-ATG AGT TAT TAG AAG TTG TTT (SEQ ID NO:5), 3′-ACC CTC TCA CTC TTC CTG AGT (SEQ ID NO:6), and 3′-GGA ACT GGG AAA GGA GAT AAC (SEQ ID NO:7) as previously described (Sohal et al., 2001).
Cre Recombination Protocol
To induce α-MHC-coupled cre recombinase in cardiomyocytes, adult TGFβRIf/fcre and TGFβRlf/wtcre double transgenic mice were treated with tamoxifen (Sigma) at a dose of 20 mg/kg per day for 7 days by subcutaneous insertion of mini-osmotic pumps (ALZET, model 200 l). A group of wild type mice was treated with tamoxifen to check whether tamoxifen itself had any effects on cardiac morphology and function. Tamoxifen was dissolved in 10% ethanol and 90% polyethyleneglycol-400 followed by a brief sonification. Mice were allowed to recover for 2 weeks prior to treatment with Ang II or vehicle.
Subcutaneous Implantation of Mini-Osmotic Pumps and Ang II Infusion
Mice of either sex weighing 24-32 g were anesthetized with 2.5% isofluorane. Under sterile conditions, a midscapular incision was made, a pocket was created in the subcutaneous tissue by a blunt dissection and a mini-osmotic pump (ALZET model 2004; ALZACorp., Palo Alto, Calif., USA) filled with saline or Ang II (0.5 mg/kg/day) was inserted. The contents of the mini-osmotic pump were delivered into the local subcutaneous space at a rate of 0.25 μl/hour for 4 weeks. In each group, 7 to 9 mice were recruited for experiments and at least 5 mice from each group completed the experiments. All the dropouts were due to death from anaesthesia except 3 animals in which LV catheterisation did not succeed.
Echocardiography
Transthoracic echocardiography was performed preoperatively and after 4-week of angII infusion in wild type, TGFβRI−/− and TGFβRl−/+ mice under 2.5% isofluorane anaesthesia. Standard views were obtained in 2D-echocardiography, end-diastolic and end-systolic internal diameters were measured and ejection fraction and fractional shortening were calculated.
Hemodynamic Measurements
Mice were anaesthetized with intraperitoneal injection of urethan. A Millar (1.4 F) catheter (Millar Instruments Inc., Houston, Tex., USA) was placed in the right common carotid artery and advanced into the left ventricle for the measurement of left intraventricular pressure. Body temperature was maintained at 37° C. using a thermally controlled surgical table and monitored with a rectal probe. The mice were then allowed to stabilize for 30 minutes prior to hemodynamic measurements.
Tissue Procurement and Myocardial Morphometry
Following hemodynamic measurements, hearts were rapidly excised, washed in 0.9% sodium chloride solution, atria were removed and the ventricles were cut into pieces. For RNA and protein isolation, samples were snap frozen in liquid nitrogen and stored in −80° C. For histological analysis, left ventricles were fixed in paraformaldehyde (1%) and embedded in paraffin. For the visualization of total collagen, picrosirius staining was performed as described previously. P38 was localized by immunostaining using anti-P38 antibody according to the manufacturer's instruction (Cell Signaling Technology, Leusden, the Netherlands).
Protein Isolation and Western Blotting
Frozen ventricles were crushed and homogenized in radioimmunoassay buffer according to the standard protocol (Santa Cruz Biotechnology, Leiden, the Netherlands). Western blotting was performed using specific antibodies against TβRI (1:1000), total and phospho (P)-Smad2, total and P-P38 (1:1000, Cell Signaling Technology, Leusden, the Netherlands), P-Smad3 (I: 5000, a kind gift from Professor E. Leof and Dr M. Wilkes, Mayo Clinic Cancer Research, Rochester, Minn., USA), collagen I (1:3000) and III (1:500) antibodies (Abcam, Leusden, the Netherlands).
TGFβ Type 1 Receptor Immunohistochemistry
Cardiac tissue sections were deparaffinised and rehydrated and antigen retrieval tissue was incubated overnight with the primary antibody (rabbit anti TGFβ receptor 1 (Santa Cruz SC-398) and subsequently the secondary antibody (Goat anti Rabbit-Biotine (DakoCytomation E0432), whereafter they were treated with Streptavidin-Horseradish Peroxidase (Renaissance TSA TM Biotin System, Perkin Elmer Precisely, Tyramide Signal Amplification kit).
All study protocols described above involving animal experiments were approved by the Animal Care and Use Committee of the Maastricht University, and were performed according to the official rules formulated in the Dutch law on care and use of experimental animals, highly similar to those of the NIH.
Statistical Analyses
Data are shown as mean±SEM. Unpaired t-test was performed to compare the difference between the means of Ang II/TGFβ/shKLFl5 and vehicle treated animals and cells. P-values of ≦0.05 were considered statistically significant.
Results
It has previously been shown that the outbred homozygous hypertensive TGR(mRen2)27 rat (Ren-2) allows to study the transition from hypertrophy towards heart failure (Schroen et al., 2004). Myocardial biopsies obtained at the age of 10 weeks were used to investigate whether altered gene expression can predict which rat later will later progress to heart failure.
Expression profiling of these biopsies revealed that suppression of the gene coding for Krüppel-like factor 15 (KLF15) characterised the hypertrophied hearts that would quickly progress to failure. This was confirmed by real-time PCR which showed that KLF15 was down-regulated in compensated LVH, but that it was significantly further suppressed in the hypertrophied hearts that quickly progressed to failure (FIG. 9a). In-situ hybridisation showed that expression of KLF15 was particularly down-regulated in cardiac myocytes (FIG. 9b). These findings extend earlier observations that KLF15 is constitutively expressed in the heart, but down-regulated in hypertrophy. That more intense suppression of KLF15 preceded the transition towards heart failure, has led to the suggestion that KLF15 has important protective properties. To explore the functional role of KLF15, a short hairpin RNA (shRNA) against KLF15 was stably introduced. Spontaneous expression of BNP, a molecular hallmark of the hypertrophy gene program, was induced more than 10-fold upon shRNA mediated suppression of KLF15 in cultured cardiac myocytes (FIG. 9c). This suggests that the constitutive presence of KLF15 is important to prevent the expression of the hypertrophy gene program.
In a parallel study, it has been shown that KLF15 null mice develop hypertrophy and cardiac function loss upon pressure loading, underlining that constitutively expressed KLF15 is essential to protect against maladaptive forms of LVH.
To explore the mechanism by which KLF15 can repress the hypertrophy gene program, its role in activation of MEF2 was studied. MEF2 is a target for hypertrophic signalling conveyed by the calcineurin and the MAPK pathway and is recognized as one of the crucial transcriptional activators of the hypertrophy gene program. A MEF2 reporter construct was used to address whether altered levels of KLF15 affect MEF2 activity in cardiac myocytes. This reporter only weakly responds to stimulation by MEF2 (Creemers, Olson unpublished data). Indeed only minor increases in MEF2 activity were observed in response to angiotensin II. However, knockdown of KLF15 significantly increased MEF2 activity (FIG. 9c) suggesting that KLF15 acts as a repressor of MEF2.
It was next sought to explore which mechanism suppresses KLF15 in cardiac myocytes. Therefore known mediators of cardiac hypertrophy were screened for their ability to inhibit KLF15 expression in cardiac myocytes. In cultured cardiac myocytes, TGFβ very robustly suppressed KLF15, so that expression of KLF15 was almost completely abolished after addition of TGFβ. Knockdown of the TGFβ type I receptor by inhibitory RNA prevented the suppression of KLF15 by TGFβ (FIG. 10a) demonstrating that classical TGFβ signalling involving its type I receptor is essential for this effect.
Therefore, to address the regulation of KLF15 by the TGFβ type I receptor in-vivo mice carrying a floxed TGFβ receptor type I gene combined with the MerCreMer allele were generated which allows to activate cre specifically in cardiac myocytes by administration of tamoxifen (Larsson et al., Sohal et al., 2001). This allowed to delete the TGFβ type I receptor specifically in cardiac myocytes in adult mice, avoiding the developmental effects of an embryonic loss of the TGFβ I receptor. Hypertension was induced by chronic angiotensin II infusion as described above in these mice to provoke hypertrophy and down-regulation of KLF15. Western blotting of whole heart homogenate revealed a significant down-regulation of the TGFβ type I receptor (FIG. 10b). Immunohistochemistry confirmed the myocyte specific down-regulation of the TGFβ type I receptor, and showed the expression of this receptor in other cell types explaining the residual signal of the TGFβ type I receptor found in the whole heart homogenate (FIG. 10c). Angiotensin II induced LVH in wild type mice, but the development of LVH was prevented in the MerCreMer-TGFβ type I mice (FIG. 10f). While in WT mice angiotensin II decreased fractional shortening, fractional shortening remained preserved in the MerCreMer-TGFβ type I mice. This indicates that loss of the TGFβ type I receptor from cardiac myocytes can prevent hypertension induced hypertrophy and function loss. As expected, the expression of KLF15 was suppressed in the hypertrophied hearts from WT mice, but this suppression was absent in the hearts of MerCreMer-TGFβ type I mice (FIG. 10g). This shows that the TGFβ type I receptor on cardiac myocytes is important for the development of hypertensive hypertrophy, and at the same time for the suppression of KLF15.
Taken together, KLF15 is the first Krüppel Like Factor to have a role in cardiac myocytes as a suppressor of cardiac hypertrophy. KLF15 inhibits MEF2 and parallel work shows it inhibits other prohypertrophic transcription factors like GAT4 as well. Consequently, it is conceivable that loss of KLF15 very robustly induces hypertrophic gene expression and is related to an adverse outcome. Suppression of KLF15 may therefore be a novel and crucial step in the development of failure prone forms of hypertrophy. It has been shown that TGFβ very robustly can suppress KLF15. Inhibitors of TGFβ, which are currently being developed in different fields, thus may have unexpected therapeutic potential as to prevent cardiac hypertrophy from progressing towards heart failure.
Conclusion
The heart hypertrophies in response to loading and injury, which often progresses towards overt heart failure. According to the present invention, a novel mechanism in this process is unveiled, where the cytokine TGFβ suppresses a novel inhibitor of hypertrophy, Krüppel Like factor 15 (KLF-15). Loss of the TGFβ type I receptor in-vivo and in-vitro prevents the suppression of KLF-15 and the development of cardiac hypertrophy and failure. The finding that TGFβ can hinder this novel mechanism that suppresses cardiac hypertrophy, opens exciting possibilities for inhibition of TGFβ signalling to prevent adverse forms of cardiac hypertrophy.
Example 3
Krüppel-Like Factor 15, a Transcriptional Repressor of Cardiac Hypertrophy
According to the invention it has been shown that the zinc-finger transcription factor, Krüppel-like factor-15 (KLF-15) is a potent transcriptional repressor of LV hypertrophy. Gene-targeting studies showed that KLF15 null mice develop normally, but in response to pressure overload, develop an exaggerated form of cardiac hypertrophy, characterized by increased heart weight, increased expression of hypertrophic genes, left ventricular cavity dilatation with increased myocyte size and reduced left ventricular systolic function. All together, these studies demonstrate a role for KLF15 in LV hypertrophy, in vivo.
Interestingly, KLF15 is down-regulated in several forms of pathological but not physiological hypertrophy, indicating that KLF15 is a regulator of pathological hypertrophy, but not of physiological hypertrophy. The fact that KLF15 counteracts hypertrophy and the additional observation that KLF15 is significantly down-regulated in pathological hypertrophy and heart failure led to the exciting possibility that interventions aimed at preventing the decrease of KLF15 levels could prevent or even reverse pathological growth.
In Vivo Experiment
To test the intriguing possibility that preventing the loss of KLF15 during pathological hypertrophy may limit pathological growth of the heart, KLF15 was overexpressed specifically in the mouse heart using recombinant adeno-associated virus (rAAV)-mediated gene delivery under the control of the cardiac troponin I promoter (Vandedriessche et al., 2007). In particular, rAAV9 vectors have been shown to achieve a robust increase of transgene expression in cardiac tissue for several weeks following intravenous administration.
Mice were intravenously injected with 1×1010 vg AAV9-KLF15 or AAV9-GFP, after which hypertrophy was induced by Angiotensin II (AngII) treatment (4 weeks, through osmotic minipumps). As shown in FIG. 11 (upper panel) KLF15 was overexpressed in the heart. Strikingly, mice allocated to AAV9-KLF15 gene transfer developed significantly less hypertrophy upon AngII stimulation, compared to AngII treated mice that received AAV9-GFP. (see FIG. 11, lower panel). Together, these-data show that forced expression of KLF-15 in cardiac myocytes suffices to reduce cardiac hypertrophy.
Conclusion
Loss of KLF15 is a vital step in the development of hypertrophy and the transition towards heart failure. The observation that cardiac overexpression of KLF15 inhibits the development of pathological hypertrophy opens exciting possibilities for strategies that prevent the down-regulation of KLF15 in vivo to prevent hypertrophy and subsequent heart failure







TABLE 1







List of primers for SYBR Green PCR and for


shLIMP-2 production









Gene
Primer
Sequence





Mouse-BNP
F
5′-GTTTGGGCTGTAACGCACTGA-3′




(SEQ ID NO: 8)



R
5′-GAAAGAGACCCAGGCAGAGTCA-3′




(SEQ ID NO: 9)


 


Mouse-ANF
F
5′-ATTGACAGGATTGGAGCCCAGAGT-3′




(SEQ ID NO: 10)



R
5′-TGACACACCACAAGGGCTTAGGAT-3′




(SEQ ID NO: 11)


 


Mouse-aska
F
5′-TGAGACCACCTACAACAGCA-3′




(SEQ ID NO: 12)



R
5′-CCAGAGCTGTGATCTCCTTC-3′




(SEQ ID NO: 13)


 


Mouse-PPIAa
F
5′-CAAATGCTGGACCAAACACAA-3′




(SEQ ID NO: 14)



R
5′-GCCATCCAGCCATTCAGTCT-3′




(SEQ ID NO: 15)


 


Human-LIMP-2
F
5′-GTTTGGGCTGTAACGCACTGA-3′




(SEQ ID NO: 16)



R
GAAAGAGACCCAGGCAGAGTCA-3′




(SEQ ID NO: 17)


 


Human-GAPDHa
F
5′-ACCCACTCCTCCACCTTTGAC-3′




(SEQ ID NO: 18)



R
5′-ACCCTGTTGCTGTAGCCAAATT-3′




(SEQ ID NO: 19)


 


Rat-LIMP-2
F
5′-TGCGTCCAAACAAGGAAGAAC-3′




(SEQ ID NO: 20)



R
5′-AATCTCTTGGCCCCTCTTAAAATAA-3′




(SEQ ID NO: 21)


 


Rat-PGK-1a
F
5′-CGGAGACACCGCCACTTG-3′




(SEQ ID NO: 22)



R
5′-AAGGCAGGAAAATACTAAACATTGC-3′




(SEQ ID NO: 23)


 


Rat-shLIMP-2b
Sense
5′-GGAAGAACATGAGTCATTT 




AAATGACTCATGTTCTTCCTTTTTC-3′




(SEQ ID NO: 24)



Anti-
5′-TCGAGAAAAAGGAAGAACATGAGTCATT



sense
T AAATGACTCATGTTCTTC




C-3′




(SEQ ID NO: 25)





aHousekeeping genes: cyclophilin A (PPIA), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase 1 (PGK-1)


bRat-shLIMP-2 oligonucleotides; hairpin structure in bold italic













TABLE 2







Genes that are differentially expressed in biopsies of failure-prone


Ren-2 rats as compared to compensated Ren-2 rats.










Probe Set

Fold



IDa
p-valueb
Changec
Gene Named













1374153_at
0.000052
4.64
Transcribed locus


1393098_at
0.000074
−1.39
similar to Lethal giant larvae homolog 2


1374120_at
0.000116
−1.89
similar to KIAA1126 protein (predicted)


1382598_at
0.000201
1.49
heat shock factor 2


1385234_at
0.000237
−1.67
Transcribed locus


1389074_at
0.000515
1.36
FCH and double SH3 domains 2 (predicted)


1376763_at
0.000520
1.23
Transcribed locus


1369722_a_at
0.000529
−1.31
xylosyltransferase II


1377000_at
0.000593
−3.11
similar to junction-mediating and regulatory





protein; p300 transcriptional cofactor JMY


1374560_at
0.000652
1.56
similar to RIKEN cDNA 3110038B19


1379466_at
0.000692
−1.50
Shadow of prion protein


1385586_at
0.000774
−1.41
Solute carrier family 2 (facilitated glucose





transporter), member 6 (predicted)


1370265_at
0.000784
1.82
Arrestin, beta 2


1375827_at
0.001303
2.46
similar to zinc-finger protein


1370102_at
0.001335
−1.89
potassium intermediate/small conductance





calcium-activated channel, subfamily, N,





member 1


1384938_at
0.001399
−1.28
Rho GTPase activating protein 1 (predicted)


1375415_at
0.001433
1.22
similar to U7 snRNP-specific Sm-like protein





LSM10


1380961_at
0.001458
−1.59
CCAAT/enhancer binding protein (C/EBP),





gamma


1392644_s_at
0.001475
−2.35
similar to RIKEN cDNA 2610019F03


1377928_at
0.001490
−1.95
similar to RIKEN cDNA 1810018L02


1368950_a_at
0.001579
−2.06
glutamate receptor, ionotropic, NMDA2D


1368553_at
0.001633
1.47
activin A receptor type II-like 1


1389569_at
0.001702
1.31
similar to BRIX (predicted)


1374495_at
0.001744
−1.30
LPS-responsive beige-like anchor (predicted)


1397694_at
0.001928
−2.94
potassium channel modulatory factor 1





(predicted)///similar to RNA binding motif





and ELMO domain 1


1397750_at
0.001951
1.36
Transcribed locus


1373541_at
0.002074
−1.29
Rho guanine nucleotide exchange factor (GEF)





17 (predicted)


1368998_at
0.002089
−1.93
NK6 transcription factor related, locus 1





(Drosophila)


1382183_at
0.002205
1.62
Transcribed locus


1381635_at
0.002217
−1.60
Collagen, type XVIII, alpha 1


1374536_at
0.002228
−1.15
LOC499569


1385494_at
0.002248
−2.24
similar to RIKEN cDNA 4930451A13 (predicted)


1390663_at
0.002310
−1.36
Transcribed locus


1395547_at
0.002465
−2.57
Guanine nucleotide binding protein, alpha q





polypeptide


1390818_at
0.002500
−1.29
ATPase, Na+/K+ transporting, beta 3





polypeptide


1381396_s_at
0.002502
−2.02
Kruppel-like factor 15


1374216_at
0.002528
−1.25
Transcribed locus


1386857_at
0.002661
1.23
Stathmin 1


1372140_at
0.002774
−1.33
similar to chromosome 6 open reading frame





80; chemokine C-C motif receptor-like 1





adjacent (predicted)


1379930_at
0.002805
−3.02
Transcribed locus


1376179_at
0.002832
−1.51
Transcribed locus


1399140_at
0.002847
1.14
Transcribed locus


1387923_at
0.002922
−1.47
zinc finger protein 179


1372789_at
0.002997
1.35
zinc finger protein 1


1395400_at
0.003131
−2.65
similar to hypothetical protein MGC23280


1390600_at
0.003208
−1.42
alpha-2,6-sialyltransferase ST6GalNAc IV


1368024_at
0.003228
−1.32
Quiescin Q6


1387555_at
0.003235
−1.90
amiloride-sensitive cation channel 2,





neuronal


1395863_at
0.003299
1.34
nuclear receptor subfamily 2, group F,





member 2


1394609_at
0.003309
−1.58
actin-binding LIM protein 2


1381045_at
0.003350
1.54
Transcribed locus


1377956_at
0.003355
−1.67
Cofilin 2, muscle (predicted)


1392061_at
0.003497
−1.89
minichromosome maintenance deficient 10





(S. cerevisiae) (predicted)


1394986_at
0.003538
−1.42
Similar to KIAA1838 protein (predicted)


1397855_at
0.003753
2.68
Similar to cysteine sulfinic acid





decarboxylase


1375291_at
0.003813
−1.76
Transcribed locus, strongly similar to





NP_733751.1 myeloid/lymphoid or mixed-





lineage leukemia 3; myeloid/lymphoid or





mixed-lineage leukemia3; ALR-like protein





[Homo sapiens]


1370720_at
0.003856
−2.07
Putative pheromone receptor VN6


1373533_at
0.003878
1.25
EST


1391763_at
0.003988
−1.33
Transcribed locus, weakly similar to





XP_516348.1 PREDICTED: similar to glycerol-





3-phosphate dehydrogenase 1-like





[Pan troglodytes]


1379258_at
0.004084
1.30
kelch-like 5 (Drosophila) (predicted)


1372855_at
0.004101
1.80
Bromodomain containing 4 (predicted)


1377342_s_at
0.004128
1.46
Rapostlin


1372030_at
0.004292
−1.12
zinc finger, FYVE domain containing 21





(predicted)


1385789_at
0.004371
−2.09
EST


1378878_at
0.004442
−2.84
similar to hypothetical protein FLJ25530





(predicted)


1369748_at
0.004471
−1.63
serine (or cysteine) proteinase inhibitor,





clade I, member 2


1385103_at
0.004588
−1.29
fused toes (predicted)


1384518_at
0.004619
−1.32
similar to PHD finger protein 14 isoform 1


1368323_at
0.004645
1.38
tissue factor pathway inhibitor


1387230_at
0.004717
−1.64
solute carrier family 12, member 3


1383457_at
0.005114
−1.86
similar to hypothetical protein





DKFZp761N1114


1392702_at
0.005181
1.41
EST


1370866_at
0.005191
1.41
Ribosomal protein L41


1371958_at
0.005199
−1.36
poly(A) binding protein, nuclear 1


1390189_at
0.005346
1.15
similar to Zinc finger protein 277


1374029_at
0.005356
1.66
EST


1386917_at
0.005360
−1.50
Pyruvate carboxylase


1373245_at
0.005366
1.22
procollagen, type IV, alpha 1 (predicted)


1385709_x_at
0.005519
−1.24
Progressive ankylosis homolog (mouse)


1394995_at
0.005638
−1.83
Cobl-like 1 (predicted)


1383147_at
0.005643
1.31
Transcribed locus


1397631_at
0.005720
−1.34
Ubiquitin specific protease 8 (predicted)


1398290_at
0.005734
1.27
Potassium channel, subfamily K, member 13


1371572_at
0.005800
1.26
amyloid beta (A4) precursor protein


1379651_at
0.005994
−1.30
Forkhead box P1 (predicted)


1387215_at
0.006008
−1.51
alanine-glyoxylate aminotransferase


1379418_at
0.006108
−1.53
LOC501008


1375358_at
0.006302
1.38
Transcribed locus


1394163_at
0.006408
2.23
SNF related kinase


1372025_at
0.006485
−1.45
Paternally expressed 3 (predicted)


1386016_at
0.006532
−2.45
EST


1376964_at
0.006542
1.56
similar to Ofd1 protein


1367750_at
0.006592
1.22
phosphoribosyl pyrophosphate synthetase-





associated protein 1


1388755_at
0.006685
1.22
SEC23A (S. cerevisiae) (predicted)


1390854_at
0.006734
−1.41
transmembrane protein 24 (predicted)


1376014_at
0.006832
−1.55
Transcribed locus


1379754_at
0.006998
−1.31
Staufen, RNA binding protein, homolog 2





(Drosophila)


1395327_at
0.007147
1.29
Lysosomal integral membrane protein-2





(LIMP-2)


1373262_at
0.007220
1.27
Similar to 2310014H01Rik protein (predicted)


1391108_at
0.007232
2.13
Transcribed locus


1387938_at
0.007304
−2.17
brain and acute leukemia, cytoplasmic


1391819_at
0.007324
−1.68
similar to hypothetical protein ET





(predicted)


1383216_at
0.007326
−1.44
Cohen syndrome homolog 1 (predicted)


1367744_at
0.007456
1.58
Melanoma antigen, family D, 2


1395869_at
0.007484
1.20
Similar to RIKEN cDNA A230063L24 gene


1384147_at
0.007519
1.43
eukaryotic translation initiation factor 1A





(predicted)


1372476_at
0.007698
1.37
fatty acid desaturase 3


1387836_at
0.007703
1.62
Prenylated SNARE protein


1378958_at
0.007759
1.22
EST


1385885_at
0.007837
−1.48
Transcribed locus, moderately similar to





XP_418312.1 PREDICTED: similar to Snf7





homologue associated with Alix 3





[Gallus gallus]


1372621_at
0.007920
1.44
similar to 2610027C15Rik protein (predicted)


1386228_at
0.007970
−2.39
Similar to PHD finger protein 20-like 1





isoform 1


1388798_at
0.007986
−1.26
ubiquitin-conjugating enzyme E2E 2 (UBC4/5





homolog, yeast) (predicted)


1373584_at
0.008209
−1.29
similar to hypothetical protein A430031N04


1383237_at
0.008308
1.25
Myoneurin (predicted)


1394721_at
0.008493
−1.38
similar to TTF-I interacting protein 5


1378315_at
0.008560
1.82
Transcribed locus


1381519_at
0.008621
−1.76
AT rich interactive domain 1A (Swil like)





(predicted)


1376059_at
0.008765
−1.53
similar to hypothetical protein MGC38689


1388377_at
0.008789
1.10
coatomer protein complex subunit alpha





(predicted)


1374247_at
0.008841
1.31
Stabilin 1 (predicted)


1373077_at
0.008994
1.39
similar to hypothetical protein D11Ertd497e





(predicted)


1376484_at
0.009158
−1.56
Transcribed locus


1388910_at
0.009255
−1.13
mitochondrial ribosomal protein S24





(predicted)


1393574_at
0.009262
−1.55
Similar to Ccl-6


1393164_at
0.009350
−1.45
mitochondrial ribosomal protein S27





(predicted)


1373697_at
0.009502
1.66
myosin binding protein C, fast-type





(predicted)


1390317_at
0.009509
2.80
Transcribed locus


1397642_at
0.009553
1.27
RAD50 homolog (S. cerevisiae)


1397352_at
0.009668
−2.04
Transcribed locus


1392557_at
0.009692
1.26
Transcribed locus


1384672_at
0.009749
−2.83
similar to RIKEN cDNA 4930434E21


1396724_at
0.009932
−1.29
EST


1393135_at
0.009960
−1.24
Transcribed locus


1388478_at
0.009986
1.27
Transcribed locus


1393318_at
0.010526
−1.32
EST


1394773_at
0.010614
−1.31
Transcribed locus, moderately similar to





XP_580018.1 PREDICTED: hypothetical protein





XP_580018 [Rattus norvegicus]


1397268_at
0.010662
−1.67
similar to solute carrier family 17 (sodium





phosphate), member 4; Na/PO4 cotransporter


1371289_at
0.011056
−1.77
nitric oxide synthase 2, inducible


1390885_at
0.011168
1.34
Transcribed locus


1392299_at
0.011420
−1.56
C-terminal PDZ domain ligand of neuronal





nitric oxide synthase


1394767_at
0.012694
−1.52
EST


1373120_at
0.019354
−1.40
Spermatogenesis associated 2





aProbe Set ID, Affymetrix probe set number


bp-value, P < 0.05 is considered statistically significant


cFold-change, fold-change in gene expression of failure-prone Ren-2 rats as compared to compensated Ren-2 rats. For example, negative sign means down-regulated in failure-prone Ren-2 rats.


dGene Name, name of gene associated with the Probe Set ID













TABLE 3







Echocardiographic parameters in LIMP-2 KO and WT mice at


baseline, and after 14 and 28 days of AngII treatment











Baseline
Day 14
Day 28















IVSda
KO(n = 11)
0.10 ± 0.00
0.10 ± 0.01$
0.10 ± 0.01$$


(cm)
WT(n = 10)
0.10 ± 0.01
0.13 ± 0.01
0.13 ± 0.00*


LVIDda
KO(n = 11)
0.34 ± 0.01
0.38 ± 0.01$$
0.38 ± 0.01$$,*


(cm)
WT(n = 10)
0.34 ± 0.01
0.33 ± 0.02
0.33 ± 0.01


LVPWda
KO(n = 11)
0.10 ± 0.01
0.09 ± 0.01$$
0.09 ± 0.00$$


(cm)
WT(n = 10)
0.10 ± 0.00
0.12 ± 0.01
0.15 ± 0.01*


LVAdb
KO(n = 11)
0.21 ± 0.01
0.27 ± 0.01$$,*
0.28 ± 0.02$,*


(cm)
WT(n = 10)
0.21 ± 0.01
0.23 ± 0.01
0.22 ± 0.00


LVLdb
KO(n = 11)
0.73 ± 0.01
0.85 ± 0.02$,*
0.84 ± 0.03$$,*


(cm)
WT(n = 10)
0.73 ± 0.01
0.79 ± 0.02,*
0.79 ± 0.02


FSa
KO(n = 11)
28.7 ± 1.9
20.1 ± 3.1
22.2 ± 3.0


(%)
WT(n = 10)
27.4 ± 2.1
25.8 ± 1.9
25.5 ± 2.9





Averages ± SEM


*P < 0.005 vs baseline KO or WT


$P < 0.05 vs age-matched WT


$$P < 0.001 vs age-matched WT


aMeasured from short axis: IVSd, Interventricular septum in diastole; LVIDd, Left ventricular inner diameter in diastole; LVPWd, Left ventricular posterial wall thickness in diastole; FS (%), Percentage fractional shortening


bMeasured from long axis: LVAd, Left ventricular area in diatole; LVLd, Left ventricular length in diastole






LITERATURE


    Gamp et al., Hum. Mol. Genet. 12: 631-646, 2003.
    Van Haaften et al., BMC Bioinformatics 7: online, 2006-09-21.
    Schroen et al., Circ. Res. 110: 3121-3128, 2004.
    Heymans et al., Circulation 112: 1136-1144, 2005.
    Junqueira et al., Histochem. J. 11: 447-455, 1979.
    De Windt et al., J. Mol. Cell. Cardiol. 29: 2095-2106, 1997.
    Crombie et al., J. Biol. Chem. 273: 4855-4863, 1998.
    Eskelinen et al., Trends Cell. Biol. 13: 137-145, 2003.
    Nishino et al., Nature 406: 906-910, 2000.
    Stypmann et al., Proc. Natl. Acad. Sci. USA 99: 6234-6239, 2002.
    Stilli et al., Exp. Physiol. 2006.
    Perriard et al., Trends Cardiovasc. Med. 13: 30-38, 2003.
    Gumbiner, J. Cell. Biol. 148: 399-404, 2000.
    Ferreira-Cornwell et al., J. Cell. Sci., 115: 1623-1634, 2002.
    Sohal et al., Circ. Res. 89: 20-25, 2001.
    Larsson et al., Embo J. 20: 1663-1673
    Vandendriessche et al., J. Thromb. Haemost. 5(1): 16-24, 2007.

## Claims

1. A method for identifying a subject at risk of developing heart failure, comprising:
(a) determining a level of one or more biological markers in a biological sample of said subject;
(b) comparing the level of said biological marker to a standard level of the same biological marker; and
(c) determining whether the level of the biological marker is indicative of a risk for developing heart failure, wherein the biological marker is a gene coding for a protein selected from the group consisting of KLF15 (SEQ ID NO: 27) and LIMP-2 (SEQ ID NO:30).

2. The method claimed in claim 1, wherein the method is performed in vitro.

3. The method claimed in claim 1 or 2, wherein the biological sample is selected from the group consisting of blood, plasma, serum, and cardiac tissue.

4. The method claimed in claim 1, wherein a decreased level of KLF15 gene expression, as compared to a standard level, is indicative of a risk of developing heart failure.

5. The method claimed in claim 1, wherein an increased level of LIMP-2 gene expression, as compared to a standard level, is indicative of a risk of developing heart failure.