WO2009121031A1

WO2009121031A1 - Methods of novel therapeutic candidate identification through gene expression analysis in vascular-related diseases

Info

Publication number: WO2009121031A1
Application number: PCT/US2009/038685
Authority: WO
Inventors: David Marshall Mann
Original assignee: Vascular Biosciences, Inc.
Priority date: 2008-03-27
Filing date: 2009-03-27
Publication date: 2009-10-01
Also published as: US20170145505A1; US8741861B2; US20210010082A1; WO2009121031A4; US20110091421A1; EP2279267A1; EP2977468A2; US20140323335A1; EP2977468B1; EP2279267A4; US9499816B2; EP2977468A3

Abstract

The present invention discloses multiple treatment regimens for vascular-related diseases and disorders. The present invention provides for methods of treating vascular-related disorders based on gene expression studies from samples collected from individuals having symptoms of vascular-related disorders. Additionally, methods are disclosed involving diagnostic techniques to focus treatment regimens. Finally, methods of treating vascular-related disorder involving targeting microRNAs are also disclosed.

Description

METHODS OF NOVEL THERAPEUTIC CANDIDATE IDENTIFICATION THROUGH GENE EXPRESSION ANALYSIS IN VASCULAR-RELATED DISEASES

By David Marshall Mann

CROSS-REFERENCES

This application claims the benefit of priority of U.S. Provisional Application Ser. No. 61/040,065, filed on March 27, 2008, the disclosure of which is hereby incorporated by referenced in its entirety.

FIELD OF THE INVENTION

The present invention relates to assessment and identification of expression of genes related to vascular- related diseases. The present invention also includes methods of comparing gene expression patterns with respect to various disease states.

BACKGROUND OF THE INVENTION

Pulmonary arterial hypertension (PAH) is an occlusive disease of the pulmonary arteries leading to serious hemodynamic abnormality, right heart failure, and premature death. The molecular mechanisms behind PAH are still unclear. Without a more complete understanding of PAH and how its complex vascular dysfunctions relate to one another, patients will suffer from imprecise diagnosis and drug therapy that may be less than optimal . Despite recent advances and introduction of new clinically approved drugs, the 5 -year survival from pulmonary hypertension remains an estimated 50% (Archer and Rich, 2000) . Consequently, treatment for PAH, while recently improved, still offers significant and long-lasting improvement in only a minority of patients. A methodology to elucidate the molecular pathways associated with PAH could guide the development of new therapies for this disease.

Though platelets and other cells may have a role in PAH, pulmonary endothelial cells and pulmonary smooth muscle cells appear to be the primary sites of disease progression (Humbert et al 2004) . Molecular pathways that show abnormality in pulmonary endothelial cells and pulmonary smooth muscle cells during PAH include endothelin-1 (Giaid et al 1993) , serotonin & serotonin transporter (Marcos et al 2003) , thromboxane (Walmrath et al 1997) , nitric oxide synthase (Kobs and Chesler 2006) , prostacyclins (Gailes, et al 2001) , potassium channels (Mandegar et al 2002) , BMP signaling (Eddahibi et al 2002) , and survivin (McMurtry et al 2005) . PAH impairs normal signaling and growth in both pulmonary endothelial and pulmonary smooth muscle cells, yet the cellular abnormalities seem to shift over time in unpredictable patterns that has thus far escaped concise definition (Michelakis, 2006) .

PAH may be understood as proceeding in phases. In early PAH, endothelial apoptosis occurs, probably resulting in pulmonary arteriole plugging and an increase in pulmonary vascular pressure (Michelakis, 2006) . In late PAH, chronic exposure to elevated pulmonary artery pressure together with dysfunctional endothelial signaling initiates hyperproliferation of smooth muscle cells {McMurtry et al 2005) . Increased concentric pulmonary smooth muscle cell proliferation leads to ever increasing pulmonary artery pressure, right ventricular failure, and death.

Lung pathology in all PAH patients show thickening throughout the arterial wall of the pulmonary vascular bed. In some forms of the disease, the pulmonary vascular lesions are reversible (e.g. in newborns with congenital heart defects) . In other patients, such as those with the idiopathic form, the lesions are irreversible. It is unknown how these variations in PAH relate to one another on a molecular basis (Pearl et al 2002) .

Current therapies for PAH patients primarily target vascular tone. Treatments that aim at correcting potassium channel dysfunction (Machado et al 2001) , nitric oxide impairment (Humbert et al 2004) , prostacyclin impairment (Tuder et al 1999, Christman et al 1992) , and endothelin-1 expression (Giaid et al 1993) have all been clinically available for several years. These therapies offer some relief from hemodynamic symptoms, but most patients show only a transient response. The proliferative disease continues to progress in most PAH patients, resulting in a five year mortality rate that remains at around 50% (Newman et al 2004) .

Currently, there are no clinically available routine means to obtain endothelial and smooth muscle samples from the pulmonary arteries of pulmonary hypertension patients for diagnosis, disease staging or drug discovery. Applicant's earlier invention, described in US Patent No. 5,406,959, describes an endoarterial biopsy catheter that has demonstrated its safety and effectiveness in normal canines (Rothman, Mann et al. , 1996) , canines with experimentally- induced pulmonary hypertension (Rothman, Mann et al . , 1998) , and canines with single-sided lung transplant rejection (Rothman, Mann et al . , 2003) . Preliminary studies have also demonstrated the safety and efficacy of a catheter-based method to obtain endovascular samples from a porcine model of PAH. Percutaneously-obtained pulmonary endoarterial biopsy samples were found to be of sufficient quantity and quality for porcine whole genome mRNA microarray analysis and microRNA analysis. Whole genome microarray analysis revealed time- sensitive variations in gene expression values as PAH progressed in the subject animal model. Genes previously shown to be associated with PAH displayed changes characteristic of the disease, and genes previously unassociated with PAH also displayed expression level dysregulation . These findings raise the possibility that the endoarterial biopsy catheter combined with microarray analysis may provide a valuable platform for the discovery of novel drug and biomarker targets in pulmonary hypertension and a platform to deliver individualized pharmacotranscriptomics .

MicroRNA analysis revealed pressure sensitive changes in microRNA expression. As our surgical shunt model of pulmonary hypertension progressed from a high flow low pressure (HFLP) manifestation to a high flow high pressure (HFHP) manifestation, different microRNAs became dysregulated either increasing or decreasing in expression relative to our baseline normal values.

Most new therapies promise to focus on arresting either the endothelial apoptosis that characterizes early PAH (angiopoetin- 1 Sc endothelial nitric oxide synthase cell -base gene transfer (Zhao et al 2003; 2005} , caspase inhibitors (Taraseviciene- Stewart et al 2001) ) or the smooth muscle cell proliferation typical of late PAH (dichloroacetate (McMurtry et al 2004) , simvastatin (Nishimura et al 2003) , sidenafil (Wharton et al 2005) , imatinib (Schermuly et al 2005) , anti-survivin (McMurtry et al 2005) , K+ channel replacement gene therapy (Pozeg et al 2003) ) .

Before administering therapies, however, it would be extremely valuable to determine which genes are dysregulated in each PAH patient at any stage of their individual disease progression. Without knowing what genes are aberrant during any point in the patient's disease course, targeted therapies may miss the mark in some patients. Life threatening side effects may emerge if the wrong cells, at the wrong time, are encouraged to die or proliferate in patients with compromised pulmonary vascular health.

A powerful method for determining the gene expression levels of thousands of genes simultaneously are DNA microarrays. Initially used for the classification of cancers that were difficult to discriminate histologically (Golub et al 1999, Bhattacharj ee et al 2001, and Ramaswamy et al 2001) , microarrays have been more recently applied to PAH (Geraci et al 2001) . PAH microarray studies have been performed on whole lung homogenates in humans (Fantozzi et al 2005) and rats (Hoshikawa et al 2003) , surgically-dissected pulmonary arteries in pigs (Medhora et al 2002) , laser-tnicrodissected pulmonary arteries in rats (Kwapiszewska et al 2005) , and mononuclear peripheral blood in humans (Bull et al 2004) . These studies have been performed to discover potentially novel PAH disease pathways, biomarkers, therapeutic targets and patient classification gene expression profiles .

To advance PAH microarray studies into practical clinical use, tissue procurement methodologies are required that do not require surgical explant or postmortem procurement, and peripheral blood has thus far proven to be inadequate to discriminate gene expression signatures between subgroups of PAH patients (Bull et al 2004; Bull et al 2007) . To take advantage of the full power of microarray technologies in PAH patients, a safe and effective minimally invasive means for the repeat procurement of endovascular samples from living PAH patients is required.

The present invention provides for the use of a novel interventional catheter, an endoarterial biopsy catheter, to obtain serial biopsy specimens from hypertensive pulmonary vessels for analysis. The ability to procure endothelial and smooth muscle samples in a minimally invasive manner will allow physicians to use microarray profiling and other techniques to classify patients upon initial presentation according to their gene expression signatures, prescribe therapies that target genes empirically found to be dysregulated in each individual patient, and monitor and adjust PAH patient therapy according to subsequent biopsy findings. A greater understanding of the complex molecular pathways underlying each patient' s PAH should enable more precise diagnosis and the delivery of more effective therapies. Also of importance is the ability to discover new uses for existing drugs as well as discovering new drug targets.

Individualized pharmacotranscriptomics based on endoarterial biopsy and microarray analysis represents a reasonable choice for researchers struggling with the complexities and contradictions of PAH and other vascular diseases. The huge literature generated from in vitro and animal studies falls short, at times, in addressing the actual facts of patient health. Many commentators describe this dilemma as the "bench-to-bedside gap" , where in vitro and animal laboratory data fails to model human disease circumstances (Aird, 2004) . Bridging that gap through catheter-based access to the vasculature in a model that recapitulates the clinical and histopathological manifestations of a form of human pulmonary hypertension will likely enable closer correlations between animal studies and patient care, and serve as a model for other vascular-based diseases such as atherosclerosis, congestive heart failure, sickle cell disease, organ transplant rejection, connective tissue diseases, chronic obstructive pulmonary disease, pulmonary embolism, asthma, systemic inflammatory response, battlefield trauma, cancer, sepsis and acute respiratory distress syndrome. There is a need in the art to provide data from gene expression analyses in order to target novel candidates for use in treating or preventing PAH.

SUMMARY OF THE INVENTION

One aspect of the present invention provides for methods of treating an individual suffering from a vascular-related disease comprising the steps of : a) obtaining a biopsy sample from the individual' s pulmonary artery; b) analyzing gene expression levels of the biopsy sample from the pulmonary artery of the individual and a non-diseased control ; c) comparing the gene expression levels between the biopsy sample from the pulmonary artery of the individual and the non-diseased control; d) identifying at least one gene from step c) that is upregulated or downregulated in the biopsy sample based on the non-diseased control; e) obtaining gene products from the genes identified in step c) ; and f) selecting pharmaceutical agents which are known inhibitors of the gene products from the at least one upregulated gene or known promoters of the gene products from the at least one downregulated gene. An additional aspect to the present invention provides for the pharmaceutical agents selected for administration to the individual suffering from the vascular-related disease. In yet another aspect, the individual is categorized based on progression of the vascular-related disease, with the treatment being based on the timing of the disease .

Another aspect of the present invention provides for a means of comparing varying levels of gene expression based on an animal model for pulmonary arterial hypertension. In a preferred embodiment, the genes expressed in the animal model are genes found to be either upregulated or downregulated. In a more preferred embodiment, the upregulated or downregulated genes are time -dependent based on the time after exposure to the PAH.

Another aspect of the present invention provides for methods of identifying genes involved in the pathway of PAH based on differential gene expression studies in a time- dependent animal model for PAH. In one embodiment, the genes are compared to other known genes which are upregulated or downregulated in the known PAH pathway.

Yet another aspect of the present invention provides for methods of diagnosing a vascular-related disease in an individual comprising the steps of: a) identifying at least one gene that is upregulated or downregulated in the vascular-related disease comprising the steps of :

1) obtaining a biopsy sample from the individual' s pulmonary artery during progression of the vascular-related disease;

2) obtaining a pulmonary artery sample from a non- diseased control;

3) extracting RNA from the samples in steps 1) and 2} ;

4) obtaining gene products from the RNA extracted in step 3 ) ; and

5) comparing gene expression levels from the biopsy sample with the non-diseased control, and b) associating the genes upregulated in the biopsy sample with an inhibitor of the gene products for administration to the individual and genes downregulated in the biopsy sample with a promoter of the gene products for administration to the individual .

Another aspect of the present invention provides for methods of treating an individual having a vascular-related disease by targeting microRNAs comprising the following steps: a) assessing a stage of the vascular-related disease in the individual; b) identifying whether microRNAs are upregulated or downregulated; c) selecting the microRNAs to target based on the stage of the vascular-related disease and whether the microRNAs are upregulated or downregulated; and d) administering an agent known to inhibit an upregulated microRNA or an agent known to promote a downregulated microRNA to the individual. A variation of this embodiment provides for the stage of the vascular-related disease being based on flow rates and blood pressure within an artery of the individual.

Another aspect of the present invention provides for methods of therapeutically targeting microRNA dysregulated in PAH comprising the steps of :

(a) obtaining a biopsy sample from the pulmonary artery during the progression of PAH;

(b) obtaining a pulmonary artery sample from a non- diseased control;

(c) extracting RNA from the artery samples;

(d) converting the RNA to cDNA;

(e) comparing levels of microRNA expression at the two differing times;

(f) identifying microRNA dysregulated in PAH relative to baseline; and

(g) inhibiting upregulated microRNA or promoting downregulated micro RNA identified in PAH biopsies.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 depicts a surgical shunt model of PAH and its association with congenital heart disease (CHD) .

Figure 2 depicts the endoarterial biopsy procedural configuration.

Figure 3 depicts biopsies: normal vessels at baseline, hypertensive LPA at 7, 21, 60 and 180 days post shunt. Figure 4 depicts GeneSpring downstream analysis of microarray data.

DETAILED DESCRIPTION OP THE INVENTION

The model described in the present invention is surgically- induced PAH in pigs. Our model mimics human Eisenmenger syndrome (a form of PAH related to congenital heart malformation) in both symptoms and pathology (Corno et al 2003) . The size of the animals makes the pulmonary vessels available to the catheter, providing a ready transition to human clinical use. And finally, the commercial availability of whole genome porcine microarrays (Bai et al 2003) makes the species ideal for our purposes in the study, and renders the use of cross species microarrays unnecessary (Medhora et al 2002) .

By obtaining pulmonary endovascular samples at early, intermediate and late time points in PAH progression, and analyzing these samples using porcine whole genome microarrays, a time-sensitive microarray based map of the underlying molecular biology of PAH may be obtained. Improved knowledge of the molecular mechanisms underlying PAH progression can lead to the identification of stage-specific biomarkers, new therapeutic targets for drug intervention, and novel signaling pathways involved in the pathogenesis of PAH. These novel target genes can then be validated using quantitative PCR and immunohistochemical stains on porcine endoarterial biopsy samples procured concurrently. At the same time, the combination of minimally invasive endoarterial biopsy and whole genome microarray analysis can serve as an animal model for subsequent studies in PAH patients. The following examples provided in this disclosure provide a profile gene expression in pulmonary hypertensive pigs by surgical anastomosis of the left pulmonary artery to the descending aorta. Endoarterial biopsy samples are collected from animals with a surgical shunt model of pulmonary hypertension at multiple time points over a 6-month time course. Gene expression analysis of the biopsy samples was performed on porcine microarrays. Microarray analysis was performed to detect dysregulated genes previously unassociated with PAH, discover novel biomarkers of pulmonary hypertension and novel targets for therapeutic intervention and advance knowledge of the molecular mechanisms of pulmonary hypertension. These studies will also help validate a new platform for PAH diagnosis and drug discovery, endoarterial biopsy and microarray analysis, for eventual clinical practice.

EXAMPLES

Example I : Construction of a microarray-based map of changes in gene expression during the progression of PAH and the identification of novel therapeutic candidates

In an animal model of PAH created by Antonio Corno and colleagues, pigs undergo surgery that redirects systemic circulation into the left pulmonary artery mimicking pulmonary hypertension secondary to congenital heart disease. The surgery elevates PA pressure and creates the same hemodynamic conditions that PAH patients experience. The present study investigates how the elevated pressure remodels the pulmonary vasculature. In Corno' s studies, histology on necropsy confirmed intimal hyperplasia in the pulmonary arteries, evidence that the surgical shunt surgery described will cause endovascular remodeling {Corno et al 2003) . Biopsy Extraction and Surgery Protocol

20-30 kg Yucatan Micropigs (Sus scrota, Yucatan micro breed) underwent surgical anastomosis of the left pulmonary artery to the descending aorta, resulting in left pulmonary arterial hypertension of at least % systemic levels. Animals are penned in the laboratory for no less than one week prior to surgery and fed normal chow. On surgery day, animals were premedicated with 20mg/kg intramuscular ketamine and 0.1 mg/kg intramuscular midazolam. After 0.25 mg of intramuscular atropine, anesthesia was induced with 1 mg/kg intravenous midazolam and 0.1 mg/kg intravenous fentanyl and maintained with 0.1 mg/kg/hr intravenous pancuronium bromide. Pigs were ventilated with an inspired oxygen fraction (FiO2) of 0.4, a tidal volume of 15 ml/kg, and a respiratory rate of 12 breaths/minute. One gram of intravenous cefazolin was given before and 2 hours after the surgical procedure. Surgical and catheter procedures were performed under general anesthesia with endo- tracheal intubation. Sedation medications and anesthetics were administered by an anesthesiologist. Intra-cardiac and intravascular pressures, EKG, and blood oxygen saturations were monitored continuously.

Under sterile conditions (the thoracic area was shaved and prepared with betadine, a left thoracotomy was performed through the fourth intercostal space, about 5 centimeters, to expose the great arteries. The main pulmonary artery (MPA) and its branches were identified and freed from surrounding tissue. Two clamps were placed on the proximal left pulmonary artery (LPA) . The proximal LPA was sutured closed, using prolene, and the distal LPA was sutured end to side in a clamped region in the descending aorta (Figure 1) , using cardiovascular prolene. Pieces of LPA endoarterial tissue were taken for histology. The clamps were removed and an IV dose of 1 mg/kg Furosemide immediately given. Hemostasis was obtained with sutures and cautery. Direct needle blood pressures were recorded in the main pulmonary artery and in the newly anastomosed left pulmonary artery. The chest was closed with sutures, both subcutaneous and cutaneous layers, using prolene and surgical wire. The animals then were weaned from anesthesia and mechanical ventilation. Postoperative analgesia was provided with morphine four times a day and a 1-2 mg/kg dose from 0.25% solution of IV Bupivacaine, a local anesthetic. A circulating warming blanket was used during surgery and recovery.

Endoarterial biopsies were performed at baseline prior to surgery to obtain unaffected tissue, and at post-shunt timepoints to obtain hypertensive biopsy samples (Figure 2) . Follow up endoarterial biopsy procedures were scheduled 7, 21, 60 and 180 days after surgery. On each catheterization day, animals were premedicated with 10 mg/kg of IV propofol, were intubated and ventilated at a rate of 12 breaths/min and were maintained under anesthesia with 1.5% halpthane. A femoral artery line was placed for monitoring. To obtain biopsies from the hypertensive left lung, an 8F introducer is placed in a carotid artery, and a 7F endhole catheter is advanced into the aorta. An angiogram is performed to visualize the LPA- aortic anastomosis. The 7F endhole catheter is then threaded through the anastomosis with X-ray fluroscopic guidance. An angiogram of the hypertensive left pulmonary vascular tree is then performed, and the catheter is advanced to the distal pulmonary artery selected for biopsy. A 0.038 in, 260 cm extra stiff Amplatz exchange guide wire will then be passed through the end-hole catheter. The end-hole catheter was exchanged for a long flexible 8F introducer sheath that is adapted with a radio opaque band at the distal end and shaped to conform to the vascular pathway. A 7F angiographic catheter was advanced through the sheath in to a 2.5 mm to 3.0 mm distal pulmonary artery branch, where an angiogram was obtained. The angiographic catheter will serve as a guide to advance the stiff sheath into a small vessel targeted for biopsy and will then be exchanged for the endoarterial biopsy catheter.

The endoarterial biopsy catheter has an external diameter of 2.5 mm and is composed of two flexible polymeric tubes that slide relative to each other. The inner tube has a stainless steel distal end with a beveled opening that is designed to accommodate arterial tissue. A vacuum is coupled to the inner tube and channeled to the beveled opening. The outer tube terminates in a stainless steel cutting tube. The proximal ends of the two tubes are with a spring powered operating mechanism. To obtain the biopsy sample a vacuum is transmitted to the beveled opening of the inner tube, causing a tissue sample to be drawn in. The outer tube is then advanced over the inner tube, severing the tissue sample. With this design, the area of artery contacted by the outer periphery of the beveled opening is larger than the inner aperture connected to the vacuum, this maintaining the tissue sample with its orientation preserved. After each biopsy, the catheter was removed and the tissue sample was placed in the appropriate solution for further processing and analysis. After the biopsy procedures were completed, repeated angiograms were obtained to assess the degree of vascular injury. At the end of the procedure, the biopsy catheter and introducer sheath were removed and hemostasis was obtained by surgical repair of the carotid artery. The animals will then be weaned from anesthesia and mechanical ventilation. Postoperative analgesia was provided with morphine four times a day and or fentanyl patches and nonsteroidal anti- inflammatory drugs four times a day.

Tissue processing

For microarray analysis, biopsy samples are placed in a test tube containing RNAlater (Qiagen) , flash frozen in dry ice, and kept frozen until RNA extraction. Additional samples are preserved in formalin, OCT freezing solution, or Bouin's solution for subsequent immunohistochemical and quantitative PCR analysis .

Porcine Genome Arrays

The Affymetrix GeneChip^® Porcine Genome Array provides comprehensive coverage of the Sus scrofa transcriptome . The array contains 23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 Sus scrofa genes.

The sequence information for this array was selected from public data sources including UniGene Build 28 (August 2004) , GenBank^® mRNAs up to August 24, 2004, and GenBank^® porcine mitochondrial and rRNA sequences. Probe sets consist of up to eleven probe pairs. The array format consists of eleven micron features synthesized on the 100 format.

RNA Extraction from Endoarterial Biopsy Samples

RNA was prepared from fresh frozen endoarterial biopsy samples in a segregated laboratory, specially prepared and cleaned regularly to destroy nucleases. Specimens were homogenized using QIAshredder columns (Qiagen, Valencia, CA) utilized in a FastPrep FP120 Homogenizer (Thermo Electron Corporation, Waltham, MA) . RNA was isolated using RNeasy Mini columns (Qiagen, Valencia, CA) as per manufacturer's protocol. All total RNA was eiuted in nuclease free water, and quantity was established by UV spectrophotometer. Final RNA integrity was evaluated by capillary electrophoresis on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) .

Gene Expression

Before target production, the quality and quantity of each RNA sample was assessed using a 2100 BioAnalyzer (Agilent) . Target was prepared and hybridized according to the "Affymetrix Technical Manual" . Total RNA (ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo (dT)24 primer that contains T7 promoter sequences (GenSet) . After first strand synthesis, residual RNA was degraded by the addition of RNaseH and a double- stranded cDNA molecule was generated using DNA Polymerase I and DNA Ligase. The cDNA will then be purified and concentrated using a phenol : chloroform extraction followed by ethanol precipitation. The cDNA products will then be incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Enzo Diagnostics) . One-half of the cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94 ° C for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc) . The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin- labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix) . The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip^® cartridge. The GeneChip^® array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips^® were washed with a series of nonstringent (25°C) and stringent (5O°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays will then be stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution. Fluorescent images were detected in a GeneChip^® Scanner 3000 and expression data was extracted using the GeneChip^® Operating System v 1.1 (Af fymetrix) . All GeneChips^® were scaled to a median intensity setting of 500. Gene expression levels were compared between biopsy samples taken from the control distal pulmonary vasculature (baseline LPA and RPA) and PAH distal pulmonary arteries (surgical shunt LPA) .

Gene Expression Analysis

After RNA preparation, array hybridization and scanning of the Porcine GeneChips^® exactly as recommended by Af fymetrix, the data produced are processed using the Affymetrix tools in the R- Bioconductor package called /Af fy/. This tool set allows for various probe level analyses of the data as well as probe level quality control. The MAS5 algorithm was used, taking into account both the MM and PM probe data, and generating "Present" or "Absent" calls for each gene on each chip. If boxplots of the porcine probe level data reveal that any of the hybridizations are of low quality, the data from these chips was removed from any downstream analysis. MASS with the non- linear Quantiles normalization (Af fy package /normalize . quantiles) / was used with this data set to produce data almost free of artificial correlations. The Present/Absent calls are also used to remove from the analysis the genes that were never expressed in any of the samples examined (this is analogous to using a P-value for gauging a gene's data quality on a chip, and then filtering) . Based on the first dozen chips processed, after normalization and quality control -19,000 genes were moved on to the next stage of the analysis. The commercial package GeneSpring was used to assess differential gene expression and perform tests using clustering algorithms. Thus far, hierarchical clustering has revealed that the time-point replicates have the greatest similarity to one another.

Gene expression fold changes for 7, 21 60 and 180 days post-surgery relative to baseline were then loaded into GSEA

(gene set enrichment analysis) or specially written PERL scripts which carry out KS (Kolmogorov-Smirnov) statistical analysis in order to identify novel therapeutic candidates.

Novel Therapeutic Identification

During PAH the best therapeutic targets are those which are upregulated as the disease state progresses. Thus drugs which are known to counter the action of any upregulated genes and their products would be of the greatest potential therapeutic value. Therefore, lists of upregulated genes were then matched to drugs which target their gene products.

In addition, many drugs interact with multiple targets in the body's tissues. Lists of the targets (called genesets) for each of -2000 characterized drugs were obtained from the literature and online databases. These genesets were then used to search for drugs which would be most likely to have therapeutic value in PAH.

This was done by using KS statistics which computes the Kolmogorov-Smirnov score for a geneset for a particular drug within an ordered list. The KSscσre task is used to examine the enrichment of a set of genes at the top of an ordered list. The KS score is high when the tags appear early {i.e. near the top) of the ordered list. The significance of the KS score for a particular test may be examined by computing KS scores for multiple sets of X query genes selected at random from the dataset (note that the KS score is not independent of the number of members of the query gene set) . Using this approach we were able to identify in our messenger RNA expression dataset drugs which are currently used as therapeutics for PAH (see Fig IA) . Importantly, using the same approach we were also able to identify additional potential therapeutics, within the existing pool of characterized drugs. This process identified existing drugs as novel therapeutics for PAH.

Example II: Gene expression analysis from porcine animal model data

Gene Expression Analysis

The porcine studies indicate that single endoarterial biopsy samples obtained in the porcine model of surgical shunt PAH contain sufficient RNA for microarray analysis, as we were able to analyze the mRNAs in whole genome porcine microarrays. We obtained endoarterial biopsies and measured pulmonary arterial pressure (PAP) at baseline prior to surgery, and at approximately 7, 21, 60 and 180 days post-PAH surgery from several animals. Porcine whole genome expression values were obtained for biological replicates with 2 samples from each time point. These replicates produced 5 sets of high quality replicated expression data (baseline, day 7 , day 21, day 60 and day 180; see Table 1 for PAP data) . Downstream data analysis was carried out using commercial (Ingenuity; GeneSpring) and free/open source software (R; Bioconductor ,- GSEA) . Mean expression values were obtained for each gene by averaging the gene expression values of the two biopsies at each tiπiepoint. The resulting gene expression mean values were used to calculate fold changes between day 7, 21, 60 and day 180 gene expression relative to baseline.

Validity of the model was confirmed by examining the gene expression changes for selected genes previously found to be dysregulated in PAH (Table 2) . Endothelin 1 and protein-tyrosine kinase Tie2 both displayed upregulation in accordance with explanted tissue from IPAH transplant recipients (Dewatcher et al 2006) , and platelet-derived growth factor receptor alpha, serotonin receptors 2B and ID, calmodulin, transcription factor STATBb, voltage -dependent anion channels 1,2 and 3, and RAS p21 protein activator 1 also increased in our model while tumor necrosis factor and plasminogen activator inhibitor-1 were found to be downregulated in our model in a similar fashion with IPAH explant tissue results (Fantozzi et al 2005) . Survivin was upregulated in our model in a similar fashion to published findings (McMurtry et al 2005) , and FYN and VAV-I oncogenes, requiem homolog, inward rectifier K + channel, and chloride channel 1 also increased while DEAD/H box polypeptide 3 and angiopoietin 1 displayed decreased expression in agreement with patient findings (Geraci et al 2001) . We also observed decreased expression of peroxisome proliferator-activated receptor gamma (Ameshima et al 2003) , and downregulated vascular endothelial growth factor B (Louzier et al 2003) in correspondence with previous results. The concordance between genes previously found to be aberrant in published PAH studies and altered gene expression in our model attest to the validity and potential usefulness of gene expression data derived from endoarterial biopsies. The time dependent nature of gene expression dysregulation found in our model further demonstrates the utility of obtaining endoarterial biopsies at multiple time points in PAH progression.

While several of these genes have been previously associated with PAH (for example, KCBNl, CASP3 , TLR4 , ILlB, IL6 , HMGCR, TOPl, FYN, PRKCA, EDNRB, PDGFRA, and HRT2B) , several have not (for example, HSPE, YESl, CFTR, MAOA, MAOB, and CACND21) , raising the intriguing possibility that known existing drugs that target upregulated genes previously unassociated with PAH may be effective in treatment of the disease.

Example III: Identification of dysregulated microRNA during the progression of PAH

Endoarterial biopsy samples percutaneously obtained during the progression of PAH were analyzed to correlate changes in microRNA expression to disease progression.

microRNA Expression data analysis

Data analysis was done in three stages. First, expression intensities were calculated for each miRNA probed on the array for all hybridizations (12 in total) using illumina's Beadstudio Version 3.0 software. Second, intensity values were quality controlled and normalized: quality control was carried out by using the illumina Beadstudio detection P-value set to <0.05 as a cutoff. This removed miRNAs which were effectively absent from the arrays (that is, were never detected) . After this step, the initial 1145 miRNAs were reduced to 1094. All the arrays were then normalized using the normalize .quant Hes routine from the Af fY package in Bioconductor . This procedure accounted for any variation in hybridization intensity between the individual arrays

Finally, these normalized data were imported into GeneSpring and analysed for differentially expressed miRNAs. The groups of biological replicates were described to the software and significantly differentially expressed genes determined on the basis of Welch t-tests and fold difference changes in expression level. The determination of raiRNA targets genes was done using a publicly available database of miRNA target sequences and a specially written PERL programming script.

miRNA Pressure Related Analysis

The data was also looked at to reflect the stages of the disease (based on blood pressure and flow rates) , as opposed to the time point or the individual pigs. Three groups were defined (1) Normal (baseline) ; (2) High Flow Low Pressure ¹HFLP' and (3) High Flow High Pressure 'HFHP' (see Table 11) . The groups were compared back to the baseline and the statistically significantly differentially regulated miRNAs determined (Tables 12, 13, 14 & 15) .

Using illumina microRNA expression microarrays, fluctuations in the level of expression of -1200 microRNAs were determined during the onset and progression of PAH. Porcine and Homo sapiens miRNA sequences are very often highly conserved. Expression comparisons were done on a timepoint basis, taking in account the available replicates and the statistical significance of the expression changes. The data was also looked at to reflect the stages of the disease (based on blood pressure and flow rates) , as opposed to the time point or the individual pigs. Three groups were defined (1) Normal (baseline) ; (2) High Flow Low Pressure ¹HFLP' and (3) High Flow High Pressure ¹HFHP' . The groups were compared back to the baseline and the statistically significantly differentially regulated miRNAs determined.

Finding micro RNAs with potential as therapeutic targets

The messenger RNA expression data set was analysed looking for expression changes in sets of genes with known target sites for particular miRNAs. miRNAs are known to negatively regulate gene expression at the level of translation by binding to upstream regions of mRNA and blocking events required for translation of the mRNA into protein. This was again done using Gene Set Enrichment Analysis (GSEA) and the publicly available miRNA genesets. "Cross-talk" is seen between the messenger RNA gene expression changes and the microRNA expression changes. The messenger RNA expression analysis directly revealed the differential expression of groups of genes competent to be regulated by these miRNA.

Example IV: Personalizing Therapeutic Regimens for Vascular- based Diseases

The use of gene expression data to shape individual drug therapies has been postulated as the next phase in personalized medicine. The bioinf ormatic processing of an individual's gene expression data can be used to generate a ranked list of therapies suitable for that individual. PAH disease pathology varies greatly over time, and is also likely to be specific for particular individuals. The analysis of the RNA in the PAH biopsy samples allows therapies to be tailored to the individual at that particular stage of the diseases progression. The genes and biochemical pathways changing the most at the level of gene expression can be determined by comparing the PAH biopsy samples to a baseline control of normal healthy vasculature tissue. Observations show time-dependent extensive changes in gene expression with the progression of PAH. Known targets for approved PAH therapeutics can be seen Up- regulated in the diseased state.

Drug therapies can be ranked by using the known targets of drugs as genesets. These drug signature lists can then be used in a process such as Gene Set Enrichment Analysis, or KS statistics. KS Statistics returns a score for how well ranked a particular drug would be for a particular patient.

A drug is represented as the set of its known target genes; this can be in the dozens for some bioactive compounds. Genesets for -2000 drugs were assembled. KS Statistics yields a value (^VKS score') representing the positional distribution of the set of query genes (here, the drug targets) within an ordered list of genes (genes induced in PAH) . The ordered list is produced by looking at the fold change in a mRNAs expression between time X and the baseline, and sorting on this value. The gene with the greatest fold change is ranked as #1, second greatest fold change is ranked as #2, etc. KS score is computed in accordance with the Kolmogorov-Smirnov non-parametric rank statistic where X is the number of genes in the query gene set, Z is the number of genes in the ordered list, and Y = Z - X. A suitable baseline is generated using gene expression from artery samples from non-diseased controls. These samples can be obtained surgically, percutaneously or post-mortem. This process can be repeated for all the PAH time points and the resulting table of KS scores for each drug hierarchically clustered . This reveals which drugs are potent ially of the greatest therapeutic value for a patient .

This supports the idea of achieving personalized treatments for vascular-based diseases by generating individual ized drug prescriptions based on the bioinforraatic processing of gene expression data f rom endoarterial biopsy samples obtained from diseased arteries . Similarly , this enables personalized treatments for vascular-based diseases by generating lists of dysregulated microRNA f rom the bioinformatic processing of microRNA expression data f rom endoarteriai biopsy samples f rom diseased arteries .

O

Claims

We claim:

1. A method of treating an individual suffering from a vascular-related disease comprising the steps of: a) obtaining a biopsy sample from the individual's pulmonary artery,- b) analyzing gene expression levels of the biopsy sample from the pulmonary artery of the individual and a non-diseased control ; c) comparing the gene expression levels between the biopsy sample from the pulmonary artery of the individual and the non-diseased control; d) identifying at least one gene from step c) that is upregulated or downregulated in the biopsy sample based on the non-diseased control; e) obtaining gene products from the genes identified in step c) ; and f) selecting pharmaceutical agents which are known inhibitors of the gene products from the at least one upregulated gene or known promoters of the gene products from the at least one downregulated gene, wherein the pharmaceutical agents selected are administered to the individual suffering from the vascular-related disease.

2. The method of claim 1, wherein the vascular-related disease is pulmonary arterial hypertension.

3. The method of claim 1, wherein the biopsy sample is extracted using an endoarterial catheter.

4. The method of claim 1, wherein the gene expression levels are analyzed by extracting RNA from the biopsy sample.

5. The method of claim 4, wherein the RNA is converted to cDNA and the cDNA is compared in step c) .

6. The method of claim 1, wherein step b) is accomplished using a microarray.

7. The method of claim 1, wherein the vascular-related disease is identified as early, early-mid, late-mid or late stage.

8. The method of claim 1, wherein the analyzing gene expression levels are for genes previously associated with the vascular-related disease.

9. The method of claim 1, wherein the analyzing gene expression levels are for genes not previously associated with the vascular-related disease.

10. A method of diagnosing a vascular-related disease in an individual comprising the steps of : a) identifying at least one gene that is upregulated or downregulated in the vascular-related disease comprising the steps of :

1) obtaining a biopsy sample from the individual's pulmonary artery during progression of the vascular-related disease ;

2) obtaining a pulmonary artery sample from a non- diseased control ;

3) extracting RNA from the samples in steps 1) and 2) ; 4) obtaining gene products from the RNA extracted in step 3 ) ; and

11. The method of claim 10, wherein the vascular-related disease is pulmonary arterial hypertension.

12. The method of claim 10, wherein the biopsy sample is extracted using an endoarterial catheter.

13. A method of identifying microRNA dysregulated in an individual having a vascular-related disease comprising the steps of : a) obtaining a biopsy sample from the individual's pulmonary artery during progression of the vascular- related disease; b) obtaining a pulmonary artery sample from a non- diseased control; c) extracting RNA from the samples in steps a) and b) ; d) converting the RNA to cDNA; e) comparing levels of microRNA expression from the biopsy sample with the non-diseased control; and f) identifying the microRNA dysregulated in the vascular- related disease relative to baseline.

14. The method of claim 13, wherein the vascular- related disease is pulmonary arterial hypertension.

15. The method of claim 13, wherein the microRNA is measured according to stages of progression of the vascular-related disease .

16. A method of treating an individual having a vascular- related disease by targeting raicroRNAs comprising the following steps : a) assessing a stage of the vascular-related disease in the individual; b) identifying whether microRNAs are upregulated or downregulated ; c) selecting the microRNAs to target based on the stage of the vascular-related disease and whether the microRNAs are upregulated or downregulated; and d) administering an agent known to inhibit an upregulated microRNA or an agent known to promote a downregulated microRNA to the individual, wherein the stage of the vascular-related disease is based on flow rates and blood pressure within an artery of the individual .

17. The method of claim 16, wherein the vascular-related disease is pulmonary arterial hypertension.

18. The method of claim 16, wherein the microRNAs to target are any microRNAs listed in Tables 12-17.

19. The method of claim 16, wherein the stage of the vascular- related disease is one of high flow and high pressure within the artery of the individual.

20. The method of claim 19, wherein the upregulated microRNAs to inhibit under the stage of high flow and high pressure comprise at least one member selected from the group consisting of hsa-miR-520g, hsa-miR-331-5p, hsa-miR-410, hsa-let-7d, hsa- miR-187, hsa-miR-16-2, hsa-miR-130a , hsa-miR-548n, hsa-miR-127- 5p, solexa-2580-353, HS_206, hsa-miR-663, solexa-7534-111 , hsa- let-7g, HS_157, hsa-miR-610 , HS_251.1, hsa-miR-519e , hsa-miR- 1237, hsa-miR-1185, HS_151.1, HS_135, solexa-3126-285 , hsa-miR- 30a, hsa-miR-192, hsa-miR-568, hsa-miR-1203, hsa-miR-28-5p, HS_262.1, HS_170, hsa-miR- 1273 , hsa-miR-602, hsa-miR-374a and hsa-miR-29a .

21. The method of claim 16, wherein the stage of the vascular- related disease is one of high flow and low pressure within the artery of the individual .

22. The method of claim 21, wherein the upregulated microRNAs to inhibit under the stage of high flow and low pressure comprise at least one member selected from the group consisting of HS_70, hsa-let-7d, hsa-miR-187, solexa-2580-353, HS_157, solexa-7534-111, hsa-miR-130a, HS_135, hsa-miR-192, hsa-miR-154, hsa-miR-151: 9.1, hsa-miR-1203, hsa-miR-525-3p and HS_199.

23. The method of claim 19, wherein the downregulated microRNAs to promote under the stage of high flow and high pressure comprise at least one member selected from the group consisting of solexa-603 -1846 , hsa-miR-586, hsa-miR-1201 , hεa-miR-33a, HS_56, hsa-miR-520d:9.1, hsa-miR-521, hsa-miR-519a, HS_134, HS_169, HS_221, hsa-miR-496, hsa-miR-935, hsa-miR-542-5p, solexa-5620-151, hsa-miR-99a, hsa-miR-212, hsa-let-7f -2 , hsa- miR-494, hsa-miR-1321 , hsa-miR-219-2-3p, hsa-miR-95, hsa-miR- 128b:9.1, hsa-miR-33a, hsa-miR-495, hsa-miR-1229 , hεa-miR-1205 , hsa-miR-524-3p, HS_150, hεa-miR-135a, hsa-miR-483 -5p, hsa-miR- 124a:9.1, hsa-miR-29b-l , hsa-miR-548c-5p, hsa-miR~551a, hsa-miR- 377 and hsa-miR-1304.

24. The method of claim 21, wherein the downregulated microRNAs to promote under the stage of high flow and low pressure comprise at least one member selected from the group consisting of HS_104, hsa-miR-548a-5p, hsa-miR-556-5p, HS_169, HS_140, hsa- miR-542-5p, HS_134 , hsa-miR-212, hsa-miR-363, HS_59, hsa-miR~ 586, hsa-miR-494, hsa-miR-1205 , hsa-let-7f -2 , hsa-miR-483 -5p, HS_150, hsa-miR-1229, HS_156, hsa-miR-619, hsa-miR-lOb and hsa- miR-371-5p.

25. A method of treating an individual having a vascular- related disease according to claim 1, further wherein the individual is categorized based on progression of the vascular- related disease.

26. The method of claim 25, wherein the progression of the vascular-related disease is selected from the group consisting of early stage, mid stage and late stage.

27. The method of claim 26, wherein the pharmaceutical agent to treat the early stage progression of the vascular-related disease is at least one member selected from the group consisting of the drugs listed in Table 3.

28. The method of claim 26, wherein the pharmaceutical agent to treat the raid stage progression of the vascular-related disease is at least one member selected from the group consisting of the drugs listed in Tables 4 and 5.

29. The method of claim 26, wherein the pharmaceutical agent to treat the late stage progression of the vascular-related disease is at least one member selected from the group consisting of the drugs listed in Table 6.

30. The method of claim 1, wherein the treatment of the individual may be modified over the course of disease progression.