Patent Document:

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 . 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 &# 39 ; 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 ). 20 - 30 kg yucatan micropigs ( sus scrofa , 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 20 mg / 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 ( fig1 ), 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 ( fig2 ). follow up endoarterial biopsy procedures were scheduled 7 , 21 , 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 non - steroidal anti - inflammatory drugs four times a day . 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 &# 39 ; s solution for subsequent immunohistochemical and quantitative pcr analysis . 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 aug . 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 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 , calif .) utilized in a fastprep fp120 homogenizer ( thermo electron corporation , waltham , mass .). rna was isolated using rneasy mini columns ( qiagen , valencia , calif .) as per manufacturer &# 39 ; s protocol . all total rna was eluted 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 , calif .). 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 ( 20 ug ) 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 ( 50 ° 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 ( affymetrix ). 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 ). after rna preparation , array hybridization and scanning of the porcine genechips ® exactly as recommended by affymetrix , the data produced are processed using the affymetrix tools in the r - bioconductor package called / affy /. this tool set allows for various probe level analyses of the data as well as probe level quality control . the mass 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 ( affy 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 &# 39 ; 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 . 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 &# 39 ; 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 ksscore 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 fig1 a ). 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 . 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 timepoint . 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 1d , calmodulin , transcription factor stat5b , 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 - 1 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 , kcbn1 , casp3 , tlr4 , il1b , il6 , hmgcr , top1 , fyn , prkca , ednrb , pdgfra , and hrt2b ), several have not ( for example , hspe , yes1 , 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 . endoarterial biopsy samples percutaneously obtained during the progression of pah were analyzed to correlate changes in microrna expression to disease progression . 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 &# 39 ; 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 & lt ; 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 . quantiles routine from the affy 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 mirna targets genes was done using a publicly available database of mirna target sequences and a specially written perl programming script . 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 ‘ hflp ’ 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 & amp ; 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 ‘ hflp ’ and ( 3 ) high flow high pressure ‘ hfhp ’. the groups were compared back to the baseline and the statistically significantly differentially regulated mirnas determined . 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 . the use of gene expression data to shape individual drug therapies has been postulated as the next phase in personalized medicine . the bioinformatic processing of an individual &# 39 ; 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 (‘ ks 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 potentially of the greatest therapeutic value for a patient . this supports the idea of achieving personalized treatments for vascular - based diseases by generating individualized drug prescriptions based on the bioinformatic processing of gene expression data from endoarterial biopsy samples obtained from diseased arteries . similarly , this enables personalized treatments for vascular - based diseases by generating lists of dysregulated microrna from the bioinformatic processing of microrna expression data from endoarterial biopsy samples from diseased arteries .

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