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Paper text:
somatostatin ( sst ) is a highly evolutionarily conserved peptide hormone that is expressed in many tissues .
indeed , it was first discovered as an inhibitor of growth hormone ( gh ) release from the pituitary gland .
sex - specific properties of pulsatile gh secretion induce well - characterized sexually dimorphic gene expression patterns in the mouse liver . to test the involvement of sst in this phenomenon
, we generated sst - knockout ( ko ) mice and performed microarray gene expression profiling on rna isolated from the liver of knockouts and wildtype controls of both sexes .
we confirmed that sst is essential for the sexually dimorphic hepatic expression of a large panel of genes .
we also found a non - overlapping subset of differentially expressed genes , discussed here , that appear to be regulated independently of sexually dimorphic gh signaling .
the mutant allele was backcrossed onto the c57bl/6j background for 14 generations and heterozygous breeding pairs were used to produce the experimental mice for this study .
all mice were housed in a temperature- and light - controlled murine - specific pathogen free environment ( 72    2  f , lights on 7:00  am to 7:00  pm ) with free access to standard laboratory chow and water .
all animal studies were approved by the iacuc at oregon health and science university . experimental knockout and wildtype control mice
( 12 total , 3 biological replicates per sex and genotype ) were euthanized by cervical dislocation between 9:00  am and 12:00  pm at age 16  weeks .
liver tissue was immediately dissected , frozen on dry ice and stored at   80  c until rna extraction . as controls for a separate experiment ,
the female mice of both genotypes had received a single subcutaneous injection of 10  l sterile sesame oil at postnatal day 1 , and had an empty 1  cm long piece of medical grade silastic tubing ( dow corning , 0.0635 inner diameter ) implanted subcutaneously between the shoulder blades under anesthesia with 2% avertin at age 8  weeks .
male mice of both genotypes underwent 2 sham gonadectomy surgeries at postnatal day 1 and at 8  weeks of age under general anesthesia either by hypothermia or 2% avertin , respectively .
for both surgeries , a small incision was made over the lower abdomen and the gonads were visualized , then the skin incision was closed with either medical grade super glue ( neonates ) or stainless steel wound clips ( adults ) . during the second surgery , an empty piece of silastic tubing was inserted between the shoulder blades as described for the females .
we have no reason to believe that these interventions , performed on both genotypes of mice , would result in altered hepatic gene expression patterns 8  weeks later .
100  mg of liver from each mouse was homogenized in 1  ml of trizol reagent ( invitrogen ) for 60  s using a rotor  stator mechanical homogenizer .
all subsequent centrifugation steps were carried out for 10  min at 12,000  rpm and 4  c .
first , samples were centrifuged and the upper phase was transferred to a new tube with addition of 200  l chloroform . following an additional centrifugation , the aqueous ( upper ) phase was carefully removed and the rna precipitated with 500  l isopropanol .
samples were centrifuged again and a pellet containing rna was obtained and washed first with 1  ml of 4  m licl and then with 70% etoh .
the pellet was allowed to air dry and then the rna was resuspended in 100  l of diethylpyrocarbonate ( depc)-treated h2o .
concentrations were between 420 and 1200  ng/l with od 260:280 values ranging from 1.94 to 2.06 and od 260:230 values from 1.81 to 2.24 .
further quality control was performed using agilent 2100 bioanalyzer chips and the rna integrity numbers ( rins ) ranged from 7.47.9 .
rna samples were submitted to the university of michigan microarray core facility , where 250  ng total rna per sample was used to synthesize cdna , generate biotin - modified amplified rna and prepare the arna for hybridization utilizing 3 ivt express kits ( affymetrix ) .
16  g of arna per sample were then hybridized to genechip mouse genome 430 2.0 arrays ( affymetrix ) for 16  h at 45  c in hyb oven 640 ( affymetrix ) .
washing and staining of the genechips was performed according to the manufacturer 's protocol using fluidics station 450 ( affymetrix ) and genechips were scanned using the 3000 7 g genechip scanner with autoloader ( affymetrix ) .
the distributions of the perfect match ( pm ) probes for each chip were compared .
rna degradation was examined and all samples were determined to be adequate ( fig . 
a probe - level model was fitted and standard error ( se ) estimates from each gene on each array are shown in a boxplot summary ( fig . 
sample 2 ( mouse 58 , wild - type female replicate # 2 ) showed a slightly elevated se compared to the other 11 samples .
log2-transformed expression values for each gene were calculated using robust multi - array average ( rma ) . a principal components analysis ( pca ) was performed and the first two principal components plotted .
biological replicates from each group clustered together , but there was a clear separation between the 4 groups ( fig . 
linear models specifically designed for microarray analysis   were fitted to the data and samples were weighted based on a gene - by - gene algorithm designed to down - weight chips that are deemed less reproducible , such as sample 2 .
the specific contrasts of male wildtype versus male sst - ko and female wildtype versus female sst - ko were computed .
probe - sets with a log2 fold change   1 and an adjusted p - value of   0.05 were selected .
analyses were conducted in the r statistical environment implementing the affy , affyplm , and limma   packages .
376 annotated genes / cdnas and 29 non - annotated sequences that showed no sexual dimorphism in wildtype mice were found to be differentially regulated in the liver of one or rarely both sexes of sst - ko compared to wt mice ( supplemental table 1 ) . of these ,
126 were down - regulated and 279 were up - regulated in sst - ko mice .
some of the more highly differentially expressed genes in this subset have been reported to be sexually dimorphic in other publications , , , , and therefore may belong in the group of genes regulated by gh , which was the topic of our previously published article .
regardless , using the david tool to functionally cluster all 405 of these differentially regulated sequences by similarly annotated gene ontology ( go ) biological process terms , we found that six of the seven significantly enriched annotation clusters were related to the immune system and included terms such as defense response , inflammatory response , mhc protein complex , cell chemotaxis and leukocyte migration ( supplemental table 2 ) .
our study was not designed to differentiate between direct and indirect effects of the absence of sst on gene expression in the liver , although there are limited reports of sst receptor expression on hepatocytes .
accumulating evidence has indicated that it is likely not hepatocytes that account for the bulk of sst receptor expression in the liver , but rather hepatic stellate cells ( hscs ) , which particularly begin to express sst - receptors after activation by various signals . because hscs have recently been identified as an important component of the innate immune system , it is tempting to speculate that the enriched clusters of immune response genes that we found to be differentially expressed in the liver of sst - ko mice are being expressed in hscs and not hepatocytes . clearly , further experiments are required , but this finding is consistent with the proposal that extra - hypothalamic sst plays a gh - independent regulatory role in tissue - specific innate immune system activation and the observation that a lack of sst results in an activation of the immune system in the stomach .
the following are the supplementary data related to this article.supplementary table 1list of all probes found to be differentially expressed between wildtype and somatostatin - knockouts of either sex , arranged in alphabetical order of gene symbol.supplementary table 2list of most highly enriched functional annotation clusters found in the list of genes in supplementary table 1 as determined by gene ontology analysis .
list of all probes found to be differentially expressed between wildtype and somatostatin - knockouts of either sex , arranged in alphabetical order of gene symbol .
list of most highly enriched functional annotation clusters found in the list of genes in supplementary table 1 as determined by gene ontology analysis .
somatostatin is a neuropeptide hormone that inhibits pituitary growth hormone ( gh ) release . using microarray analysis of gene expression in the livers of wildtype control and somatostatin knockout mice , 
 we have previously identified a panel of genes whose gh - dependent and sexually dimorphic expression patterns are significantly altered by the absence of somatostatin ( 1 ) . here , we provide methodological and analytical details of that study , the raw data of which is deposited in the gene expression omnibus as data set gse56520 . 
 in addition , we performed further gene ontology analysis of the data and found that the differential expression of a second subset of genes in the livers of somatostatin - knockout mice versus wildtype controls is likely independent of gh signaling and involved in the innate immune response .