Profiling the adult human liver transcriptome: analysis by cDNA array hybridization.

BACKGROUND/AIMS: A comprehensive profile of genes expressed at the mRNA level (transcriptome) in human liver tissue is important for elucidating the pathogenesis and treatment of hepatic diseases. The recent development of cDNA array hybridization allows the parallel monitoring of thousands of genes expressed in a single organ. METHODS: High-density microarrays containing 4043 known and unique human cDNA gene targets were used to quantitatively analyze the expression of genes in human livers. Expressed gene transcripts were classified by function and listed with information of their chromosomal positions. Computational analysis was used to cluster genes according to similarity in pattern of gene expression. RESULTS: A total of 2418 unique gene transcripts were detected in five liver specimens. Through relational database analysis, we determined 1212 genes that were commonly expressed in 4 of the five liver specimens. Furthermore, analysis of the total 2418 expressed genes by self-organizing maps and hierarchical clustering unexpectedly revealed a genomic acute phase response in two of the liver specimens. CONCLUSIONS: These findings represent a comprehensive preliminary molecular index of genes transcribed in the adult human liver. The information may serve as a resource for speeding up the discovery of genes underlying human hepatic diseases.

The N-glycans determine the differential blood clearance and hepatic uptake of human immunoglobulin (Ig)A1 and IgA2 isotypes.

Human immunoglobulin (Ig)A exists in blood as two isotypes, IgA1 and IgA2, with IgA2 present as three allotypes: IgA2m(1), IgA2m(2), and IgA2m(n). We now demonstrate that recombinant, chimeric IgA1 and IgA2 differ in their pharmacokinetic properties. The major pathway for the clearance of all IgA2 allotypes is the liver. Liver-mediated uptake is through the asialoglycoprotein receptor (ASGR), since clearance can be blocked by injection of excess galactose-Ficoll ligand and suppressed in ASGR-deficient mice. In contrast, only a small percentage of IgA1 is cleared through this pathway. The clearance of IgA1 lacking the hinge region with its associated O-linked carbohydrate was more rapid than that of wild-type IgA1. IgA1 and IgA2 that are not rapidly eliminated by the ASGR are both removed through an undefined ASGR-independent pathway with half-lives of 14 and 10 h, respectively. The rapid clearance of IgA2 but not IgA1 through the liver may in part explain why the serum levels of IgA1 are greater than those of IgA2. In addition, dysfunction of the ASGR or altered N-linked glycosylation, but not O-glycans, that affects recognition by this receptor may account for the elevated serum IgA seen in liver disease and IgA nephropathy.

Comprehensive gene expression profile of the adult human renal cortex: analysis by cDNA array hybridization.

BACKGROUND: Profiling of gene expression in healthy and diseased renal tissue is important for elucidating the pathogenesis of renal diseases. Comprehensive information about the genes expressed in renal tissue is unavailable. The recently developed cDNA array hybridization methodology allows simultaneous monitoring of thousands of genes expressed renal tissue. METHODS: Complex [alpha-33P]-labeled cDNA probes were prepared from histopathologically uninvolved remnants of nine renal tissues obtained by nephrectomy. Each probe was hybridized to a high-density array of 18,326 paired target genes. The radioactive hybridization signals by phosphorimager screens were quantitated by special software. Bioinformatics from public genomic databases were used to assign a chromosomal location of each expressed transcript and gene function. Cluster analysis was used to arrange genes according to the similarity in pattern of gene expression. RESULTS: A total of 7563 different gene transcripts was detected in the nine tissue samples. Approximately 870 of these genes were full-length mRNA human transcripts (HT), and the remaining 6693 were expressed sequence tags (ESTs). The full-length transcripts were classified by function of the gene product and were listed with information of their chromosomal positions. To allow a comparison between gene expression in clinical and experimental studies, the mouse genes with known similar function to the human counterpart were included in the bioinformatics analysis. Cluster analysis of 502 full-length genes that are expressed in four or more renal tissues revealed more than 110 genes that are highly expressed in all the renal specimens. CONCLUSIONS: The presented data constitute a comprehensive preliminary transcriptional map of the adult human renal cortex. The information may serve as a resource for speeding up the discovery of genes underlying human renal disease. The integrated listing of the full-length expressed human and mouse genes is available through e-mail (Abdalla_Rifai@Brown.edu).

Gene expression of 5-lipoxygenase and LTA4 hydrolase in renal tissue of nephrotic syndrome patients.

Leukotrienes (LT) of the 5-lipoxygenase pathway constitute a class of potent biological lipid mediators of inflammation implicated in the pathogenesis of different models of experimental glomerulonephritis. The key enzyme, 5-lipoxygenase (5-LO), catalyses oxygenation of arachidonic acid to generate the primary leukotriene LTA4. This LT, in turn, serves as a substrate for either LTA4 hydrolase, to form the potent chemoattractant LTB4, or LTC4 synthase, to produce the powerful vasoconstrictor LTC4. To investigate the potential role of LT in the pathogenesis of human glomerulonephritis with nephrotic syndrome, we examined the gene expression of 5-LO and LTA4 hydrolase in renal tissue of 21 adult patients with nephrotic syndrome and 11 controls. The patients consisted of 11 cases of membranous nephropathy (MN), seven focal and segmental glomerulosclerosis (FSGS), two non-IgA mesangial glomerulonephritis and one minimal change disease. Total RNA purified from renal tissue was reverse transcribed into cDNA and amplified with specific primers in a polymerase chain reaction (RT-PCR). Eight patients' renal tissue, four MN and four FSGS, co-expressed 5-LO and LTA4 hydrolase. In situ hybridization analysis revealed 5-LO expression and distribution limited to the interstitial cells surrounding the peritubular capillaries. Comparative clinical and immunohistological data showed that these eight patients had impaired renal function and interstitial changes that significantly correlated with 5-LO expression. These findings suggest that leukotrienes may play an important role in the pathogenesis of MN and FSGS. These results are also relevant to elucidating the pathophysiologic mechanisms which underlie progression to renal failure in these diseases.

Steroid metabolism along the gastrointestinal tract of the cannulated pig.

Steroid metabolism along the gastrointestinal tract of the cannulated pig was studied. Thi was achieved by fitting simple gut cannulas in the terminal ileum, caecum and mid-colon of three Landrace x large white boars, which enabled convenient collection of digesta and faecal samples at defined time points. Biochemical analyses showed that the neutral steroid profile of the pig is similar to that of man, dominated by cholesterol and its bacterial metabolite coprostanol. In contrast, pigs consuming a normal diet excrete appreciably lower quantities of neutral sterols in faeces. The major primary bile acids detected were the glycine and taurine amidates of hyocholic and chenodeoxycholic acids, which were rapidly converted to the free bile acids and subsequently dehydroxylated to hyodeoxycholic and lithocholic acids respectively, in the terminal ileum and caecum. Bacterial deconjugation and 7 alpha-dehyrdoxylation are virtually complete in the caecum with negligible further metabolism in the colon and faeces. On a wet weight basis the concentration of both neutral and acid steroids was shown to increase aborally. Inclusion of dietary fibre in the form of cellulose (Solka floc) and guar gum reduced steroid concentration considerably at all sites of the large intestine, which is consistent with their stool bulking effects. In conclusion, this study shows that intestinal steroid metabolism in the pig is similar to that in man despite slightly different bile acid profiles and, therefore, the multicannulated pig may serve as a useful model of man in chemoprevention studies of colorectal cancer.

Phenotypic characterization of cytokine expression in patients with IgA nephropathy.

To identify the cytokines that play a relevant role in the pathogenesis of IgA nephropathy, we analyzed and compared the gene expression of proinflammatory cytokines, immuno-regulatory cytokines, and growth factors in peripheral blood mononuclear cells (PBMC). Expression of IL-1 alpha, IL-1 beta, IL-2, IL-4, IL-6, IL-10, IL-12, IFN-gamma, TGF-beta, TNF-alpha, and PDGF was examined in 28 patients with IgA nephropathy (IgAN), 20 patients with non-IgA mesangial proliferative glomerulonephritis (mesPGN), and 19 healthy controls. Compared with healthy controls, a significant number of IgAN and mesPGN patients showed increased expression of IL-1 beta, IL-4, IL-10, IL-12, and IFN-gamma. The cytokine profile of renal tissue of 10 IgAN and 5 mesPGN biopsies was simultaneously analyzed and compared with that of PBMC. The proinflammatory IL-1 alpha and growth factor PDGF-B were expressed more in renal tissues than in PBMC. Furthermore, the renal profile of IL-alpha, IFN-gamma, and TNF-alpha expression was associated with the expression of IFN-gamma in PBMC. The serum level of IFN-gamma of IgAN correlated significantly (P = 0.0003) with that of IL-12, suggesting a potential role for cross-stimulation. More importantly, expression of IFN-gamma in PBMC and the elevated serum level correlated with the decline in glomerular filtration rate (P = 0.0012) and severity of renal histopathologic grade. To elucidate the role of leukocytes in renal cytokine expression, surface markers of T cells (CD3), monocytes (CD14), natural killer cells (CD16), and B cells (CD19) were also examined in renal tissues. The prominent renal expression of CD3, CD14, and CD16 implicates the leukocytes as the major source of proinflammatory cytokines in IgAN. Collectively, these findings indicate that IFN-gamma plays a prominent role in an interactive network of cytokines that contribute to the pathogenesis and progression of IgA nephropathy.

Effect of fibre on bile acid metabolism by human faecal bacteria in batch and continuous culture.

The effect of various fibres on bile acid metabolism by human faecal bacteria was studied in batch and continuous culture models of the large intestine. The metabolism of the primary bile acids--chenodeoxycholic and cholic-was entirely oxidative in aerobic conditions, and the major metabolites were the 7-oxo-derivatives of the parent bile acids. Addition of both undigested and digested wheat bran and pea fibre to aerobic batch cultures reduced metabolism in a dose-dependent manner with undigested fibre being far more effective. In anaerobic conditions, the metabolism of primary bile acids was predominantly reductive: the major metabolites were the 7 alpha-dehydroxylated products of the parent bile acids--namely lithocholic acid (from chenodeoxycholic acid) and deoxycholic acid (from cholic acid), respectively. Addition of undigested crude fibre to batch cultures reduced 7 alpha-dehydroxylation in a dose-dependent manner; addition of digested crude fibre to anaerobic continuous cultures had no significant effect on bile acid metabolism. The soluble fibre lactulose needed to be added to reduce pH sufficiently (> or = 5.5), to prevent 7 alpha-dehydroxylation of primary bile acids. Reduction of 7 alpha-dehydroxylation was also associated with a substantial decrease in Bacteroides spp and a concomitant increase in Lactobacillus spp in the cultures. The failure of digested wheat bran to reduce bile acid metabolism in continuous culture is attributed mainly to the physical constraints of the systems which can handle no more than 4-6% particulate material due to blockage. It is concluded that anaerobic continuous culture systems with human faecal bacteria have some value as models of the human large intestinal environment, but further modifications are required before the effect of particulate fibres on the metabolism of bile acids can be fully addressed.

Clearance kinetics, biodistribution, and organ saturability of phosphorothioate oligodeoxynucleotides in mice.

We examined the dynamics of removal from circulation, tissue distribution, and persistence of phosphorothioate oligodeoxynucleotides (S-ODN) anti-tumor-necrosis-factor and a control of random sequence (randomer) in mice. After intravenous injection, the majority (96%) of S-ODN cleared rapidly from the circulation in the first two phases. In the first phase, 37.8 +/- 2.3% of the radioactivity had a mean half-life (t1/2) of 2.0 +/- 0.4 minutes. In the second phase, 58.1 +/- 1.5% of the radioactivity cleared with t1/2 of 12.6 +/- 0.2 minutes. The catabolic phase, constituting a minor proportion (4.1 +/- 0.8% of the total radioactivity), had a mean t1/2 of 2.7 +/- 0.5 hours. At a low dose (1 microgram) tissue distribution of both S-ODN anti-tumor-necrosis-factor and randomer were similar. The liver and kidneys were the major organs involved in uptake and removal of S-ODN. Autoradiographic studies showed the liver Kupffer cells to be the major site of uptake and renal urinary space for elimination. The clearance rate from the circulation was increased with the dose of S-ODN. In contrast, the fraction of radioactivity localized in the kidneys, liver, and spleen was decreased with increase in dosage. Furthermore, at a high dose (200 micrograms), the tissue distribution of the S-ODN anti-tumor-necrosis-factor differed significantly from the randomer. These findings have general significance in showing that the liver and kidneys are the major organs for removal of S-ODN and these organs are saturable at high doses. In addition, the results have specific importance in defining different parameters, dose and base composition, that affect utilization of antisense oligonucleotides for controlling gene expression in vivo.

Lack of production and growth-modulating effects of 1a,25-dihydroxyvitamin D3 in cultured fetal rat hepatocytes.

1a,25-Dihydroxyvitamin D3 [1,25(OH)2D3], the hormonal form of vitamin D3, has been shown to play a role in the regulation of growth of the regenerating adult rat liver following partial hepatectomy. In addition, a recent study implicated the neonatal liver as a possible extrarenal site of 1,25(OH)2D3 synthesis. Therefore, in our present study we used rapidly growing fetal hepatocytes in culture as a model cell line for regenerating hepatocytes and tested the hypothesis that fetal hepatocytes locally produce 1,25(OH)2D3 which in turn regulates their growth. Hepatocytes isolated from 19-day rat fetuses were grown in culture for 24 h in minimal essential medium without added serum or mitogens. To identify 1,25(OH)2D3 production, we incubated fetal hepatocytes in culture with 3H-25-hydroxyvitamin D3 (3H-25-OH D3) for 2, 6 and 24 h. High-pressure liquid chromatographic analysis of the lipid extract of the medium and cells revealed no evidence of conversion of 3H-25-OH D3 into 3H-1,25(OH)2D3. Additionally, to investigate the effect of 1,25(OH)2D3 on DNA synthesis in fetal liver, we measured 3H-thymidine incorporation by the cultured fetal hepatocytes following 24 h of exposure to various concentrations of 1,25(OH)2D3. The results of DNA synthesis revealed no effect of 1,25(OH)2D3 on fetal hepatocyte growth. As alterations in growth regulation by 1,25(OH)2D3 in other cells are thought to be mediated by intracellular vitamin D receptors (VDR), the expression of the VDR message in the fetal and maternal tissues of a pregnant rat was studied. RNA was first isolated from fetal liver, fetal kidney, maternal liver and maternal kidney, and the corresponding cDNA was then generated by reverse transcription.(ABSTRACT TRUNCATED AT 250 WORDS)

Serial renal sonographic evaluation of patients with Lesch-Nyhan syndrome.

The objective of this study was to review sequential renal sonograms of patients with Lesch-Nyhan syndrome obtained over several years to determine different sonographic patterns, the alterations in the patterns occurring over time and the relationship to management. Additional objectives were to evaluate the size of the kidneys, and to correlate the metabolic constituents of calculi with the therapeutic regimens and with the renal sonographic patterns. Serial sonograms of six patients with Lesch-Nyhan syndrome were reviewed for periods varying between 2 and 7 years with a mean of 4 years. The ages of the patients at the conclusion of the study were between 10 and 22 years. Three patterns of abnormal echogenicity were found; a punctate increase in echogenicity in the renal medullary pyramids, a diffuse increase in medullary pyramid echogenicity, and a pattern of increased echogenicity in the collecting system. These patterns were progressive but did not alternate on sequential scans, regardless of increasing or constant therapy. Analysis of calculi suggested patients were precipitating various metabolites concurrently; the incidence of metabolites appeared to be unrelated to therapy. Those patients with shadowing opacities, whether in the renal medulla or collecting system, were more likely to develop renal colic. Renal dimensions were small with renal function remaining normal.

Extrarenal cytokines modulate the glomerular response to IgA immune complexes.

Clinical episodes of IgA nephropathy coincide recurrently with microbial infections. Cytokines produced during such infections may play a role in the pathogenesis of IgA-associated glomerulonephritis. To test this hypothesis, we examined the influence of passively administered proinflammatory cytokines (IL-1, IFN-gamma and IL-6) on the development of glomerulonephritis in an experimental model of IgA nephropathy. Glomerular IgA immune deposits were induced in mice by administration of IgA anti-phosphorylcholine (PC) with either a PC-containing carbohydrate antigen of Pneumococcal C polysaccharide (PnC) or a protein antigen of PC-conjugated bovine serum albumin (PC-BSA). The effect of IL-1 on the IgA-PC-BSA induced glomerular changes resulted in an increase of mesangial hypercellularity that was associated with mild proteinuria and hematuria. Mice treated with IL-1 and IgA-PnC developed diffuse proliferative glomerulonephritis with proteinuria and hematuria. In contrast, IL-6 treatment with IgA-PC-BSA of IgA-PnC failed to exert any significant renal effect. The combination of IL-6 and IL-1, however, intensified the mesangial hypercellularity of the IgA-PC-BSA, and induced severe proliferative glomerulonephritis with inflammatory monocytes and neutrophils infiltrates in the IgA-PnC treated mice. These glomerular changes were also accompanied by increased proteinuria and hematuria. Similarly, the combination of IFN with IL-1 produced histologic changes and compromised renal function more than IFN or IL-1 exerted independently. These results suggest that extrarenal cytokines influence the renal response to IgA immune deposits. We also conclude that a synergy of multiple cytokines and nephritogenic antigens immobilized in glomerular IgA immune deposits may lead to rapid progression of IgA-associated glomerulonephritis.

Faecal steroids and colorectal cancer: the effect of lactulose on faecal bacterial metabolism in a continuous culture model of the large intestine.

The effect of lactulose on intestinal bacterial metabolism in two identical single-stage chemostats has been studied. The study was designed as a single stage crossover. Both cultures were inoculated and treated in an identical manner except that whilst one fermenter was subject to pH control the other was not and vice versa. Complex bacterial populations were maintained for 23 days and many of the metabolic functions carried out by the micro-organisms in vivo were demonstrated in vitro. The predominant organisms belonged to the genera Bacteroides, Bifidobacterium and Clostridium with abundant levels of anaerobic Gram-positive rods. The redox potential in each fermenter showed considerable variation with maximum values of below -300 eV being attained. An indication of the stability of the bacterial communities was the production of short-chain volatile fatty acids; during steady-state conditions the mean ratio of the major acids acetic, propionic and butyric being 3.90:0.69:1.00 and 3.65:0.76:1.00 in each fermenter, respectively. During steady-state conditions, 7 alpha-dehydroxylation of the primary bile acid chenodeoxycholic acid was maintained at a constant rate with lithocholic acid representing over 85% of total steroid. Addition of the soluble fibre lactulose to the cultures had a profound effect on many of the parameters tested. Without pH control the culture pH dropped to below 5.0 and this coincided with a substantial decrease in total anaerobes, especially Bacteroides spp., an increase in Lactobacillus spp. (concomitant with an increase in lactic acid), a decrease in the concentration of short-chain volatile fatty acids and a substantial decrease in 7 alpha-dehydroxylation of chenodeoxycholic acid. These results show that it is possible to maintain viable intestinal bacteria in vitro using a continuous culture chemostat and that the cultures respond to changing conditions as evinced by the inhibition of 7 alpha-dehydroxylation of chenodeoxycholic acid on addition of lactulose. This indicates that the model may be of further use in studying the modulation of secondary bile acid formation, a possible risk factor in colorectal carcinogenesis.

Measurement of transit time of digesta through sections of gastrointestinal tract of pigs fed with diets containing various sources of dietary fibre (non-starch polysaccharides).

The effects of various sources of dietary fibre (defined as non-starch polysaccharides (NSP] on the transit time (TT) of digesta through sections of digestive tract were measured in pigs of 30-85 kg. The pigs were fitted with simple cannulas in the terminal ileum, caecum and mid-colon. Diets in experiments 1-3 were based on barley, wheat, soya bean meal and fish meal with NSP added in the form of wood cellulose (experiment 1), guar gum (experiment 2), wheat bran, pectin (experiment 3). Lactulose was also included in experiment 3 because of its NSP-like effects. Diets in experiments 4 and 5 were based on starch and casein and contained Phaseoluos vulgaris or Pisum sativum (experiment 4) and sugar beet pulp or wheat bran (experiment 5). Transit time (TT) was measured using 103Ruthenium phenanthroline to label solids and 51Chromium complexed to EDTA for liquids. Samples were taken every 3 h after marker administration for 51 h from all cannulas and the faecal output was collected every 3 h. The values obtained were very variable. The range of TT (h) defined as first arrival of markers and peak marker level was 3-12.2 and 3-12.2 to the ileum, 3-22.3 and 4.5-22.3 to the caecum, 4.5-50.3 and 16.5-48.8 to the colon and 24- less than 51 and 30- less than 51 to the rectum respectively.