Detecting patterns of protein distribution and gene expression in silico

Most biological information is contained within gene and genome sequences. However, current methods for analyzing these data are limited primarily to the prediction of coding regions and identification of sequence similarities. We have developed a computer algorithm, CoSMoS (for context sensitive motif searches), which adds context sensitivity to sequence motif searches. CoSMoS was challenged to identify genes encoding peroxisome-associated and oleate-induced genes in the yeast Saccharomyces cerevisiae. Specifically, we searched for genes capable of encoding proteins with a type 1 or type 2 peroxisomal targeting signal and for genes containing the oleate-response element, a cis-acting element common to fatty acid-regulated genes. CoSMoS successfully identified 7 of 8 known PTS-containing peroxisomal proteins and 13 of 14 known oleate-regulated genes. More importantly, CoSMoS identified an additional 18 candidate peroxisomal proteins and 300 candidate oleate-regulated genes. Preliminary localization studies suggest that these include at least 10 previously unknown peroxisomal proteins. Phenotypic studies of selected gene disruption mutants suggests that several of these new peroxisomal proteins play roles in growth on fatty acids, one is involved in peroxisome biogenesis and at least two are required for synthesis of lysine, a heretofore unrecognized role for peroxisomes. These results expand our understanding of peroxisome content and function, demonstrate the utility of CoSMoS for context-sensitive motif scanning, and point to the benefits of improved in silico genome analysis.     

In silico dissection of cell-type-associated patterns of gene expression in prostate cancer

Prostate tumors are complex entities composed of malignant cells mixed and interacting with nonmalignant cells. However, molecular analyses by standard gene expression profiling are limited because spatial information and nontumor cell types are lost in sample preparation. We scored 88 prostate specimens for relative content of tumor, benign hyperplastic epithelium, stroma, and dilated cystic glands. The proportions of these cell types were then linked in silico to gene expression levels determined by microarray analysis, revealing unique cell-specific profiles. Gene expression differences for malignant and nonmalignant epithelial cells (tumor versus benign hyperplastic epithelium) could be identified without being confounded by contributions from stroma that dominate many samples or sacrificing possible paracrine influences. Cell-specific expression of selected genes was validated by immunohistochemistry and quantitative PCR. The results provide patterns of gene expression for these three lineages with relevance to pathogenetic, diagnostic, and therapeutic considerations.     

Ghrelin tissue distribution: comparison between gene and protein expression

Ghrelin, the natural ligand of the GH secretagogue (GHS) receptor, was originally isolated from the stomach and detected in several tissues, but a systematic study of its tissue distribution has not been performed. In the present investigation, we evaluated ghrelin gene expression (by RT-PCR technique) and ghrelin protein concentration (by enzyme immunoassay technique) in tissues obtained from control rats as well as in rats subjected to 48-h fasting. The ghrelin gene was expressed in stomach, small intestine, brain, cerebellum, pituitary, heart, pancreas, salivary gland, adrenal, ovary and testis, with maximum expression occurring in the stomach, while no significant expression was detected by standard RT-PCR in liver, lung, kidney and skeletal muscle. Ghrelin protein was detected in stomach, small intestine, brain, cerebellum, pituitary, lung, skeletal muscle pancreas, salivary gland, adrenal, ovary and testis, at concentrations ranging from 0.05 to 1.43 ng/mg of homogenate protein (the highest concentration occurred in the lung, followed by the brain). Ghrelin was not detectable in the heart, liver and kidney. Therefore, gene and protein expression were dissociated. Fasting did not produce significant changes in ghrelin gene expression, while the distribution of ghrelin between different tissues was significantly modified: protein concentration increased in the brain, cerebellum, lung and salivary gland, while it decreased in the stomach.     

Developmental gene expression and tissue distribution of the CHIP28 water-channel protein.

The CHIP28 water channel is a major component of red cell and renal tubule membranes; however, its ontogeny and tissue distribution remain undefined. Three patterns of expression were identified when CHIP28 mRNA was surveyed by in situ hybridization histochemistry in rats between embryonic day 14 and maturity. (i) CHIP28 mRNA and protein were very abundant in hematopoietic tissue and kidneys of mature rats, but strong expression did not occur until after birth, when it appeared in renal proximal tubules and descending thin limbs, red pulp of the spleen, and membranes of circulating red cells. (ii) CHIP28 mRNA was abundant in choroid plexus epithelium throughout fetal development and maturity. (iii) CHIP28 mRNA was transiently observed in periosteum, heart, vascular endothelium, and cornea during fetal development. The ontogeny of kidney and red cell CHIP28 expression coincides with the ability of kidneys to concentrate urine, suggesting that CHIP28 promotes water reabsorption in the proximal nephron and provides red cell osmoregulation needed for passage through the hypertonic medulla. Its presence in the choroid plexus suggests that CHIP28-mediated water transport contributes to secretion of cerebrospinal fluid. The functional role of CHIP28 in developing bone, heart, and eye is unclear. These findings further establish the general physiologic role of CHIP28 as a water channel involved in reabsorption, osmoregulation, and secretion. The studies also suggest other possible functions during fetal development and predict that complex mechanisms will be needed for regulation of CHIP28 gene expression in diverse tissues at distinct points in development.     

Identification of novel epididymal genes by expression profiling and in silico gene discovery

We have used both the UniGene RIKEN epididymal EST library and the Affymetrix microarray profiling for identifying novel epididymal genes in mouse. The use of ESTs is a complementary approach to Affymetrix arrays for identifying novel epididymal genes, while only 32% and 28% of ESTs of unknown genes were present in the U74v.2Set and MG 430 2.0 version Affymetrix arrays, respectively. As expected, the probe set for a notably larger proportion of known genes was present in the Affymetrix arrays, and the coverage was greatly improved by the newer array version. Furthermore, many genes with more than five ESTs in the UniGene library showed variable levels of expression in both versions of the Affymetrix arrays. However, both the Affymetrix and EST data correlated well with that obtained by quantitative RT-PCR, and thus, we conclude that the findings of high EST number but only limited expression in the arrays could be considered as false negatives in the Affymetrix arrays.     

Lineage specificity of gene expression patterns

The hematopoietic system offers many advantages as a model for understanding general aspects of lineage choice and specification. Using oligonucleotide microarrays, we compared gene expression patterns of multiple purified hematopoietic cell populations, including neutrophils, monocytes, macrophages, resting, centrocytic, and centroblastic B lymphocytes, dendritic cells, and hematopoietic stem cells. Some of these cells were studied under both resting and stimulated conditions. We studied the collective behavior of subsets of genes derived from the Biocarta database of functional pathways, hand-tuned groupings of genes into broad functional categories based on the Gene Ontology database, and the metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. Principal component analysis revealed strikingly pervasive differences in relative levels of gene expression among cell lineages that involve most of the subsets examined. These results indicate that many processes in these cells behave differently in different lineages. Much of the variation among lineages was captured by the first few principal components. Principal components biplots were found to provide a convenient visual display of the contributions of the various genes within the subsets in lineage discrimination. Moreover, by applying tree-constructing methodologies borrowed from phylogenetics to the expression data from differentiated cells and stem cells, we reconstructed a tree of relationships that resembled the established hematopoietic program of lineage development. Thus, the mRNA expression data implicitly contained information about developmental relationships among cell types.     

Divergent and nonuniform gene expression patterns in mouse brain

Considerable progress has been made in understanding variations in gene sequence and expression level associated with phenotype, yet how genetic diversity translates into complex phenotypic differences remains poorly understood. Here, we examine the relationship between genetic background and spatial patterns of gene expression across seven strains of mice, providing the most extensive cellular-resolution comparative analysis of gene expression in the mammalian brain to date. Using comprehensive brainwide anatomic coverage (more than 200 brain regions), we applied in situ hybridization to analyze the spatial expression patterns of 49 genes encoding well-known pharmaceutical drug targets. Remarkably, over 50% of the genes examined showed interstrain expression variation. In addition, the variability was nonuniformly distributed across strain and neuroanatomic region, suggesting certain organizing principles. First, the degree of expression variance among strains mirrors genealogic relationships. Second, expression pattern differences were concentrated in higher-order brain regions such as the cortex and hippocampus. Divergence in gene expression patterns across the brain could contribute significantly to variations in behavior and responses to neuroactive drugs in laboratory mouse strains and may help to explain individual differences in human responsiveness to neuroactive drugs.     

Individuality and variation in gene expression patterns in human blood

The nature and extent of interindividual and temporal variation in gene expression patterns in specific cells and tissues is an important and relatively unexplored issue in human biology. We surveyed variation in gene expression patterns in peripheral blood from 75 healthy volunteers by using cDNA microarrays. Characterization of the variation in gene expression in healthy tissue is an essential foundation for the recognition and interpretation of the changes in these patterns associated with infections and other diseases, and peripheral blood was selected because it is a uniquely accessible tissue in which to examine this variation in patients or healthy volunteers in a clinical setting. Specific features of interindividual variation in gene expression patterns in peripheral blood could be traced to variation in the relative proportions of specific blood cell subsets; other features were correlated with gender, age, and the time of day at which the sample was taken. An analysis of multiple sequential samples from the same individuals allowed us to discern donor-specific patterns of gene expression. These data help to define human individuality and provide a database with which disease-associated gene expression patterns can be compared.     

Spatial patterns of gene expression in the olfactory bulb

How olfactory sensory neurons converge on spatially invariant glomeruli in the olfactory bulb is largely unknown. In one model, olfactory sensory neurons interact with spatially restricted guidance cues in the bulb that orient and guide them to their target. Identifying differentially expressed molecules in the olfactory bulb has been extremely difficult, however, hindering a molecular analysis of convergence. Here, we describe several such genes that have been identified in a screen that compiled microarray data to create a three-dimensional model of gene expression within the mouse olfactory bulb. The expression patterns of these identified genes form the basis of a nascent spatial map of differential gene expression in the bulb.     

Systemic and cell type-specific gene expression patterns in scleroderma skin

We used DNA microarrays representing >12,000 human genes to characterize gene expression patterns in skin biopsies from individuals with a diagnosis of systemic sclerosis with diffuse scleroderma. We found consistent differences in the patterns of gene expression between skin biopsies from individuals with scleroderma and those from normal, unaffected individuals. The biopsies from affected individuals showed nearly indistinguishable patterns of gene expression in clinically affected and clinically unaffected tissue, even though these were clearly distinguishable from the patterns found in similar tissue from unaffected individuals. Genes characteristically expressed in endothelial cells, B lymphocytes, and fibroblasts showed differential expression between scleroderma and normal biopsies. Analysis of lymphocyte populations in scleroderma skin biopsies by immunohistochemistry suggest the B lymphocyte signature observed on our arrays is from CD20+ B cells. These results provide evidence that scleroderma has systemic manifestations that affect multiple cell types and suggests genes that could be used as potential markers for the disease.     

A typology of photoreceptor gene expression patterns in the mouse

Mutations in photoreceptor-enriched genes have been implicated in dozens of human retinal diseases, yet no systematic analysis of rod and cone gene expression patterns has been carried out. In addition, although cone photoreceptor loss accounts for much of the morbidity of retinal disease, relatively few cone-specific genes are known. In this study, we carried out microarray and in situ hybridization analyses of the mouse Neural retina leucine zipper gene (Nrl) mutant, which shows an en masse conversion of rods into cones, to establish a typology of photoreceptor gene expression and to identify novel cone-specific genes. We found a total of 18 new cone-enriched genes, some of which map near uncloned retinal disease loci. Several of these genes have a dorsal-ventral (D-V) pattern of expression similar to that of short- or medium-wavelength opsins. We carried out microarray analysis of dorsal and ventral microdissected WT retina and found additional photoreceptor genes with an asymmetric distribution. Overall, we found that photoreceptor genes fall on an expression spectrum from rod-specific to cone-specific, with many showing varying degrees of rod and cone coexpression. These expression patterns can be reliably predicted from microarray data alone. Our results demonstrate definitive molecular differences between rods and cones that may underlie the physiological differences between these two classes of photoreceptors.     

蛋白翻译起始因子C2在肝癌、胃癌中的表达与分布

目的 研究C2基因在肝细胞癌（HCC）、胃癌中的表达、分布及意义。方法 利用免疫组化法检测C2蛋白在60例HCC、58例胃癌组织中的表达，Western blot法检测C2蛋白在10例HCC及其癌旁组织中的表达。结果 60例HCC及42例癌旁组织中，C2蛋白阳性率分别为27．3％（17／60例）和83．3％（35／42例），C2蛋白在HCC癌组织中表达明显低于其癌旁组织（P＜0．001）；C2的表达与病人年龄、HBsAg及AFP明显关系（P＜0．05）。Western blot结果与免疫组化一致。在HBXAg阳性的49例HCC中，C2蛋白阳性率为20．4％，在HBXAg阴性的11例HCC中，C2蛋白阳性率为63．6％。C2在HBXAg阳性的HCC中的表达明显低于HBXAg阴性者（P＜0．05）。58例原发性胃癌及44例癌旁组织中，C2蛋白阳性率分别占41．4％（24／58例）和77．3％（34／44例）。C2蛋白在胃癌组织中表达明显低于其癌旁组织（P＜0．05），且与胃癌组织的分化程度、浆膜浸润、肿瘤大小有明显的关系（P＜0．05）。结论 C2基因表达下调可能与HCC、胃癌的发生、发展有关。HBXAg对C2的抑制作用可能与HCC的发生，发展有关。C2可能是一潜在的抑癌基因。     

hClock基因mRNA及其蛋白在结直肠肿瘤中表达的研究

目的探讨人类生物钟基因hClockmRNA及其蛋白在不同Dukes分期结直肠肿瘤中的表达,研究它们的表达与结直肠肿瘤的侵袭及转移的关系。方法采用原位杂交检测结直肠癌与相应癌旁组织中hClock基因mRNA的表达,并采用免疫组织化学检测相应标本中hCloek基因蛋白产物（CLOCK蛋白）的表达。结果21例结直肠肿瘤中hCloekmRNA弱阳性表达率47．62％,中或强阳性表达率52．38％,且与Dukes分期相关（P〈0．05）;CLOCK蛋白均呈中或强阳性表达。相应癌旁组织中hClockmRNA及蛋白呈弱阳性表达（P〈0．01）。结论hCloek基因可能与结直肠肿瘤的发生、发展及侵袭、转移有相关性。     

Zone‐specific gene expression patterns in articular cartilage

Objective

To identify novel genes and pathways specific to the superficial zone (SZ), middle zone (MZ), and deep zone (DZ) of normal articular cartilage.

Methods

Articular cartilage was obtained from the knees of 4 normal human donors. The cartilage zones were dissected on a microtome. RNA was analyzed on human genome arrays. The zone‐specific DNA array data obtained from human tissue were compared to array data obtained from bovine cartilage. Genes differentially expressed between zones were evaluated using direct annotation for structural or functional features, and by enrichment analysis for integrated pathways or functions.

Results

The greatest differences in genome‐wide RNA expression data were between the SZ and DZ in both human and bovine cartilage. The MZ, being a transitional zone between the SZ and DZ, thereby shared some of the same pathways as well as structural/functional features of the adjacent zones. Cellular functions and biologic processes that were enriched in the SZ relative to the DZ included, most prominently, extracellular matrix–receptor interactions, cell adhesion molecule functions, regulation of actin cytoskeleton, ribosome‐related functions, and signaling aspects such as the IFN, IL4, Cdc42/Rac, and JAK/STAT signaling pathways. Two pathways were enriched in the DZ relative to the SZ, including PPARG and EGFR/SMRTE.

Conclusion

These differences in cartilage zonal gene expression identify new markers and pathways that govern the unique differentiation status of chondrocyte subpopulations.

     

免疫球蛋白结合蛋白在氟中毒大鼠骨组织中的表达研究

目的 观察内质网应激标志性分子免疫球蛋白结合蛋白(BiP)在氟中毒大鼠股骨组织的表达,探讨内质网应激在氟骨症发病机制中的可能作用。方法 60只Wistar大鼠,按体质量随机分成4组,每组15只。对照组饲以常规饲料（含钙量为0.79％）,低钙组饲以自制低钙饲料（含钙量为0.063％）,饮用自来水(氟化钠水平＜1 mg/L);高氟组和低钙高氟组分别饲以常规饲料、自制低钙饲料,饮用自来水中加氟(氟化钠水平为221 mg/L)。实验期间动物自由进食、进水,每周测体质量1次。实验周期为12周。通过免疫组化和RT-PCR技术分析BiP在股骨组织中基因和蛋白水平的表达变化。结果 高氟组、低钙组、低钙高氟组大鼠股骨矿物质水平[(0.131±0019)、(0.097±0.011)、(0.083±0.007) g/cm]均低于对照组[(0.159±0.029)g/cm,P均＜0.05];低钙组、低钙高氟组的骨密度[(0.243±0.018)、(0.223±0.022)g/cm2]均低于对照组[(0.296±0.046)g/cm2,P 均＜0.05]。免疫组化技术检测到低钙组和低钙高氟两组大鼠股骨内抗BiP阳性染色的成骨细胞较对照组显著增加,而且低钙高氟组明显比低钙组的阳性成骨细胞多。RT-PCR分析显示出低钙加氟组大鼠骨组织的骨桥蛋白(OPN)、骨钙蛋白(OCN)mRNA表达水平(1.36±0.20、1.31±0.11)高于对照组(0.82±0.16、0.85±0.15,P均＜ 0.05);与加氟组(0.97±0.29)比较,低钙加氟组(1.36±0.20)大鼠骨组织的OPN表达明显提高(P＜0.05);低钙组和低钙高氟组BiP基因表达(1.38±0.24、1.35±0.12)高于对照组（1.14±0.06.P均＜0.05）。结论 投氟或联合低钙饮食刺激了大鼠股骨BiP基因和蛋白的表达,说明高氟或低钙高氟条件下大鼠骨组织出现不同程度的内质网应激。     

In silico cloning of mouse Muc5b gene and upregulation of its expression in mouse asthma model

Using a BLAST-searching approach, we identified a mouse expressed sequence tag (EST) clone (AA038672) showing great similarity to the 3' end of the human MUC5B gene. The clone was named "3pmmuc5b-1" after complete nucleotide sequencing (Genbank Accession, AF369933). A subsequent search of the mouse genome database with the 3pmmuc5b-1 sequence identified two overlapping genomic clones (AC020817 and AC020794) that contained the sequence of both 3pmmuc5b-1 and the mouse Muc5ac gene. Like their human homologs, the genomic order of the mouse Muc genes is 5'-Muc5ac-Muc5b-3'. These results suggest that the newly identified EST clone, 3pmmuc5b-1, is part of the 3' portion of the mouse Muc5b gene. In situ hybridization demonstrated that this putative mouse Muc5b message was expressed in a restricted manner in the sublingual gland region of the tongue and the submucosal gland region of the mouse trachea in a normal animal. However, the gene expression was greatly enhanced in airway surface epithelium and the submucosal gland region in ovalbumin-induced asthmatic mice. These results were consistent with previous studies of human airway tissues. We therefore conclude that this newly cloned mouse Muc5b gene could be used as a marker for studying aberrant mucin gene expression in mouse models of various airway diseases.