Human Gene Probe Research Articles

Down-regulation of focal adhesion signaling in response to cyclophilin A knockdown in human endometrial cancer cells, implicated by cDNA microarray analysis

ObjectiveCypA had been identified as a potential therapeutic target to endometrial cancer in our previous research. Herein, we aimed to further elucidate the underlying comprehensive mechanisms of CypA knockdown-associated anticancer effects by cDNA microarray-based approach. MethodsLV-shCypA was constructed and transfected into HEC-1-B cells. The efficiency of CypA knockdown was determined by qRT-PCR and Western blotting. The migratory/invasive capacity was examined by transwell assay. CypA knockdown-induced comprehensive gene expression alterations were analyzed using NimbleGen Human Gene Expression Microarray consisting of 45,033 probes for human genes. Functional analysis of the microarray data was performed using KEGG and Gene Ontology analyses. The selected differentially expressed genes were validated by qRT-PCR. ResultsKnockdown of CypA by LV-shCypA led to a significant decrease of migratory/invasive cell proportions in HEC-1-B cells. Microarray analysis showed 3533 and 2772 genes to be up-regulated and down-regulated in CypA-knockdown cells, respectively. Functional analysis showed 50 up-regulated pathways and 14 down-regulated pathways in CypA-knockdown cells, and focal adhesion signaling was one of the most enriched down-regulated pathways. The expression patterns of 16 genes in focal adhesion signaling, which encoded MAPK kinases, focal adhesion kinase (FAK), integrin subunits and laminin subunits, were validated by qRT-PCR and the consistency percentage with microarray data reached 100%. ConclusionsSuppression of migratory/invasive capacity by CypA knockdown is likely associated with the down-regulation of focal adhesion signaling, which may contribute to the understanding of the role of CypA as a potential therapeutic target for endometrial cancer.

Prognostic index reflecting genetic alteration related to disease-free time for gastric cancer patient

The study purpose was to develop a patient's prognostic index (PI) reflecting the genetic information in cDNA microarray-based CGH experiment data for estimating a gastric cancer patient's survival time. The developed methodology was fit to and validated using data from the Cancer Metastasis Research Center at Yonsei University; 30 pairs of gastric tumors and normal gastric tissues were used in the cDNA microarray-based CGH. The cDNA microarrays containing 17,000 sequence-verified human gene probes were directly compared. Genetic alteration score (GAS) was constructed based on the genes that had a high frequency of alteration among all the genes displaying small variations across the arrays. GAS was determined using a technique that finds linear combinations of the original variables that best account for the variability in the data. When classifying cancer patients with the PI predicted by the model incorporating GAS, the correct classification rate for recurrence was 83.33%. In conclusion, GAS allowed for providing an independent patient's PI that reflects the genetic information for prognosis on hazard rate of recurrence, which was capable of distinguishing a patient's recurrence status, survival status and cancer stage status. The predicted PI also provided each patient's estimated disease-free survival rate. In this study, 82 genes were selected for analysis based on a high frequency of alteration and small variations across the arrays. In addition, 13 genes displaying a possible relationship with disease-free survival time were identified. GAS was found to be associated with the recurrence status and survival status.

Downstream targets of heterogeneous nuclear ribonucleoprotein A2 mediate cell proliferation

Over-expression of heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 is regarded as an early marker for several cancers. This protein is associated with proto-oncogenes and tumor suppressor genes and has itself been described as a proto-oncogene. Our earlier experiments drew a connection between hnRNP A2/B1 levels and cell proliferation and raised the possibility that this protein contributes to the uncontrolled cell division that characterizes cancer. Limited knowledge of the downstream targets of hnRNP A2/B1 has, however, precluded a clear understanding of their roles in cancer cell growth. To define the pathways in which this protein acts we have now carried out microarray experiments with total RNA from Colo16 epithelial cells transfected with an shRNA that markedly suppresses hnRNP A2/B1 expression. The microarray data identified 123 genes, among 22 283 human gene probe sets, with altered expression levels in hnRNP A2/B1-depleted cells. Ontological analysis showed that many of these downstream targets are involved in regulation of the cell cycle and cell proliferation and that this group of proteins is significantly over-represented amongst the affected proteins. The changes detected in the microarray experiments were confirmed by real-time PCR for a subset of proliferation-related genes. Immunoprecipitation-RT-PCR demonstrated that hnRNP A2/B1 formed complexes with the transcripts of many of the verified downstream genes, suggesting that hnRNP A2/B1 contributes to the regulation of these genes. These results reinforce the conclusion that hnRNP A2/B1 is associated with cellular processes that affect the cell cycle and proliferation.

Persistence of Host Response Signatures of Pathogens Despite Evidence of Stress‐Induced Immune Suppression

The aim of this study was to determine the impact of battlefield-like stress on immune function and to determine if host genomic responses to dengue, plague and staphylococcal enterotoxin B (SEB) can still predict such exposures despite the “background” effects of immune suppression due to stress. Leucocytes isolated from blood samples of 15 US Army Ranger Training Battalion (RTB) Cadets (collected before and after 8 weeks training) were exposed in vitro to the three pathogens to analyze pathogen- and/or stress-induced regulation of gene expression profiles using cDNA arrays of ~9,000 human gene probes. After the RTB course, trainees had lost weight and showed metabolite patterns of severe stress. Statistically significant host response genes both in the presence and absence of the RTB stressors were determined. In each case of the matched pairs of before/after training, the gene profiles showed consistent suppression of immune related genes. Though a number of genes showed regulation when RTB stressors acted alone or in concert with pathogenesis, yet we were able to identify other genes that showed consistent differential expression specific to dengue, plague and SEB both before and after RTB stressors. Some of the significantly regulated genes are involved in defense, stress response, signal transduction, transcriptional and growth regulations. We are grateful to the Defense Threat Reduction Agency for funding.

Gene Copy Number Change Events at Chromosome 20 and Their Association with Recurrence in Gastric Cancer Patients

This study examined the gene copy number change events at chromosome 20 in gastric cancer, and their possible relationship with recurrence using cDNA microarray-based comparative genomic hybridization. Thirty pairs of gastric tumor and normal gastric tissues were used in the cDNA microarray-based comparative genomic hybridization. The cDNA microarrays containing 17,000 sequence-verified human gene probes were used in a direct comparison design, where genomic DNAs from the normal and tumor tissues were labeled with fluorescent dyes Cy3 and Cy5, respectively, and cohybridized. Genes with log(2) (Cy5/Cy3) > or = 0.58 in at least one case were selected as the amplified genes. In order to search for the association between gene copy number changes and the recurrence status, patients were grouped according to their recurrence status. Gene selection between the two groups was done, and each patient was given a score based on the sum of the selected genes' ratios. Logistic regression analysis was carried out in order to determine if the score of a group of patients was correlated with a recurrence. A group of genes including NCOA6, CYP24A1, PTPN1, and ZNF217 was amplified in gastric cancer. Another group of 39 genes, whose sum of copy number change levels was significantly associated with a poor prognosis for recurrence, was selected (P < 0.05). Ninety-six amplified genes at chromosome 20 of gastric cancer are reported. A scoring system based on gene copy changes at chromosome 20 can provide an independent patient grouping system that can distinguish patient recurrence status and survival.

Characterization of Waldenström Macroglobulinemia Subtypes using Global Gene Expression Profiling.

Waldenström macroglobulinemia (WM) is a lymphoid neoplasm associated with accumulation of lymphoplasmacytic cells in the bone marrow and an elevated monoclonal IgM in the serum. Although the genetic and molecular mechanisms behind the pathogenesis of WM are not well understood, losses of the long arm of chromosome 6 have been found as the only recurrent genomic aberration. These deletions, mostly starting at 6q21, are observed in upwards of 50% of patients and involve the majority of the clonal cells. To better characterize pathologic gene expression signatures in different types of WM at the molecular level (6q deleted versus not), we examined gene expression level changes of more than 20000 human gene probes in bone marrow tissues of clinically proven WM patients. We used Affymetrix HG-U133A v2 chips (n = 24). Clonal cells were purified using a combination of anti-CD138 and anti-CD19 Miltenyi™ magnetic microbeads. Based on cIgM-FISH results, we classified samples into two groups - 6q normal (ND) group and 6q deletion (D) group. We then proceeded to identify genes that showed differential expression between the two groups. We selected 165 differentially expressed genes (DEG) using SAM, and underwent further investigation of biological annotations of them using Gene Ontology™ (GO) terms. Among165 DEG, only 32 showed high level of expression in ND group compared to D group while 133 showed high level of expression in D group. As expected, all genes that reside in 6q region showed under-expression in D group, constituting 53% (17 genes) of genes under-expressed in D group (32 genes). According to GO analysis, the 6q-deletion-induced under-expression affects many biological processes, and is associated with a transcriptional upregulation of downstream genetic cascades. This likely indicates release of regulatory control by a tumor suppressor gene. Genes involved in cell growth and maintenance, cell communication and morphogenesis are also over-expressed in D group. Interestingly, a gene that is involved in innate immune response and inflammatory response shows under-expression in D group but is not accounted for by other mechanisms. In similar vein, a gene that is involved in negative regulation of cytokine biosynthesis showed over-expression in D group. We think these transcriptional characteristics can provide basic framework for differentiating subtypes of WM and search for genes associated with WM pathogenesis

Gene expression profiles of the developing human retina

Retina is a multilayer and highly specialized tissue important in converting light into neural signals. In humans, the critical period for the formation of complex multiplayer structure takes place during embryogenesis between 12 and 28 weeks. The morphologic changes during retinal development in humans have been studied but little is known about the molecular events essential for the formation of the retina. To gain further insights into this process, cDNA microarrays containing 16361 human gene probes were used to measure the gene expression levels in retinas. Of the 16361 genes, 68.7%, 71.4% and 69.7% showed positive hybridization with cDNAs made from 12–16 week fetal, 22–26 week fetal and adult retinas. A total of 814 genes showed a minimum of 3-fold changes between the lowest and highest expression levels among three time points and among them, 106 genes had expression levels with the hybridization intensity above 100 at one or more time points. The clustering analysis suggested that the majority of differentially expressed genes were down-regulated during the retinal development. The differentially expressed genes were further classified according to functions of known genes, and were ranked in decreasing order according to frequency: development, differentiation, signal transduction, protein synthesis and translation, metabolism, DNA binding and transcription, DNA synthesis-repair-recombination, immuno-response, ion channeltransport, cell receptor, cytoskeleton, cell cycle, pro-oncogene, stress and apoptosis related genes. Among these 106 differentially expressed genes, 60 are already present in NEI retina cDNA or EST Databank but the remaining 46 genes are absent and thus identified as “function unknown”. To validate gene expression data from the microarray, real-time RT-PCR was performed for 46 “function unknown” genes and 6 known retina specific expression genes, and β-actin was used as internal control. Twenty-seven of these genes showed very similar expression profiles between the microarray and real-time RT-PCR data. In situ hybridization revealed both expression level and cellular distribution of NNAT in retina. Finally, the chromosomal locations of 106 differentially expressed genes were also searched and one of these genes is associated with autosomal dominant cone or cone-rod dystrophy. The data from present study provide insights into understanding genetic programs during human retinal development and help identify additional retinal disease genes.

Discovery of Gene Families and Alternatively Spliced Variants by RecA-Mediated Cloning

Probing the functional complexity of the human genome will require new gene cloning techniques, not only to discover intraspecies gene homologs and interspecies gene orthologs, but also to identify alternatively spliced gene variants. We report homologous cDNA cloning methods that allow cloning of gene family members, genes from different species, and alternatively spliced gene variants. We cloned human 14-3-3 gene family members using DNA probes with as much as 35% sequence divergence, cloned alternatively spliced gene forms of Rad51D, and cloned a novel splice form of the human 14-3-3 theta gene with a unique expression pattern. Interspecies gene cloning was demonstrated for the mouse Rad51C and mouse β-actin genes using human gene probes. The gene family cloning method is fast, efficient, and free from PCR errors; moreover, it exploits the abilities of RecA protein to pair homologous or partially homologous DNA sequences stably in kinetically trapped, multistranded DNA hybrids that can be used for subsequent gene clone enrichment.

A Comparative Transcriptional Map of a Region of 250 kb on the Human and Mouse X Chromosome between the G6PD and the FLN1 Genes

The transcriptional organization of the region of the mouse X chromosome between the G6pd and the Fln1 genes was studied in detail, and it was compared with the syntenic region of the human chromosome. A cosmid contig of 250 kb was constructed by screening mouse cosmid libraries with probes for human genes and with whole cosmids. Overlapping cosmids were aligned by comparing EcoRI and rare-cutter restriction enzyme digestions. The gene order and the orientation of transcription were determined by hybridization with fragments from the 5′ and 3′ moieties of each cDNA. Our work demonstrates that all of the new genes identified in human are present in the mouse. The size of the region, 250 kb, is also very similar, as are gene order and gene organization: the transcriptional organization in "domains" described in human is found to be identical in the mouse. The major difference detected is the much lower content in rare-cutter restriction sites, which is related to the lower G+C and CpG content of mouse DNA. The very high conservation that we have described suggests that a potent selective pressure has contributed to such conservation of gene organization.

Glutathione peroxidase and other antioxidant enzyme function in marine invertebrates ( Mytilus edulis, Pecten maximus, Carcinus maenas and Asterias rubens)

Selenium-dependent glutathione peroxidase (Se-GPX) and other antioxidant enzyme function was studied in four marine invertebrates, viz. mussel M. edulis (euryoxic herbivore), scallop P. maximus (stenoxic herbivore), crab C. maenas (euryoxic omnivore) and starfish A. rubens (euryoxic carnivore). Se-GPX, Superoxide dismutase and catalase activities were generally highest in the major digestive detoxication tissue of each species (digestive gland, hepatopancreas or pyloric caeca), consistent with pro-oxidant xenobiotics being a major source of oxyradical production. Total GPX activity was more similar between tissues, presumably due to a wider tissue distribution of glutathione S-transferases with GPX activity. Levels of putative Se-GPX mRNA (slot-blot analysis with 1.4 kb human gene probe) paralleled Se-GPX activity in the two mollusc species, indicating regulation of enzyme function at the level of mRNA. In vitro endogenous potential for NAD(P)H-dependent hydroxyl radical production (iron-mediated 2-keto-4-methiolbutyric acid oxidation) was similar in the digestive tissues of the four species, whereas differences in antioxidant enzyme activities were greater, indicating that exogenous sources of oxyradical production may be important in determining levels of antioxidant defences.

Detection of canine homologs of human MYC, BCL2, IGH, and TCRB genes by Southern blot analysis

Subsets of non-Hodgkin's lymphoma in humans have been shown to involve activation of protooncogenes such as MYC and BCL2 resulting from chromosome translocation involving the IGH and TCR genes. Malignant lymphomas in the canine present histologic and clinical subsets similar to those in humans. To study the genetic nature of these lymphomas, we undertook this study to determine, by Southern blotting analysis, the extent of homology between the human and canine genes MYC, BCL2, IGH, and TCRB using human gene probes. Our results, presented here, show that the organization of these genes in the two species is very similar.

Identification of LDL receptor gene marker associated with altered levels of LDL cholesterol and apolipoprotein B in baboons.

We are studying the genetic factors underlying the common forms of heart disease by identifying genes that affect normal variations in plasma lipid, lipoprotein, and apolipoprotein concentrations in baboons. For these studies we are using cloned human gene probes to identify restriction fragment length polymorphisms (RFLPs) at loci encoding the proteins of cholesterol metabolism. In this report we present the identification and mapping of a polymorphic Ava II cleavage site in intron 17 of the baboon low density lipoprotein (LDL) receptor gene. We determined genotypes for this RFLP on a population of 253 pedigreed baboons and assessed the effect of LDL receptor RFLP genotypes on serum concentrations of LDL cholesterol (LDL-C) and apolipoprotein B (apo B). These measures were obtained for each baboon on each of two diets: a low cholesterol, low fat (basal) diet and a high cholesterol, high saturated fat (atherogenic) diet. Statistical analysis detected a significant association between LDL receptor genotype and serum LDL-C and apo B concentrations on both diets. Homozygotes for the rarer allele had lower serum concentrations of LDL-C and apo B than did homozygotes for the common allele, and with the exception of apo B levels on the basal diet, intermediate levels were observed in heterozygotes. The LDL receptor RFLP accounted for approximately 3% to 7% of the variation in serum LDL-C and apo B concentrations on both diets.

Restriction fragment length polymorphism analysis of the VX locus in human lupus

To evaluate the degree of genetic polymorphism of the V kappa repertoire in systemic lupus erythematosus (SLE), we performed Southern blot hybridizations with human gene probes corresponding to the four human V kappa gene families. In a comparative analysis, non-lymphoid cell DNA samples from three patients with idiopathic SLE, eight subjects with susceptibility to drug-induced lupus and seven control individuals were digested with the restriction endonucleases Bam HI, Bg 1 II, Eco RI and Hind III, and hybridized sequentially to the four V kappa family-specific probes. The restriction patterns on Southern blots revealed a low degree of polymorphism of the human V kappa gene repertoires of SLE patients and control individuals. This analysis, together with previous parallel studies of the V kappa locus in lupus-prone mice, implies that autoantibody hyperproduction in lupus is not associated with major modifications in the structure or genomic organization of immunoglobulin light chain genes.

Yeast artificial chromosomes with 200- to 800-kilobase inserts of human DNA containing HLA, V kappa, 5S, and Xq24-Xq28 sequences.

Sequences hybridizing to several human gene probes have been recovered as cloned inserts in yeast artificial chromosomes (YACs). Among 2300 YACs made from human leukocyte DNA (totaling about 0.1 genomic equivalent of human DNA) we have found two, 200 and 780 kilobases (kb), containing sequences of V kappa I immunoglobulin (V = variable); one, 240 kb, with class I HLA; and 11, 200-800 kb, with 5S rRNA-encoding DNA (rDNA). Fifty human YACs from a hamster-human cell hybrid with only the Xq24-Xq28 portion of the X chromosome include one that contains two anonymous probe sequences, DX13 and St14, previously inferred by indirect means to lie within about 70 kb of one another in Xq28. The YACs specific for human DNA arise at a frequency equivalent to the fraction of cellular DNA that is human-specific. Furthermore, the human YACs, formed in a 280-fold excess of hamster DNA, do not hybridize to a hamster DNA probe, indicating that individual YACs do not contain a combination of human and hamster DNA. To confirm that sequences are not scrambled, the YACs containing V kappa I or DX13 and St14 sequences were shown to produce restriction fragments identical in mobility to fragments detected by the same probes in total human DNA digested with the same enzymes. YACs may therefore provide large clones to bridge gene mapping at the chromosome level to molecular analyses of small fragments of genomic DNA.

Transfer of nonselectable genes into mouse teratocarcinoma cells and transcription of the transferred human beta-globin gene.

Teratocarcinoma (TCC) stem cells can function as vehicles for the introduction of specific recombinant genes into mice. Because most genes do not code for a selectable marker, we investigated the transformation efficiency of vectors with a linked selectable gene. In one series, TCC cells first selected for thymidine kinase deficiency were treated with DNA from the plasmid vector PtkH beta 1 containing the human genomic beta-globin gene and the thymidine kinase gene of herpes simplex virus. A high transformation frequency was obtained after selection in hypoxanthine-aminopterin-thymidine medium. Hybridization tests revealed that the majority of transformants had intact copies of the human gene among three to six total copies per cell. These were associated with cellular DNA sequences as judged from the presence of additional new restriction fragments and from stability of the sequences in tumors produced by injecting the cells subcutaneously. Total polyadenylate-containing RNA from cell cultures of two out of four transformants examined showed hybridization to the human gene probe: one RNA species resembled mature human beta-globin mRNA transcripts; the others were of larger size. In differentiating tumors, various tissues, including hematopoietic cells of TCC provenance could be found. In a second model set of experiments, wild-type TCC cells were used to test a dominant-selection scheme with pSV-gpt vectors. Numerous transformants were isolated, and their transfected DNA was apparently stably integrated. Thus, any gene of choice can be transferred into TCC stem cells even without mutagenesis of the cells, and selected cell clones can be characterized. Cells of interest may then be introduced into early embryos to produce new mouse strains with predetermined genetic changes.

Transfer of nonselectable genes into mouse teratocarcinoma cells and transcription of the transferred human beta-globin gene.

Teratocarcinoma (TCC) stem cells can function as vehicles for the introduction of specific recombinant genes into mice. Because most genes do not code for a selectable marker, we investigated the transformation efficiency of vectors with a linked selectable gene. In one series, TCC cells first selected for thymidine kinase deficiency were treated with DNA from the plasmid vector PtkH beta 1 containing the human genomic beta-globin gene and the thymidine kinase gene of herpes simplex virus. A high transformation frequency was obtained after selection in hypoxanthine-aminopterin-thymidine medium. Hybridization tests revealed that the majority of transformants had intact copies of the human gene among three to six total copies per cell. These were associated with cellular DNA sequences as judged from the presence of additional new restriction fragments and from stability of the sequences in tumors produced by injecting the cells subcutaneously. Total polyadenylate-containing RNA from cell cultures of two out of four transformants examined showed hybridization to the human gene probe: one RNA species resembled mature human beta-globin mRNA transcripts; the others were of larger size. In differentiating tumors, various tissues, including hematopoietic cells of TCC provenance could be found. In a second model set of experiments, wild-type TCC cells were used to test a dominant-selection scheme with pSV-gpt vectors. Numerous transformants were isolated, and their transfected DNA was apparently stably integrated. Thus, any gene of choice can be transferred into TCC stem cells even without mutagenesis of the cells, and selected cell clones can be characterized. Cells of interest may then be introduced into early embryos to produce new mouse strains with predetermined genetic changes.