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PubMed2006

Gene expression profiles in the liver of mice irradiated with (60)Co gamma rays and treated with soybean isoflavone.

PURPOSE: To better understand the molecular mechanisms underlying the radio-protective effect of soybean isoflavone that we observed in our recent animal experiments. MATERIALS AND METHODS: We utilized a cDNA microarray to investigate the expression profiles of 4,096 known genes in the livers of irradiated-mice with or without soybean isoflavone treatment. Dye swap approach was employed to control for gene-specific dye bias and quantitative real-time RT-PCR was performed on several genes to validate the cDNA microarray data. RESULTS: Compared with the control group, 68 genes were up-regulated and 28 genes were down-regulated in mice treated with irradiation alone, whereas only 6 genes were down-regulated and 35 genes were up-regulated in mice treated with soybean isoflavone. Interestingly, some of the down-regulated genes in the irradiated group, such as DNA repair and stress response genes and cytoskeleton-associated genes, which are markers of cellular damage after irradiation, were maintained at close to normal expression levels after soybean isoflavone treatment. CONCLUSIONS: Comparison of gene expression profiles in the livers of irradiated-mice treated with or without soybean isoflavone suggested that soybean isoflavone may be an efficient tool to reverse irradiation damage of the liver through multiple-pathways and also provides important clues to further pursue the molecular mechanisms underlying the radio-protective activity of soybean isoflavone.

Animals↗

PubMed2006

Effect of vasoconstrictor coupling factor 6 on gene expression profile in human vascular endothelial cells: enhanced release of asymmetric dimethylarginine.

BACKGROUND: Coupling factor 6 (CF6), a component of ATP synthase, inhibits phospholipase A2 and induces vasoconstriction. However, because arachidonic acid acts in the widespread fields of vascular biology, CF6 might exert profound effects in addition to vasoconstriction. We investigated the effect of CF6 on the gene expression profile in human umbilical vein endothelial cells. METHODS AND RESULTS: The increased gene expression after 24-h exposure to CF6 at 10 mol/l, assessed by cDNA microarray (n = 3), included neuregulin-1 (1.84 +/- 0.07 fold compared with control, P < 0.05) and relaxin-1 (1.74 +/- 0.20, P < 0.05), both relating to congestive heart failure, urokinase type plasminogen activator receptor (1.77 +/- 0.24, P = 0.06) and estrogen receptor beta (1.74 +/- 0.36, P = 0.08), both relating to vascular inflammation and cell infiltration, and protein arginine methyltransferase (PRMT-1; 1.73 +/- 0.20, P < 0.05). Out of these genes, the enzyme relating to the synthesis (PRMT-1) of asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide synthase (NOS), was further examined concomitantly with the degradation enzyme, dimethylarginine dimethylaminohydrolase 2 (DDAH-2). The ratio of PRMT-1 to glyceraldehyde 3-phosphate dehydrogenase (GAPDH) mRNA, measured by real-time quantitative reverse transcription-polymerase chain reaction, was increased by 9 +/- 2% (n = 10, P < 0.01) at 48 h after CF6 at 10 mol/l, whereas the ratio of DDAH-2 to GAPDH was decreased by 12 +/- 2% (n = 8, P < 0.01). DDAH-2 protein and activity were decreased by 28 +/- 5% (n = 5, P < 0.01) and 19 +/- 2% (n = 6, P < 0.01) by CF6, respectively. ADMA release was enhanced by 20 +/- 8% and NOS activity was decreased by 13 +/- 1% (both n = 8, P < 0.05) by CF6. CONCLUSIONS: CF6 changes the gene expression profile to be proatherogenic and functions as a novel stimulator for ADMA release by enhancing its synthesis and suppressing its degradation.

Amidohydrolases↗

PubMed2004

Gene expression profiling of human cancers.

DNA microarrays allow us to visualize simultaneously the expression of potentially all genes within a cell population or tissue sample-revealing the "transcriptome." The analysis of this type of data is commonly called "gene expression profiling" (GEP) because it provides a comprehensive picture of the pattern of gene expression in a particular biological sample. For this reason microarrays are revolutionizing life sciences research and are leading to the development of novel and powerful methods for investigating cancer biology, classifying cancers, and predicting clinical outcome of cancers. Several recent high-profile reports have revealed how clustering of GEP data can clearly identify clinically (and prognostically) important subtypes of cancer among patients considered by established clinicopathological criteria to have similar tumors. Accurate "prognostic signatures" can be obtained from GEP data, which represent relatively small numbers of genes. These signatures can be valuable in directing appropriate treatment and in predicting clinical outcome, and they generally outperform other systems based on clinical and histological criteria. In this paper the basic principles of DNA microarray technology and the different types of microarray platforms available will be introduced, and the power of the technique will be illustrated by reviewing some recent GEP studies on selected cancers, including a preliminary analysis of hepatocellular carcinoma from our Palermo laboratory. GEP is likely to be adopted in the future as a key decision-making tool in the clinical arena. However, several issues relating to data analysis, reproducibility, cross-comparability, validation, and cost need to be resolved before the technology can be adopted broadly in this context.

Carcinoma, Hepatocellular↗

PubMed2006

[Differential gene expression profile of keloids: a study with cDNA microarray].

OBJECTIVE: To investigate the differentially expressed genes in keloids in comparison with normal skin using cDNA microarray. METHODS: The cDNA microarray consisting of 8064 clones of human genes was employed to detect and screen the differentially expressed genes in keloid and normal skin tissues. Semi-quantitative RT-PCR was applied to verify the results of gene microarray. RESULTS: Totally 277 differentially expressed genes were identified in keloids in comparison with normal skin tissue, including 163 up-regulated genes and 114 down-regulated ones according to the designed data filter criteria. These differentially expressed genes belonged to 26 different functional gene families involving different biological processes. RT-PCR yielded results were consistent with those of microarray study. CONCLUSION: A variety of genes are involved in the formation of keloids. The 277 differentially expressed genes comprise the differential gene expression profile of keloids and describe the general changes in the gene expressions in keloid at transcriptional level. Further analysis of the identified genes might help reveal the molecular mechanism of abnormal scarring.

Connective Tissue Growth Factor↗

PubMed2004

Altered response to mirtazapine on gene expression profile of lymphocytes from Alzheimer's patients.

Antidepressants are widely used in the treatment of mood disorders associated with dementia, however little information is available on their effect at the molecular level. We have demonstrated that gene expression profiles of lymphocytes from patients with Alzheimer dementia differ from that seen with controls, with alpha(2)-adrenoceptor being the most highly repressed transcript. To address this issue in light of antidepressant treatment, we used lymphocytes derived from Alzheimer patients and control individuals to assess the impact of mirtazapine, the novel antidepressant with alpha(2)-adrenoceptor antagonistic activities, on gene expression using a cDNA microarray representing 3200 distinct human genes. Sequences that are differentially regulated after treatment with mirtazapine were identified and categorized based on similarities in biological functions. This analysis revealed that selected biological processes, including protein metabolism, cytoskeleton integrity, immune response, cellular plasticity, and neurotransmission, are involved in early phases of administration of this antidepressant. In addition, although it was possible to identify common targets, the expression profiles of Alzheimer lymphocytes differed mainly in their magnitude from those seen with controls. These results confirm the usefulness of the gene array approach for studying Alzheimer-specific changes in the periphery and suggest that the expression of genes of Alzheimer lymphocytes is modulated differently by mirtazapine, which correlates with the pathology.

Aged↗

PubMed2004

Gene expression profiles from hypertrophic scar fibroblasts before and after IL-6 stimulation.

The structural rearrangement of collagen fibres in hypertrophic scar causes abnormal contracture, low tensile strength, and raised scars, which cause functional impairment and disfigurement. It is hypothesized that changes in the genes of cytokines, extracellular matrix proteins, and proteins regulating programmed cell death are related to hypertrophic scar formation. To test this hypothesis, fibroblasts were cultured from hypertrophic scars and their response to interleukin-6 (IL-6) stimulation was studied by defining their gene expression profiles. Affymetrix gene chip analysis was used to identify up- or down-regulation in the 12 625 genes present in the affymetrix array. RT-PCR and ELISA assays were used to validate microarray expression profiles further. Comparison of gene profiles showed an increase of 12 genes in hypertrophic scar fibroblasts compared with normal skin fibroblasts, while the expression of 14 genes decreased. Thirty-three genes were affected by IL-6 treatment in the hypertrophic scar fibroblasts, while 57 genes were affected in normal skin fibroblasts. Messenger RNA to beta-actin ratios for matrix metalloproteinase-1 (MMP-1) and MMP-3 were increased with IL-6 in normal skin fibroblasts from 2.43 +/- 0.06 to 5.50 +/- 0.45 and from 0.75 +/- 0.09 to 1.98 +/- 0.01, respectively. No change in these matrix metalloproteinases could be shown with IL-6 stimulation in hypertrophic scar fibroblasts. Secreted protein levels of pro-MMP-1 and MMP-3 were elevated in the supernatants from normal skin fibroblasts from 2.00 +/- 0.09 and 1.72 +/- 0.10 ng/ml to 4.60 +/- 0.12 and 3.41 +/- 0.20 ng/ml, respectively, after treatment with IL-6 (p < 0.05). No changes were observed in hypertrophic scar fibroblasts treated with IL-6. Values are means +/- SEM. The absence of any up-regulation of MMP-1 and MMP-3 in hypertrophic scar fibroblasts, in response to IL-6, suggests that suppression of matrix metalloproteinases may play a role in the excessive accumulation of collagen formed in hypertrophic scars. While the pathogenesis of abnormal hypertrophic scars remains poorly understood, the use of gene expression arrays may prove helpful in identifying the mechanisms responsible for this type of abnormal scar formation and in formulating an effective therapeutic protocol.

Cells, Cultured↗

PubMed2003

Expression profiling of human breast cancers and gene regulation by progesterone receptors.

Even the first expression profiling studies of breast cancers have generated new insights. They suggest for example, that information about tumor aggressiveness, prognosis, metastatic potential, or treatment outcome is encoded in, and can be deduced from, the primary tumor. On the other hand no clinical genomic array data have yet been published that deal with hormonal aspects of breast tumorigenesis, tumor progression, or therapeutics. Rather, studies have focused on experimental model systems. We review below the currently published data on array profiling in clinical breast cancer, then describe our studies in breast cancer cell lines and xenograft models dealing with progesterone receptors (PRs) and the role of progesterone. We demonstrate that the two PR isoforms, PR-A and PR-B, have mostly nonoverlapping molecular signatures when liganded by progesterone, with PR-B the more active form. Additionally, we document the surprising finding that unliganded PRs can regulate gene transcription, with PR-A the more active form. In ovariectomized mice supplemented with estradiol but lacking measurable progesterone, PR-B-expressing tumors grow to twice the size of PR-A-expressing ones. We conclude that in breast cancers, PRs are more than simple markers of estrogen receptor function. Rather, presence of PRs and the ratio of the two isoforms directly influence tumor phenotype, even in the absence of ligand.

Animals↗

PubMed2003

Effects of oral adsorbent on gene expression profile in uremic rat kidney: cDNA array analysis.

BACKGROUND: An oral adsorbent, AST-120, is effective in removing such uremic toxins as indoxyl sulfate and delays the progression of chronic renal failure. To elucidate the molecular mechanisms underlying the renoprotective effects of AST-120, the complementary DNA (cDNA) array method was used to survey the alteration in gene expression profiles of uremic rat kidneys in response to AST-120. METHODS: Six weeks after five-sixth nephrectomy, 10 uremic rats were divided into two groups: those administered AST-120 and control uremic rats. Rats subjected to sham operation also were included as normal rats. After administration of AST-120 for 18 weeks, renal tissues were analyzed by cDNA array. RESULTS: Among the 343 genes selected as expressed, control uremic rats showed significantly increased levels of 139 genes and significantly decreased levels of 45 genes compared with normal rats. AST-120 treatment attenuated expression levels of 43 of the 139 upregulated renal genes and 21 of the 45 downregulated renal genes in uremic rat kidney. Those genes could be subdivided into several functional categories, including cytokine (transforming growth factor-beta1 [TGF-beta1], etc), intracellular signaling, transcription, translation, channel and transporter (organic anion transporter 1 [OAT1], etc), metabolism, and protease and its inhibitor. Quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) analysis showed that AST-120 significantly increased OAT1 renal expression and tended to decrease TGF-beta1, tissue inhibitor of metalloproteinase-1 (TIMP-1), and endothelin-1 renal expression in uremic rats. There were statistically significant positive correlations between cDNA array-based and RT-PCR-based gene expression levels of TGF-beta1, TIMP-1, and endothelin-1. CONCLUSION: The cDNA array method determines changes in the gene expression profile in uremic rat kidney in response to AST-120 and provides new insights into elucidation of the molecular mechanism underlying the renoprotective effects of AST-120.

Administration, Oral↗

PubMed2002

Gene expression profiling of advanced head and neck squamous cell carcinomas and two squamous cell carcinoma cell lines under radio/chemotherapy using cDNA arrays.

BACKGROUND AND PURPOSE: The response of squamous cell carcinomas of the head and neck (HNSCC) to radio/chemotherapy is accompanied by complex changes in patterns of gene expression. It is highly probable that a better understanding of molecular and genetic changes can help to optimize the treatment of HNSCC. cDNA arrays provide a powerful tool for high-throughput monitoring of gene expression in small clinical specimens. MATERIALS AND METHODS: We used tumour biopsies from four patients with HNSCC which have been taken prior to and during radio/chemotherapy. The patterns of gene expression obtained from clinical samples were compared with gene expression profiles of two squamous cell carcinoma cell lines (FaDU and UD-7A). RESULTS: The experimental data analysis revealed changes in expression levels of several genes during radio/chemotherapy. Despite treatment, independent samples taken from the same cell line or tumour in situ were more similar to each other than either was to other specimens. The data indicate a high gene heterogeneity of HNSCC that is preserved during treatment. CONCLUSIONS: From our preliminary results we conclude that the cDNA array experimental approach can detect differences in gene expression between treated and untreated small tumour biopsies, as well as inter-individual differences in expression profiles between HNSCC tumours. The examination of a greater sample size will be needed to make this preliminary evaluation useful to elucidate the functional significance of individual genes which exhibit altered levels of expression under radiation therapy.

Carcinoma, Squamous Cell↗

PubMed2005

Extremely low-frequency electromagnetic fields do not affect DNA damage and gene expression profiles of yeast and human lymphocytes.

We studied the effects of extremely low-frequency (50 Hz) electromagnetic fields (EMFs) on peripheral human blood lymphocytes and DBY747 Saccharomyces cerevisiae. Graded exposure to 50 Hz magnetic flux density was obtained with a Helmholtz coil system set at 1, 10 or 100 microT for 18 h. The effects of EMFs on DNA damage were studied with the single-cell gel electrophoresis assay (comet assay) in lymphocytes. Gene expression profiles of EMF-exposed human and yeast cells were evaluated with DNA microarrays containing 13,971 and 6,212 oligonucleotides, respectively. After exposure to the EMF, we did not observe an increase in the amount of strand breaks or oxidated DNA bases relative to controls or a variation in gene expression profiles. The results suggest that extremely low-frequency EMFs do not induce DNA damage or affect gene expression in these two different eukaryotic cell systems.

Blood Proteins↗

PubMed2006

Single-cell expression profiling of human epidermal stem and transit-amplifying cells: Lrig1 is a regulator of stem cell quiescence.

Considerable progress has been made in characterizing epidermal stem cells by microarray analysis of FACS-selected populations. One limitation of this approach is that the gene expression profiles represent the average of the cell population, potentially masking cellular heterogeneity of functional significance. To overcome this problem, we have performed single-cell expression profiling. We have generated cDNA libraries from single human epidermal cells, designated as stem or transit-amplifying cells on the basis of Delta1 and melanoma-associated chondroitin sulfate proteoglycan expression. Of the 14 putative stem cell markers identified, we selected one, the EGF receptor antagonist leucine-rich repeats and immunoglobulin-like domains 1 (Lrig1), for further study. Lrig1 was expressed in groups of basal cells in human interfollicular epidermis previously identified as enriched for stem cells. Overexpression of Lrig1 decreased keratinocyte proliferation but did not affect the proportion of stem and transit-amplifying cells, as judged by clonal growth characteristics. Down-regulation of Lrig1 using siRNA increased cell-surface EGF receptor levels, enhanced activation of downstream pathways, and stimulated proliferation. Lrig1 acted in part by negatively regulating the Myc promoter. We propose that Lrig1 maintains epidermal stem cells in a quiescent nondividing state, and that Lrig1 down-regulation triggers proliferation.

Biological Transport↗

PubMed2005

Right- and left-sided colorectal cancers display distinct expression profiles and the anatomical stratification allows a high accuracy prediction of lymph node metastasis.

Accurate preoperative prediction of lymph node metastasis and degree of tumor invasion would facilitate an appropriate decision of the extent of surgical resection of cancers to reduce unnecessary complication or to minimize the risk of recurrence in patients. We analyzed gene expression profiles characteristic of the invasiveness of colorectal carcinoma in a total of 89 cases, using a cDNA array and pattern classification algorithms. We set binary classes for a panel of clinicopathologic parameters, each of which was divided at different levels for categories (discrete) or values (continuous). We searched an optimal combination of genes to discriminate the classes by using of a feature subset selection algorithm, which was applied to a set of genes preselected on the basis of statistical difference in expression (two-sided t test, P < or = 0.05). We used a sequential forward feature selection which additively searched a combination of genes, giving a minimal leave-one-out classification error rate of a k-nearest neighbor classifier. In the process of gene preselection, we found a remarkable difference in the expression pattern of genes according to the anatomical location of cancers. The difference was most prominent when the classes were set for cecum, ascending colon, transverse colon, and descending colon (CATD) versus sigmoid colon and rectum (SR). By stratifying these two locations, we were able to extract gene expression profiles characteristic of the classes of the presence versus absence of lymph node metastasis, lymphatic invasion, vascular invasion and degree of mural invasion, and pathological stages, with an accuracy of more than 90%. These results suggest that colorectal cancers harbor distinct molecular pathophysiological statuses according to their right-to-left locations, of which stratification is important for pattern classification of cDNA array data.

Adult↗

PubMed2001

Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile.

Gastrointestinal stromal tumors (GISTs), the most common mesenchymal tumors of the digestive tract, are believed to arise from the interstitial cells of Cajal. GISTs are characterized by mutations in the proto-oncogene KIT that lead to constitutive activation of its tyrosine kinase activity. The tyrosine kinase inhibitor STI571, active against the BCR-ABL fusion protein in chronic myeloid leukemia, was recently shown to be highly effective in GISTs. We used 13,826-element cDNA microarrays to define the expression patterns of 13 KIT mutation-positive GISTs and compared them with the expression profiles of a group of spindle cell tumors from locations outside the gastrointestinal tract. Our results showed a remarkably distinct and uniform expression profile for all of the GISTs. In particular, hierarchical clustering of a subset of 113 cDNAs placed all of the GIST samples into one branch, with a Pearson correlation >0.91. This homogeneity suggests that the molecular pathogenesis of a GIST results from expansion of a clone that has acquired an activating mutation in KIT without the extreme genetic instability found in the common epithelial cancers. The results provide insight into the histogenesis of GIST and the clinical behavior of this therapeutically responsive tumor.

Adult↗

PubMed2003

Discovery of distinctive gene expression profiles in rheumatoid synovium using cDNA microarray technology: evidence for the existence of multiple pathways of tissue destruction and repair.

Rheumatoid arthritis (RA) is a heterogeneous disease. We used cDNA microarray technology to subclassify RA patients and disclose disease pathways in rheumatoid synovium. Hierarchical clustering of gene expression data identified two main groups of tissues (RA-I and RA-II). A total of 121 genes were significantly higher expressed in the RA-I tissues, whereas 39 genes were overexpressed in the RA-II tissues. Among the 121 genes overexpressed in RA-I tissues, a relative majority of nine genes are located on chromosome 6p21.3. An interpretation of biological processes that take place revealed that the gene expression profile in RA-I tissues is indicative for an adaptive immune response. The RA-II group showed expression of genes suggestive for fibroblast dedifferentiation. Within the RA-I group, two subgroups could be distinguished; the RA-Ia group showed predominantly immune-related gene activity, while the RA-Ib group showed an additional higher activity of genes indicative for the classical pathway of complement activation. All tissues except the RA-Ia subgroup showed elevated expression of genes involved in tissue remodeling. These results confirm the heterogeneous nature of RA and suggest the existence of distinct pathogenic mechanisms that contribute to RA. The differences in expression profiles provide opportunities to stratify patients based on molecular criteria.

Arthritis, Rheumatoid↗

PubMed2006

Isolation, sequence analysis and expression profile of a novel porcine gene, NIP7, differentially expressed in the Longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs.

In order to detect the molecular mechanism of heterosis in pigs, the mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 180 amino acids that contains the conserved putative RNA-binding domain in PseudoUridine synthase and Archaeosine transglycosylase (PUA) and has high homology with the 60S ribosome subunit biogenesis protein NIP7 homolog of three species--human (98%), mouse (97%) and rat (96%)--so that it can be defined as swine 60S ribosome subunit biogenesis protein NIP7 homolog (NIP7). The tissue expression analysis indicated that the swine NIP7 gene is over expressed in muscle, heart, liver, fat, kidney, and lung, but weakly expressed in small intestine, ovary, and spleen. The genomic DNA sequence of swine NIP7 gene was finally amplified and result revealed that the swine NIP7 gene contains five exons and four introns. Our experiment is the first to establish the primary foundation for further research on the swine NIP7 gene.

Amino Acid Sequence↗

PubMed2006

Pathway-specific apoptotic gene expression profiling in chronic lymphocytic leukemia and follicular lymphoma.

Defects in the apoptotic pathway are pathogenetically important in chronic lymphocytic leukemia and follicular lymphoma. To further understand these defects, we profiled the apoptotic gene expression of these two neoplasms. Oligonucleotide arrays with 112 apoptotic genes were used, and data analysis was performed on seven chronic lymphocytic leukemia and 10 follicular lymphoma frozen tumor samples from six and seven patients, respectively. The overall gene expression pattern was strikingly similar among all 17 samples, regardless of the type of lymphoma and history of chemotherapy exposure. MCL1, TNFRSF1B and TNFRSF7 were highly expressed in most cases. The apoptotic gene expression between the groups of untreated chronic lymphocytic leukemia (n=3) and untreated follicular lymphoma (n=6) was also similar (Pearson correlation coefficient, 0.94). Comparison between the groups of untreated chronic lymphocytic leukemia (n=3) and postchemotherapy chronic lymphocytic leukemia (n=4) revealed six genes with >2-fold changes, including BIRC5/Survivin that was higher in the postchemotherapy samples. This finding was validated by immunohistochemistry. Similar analysis of follicular lymphoma cases did not identify any significant differences. To conclude, our findings suggest that chronic lymphocytic leukemia and follicular lymphoma share common apoptotic defects, and highlight the importance of MCL1 and the TNF pathway. Upregulation of survivin may be one of the mechanisms by which chronic lymphocytic leukemia becomes desensitized to chemotherapy.

Aged↗

PubMed2004

Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation.

BACKGROUND: The microRNAs (miRNAs) are an extensive class of small noncoding RNAs (18 to 25 nucleotides) with probable roles in the regulation of gene expression. In Caenorhabditis elegans, lin-4 and let-7 miRNAs control the timing of fate specification of neuronal and hypodermal cells during larval development. lin-4, let-7 and other miRNA genes are conserved in mammals, and their potential functions in mammalian development are under active study. RESULTS: In order to identify mammalian miRNAs that might function in development, we characterized the expression of 119 previously reported miRNAs in adult organs from mouse and human using northern blot analysis. Of these, 30 miRNAs were specifically expressed or greatly enriched in a particular organ (brain, lung, liver or skeletal muscle). This suggests organ- or tissue-specific functions for miRNAs. To test if any of the 66 brain-expressed miRNAs were present in neurons, embryonal carcinoma cells were treated with all-trans-retinoic acid to promote neuronal differentiation. A total of 19 brain-expressed miRNAs (including lin-4 and let-7 orthologs) were coordinately upregulated in both human and mouse embryonal carcinoma cells during neuronal differentiation. The mammalian ortholog of C. elegans lin-28, which is downregulated by lin-4 in worms via 3' untranslated region binding, was also repressed during neuronal differentiation of mammalian embryonal carcinoma cells. Mammalian lin-28 messenger RNAs contain conserved predicted binding sites in their 3' untranslated regions for neuron-expressed miR-125b (a lin-4 ortholog), let-7a, and miR-218. CONCLUSIONS: The identification of a subset of brain-expressed miRNAs whose expression behavior is conserved in both mouse and human differentiating neurons implicates these miRNAs in mammalian neuronal development or function.

Adult↗

PubMedDate not supplied

Alterations in cell cycle genes in early stage lung adenocarcinoma identified by expression profiling.

In normal lung epithelial cells, cellular division is an ordered, tightly regulated process involving multiple checkpoints that assess extracellular growth signals, cell size, and DNA integrity. In contrast, neoplastic lung cells develop the ability to bypass several of these checkpoints, particularly at the G1/S and G2/M boundaries. We used genomic profiling to compare gene expression levels in early stage lung adenocarcinomas and non-neoplastic pulmonary tissue in order to comprehensively identify alterations in the process of cell cycling. RNA extracted from node negative, poorly differentiated lung adenocarcinomas (15 patients) and non-neoplastic pulmonary tissue (5 patients) was hybridized to oligonu-cleotide microarray filters containing 44,363 genes. Ontological classification was used to extract genes involved with cell cycle progression. Further analysis discovered a subset of differentially expressed genes for further study. Of the 624 cell cycle genes on the microarray filters, 40 genes were predicted to be differentially expressed in lung adeno-carcinomas. Alterations in several genes (i.e., cyclin B1, cyclin D1, p21, MDM2) are consistent with published data in the literature. We also identified 19 novel genes that have neither been described in non-small cell lung cancer (i.e., cdc2, cullin 4A, ZAC, p57, DP-1, GADD45, PISSLRE, cdc20) nor in any other tumors (i.e., cyclin F, cullin 5, p34). These results identified several potential cell cycle genes altered in lung cancer.

Adenocarcinoma↗