Gene expression profiling studies on Caenorhabditis elegans dystrophin mutants dys-1(cx-35) and dys-1(cx18).

The Caenorhabditis elegans genome contains a single dystrophin/utrophin orthologue, dys-1. Point mutations in this gene, dys-1(cx35) and dys-1(cx18), result in truncated proteins. Such mutants offer potentially valuable worm models of human Duchenne muscular dystrophy. We have used microarrays to examine genes expressed differentially between wild-type C. elegans and dys-1 mutants. We found 106 genes (115 probe sets) to be differentially expressed when the two mutants are compared to wild-type worms, 49 of which have been assigned to six functional categories. The main categories of regulated genes in C. elegans are genes encoding intracellular signalling, cell-cell communication, cell-surface, and extracellular matrix proteins; genes in these same categories have been shown by others to be differentially expressed in muscle biopsies of muscular dystrophy patients. The C. elegans model may serve as a convenient vehicle for future genetic and chemical screens to search for new drug targets.

Aging is associated with increased T-cell chemokine expression in C57BL/6 mice.

To better understand the contribution of the chemokine system in immune senescence, we determined the aging effect on CD4+ and CD8+ T-cell chemokine expression by microarray screening and ribonuclease protection assays. Compared with young C57BL/6 mice, freshly isolated CD4+ cells from aged mice express increased level of interferon-gamma-inducible protein 10 (IP-10), macrophage inflammatory protein (MIP)-1alpha, MIP-1beta, regulated upon activation, normal T-cell expressed and secreted (RANTES), and lymphotactin (Ltn). T-cell receptor (TCR)/coreceptor stimulation up-regulates MIP-1alpha, MIP-1beta, and Ltn, and down-regulates IP-10 and RANTES expression in CD4+ T cells. A similar increase in chemokine expression was demonstrated in the CD8+ T cell. Enzyme-linked immunosorbent assays confirmed increased T-cell chemokine protein production in old CD4+ and CD8+ T cells. Finally, supernatant of cultured T cells from old animals caused an enhanced leukocyte chemotaxis response compared with that from young animals, suggesting that the age-related difference in T-cell chemokine expression has an important functional consequence.

Molecular profiling of the immune response in colon cancer using protein microarrays: occurrence of autoantibodies to ubiquitin C-terminal hydrolase L3.

We implemented a protein microarray approach to identify proteins that induce a humoral response in colon cancer. Solubilized proteins from the LoVo colon adenocarcinoma cell line were separated into 1760 fractions, arrayed onto nitrocellulose-coated slides, and hybridized with individual sera from 15 newly diagnosed patients with colon cancer, 15 with lung cancer, and 15 healthy subjects. 39/1760 fractions showed enhanced reactivity with sera from patients with colon cancer (p < 0.01) relative to healthy controls. A distinct pattern of reactivity was observed with sera from colon cancer relative to lung cancer. One fraction that exhibited reactivity with 9/15 colon cancer sera was subjected to mass spectrometry leading to the identification of ubiquitin C-terminal hydrolase isozyme 3 (UCH-L3) as a constituent. To validate the occurrence of autoantibodies to UCH-L3, independent analysis was done by means of Western blots. UCH-L3 antibodies were detected in 19/43 sera from patients with colon cancer, and in 0/54 sera from subjects with lung cancer (24), colon adenoma (15) or otherwise healthy (15). Our findings indicate the occurrence of an immune response to a broad set of antigens in colon cancer and the feasibility of identifying the antigenic targets using a combination of protein microarrays and mass spectrometry.

T cell chemokine receptor expression in aging.

Changes in chemokine receptor expression are important in determining T cell migration and the subsequent immune response. To better understand the contribution of the chemokine system in immune senescence we determined the effect of aging on CD4(+) T cell chemokine receptor function using microarray, RNase protection assays, Western blot, and in vitro chemokine transmigration assays. Freshly isolated CD4(+) cells from aged (20-22 mo) mice were found to express a higher level of CCR1, 2, 4, 5, 6, and 8 and CXCR2-5, and a lower level of CCR7 and 9 than those from young (3-4 mo) animals. Caloric restriction partially or completely restored the aging effects on CCR1, 7, and 8 and CXCR2, 4, and 5. The aging-associated differences in chemokine receptor expression cannot be adequately explained by the age-associated shift in the naive/memory or Th1/Th2 profile. CD4(+) cells from aged animals have increased chemotactic response to stromal cell-derived factor-1 and macrophage-inflammatory protein-1alpha, suggesting that the observed chemokine receptor changes have important functional consequences. We propose that the aging-associated changes in T cell chemokine receptor expression may contribute to the different clinical outcome in T cell chemokine receptor-dependent diseases in the elderly.

An altered cellular response to interferon and up-regulation of interleukin-8 induced by the hepatitis C viral protein NS5A uncovered by microarray analysis.

There is evidence for an inhibition of interferon-alpha antiviral activity by the hepatitis C viral protein, NS5A. To identify the mechanisms through which NS5A blocks interferon activity, we compared the gene expression profile of interferon-treated Huh7 cells, stably expressing NS5A with control, using microarrays. Following interferon treatment, 50 genes were up-regulated by at least twofold in control clones, whereas induction of 9 of the 50 genes was significantly reduced in NS5A-expressing clones. The strongest effect of NS5A on interferon response was observed for the OAS-p69 gene. Remarkably, Huh7 cells expressing NS5A showed an up-regulation of interleukin-8. Up-regulation of interleukin-8 was also observed upon transient expression of NS5A mutants isolated from patients responsive or resistant to interferon therapy. Addition of interleukin-8 to Huh7 cells inhibited the antiviral activity of interferon and, similarly to NS5A, reduced the induction by interferon-alpha of selective genes including OAS-p69. Our findings provide a mechanism for NS5A-mediated interferon resistance.

Food deprivation-induced expression of minoxidil sulfotransferase in the hypothalamus uncovered by microarray analysis.

We used oligonucleotide microarrays to analyze comprehensively hypothalamic gene expression changes that correlate with energy homeostasis. We compared the hypothalamic gene expression profiles of freely fed and 48-h fasted rats using 26,379 oligonucleotide probe sets. Expression of 96 genes was up-regulated and expression of 73 genes was down-regulated in a statistically significant manner with fasting. The gene encoding the enzyme minoxidil sulfotransferase, an enzyme that catalyzes the transfer of sulfonate groups to biogenic amines and other substrates, was foremost among a set of genes whose mRNAs were uniformly detectable and displaying the greatest transcriptional changes with fasting. Northern blot analysis indicated that minoxidil sulfotransferase mRNA is up-regulated in the fasted rat and mouse, ob/ob mouse, and fa/fa rat. Results of reverse transcription quantitative PCR indicated that minoxidil sulfotransferase mRNA is also up-regulated in the microdissected arcuate and paraventricular nuclei of the fasted rat. Several index genes known to be either up-regulated (neuropeptide Y) or down-regulated (amphetamine-regulated transcript and proopiomelanocortin) with fasting were also found to be present among our set of "differentially expressed" genes. This study identifies a novel gene induced by fasting and demonstrates the feasibility of using oligonucleotide microarrays for the study of complex neuronal processes.