A differential display protocol to identify differentially expressed mRNAs in potassium-deprived cerebellar granule cells

Gene expression variance based on random sequencing in rat remnant kidney

BACKGROUND

Several examinations have been performed to identify the genes involved in chronic renal failure using 5/6 nephrectomized rats. Recently, many systematic techniques for examining molecular expression have been developed. They might also be effective in elucidating the molecular mechanism of progressive renal failure. In this study, digital expression profiling was carried out to construct a subtractive mRNA expression database for the 5/6 nephrectomized kidney.

METHODS

One thousand clones were randomly sequenced from 5/6 nephrectomized and sham-operated rat kidney cDNA libraries, respectively, and defined by BLAST search. In silico subtractive analysis was performed to search for genes up- or down-regulated in the 5/6 nephrectomized kidney.

RESULTS

The growth factor-related mRNAs and the mRNAs encoding cytoskeletal or membrane proteins were up-regulated, but the transporter-related mRNAs were down-regulated in the 5/6 nephrectomized kidney database. In silico subtraction revealed that 63 mRNAs were increased and 59 were decreased in the 5/6 nephrectomized kidney. To confirm whether the in silico subtractive database reflected the actual expression of mRNA or protein, 12 known genes were examined by Northern blotting or immunoblotting, respectively. The actual expression of the 12 genes was comparable with the results of in silico subtraction. In addition, we successfully isolated five unknown genes, two up-regulated and three down-regulated in the 5/6 nephrectomized kidney.

CONCLUSION

We constructed a subtractive mRNA expression database for 5/6 nephrectomized kidney, which reflects the actual alterations in mRNA expression after subtotal nephrectomy. This database may be useful for elucidation of the molecular mechanism of progressive renal failure.

Reduced KIAA0471 mRNA expression in Alzheimer's patients: a new candidate gene product linked to the disease?

Alzheimer's disease (AD) phenotype complexity raises the question whether genetic features remain unknown. Although a few percentage of patients are familial cases linked to mutations in amyloid precursor protein, presenilin 1 or presenilin 2 genes, the remainder are considered mainly sporadic late-onset cases with a complex etiology. However, changes in gene expression or other genetic features of the individual can clearly contribute to develop the illness. Consequently, in this paper we have focused on the identification of new genes, the expression of which is altered in AD. We used the technique of differential display reverse transcriptase-polymerase chain reaction (DDRT-PCR) in order to study the gene expression differences in brain tissue from patients in an advanced stage of AD. After studying medial septum and hippocampus brain areas, we found an inhibition of the KIAA0471 gene expression in three out of six AD patients, including one with a presenilin 1 gene mutation. This gene encodes for a large protein that presents, in its predicted form, 95% homology with IDN4-GGTR sequences. These results may provide significant clues for understanding the molecular mechanisms underlying septohippocampal neurodegeneration. In addition, they may open a new area of research for diagnostic and therapeutic tools, the relevance of which is also considered.

Variation in gene expression in response to stress in two populations of Fundulus heteroclitus

We used differential display PCR to identify hepatic genes responsive to handling stress and genes that differ in expression between populations of a fish, Fundulus heteroclitus, from different thermal environments. Despite substantial inter-individual variation, we cloned 20 putatively stress-regulated bands from Northern fish, 10 of which had high similarity to genes of known function. We selected five of these genes for further analysis based on their known roles in the stress response. Three of these genes (glucokinase, serine-threonine kinase 10 and cRAF) were confirmed as stress-responsive using real-time PCR. These genes increased in expression in response to a 7-day chronic stress protocol in fish from the Southern population of F. heteroclitus, but did not change significantly in fish from the Northern population. These three genes also differed in expression between populations in control fish, suggesting a link between the response to chronic stress and inter-population differences in gene expression in unstressed laboratory-acclimated fish. Two genes that did not respond to stress (glycogen synthase kinase and warm acclimation-related protein (WAP)) also differed between populations. Expression of WAP was eight-fold higher in Southern than in Northern fish, consistent with a previously suggested role for this gene in thermal acclimation or adaptation in fish.

Inhibition of insulin-like growth factor I activity contributes to the premature apoptosis of cerebellar granule neuron in weaver mutant mice: in vitro analysis

Evidence from transgenic mice and cultured cerebellar neurons supports an important role for insulin-like growth factor I (IGF-I) in the formation of cerebellar cytoarchitecture. To understand IGF-I's function during cerebellar development, we examined the involvement of IGF-I in the premature apoptosis of granule neurons derived from the cerebella of weaver (wv) mutant mice. Before their demise, wv granule neurons increased the expression and secretion of IGFBP5 in a gene dose-dependent manner. Because IGFBP5 may interfere with the interaction of IGF-I and its receptor, the abnormally high IGFBP5 levels in wv granule neurons suggest that a lack of IGF-I activation may contribute to their premature apoptosis. This hypothesis is supported by a gene dose-dependent decrease in IGF-I receptor (IGF-IR) phosphorylation. More importantly, there is a parallel gene dose-dependent decrease in Akt activity, which was inversely correlated with the activity levels of caspase 3. On the other hand, adding IGFBP5 antibody into culture media increased the survival of wv granule neurons, whereas adding IGFBP5 decreased the survival of wild-type granule neurons. To delineate the interaction between IGF-I and IGFBP5 on wv granule neurons, we examined neuronal survival after treating with IGF-I, des(1-3) IGF-I, or IGFBP5 antibody. At the same concentration, des(1-3) IGF-I was more effective than IGF-I in promoting survival, in increasing Akt activity, and in decreasing caspase 3 activity. These results indicate that IGF-I's actions on wv granule neurons are normally inhibited by excess IGFBP5, and sufficient IGF-I receptor activation rescues wv granule neurons via stimulating the Akt signaling pathway.

Rapid induction and Ca(2+) influx-mediated suppression of vitamin D3 up-regulated protein 1 (VDUP1) mRNA in cerebellar granule neurons undergoing apoptosis

Cerebellar granule neurons (CGNs) grown under depolarizing conditions with high K(+) (HK; 30 mM) undergo apoptosis following replacement of HK by physiological K(+) (5.4 mM). Differential display analysis identified eight genes up-regulated in this paradigm of apoptosis. Vitamin D3 up-regulated protein 1 (VDUP1) mRNA was markedly up-regulated as early as 2 h following HK withdrawal. VDUP1 mRNA was up-regulated in other paradigms of neuronal apoptosis as well both in vitro and in vivo. HK effectively suppressed the up-regulation of VDUP1 mRNA in CGNs undergoing apoptosis via Ca(2+) influx through voltage-dependent L-type Ca(2+) channels, which did not require de novo protein synthesis. The up-regulation occurred in parallel with that of the c-jun transcript and c-jun protein phosphorylation. Moreover, SB203580, p38 mitogen-activated protein kinase inhibitor, suppressed up-regulation of both c-jun and VDUP1 mRNAs, and c-jun phosphorylation in CGNs undergoing apoptosis. IGF-1, one of the neuroprotective agents for CGNs, also inhibited VDUP1 mRNA up-regulation through a phosphoinositide 3 kinase-dependent pathway. These results suggest that the VDUP1 gene is a novel member of early response genes in neuronal apoptosis whose expression is directly regulated by Ca(2+) influx and coordinately regulated with the transcription factor c-jun in CGNs.

Single strand mRNA differential display (SSDD) applied to the identification of serine/threonine phosphatases regulated during cerebellar development

Differential display is a used widely and useful technique for the study of differentially expressed genes. However, very poor results have been obtained in the past when particular gene families were studied. Initially, we attempted to study the mRNA expression of catalytic subunits of serine/threonine phosphatases, using two primers specific to consensus sequences of these phosphatases. When differential display was applied, two wide, unresolved bands were isolated that contained cDNA of several phosphatases, together with that of many other unrelated transcripts. To overcome this problem, we used an alternative strategy, referred to as single strand differential display (SSDD), which is a combination of differential display and single strand conformation polymorphism (SSCP). After initial PCR amplification with specific primers, we ran a polyacrylamide (or agarose) gel, pre-selecting the region that contained fragments of the size expected for the consensus region (250-350 bp). The DNA eluted from this zone was then separated on a non-denaturing (SSCP) gel. Using this approach, we were able to characterize the expression of five ser/thr phosphatases, and a previously unreported splice variant of one of them, PP1gamma. All these phosphatases show varying levels of expression during development, indicating a very complex regulation of protein phosphorylation-dephosphorylation during the period of synaptogenesis in the mouse cerebellum.

Ubiquitin-binding protein p62 expression is induced during apoptosis and proteasomal inhibition in neuronal cells

Neuronal apoptosis is involved in several pathological conditions of the brain. Using cDNA arrays, we observed upregulation of ubiquitin-binding protein p62 expression during serum withdrawal-induced apoptosis in Neuro-2a cells. We demonstrate here that the expression levels of p62 mRNA and protein were increased in Neuro-2a cells and cultured rat hippocampal neurons by different types of proapoptotic treatments, including serum deprivation, okadaic acid, etoposide, and trichostatin A. Ubiquitin-binding protein p62 is a widely expressed cytoplasmic protein of unclear function. The ability of p62 to bind noncovalently to ubiquitin and to several signalling proteins suggests that p62 may play a regulatory role connected to the ubiquitin system. Accordingly, we show that proteasomal inhibitors MG-132, lactacystin, and PSI caused a prominent upregulation of p62 mRNA and protein expression, with a concomitant increase in ubiquitinated proteins. To conclude, p62 upregulation appears to be a common event in neuronal apoptosis. Results also suggest that the induction of p62 expression by proteasomal inhibitors may be a response to elevated levels of ubiquitinated proteins, possibly constituting a protective mechanism.

Insulin-like growth factor binding protein 5 and type-1 insulin-like growth factor receptor are differentially regulated during apoptosis in cerebellar granule cells

Neuronal apoptosis is considered to play a significant role in several neuropathological conditions. However, the molecular mechanisms underlying neuronal apoptosis are poorly understood. Insulin-like growth factor (IGF) signalling is considered to be an important regulator of neuronal differentiation, survival and apoptosis. We have examined the expression of two members of the IGF system, insulin-like growth factor binding protein 5 (IGFBP-5) and the type-1 IGF receptor (IGF1R), during apoptosis of rat cerebellar granule cells (CGCs) in vitro. We describe a prominent downregulation of IGFBP-5 mRNA and protein expression. We also show that IGF-I increases IGFBP-5 expression in CGCs and that the downregulation of IGFBP-5 mRNA can be suppressed by inhibiting mRNA synthesis with actinomycin D. The expression of IGF1R mRNA showed a transient upregulation during potassium chloride (KCl) deprivation induced apoptosis, in contrast to the IGF1R protein level, which was downregulated during KCl deprivation. Our results provide insight into the expression of IGF-related genes during neuronal apoptosis, and indicate that they mediate a protective response to the withdrawal of trophic stimulation. It seems that the expression of IGFBP-5 and IGF1R is regulated to maximize the availability of IGF and the activity of IGF-triggered survival signalling.