Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein.

Previous evidence indicates that a number of proteins are able to interact with cognate mRNAs. These autogenous associations represent important regulatory mechanisms that control gene expression at the translational level. Using the catRAPID approach to predict the propensity of proteins to bind to RNA, we investigated the occurrence of autogenous associations in the human proteome. Our algorithm correctly identified binding sites in well-known cases such as thymidylate synthase, tumor suppressor P53, synaptotagmin-1, serine/ariginine-rich splicing factor 2, heat shock 70 kDa, ribonucleic particle-specific U1A and ribosomal protein S13. In addition, we found that several other proteins are able to bind to their own mRNAs. A large-scale analysis of biological pathways revealed that aggregation-prone and structurally disordered proteins have the highest propensity to interact with cognate RNAs. These findings are substantiated by experimental evidence on amyloidogenic proteins such as TAR DNA-binding protein 43 and fragile X mental retardation protein. Among the amyloidogenic proteins, we predicted that Parkinson's disease-related α-synuclein is highly prone to interact with cognate transcripts, which suggests the existence of RNA-dependent factors in its function and dysfunction. Indeed, as aggregation is intrinsically concentration dependent, it is possible that autogenous interactions play a crucial role in controlling protein homeostasis.

Accurate expression profiling of very small cell populations.

BACKGROUND: Expression profiling, the measurement of all transcripts of a cell or tissue type, is currently the most comprehensive method to describe their physiological states. Given that accurate profiling methods currently available require RNA amounts found in thousands to millions of cells, many fields of biology working with specialized cell types cannot use these techniques because available cell numbers are limited. Currently available alternative methods for expression profiling from nanograms of RNA or from very small cell populations lack a broad validation of results to provide accurate information about the measured transcripts. METHODS AND FINDINGS: We provide evidence that currently available methods for expression profiling of very small cell populations are prone to technical noise and therefore cannot be used efficiently as discovery tools. Furthermore, we present Pico Profiling, a new expression profiling method from as few as ten cells, and we show that this approach is as informative as standard techniques from thousands to millions of cells. The central component of Pico Profiling is Whole Transcriptome Amplification (WTA), which generates expression profiles that are highly comparable to those produced by others, at different times, by standard protocols or by Real-time PCR. We provide a complete workflow from RNA isolation to analysis of expression profiles. CONCLUSIONS: Pico Profiling, as presented here, allows generating an accurate expression profile from cell populations as small as ten cells.

Islet graft response to transplantation injury includes upregulation of protective as well as apoptotic genes.

Pancreatic islets are particularly vulnerable in the initial days after transplantation when multiple factors converge to damage the islet graft. The aim of this study was to investigate the expression profile of genes involved in damage and protection of beta-cells in the initial days after syngeneic islet transplantation. We studied the expression of a set of selected genes involved in apoptosis (Bcl2, Bclx(L), Bax, Bad, Bid, and CHOP), cytokine defense, (SOCS-1 and SOCS-3), or free radical protection (Hmox1, Cu/Zn-SOD, Mn-SOD, and Hsp70). Because hyperglycemia has deleterious effects on islet transplantation outcome, we studied its effect on the expression of these genes. Five hundred islets were syngeneically transplanted under the kidney capsule of normoglycemic or streptozotocin-induced diabetic Lewis rats. Gene expression was analyzed by quantitative real-time RT-PCR in grafts 1, 3, and 7 days after transplantation, and in freshly isolated islets. The expression of proapoptotic genes Bid and CHOP, as well as protective genes Bclx(L), Socs1, Socs3, Hmox1, and MnSod, was maximally increased 1 day after transplantation, and in most cases it remained increased 7 days later, indicating the presence of a protective response against cell damage. In contrast, the expression of Bcl2, Bax, Bad, Cu/ZnSod, and Hsp70 genes did not change. Hyperglycemia did not modify the expression of most studied genes. However, MnSod and Ins2 expression was increased and reduced, respectively, on day 7 after transplantation to diabetic recipients, suggesting that hyperglycemia increased oxidative stress and deteriorated beta-cell function in transplanted islets.

Selection of a suitable internal control gene for expression studies in pancreatic islet grafts.

The use of real-time reverse transcription polymerase chain reaction to compare gene expression in different tissues and conditions requires normalization to an internal control that must be expressed at a constant level. Although a previous validation step is required to confirm that an internal control is appropriate, no comparison of frequently used "housekeeping" genes is available for islet grafts. We have investigated the effect of transplantation and metabolic environment on the expression of 18S, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta-actin, and cyclophilin A genes in pancreatic islets. The expression of these genes was determined on days 1, 3, and 7 after transplantation into normoglycemic or hyperglycemic rats and in isolated islets. Only 18S gene expression remained stable in all studied conditions, indicating that it is the best internal control for gene expression analysis in islet grafts. The significant variation found in other housekeeping genes, particularly GAPDH and beta-actin, question their use as internal controls in islet grafts.

Expression of concentrative nucleoside transporters SLC28 (CNT1, CNT2, and CNT3) along the rat nephron: effect of diabetes.

BACKGROUND: The renal reabsorption of natural nucleosides and a variety of nucleoside-derived drugs relies on the function of the apically located, Na(+)-dependent, concentrative nucleoside transporters CNT1, CNT2, and CNT3 (SLC28A1, SLC28A2, and SLC28A3). The aims of this study were to determine the segmental localization of the three SLC28 family members and to establish whether streptozotocin-induced diabetes alters their expression. METHODS: SLC28 expression was measured by real-time polymerase chain reaction (PCR) on microdissected sections of rat nephrons. Diabetes was induced by streptozotocin treatment and the biochemical profiles of control, diabetic, and insulin-treated rats were established. The effect of diabetes on SLC28 expression was assessed in those segments that significantly express SLC28 genes. RESULTS: CNT1-3 mRNAs were expressed in the proximal tubule and glomerulus. In addition, CNT2 and CNT3 mRNAs were expressed in the outer medullary and cortical collecting duct, respectively. Diabetes reduced expression of the three CNTs in almost all nephron segments, and this effect was not prevented by an insulin treatment that normalized all blood and urine parameters. Diabetes increased CNT1 and CNT3 expression in the glomerulus and insulin treatment decreased it. CONCLUSION: The relative distribution of SLC28 gene expression suggests a role for the proximal tubule in renal nucleoside clearance and an accessory role for CNT2 and CNT3, in adenosine-mediated regulation of collecting duct functions. Diabetes probably may impair nucleoside clearance independently of insulin.

The osmoregulatory and the amino acid-regulated responses of system A are mediated by different signal transduction pathways.

The osmotic response of system A for neutral amino acid transport has been related to the adaptive response of this transport system to amino acid starvation. In a previous study (Ruiz-Montasell, B., M. Gómez-Angelats, F.J. Casado, A. Felipe, J.D. McGivan, and M. Pastor-Anglada. 1994. Proc. Natl. Acad. Sci. USA. 91:9569-9573), a model was proposed in which both responses were mediated by different mechanisms. The recent cloning of several isoforms of system A as well as the elucidation of a variety of signal transduction pathways involved in stress responses allow to test this model. SAT2 mRNA levels increased after amino acid deprivation but not after hyperosmotic shock. Inhibition of p38 activity or transfection with a dominant negative p38 did not alter the response to amino acid starvation but partially blocked the hypertonicity response. Inhibition of the ERK pathway resulted in full inhibition of the adaptive response of system A and no increase in SAT2 mRNA levels, without modifying the response to hyperosmolarity. Similar results were obtained after transfection with a dominant negative JNK1. The CDK2 inhibitor peptide-II decreased the osmotic response in a dose-dependent manner but did not have any effect on the adaptive response of system A. In summary, the previously proposed model of up-regulation of system A after hypertonic shock or after amino acid starvation by separate mechanisms is now confirmed and the two signal transduction pathways have been identified. The involvement of a CDK-cyclin complex in the osmotic response of system A links the activity of this transporter to the increase in cell volume previous to the entry in a new cell division cycle.