Does metabolic radiolabeling stimulate the stress response? Gene expression profiling reveals differential cellular responses to internal beta vs. external gamma radiation

Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants

Protein turnover is an important aspect of the regulation of cellular processes for organisms when responding to developmental or environmental cues. The measurement of protein turnover in plants, in contrast to that of rapidly growing unicellular organismal cultures, is made more complicated by the high degree of amino acid recycling, resulting in significant transient isotope incorporation distributions that must be dealt with computationally for high throughput analysis to be practical. An algorithm in R, ProteinTurnover, was developed to calculate protein turnover with transient stable isotope incorporation distributions in a high throughput automated manner using high resolution MS and MS/MS proteomic analysis of stable isotopically labeled plant material. ProteinTurnover extracts isotopic distribution information from raw MS data for peptides identified by MS/MS from data sets of either isotopic label dilution or incorporation experiments. Variable isotopic incorporation distributions were modeled using binomial and beta-binomial distributions to deconvolute the natural abundance, newly synthesized/partial-labeled, and fully labeled peptide distributions. Maximum likelihood estimation was performed to calculate the distribution abundance proportion of old and newly synthesized peptides. The half-life or turnover rate of each peptide was calculated from changes in the distribution abundance proportions using nonlinear regression. We applied ProteinTurnover to obtain half-lives of proteins from enriched soluble and membrane fractions from Arabidopsis roots.

Pulse-chase analysis of procollagen biosynthesis by azidohomoalanine labeling

Disruptions in procollagen synthesis, trafficking and secretion by cells occur in multiple connective tissue diseases. Traditionally, these disruptions are studied by pulse-chase labeling with radioisotopes. However, significant DNA damage, excessive accumulation of reactive oxygen species and formation of other free radicals have been well documented in the literature at typical radioisotope concentrations used for pulse-chase experiments. Therefore, it is important to keep in mind that the resulting cell stress response might affect interpretation of the data, particularly with respect to abnormal function of procollagen-producing cells. In this study, we describe an alternative method of pulse-chase procollagen labeling with azidohomoalanine, a noncanonical amino acid that replaces methionine in newly synthesized protein chains and can be detected via highly selective click chemistry reactions. At least in fibroblast culture, this approach is more efficient than traditional radioisotopes and has fewer, if any, unintended effects on cell function. To illustrate its applications, we demonstrate delayed procollagen folding and secretion by cells from an osteogenesis imperfecta patient with a Cys substitution for Gly766 in the triple helical region of the α1(I) chain of type I procollagen.

Protein turnover on the scale of the proteome

Protein turnover is a neglected dimension in postgenomic studies, defining the dynamics of changes in protein expression and forging a link between transcriptome, proteome and metabolome. Recent advances in postgenomic technologies have led to the development of new proteomic techniques to measure protein turnover on a proteome-wide scale. These methods are driven by stable isotope metabolic labeling of cells in culture or in intact animals. This review considers the merits and difficulties of different methods that allow access to proteome dynamics.

Dissection of a complex transcriptional response using genome-wide transcriptional modelling

Modern genomics technologies generate huge data sets creating a demand for systems level, experimentally verified, analysis techniques. We examined the transcriptional response to DNA damage in a human T cell line (MOLT4) using microarrays. By measuring both mRNA accumulation and degradation over a short time course, we were able to construct a mechanistic model of the transcriptional response. The model predicted three dominant transcriptional activity profiles—an early response controlled by NFκB and c-Jun, a delayed response controlled by p53, and a late response related to cell cycle re-entry. The method also identified, with defined confidence limits, the transcriptional targets associated with each activity. Experimental inhibition of NFκB, c-Jun and p53 confirmed that target predictions were accurate. Model predictions directly explained 70% of the 200 most significantly upregulated genes in the DNA-damage response. Genome-wide transcriptional modelling (GWTM) requires no prior knowledge of either transcription factors or their targets. GWTM is an economical and effective method for identifying the main transcriptional activators in a complex response and confidently predicting their targets.

Proteomic analysis of phosphoproteins regulated by abscisic acid in rice leaves

Abscisic acid (ABA) is a hormone that regulates plant development and adaptation to environmental stresses. Protein phosphorylation has been recognized as an important mechanism for ABA signaling. However, the target phosphoproteins regulated by ABA are still largely unknown. Here, we report the identification of ABA-regulated phosphoproteins in rice using proteomic approaches. Six ABA-regulated phosphoproteins were identified as G protein beta subunit-like protein, ascorbate peroxidase, manganese superoxide dismutase, triosephosphate isomerase, putative Ca(2+)/H(+) antiporter regulator protein, and glyoxysomal malate dehydrogenase. These results provide new insight into the regulatory mechanism for some ABA signaling proteins and implicate several previously unrecognized proteins in ABA action.

Gene expression changes in cervical squamous cell carcinoma after initiation of chemoradiation and correlation with clinical outcome

PURPOSE

The purpose of this study was to investigate early gene expression changes after chemoradiation in a human solid tumor, allowing identification of chemoradiation-induced gene expression changes in the tumor as well as the tumor microenvironment. In addition we aimed to identify a gene expression profile that was associated with clinical outcome.

METHODS AND MATERIALS

Microarray experiments were performed on cervical cancer specimens obtained before and 48 h after chemoradiation from 12 patients with Stage IB2 to IIIB squamous cell carcinoma of the cervix treated between April 2001 and August 2002.

RESULTS

A total of 262 genes were identified that were significantly changed after chemoradiation. Genes involved in DNA repair were identified including DDB2, ERCC4, GADD45A, and XPC. In addition, significantly regulated cell-to-cell signaling pathways included insulin-like growth factor-1 (IGF-1), interferon, and vascular endothelial growth factor signaling. At a median follow-up of 41 months, 5 of 12 patients had experienced either local or distant failure. Supervised clustering analysis identified a 58-gene set from the pretreatment samples that were differentially expressed between patients with and without recurrence. Genes involved in integrin signaling and apoptosis pathways were identified in this gene set. Immortalization-upregulated protein (IMUP), IGF-2, and ARHD had particularly marked differences in expression between patients with and without recurrence.

CONCLUSIONS

Genetic profiling identified genes regulated by chemoradiation including DNA damage and cell-to-cell signaling pathways. Genes associated with recurrence were identified that will require validation in an independent patient data set to determine whether the 58-gene set associated with clinical outcome could be useful as a prognostic assay.

Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells

Background

This study assesses the whole-genome gene expression changes in a panel of primary human cell lines in response to DNA damage mediated by decay of DNA-incorporated radioiodinated thymidine analog 5-[¹²⁵I]iodo-2'-deoxyuridine (¹²⁵I-IUdR). Three normal human cell lines of different origin, namely, gingival fibroblasts AG09319, fetal skin fibroblasts GM05388 and neonatal foreskin epidermal keratinocytes (NHFK) were used in this study. DNA molecules were radiolabeled by incubation of cells in culture in a medium supplemented with either 3.7 kBq/ml or 18.5 kBq/ml of ¹²⁵I-IUdR for 24 h followed by incubation in IUdR-free medium for additional 24 hours. Each experiment was carried out in quadruplicate. ¹²⁵I-IUdR uptake was monitored by measuring DNA-associated radioactivity. The whole-genome gene expression changes were evaluated using Agilent Human Whole Genome oligo microarrays containing 44,290 elements representing all known and predicted human genes. DNA microarray dataset was independently partially validated with quantitative real-time PCR (RT-PCR).

Results

AG09319 gingival cells in culture responded to ¹²⁵I-IUdR treatment by changing the expression level of 335 genes in total, whereas under the same conditions GM05388 and NHFK cells differentially expressed 49 genes and 27 genes, respectively. However, for GM05388 cells the number of differentially expressed genes increases with the rise of ¹²⁵I-IUdR concentrations in cell culture media. The key up-regulated biological processes in a chosen panel of cell lines concern the regulation of protein kinase activities and/or cell death. Genes repressed in response to ¹²⁵I-IUdR treatment are involved in cytokinesis, M phase of the cell cycle, chromosome architecture and organization, DNA metabolism, DNA packaging, DNA repair and response to DNA damage. Despite the disparate nature of the gene patterns elicited by ¹²⁵I-induced DNA damage among the different cell lines, the differentially expressed transcripts reveal strikingly non-random chromosomal distribution in all the cell lines we used.

Conclusion

Our data suggest that DNA-targeted ionizing radiation produced by ¹²⁵I-IUdR results in changes in expression of only a limited subset of genes in primary human cells. The responsive genes are distributed non-randomly among the chromosomes; and a significant fraction of them is p53-dependent in the transcriptional regulation.

Proteome analysis of proliferative response of bystander cells adjacent to cells exposed to ionizing radiation

Recently (Cytometry 2003, 56A, 71-80), we reported that direct cell-to-cell contact is required for stimulating proliferation of bystander rat liver cells (WB-F344) cocultured with irradiated cells, and neither functional gap junction intercellular communication nor long-range extracellular factors appear to be involved in this proliferative bystander response (PBR). The molecular basis for this response is unknown. Confluent monolayers of WB-F344 cells were exposed to 5-Gray (Gy) of gamma-rays. Irradiated cells were mixed with unirradiated cells and co-cultured for 24 h. Cells were harvested and protein expression was examined using 2-DE. Protein expression was also determined in cultures of unirradiated and 5-Gy irradiated cells. Proteins were identified by MS. Nucleophosmin (NPM)-1, a multifunctional nucleolar protein, was more highly expressed in bystander cells than in either unirradiated or 5-Gy irradiated cells. Enolase-alpha, a glycolytic enzyme, was present in acidic and basic variants in unirradiated cells. In bystander and 5-Gy irradiated cells, the basic variant was weakly expressed, whereas the acidic variant was overwhelmingly present. These data indicate that the presence of irradiated cells can affect NPM-1 and enolase-alpha in adjacent bystander cells. These proteins appear to participate in molecular events related to the PBR and suggest that this response may involve cellular defense, proliferation, and metabolism.

Microarray analysis of differentially expressed genes after exposure of normal human fibroblasts to ionizing radiation from an external source and from DNA-incorporated iodine-125 radionuclide

Exposure of cells to ionizing radiation (IR) produces changes in the expression level of a large number of genes. However, less is known of gene-expression changes caused by local radiation exposure from radionuclides within cells. We studied changes in the genome-wide gene expression induced by decay of 125I incorporated into DNA as [125I]-iododeoxyuridine (125I-IUdR) in normal IMR-90 human lung fibroblasts and compared them with the changes produced by external gamma-radiation delivered at high (HDR) or low (LDR) dose rate. We found that more than 2000 genes were consistently up- or down-regulated following HDR and LDR gamma-radiation. The profiles of differentially expressed genes following HDR and LDR shared about 64% (up) and 74% (down) genes in common, with many genes identified as radiation-responsive for the first time. In contrast, in all only 206 genes changed their expression level in the 125I-IUdR-treated cells, even though the total number of DNA double-strand breaks (DSB) produced by 125I-IUdR exceeded that produced by the gamma-radiation. With few exceptions, the expression levels of 125I-IUdR-responsive genes were also altered following gamma-irradiation. Therefore, nuclear DNA-localized decays of 125I produce 10 times fewer differentially expressed genes than whole-cell exposure to gamma-radiation of comparable dose. These results suggest that the effect of IR on the changes in global gene expression depends on the distribution of energy depositions within the cell. In contrast to cell survival, DNA DSB may not be the major factor modulating changes in gene expression following irradiation.

Ranked prediction of p53 targets using hidden variable dynamic modeling

Hidden Variable Dynamic Modelling is a new approach to microarray analysis that quantitatively predicts the regulation of gene activity.

Full exploitation of microarray data requires hidden information that cannot be extracted using current analysis methodologies. We present a new approach, hidden variable dynamic modeling (HVDM), which derives the hidden profile of a transcription factor from time series microarray data, and generates a ranked list of predicted targets. We applied HVDM to the p53 network, validating predictions experimentally using small interfering RNA. HVDM can be applied in many systems biology contexts to predict regulation of gene activity quantitatively.

Synergistic activity of the proteasome inhibitor PS-341 with non-myeloablative 153-Sm-EDTMP skeletally targeted radiotherapy in an orthotopic model of multiple myeloma

Multiple myeloma is a highly radiosensitive skeletal malignancy, but bone-seeking radionuclides have not yet found their place in disease management. We previously reported that the proteasome inhibitor PS-341 selectively sensitizes myeloma cells to the lethal effects of ionizing radiation. To extend these observations to an in vivo model, we combined PS-341 with the bone-seeking radionuclide 153-Sm-EDTMP. In vitro clonogenic assays demonstrated synergistic killing of myeloma cells exposed to both PS-341 and 153-Sm-EDTMP. Using the orthotopic, syngeneic 5TGM1 myeloma model, the median survivals of mice treated with saline, 2 doses of PS-341 (0.5 mg/kg), or a single nonmyeloablative dose of 153-Sm-EDTMP (22.5 MBq) were 21, 22, and 28 days, respectively. In contrast, mice treated with combination therapy comprising 2 doses of PS-341 (0.5 mg/kg), 1 day prior to and 1 day following 153-Sm-EDTMP (22.5 MBq) showed a significantly prolonged median survival of 49 days (P < .001). In addition to prolonged survival, this treatment combination yielded reduced clonogenicity of bone marrow-resident 5TGM1 cells, reduced serum myeloma-associated paraprotein levels, and better preservation of bone mineral density. Myelosuppression, determined by peripheral blood cell counts and clonogenicity assays of hematopoietic progenitors, did not differ between animals treated with 153-Sm-EDTMP alone versus those treated with the combination of PS-341 plus 153-Sm-EDTMP. PS-341 is a potent, selective in vivo radiosensitizer that may substantially affect the efficacy of skeletal-targeted radiotherapy in multiple myeloma.

Genome-wide gene expression changes in normal human fibroblasts in response to low-LET gamma-radiation and high-LET-like 125IUdR exposures

Functional genomics studies were carried out to characterize the transcriptional response of normal human fibroblasts to ionizing radiation (IR) of different types. To this end, lung fibroblast IMR-90 cultures were exposed either to external beam gamma-radiation or to internal irradiation from decay of (125)I-labeled deoxyuridine ((125)IUdR) incorporated into the cellular DNA. A relatively small dose of 1 Gy of gamma-radiation was delivered to cell cultures either at a high dose-rate (HDR, 1 Gy, 1 min) or at a low dose-rate (LDR, 1 Gy, 22 h). More than 41,000 transcripts were assayed by oligo DNA microarray featuring all known and predicted genes in human genome. Gene expression profiles following gamma-radiation and decays of high-linear energy transfer (LET)-like (125)I share the majority of genes in common, indicating the involvement of similar pathways in signal transduction after IR exposures of different modalities. Gene Ontology (GO) analysis revealed that the oxidative phosphorylation, metabolism of nt, protein kinase cascade and cell cycle are among the up-regulated biological processes mostly affected by gamma-radiation in IMR-90 cells. The translational elongation, negative regulation of cell growth, antigen processing and protein targeting are down-regulated following IR exposures. About one-third of genes differentially expressed following either HDR or LDR gamma-radiation exposures in the same absorbed dose were different, indicating the involvement of distinct transcriptional programs in cellular response to irradiation delivered with the different dose rates.

Low-dose irradiation alters the transcript profiles of human lymphoblastoid cells including genes associated with cytogenetic radioadaptive response

Low-dose ionizing radiation alters the gene expression profiles of mammalian cells, yet there is little understanding of the underlying cellular mechanisms responsible for these changes or of their consequences for genomic stability. We investigated the cytogenetic adaptive response of human lymphoblastoid cell lines exposed to 5 cGy (priming dose) followed by 2 Gy (challenge dose) compared to cells that received a single 2-Gy dose to (a) determine how the priming dose influences subsequent gene transcript expression in reproducibly adapting and non-adapting cell lines, and (b) identify gene transcripts that are associated with reductions in the magnitude of chromosomal damage after the challenge dose. The transcript profiles were evaluated using oligonucleotide arrays and RNA obtained 4 h after the challenge dose. A set of 145 genes (false discovery rate = 5%) with transcripts that were affected by the 5-cGy priming dose fell into two categories: (a) a set of common genes that were similarly modulated by the 5-cGy priming dose irrespective of whether the cells subsequently adapted or not and (b) genes with differential transcription in accordance with the cell lines that showed either adaptive or non-adaptive outcomes. The common priming-dose response genes showed up-regulation for protein synthesis genes and down-regulation of metabolic and signal transduction genes (>10-fold differences). The genes associated with subsequent adaptive and non-adaptive outcomes involved DNA repair, stress response, cell cycle control and apoptosis. Our findings support the importance of TP53-related functions in the control of the low-dose cytogenetic radioadaptive response and suggest that certain low-dose-induced alterations in cellular functions are predictive for the risk of subsequent genomic damage.

Low-level radiocaesium exposure alters gene expression in roots of Arabidopsis

Radiocaesium is one of the main anthropogenic sources of internal and external exposure to beta- and gamma-radiation (e.g. from global fallout of atmospheric atomic bomb testing and from the Chernobyl reactor accident). Here we investigated gene expression by suppression subtractive hybridization (SSH) and reverse transcription-polymerase chain reaction (RT-PCR) in Arabidopsis thaliana, which was induced by the root uptake of 134Cs. SSH analysis resulted in the isolation of 46 clones that were differentially expressed at 30 Bq cm(-3) 134Cs. Most of the expressed sequence tags identified belonged to genes encoding proteins that were involved in cell growth, cell division and the development of plants, and in proteins controlling translation, general metabolism and stress defence, including a DNA excision repair protein. The accumulation of caesium in plant material was measured in plants grown for 5 wk on agar contaminated by up to 60 Bq cm(-3) 134Cs. 134Cs was found to accumulate, in particular, in leaf rosettes and was dependent on the activity concentration in the growth media. The data indicate that low-level ionizing radiation influences important cellular responses, resulting in a changed gene-expression profile.

Bystander cell proliferation is modulated by the number of adjacent cells that were exposed to ionizing radiation

BACKGROUND

Direct cell-to-cell contact appears to be a prerequisite for the proliferative response of bystander WB-F344 cells co-cultured with irradiated cells; however, neither gap junctional intercellular communication nor long-range factors released into the medium appear to be involved (Cytometry 2003;56A:71-80). The present work investigated whether the proliferative bystander response depends on the number of irradiated cells (cells exposed to external gamma-rays or cells exposed to short-range beta-particles emitted by DNA-incorporated (3)H-thymidine) that are adjacent to unirradiated bystander cells.

METHODS

Subconfluent monolayers of rat liver epithelial cells (WB-F344) were incubated in the presence of (methyl-(3)H)thymidine at a concentration of 5.8 kBq/ml for 18 h. Radiolabeled cells containing 0.7 x 10(-3) Bq/cell (absorbed dose: 0.14 Gy) were plated together with unlabeled cells in proportions of 6% and 94%, 12% and 88%, 25% and 75%, 50% and 50%, and 75% and 25%, respectively, keeping constant the total number of plated cells. In a parallel experiment, cells acutely exposed to 5 Gy of (137)Cs gamma-rays were plated with unirradiated cells in the same proportions. In both experiments, cells were co-cultured for 24 h followed by a flow cytometric study of their proliferation. The two cell populations in the co-cultures were distinguished by staining one population with carboxyfluorescein diacetate, succinimidyl ester, which metabolizes intracellularly.

RESULTS

Increasing the fraction of irradiated cells relative to unirradiated bystander cells led to an increase in proliferation of bystander cells. Specifically, in co-cultures in which irradiated cells were initially mixed with unirradiated cells in proportions of 50% and 50% and of 75% and 25%, respectively, bystander cells showed a statistically significant increase of their proliferation compared with the controls.

CONCLUSIONS

The proliferative response of WB-F344 bystander cells is modulated by the number of adjacent cells that are exposed to ionizing radiation from external gamma-rays or intracellularly emitted (3)H beta-particles.

Proliferative response of bystander cells adjacent to cells with incorporated radioactivity

BACKGROUND

In a recent study, we showed that cells irradiated with gamma-rays stimulate cell growth of unirradiated (bystander) cells, when the two populations are co-cultured as a mixture. Direct cell-to-cell contact appears to be a prerequisite for the proliferative response of the bystander cells. The aim of the current work is to investigate the possible proliferative bystander effects caused by intracellular irradiation with incorporated radionuclides, specifically the short-range beta particle emitter, tritium ((3)H).

METHODS

Subconfluent monolayers of rat liver epithelial cells (WB-F344) were incubated in the presence of (methyl-(3)H)thymidine ((3)HTdR) at concentrations ranging between 5.2 kBq/ml and 57.8 kBq/ml for 18 h. Radiolabeled cells, containing between 0.7 x 10(-3) Bq/cell and 8.8 x 10(-3) Bq/cell were mixed with unlabeled (i.e., bystander) cells in a ratio of 1:1 and cultured together for 24 h followed by an flow cytometry (FCM) study of their proliferation. In order to discriminate the two populations of co-cultured cells, one cell population (unlabeled bystander cells) was stained with carboxyfluorescein diacetate, succinimidyl ester (CFDA SE), which metabolizes intracellularly. The absorbed doses received by the radiolabeled cells that contained 0.7 x 10(-3), 2.5 x 10(-3), and 8.8 x 10(-3) Bq/cell were 0.14, 0.49, and 1.7 Gy, respectively.

RESULTS

Cells that were not treated with tritiated thymidine (unlabeled cells), in the presence of radiolabeled cells that received absorbed doses from 0.14-1.7 Gy, showed enhanced cell growth by approximately 9 to 10%.

CONCLUSIONS

Cells labeled with (3)HTdR can induce increased proliferation in neighboring unlabeled bystander cells. FCM provides an excellent basis for characterization of proliferative bystander effects in co-culture systems.

Sensitization to Radiation from an Implanted125I Source by Sustained Intratumoral Release of Chemotherapeutic Drugs

We have investigated tumor response to low-dose-rate irradiation from an implanted 125I source alone or in conjunction with intratumoral drug administration. The drug (cis-DDP or 5-FU) was incorporated homogeneously into the co-polymer CPP-SA, 20:80, and the polymer/drug rods were implanted in the RIF-1 fibrosarcomas growing subcutaneously in C3H mice. Twenty-four hours later, the tumor was implanted with an 125I seed. Tumor growth time was the end point in these experiments. For implanted 125I sources of different dose rates and implant times giving a range of total doses, a consistent dose-response relationship was shown between tumor growth time and total dose. In other experiments, 125I sources of different specific activities were implanted for periods of time adjusted so that the total dose to the tumor was always the same. When the 125I implant was combined with 5-FU, greater than additive responses were seen for both short (30 h) and long (96 h) 125I treatment times. In contrast, a short-duration (30 h) 125I implant combined with cis-DDP was the least effective treatment, giving a combined response that was no better than additive, whereas 96 h exposure to 125I combined with cis-DDP was the most effective combined treatment. It is conjectured that this inverse dose-rate effect seen when cis-DDP is combined with low-dose rate radiation is related to a cell cycle effect and/or to inhibition of repair of radiation damage by cis-DDP.