Early Changes In Protein Expression Research Articles

CBIO-01. THE EARLY CHANGES IN PROTEIN EXPRESSION IN THE RHESUS OPTIC NERVES INJURED BY A SINGLE DOSE/FRACTIONATION STEREOTACTIC RADIOSURGERY

Radiation-induced optic neuropathy (RION) is a severe complication when we use stereotactic radiosurgery (SRS) to treat anterior visual disease. This study was designed to analyze the early changes in protein expression in rhesus optic nerves injured by SRS. The left side intraorbital optic nerves of 3 rhesus monkeys (6-8 years)were injured by gamma knife surgery (GKS) (marginal dose of 15 Gy, 50% isodose curve), while the contralateral optic nerves served as the control. The bilateral intraorbital optic nerves of 3 rhesus monkeys were dissected and performed a non-marker quantitative proteomic analysis at 72 hours after GKS. The differential expression protein information was obtained. The functional information of those proteins was obtained through the BLAST sequence alignment with the human proteomic. The result showed that 41 proteins fit the criteria for differential expression (change>2.0-fold, P value<0.05 or exclusive expression). 7 proteins were significantly down-regulated (change>2.0-fold, P value<0.05) at the injured optic nerves. 18 proteins were exclusively expressed in the contralateral optic nerves. And 16 proteins were exclusively expressed in the injured optic nerves. In general, this study indicated that the single dose of 15 Gy on a 50% isodose curve in the optic nerve had a significant impact on protein expression at 72 hours after GKS. Non-marker quantitative analysis based on high-resolution LCMS/MS can be used to detect the early protein expression change in RION. At 72h after GKS, The cell’s endocytosis and pinocytosis were declined and shown a significant inflammation and immunization. The proliferation of those cell were declined and the genetic transcription and translation were increased in the injury optic.

Inhibition of MAPKs and type IV phosphodiesterase during the early phase of acute pancreatitis: A shotgun proteomics approach

Introduction: Early changes in protein expression and signaling mechanisms (MAPKs cascade or the cAMP pathway) in acute pancreatitis (AP) play important roles in the further development of the disease. Therefore, proteomic analyses of pancreatic subcellular fractions might be very useful for deciphering AP at the molecular level. Aims:WereportedhereaTandemMassTag(TMT)proteomicsanalysisof the soluble fraction of the pancreas during the early phase of experimental AP and under MAPKs or type IV phosphodiesterase (PDEIV) inhibition. Materials & methods: The early phase of AP was induced in rats by two subcutaneous injections of 20 mg of cerulein (Cer)/kg body weight at hourly intervals. PDEIV and the MAPKs cascade were inhibited by rolipram and SP600125 or PD98059, respectively, before the induction of AP. TMT 6 analysis weredesignedtocharacterizeeachexperimentalconditioninacross-sectional study. Changes in protein expression were validated by immunoblotting. Results: Out of the around 540 identified proteins, 298 were differentially expressed during the early phase of AP (Isobar, p < 0.05). Also, we identified 27 (SP600125), 39 (PD98059) or 38 (rolipram) proteins differentially regulated by the distinct pretreatments compared to the Cer class. These proteins are mainly involved in protein and membrane trafficking, apoptosis, mitochondrial function, calcium signaling and cytoskeleton impairment. We are currently characterizing novel candidates that might be relevant to AP pathogenesis. Conclusion: These data should provide valuable information for unraveling the early pathophysiologic mechanisms of Cer-induced AP and might unmask new potential biomarkers of the disease.

Proteins related to early changes in carcinogenesis of hepatic oval cells after treatment with methylnitronitrosoguanidine

Hepatic oval cells are considered as facultative progenitor/stem cells of liver and able to differentiate into either hepatocytes or biliary epithelial cells. The transformed oval cells by carcinogen possess potential to develop carcinomas in animal models. In order to better understand the molecular mechanism in carcinogenetic process, we used a proteomic approach to assess the early changes in protein expression of oval cells (OC3W3-15) initiated by methylnitronitrosoguanidine (MNNG). Meanwhile, we compared cell biologic characteristics of the MNNG treated OC3W3-15 cells and control oval cells by electron microscopy, flow cytometry, karyotype and soft agar assay. The mRNA levels of GGT and GSTP1 determined by real-time PCR were also detected in both cell lines. Our results showed that MNNG-treated OC3W3-15 cells exhibited characteristics of malignant transformation, including growth rate, chromosomal aberrations, abnormal DNA content, and the ability to form colonies. The cells expressed higher levels of the tumor marker AFP, GGT and GSTP1 mRNA than that of control cells. Significant changes of several proteins involved in the malignant transformation process, including cell cycle related proteins, proteins involved in organism development and cell differentiation, are found in OC3W3-15 cells. The proteins may provide early affection in malignant transformation of hepatic oval cells, and yield further insight into mechanism of carcinogenesis of hepatocellular carcinoma.

Early Changes in mRNA and Protein Expression Related to Cancer Treatment by Modulated Electrohyperthermia

Modulated electrohyperthermia (mEHT), generated by capacitive coupled, modulated 13.56 MHz radiofrequency, is a noninvasive technique for targeted tumor treatment based on elevated ion concentration and electric admittance in malignant tumors. In this study, we tested early changes in protein expression related to tumor destruction upon a single shot of 30-minute mEHT treatment of xenografted human colorectal cell line (HT29) implanted into the femoral region of Balb/c nu/nu mice. Treatment-related mRNA expression profiling was done using the human genome U133 Plus 2.0 Arrays. Apoptosis protein arrays and immunohistochemistry were performed for validating changes at the protein level. The mEHT treatment resulted in major expression changes in 48 genes including several heat-shock proteins. Apoptosis protein arrays revealed the upregulation of death receptors, Bcl-2 superfamily mitochondrial apoptosis regulatory proteins, and heat-shock proteins, which were also confirmed in situ. Within 24-hour post-treatment, mEHT resulted in the upregulation apoptosis induction and heat-shock-related gene and protein expression in HT29 colorectal cancer xenografts contributing to tumor destruction.

Proteomics of Genetically Engineered Mouse Mammary Tumors Identifies Fatty Acid Metabolism Members as Potential Predictive Markers for Cisplatin Resistance

In contrast to various signatures that predict the prognosis of breast cancer patients, markers that predict chemotherapy response are still elusive. To detect such predictive biomarkers, we investigated early changes in protein expression using two mouse models for distinct breast cancer subtypes who have a differential knock-out status for the breast cancer 1, early onset (Brca1) gene. The proteome of cisplatin-sensitive BRCA1-deficient mammary tumors was compared with that of cisplatin-resistant mammary tumors resembling pleomorphic invasive lobular carcinoma. The analyses were performed 24 h after administration of the maximum tolerable dose of cisplatin. At this time point, drug-sensitive BRCA1-deficient tumors showed DNA damage, but cells were largely viable. By applying paired statistics and quantitative filtering, we identified highly discriminatory markers for the sensitive and resistant model. Proteins up-regulated in the sensitive model are involved in centrosome organization, chromosome condensation, homology-directed DNA repair, and nucleotide metabolism. Major discriminatory markers that were up-regulated in the resistant model were predominantly involved in fatty acid metabolism, such as fatty-acid synthase. Specific inhibition of fatty-acid synthase sensitized resistant cells to cisplatin. Our data suggest that exploring the functional link between the DNA damage response and cancer metabolism shortly after the initial treatment may be a useful strategy to predict the efficacy of cisplatin.

Identification of proteins related to early changes observed in Human hepatocellular carcinoma cells after treatment with the mycotoxin Zearalenone

Zearalenone (ZEA) is a mycotoxin produced by some Fusarium species. ZEA often occur as a contaminant in cereal grains and animal feeds. Human exposure occurs by ingestion of mycotoxin-contaminated products and can cause serious health problems. It was established that this mycotoxin have an hepato, haemato, immuno and genotoxic properties (Maaroufi et al., 1996; Lioi et al., 2004). While most ZEA toxic effects have been quite well investigated, more studies are required to elucidate its mechanisms of toxicity. In order to better understand the molecular mechanisms involved in ZEA toxicity, we used a proteomic approach, to assess the early changes in protein expression initiated by ZEA in HepG2 cells. Our results showed that, after 8h of exposure, cells were still viable and showed a significant change in a number of proteins involved in diverse cellular processes. These changes may provide the early affected functions and yield further insight into mechanisms underlying the involvement of mycotoxin-induced diseases.

Noise induced changes in the expression of p38/MAPK signaling proteins in the sensory epithelium of the inner ear

Noise exposure is a major cause of hearing loss. Classical methods of studying protein involvement have provided a basis for understanding signaling pathways that mediate hearing loss and damage repair but do not lend themselves to studying large networks of proteins that are likely to increase or decrease during noise trauma. To address this issue, antibody microarrays were used to quantify the very early changes in protein expression in three distinct regions of the chinchilla cochlea 2h after exposure to a 0.5-8 kHz band of noise for 2h at 112 dB SPL. The noise exposure caused significant functional impairment 2h post-exposure which only partially recovered. Distortion product otoacoustic emissions were abolished 2h after the exposure, but at 4 weeks post-exposure, otoacoustic emissions were present, but still greatly depressed. Cochleograms obtained 4 weeks post-exposure demonstrated significant loss of outer hair cells in the basal 60% of the cochlea corresponding to frequencies in the noise spectrum. A comparative analysis of the very early (2h post-exposure) noise-induced proteomic changes indicated that the sensory epithelium, lateral wall and modiolus differ in their biological response to noise. Bioinformatic analysis of the cochlear protein profile using "The Database for Annotation, Visualization and Integrated Discovery 2008" (DAVID - http://david.abcc. ncifcrf.gov) revealed the initiation of the cell death process in sensory epithelium and modiolus. An increase in Fas and phosphorylation of FAK and p38/MAPK in the sensory epithelium suggest that noise-induced stress signals at the cell membrane are transmitted to the nucleus by Fas and focal adhesion signaling through the p38/MAPK signaling pathway. Up-regulation of downstream nuclear proteins E2F3 and WSTF in immunoblots and microarrays along with their immunolocalization in the outer hair cells supported the pivotal role of p38/MAPK signaling in the mechanism underlying noise-induced hearing loss.

Proteomic Analysis Uncovers Novel Actions of the Neurosecretory Protein VGF in Nociceptive Processing

Peripheral tissue injury is associated with changes in protein expression in sensory neurons that may contribute to abnormal nociceptive processing. We used cultured dorsal root ganglion (DRG) neurons as a model of axotomized neurons to investigate early changes in protein expression after nerve injury. Comparing protein levels immediately after DRG dissociation and 24 h later by proteomic differential expression analysis, we found a substantial increase in the levels of the neurotrophin-inducible protein VGF (nonacronymic), a putative neuropeptide precursor. In a rodent model of nerve injury, VGF levels were increased within 24 h in both injured and uninjured DRG neurons, and the increase persisted for at least 7 d. VGF was also upregulated 24 h after hindpaw inflammation. To determine whether peptides derived from proteolytic processing of VGF participate in nociceptive signaling, we examined the spinal effects of AQEE-30 and LQEQ-19, potential proteolytic products shown previously to be bioactive. Each peptide evoked dose-dependent thermal hyperalgesia that required activation of the mitogen-activated protein kinase p38. In addition, LQEQ-19 induced p38 phosphorylation in spinal microglia when injected intrathecally and in the BV-2 microglial cell line when applied in vitro. In summary, our results demonstrate rapid upregulation of VGF in sensory neurons after nerve injury and inflammation and activation of microglial p38 by VGF peptides. Therefore, VGF peptides released from sensory neurons may participate in activation of spinal microglia after peripheral tissue injury.

Proteomic Analysis of the Balance between Survival and Cell Death Responses in Cisplatin-Mediated Ototoxicity

Cisplatin, a widely used anticancer drug, preferentially damages outer hair cells (OHCs) of the inner ear. In this study, an antibody microarray was used to identify early changes in protein expression in the rat cochlea induced by cisplatin. Only small changes in hearing thresholds (4-34 dB elevation) were detected two days after cisplatin treatment (12 mg/kg). OHC function, measured by otoacoustic emissions, was slightly depressed (10 dB), and little or no receptor cell loss was observed. However, cisplatin induced large changes in the expression of 19 proteins involved in apoptosis, cell survival, or progression through the cell cycle. Fifteen of the proteins are novel to the study of the inner ear. Immunoblotting confirmed increases in the levels of the pro-survival activating transcription factor 2 (ATF2), of pro-apoptotic serine-threonine protein kinase, receptor interacting protein, and a 70/75 kDa nitrotyrosine bearing doublet of unknown function. Anti-nitrotyrosine antibodies localized these oxidatively damaged proteins to the stereocilia of OHCs, the Golgi-centrosome region of Hensen's cells, nuclei of outer pillar cells, and tunnel crossing fibers innervating OHCs. The results of this proteomic analysis reflect the commencement of ototoxic and cell survival responses before the observation of a significant functional or anatomical loss.

Proteomic analysis of cisplatin-induced cochlear damage: Methods and early changes in protein expression

To identify early changes in protein expression associated with cisplatin ototoxicity, we used two dimensional-difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption-time-of-flight (MALDI-TOF) mass spectrometry to analyze proteins from P3 rat cochleae that were cultured for 3 h with or without 1 mM cisplatin. Replicate analysis of fluorescent images from six gels revealed significant ( p < 0.01) cisplatin-induced changes (greater than 1.5-fold) in expression of 22 cochlear proteins. These include increases in the expression of five proteins, four of which were identified as nucleobindin 1, a nuclear calcium signaling and homeostasis protein (2.1-fold), heterogeneous nuclear ribonucleoprotein C, an RNA processing protein (1.8-fold), a 55 kDa protein that is either endothelial differentiation-related factor 1 or alpha-6 tubulin (1.7-fold), and calreticulin, a calcium binding chaperone of the endoplasmic reticulum (ER, 1.6-fold). The expression of 17 proteins was significantly ( p < 0.01) decreased by greater than 1.5-fold. These include ribonuclease/angiogenin inhibitor 1 (1.6-fold), RAS-like, family 12 (predicted), ras association (RalGDS/AF-6) domain family 5 (4.5-fold), homologous the RAS family of GTPase signaling proteins (2.4-fold), and Protein tyrosine phosphatase domain containing 1 (predicted, 6.1-fold). We identified seven cochlear proteins with either smaller (1.2–1.5-fold) or less significant ( p < 0.05) cisplatin-induced changes in expression. Notably, heat shock 70 kDa protein 5 (Hspa5, Grp78, and BiP), an ER chaperone protein involved in stress response, decreased 1.7-fold. We observed changes consistent with phosphorylation in the level of isoforms of another ER stress-induced protein, glucose-regulated protein Grp58. Changes in cisplatin-induced protein expression are discussed with respect to known or hypothesized functions of the identified proteins.

Comparative proteomic analysis reveals differential expression of Hsp25 following the directed differentiation of mouse embryonic stem cells

Murine embryonic stem (ES) cells can be committed to neural differentiation with high efficiency in culture through the use of feeder- and serum-free media. This system is proving to be an excellent model to study processes involved in ES cell commitment to neural cell fate. We used this approach to generate neurogenic embryoid bodies (NEBs) in a serum-free culture system to perform proteomic analysis of soluble fractions and identify early changes in protein expression as ES cells differentiate. Ten candidate proteins were altered significantly in expression levels. One of the most significant alterations was for the small heat shock protein Hsp25. Three species of Hsp25 are detected in ES cells, and this expression pattern changes during the first 24 h of differentiation until expression is decreased to levels that are barely detectable at 4 days following differentiation. We used immunofluorescence studies to confirm that following ES cell differentiation, expression of Hsp25 becomes excluded from neural precursors as well as other differentiating cells, making it a potentially useful marker of early ES cell differentiation.

β‐Phenylethyl isothiocyanate mediated apoptosis: A proteomic investigation of early apoptotic protein changes

beta-Phenylethyl isothiocyanate (PEITC) is a promising chemopreventative agent found in abundance in watercress (Rorripa nasturtium aquaticum) as its glucosinolate precursor. In the present investigation, we sought to determine the early changes in protein expression that contribute to the mechanism(s) of PEITC-mediated apoptosis in the human hepatoma HepG2 cell line. Such data may invariably identify new molecular targets of PEITC, contributing to a greater understanding of the mechanism(s) by which isothiocyanates mediate apoptotic cascades. Using two-dimensional difference gel electrophoresis we determined the changes in global protein expression between control (0.01% dimethyl sulfoxide) and PEITC (IC50 approximately 20 microM) treated cells after 3 and 6 h, such time points being used to circumvent the effects of caspase mediate proteolysis. Comparison between PEITC treated cells with their respective controls showed that 17 protein spots were differentially expressed. Fourteen of these spots, representing 9 unique proteins, were successfully identified using matrix-assisted laser desorption / ionization-time of flight (MALDI-TOF) and MALDI tandem time of flight (TOF/TOF) mass spectrometry. We observed significant shifts in isoelectric points on two-dimensional electrophoresis gels in heat shock 27 kDa protein (HSP27), macrophage migration inhibition factor and heterogeneous nuclear ribonucleoprotein K (hnRNP K) indicating that these proteins are probably involved in protein phosphorylation. Indeed, hnRNP K was determined to be phosphorylated on key tyrosine residues as assessed by using antiphosphotyrosine antibodies. In separate experiments we also showed that c-myc is up-regulated in PEITC treated cells, and since hnRNP K is reported to induce overexpression of c-myc, we proposed that PEITC-induced apoptosis may involve a c-myc dependent apoptotic pathway in HepG2 cells.

Early Changes in Protein Expression Detected by Mass Spectrometry Predict Tumor Response to Molecular Therapeutics

Biomarkers that predict therapeutic response are essential for the development of anticancer therapies. We have used matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to directly analyze protein profiles in mouse mammary tumor virus/HER2 transgenic mouse frozen tumor sections after treatment with the erbB receptor inhibitors OSI-774 and Herceptin. Inhibition of tumor cell proliferation and induction of apoptosis and tumor reduction were predicted by a >80% reduction in thymosin beta4 and ubiquitin levels that were detectable after 16 hours of a single drug dose before any evidence of in situ cellular activity. These effects were time- and dose-dependent, and their spatial distribution in the tumor correlated with that of the small-molecule inhibitor OSI-774. In addition, they predicted for therapeutic synergy of OSI-774 and Herceptin as well as for drug resistance. These results suggest that drug-induced early proteomic changes as measured by MALDI-MS can be used to predict the therapeutic response to established and novel therapies.