Differential Proteomic Expression Research Articles

Mechanoregulation of titanium dioxide nanoparticles in cancer therapy.

Titanium dioxide (TiO2) nanoparticles (NPs), first developed in the 1990s, have been applied in numerous biomedical fields such as tissue engineering and therapeutic drug development. In recent years, TiO2-based drug delivery systems have demonstrated the ability to decrease the risk of tumorigenesis and improve cancer therapy. There is increasing research on the origin and effects of pristine and doped TiO2-based nanotherapeutic drugs. However, the detailed molecular mechanisms by which drug delivery to cancer cells alters sensing of gene mutations, protein degradation, and metabolite changes as well as its associated cumulative effects that determine the microenvironmental mechanosensitive metabolism have not yet been clearly elucidated. This review focuses on the microenvironmental influence of TiO2-NPs induced various mechanical stimuli on tumor cells. The differential expression of genome, proteome, and metabolome after treatment with TiO2-NPs is summarized and discussed. In the tumor microenvironment, mechanosensitive DNA mutations, gene delivery, protein degradation, inflammatory responses, and cell viability affected by the mechanical stimuli of TiO2-NPs are also examined.

Abstract 657: The comparison of calcium-induced differentiation in colonoid cultures derived from the normal human colon tissue and colonic adenomas

Abstract Introduction: Previous ex vivo studies with colon cancer cell lines and human colon adenoma derived colonoid cultures have demonstrated that calcium and Aquamin (a calcium-rich, multi-mineral natural product) suppressed proliferation and induced differentiation. Aquamin was effective at a lower dose as compared to calcium. Methods: Colonoid cultures were established from histologically-normal human colon tissue and maintained in a low-calcium (0.25 mM) medium (control) or supplemented with an amount of calcium or Aquamin (1.5 mM), that was shown previously to induce differentiation in human adenoma colonoids. Quantitative immunohistochemistry and differential proteomic expression were assessed after 4 weeks of in vitro intervention with calcium or Aquamin, as performed in the past with adenoma-derived cultures. Results: The normal colonoids underwent differentiation as indicated by morphological features, a low proliferative index and high-level expression of cytokeratin 20 (CK20) under control conditions. Only modest additional changes were seen in these parameters with either calcium alone or Aquamin (providing up to 3.0 mM calcium). This was an altered response as compared to adenoma-derived colonoids which differentiated in response to calcium or Aquamin at 1.5mM calcium. In spite of this, proteomic analysis and immunohistochemistry of normal colonoids revealed that both interventions induced strong up-regulation of several proteins involved in cell-cell and cell-matrix interaction and in barrier formation. Among these were cadherins, keratins, claudins, CAECAMS, laminin subunits, and desmosomal proteins. Transmission electron microscopy showed an increase in desmosomes in response to intervention. Conclusion: These findings suggest that normal colonoids were inherently more calcium-sensitive than adenoma colonoids and were readily differentiated at a lower calcium concentration as present in the control. Table:Quantitative expression of immunohistochemical markers in colonoid culturesHuman Colonic Adenoma (n=3)Normal Colon (n=3)IHC MarkersControlCalcium 1.5mMAquamin 1.5mMControlCalcium 1.5mMAquamin 1.5mMKi6784.8±9.250.1±14.8*41.8±23.6*33.2±26.127.5±26.827.1±24.3CK200.23±0.130.54±0.13*0.53±0.10*0.78±0.190.73±0.220.76±0.20E-Cadherin0.44±0.060.70±0.09*0.70±0.07*0.49±0.100.61±0.09*0.58±0.08**reflects significance as compared to the corresponding control (p<0.05).Each condition has 20-30 crypts in colonoid culture per adenoma or normal colon. Citation Format: Muhammad N. Aslam, Shannon D. McClintock, Areeba H. Rizvi, Durga Attili, Shailja Pandya, Humza Rehman, Daniyal M. Nadeem, D. Kim Turgeon, James Varani. The comparison of calcium-induced differentiation in colonoid cultures derived from the normal human colon tissue and colonic adenomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 657.

Differential expression of leaf proteome of tolerant and susceptible maize (Zea mays L.) genotypes in response to multiple abiotic stresses.

In the present work, tropical maize genotypes were evaluated for multiple stresses (drought × low-N and waterlogging × low-N) applied simultaneously to 30-day-old maize seedlings. Two-dimensional gel electrophoresis was used to examine the protein changes induced by combined stress, in leaves, of tolerant and susceptible genotypes. Moreover, physiological and biochemical parameters were assessed to understand the physiological status of tolerant and susceptible genotypes under combined stress. The results show that up-regulated proteins of the tolerant genotype have a significant role in activating defense response, restoration of plant growth, and to maintain metabolic homeostasis under stressful conditions. Therefore, they contribute to improve and maintain the state of acclimation of the genotype under stress. Alternatively in the susceptible genotype, the up-regulated proteins are representative biomarkers of stress or are involved in the defense against pathogens and efforts to maintain energy metabolism. Thus, protecting the survival of the genotype under multiple stress conditions. We conclude that depending on the given stress treatment, tolerant and susceptible genotypes differed in stress-enduring approaches. Therefore, the study provides insight to comprehend the response of tolerant and susceptible genotypes under combined stress conditions, which could be valuable for further research and will demonstrate that it is advantageous to select combined stress-tolerant genotypes.

Inactivation of ntcA gene revealed differential proteome expression and induction of some hypothetical proteins in the cyanobacterium Anabaena sp. PCC 7120 and its derivative ntcA mutant under different levels of calcium

Calcium is an important macronutrient for both prokaryotes and eukaryotes. It acts as an important second messenger mediating rapid response to environmental conditions. The present investigation deals with proteome profiling of Anabaena 7120 and its derivative ntcA mutant in response to varied calcium doses (0, 1 and 10 mM CaCl2). Concentration of 1 mM CaCl2 salt was the optimum concentration whereas 10 mM CaCl2 was the inhibitory concentration for both the wild type and mutant strains. The results showed highly significant alteration in terms of protein abundance and differential response related to key processes of photosynthesis, energy and metabolism, nitrogen metabolism, oxidative and antioxidative defence, transport and signalling and fatty acid metabolism. In the wild type proteins related to photosynthesis and nitrogen metabolism showed upregulation at 1 mM CaCl2 concentration while antioxidative defence related proteins were down-regulated. In the mutant however, proteins related to photosynthesis and nitrogen metabolism exhibited severe down-regulation. Some hypothetical proteins were also realized during proteome analysis. Overall, our results suggested that NtcA have a potential role in regulation of calcium ion dependent key processes underlying in various metabolic activities of the cyanobacterium Anabaena 7120.

Proteomic Identification of Biomarkers Associated with Eating Control and Bariatric Surgery Outcomes in Patients with Morbid Obesity.

The current therapeutics of morbid obesity could be significantly improved after the identification of novel biomarkers associated with the food addiction endophenotype of obesity and with bariatric surgery outcomes. We applied differential expression proteomics and enzyme-linked immunosorbent confirmatory assays to identify (a) proteins that varied according to loss of control over eating in morbidly obese patients and (b) proteins that varied between normoweight controls and patients before and 1year after bariatric surgery. Clusterin was the only protein that consistently varied according to eating control in patients. Patients showed increased levels of serum amyloid P protein, apolipoprotein A4, serotransferrin, complement factors B and C3 and haptoglobin with respect to controls; the levels of all these proteins tended to return to control values 1year after surgery. In contrast, apolipoprotein A1 and transthyretin were initially downregulated in patients and were scarcely changed by surgery. Leucine-rich alpha-2-glycoprotein was markedly increased in patients only after surgery. Clusterin could be of interest as a putative biomarker for food addiction diagnosis in people with morbid obesity. In addition, postsurgical normalization of the proteins initially dysregulated in obese subjects might help monitor clinical improvements after surgery, while lasting or newly detected alterations (i.e., those affecting transthyretin and leucine-rich alpha-2-glycoprotein) could reflect partial refractoriness and/or contribute to the early prediction of clinical problems.

Proteomic analysis to investigate color changes of chilled beef longissimus steaks held under carbon monoxide and high oxygen packaging

This study investigated the proteome basis for color stability variations in beef steaks packaged under two modified atmosphere packaging (MAP) methods: HiOx-MAP (80% O2/20% CO2) and CO-MAP (0.4% CO/30% CO2/69.6% N2) during 15 days of storage. The color stability, pH, and sarcoplasmic proteome analysis of steaks were evaluated on days 0, 5, 10 and 15 of storage. Proteomic results revealed that the differential expression of the sarcoplasmic proteome during storage contributed to the variations in meat color stability between the two MAP methods. Compared with HiOx-MAP steaks, some glycolytic and energy metabolic enzymes important in NADH regeneration and antioxidant processes, antioxidant peroxiredoxins (thioredoxin-dependent peroxide reductase, peroxiredoxin-2, peroxiredoxin-6) and protein DJ-1 were more abundant in CO-MAP steaks. The over-expression of these proteins could induce CO-MAP steaks to maintain high levels of metmyoglobin reducing activity and oxygen consumption rate, resulting in CO-MAP steaks exhibiting better color stability than HiOx-MAP steaks during storage.

Differential expression of proteome in aqueous humor in patients with and without glaucoma

Abstract Objective To determine quantitative and qualitative differences of aqueous humor proteome in patients with and without glaucoma. Method Observational, descriptive and cross-sectional study of 12 patients (8 men; 4 women) with and without glaucoma. There are 3 groups of minority proteins with serum equimolar contribution of each of the patients. Specimens were obtained during cataract surgery from patients without glaucoma (performed with retrobulbar anesthesia [cataract retrobulbar patient – CRP; n = 4] or topical [cataract topical patient – CTP; n = 4]), or from patients with glaucoma (performed with retrobulbar anesthesia [glaucoma retrobulbar patient – GRP; n = 4]). The humor proteome samples were frozen at −80 °C until processing by trypsin digestion to obtain tryptic peptides, and then performing liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) to obtain the proteome and its differential expression between groups. Statistical analysis was performed using the SPSS v.17 program. Results The study included 12 patients, aged (mean ± standard deviation) 74.50 ± 9.53 years. Concentrations obtained: 0.48 ± 0.25 μg/μl for CRP, 0.28 ± 0.04 μg/μl for CTP, and 0.35 ± 0.16 μg/μl for GRP. A total of 309 proteins were identified, of which 205, 210, and 182 were in CRP, CTP, and GRP, respectively. A total of 114 proteins were common to all three groups, 50 were exclusive to CRP, 58 to CTP, and 27 to GRP. Conclusions In this pilot study, a quantitative difference was found in the protein expression of humor among patients with glaucoma, there being 27 proteins unique to patients with glaucomatous disease.

Physiological and proteomic responses to corticosteroid treatments in Eurasian perch, Perca fluviatilis: Investigation of immune-related parameters

The comparative effects of cortisol and 11-deoxycorticosterone (DOC), two major corticosteroids in fish, have yet received little attention in teleosts. We evaluated the proteomic and immune responses of Eurasian perch to chronic corticosteroid treatments. We implanted immature perch with cortisol (80mg/kg) or DOC (4mg/kg) and measured the proportions of blood leucocytes, immune indices in the plasma, spleen and liver (complement and lysozyme activity, total immunoglobulin and immune gene expression in the tissues) and differential proteome expression (corticosteroid versus control) in the liver and the spleen on days 2, 4 and 14 post-treatment. Implantation of cortisol decreased the ratio of blood leucocytes and depressed Ig levels in both organs while DOC modulated the proportion of leucocyte sub-populations (increase in lymphocytes and decrease in granulocytes). In contrast, the innate humoral immunity was not strongly influenced by any of corticosteroid implants. The only immune parameter that was significantly affected was lysozyme, after DOC treatment. A number of proteins were differentially regulated by these hormones and some were identified in the liver (21 for cortisol and 8 for DOC) and in the spleen (10 for cortisol and 10 for DOC). None of the proteins was directly linked to immunity, except the natural killer enhancing factor, which was repressed by cortisol in the spleen. Our results also confirm that the proteins involved in energetic and glucose metabolism are affected by corticosteroids. Furthermore, these corticosteroids differently regulate immune status in Eurasian perch and they primarily impact leucocytes, as opposed to innate immune function.

Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses.

Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS) via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs) that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular homeostasis and metabolic balance under stress. In conclusion, our results provide a better understanding of the global metabolic adaptations of B. abortus associated with distinct environmental stresses. The identification of proteins necessary for stress resistance is crucial toward elucidating the infectious process in order to control brucellosis, and may facilitate the discovery of novel therapeutic targets and effective vaccines.

Differential proteome expression analysis of androgen-dependent and -independent pathways in LNCaP prostate cancer cells

Prostate cancer (PC) is one of the leading causes of cancer death in men. It commonly develops in older males, but the number of younger men diagnosed with the disease has increased in recent years. Hormone therapies, such as chemical and surgical methods that inhibit androgen synthesis or androgen receptor (AR) activation, have been used for advanced disease. However, castration-resistant PC (CRPC), which exhibits androgen-independent mechanisms for activating AR, develops after a few years of such treatment and no therapy is available. In this study, we examined differences in the proteomes associated with the androgen-dependent (DHT treatment) and -independent (FSK, forskolin treatment) AR signaling conditions in LNCaP prostate cancer cells. Moreover, we used EPI-001, which inhibits AR-mediated transcriptional activity, to examine whether the observed differences in protein expression were directly affected by AR-mediated mechanisms. A total of 213 protein spots were matched in our 2-dimensional gel electrophoresis (2DE) analysis and 8 proteins with significant expression changes in our 5 different treatment groups were identified by mass spectrometry. Among these proteins, expression levels of PEPCK-M, catalase, tubulin alpha chain, alpha-enolase, and endoplasmic reticulum resident protein 29 were significantly altered by DHT and the levels of HSP 90 and EF-Tu were changed by FSK. These changes were blocked by EPI-001 in DHT-regulated proteins, PEPCK-M, catalase, and tubulin alpha chain and FSK-regulated EF-Tu protein. The results from our immunohistochemical analysis using in vivo xenograft models were consistent with the 2DE data. We therefore report the first identification of differences in proteins that are significantly regulated under androgen-dependent and -independent AR signaling conditions. Our findings could suggest a possible molecular mechanism through which AR is activated in the absence and/or presence of androgen, and might help explain the inhibitory action of EPI-001 on CRPC.

Phenotypic and proteomic analysis of positively regulated gellan biosynthesis pathway in Sphingomonas elodea

ABSTRACTSphingomonas elodea is a Gram-negative bacterium capable of producing ‘gellan gum’ exopolysaccharide that is the most extensively studied expolysaccharides of microbial origin. In this study, we investigated the phenotypic and proteomic alterations in S. elodea by homogeneously expressing both gelA and gelN involved in positive regulation and extracellular secretion of metabolites in gellan biosynthesis, respectively. Expression of six histidine-tagged GelA and GelN was determined by Western blot analysis. Successful expression of GelA and GelN resulted in both morphological changes of colonies and enhanced secretion of gellan into the growth medium (GelA, 21.2% more and GelN, 48.3% more) overexpressed compared to the wile-type. Comparative two-dimensional gel electrophoresis analysis revealed a differential proteome expression in S. elodea overexpressing GelA and GelN. Proteins up- or down-regulated by GelA and GelN overexpression were found to be mainly sugar transportation proteins, two-component regulatory proteins, and proteins involved in secretion pathways. The results suggest that the effect of GelA and GelN overexpression on gellan biosynthesis might be mainly caused by increased transportation of sugar units or enhanced exportation of gellan.

Differential proteomics of the synovial membrane between bilateral and unilateral knee osteoarthritis in surgery‑induced rabbit models.

The present study investigated the differential proteomics of synovial membranes between bilateral and unilateral anterior cruciate ligament transection (ACLT) in rabbits with knee osteoarthritis (KOA), in order to elucidate the pathological biomarkers of different degrees of KOA. A total of 6New Zealand rabbits were randomly divided into groups AandB (three rabbits per group). The two groups were subjected to bilateral and unilateral ACLT, respectively. A total of 6weeks following surgery, proteins were extracted from the knee joint synovial membranes of KOA rabbits and were separated by two‑dimensional polyacrylamide gel electrophoresis. The differentially expressed proteins in the OA synovial membranes were selected for further analysis by linear ion trap‑Fourier transform ion cyclotron resonance mass spectrometry. Ten protein spots were identified to be different between the synovial membranes of the bilateral and unilateral KOA rabbits. Protein disulfide‑isomerase and creatine kinaseM‑type were identified in the unilateral KOA rabbit synovial membranes. Serum albumin (three spots), lumican, α‑2‑HS‑glycoprotein and three uncharacterized proteins were identified in the synovial membranes of the bilateral KOA rabbits. The differential proteomic expression demonstrated the different biomarkers associated with bilateral and unilateral KOA, and indicated that spontaneous and secondary KOA require diverse methods of treatment; thus the underlying mechanism of KOA requires further investigation.

Bioinformatic and Functional Analysis of Venom from the Jewel Wasp Ampulex compressa

The parasitoid jewel wasp Ampulex compressa exploits its host, the American cockroach Periplaneta americana, as a food source for its young. The host is subdued through direct envenomation into the central nervous system, inducing a days‐long “zombie‐like state” referred to as hypokinesia. Hypokinesia is a specific, venom‐induced behavioral state characterized by suppression of the escape response and reduced spontaneous walking, leaving other motor functions intact. This condition is reversible, provided that egg deposition is prevented. To facilitate elucidation of biochemical mechanisms underlying venom‐induced hypokinesia, we developed a comprehensive inventory of the venom by combining: 1) next‐generation RNA sequencing, transcriptomic analysis of venom gland components, and 2) proteomics of venom apparatus extracts and whole milked venom via mass spectroscopy‐based Multi‐Dimensional Protein Identification Technology. These analyses yielded a total of 201 proteins and peptides in the venom, 105 with Pfam domains, 146 similar to other proteins in the NCBI‐nr or Uniprot databases, and 45 novel proteins absent in global databases. A. compressa venom proteins include members of the M13 family of proteases (11), phospholipase A2 isoforms (10), along with hyaluronidase, chitinase, icarapin, venom acid phosphatase, serpins, and signaling peptides including tachykinin, corazonin, and myosuppressin. Differential expression analysis and proteomics of the two major tissues of the venom apparatus ‐ venom sac and venom gland ‐identified tissue‐specific expression of key venom components.We show that A. compressa venom tachykinins (AcVTK) are able to activate the cockroach brain tachykinin receptor with high affinity (EC50 ~1 nM) in vitro. Injection of synthetic AcVTK into the subesophageal ganglion, an established target of the wasp venom, increases escape response threshold for one hour post‐treatment. These results indicate that tachykinin may participate in the behavioral changes resulting from envenomation of cockroach cerebral ganglia.We isolated and characterized two novel, paralogous venom sac peptides found in milked venom. These peptides are alpha‐helical, amphipathic, and constitute a new family of venom toxins termed ampulexins. Injection of the most abundant venom peptide, ampulexin‐1, into the subesophageal ganglion of cockroaches resulted in a short‐term increase in escape threshold.Our findings show that the venom of A. compressa is a rich collection of both well‐known and novel, pharmacologically diverse compounds. Our study provides new and comprehensive information on A. compressa venom contents that inform hypotheses regarding its mode of action.

Proteome profiling reveals regional protein alteration in cerebrum of common marmoset (Callithrix jacchus) exposed to methylmercury.

Methylmercury (MeHg) is known to selectively damage the calcarine and precentral cortices along deep sulci and fissures in adult cases, but the detailed mechanism is still unclear. This study aims to identify and analyze the differential proteome expression in two regions of the cerebrum (the frontal lobe and the occipital lobe including the calcarine sulcus) of the common marmoset exposed to MeHg using a shot-gun proteomic approach. A total of 1045 and 1062 proteins were identified in the frontal lobe (FL) and occipital lobe (OL), of which, 62 and 89 proteins were found significantly changed with MeHg exposure. Functional enrichment/depletion analysis showed that the lipid metabolic process and proteolysis were affected in both two lobes. Functional changes in FL were characterized in cell cycle and cell division, sulfur compound metabolic process, microtubule-based process and glycerolipid metabolic process. In comparison, proteins were enriched in the functions of transport, carbohydrate metabolic process, chemical caused homeostasis and regulation of body fluid levels in OL. Pathway analysis predicted that vasopressin-regulated water reabsorption was disturbed in MeHg-treated FL. Our results showed that MeHg induced regional specific protein changes in FL and OL but with similar endpoint effects such as energy diminish and disruption of water transport. APOE and GPX1 were shown to be possible key proteins targeted by MeHg leading to multiple functional changes in OL. This is the first report of the whole proteome changes of primate cerebrum for MeHg neurotoxicity, and the results will contribute to the understanding of molecular basis of MeHg intoxication in humans.

Differential proteomic expression of human placenta and fetal development following e-waste lead and cadmium exposure in utero

Prenatal exposure to lead (Pb) and cadmium (Cd) has been associated with a series of physiological problems resulting in fetal growth restriction. We aimed to investigate the effects of Pb and Cd exposure on placental function and the potential mechanisms involved in fetal development. Placental specimens and questionnaires were collected from an e-waste area and a reference area in China. Two-dimensional electrophoresis combined with MALDI-TOF-MS/MS and molecular network relationship were performed to analyze differentially expressed proteins using a compositing sample pool. Compared with the reference group, the exposed group exhibited significantly higher levels of placental Pb and Cd (p<0.01), shorter body length and higher gestational age (p<0.01). After bivariate adjustment in a linear regression model, decreases of 205.05g in weight and 0.44cm in body length were associated with a 10ng/g wt increase in placental Cd. Pb showed a negative trend but lacked statistical significance. Proteomic analysis showed 32 differentially-expressed proteins and were predominantly involved in protein translocation, cytoskeletal structure, and energy metabolism. Fumarate hydratase was down-regulated in the exposed placenta tissues and validated by ELISA. Alterations in placental proteome suggest that imbalances in placental mitochondria respiration might be a vital pathway targeting fetal growth restriction induced by exposure to Cd.

Journal Digest

Journal Digest

Feasibility of investigating differential proteomic expression in depression: implications for biomarker development in mood disorders.

The objective of this study was to determine whether proteomic profiling in serum samples can be utilized in identifying and differentiating mood disorders. A consecutive sample of patients with a confirmed diagnosis of unipolar (UP n=52) or bipolar depression (BP-I n=46, BP-II n=49) and controls (n=141) were recruited. A 7.5-ml blood sample was drawn for proteomic multiplex profiling of 320 proteins utilizing the Myriad RBM Discovery Multi-Analyte Profiling platform. After correcting for multiple testing and adjusting for covariates, growth differentiation factor 15 (GDF-15), hemopexin (HPX), hepsin (HPN), matrix metalloproteinase-7 (MMP-7), retinol-binding protein 4 (RBP-4) and transthyretin (TTR) all showed statistically significant differences among groups. In a series of three post hoc analyses correcting for multiple testing, MMP-7 was significantly different in mood disorder (BP-I+BP-II+UP) vs controls, MMP-7, GDF-15, HPN were significantly different in bipolar cases (BP-I+BP-II) vs controls, and GDF-15, HPX, HPN, RBP-4 and TTR proteins were all significantly different in BP-I vs controls. Good diagnostic accuracy (ROC-AUC⩾0.8) was obtained most notably for GDF-15, RBP-4 and TTR when comparing BP-I vs controls. While based on a small sample not adjusted for medication state, this discovery sample with a conservative method of correction suggests feasibility in using proteomic panels to assist in identifying and distinguishing mood disorders, in particular bipolar I disorder. Replication studies for confirmation, consideration of state vs trait serial assays to delineate proteomic expression of bipolar depression vs previous mania, and utility studies to assess proteomic expression profiling as an advanced decision making tool or companion diagnostic are encouraged.

Differential proteomic and tissue expression analyses identify valuable diagnostic biomarkers of hepatocellular differentiation and hepatoid adenocarcinomas

The exact discrimination of lesions with true hepatocellular differentiation from secondary tumours and neoplasms with hepatocellular histomorphology like hepatoid adenocarcinomas (HAC) is crucial. Therefore, we aimed to identify ancillary protein biomarkers by using complementary proteomic techniques (2D-DIGE, label-free MS). The identified candidates were immunohistochemically validated in 14 paired samples of hepatocellular carcinoma (HCC) and non-tumourous liver tissue (NT). The candidates and HepPar1/Arginase1 were afterwards tested for consistency in a large cohort of hepatocellular lesions and NT (n = 290), non-hepatocellular malignancies (n = 383) and HAC (n = 13). Eight non-redundant, differentially expressed proteins were suitable for further immunohistochemical validation and four (ABAT, BHMT, FABP1, HAOX1) for further evaluation. Sensitivity and specificity rates for HCC/HAC were as follows: HepPar1 80.2%, 94.3% / 80.2%, 46.2%; Arginase1 82%, 99.4% / 82%, 69.2%; BHMT 61.4%, 93.8% / 61.4%, 100%; ABAT 84.4%, 33.7% / 84.4%, 30.8%; FABP1 87.2%, 95% / 87.2%, 69.2%; HAOX1 95.5%, 36.3% / 95.5%, 46.2%. The best 2×/3× biomarker panels for the diagnosis of HCC consisted of Arginase1/HAOX1 and BHMT/Arginase1/HAOX1 and for HAC consisted of Arginase1/FABP1 and BHMT/Arginase1/FABP1. In summary, we successfully identified, validated and benchmarked protein biomarker candidates of hepatocellular differentiation. BHMT in particular exhibited superior diagnostic characteristics in hepatocellular lesions and specifically in HAC. BHMT is therefore a promising (panel based) biomarker candidate in the differential diagnostic process of lesions with hepatocellular aspect.

Differential Expression of Durum Wheat Gluten Proteome under Water Stress during Grain Filling

Environmental stress during grain filling may affect wheat protein composition, thus influencing its final quality. A proteomic approach was used to evaluate changes in storage protein composition under water stress of two Italian durum wheat (Triticum turgidum ssp. durum) cultivars, Ciccio and Svevo. The high-molecular-weight glutenin region increased progressively in both cultivars and under two water regimens. The L48-35 region, corresponding to low-molecular-weight (LMW) glutenin subunits, increased slightly during grain development and decreased under water stress in both cultivars. In particular, an s-type LMW related to superior technological quality was down-expressed in the early-mid period in Svevo and in the mid-late period in Ciccio. Finally, the L<35 region, corresponding to gliadin-like proteins, decreased slightly during grain development and increased under stress in both cultivars. Several α-gliadins, associated with immunological potential, increased their expression under water stress, especially in Svevo in the early-mid stage of grain filling.

Proteomic and gene expression analysis of zebrafish brain undergoing continuous light/dark stress.

Several organisms irrespective of their complexity in structure and function have an inbuilt circadian rhythm. Zebrafish could be used as an alternate model animal in sleep research as it exhibits similar sleep-wake dynamics as mammals and Drosophila. In this study, we have analysed the adult zebrafish brain for its differential proteome and gene expression during perturbed light/dark cycle. A total of 53 and 25 proteins including sncb, peroxiredoxins and TCR alpha were identified based on two-dimensional gel electrophoresis Fourier transform mass spectrometer/ion trap tandem mass spectrometer and differential in-gel electrophoresis MALDI TOF MS/MS analysis, respectively, with at least 1.5-fold changes between the control and experimental brains. Real time-polymerase chain reaction revealed that many circadian pathway-associated genes, such as per1b, bmal1b, cry1b, bmal2 and nr1d2, were differentially regulated during continuous light/dark exposures. It is hypothesized that the differential regulation of these genes might lead to the discovery of potential diagnostic markers for gaining insight into the light/dark-associated stress in humans.