RNAIII-inhibiting peptide improves efficacy of clinically used antibiotics in a murine model of staphylococcal sepsis

RNAIII-inhibiting peptide (RIP, YSPWTNF-NH2) is a quorum-sensing peptide inhibitor that prevents Staphylococcus aureus toxin production and biofilm formation. A mouse sepsis model was used to test the efficacy of RIP alone or in combination with conventional antibiotics in suppressing S. aureus-induced sepsis. Mice were injected intravenously with 3.0x10(6)CFU of S. aureus ATCC 25923 or with 3.0x10(6)CFU of S. aureus strain Smith diffuse. All animals were randomized to receive intravenously isotonic sodium chloride solution as a control, or 20 mg/kg RIP alone or combined with 20 mg/kg cefazolin, 10 mg/kg imipenem, or 10 mg/kg vancomycin immediately or 6 h after bacterial challenge. Main outcome measures were bacteremia and lethality. All compounds reduced lethality when compared to controls. Although, in general combined-treated groups had significant lower bacterial counts when associated to singly-treated groups only the combination between RIP and vancomycin with respect to cefazolin gave a statistically significant decrease in the lethality rate. Lowest lethality rates (10%) and bacteremia (<10(2)CFU/ml) were obtained when RIP was administered in combination with vancomycin. Because RIP can be synergistic with current antibiotic therapies and help to reduce S. aureus exotoxins production, it can be considered a promising agent to associate with antibiotics for further clinical research into treatment of sepsis.     

Antibiotic susceptibility of clinically relevant anaerobes in Estonia from 1999 to 2001

At present little or no data is available regarding the resistance profiles of anaerobic bacteria in relation to the general usage of antibiotics. The objective of this study was to assess whether any potential relationship exists between the dynamics of antibiotic resistance of anaerobic bacteria and the consumption of antibiotics during the last 3 years within the Estonian population. In total, 416 anaerobic isolates were investigated from various clinical samples. The anaerobes were isolated on Wilkins-Chalgren Agar, incubated in an anaerobic glove box and identified by standard methods. beta-lactamase negative strains were tested against metronidazole, clindamycin, benzylpenicillin and the positive strains were further tested against metronidazole, clindamycin, and ampicillin/sulbactam by E-tests. The results of the susceptibility tests were interpreted according to the current criteria of NCCLS. Data from the Estonian State Agency of Medicines was used to assess the antibiotic consumption rate in the population (Defined Daily Doses per 1000 inhabitants annually). The following species of anaerobes were isolated: B. fragilis group, Bacteroides sp., Fusobacterium sp., Porphyromonas sp., Prevotella sp., Peptostreptococcus sp., in addition to various unidentified Gram-positive rods. Metronidazole resistance was not found among Gram-negative bacteria despite a relatively high consumption of this antimicrobial agent in Estonia. Only ampicillin/sulbactam demonstrated excellent in vitro activity against all anaerobes. Unexpectedly despite a relatively low rate of consumption of clindamycin a high rate of resistance to this agent occurred; a similar situation was noted for penicillin. In the present study we did not observe a relationship between the changes in antibiotic consumption (DDD/1000) rate and the resistance pattern of anaerobic bacteria to metronidazole, clindamycin, penicillin and ampicillin/sulbactam during a 3-year follow-up period. High resistance to penicillin among some species and also to clindamycin is similar to the global trend and argues for limited use of these antibiotics in empirical treatment. We would suggest that monitoring of local susceptibility pattern is necessary for the selection of initial empirical therapy.     

Current issues with acetaminophen hepatotoxicity--a clinically relevant model to test the efficacy of natural products

There is a significant need to evaluate the therapeutic potential of natural products and other compounds purported to be hepatoprotective. Acetaminophen-induced liver injury, especially in mice, is an attractive and widely used model for this purpose because it is both clinically relevant and experimentally convenient. However, the pathophysiology of liver injury after acetaminophen overdose is complex. This review describes the multiple steps and signaling pathways involved in acetaminophen-mediated cell death. The toxicity is initiated by the formation of a reactive metabolite, which depletes glutathione and binds to cellular proteins, especially in mitochondria. The resulting mitochondrial oxidant stress and peroxynitrite formation, in part through amplification by c-jun-N-terminal kinase activation, leads to mitochondrial DNA damage and opening of the mitochondrial permeability transition pore. Endonucleases from the mitochondrial intermembrane space and lysosomes are responsible for nuclear DNA fragmentation. Despite the oxidant stress, lipid peroxidation is not a relevant mechanism of injury. The mitochondrial dysfunction and nuclear DNA damage ultimately cause oncotic necrotic cell death with release of damage-associated molecular patterns that trigger a sterile inflammatory response. Current evidence supports the hypothesis that innate immune cells do not contribute to injury but are involved in cell debris removal and regeneration. This review discusses the latest mechanistic aspects of acetaminophen hepatotoxicity and demonstrates ways to assess the mechanisms of drug action and design experiments needed to avoid pitfalls and incorrect conclusions. This review should assist investigators in the optimal use of this model to test the efficacy of natural compounds and obtain reliable mechanistic information.     

Further characterization of a clinically relevant model of melanoma metastasis and an effective vaccine

A major problem in evaluating the effectiveness of tumor cell vaccination and other biological therapies is the variability of experimental models. In this study we have further developed and characterized a model for metastatic melanoma that approximates the major clinical stages of metastatic dissemination: stage I-growth of the primary (local) tumor, stage II-dissemination to regional lymph nodes, and stage III-metastasis to distant organs (lungs). C57BL/6 mice were challenged subcutaneously with B16 F10 murine melanoma cells in the midtail, and within 3 weeks 100% of the mice had local tumors growing in their tails. By 5–7 weeks after challenge, most of the mice had developed metastases to the inguinal lymph nodes and subsequently had metastatic colonies in the lungs and in the bone marrow. Preimmunization of mice with a formalinized extracellular antigen vaccine, derived from B16F10 melanoma cells, provided partial inhibition of the growth of the primary melanoma tumors, as well as reducing the number of metastases to the regional (inguinal) lymph nodes and lungs along with concomitantly increasing survival time. This model for melanoma metastasis provides a reasonable and reproducible test system for the study of anti-melanoma immunity and the different cellular and humoral mechanisms involved.This work was supported in part by National Institutes of Health grants R37 CA45148 and R30 CA13943     

Propofol is cardioprotective in a clinically relevant model of normothermic blood cardioplegic arrest and cardiopulmonary bypass

The general anesthetic propofol has been shown to be cardioprotective. However, its benefits when used in cardioplegia during cardiac surgery have not been demonstrated. In this study, we investigated the effects of propofol on metabolic stress, cardiac function, and injury in a clinically relevant model of normothermic cardioplegic arrest and cardiopulmonary bypass. Twenty anesthetized pigs, randomized to propofol treatment (n = 8) and control (n = 12) groups, were surgically prepared for cardiopulmonary bypass (CPB) and cardioplegic arrest. Doses of warm blood cardioplegia were delivered at 15-min intervals during a 60-min aortic cross-clamped period. Propofol was continuously infused for the duration of CPB and was therefore present in blood cardioplegia. Myocardial biopsies were collected before, at the end of cardioplegic arrest, and 20 mins after the release of the aortic cross-clamp. Hemodynamic parameters were monitored and blood samples collected for cardiac troponin I measurements. Propofol infusion during CPB and before ischemia did not alter cardiac function or myocardial metabolism. Propofol treatment attenuated the changes in myocardial tissue levels of adenine nucleotides, lactate, and amino acids during ischemia and reduced cardiac troponin I release on reperfusion. Propofol treatment reduced measurable hemodynamic dysfunction after cardioplegic arrest when compared to untreated controls. In conclusion, propofol protects the heart from ischemia-reperfusion injury in a clinically relevant experimental model. Propofol may therefore be a useful adjunct to cardioplegic solutions as well as being an appropriate anesthetic for cardiac surgery.     

Effects of ischemic preconditioning and adenosine pretreatment on myocardial function and energetics in a clinically relevant model

Preconditioning (PC) is a potential approach to myocardial protection. We hypothesize that brief ischemia or adenosine given prior to an extended period of warm ischemia may prevent myocardial stunning by altering myocardial metabolism. Using a global ischemia model, 19 dogs were subjected to no PC(control), two episodes of ischemia (2 min of global ischemia followed by 3 min of reperfusion) (IPC), or 30 min of pulmonary artery adenosine infusion (AP), to a maximum of 350 microg/kg/min, followed by 20 min of global warm ischemia on cardiopulmonary bypass. Left ventricular pressure-volume loops and myocardial oxygen consumption (MVO(2)) were measured at baseline and after 60 min of reperfusion, on right heart bypass. All data were compared between baseline and reperfusion. Load independent left ventricular function, defined as preload recruitable stroke work (PRSW), decreased in control and IPC groups (72+/-7%, 71+/-12%, respectively). AP blunted the decrease in PRSW (45+/-9%, p<.05 compared to control). Myocardial energetic conversion efficiency, defined as the slope of the MVO(2)-Stroke work relationship was not significantly changed for controls (2.17+/-0.47 to 1.84+/-0.68) and IPC (2.99+/-0.45 to 2.16+/-0.65), but was for AP (1.16+/-0.88 to 5.71+/-1.66, p<0.04). IPC did not prevent ventricular stunning or alter myocardial energetics. AP reduced ventricular stunning but resulted in worsened myocardial energy efficiency. The benefits to ventricular function of the adenosine pretreatment protocol used in this study were only possible at a cost of higher metabolic requirements.     

Cryopreservation of primary porcine liver cells in an organotypical sandwich model in a clinically relevant flat membrane bioreactor

To overcome the logistical difficulties of continuously supplying freshly-isolated, primary porcine liver cells to bioartificial liver support bioreactors, we developed a cryopreservation method using an organotypical sandwich model in a flat membrane bioreactor (FMB). We measured albumin secretion rate, urea synthesis rate and 7-ethoxy coumarin (ECOD) in long-term cultures of cryopreserved cells (up to 14 days). The albumin secretion rate was 62% that of non-cryopreserved cells at days 11 and 14. The ECOD activity was 54% that of fresh, control cells initially and increased up to 79% by the 14th day. The urea synthesis rate was stable at 60% that of the control. This study showed that cryopreserved cells can recover liver-specific functions. This result has the potential to dramatically expand the clinical application of bioartificial liver supports.     

Measuring clinically relevant knee motion with a self-calibrated wearable sensor

Low-cost sensors provide a unique opportunity to continuously monitor patient progress during rehabilitation; however, these sensors have yet to demonstrate the fidelity and lack the calibration paradigms necessary to be viable tools for clinical research. The purpose of this study was to validate a low-cost wearable sensor that accurately measured peak knee extension during clinical exercises and needed no additional equipment for calibration. Sagittal plane knee motion was quantified using a 9-axis motion sensor and directly compared to motion capture data. The motion sensor measured the field strength of a strong earth magnet secured to the distal femur, which was correlated with knee angle during a simple calibration process. Peak knee motions and kinematic patterns were compared with motion capture data using paired t-tests and cross correlation, respectively. Peak extension values during seated knee extensions were accurate within 5 degrees across all subjects (root mean square error: 2.6 degrees, P = 0.29). Knee flexion during gait strongly correlated (0.84 ≤ r_xy ≤ 0.99) with motion capture measurements but demonstrated peak flexion errors of 10 degrees. In this study, we present a low-cost sensor (≈$ 35 US) that accurately determines knee extension angle following a calibration procedure that did not require any other equipment. Our findings demonstrate that this sensor paradigm is a feasible tool to monitor patient progress throughout physical therapy. However, dynamic motions that are associated with soft-tissue artifact may limit the accuracy of this type of wearable sensor.     

Structural basis of antigen mimicry in a clinically relevant melanoma antigen system

Although mimics of human tumor antigens are effective immunogens to overcome host unresponsiveness to the nominal antigen, the structural basis of this mimicry remains poorly defined. Therefore, in this study we have characterized the structural basis of the human high molecular weight-melanoma-associated antigen (HMW-MAA) mimicry by the mouse anti-idiotypic (anti-id) monoclonal antibody (mAb) MK2-23. Using x-ray crystallography, we have characterized the three-dimensional structure of the anti-id mAb MK2-23 Fab' and shown that its heavy chain complementarity-determining region (CDR3) (H3) and its light chain CDR1 (L1) are closely associated. These moieties are the source of HMW-MAA mimicry, since they display partial amino acid sequence homology along with a similar structural fold with the HMW-MAA core protein. Furthermore, a 15-residue peptide comprising the H3 loop of anti-id mAb MK2-23 demonstrates HMW-MAA-like in vitro and in vivo reactivity. This peptide in conjunction with the structural data will facilitate the characterization of the effect of the degree of antigen mimicry on the induction of a self-antigen-specific immune response by a mimic.     

Refinement of a thyroid cultured cell system used in clinically relevant bioassays

Thyroid cultured cells are now used worldwide in clinical bioassays of TSH and of thyroid autoantibodies. Having originally developed the thyroid cell cultures (Ambesi-Impiombato et al. 1980) from rat glands in our laboratory, we now aim to improve the system, moving in two directions: a) TSH-independent mutants have been produced and characterized, which can be used in clinical bioassays without starvation from the hormone. b) Human cultures have been attempted using our experience with rat cells, as well as innovative strategies. Preliminary results now indicate that human normal differentiated cells may be available for clinical studies in vitro, when species-specific differences may be critical.     

Proteomics as a tool for clinically relevant biomarker discovery and validation

The excitement associated with clinical applications of proteomics was initially focused on its potential to serve as a vehicle for both biomarker discovery and drug discovery and routine clinical sample analysis. Some approaches were thought to be able to "identify" mass spectral characteristics that distinguished between control and disease samples, and thereafter it was believed that the same tool could be employed to screen samples in a high-throughput clinical setting. However, this has been difficult to achieve, and the early promise is yet to be fully realized. While we see an important place for mass spectrometry in drug and biomarker discovery, we believe that alternative strategies will prove more fruitful for routine analysis. Here we discuss the power and versatility of 2D gels and mass spectrometry in the discovery phase of biomarker work but argue that it is better to rely on immunochemical methods for high-throughput validation and routine assay applications.     

Detection of clinically relevant point mutations by a novel piezoelectric biosensor

Piezoelectric sensing is here applied to point mutation detection in human DNA. The mutation investigated is in the TP53 gene, which results inactivated in most cancer types. TP53 gene maps on chromosome 17 (17p13.1). It contains 11 exons and codifies for the relative protein, involved in cell proliferation. The TP53 gene has a wide mutation spectrum that is related to different tumours. In particular, those occurring in the structurally important L2 and L3 zinc-binding domains, have been linked to patient prognosis and more strongly to radiotherapy and chemotherapy resistance in several major cancers. For this reason, the identification of these mutations represents an important clinical target and biosensors could represent good candidate for fast mutation screening. In this paper, a DNA-based piezoelectric biosensor for the detection of the TP53 gene mutation at codon 248 is reported. A biotinylated probe was immobilised on the sensor surface via dextran-streptavidin modified surfaces. The sensor was optimised using synthetic oligonucleotides. Finally, the sensor system was successfully applied to polymerase chain reaction (PCR)-amplified real samples of DNA extracted from two cell lines, one normal (wild-type) and one mutated, carrying the mutation at codon 248 of the TP53 gene. The results obtained demonstrate that the DNA-based piezoelectric biosensor is able to detect the point mutations in PCR-amplified samples showing the potentialities of this approach for routine analysis.     

RhoA as a mediator of clinically relevant androgen action in prostate cancer cells

Recently, we have identified serum response factor (SRF) as a mediator of clinically relevant androgen receptor (AR) action in prostate cancer (PCa). Genes that rely on SRF for androgen responsiveness represent a small fraction of androgen-regulated genes, but distinguish benign from malignant prostate, correlate with aggressive disease, and are associated with biochemical recurrence. Thus, understanding the mechanism(s) by which SRF conveys androgen regulation to its target genes may provide novel opportunities to target clinically relevant androgen signaling. Here, we show that the small GTPase ras homolog family member A (RhoA) mediates androgen-responsiveness of more than half of SRF target genes. Interference with expression of RhoA, activity of the RhoA effector Rho-associated coiled-coil containing protein kinase 1 (ROCK), and actin polymerization necessary for nuclear translocation of the SRF cofactor megakaryocytic acute leukemia (MAL) prevented full androgen regulation of SRF target genes. Androgen treatment induced RhoA activation, increased the nuclear content of MAL, and led to MAL recruitment to the promoter of the SRF target gene FHL2. In clinical specimens RhoA expression was higher in PCa cells than benign prostate cells, and elevated RhoA expression levels were associated with aggressive disease features and decreased disease-free survival after radical prostatectomy. Overexpression of RhoA markedly increased the androgen-responsiveness of select SRF target genes, in a manner that depends on its GTPase activity. The use of isogenic cell lines and a xenograft model that mimics the transition from androgen-stimulated to castration-recurrent PCa indicated that RhoA levels are not altered during disease progression, suggesting that RhoA expression levels in the primary tumor determine disease aggressiveness. Androgen-responsiveness of SRF target genes in castration-recurrent PCa cells continued to rely on AR, RhoA, SRF, and MAL and the presence of intact SRF binding sites. Silencing of RhoA, use of Rho-associated coiled-coil containing protein kinase 1 inhibitors, or an inhibitor of SRF-MAL interaction attenuated (androgen-regulated) cell viability and blunted PCa cell migration. Taken together, these studies demonstrate that the RhoA signaling axis mediates clinically relevant AR action in PCa.     

Protective effects of resveratrol in ischemia-reperfusion injury of skeletal muscle: A clinically relevant animal model for lower extremity ischemia

Ischemia and reperfusion injury of the skeletal muscle is a common and serious condition observed in patients admitting to peripheral vascular surgery, interventional radiology and cardiology departments. Resveratrol (RVT) being a strong natural antioxidant is found in deal of red wine and Mediterranean diet. In the present study, male Spraque-Dawley rats were randomized into two groups of equal size. The first group was the control group, and these rats were administered with tap water with a gastric tube for fourteen consecutive days once daily. According to the same protocol, the rats in the second group were treated with tap water containing 20 mg/kg RVT. All the rats in the two groups were subjected to acute hind limb ischemia through clamping of the abdominal aorta for 120 min. Following this procedure, 60 minutes of reperfusion was applied by reestablishing blood flow in both iliac arteries. Ischemic damage in the skeletal muscle tissue was assessed by measuring myoglobin, lactate dehydrogenase, creatinine phosphokinase, aspartate transaminase enzymes in venous blood samples obtained at the end of the reperfusion period. Oxidative stress caused by reperfusion was determined by measuring MDA, carbonyl and protein sulphydryl levels in quadriceps muscle tissue retrieved at the end of the experiment. In Group II rats, all the measured ischemic enzymes and the markers of oxidative stress reflected robust anti-ischemic properties obtained by RVT administration. The data from both groups revealed statistically significant protection against acute skeletal muscle ischemia and reperfusion injury in Group II rats, compared to Group I. As a major dietary flavonoid RVT can protect the skeletal muscle tissue against global ischemia and reperfusion injury because of its strong antioxidant and cytoprotective properties.     

Structural and biophysical properties of a synthetic channel-forming peptide: Designing a clinically relevant anion selective pore

The design, synthesis, modeling and in vitro testing of channel-forming peptides derived from the cys-loop superfamily of ligand-gated ion channels are part of an ongoing research focus. Over 300 different sequences have been prepared based on the M2 transmembrane segment of the spinal cord glycine receptor α-subunit. A number of these sequences are water-soluble monomers that readily insert into biological membranes where they undergo supramolecular assembly, yielding channels with a range of selectivities and conductances. Selection of a sequence for further modifications to yield an optimal lead compound came down to a few key biophysical properties: low solution concentrations that yield channel activity, greater ensemble conductance, and enhanced ion selectivity. The sequence NK(4)-M2GlyR T19R, S22W (KKKKPARVGLGITTVLTMRTQW) addressed these criteria. The structure of this peptide has been analyzed by solution NMR as a monomer in detergent micelles, simulated as five-helix bundles in a membrane environment, modified by cysteine-scanning and studied for insertion efficiency in liposomes of selected lipid compositions. Taken together, these results define the structural and key biophysical properties of this sequence in a membrane. This model provides an initial scaffold from which rational substitutions can be proposed and tested to modulate anion selectivity. This article is part of a Special Issue entitled: Protein Folding in Membranes.     

Current strategies and findings in clinically relevant post-translational modification-specific proteomics

Mass spectrometry-based proteomics has considerably extended our knowledge about the occurrence and dynamics of protein post-translational modifications (PTMs). So far, quantitative proteomics has been mainly used to study PTM regulation in cell culture models, providing new insights into the role of aberrant PTM patterns in human disease. However, continuous technological and methodical developments have paved the way for an increasing number of PTM-specific proteomic studies using clinical samples, often limited in sample amount. Thus, quantitative proteomics holds a great potential to discover, validate and accurately quantify biomarkers in body fluids and primary tissues. A major effort will be to improve the complete integration of robust but sensitive proteomics technology to clinical environments. Here, we discuss PTMs that are relevant for clinical research, with a focus on phosphorylation, glycosylation and proteolytic cleavage; furthermore, we give an overview on the current developments and novel findings in mass spectrometry-based PTM research.     

Determining clinically relevant features in cytometry data using persistent homology

Cytometry experiments yield high-dimensional point cloud data that is difficult to interpret manually. Boolean gating techniques coupled with comparisons of relative abundances of cellular subsets is the current standard for cytometry data analysis. However, this approach is unable to capture more subtle topological features hidden in data, especially if those features are further masked by data transforms or significant batch effects or donor-to-donor variations in clinical data. We present that persistent homology, a mathematical structure that summarizes the topological features, can distinguish different sources of data, such as from groups of healthy donors or patients, effectively. Analysis of publicly available cytometry data describing non-naïve CD8+ T cells in COVID-19 patients and healthy controls shows that systematic structural differences exist between single cell protein expressions in COVID-19 patients and healthy controls. We identify proteins of interest by a decision-tree based classifier, sample points randomly and compute persistence diagrams from these sampled points. The resulting persistence diagrams identify regions in cytometry datasets of varying density and identify protruded structures such as ‘elbows’. We compute Wasserstein distances between these persistence diagrams for random pairs of healthy controls and COVID-19 patients and find that systematic structural differences exist between COVID-19 patients and healthy controls in the expression data for T-bet, Eomes, and Ki-67. Further analysis shows that expression of T-bet and Eomes are significantly downregulated in COVID-19 patient non-naïve CD8+ T cells compared to healthy controls. This counter-intuitive finding may indicate that canonical effector CD8+ T cells are less prevalent in COVID-19 patients than healthy controls. This method is applicable to any cytometry dataset for discovering novel insights through topological data analysis which may be difficult to ascertain otherwise with a standard gating strategy or existing bioinformatic tools.     

Late effects in the mouse small intestine after a clinically relevant multifractionated radiation treatment

Late radiation effects were investigated in the mouse small intestine after a daily fractionated radiation treatment. Mice were given 14 X 3 Gy in 2 weeks over a partial abdominal irradiation field. There was evidence for late injury in the intestinal epithelium, the submucosa, and the subserosa. Late damage in the epithelium was shown histologically by a reduced crypt number and villus atrophy at 3 and 6 months but not at 24 h after the end of treatment. The reduction in crypt number was significant in the ileum at 3 and 6 months after irradiation: 100 +/- 4 and 98 +/- 5 (SEM) per circumference, respectively, versus 132 +/- 3 and 146 +/- 6 in age-matched controls (P less than 0.01, t test). The mitotic activity in the crypts of the irradiated animals was significantly increased at all investigated times, suggesting a prolonged but insufficient compensatory response to maintain the mucosal integrity. The repercussion on intestinal epithelial function was, at least in part, reflected by a progressively reduced body weight gain up to 5 g at 3 months after treatment. The ability of the surviving crypt stem cells to form microcolonies after irradiation, however, was not impaired. Evidence for injury in the submucosa was provided from macroscopic and histological examination. Macroscopically, at 6 months after treatment, narrowed and rigid bowel segments surrounded by fibrotic adhesions were observed, causing partial intestinal obstruction. In addition, sometimes focal areas of hemorrhage and infarction in small bowel segments were present. Histologically, diffuse and pronounced submucosal edema without increased fibrosis was seen, together with markedly dilated small blood vessels in focal areas of macroscopic intestinal infarction. The intestinal perfusion, as assessed by 86Rb extraction, was significantly but transiently reduced at 3 months after irradiation. These data suggest mainly late effects in the small intestine after this daily fractionated irradiation treatment. The reduced number of epithelial cells and the submucosal edema are possibly mediated by radiation injury in the intestinal microvasculature.