Multiple Protein Analysis of Formalin-fixed and Paraffin-embedded Tissue Samples with Reverse phase Protein Arrays

Reverse-phase protein arrays (RPPAs) have become an important tool for the sensitive and high-throughput detection of proteins from minute amounts of lysates from cell lines and cryopreserved tissue. The current standard method for tissue preservation in almost all hospitals worldwide is formalin fixation and paraffin embedding, and it would be highly desirable if RPPA could also be applied to formalin-fixed and paraffin embedded (FFPE) tissue. We investigated whether the analysis of FFPE tissue lysates with RPPA would result in biologically meaningful data in two independent studies. In the first study on breast cancer samples, we assessed whether a human epidermal growth factor receptor (HER) 2 score based on immunohistochemistry (IHC) could be reproduced with RPPA. The results showed very good concordance between the IHC and RPPA classifications of HER2 expression. In the second study, we profiled FFPE tumor specimens from patients with adenocarcinoma and squamous cell carcinoma in order to find new markers for differentiating these two subtypes of non-small cell lung cancer. p21-activated kinase 2 could be identified as a new differentiation marker for squamous cell carcinoma. Overall, the results demonstrate the technical feasibility and the merits of RPPA for protein expression profiling in FFPE tissue lysates.Many diseases are characterized by the expression of specific proteins and the activation status of distinct signaling pathways (1). Thus, protein expression profiling and activation patterns are instrumental for understanding disease, the development of effective treatments, and the identification of patients who will respond to particular therapies. Traditional ways of analyzing protein expression (e.g. Western blot) can be used for these purposes but often are labor intensive, have low throughput, and consume high sample volumes. Reverse-phase protein array (RPPA)¹ technology is a very promising method that circumvents these issues (2–4). For RPPA, minute amounts of whole protein lysates from a multitude of samples are spotted onto slides, and individual proteins are detected via protein-specific antibodies. This enables medium- to high-throughput analysis of precious low-volume sample material.Lysates for RPPA have so far been generated mainly from cell lines or fresh frozen tissue. However, because of the high amount of effort involved in the use of liquid nitrogen for sample preservation, in almost all hospitals worldwide formalin fixation and paraffin embedding is the preferred method for tissue preservation. Therefore, it would be highly desirable if protein-specific epitopes could be quantitatively extracted and analyzed from formalin-fixed and paraffin embedded (FFPE) tissue, as this would make the majority of clinical specimens accessible for mechanistic protein-based research.In recent years, several research groups have established protocols for protein extraction from FFPE tissue. Common to all of them is the use of high concentrations of ionic detergents, such as sodium dodecyl sulfate, and high temperature. It was shown that these methods even make it possible to extract full-length proteins from FFPE tissue (5–12). The coefficient of variation of the relative extraction efficiency based on Western blot and densitometric assessment of actin typically is below 20% (13). To assess whether the analysis of FFPE tissue lysates would result in biologically meaningful data, we analyzed FFPE breast cancer tissue samples by RPPA for the expression of human epidermal growth factor receptor 2 (HER2) and compared it to HER2 assessment by the gold standard used in clinical practice, which is based on immunohistochemistry (IHC). Successful recovery of HER2 from FFPE tissue should result in concordant HER2 classification between RPPA and IHC.In the second part of the study, FFPE samples of non-small cell lung cancer (NSCLC) were examined via RPPA. Samples from two subtypes of NSCLC, adenocarcinoma (AC) and squamous cell carcinoma (SCC), were analyzed for more than 150 proteins, including two proteins that are known to be differentially expressed between the two subtypes. The objectives of this analysis were to further assess the validity of the approach by confirming the two positive controls and to identify new markers for the differentiation of the two subtypes of NSCLC.     

A quality of life in chronic combat related posttraumatic stress disorder--a study on Croatian War veterans

The main objective of this study was to examine an association of various symptoms in chronic combat-related post traumatic stress disorder (PTSD) and the quality of life in this population. 248 Croatian male war veterans all diagnosed with chronic PTSD were consecutively enrolled in this study as they showed up at the routine check-up. They were given self report questionnaires Trauma Symptom Inventory (TSI-A) evaluating different PTSD symptoms and WHO Quality of Life-BREF assessing four different domains of the quality of life. After independent sample t- test was performed, the presence of each symptom defined by Trauma Symptom Inventory indicated the impairment of all four quality of life domains in a group of subject suffering from it, except of intrusive experience not being associated with the lesser quality in social domain. All quality of life domains were significantly correlated with various PTSD symptoms; however Pearson correlation factors ranged from small to medium value. As expected, PTSD symptoms are associated with lesser quality of life in the affected population. The further research is needed to show possible causal relationship between PTSD and, especially, physical health of these patients.     

Leptin action via neurotensin neurons controls orexin, the mesolimbic dopamine system and energy balance

Leptin acts on leptin receptor (LepRb)-expressing neurons throughout the brain, but the roles for many populations of LepRb neurons in modulating energy balance and behavior remain unclear. We found that the majority of LepRb neurons in the lateral hypothalamic area (LHA) contain neurotensin (Nts). To investigate the physiologic role for leptin action via these LepRb(Nts) neurons, we generated mice null for LepRb specifically in Nts neurons (Nts-LepRbKO mice). Nts-LepRbKO mice demonstrate early-onset obesity, modestly increased feeding, and decreased locomotor activity. Furthermore, consistent with the connection of LepRb(Nts) neurons with local orexin (OX) neurons and the ventral tegmental area (VTA), Nts-LepRbKO mice exhibit altered regulation of OX neurons and the mesolimbic DA system. Thus, LHA LepRb(Nts) neurons mediate physiologic leptin action on OX neurons and the mesolimbic DA system, and contribute importantly to the control of energy balance.     

Simultaneous isolation of human kidney cathepsins B, H, L and C and their characterisation

A procedure for the simultaneous isolation of four cysteine proteinases, cathepsins B, H, L and C, from human kidney is described. The method includes concentration of the acidified homogenate by ammonium sulphate precipitation. The resuspended and dialysed precipitate was chromatographed on DEAE-cellulose DE-32, to allow separation of cathepsins H and C from cathepsins B and L. The main isoform of cathepsin H was separated from cathepsin C by cation-exchange chromatography on CM-Sephadex C-50. These two enzymes were further purified by covalent chromatography on thiopropyl Sepharose and gel permeation on Sephacryl S-200. The last step allowed separation of cathepsin C and the minor isoform of cathepsin H. Purification of the other two enzymes, cathepsins B and L, was carried out on thiol Sepharose, followed by chromatography on CM-Sepharose C-50. In this step, pure cathepsin L was obtained, while two isoforms of cathepsin B had to be finally purified on Sephacryl S-200 columns. The purity of each enzyme was analysed by sodium dodecyl sulphate polyacrylamide gel electrophoresis, isoelectric focusing on polyacrylamide gels and N-terminal sequencing. The activities of the purified cathepsins B, H and L were determined in terms of k_cat/K_M for three substrates, Z-Phe-Arg-MCA, Z-Arg-Arg-MCA and Arg-MCA. The method produced 25 mg of cathepsin B, 6.5 mg of cathepsin H, 1.5 mg of cathepsin L and 3.8 mg of cathepsin C from 3.5 kg of human kidney.     

Human plasma kininogens are identical with alpha-cysteine proteinase inhibitors. Evidence from immunological, enzymological and sequence data

Human high- and low-Mr kininogens were shown to be potent inhibitors of cysteine proteinases such as cathepsin L and papain (Ki = 17-48 pM). A strong immunological cross-reaction between the kininogens and low-Mr alpha-cysteine proteinase inhibitor from human plasma was found. Comparison of partial amino acid sequences from high- and low-Mr kininogen and low-Mr alpha-cysteine proteinase inhibitor demonstrated sequence identity for all segments analyzed. These findings suggest that the kininogens and the alpha-cysteine proteinase inhibitors from human plasma are identical proteins.     

Influence of denervation on the molecular forms of junctional and extrajunctional acetylcholinesterase in fast and slow muscles of the rat.

Acetylcholinesterase (AChE) molecular forms in denervated rat muscles, as revealed by velocity sedimentation in sucrose gradients, were examined from three aspects: possible differences between fast and slow muscles, response of junctional vs extrajunctional AChE, and early vs late effects of denervation. In the junctional region, the response of the asymmetric AChE forms to denervation is similar in fast extensor digitorum longus (EDL) and slow soleus (SOL) muscle: (a) specific activity of the A12 form decreases rapidly but some persists throughout and even increases after a few weeks; (b) an early and transient increase of the A4 AChE form lasting for a few weeks may be due to a block in the synthetic process of the A12 form. In the extrajunctional regions, major differences with regard to AChE regulation exist already between the normal EDL and SOL muscle. The extrajunctional asymmetric AChE forms are absent in the EDL because they became completely repressed during the first month after birth, but they persist in the SOL. Differences remain also after denervation and are, therefore, not directly due to different neural stimulation patterns in both muscles: (a) an early but transient increase of the G4 AChE occurs in the denervated EDL but not in the SOL; (b) no significant extrajunctional activity of the asymmetric AChE forms reappears in the EDL up till 7 wk after denervation. In the SOL, activity of the asymmetric AChE forms is decreased early after denervation but increases thereafter.(ABSTRACT TRUNCATED AT 250 WORDS)     

Iodide, thiocyanate and cyanide ions as capturing reagents in one-step copper-thiocholine method for cytochemical localization of cholinesterase activity.

The necessity of the presence of iodide in Cu-ThCh reaction was investigated by following the precipitate formation "in vitro" and by evaluating the ultrastructural localization of the precipitate in sympathetic ganglion cells of the frog and in the end-plate regions of the rat diaphragm. It was found that thiocyanate or cyanide is the only anion that can be substituted for iodide as the capturing agent in precipitation. The optimal concentration in the preincubation and incubation media of any one of the three anions is from 2 to 5 mM. At a concentration below 1 mM precipitation "in vitro" is considerably delayed as a result of which in electron microscopy diffusion artefacts appear in tissue sections. The unconverted primary precipitate obtained in the presence of iodide had been used for ultrastructural localization of ChE activity and now this use has been extended to precipitates obtained in the presence of CN- or CNS-. Better-quality localization in the presence of either one of the latter anions suggests that they, and particularly CN-, should be substituted for I- in the one-step Cu-ThCh method for the cytochemistry of cholinesterases.     

THE APPEARANCE OF ACETYLCHOLINESTERASE IN THE DORSAL ROOT NEUROBLAST OF THE RABBIT EMBRYO : A Study by Electron Microscope Cytochemistry and Microgasometric Analysis with the Magnetic Diver

In the nine day old embryo, acetylcholinesterase (AChE) is found in the reticulum, i.e. the nuclear envelope, endoplasmic reticulum, and Golgi complex, of a few cells in the neural crest. When the neurite first enters the neural tube, reticulum-bound enzyme is present also in the varicosity of the growth cone of the bipolar neuroblast. At later stages, AChE in the neuroblast has a dual distribution; in addition to the reticulum, activity also appears at the axolemmal surface. The axolemmal activity is found initially on the distal portions of axons in the posterior fasciculus and then progressively appears along the nerve roots in a distal to proximal direction. Very little reticulum-bound enzyme is present within the axon proper. After the 13th day the levels of AChE activity in the posterior fasciculus greatly exceed those in the dorsal root or in the ganglion. Enzymatic activity in the dorsal root equals or exceeds that in the posterior fasciculus by day 16, and both areas are considerably more active than the ganglion.     

Recovery of Acetylcholinesterase in the Diaphragm, Brain, and Plasma of the Rat After Irreversible Inhibition by Soman: A Study of Cytochemical Localization and Molecular Forms of the Enzyme in the Motor End Plate

Abstract Recovery of AChE activity in the motor end plate region and end plate free region of the rat diaphragm was studied after irreversible inhibition by soman. Recovery was slow during the first 2 days and only 4 S and 10 S molecular forms of AChE were present in the end plate region. However, cytochemical evidence indicates that synaptic AChE has already started to accumulate and that the synthesis of AChE in muscle and Schwann cell might even be enhanced. Tubular structures, observed underneath the motor end plate, may serve to transport the enzyme from its sites of synthesis in the sarcoplasmic reticulum. Asymmetric molecular forms of AChE in the end plate region appeared later during recovery and, one week after poisoning, their activity was only about 50% of normal value. The limited ability of newly synthesized AChE to attach to the subcellular structures and, therefore, to be retained in the muscle, may explain the phase of slow recovery. In accordance with this view, AChE activity in brain recovered in a similar way as in muscle, whereas soluble plasma cholinesterases recovered faster, apparently without a slow initial phase.