Proteomics analysis of prefrontal cortex of Alzheimer's disease patients revealed dysregulated proteins in the disease and novel proteins associated with amyloid-β pathology

BACKGROUND

Alzheimer's disease (AD) is a progressive, chronic, and neurodegenerative disease, and the most common cause of dementia worldwide. Currently, the mechanisms underlying the disease are far from being elucidated. Thus, the study of proteins involved in its pathogenesis would allow getting further insights into the disease and identifying new markers for AD diagnosis.

METHODS

We aimed here to analyze protein dysregulation in AD brain by quantitative proteomics to identify novel proteins associated with the disease. 10-plex TMT (tandem mass tags)-based quantitative proteomics experiments were performed using frozen tissue samples from the left prefrontal cortex of AD patients and healthy individuals and vascular dementia (VD) and frontotemporal dementia (FTD) patients as controls (CT). LC-MS/MS analyses were performed using a Q Exactive mass spectrometer.

RESULTS

In total, 3281 proteins were identified and quantified using MaxQuant. Among them, after statistical analysis with Perseus (p value < 0.05), 16 and 155 proteins were defined as upregulated and downregulated, respectively, in AD compared to CT (Healthy, FTD and VD) with an expression ratio ≥ 1.5 (upregulated) or ≤ 0.67 (downregulated). After bioinformatics analysis, ten dysregulated proteins were selected as more prone to be associated with AD, and their dysregulation in the disease was verified by qPCR, WB, immunohistochemistry (IHC), immunofluorescence (IF), pull-down, and/or ELISA, using tissue and plasma samples of AD patients, patients with other dementias, and healthy individuals.

CONCLUSIONS

We identified and validated novel AD-associated proteins in brain tissue that should be of further interest for the study of the disease. Remarkably, PMP2 and SCRN3 were found to bind to amyloid-β (Aβ) fibers in vitro, and PMP2 to associate with Aβ plaques by IF, whereas HECTD1 and SLC12A5 were identified as new potential blood-based biomarkers of the disease.

Targeted proteomics on its way to discovery

For a long time, targeted and discovery proteomics covered different corners of the detection spectrum, with targeted proteomics focused on small target sets. This changed with the recent advances in highly multiplexed analysis. While discovery proteomics still pushes higher numbers of identified and quantified proteins, the advances in targeted proteomics rose to cover large parts of less complex proteomes or proteomes with low protein detection counts due to dynamic range restrictions, like the blood proteome. These new developments will impact, especially on the field of biomarker discovery and the possibility of using targeted proteomics for diagnostic purposes. This article is protected by copyright. All rights reserved.

Analysis of the Dynamic Proteasome Structure by Cross-Linking Mass Spectrometry

The 26S proteasome is a macromolecular complex that degrades proteins maintaining cell homeostasis; thus, determining its structure is a priority to understand its function. Although the 20S proteasome's structure has been known for some years, the highly dynamic nature of the 19S regulatory particle has presented a challenge to structural biologists. Advances in cryo-electron microscopy (cryo-EM) made it possible to determine the structure of the 19S regulatory particle and showed at least seven different conformational states of the proteasome. However, there are still many questions to be answered. Cross-linking mass spectrometry (CLMS) is now routinely used in integrative structural biology studies, and it promises to take integrative structural biology to the next level, answering some of these questions.

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Assessment of the global profile of ubiquitin chain topologies within a proteome is of interest to answer a wide range of biological questions. The protocol outlined here takes advantage of the di-glycine (-GG) modification left after the tryptic digestion of ubiquitin incorporated in a chain. By quantifying these topology-characteristic peptides the relative abundance of each ubiquitin chain topology can be determined. The steps required to quantify these peptides by a parallel reaction monitoring experiment are reported taking into consideration the stabilization of ubiquitin chains. Preparation of heavy controls, cell lysis, and digestion are described along with the appropriate mass spectrometer setup and data analysis workflow. An example data set with perturbations in ubiquitin topology is presented, accompanied by examples of how optimization of the protocol can affect results. By following the steps outlined, a user will be able to perform a global assessment of the ubiquitin topology landscape within their biological context.

An integrated workflow for crosslinking mass spectrometry

We present a concise workflow to enhance the mass spectrometric detection of crosslinked peptides by introducing sequential digestion and the crosslink identification software xiSEARCH. Sequential digestion enhances peptide detection by selective shortening of long tryptic peptides. We demonstrate our simple 12‐fraction protocol for crosslinked multi‐protein complexes and cell lysates, quantitative analysis, and high‐density crosslinking, without requiring specific crosslinker features. This overall approach reveals dynamic protein–protein interaction sites, which are accessible, have fundamental functional relevance and are therefore ideally suited for the development of small molecule inhibitors.

Analysis of ubiquitin signaling and chain topology cross-talk

Protein ubiquitination is a powerful post-translational modification implicated in many cellular processes. Although ubiquitination is associated with protein degradation, depending on the topology of polyubiquitin chains, protein ubiquitination is connected to non-degradative events in DNA damage response, cell cycle control, immune response, trafficking, intracellular localization, and vesicle fusion events. It has been shown that a ubiquitin chain can contain two or more topologies at the same time. These branched chains add another level of complexity to ubiquitin signaling, increasing its versatility and specificity. Mass spectrometry-based proteomics has been playing an important role in the identification of all types of ubiquitin chains and linkages. This review aims to provide an overview of ubiquitin chain topology and associated signaling pathways and discusses the MS-based proteomic methodologies used to determine such topologies. SIGNIFICANCE: Ubiquitination plays important roles in many cellular processes. Proteins can be monoubiquitinated or polyubiquitinated forming non-branched or branched chains in a high number of possible combinations, each associated with different cellular processes. The detection and the topology of ubiquitin chains is thus of extreme importance in order to explain such processes. Advances in mass spectrometry based proteomics allowed for the discovery and topology mapping of many ubiquitin chains. This review revisits the state of the art in ubiquitin chain identification by mass spectrometry and gives an insight on the implication of such chains in many cellular processes.

Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer

We compared the five different ways of fragmentation available on a tribrid mass spectrometer and optimized their collision energies with regard to optimal sequence coverage of cross-linked peptides. We created a library of bis(sulfosuccinimidyl)suberate (BS3/DSS) cross-linked precursors, derived from the tryptic digests of three model proteins (Human Serum Albumin, creatine kinase, and myoglobin). This enabled in-depth targeted analysis of the fragmentation behavior of 1065 cross-linked precursors using the five fragmentation techniques: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), and the combinations ETciD and EThcD. EThcD gave the best sequence coverage for cross-linked m/z species with high charge density, while HCD was optimal for all others. We tested the resulting data-dependent decision tree against collision energy-optimized single methods on two samples of differing complexity (a mix of eight proteins and a highly complex ribosomal cellular fraction). For the high complexity sample the decision tree gave the highest number of identified cross-linked peptide pairs passing a 5% false discovery rate (on average ∼21% more than the second best, HCD). For the medium complexity sample, the higher speed of HCD proved decisive. Currently, acquisition speed plays an important role in allowing the detection of cross-linked peptides against the background of linear peptides. Enrichment of cross-linked peptides will reduce this role and favor methods that provide spectra of higher quality. Data are available via ProteomeXchange with identifier PXD006131.

Meloidogyne javanica on Peanut in Florida

A mixed population of Meloidogyne arenaria race 1 and M. javanica race 3 is reported on peanut from a field in Levy County, Florida. Confirmation of M. javanica on peanut is based on esterase and malate dehydrogenase isozyme patterns resolved on polyacrylamide slab gels following electrophoresis, and perineal patterns. Up to 29% of 290 individual females collected from peanut roots in the field in autumn 2002 showed a typical esterase J3 phenotype for M. javanica. This is the third report of M. javanica infecting peanut in the United States.

Sulfation of intrinsic glycoproteins of the rabbit vitreous

The experiments reported here were designed to characterize the intrinsic vitreous glycoproteins and to understand the process of their sulfation. Rabbits were injected intravitreally with 35S-sodium sulfate and killed at several time intervals after injection. In another series of experiments, rabbits were injected either with 35S-sodium sulfate, 3H-fucose or 3H-tyrosine, associated or not associated with tunicamycin administration. Vitreous from the control eyes was also digested with N-glycosidase. Furthermore, ciliary bodies, the putative source of the intrinsic vitreous glycoproteins, were incubated with 35S-sodium sulfate in the presence or absence of the protein synthesis inhibitor cycloheximide, and the culture media recovered for analysis. These and the vitreous samples of the other experiments were processed for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and fluorography. Except for serum albumin, practically all polypeptide bands of the vitreous and culture media were labeled with radioactive sulfate and were shown to undergo renewal. The experiments using tunicamycin or enzyme treatment suggest that radioactive sulfate was incorporated not only into the carbohydrate side chains of the glycoproteins but also into the amino acid tyrosine of the polypeptide backbone of these glycoproteins.

Medical care in old age: what do nurses in long-term care consider appropriate?

OBJECTIVES

To determine whether nurses working in a long-term care institution, who are knowledgeable about the full range of conditions common among older people, favor limitations of treatment in old age; and to study whether the level of intensity of care they regard as appropriate varies with the overall health status of the older individual.

DESIGN

Participants were asked to complete an intervention-specific advance directive for themselves, with scenarios representing terminal illness, dementia plus chronic illness, chronic illness in a nursing home resident, chronic illness in a community-dwelling older person, and a robust, community-dwelling older person.

SETTING

A 725-bed long-term care institution, with residents having a mean age of 88 years and a wide range of physical and cognitive deficits.

PARTICIPANTS

Full-time nurses at the long-term care facility were eligible and were given survey instruments; 102 of the 145 eligible nurses completed the questionnaire.

MEASUREMENTS

The unit of analysis is the refusal rate, defined as the mean number of refusals of interventions for each respondent.

MAIN RESULTS

The overall refusal rate for all five scenarios taken together was 72.1%. The refusal rate in the case of terminal illness was 90.9%, in the case of dementia plus chronic illness 81.8%, in the case of dementia in a nursing home 69.1%, for a homebound older person with chronic illness 70.9%, and for a previously healthy 85-year-old person living in the community, 50.0% (P < .001).

CONCLUSIONS

Nurses working in a long-term care institution have strong preferences about limiting a variety of interventions in old age. The greater the degree of physical and cognitive impairment, the more limitations they favor. This suggests the necessity of expanding advance planning to include a discussion of what constitutes appropriate treatment in a broad range of circumstances.

Interleukin-1 and interleukin-2 defects associated with murine graft-versus-host-induced immunodeficiency

In this study we investigated the mechanism, or mechanisms, involved in graft-versus-host (GVH)-induced T cell immunodeficiency. Chronic GVH reactions were induced in normal CBA X A F1 (BAF1) hybrid mice by the injection of parental A strain lymphoid cells. At various times (43-91 days) after GVH induction, the functional status of GVH T cells was assessed using interleukin-1 (IL-1) and interleukin-2 (IL-2) as probes. The response of GVH thymocytes to IL-1 was depressed when compared with normal thymocytes. Although GVH peanut-agglutinin-negative (PNA-) thymocytes did respond to IL-2 alone or IL-2 plus phytohemagglutinin (PHA), this response was significantly lower than the response of PNA- thymocytes from normal mice. In addition, GVH spleen cells failed to produce significant amounts of IL-2 when stimulated with concanavalin A. These results suggest that the long term immunosuppression associated with murine chronic GVH disease is due, at least in part, to a decrease in the responsiveness to IL-1 and IL-2, and to a marked deficiency in IL-2 production.