Contributions to our understanding of T cell physiology through unveiling the T cell proteome

AutophagosOMES: identification of autophagosomal cargo in CD4+ T cells by proteomics

Macroautophagy/autophagy, a cellular process that sequesters and breaks down cellular components in the lysosome/vacuole, is important in various events where cell composition undergoes changes. Broadly, autophagy is involved in T cell regulation including maintaining cell homeostasis. One process where a cell alters its composition is in the activation of helper T cells in the immune system. When helper (CD4+) T cells are activated by antigens, they both grow and alter their cellular components to become effector T cells. Autophagy is the process that facilitates the breakdown of these cellular components and is therefore hypothesized to have a role in CD4+ T cell activation. Previous research has concluded that CD4+ T cell activation induces autophagy, providing an avenue for further research aimed at examining the ways in which this induced autophagy affects CD4+ T cell proliferation and function. Toward this end, Zhou et al. researched the autophagosomal cargo present within CD4+ T cells and the impact this cargo has on CD4+ T cell proliferation.

A sensitive S-Trap-based approach to the analysis of T cell lipid raft proteome

The analysis of T cell lipid raft proteome is challenging due to the highly dynamic nature of rafts and the hydrophobic character of raft-resident proteins. We explored an innovative strategy for bottom-up lipid raftomics based on suspension-trapping (S-Trap) sample preparation. Mouse T cells were prepared from splenocytes by negative immunoselection, and rafts were isolated by a detergent-free method and OptiPrep gradient ultracentrifugation. Microdomains enriched in flotillin-1, LAT, and cholesterol were subjected to proteomic analysis through an optimized protocol based on S-Trap and high pH fractionation, followed by nano-LC-MS/MS. Using this method, we identified 2,680 proteins in the raft-rich fraction and established a database of 894 T cell raft proteins. We then performed a differential analysis on the raft-rich fraction from nonstimulated versus anti-CD3/CD28 T cell receptor (TCR)-stimulated T cells. Our results revealed 42 proteins present in one condition and absent in the other. For the first time, we performed a proteomic analysis on rafts from ex vivo T cells obtained from individual mice, before and after TCR activation. This work demonstrates that the proposed method utilizing an S-Trap-based approach for sample preparation increases the specificity and sensitivity of lipid raftomics.

Proteomic Approaches for Biomarker Panels in Cancer

Proteomic technologies remain the main backbone of biomarkers discovery in cancer. The continuous development of proteomic technologies also enlarges the bioinformatics domain, thus founding the main pillars of cancer therapy. The main source for diagnostic/prognostic/therapy monitoring biomarker panels are molecules that have a dual role, being both indicators of disease development and therapy targets. Proteomic technologies, such as mass-spectrometry approaches and protein array technologies, represent the main technologies that can depict these biomarkers. Herein, we will illustrate some of the most recent strategies for biomarker discovery in cancer, including the development of immune-markers and the use of cancer stem cells as target therapy. The challenges of proteomic biomarker discovery need new forms of cross-disciplinary conglomerates that will result in increased and tailored access to treatments for patients; diagnostic companies would benefit from the enhanced co-development of companion diagnostics and pharmaceutical companies. In the technology optimization in biomarkers, immune assays are the leaders of discovery machinery.

Cell-selective labelling of proteomes in Drosophila melanogaster

The specification and adaptability of cells rely on changes in protein composition. Nonetheless, uncovering proteome dynamics with cell-type-specific resolution remains challenging. Here we introduce a strategy for cell-specific analysis of newly synthesized proteomes by combining targeted expression of a mutated methionyl-tRNA synthetase (MetRS) with bioorthogonal or fluorescent non-canonical amino-acid-tagging techniques (BONCAT or FUNCAT). Substituting leucine by glycine within the MetRS-binding pocket (MetRS^LtoG) enables incorporation of the non-canonical amino acid azidonorleucine (ANL) instead of methionine during translation. Newly synthesized proteins can thus be labelled by coupling the azide group of ANL to alkyne-bearing tags through ‘click chemistry'. To test these methods for applicability in vivo, we expressed MetRS^LtoG cell specifically in Drosophila. FUNCAT and BONCAT reveal ANL incorporation into proteins selectively in cells expressing the mutated enzyme. Cell-type-specific FUNCAT and BONCAT, thus, constitute eligible techniques to study protein synthesis-dependent processes in complex and behaving organisms.

Mutated tRNA synthetases can incorporate non-canonical amino acids into proteins. Erdmann et al. exploit this property to metabolically label newly synthesized proteins in selected cell types in Drosophila, and demonstrate their detection using proteomics (BONCAT) and fluorescence imaging (FUNCAT).

Immunomics in Skin Cancer - Improvement in Diagnosis, Prognosis and Therapy Monitoring

This review will focus on the elements of the skin’s immune system, immune cells and/or non-immune cells that support immune mechanisms, molecules with immune origin and/or immune functions that are involved in skin carcinogenesis. All these immune elements are compulsory in the development of skin tumors and/or sustainability of the neoplastic process. In this light, recent data gathered in this review will acknowledge all immune elements that contribute to skin tumorigenesis; moreover, they can serve as immune biomarkers. These immune markers can contribute to the diagnostic improvement, prognosis forecast, therapy monitoring, and even personalized therapeutical approach in skin cancer. Immune processes that sustain tumorigenesis in non-melanoma and melanoma skin cancers are described in the framework of recent data.

Regulation of cyclin T1 and HIV-1 Replication by microRNAs in resting CD4+ T lymphocytes

The replication of integrated human immunodeficiency virus type 1 (HIV-1) is dependent on the cellular cofactor cyclin T1, which binds the viral Tat protein and activates the RNA polymerase II transcription of the integrated provirus. The activation of resting CD4(+) T cells upregulates cyclin T1 protein levels independently of an increase in cyclin T1 mRNA levels, suggesting a translational repression of cyclin T1 in resting CD4(+) T cells. Hypothesizing that microRNAs (miRNAs) repress cyclin T1 translation in resting CD4(+) T cells and that this inhibition is lifted upon cell activation, we used microarray expression analysis to identify miRNAs miR-27b, miR-29b, miR-150, and miR-223 as being significantly downregulated upon CD4(+) T cell activation. The overexpression of these miRNAs decreased endogenous cyclin T1 protein levels, while treatment with the corresponding antagomiRs increased cyclin T1 protein levels. An miR-27b binding site within the cyclin T1 3' untranslated region (3'UTR) was identified and confirmed to be functional after the mutation of key resides abrogated the ability of miR-27b to decrease the expression of a luciferase reporter upstream of the cyclin T1 3'UTR. Ago2 immunoprecipitation revealed an association with cyclin T1 mRNA that was decreased following treatment with miR-27b and miR-29b antagomiRs. Cells overexpressing miR-27b showed decreased viral gene expression levels of the HIV-1 reporter virus and a decreased replication of strain NL4.3; a partial rescue of viral transcription could be seen following the transfection of cyclin T1. These results implicate miR-27b as a novel regulator of cyclin T1 protein levels and HIV-1 replication, while miR-29b, miR-223, and miR-150 may regulate cyclin T1 indirectly.

Proteomic approaches to understanding the role of the cytoskeleton in host-defense mechanisms

The cytoskeleton is a cellular scaffolding system whose functions include maintenance of cellular shape, enabling cellular migration, division, intracellular transport, signaling and membrane organization. In addition, in immune cells, the cytoskeleton is essential for phagocytosis. Following the advances in proteomics technology over the past two decades, cytoskeleton proteome analysis in resting and activated immune cells has emerged as a possible powerful approach to expand our understanding of cytoskeletal composition and function. However, so far there have only been a handful of studies of the cytoskeleton proteome in immune cells. This article considers promising proteomics strategies that could augment our understanding of the role of the cytoskeleton in host-defense mechanisms.

Aberrant reactive oxygen and nitrogen species generation in rheumatoid arthritis (RA): causes and consequences for immune function, cell survival, and therapeutic intervention

The infiltration and persistence of hematopoietic immune cells within the rheumatoid arthritis (RA) joint results in elevated levels of pro-inflammatory cytokines, increased reactive oxygen (ROS) and -nitrogen (RNS) species generation, that feeds a continuous self-perpetuating cycle of inflammation and destruction. Meanwhile, the controlled production of ROS is required for signaling within the normal physiological reaction to perceived "foreign matter" and for effective apoptosis. This review focuses on the signaling pathways responsible for the induction of the normal immune response and the contribution of ROS to this process. Evidence for defects in the ability of immune cells in RA to regulate the generation of ROS and the consequence for their immune function and for RA progression is considered. As the hypercellularity of the rheumatoid joint and the associated persistence of hematopoietic cells within the rheumatoid joint are symptomatic of unresponsiveness to apoptotic stimuli, the role of apoptotic signaling proteins (specifically Bcl-2 family members and the tumor suppressor p53) as regulators of ROS generation and apoptosis are considered, evaluating evidence for their aberrant expression and function in RA. We postulate that ROS generation is required for effective therapeutic intervention.

Proteomic change of peripheral lymphocytes from scald injury and Pseudomonas aeruginosa sepsis in rabbits

BACKGROUND

Increased susceptibility to infection has been related to impairment of lymphocyte-regulated immune responses after severe burn. The aim of this study is to identify the differential expression of proteins in circulating lymphocytes from scald injury and Pseudomonas aeruginosa sepsis in rabbits to provide a basis for pathogenesis of burns and sepsis.

METHODS

Rabbits were subjected to sham burn (A), 30% scald (B), A+bacterial challenge (C) or B+bacterial challenge (D). Bacterial challenge was inflicted by an injection of 2.0x10(8) CFU P. aeruginosa (ATCC27853) in the auricular vein 22 h after the burn procedure. The animals were sacrificed 24 h later. Lymphocytes were isolated, and the differential proteins in the lymphocytes from the experimental and control animals were identified by two-dimensional electrophoresis (2-DE) coupled with matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS), two of which were confirmed by Western blotting.

RESULTS

Nineteen differential protein spots were found by 2-DE and 12 spots (11 proteins) were identified. Differential expression of peroxiredoxin and annexin I was validated by Western blotting. Among the identified proteins, the expression levels of cofilin, cyclophilin A, ubiquitin, nucleoside diphosphate kinase, glutamate dehydrogenase and annexin I were down-regulated in group B, excessively down-regulated in group D, but mildly in group C, and peroxiredoxin was up-regulated in groups B and D.

CONCLUSIONS

Proteome changes in lymphocytes from P. aeruginosa sepsis in the scalded rabbits were revealed, which are related to immune suppression and the pathogenesis of sepsis after scald injury.

In vivo vitamin C supplementation increases phosphoinositol transfer protein expression in peripheral blood mononuclear cells from healthy individuals

Ascorbate can act as both a reducing and oxidising agent in vitro depending on its environment. It can modulate the intracellular redox environment of cells and therefore is predicted to modulate thiol-dependent cell signalling and gene expression pathways. Using proteomic analysis of vitamin C-treated T cells in vitro, we have previously reported changes in expression of five functional protein groups associated with signalling, carbohydrate metabolism, apoptosis, transcription and immune function. The increased expression of the signalling molecule phosphatidylinositol transfer protein (PITP) was also confirmed using Western blotting. Herein, we have compared protein changes elicited by ascorbate in vitro, with the effect of ascorbate on plasma potassium levels, on peripheral blood mononuclear cell (PBMC) apoptosis and PITP expression, in patients supplemented with vitamin C (0-2 g/d) for up to 10 weeks to investigate whether in vitro model systems are predictive of in vivo effects. PITP varied in expression widely between subjects at all time-points analysed but was increased by supplementation with 2 g ascorbate/d after 5 and 10 weeks. No effects on plasma potassium levels were observed in supplemented subjects despite a reduction of K+ channel proteins in ascorbate-treated T cells in vitro. Similarly, no effect of vitamin C supplementation on PBMC apoptosis was observed, whilst ascorbate decreased expression of caspase 3 recruitment domain protein in vitro. These data provide one of the first demonstrations that proteomics may be valuable in developing predictive markers of nutrient effects in vivo and may identify novel pathways for studying mechanisms of action in vivo.