Novel insights into proteomic technologies and their clinical perspective

A report on the Proteomic Forum 2009 conference, Berlin, Germany, 29 March to 2 April, 2009

An antigen microarray protocol for COVID-19 serological analysis.

peer reviewedThe emergence of the coronavirus disease 2019 pandemic increased the interest in analysis of immunoglobulin responses. ELISA and lateral flow assays are widely used but are restricted by a single response value to an antigen or antigen pool. Here, we describe antigen microarrays, an alternative allowing simultaneous assessment of multiple interactions between antigens and the immunoglobulin content of patient sera. The technique requires minimal reagents and sample input and can be adapted to a wide variety of potential antigenic targets of interest

Statin-induced myopathic changes in primary human muscle cells and reversal by a prostaglandin F2 alpha analogue

Statin-related muscle side effects are a constant healthcare problem since patient compliance is dependent on side effects. Statins reduce plasma cholesterol levels and can prevent secondary cardiovascular diseases. Although statin-induced muscle damage has been studied, preventive or curative therapies are yet to be reported. We exposed primary human muscle cell populations (n = 22) to a lipophilic (simvastatin) and a hydrophilic (rosuvastatin) statin and analyzed their expressome. Data and pathway analyses included GOrilla, Reactome and DAVID. We measured mevalonate intracellularly and analyzed eicosanoid profiles secreted by human muscle cells. Functional assays included proliferation and differentiation quantification. More than 1800 transcripts and 900 proteins were differentially expressed after exposure to statins. Simvastatin had a stronger effect on the expressome than rosuvastatin, but both statins influenced cholesterol biosynthesis, fatty acid metabolism, eicosanoid synthesis, proliferation, and differentiation of human muscle cells. Cultured human muscle cells secreted ω-3 and ω-6 derived eicosanoids and prostaglandins. The ω-6 derived metabolites were found at higher levels secreted from simvastatin-treated primary human muscle cells. Eicosanoids rescued muscle cell differentiation. Our data suggest a new aspect on the role of skeletal muscle in cholesterol metabolism. For clinical practice, the addition of omega-n fatty acids might be suitable to prevent or treat statin-myopathy

Branching and Mixing: New Signals of the Ubiquitin Signaling System

Posttranslational modifications allow cells and organisms to adapt to their environment without the need to synthesize new proteins. The ubiquitin system is one of the most versatile modification systems as it does not only allow a simple on–off modification but, by forming a chain of ubiquitin molecules, allows conveying multiple signals. The structure of the chains is dependent on the linkage to the previous ubiquitin molecule as every lysine can serve as an acceptor point for this modification. Different chain types code for specific signals ranging from protein degradation to protein targeting different cellular compartments. Recently the code of ubiquitin signals has been further expanded as branching and mixing of different chain types has been detected. As an additional layer of complexity, modifications of the ubiquitin chain by ubiquitin-like modifiers, like NEDD8, SUMO, or ISG15, have been found. Here we will discuss the different chain types and the technical challenges which are associated with analyzing ubiquitin topology-based signaling

S-palmitoylation Is Required for the Control of Growth Cone Morphology of DRG Neurons by CNP-Induced cGMP Signaling

Genetic investigations have demonstrated that a specific form of axonal branching - the bifurcation of afferents from dorsal root ganglia (DRG), cranial sensory ganglia (CSG) and mesencephalic trigeminal neurons (MTN) – is regulated by a cGMP-dependent signaling pathway. This cascade is composed of the ligand C-type natriuretic peptide (CNP), the receptor guanylyl cyclase Npr2, and the cGMP-dependent protein kinase Iα (cGKIα). In the absence of any one of these components, axons no longer bifurcate, instead they turn in either an ascending or a descending direction. To gain further mechanistic insights into the process of axon bifurcation we applied different cell culture approaches to decipher downstream activities of cGKI in somatosensory growth cones. We demonstrate that CNP induces an enlargement of DRG growth cones via cGKI which is considered as the priming step of axon bifurcation in the spinal cord. This growth cone remodeling was both blocked by pharmacological inhibitors of S-palmitoylation and potentiated by blocking de-palmitoylation. cGKI colocalizes with the palmitoylome and vesicular structures including the endoplasmic reticulum, early endosomes, lysosomes primarily in the central domain of the growth cone as well as with the Golgi apparatus at the level of the soma. Interestingly, an acyl-biotin-exchange chemistry-based screen indicated that 8pCPT-cGMP-induced signaling induces S-palmitoylation of a restricted pool of proteins in the DRG-derived cell line F11. Overall, our data indicate that CNP-induced cGMP signaling via cGKI affects growth cone morphology of somatosensory afferents. Moreover, it also suggests that S-palmitoylation might play a role in this process

On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility

Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow

The Proteasome Activators Blm10/PA200 Enhance the Proteasomal Degradation of N-Terminal Huntingtin.

The Blm10/PA200 family of proteasome activators modulates the peptidase activity of the core particle (20S CP). They participate in opening the 20S CP gate, thus facilitating the degradation of unstructured proteins such as tau and Dnm1 in a ubiquitin- and ATP-independent manner. Furthermore, PA200 also participates in the degradation of acetylated histones. In our study, we use a combination of yeast and human cell systems to investigate the role of Blm10/PA200 in the degradation of N-terminal Huntingtin fragments (N-Htt). We demonstrate that the human PA200 binds to N-Htt. The loss of Blm10 in yeast or PA200 in human cells results in increased mutant N-Htt aggregate formation and elevated cellular toxicity. Furthermore, Blm10 in vitro accelerates the proteasomal degradation of soluble N-Htt. Collectively, our data suggest N-Htt as a new substrate for Blm10/PA200-proteasomes and point to new approaches in Huntington\u27s disease (HD) research

Simultaneous extraction of proteins and metabolites from cells in culture

Proper sample preparation is an integral part of all omics approaches, and can drastically impact the results of a wide number of analyses. As metabolomics and proteomics research approaches often yield complementary information, it is desirable to have a sample preparation procedure which can yield information for both types of analyses from the same cell population. This protocol explains a method for the separation and isolation of metabolites and proteins from the same biological sample, in order for downstream use in metabolomics and proteomics analyses simultaneously. In this way, two different levels of biological regulation can be studied in a single sample, minimizing the variance that would result from multiple experiments. This protocol can be used with both adherent and suspension cell cultures, and the extraction of metabolites from cellular medium is also detailed, so that cellular uptake and secretion of metabolites can be quantified. Advantages of this technique includes: 1. Inexpensive and quick to perform; this method does not require any kits. 2. Can be used on any cells in culture, including cell lines and primary cells extracted from living organisms. 3. A wide variety of different analysis techniques can be used, adding additional value to metabolomics data analyzed from a sample; this is of high value in experimental systems biology

Cervical Fluids Are a Source of Protein Biomarkers for Early, Non-Invasive Endometrial Cancer Diagnosis

Cervical sample; Endometrial cancer; ProteinMostra cervical; Càncer d'endometri; ProteïnaMuestra cervical; Cáncer de endometrio; ProteínaBackground: Abnormal uterine bleeding is the main symptom of endometrial cancer (EC), but it is highly nonspecific. This represents a huge burden for women’s health since all women presenting with bleeding will undergo sequential invasive tests, which are avoidable for 90–95% of those women who do not have EC. Methods: This study aimed to evaluate the potential of cervical samples collected with five different devices as a source of protein biomarkers to diagnose EC. We evaluated the protein quantity and the proteome composition of five cervical sampling methods. Results: Samples collected with a Rovers Cervex Brush® and the HC2 DNA collection device, Digene, were the most suitable samples for EC proteomic studies. Most proteins found in uterine fluids were also detected in both cervical samples. We then conducted a clinical retrospective study to assess the expression of 52 EC-related proteins in 41 patients (22 EC; 19 non-EC), using targeted proteomics. We identified SERPINH1, VIM, TAGLN, PPIA, CSE1L, and CTNNB1 as potential protein biomarkers to discriminate between EC and symptomatic non-EC women with abnormal uterine bleeding in cervical fluids (AUC > 0.8). Conclusions: This study opens an avenue for developing non-invasive protein-based EC diagnostic tests, which will improve the standard of care for gynecological patients.This research was funded by grants from the Instituto de Salud Carlos III (ISCIII) grant number PI17/02155, PI20/00644 to E.C. and S.C., and the IFI19/00029 to E.C.-d.l.-R.; from Fundación Científica Asociación Española Contra el Cáncer (AECC) grant number GCTRA1804MATI; and the INVES20051COLA to E.C.; the CIBERONC network grant number CB16/12/00328; and the ERA PerMed ERA-NET grant (PERME212443COLA funded by AECC and AEC21_2/00030 funded by ISCIII); and 2021 SGR 1157 by AGAUR. The present work has been also supported by a Televie grant 5/20/5—TLV/DD to G.D

In silico Approach for Validating and Unveiling New Applications for Prognostic Biomarkers of Endometrial Cancer

Bioinformática; Cáncer de endometrio; Biomarcador pronósticoBioinformàtica; Càncer d'endometri; Biomarcador pronòsticBioinformatics; Endometrial cancer; Prognostic biomarkerEndometrial cancer (EC) mortality is directly associated with the presence of prognostic factors. Current stratification systems are not accurate enough to predict the outcome of patients. Therefore, identifying more accurate prognostic EC biomarkers is crucial. We aimed to validate 255 prognostic biomarkers identified in multiple studies and explore their prognostic application by analyzing them in TCGA and CPTAC datasets. We analyzed the mRNA and proteomic expression data to assess the statistical prognostic performance of the 255 proteins. Significant biomarkers related to overall survival (OS) and recurrence-free survival (RFS) were combined and signatures generated. A total of 30 biomarkers were associated either to one or more of the following prognostic factors: histological type (n = 15), histological grade (n = 6), FIGO stage (n = 1), molecular classification (n = 16), or they were associated to OS (n = 11), and RFS (n = 5). A prognostic signature composed of 11 proteins increased the accuracy to predict OS (AUC = 0.827). The study validates and identifies new potential applications of 30 proteins as prognostic biomarkers and suggests to further study under-studied biomarkers such as TPX2, and confirms already used biomarkers such as MSH6, MSH2, or L1CAM. These results are expected to advance the quest for biomarkers to accurately assess the risk of EC patients.This research was funded by grants from the Instituto de Salud Carlos III (ISCIII) grant number PI17/02155, PI20/00644, and the IFI19/00029 to E.C.-d.l.R., the Ministerio de ciencia, Innovación y Universidades through a RETOS Colaboración (RTC-2017-6261-1), both co-financed by the European Regional Development Fund (FEDER); from Fundación Científica Asociación Española Contra el Cáncer (AECC) grant number GCTRA1804MATI and CIBERONC network grant number CB16/12/00328; and Grups Consolidats de la Generalitat de Catalunya (2017SGR1661). E.C. is supported by an Investigator Grant from AECC (INVES20051COLA). E.M.-G. was supported by Televie grant F5/20/5-TLV/DD