Statistics for proteomics: experimental design and 2-DE differential analysis

Proteomics relies on the separation of complex protein mixtures using bidimensional electrophoresis. This approach is largely used to detect the expression variations of proteins prepared from two or more samples. Recently, attention was drawn on the reliability of the results published in literature. Among the critical points identified were experimental design, differential analysis and the problem of missing data, all problems where statistics can be of help. Using examples and terms understandable by biologists, we describe how a collaboration between biologists and statisticians can improve reliability of results and confidence in conclusions.     

Development of proteomic tools to study protein adsorption on a biomaterial, titanium grafted with poly(sodium styrene sulfonate)

It is known that protein adsorption is the initial interaction between implanted biomaterials and biological environment. Generally, a complex protein layer will be formed on material surfaces within a few minutes and the composition of this layer at the interface determines the biological response to the implanted material, and therefore the long-term compatibility of the biomaterial. Despite different techniques exist to observe protein adsorption on biomaterials, none of them led to the identification of adsorbed proteins. In this paper, we report a chromatographic technique coupled to proteomics to analyse and identify proteins from complex biological samples adsorbed on biomaterial surfaces. This approach is based on (1) elaboration of the chromatographic support containing the biomaterial (2) a chromatography step involving adsorption of proteins on the biomaterial (3) the high-resolution separation of eluted proteins by 2-DE gel and (4) the identification of proteins by mass spectrometry. Experiments were performed with proteins from platelets rich plasma (PRP) adsorbed on a biomaterial which consist in titanium bioactivated with PolyNaSS. Our results show that chromatographic approach combined to 2-DE gels and mass spectrometry provides a powerful tool for the analysis and identification of proteins adsorbed on various surfaces.     

The Development of the Older Persons and Informal Caregivers Survey Minimum DataSet (TOPICS-MDS): A Large-Scale Data Sharing Initiative

Introduction

In 2008, the Ministry of Health, Welfare and Sport commissioned the National Care for the Elderly Programme. While numerous research projects in older persons’ health care were to be conducted under this national agenda, the Programme further advocated the development of The Older Persons and Informal Caregivers Survey Minimum DataSet (TOPICS-MDS) which would be integrated into all funded research protocols. In this context, we describe TOPICS data sharing initiative (www.topics-mds.eu).

Materials and Methods

A working group drafted TOPICS-MDS prototype, which was subsequently approved by a multidisciplinary panel. Using instruments validated for older populations, information was collected on demographics, morbidity, quality of life, functional limitations, mental health, social functioning and health service utilisation. For informal caregivers, information was collected on demographics, hours of informal care and quality of life (including subjective care-related burden).

Results

Between 2010 and 2013, a total of 41 research projects contributed data to TOPICS-MDS, resulting in preliminary data available for 32,310 older persons and 3,940 informal caregivers. The majority of studies sampled were from primary care settings and inclusion criteria differed across studies.

Discussion

TOPICS-MDS is a public data repository which contains essential data to better understand health challenges experienced by older persons and informal caregivers. Such findings are relevant for countries where increasing health-related expenditure has necessitated the evaluation of contemporary health care delivery. Although open sharing of data can be difficult to achieve in practice, proactively addressing issues of data protection, conflicting data analysis requests and funding limitations during TOPICS-MDS developmental phase has fostered a data sharing culture. To date, TOPICS-MDS has been successfully incorporated into 41 research projects, thus supporting the feasibility of constructing a large (>30,000 observations), standardised dataset pooled from various study protocols with different sampling frameworks. This unique implementation strategy improves efficiency and facilitates individual-level data meta-analysis.     

Purification of human galectin-1 produced in high-cell density cultures of recombinant Escherichia coli: a comparison with classic shake flask cultivation

The aim of the present work was to develop a highly productive and simplified process for active human galectin-1 (Gal1) production. Gal1 is a beta-galactoside binding lectin that differentially affects biological and cellular functions such as immune surveillance and apoptosis. These effects have attracted the attention of researchers in cell biology, biochemistry and immunology. However, the production of sufficient amounts of recombinant human Gal1 (rhGal1) is needed to study of the effects of Gal1 during cell treatments. To this end, an high-yield expression of rhGal1 was achieved by high-cell density fed-batch cultivation using an exponential glycerol feeding strategy and rhGal1 was purified by a one-step purification scheme using affinity chromatography.     

Externalization and binding of galectin-1 on cell surface of K562 cells upon erythroid differentiation

Galectin 1 (GAL1) is a β-galactoside-binding lectin involvedin cell cycle progression. GAL1 overexpression is associatedwith neoplastic transformation and loss of differentiation.The gene encoding for human GAL1 resides on chromosome 22(ql2;ql3), and its expression is devel-opmentally regulated. Althoughdevoid of signal peptide GAL1 can be externalized from cellsby a mechanism independent of the normal secretory process.We report here on a study of the effects of erythroid differentiationof the human leukemia cell line K562 on GAL1 protein expression.In undifferentiated K562 cells, GAL1 was expressed into thecytosol. However, the amount of GAL1 was surprisingly weakerin K562 cells than in other leukemia cell lines such as TF-1or KGla. Treatment of K562 cells with erythropoietin (EPO) orwith aphidicolin (APH), an inhibitor for DNA polymerase , inducedan erythroid pheno-type and led to the externalization of cytosolicGAL1 which was then bound to ligands on cell surface in a galactoside-inhibitablefashion. Our results demonstrate that acquisition of an erythroidphenotype is associated with an exter-nalization of GALL Theautocrine binding of GAL1 to cell surface ligands of non adherentcells such as K562 suggest that GAL1 is implicated rather insignal transduction than in cell-cell or cell-matrix interaction.Moreover, the reciprocal translocation involving chromosomes9 and 221(9;22) present in K562 cells might explain the weakexpression of GAL1 in K562 leukemia cells. galectin-l K562 cells differentiation glycoconjugates     

Oligoclonal β-galactoside-specific γ immunoglobulins allow the immunocytochemical detection of cellular antigenic determinants expressed in mouse brain after surgical injury

Histological brain sections were probed with human oligoclonal lectin-like IgGs (L-IgG) purified from normal serum. In intact brain, antigenic determinants for these IgG were restricted to some blood vessel endothelial cells. By contrast, during the inflammatory reaction following a surgical injury, these determinants were detected at the cell surface of different cell types, within and near the lesion site. The cells reacting with L-IgG consisted of endothelial cell, mature astrocytes, activated microglial and ependymal cells.     

Tropomyosin isoform switching in tumorigenic human fibroblasts.

We identified six tropomyosin (Tm) isoforms in diploid human fibroblasts. We used computerized microdensitometry of 2-dimensional protein profiles to measure the relative rates of synthesis and abundance of the individual Tm isoforms and actin, the two major structural constituents of microfilaments. In carcinogen-transformed human fibroblasts (HuT-14), the rates of synthesis of three Tm isoforms (Tm1, Tm2, and Tm6) were greatly decreased relative to normal diploid parental fibroblasts and to actin. In contrast, related nontumorigenic HuT fibroblasts which are "immortalized" and anchorage independent exhibited both slight down-regulation of Tm1 and Tm6 and 3.5-fold up-regulation of Tm3. Thus, Tm isoform switching from the predominance of the larger more avid Tm isoforms (Tm1, Tm2, Tm3, and Tm6) to the smaller, less avid Tm isoforms (Tm4 and Tm5) in microfilaments was a transformation-induced change correlated with tumorigenicity in human fibroblasts.     

Controlled cell Adhesion and aCtivity onto TAl6V TItanium alloy by grafting of the SURFace: Elaboration of orthopaedic implants capable of preventing joint prosthesis infection

The project ANR TECSAN “ACTISURF” has for main objective to propose a new generation of joint prosthesis (hip, knee, shoulder) made of TAl6V titanium alloy capable of limiting and even preventing the joint infections. A chemical modification of titanium surfaces has been set up to confer desirable functional and required properties to the joint prostheses. In order to prevent bacteria adhesion and to improve the long-term osteointegration, bioactive polymers bearing ionic groups were covalently grafted onto titanium surfaces by a grafting “from” technique. The bioactive polymer grafted surfaces named “bioactive TAl6V surfaces” (cylinder, prostheses, discs) were extensively characterized in vitro and in vivo to assess the bacteria and cell responses. The chemical treatment was industrialized by Ceraver Society, which is now able to produce the bioactive prosthesis at the industrial level. At the same time, a method to follow and/or to detect inflammation and infection in patient sera has been developed. Results showed that: (1) grafting of ionic polymers was successful by using radicals from titanium peroxides able to initiate the radical polymerization of ionic monomers; (2) anionic polymers successfully prevent bacterial adhesion and favor osteoblast cell adhesion and differentiation in vitro. In vivo results are still in process and will be delivered at the end of the year.