Biomedical subjects

Jacques Corbeil

Publications and source records attributed to Jacques Corbeil.

9 recordsLinked to original sources

PubMed2003

2HAPI: a microarray data analysis system.

SUMMARY: 2HAPI (version 2 of High density Array Pattern Interpreter) is a web-based, publicly-available analytical tool designed to aid researchers in microarray data analysis. 2HAPI includes tools for searching, manipulating, visualizing, and clustering the large sets of data generated by microarray experiments. Other features include association of genes with NCBI information and linkage to external data resources. Unique to 2HAPI is the ability to retrieve upstream sequences of co-regulated genes for promoter analysis using MEME (Multiple Expectation-maximization for Motif Elicitation) AVAILABILITY: 2HAPI is freely available at http://array.sdsc.edu. Users can try 2HAPI anonymously with pre-loaded data or they can register as a 2HAPI user and upload their data.

Algorithms↗

PubMed2003

Polyclonal proliferation and apoptosis of CCR5+ T lymphocytes during primary human immunodeficiency virus type 1 infection: regulation by interleukin (IL)-2, IL-15, and Bcl-2.

We measured apoptosis of subsets of T lymphocytes by single-cell analysis of caspase activation, to confirm high turnover of chemokine receptor CCR5(+) T cells in subjects with acute, primary human immunodeficiency virus type 1 (HIV-1) infection (PHI). High levels of spontaneous apoptosis, consisting mainly of CD8(+) T lymphocytes, were closely associated with increases in the activation markers Ki-67, CD38, and the HIV coreceptor CCR5 and with decreases in Bcl-2 and the interleukin (IL)-7 receptor at the single-cell level. Increased expression of Ki-67 and CCR5 ex vivo, as well as increased apoptosis, was seen in all T cell receptor beta-chain variable region (TCRBV) subfamilies studied. The addition of IL-2 or IL-15, but not IL-7, significantly inhibited caspase activation, increased Bcl-2 expression, and rapidly initiated proliferation in vitro of CD8(+) T cells expressing CCR5 and multiple TCRBV subfamilies. Furthermore, IL-15 receptor alpha-chain messenger RNA levels were increased in peripheral blood mononuclear cells during PHI. These results suggest that CCR5(+)Ki-67(+)Bcl-2(dim) activated T cells generated during PHI traffic via blood to tissue sites, where the cells may survive and/or further proliferate under the local influence of IL-2 or IL-15. Understanding cytokine effects on CCR5(+) T cells will be important in understanding chronic HIV-1 replication and pathogenesis.

Adult↗

PubMed2003

Effect of micromechanical stimulations on osteoblasts: development of a device simulating the mechanical situation at the bone-implant interface.

Many experimental models have been developed to investigate the effects of mechanical stimulation of cells, but none of the existing devices can simulate micromotions at the cellular-mechanical interface with varying amplitudes and loads. Osteoblasts are sensitive to mechanical stimuli, so to study the bone-implant interface it would be important to quantify their reaction in a situation mimicking the mechanical situation arising at that interface. In this study, we present the development of a new device allowing the application of micromotions and load on cells in vitro. The new device allowed the cells to be stimulated with sinusoidal motions of amplitudes comprised between +/- 5 and +/- 50 microm, frequencies between 0.5 and 2 Hz, and loads between 50 and 1000 Pa. The device, with a total length of 20 cm, was designed to work in an incubator at 37 degrees C and 100% humidity. Expression of various bone important genes was monitored by real-time RT-PCR. Micromotions and load were shown to affect the behavior of osteoblasts by down-regulating the expression of genes necessary for the creation of organic extracellular matrix (collagen type I) as well as for genes involved in the mineralization process (osteocalcin, osteonectin). The developed device could then be used to simulate different mechanical situations at the bone-implant interface.

Bone and Bones↗

PubMed2003

Surface CD4 expression modulated by a cellular factor induced by HIV type 1 infection.

Human immunodeficiency virus type 1 (HIV-1) alters gene expression in infected cells, leading to cellular dysfunction. We uncovered a number of host cell genes that are modulated in both CD4(+) T cell lines and primary CD4(+) T lymphocytes infected with HIV-1, using high-density oligonucleotide probe microarray technology. We focused on one gene in particular, nuclear factor I-B2 (NFI-B2), because of its high level of expression. NFI-B2 is a member of the nuclear factor I family of nuclear proteins, which are known to be involved in viral and cellular transcription. To better understand the role of NFI-B2 during HIV-1 infection, we generated a Jurkat T cell line that constitutively expressed NFI-B2. After infection with HIV-1, these cells produced fewer viruses because of a downregulation of surface CD4 expression. The surface expression of the coreceptor, CXCR4, remained unchanged. Furthermore, levels of CD4 mRNA were reduced in NFI-B2-producing cells, suggesting that expression of NFI-B2 impairs CD4 transcription. Modulation of NFI-B2 by HIV-1 may represent yet another mechanism by which HIV infection reduces cell surface expression of CD4.

CCAAT-Enhancer-Binding Proteins↗

PubMed2003

A new perspective on V3 phenotype prediction.

The particular coreceptor used by a strain of HIV-1 to enter a host cell is highly indicative of its pathology. HIV-1 coreceptor usage is primarily determined by the amino add sequences of the V3 loop region of the viral envelope glycoprotein. The canonical approach to sequence-based prediction of coreceptor usage was derived via statistical analysis of a less reliable and significantly smaller data set than is presently available. We aimed to produce a superior phenotypic classifier by applying modern machine learning (ML) techniques to the current database of V3 loop sequences with known phenotype. The trained classifiers along with the sequence data are available for public use at the supplementary website: http://genomiac2.ucsd.edu:8080/wetcat/v3.html and http://www.cs.waikato.ac.nz/ml/weka[corrected].

Amino Acid Sequence↗

PubMed2002

Gene expression analysis of osteoblastic cells contacted by orthopedic implant particles.

Particles generated from orthopedic implants through years of wear play an essential role in the aseptic loosening of a prosthesis. We have investigated the biocompatibility of these orthopedic particles on different osteoblast-like cells representative of different stages of osteoblast maturation. We found the particles induced a caspase-dependent apoptosis of osteoblasts, with less mature osteoblasts being the most susceptible. An analysis of gene expression was performed on the less mature osteoblasts, which were in contact with the particles. We found that the particles had a profound impact on genes that code for inflammatory cytokines and genes involved in controlling the nuclear architecture. Results from this study suggest that the peri-implant osteolysis after a total joint replacement can be due in part to a decrease of bone formation and not solely to an overstimulation of bone resorption as is generally proposed. Development of new drugs that promote normal bone formation and osteoblast survival would possibly control peri-implant osteolysis, resulting in a better prognosis for patients with orthopedic implants.

Animals↗

PubMed2002

Large-scale gene expression analysis of osteoblasts cultured on three different Ti-6Al-4V surface treatments.

To improve implant biocompatibility, we developed a simple cost-effective thermal surface treatment allowing an increase in the oxide layer thickness of a titanium (Ti) alloy used in orthopaedic implants. The goal of this study was to test in vitro the reaction of osteoblasts to the developed surface treatment and to compare it to the osteoblast reaction to two other surface treatments currently used in the practice of implant surgery. Quantification of osteoblast gene expression on a large scale was used in this study. The kinetics of gene expression over 120 h was followed for 58 genes to quantify the effect of the developed surface treatment. Twenty eight genes were further selected to compare the effects of surface treatments on osteoblasts. Based on the genes studied, we could propose a general pathway for the cell reaction according to the surface treatments used: (1) metal ion release changes the time course of gene expression in the FAK pathway; (2) once the accumulation of metal ions released from the Ti surface exceeds a threshold value, cell growth is diminished and apoptosis may be activated; (3) PTK up-regulation is also induced by metal ion release; (4) the expression of Bcl-2 family and Bax may suggest that metal ions induce apoptosis. The developed treatment seems to increase the Ti-6Al-4V biocompatibility as highlighted by the lower impact of this treatment by the different pathways studied, on the lower inflammatory reaction that could be induced, as well as by the lower induced osteoblast apoptosis compared to the two other surface treatments.

Alloys↗

PubMed2002

Effects of antiretroviral drugs on human immunodeficiency virus type 1-induced CD4(+) T-cell death.

Apoptosis of peripheral blood T cells plays an important role in the pathogenesis of human immunodeficiency virus (HIV) infection. In this study, we found that HIV type 1 (HIV-1) primes CD4(+) T cells from healthy donors for apoptosis, which occurs after CD95 ligation or CD3-T-cell receptor (TCR) stimulation. CD95-mediated death did not depend on CD4 T-cell infection, since it occurred in the presence of the reverse transcriptase inhibitor didanosine (ddI). In contrast, apoptosis induced by productive infection (CD3-TCR stimulation) is prevented by both CD95 decoy receptor and ddI. Our data suggest that HIV-1 triggers at least two distinct death pathways: a CD95-dependent pathway that does not require viral replication and a viral replication-mediated cell death independent of the CD95 pathway. Further experiments indicated that saquinavir, a protease inhibitor, at a 0.2 microM concentration, decreased HIV-mediated CD95 expression and thus cell death, which is independent of its role in inhibiting viral replication. However, treatment of peripheral blood mononuclear cells from healthy donors with a higher concentration (10 microM) of an HIV protease inhibitor, saquinavir or indinavir, induced both a loss in mitochondrial membrane potential (DeltaPsim) and cell death. Thus, protease inhibitors have the potential for both beneficial and detrimental effects on CD4(+) T cells independent of their antiretroviral effects.

Anti-HIV Agents↗

PubMed2001

Productive HIV-1 infection of primary CD4+ T cells induces mitochondrial membrane permeabilization leading to a caspase-independent cell death.

We have explored in vitro the mechanism by which human immunodeficiency virus, type 1 (HIV-1) induces cell death of primary CD4+ T cells in conditions of productive infection. Although HIV-1 infection primed phytohemagglutinin-activated CD4+ T cells for death induced by anti-CD95 antibody, T cell death was not prevented by a CD95-Fc decoy receptor, nor by decoy receptors of other members of the TNFR family (TNFR1/R2, TRAILR1/R2/OPG, TRAMP) or by various blocking antibodies, suggesting that triggering of death receptors by their cognate ligands is not involved in HIV-induced CD4 T cell death. HIV-1 induced CD4 T cell shrinkage, cell surface exposure of phosphatidylserine, loss of mitochondrial membrane potential (Deltapsim), and mitochondrial release of cytochrome c and apoptosis-inducing factor. A typical apoptotic phenotype (nuclear chromatin condensation and fragmentation) only occurred in around half of the dying cells. Treatment with benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone, a broad spectrum caspase inhibitor, prevented nuclear chromatin condensation and fragmentation in HIV-infected CD4+ T cells and in a cell-free system (in which nuclei were incubated with cytoplasmic extracts from the HIV-infected CD4+ T cells). Nevertheless, benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone did not prevent mitochondrial membrane potential loss and cell death, suggesting that caspases are dispensable for HIV-mediated cell death. Our findings suggest a major role of the mitochondria in the process of CD4 T cell death induced by HIV, in which targeting of Bax to the mitochondria may be involved.

Animals↗