Biomedical subjects

Dequan Chen

Publications and source records attributed to Dequan Chen.

10 recordsLinked to original sources

PubMed2006

Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data.

BACKGROUND: Multicategory Support Vector Machines (MC-SVM) are powerful classification systems with excellent performance in a variety of data classification problems. Since the process of generating models in traditional multicategory support vector machines for large datasets is very computationally intensive, there is a need to improve the performance using high performance computing techniques. RESULTS: In this paper, Parallel Multicategory Support Vector Machines (PMC-SVM) have been developed based on the sequential minimum optimization-type decomposition method for support vector machines (SMO-SVM). It was implemented in parallel using MPI and C++ libraries and executed on both shared memory supercomputer and Linux cluster for multicategory classification of microarray data. PMC-SVM has been analyzed and evaluated using four microarray datasets with multiple diagnostic categories, such as different cancer types and normal tissue types. CONCLUSION: The experiments show that the PMC-SVM can significantly improve the performance of classification of microarray data without loss of accuracy, compared with previous work.

Algorithms↗

PubMed2006

Dendritic cell surface calreticulin is a receptor for NY-ESO-1: direct interactions between tumor-associated antigen and the innate immune system.

How the immune system recognizes endogenously arising tumors and elicits adaptive immune responses against nonmutated tumor-associated Ags is poorly understood. In search of intrinsic factors contributing to the immunogenicity of the tumor-associated Ag NY-ESO-1, we found that the NY-ESO-1 protein binds to the surface of immature dendritic cells (DC), macrophages, and monocytes, but not to that of B cells or T cells. Using immunoprecipitation coupled with tandem mass spectrometry, we isolated DC surface calreticulin as the receptor for NY-ESO-1. Calreticulin Abs blocked NY-ESO-1 binding on immature DC and its cross-presentation to CD8+ T cells in vitro. Calreticulin/NY-ESO-1 interactions provide a direct link between NY-ESO-1, the innate immune system, and, potentially, the adaptive immune response against NY-ESO-1.

Antigens, Neoplasm↗

PubMed2006

Caspase-3 and -7 mediate apoptosis of human Chang's conjunctival cells induced by enterovirus 70.

Enterovirus 70 (EV70) is the major etiological agent of acute hemorrhagic conjunctivitis (AHC). EV70 m.o.i.- (multiplicity of infection) and time-dependently induced apoptosis in human Chang's conjunctival (HCC) cells. UV- or heat-inactivated EV70 did not induce apoptosis. EV70-induced apoptosis was inhibited by cycloheximide and methoxysuccinyl-Ala-Ala-Pro-Val-chloromethylketone (MPCMK), but not actinomycin D and guanidine.HCl (although guanidine.HCl inhibited the apoptosis induced by EV70 infection at 0.5 PFU/cell for 18 h). EV70 infection induced activation of caspase-3 and -7 and degradation of the constitutively activated caspase-6. EV70-induced apoptotic DNA ladders and activated caspase-3 and -7, correlated with virus release. Caspase inhibitor IX (Z-VD-FMK) inhibited EV70-induced apoptosis and virus release, but not intracellular viral production. The results suggest that infectious virus and the syntheses of viral proteins especially EV70 proteases, but not viral genome RNA, are required for caspase-3 and -7-mediated EV70-induced apoptosis, and that apoptosis through cell lysis promotes EV70 release from HCC cells.

Apoptosis↗

PubMed2006

Intracameral toxicity of bacterial components muramyl dipeptide and staurosporine: ciliary cyst formation, epithelial cell apoptosis and necrosis.

The uveitogenic bacterial cell wall component muramyl dipeptide (MDP) is apoptogenic in rabbit kidney cells. The purpose of this investigation was to assess the cytotoxic activity of MDP and staurosporine (STSP; induces cultured corneal and lens cells apoptosis) in rabbit ciliary body tissue. Anterior uveitis was determined by clinical symptoms and increased aqueous humor (AH) protein. Ciliary body tissue was assessed for histological changes, caspase-3 activity, dye uptake, distribution of immunoreactive caspase-3 and DNA ladders at 4 and 6 hours postinjection. Increases in caspase-3 activity, APOPercentage dye uptake, and localization of immunoreactive caspase-3 in ciliary epithelial cells were associated with ciliary cysts of detached nonpigmented epithelial (NPE) cells, as well as apoptotic and necrotic DNA ladders in ciliary body tissues from eyes injected with MDP and/or STSP. The results suggest that intracameral injection of the bacterial components MDP and STSP can induce acute endophthalmic changes in uveal tissue including formation of ciliary body, NPE and pigmented epithelial (PE) cell apoptosis, and ciliary body tissue necrosis.

Acetylmuramyl-Alanyl-Isoglutamine↗

PubMed2005

Surface calreticulin mediates muramyl dipeptide-induced apoptosis in RK13 cells.

Calreticulin (CRT) is a binding protein for apoptotic N-acetylmuramyl-L-alanyl-D-isoglutamine (L,D-MDP) or peptidoglycan in RK(13) cells. CRT on RK(13) cell surface (srCRT) forms complex(es) with tumor necrosis factor receptor 1 (TNFR1) and TNFR-associated death domain (TRADD) protein of the cell membrane. CRT polyclonal or monoclonal antibody binding to RK(13) srCRT dose-dependently inhibited L,D-MDP-induced apoptosis. In RK(13) cells, L,D-MDP up-regulated the TNFR1.TRADD complex of the plasma membrane and subsequently induced cytosolic TRADD-Fas-associated death domain protein complex. Biotinylated srCRT was capable of calcium-dependent binding of Sepharose-immobilized L,D-MDP or peptidoglycan. However, Toll-like receptors TLR-2 and TLR-4, Nod2, and CD14 of RK(13) cells did not specifically bind Sepharose-immobilized L,D-MDP. High concentrations (5-40 mm) of EGTA dose-dependently inhibited free L,D-MDP binding to purified RK(13) cell CRT and promoted free L,D-MDP dissociation from RK(13) cell CRT.MDP complex. Different concentrations of EGTA (0-40 mm) added to Dulbecco's modified essential medium with 1.8 mm calcium or phosphate-buffered saline with 0.18 mm calcium have different effects on medium free calcium concentrations but have identical inhibiting effects on L,D-MDP-induced apoptosis. More inhibition of the L,D-MDP-induced apoptotic DNA ladders and caspase-3 activity in RK(13) cells was obtained with EGTA pretreatment (83%) than just EGTA + L,D-MDP (47%). The knocking down of srCRT by antisense oligonucleotide CRTAS121 (250 nmol/ml) and stealth small interfering RNA CRT_siR479 (150 pm/ml) for 2 days (44 and 66%, respectively), resulted in the inhibition of L,D-MDP-induced caspase-3 activity (47 and 65%, respectively). The results suggest that (a) the binding of L,D-MDP to srCRT is calcium-dependent, i.e. on srCRT-bound calcium, and (b) it is srCRT, not TLR-2, TLR-4, Nod2 or CD14, that mediates L,D-MDP-induced RK(13) cell apoptosis through activating the TNFR1. TRADD-Fas-associated death domain protein apoptotic pathway.

Acetylmuramyl-Alanyl-Isoglutamine↗

PubMed2005

Immunogenicity of enterovirus 70 capsid protein VP1 and its non-overlapping N- and C-terminal fragments.

Currently no practical treatment method or effective virus vaccine is available for acute hemorrhagic conjunctivitis (AHC) caused by enterovirus 70 (EV70). Antibodies to UV-inactivated EV70 (J670/71 epidemic isolate) and to the inclusion bodies of recombinant proteins of full-length EV70 VP1 (GST-VP1m), its non-overlapping terminal fragments N138 (1-138 aa) and C170 (141-310 aa) (or GST-N138m and GST-C170) were developed in rabbits. The anti-EV70 neutralizing activities of the rabbit sera were determined by standard neutralization assays. The antibodies to UV-inactivated EV70, were immuno-reactive with EV70 capsid proteins VP1 and VP3 of four EV70 epidemic isolates (KW/97, T260/74, J670/71 and AE/72) in Western-blot analysis, and immunoprecipitated the capsid proteins VP1 and VP3 from the cell lysates of virus-infected human Chang's conjunctival (HCC) cells. The antibodies to GST-VP1m, GST-N138m and GST-C170, immunoprecipitated only the VP1 proteins of the four EV70 isolates. Anti-EV70 J670/71 antibodies and the antibodies to the three recombinant VP1 proteins were all capable of immunoprecipitating EV70 whole-virus of the four EV70 epidemic isolates grown in HCC cells. The anti-EV70 virion antibodies neutralized EV70 isolates with titers of 6000-10,000 units/ml while the antibodies to GST-VP1m, GST-N138m or GST-C170 neutralized EV70 isolates with titers of 20-320units/ml. The results suggest that (a) immunization with bacterially produced recombinant EV70 VP1 and its non-overlapping N- and C-terminal fragments, was capable of eliciting EV70-neutralizing antibodies; (b) the neutralization titers of antibodies to the recombinant VP1 proteins were lower than that of antibodies to the UV-inactivated EV70 virions; and (c) the non-overlapping N138 and C170 fragments of EV70 VP1 both harbor independent anti-EV70 neutralization antigenic sites.

Antibodies, Viral↗

PubMed2004

Calreticulin is a binding protein for muramyl dipeptide and peptidoglycan in RK13 cells.

Calreticulin (CRT) was isolated and identified as a protein in rabbit kidney RK(13) cells that binds the apoptogenic bacterial cell wall (BCW) components, muramyl dipeptide (MDP) and peptidoglycan (PG). Mannan-agarose purified RK(13) cell CRT (rCRT) selectively bound sepharose-immobilized L,D-MDP and PG, but not L,L-MDP or D,D-MDP. Purified rCRT and bovine CRT (bCRT) also bound free PG and L,D-MDP demonstrated in bioassays of RK(13) cell apoptosis. The results suggest that, in RK(13) cells, (a) CRT is a specific binding protein for both L,D-MDP and PG and (b) CRT binding L,D-MDP or PG is dependent on the stereoisomeric configuration of the dipeptide (L-alanyl-D-isoglutamine) moiety. In addition, the results also suggest that, in RK(13) cells, the binding of L,D-MDP, L,L-MDP, D,D-MDP, or PG to CRT correlates with their capacities of inducing apoptosis.

Acetylmuramyl-Alanyl-Isoglutamine↗

PubMed2004

Expression of enterovirus 70 capsid protein VP1 in Escherichia coli.

The VP1 gene of enterovirus 70 (EV70) possesses a large number of Escherichia coli low-usage codons (11.0%) and a bacterial ribosome binding site complementary sequence (RBSCS) 5'-UGUCUCCUUUUC-3' flanking the codon 139. Plasmids containing EV70 cDNA encoding the full-length VP1 failed to express in E. coli (BL21(DE3), Rosetta 2(DE3) or Rosetta (DE3)pLysS). High expression (>8% of total protein) of recombinant VP1 (rVP1m) in E. coli required engineering of the encoding cDNA (conserved modification of the native cDNA) by simultaneous substitution of a rare-codon cluster located between codons 103 and 132, and replacement of the RBSCS-TCCTTT sequence. The rare-codon frequencies of the cDNAs encoding VP1 non-overlapping terminal fragments N138 (1-138 aa) and C170 (141-310 aa) are similar (10.9 and 11.2%, respectively). However, in E. coli, high expression of recombinant C170 (rC170) required no modification of the native cDNA whereas high expression of recombinant N138 (rN138m) required minimal synonymous substitution of the above rare-codon cluster. The rare-codon cluster of EV70 VP1 gene has five least-usage arginine codons (AGG/AGA) and three tandem rare-codon pairs (AGGAGG, CUAAGG, and AGACUA). Our results suggest that the rare-codon cluster (its rare codon arrangement per se and/or its related mRNA secondary structure(s)) and the RBSCS in EV70 VP1 gene, not the rare-codon frequency, constitute the key elements that suppress its expression in E. coli.

Binding Sites↗

PubMed2003

Systemic and ocular antibody responses to inactivated acute hemorrhagic conjunctivitis (AHC) virus; enterovirus 70 (EV70).

PURPOSE: Evaluate the immune response in rabbits injected with EV70, the agent of acute hemorrhagic conjunctivitis (AHC) and AHC associated neuropathy. METHODS: Rabbits were injected intramuscularly with uv-light inactivated EV70 isolate J670/71. Neutralizing activity against EV70 was quantified in serum and tear samples and the immunoglobulin (Ig) classes of the neutralizing activity in serum identified by sucrose gradient ultra-centrifugation. Adjuvant muramyl dipeptide (MDP) was applied topically to assess the role of ocular inflammation on levels of neutralizing antibody, proteins and Ig in tears. The protective effects of human and rabbit sera and interferon-alpha (IFN-alpha) against EV70 were compared in human conjunctival and lens cells. RESULTS: Sera collected at 6 and 13 d contained 19S IgM anti-EV70 neutralizing antibody, while serum collected 21 d post injection contained 19S IgM and 7S IgG anti-EV70 neutralizing antibody. Low titers of anti-EV70 activity (< or =30 U/ml) were detected in tears of seropositive rabbits. MDP induction of conjunctivitis in seropositive rabbits increased tear IgG concentration (3-fold) and anti-EV70 neutralizing antibody titers (> or =10-fold). The protective effect of the rabbit and human sera against EV70 infection in conjunctival, but not lens epithelial cells, was enhanced by the addition of IFN-alpha. CONCLUSIONS: Immunization with uv-light inactivated EV70 elicits a classical humoral immune response in rabbits. The protective activity of serum in EV70-infected human conjunctival cells, but not lens cells, was increased by IFN-alpha. Adjuvant MDP-induced conjunctivitis, increased blood-conjunctival barrier (BCB) permeability and anti-EV70 neutralizing activity in tear of seropositive rabbits. The results suggest immunization with inactivated EV70 could provide systemic as well as ocular protection during natural EV70 infection.

Acetylmuramyl-Alanyl-Isoglutamine↗

PubMed2002

Stereo-isomer specific induction of renal cell apoptosis by synthetic muramyl dipeptide (N-acetylmuramyl-L-alanyl-D-isoglutamine).

The cytotoxicity of bacterial cell wall components, muramyl dipeptide (synthetic N-acetylmuramyl-L-alanyl-D-isoglutamine; L,D-MDP) and lipopolysaccharide (LPS), was investigated in several kidney cell lines. MDP and LPS were toxic to rabbit and monkey kidney cells, MDP was toxic to canine kidney cells, but not to human or porcine kidney cells. Notably, L,D-MDP was >100-fold more cytotoxic/microg than the D,D-MDP and L,L-MDP, as well as LPS. L,D-MDP and analogs containing L,D-MDP were the most widely cytotoxic of the MDP tested. The MDP-induced cytotoxicity was characterized as apoptosis by DAPI staining and DNA laddering. The acute rabbit kidney (RK13) cell apoptosis (cell death in < 5 h) induced by apical or basal application of MDP was associated with glutamate (Glu) release, decreased gamma-glutamyltranspeptidase (GGT) and acidosis and was suppressed by Indomethacin, Naproxen and Curcumin. The cytotoxic activity of L,D-MDP was decreased significantly by 24 h incubation in human sera. Aged (> 2 year-old) rabbits that apparently failed to quickly clear and excrete a uveitogenic dose of MDP within 24 h died in I week. The results indicate that minute amounts (5 ng/ml) of MDP containing L-alanyl-D-isoglutamine can induce renal cell apoptosis in vitro and support MDP-induced kidney cytotoxicity in rabbits. Also, the results indicate that MDP in sera can be detected utilizing the RK13 cell bioassay and that failure to rapidly clear and excrete L,D-MDP is associated with uveitis and death in aged rabbits.

Acetylmuramyl-Alanyl-Isoglutamine↗