Detection of human immunodeficiency virus type 1 proviral DNA by PCR using an electrochemiluminescence-tagged probe

Development of sensitive ddPCR assays to reliably quantify the proviral DNA reservoir in all common circulating HIV subtypes and recombinant forms

INTRODUCTION

The latent reservoir is the main barrier on the road to HIV cure, and clinical approaches towards eradication are often evaluated by their effect on proviral DNA. To ensure inclusiveness and representativeness in HIV cure studies, proviral DNA quantification assays that are able to detect all common circulating HIV clades are urgently needed. Here, three HIV DNA assays targeting three different genomic regions were evaluated for their sensitivity and subtype-tolerance using digital PCR.

METHODS

A subtype-B-specific assay targeting gag (GAG) and two assays targeting conserved sequences in ltr and pol (LTR and JO) were assessed for their sensitivity and subtype-tolerance in digital PCR (Bio-Rad QX200), using a panel of serially diluted subtype reference plasmids as well as a panel of clinical isolates. Both panels represent subtypes A, B, C, D, F, G and circulating recombinant forms (CRFs) AE and AG, which together are responsible for 94% of HIV infections worldwide.

RESULTS

HIV subtype was observed to greatly affect HIV DNA quantification results. Robust regression analysis of the serially diluted plasmid panel showed that the GAG assay was only able to linearly quantify subtype B, D and G isolates (4/13 reference plasmids, average R2 = 0.99), whereas LTR and JO were able to quantify all tested isolates (13/13 reference plasmids, respective average R2 = 0.99 and 0.98). In the clinical isolates panel, isolates were considered detectable if all replicates produced a positive result. The GAG assay could detect HIV DNA in four out of five subtype B and one out of two subtype D isolates, whereas the LTR and JO assays detected HIV DNA in all twenty-nine tested isolates. LTR and JO results were found to be equally precise but more precise than GAG.

CONCLUSIONS

The results demonstrate the need for a careful validation of proviral reservoir quantification assays prior to investigations into non-B subtype reservoirs. The LTR and JO assays can sensitively and reliably quantify HIV DNA in a panel that represents the worldwide most prevalent subtypes and CRFs (A, B, C, D, AE, F, G and AG), justifying their application in future trials aimed at global HIV cure.

Synthesis of a platinum(II) complex with 2-(4-methoxy-phenyl) imidazo [4,5-f]-[1,10] phenanthrolin and study of its antitumor activity

A new platinum(II) complex of [Pt(II)(L) (pn)]Cl·2H2O (1) (pn = 1,3-propanediamine) with 2-(4-methoxy-phenyl)imidazo [4,5-f]-[1,10]phenanthrolin (H-L) was synthesized and characterized. In complex 1, the platinum adopts a four-coordinated square planar geometry. Complex 1 exhibited selective cytotoxicity against NCI-H460, BEL-7402, SK-OV-3, SK-OV-3/DDP and HeLa cell lines with IC50 values in the micromolar range (9.7-35.8 μM), but low cytotoxicity toward normal human liver HL-7702 cells. Complex 1 caused HeLa cell cycle arrest at S phase and it induced HeLa apoptosis by the activation of caspase-3/9. Various experiments showed that complex 1 preferred to bind with G-quadruplex in c-myc. Taken together, we found that complex 1 exerted its antitumor activity mainly via inhibiting telomerase by interaction with c-myc quadruplex and activation of caspase-3/9.

Micro- and nanotechnology for HIV/AIDS diagnostics in resource-limited settings

Thirty-four million people are living with HIV worldwide, a disproportionate number of whom live in resource-limited settings. Proper clinical management of AIDS, the disease caused by HIV, requires regular monitoring of both the status of the host's immune system and levels of the virus in their blood. Therefore, more accessible technologies capable of performing a CD4+ T cell count and HIV viral load measurement in settings where HIV is most prevalent are desperately needed to enable better treatment strategies and ultimately quell the spread of the virus within populations. This review discusses micro- and nanotechnology solutions to performing these key clinical measurements in resource-limited settings.

Rapid and cost-effective detection of sequence-specific DNA by monitoring the electrochemical response of 2'-deoxyguanosine 5'-triphosphate in a PCR sample

This study describes a novel strategy for rapid and cost-effective detection of sequence-specific DNA based upon the essential utility of the polymerase chain reaction (PCR) and electrochemical technologies. A dramatic enhancement of the anodic peak current (i(pa)) and a visible decrease of overpotential towards free 2'-deoxyguanosine 5'-triphosphate (dGTP) could be realized on a glassy carbon electrode modified with short single-walled carbon nanotubes (S-SWNT/GCE). Thereby, the concentration of the free dGTP in the PCR sample mixture could be determined sensitively. The i(pa) of the free dGTP decreased remarkably after a successful PCR amplification owing to the participation of the free dGTP as one of the reactive substrates for the PCR products, namely dsDNA. Based upon this response change of the free dGTP before and after incorporation in PCR, a novel method aiming at detecting PCR results was established. One transgenic maize sample as a model was successfully detected by employing the specific sequences of 35S promoter from cauliflower mosaic virus (CaMV35S) gene and nopaline synthase (NOS) gene as markers. The result was in good accordance with that obtained with gel electrophoresis.

An improved electrochemiluminescence polymerase chain reaction method for highly sensitive detection of plant viruses

Recently, we have reported an electrochemiluminescence polymerase chain reaction (ECL-PCR) method for detection of genetically modified organisms. The ECL-PCR method was further improved in the current study by introducing a multi-purpose nucleic acid sequence that was specific to the tris(bipyridine) ruthenium (TBR) labeled probe, into the 5' terminal of the primers. The method was applied to detect plant viruses. Conserved sequence of the plant viruses was amplified by PCR. The product was hybridized with a biotin labeled probe and a TBR labeled probe. The hybridization product was separated by streptavidin-coated magnetic beads, and detected by measuring the ECL signals of the TBR labeled. Under the optimized conditions, the experiment results show that the detection limit is 50 fmol of PCR products, and the signal-to-noise ratio is in excess of 14.6. The method was used to detect banana streak virus, banana bunchy top virus, and papaya leaf curl virus. The experiment results show that this method could reliably identity viruses infected plant samples. The improved ECL-PCR approach has higher sensitivity and lower cost than previous approach. It can effectively detect the plant viruses with simplicity, stability, and high sensitivity.

Electrogenerated Chemiluminescence in Polyelectrolyte Multilayers: Efficiency and Mechanism

The presence of an ultrathin film of polyelectrolyte complex, formed by the multilayering method, on an electrode was shown to enhance the intensity of electrogenerated chemiluminescence (ECL) from the tris(2,2')bipyridylruthenium(II)/tripropylamine system. Platinum electrodes coated with up to 17 layers of poly(diallyldimethylammonium chloride) or poly(vinylmethylpyridine), alternately layered with poly(styrenesulfonate), revealed significant differences in enhancement of ECL, depending on the identity of the multilayer. ECL following deposition of each layer showed an oscillating intensity of light emission, which alludes to the importance of surface and bulk charge. This effect, along with others, such as increased output with increasing tripropylamine concentration, was used to suggest a mechanism for enhanced ECL intensity at multilayer-coated electrodes.

Fibroblast growth factor-2 increases the renal recruitment and attachment of HIV-infected mononuclear cells to renal tubular epithelial cells

The role of circulating growth factors in the pathogenesis of childhood HIV-1-associated nephropathy (HIVAN) is not clearly understood. In previous studies, we found a significant accumulation of fibroblast growth factor-2 (FGF-2) in the circulation and kidneys of children with HIVAN. The purpose of this study was to determine whether circulating FGF-2 may play a role in the pathogenesis of HIVAN by increasing the renal recruitment and attachment of HIV-infected mononuclear cells to renal epithelial cells. Using in vitro cell adhesion assays, we showed that FGF-2 increased the attachment of peripheral blood mononuclear cells (PBMCs) to fibronectin-coated tissue culture dishes by approximately threefold through a mechanism that involved the alpha5 integrin subunit. In addition, we found that FGF-2 induces a similar increase in the attachment of HIV-infected PBMCs and monocytes/macrophages to plastic tissue culture dishes and to monolayers of primary renal tubular epithelial cells harvested from the urine of HIV-infected children with renal disease. Finally, we injected 16 adult C57Bl6/J male mice with recombinant adenoviral vectors carrying either the LacZ gene or a secreted form of human FGF-2 (5 x 10(8)pfu/mouse) and demonstrated that high levels of circulating FGF-2 can increase the renal recruitment of circulating inflammatory cells and induce transient tubulointerstitial injury in vivo. These data suggest that FGF-2 may have an immunomodulatory role in the pathogenesis of HIVAN by recruiting HIV-infected cells in the kidney.

Enzyme-amplified amperometric detection of 3000 copies of DNA in a 10-microL droplet at 0.5 fM concentration

We reported earlier the detection of a 38-base DNA strand at 20 pM concentration by an enzyme-amplified sandwich-type amperometric assay. The assay utilized a carbon electrode on which a redox polymer, comprising a DNA capture sequence, was electrodeposited. When present in the tested solution, part of the probed sequence hybridized with the capture probe. Hybridization of its remaining part with a horseradish peroxidase (HRP)-labeled sequence resulted in the flow of an H2O2 electroreduction current, the redox polymer wired HRP forming an electrocatalyst. Here we report a > 10(4)-fold improvement in the detection limit of the assay. DNA was detected at 0.5 fM concentration when the earlier used 3.6-mm-diameter carbon electrode was replaced by a 10-microm-diameter microelectrode. The radial diffusion of electrons through the film on the microelectrode allowed the electrodeposition of a thicker film of the redox polymer, an increase in the loading of the capture sequence, and increased the collection efficiency of the electron vacancies originating in the electroreduced H2O2. When the volume probed by the microelectrode was 10 microL, as few as 3000 copies of DNA were detected.

Rapid monitoring of recombinant protein products: a comparison of current technologies

Specific measurement of recombinant protein titer in a complex environment during industrial bioprocessing has traditionally relied on labor-intensive and time-consuming immunoassays. In recent years, however, developments in analytical technology have resulted in improved methods for protein product monitoring during bioprocessing. The choice of product-monitoring technology for a particular bioprocess will depend on a variety of assay factors and instrument-specific factors. In this article, we have compiled an overview of the advantages and disadvantages of the most commonly used technologies used: electrochemiluminescence, optical biosensors, rapid chromatography and nephelometry. The advantages of each technology for measuring both small and large recombinant therapeutic proteins are compared with a conventional enzyme-linked immunosorbent assay (ELISA) technique.

A wireless electrochemiluminescence detector applied to direct and indirect detection for electrophoresis on a microfabricated glass device

A novel electrochemiluminescence (ECL) detector is presented in this article. The detector is applied for micellar electrokinetic chromatographic separation of dichlorotris(2,2'-bipyridyl)ruthenium(II) hydrate [Ru-(bpy)] and dichlorotris(1,10-phenanthroline)ruthenium-(II) hydrate [Ru(phen)] on a microfabricated glass device. It consists of a microfabricated "U"-shape floating platinum electrode placed across the separation channel. The legs of the U function respectively as working and counter electrode. The required potential difference for the ECL reaction is generated at the Pt electrode by the electric field available in the separation channel during electrophoretic separation. Initial experiments demonstrate a micellar electrokinetic separation and direct ECL detection of 10(-16) mol of Ru(phen) (10(-6) M) and 4.5 x 10(-16) mol of Ru(bpy) (5 x 10(-6) M). Also, preliminary results show the indirect detection of three amino acids. The high voltage at the location of detection does not interfere with the electrochemistry.

Infection of human primary renal epithelial cells with HIV-1 from children with HIV-associated nephropathy

Children affected with human immunodefficiency virus (HIV)-associated nephropathy (HIVAN) usually develop significant renal glomerular and tubular epithelial cell injury. The pathogenesis of these changes is not clearly understood. Human renal tubular epithelial cells (RTEc) do not express CD4 surface receptors, and it is not clear whether these cells can be infected by HIV-1. Certain strains of HIV-1, however, have been shown capable of infecting CD4-negative epithelial cell lines. We hypothesized that the inability of laboratory strains of HIV-1 to infect renal epithelial cells may be due to a limited tropism, as opposed to wild-type viruses derived from children with HIVAN, and that viruses derived from these children are capable of infecting RTEc from the same patient. Here, we have demonstrated that HIV-1 isolates from children with HIVAN can productively infect RTEc through a CD4 independent pathway, and that infected mononuclear cells can transfer the virus to human RTEc. Human RTEc sustained low levels of viral replication and HIV-1 inhibited the growth and survival of cultured human RTEc. Thus, HIV-1 may directly induce degenerative changes in RTEc of children with HIVAN. Infected macrophages may play a relevant role in this process by transferring viruses to RTEc.

Comparison of culture and the antigenemia assay for detection of cytomegalovirus in blood specimens submitted to a reference laboratory

We compared the antigenemia assay (AA) with tandem shell vial cultures (SVCs) and tube cultures (TCs) for detection of cytomegalovirus (CMV) in 343 blood specimens. For 249 specimens, the AA was performed in duplicate with two different commercially available monoclonal antibody reagents (Biotest Diagnostic Corporation and Argene Biosoft). Specimens considered true positives were positive in either culture system or both AAs. Only specimens which were negative in both cultures and positive in a single AA were tested retrospectively with a CMV PCR assay. CMV recovery rates were also calculated to determine if increased specimen age resulted in decreased positivity. CMV recovery rates for the AA and the combination of both cultures were 20.0 and 5.0% at 3 to 18 h, 20.2 and 14.0% at 18 to 35 h, 12.5 and 7.8% at 36 to 52 h, and 18.8 and 6.3% at 64 to 75 h, respectively. The sensitivities and specificities of the Biotest AA, the Argene AA, SVC, and TC were 84.4 and 100.0, 100.0 and 99.6, 44.4 and 100.0, and 46.0 and 100.0%, respectively. The AA was significantly more sensitive than either culture method alone and was also more sensitive than the two culture methods used in tandem (the tandem culture sensitivity was 63.5%); the Argene AA identified more positives than the Biotest AA.

Concepts, principles, and applications of selected molecular biology techniques in clinical biochemistry

The myriad molecular techniques that have been developed and are undergoing refinement have advanced our knowledge of disease processes and made available strategies for detection. While the greatest impact of molecular techniques in the diagnostic laboratory has been in the realm of infectious diseases, techniques such as flow cytometry, FISH, and multiplex-nested PCR followed by direct DNA sequencing are increasing the scope of cancer detection and treatment. The facile typing of HLA-class II genes is a major advance in the matching of donors to recipients of organ transplantation. With advances in genosensor technology and robotic automation, molecular biology techniques are clearly poised to enter the diagnostic clinical biochemistry laboratory for multiple applications.