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Original Article

Detection of Human Immunodeficiency Virus Type 1 Provirus in Mononuclear Cells by in Situ Polymerase Chain Reaction

Omar Bagasra, M.D., Ph.D., Stephen P. Hauptman, D.O., Harold W. Lischner, M.D., Mark Sachs, M.D., and Roger J. Pomerantz, M.D.

N Engl J Med 1992; 326:1385-1391May 21, 1992

Abstract
Abstract

Background

Studies of human immunodeficiency virus type 1 (HIV-1) infection have attempted to quantitate the viral load and correlate it with the degree of immune deficiency. In one study, only about 1 in 10,000 peripheral-blood mononuclear cells (PBMC) expressed HIV-1, but in other studies, at least 1 in 100 CD4-positive cells was infected and harbored the HIV-1 provirus.

Methods

We developed a new, highly sensitive in situ polymerase-chain-reaction (PCR) method that amplifies selected genetic regions within intact single cells. We used this technique to determine the proportion of PBMC carrying HIV-1 provirus in infected patients in different stages of disease.

Results

None of the PBMC from 11 HIV-1—seronegative patients were found to be positive for HIV-1 provirus by the in situ PCR method. In 56 patients infected with HIV-1, the percentage of PBMC with HIV-1 ranged from 0.1 percent to 13.5 percent. The mean percentage of infected mononuclear cells was greater in 13 patients with persistent generalized adenopathy (mean, 6.6 percent) and 19 with the acquired immunodeficiency syndrome (Stages IV-A to IV-C) (4.6 percent) than in 19 patients with asymptomatic HIV-1 infection (0.9 percent) (P<0.001). However, in five patients with Kaposi's sarcoma (Stage IV-D), an average of only 1.6 percent of mononuclear cells were infected.

Conclusions

In HIV-1 infection, the proportion of PBMC that are infected appears to be at least 10 times higher than previously described. It is likely that most infected cells contain HIV-1 provirus in a latent or defective form that was not detected in some earlier studies. (N Engl J Med 1992;326:1385–91.)

Article

SINCE human immunodeficiency virus type 1 (HIV-1) was first described as the etiologic agent of the acquired immunodeficiency syndrome (AIDS),1 , 2 the numbers of cells infected in vivo with HIV-1 have been evaluated in patients in various clinical stages of disease.3 , 4 These studies have sought to correlate levels of HIV-1 infection with the pathogenesis and the clinical course of the disease.

The initial studies of Harper et al.4 demonstrated that with the use of in situ hybridization for HIV-1-specific RNA, only 1 in 10,000 to 1 in 100,000 peripheral-blood mononuclear cells (PBMC) and lymph-node cells can be identified as positive for HIV-1 in vivo. Of course, these findings did not rule out the possibility that HIV-1 may be present in a higher proportion of PBMC as a nonreplicating provirus. These data, though, make it difficult to understand how such a low number of HIV-1—infected cells could cause such a severe depletion of CD4-positive lymphocytes. Recent data suggest that the number of PBMC containing HIV-1—specific RNA is higher in patients with the infection.5 Ho et al.,6 using limitingdilution assays, have shown that infectious HIV-1 can be isolated from an average of 1 in 400 PBMC obtained from patients with AIDS, although higher levels have been detected during acute seroconversion to HIV-1.7 , 8

Since the introduction of Taq, the thermostable polymerase that brought automation and convenience to the polymerase-chain-reaction (PCR) method, special attention has been directed to the study of HIV-1 infection.9 10 11 12 13 14 15 Various modifications of the PCR method have been used to assess quantitatively or semiquantitatively the relative frequencies of HIV-1—infected cells in lymph nodes, PBMC, and other cell types.16 17 18 19 20 21 Schnittman et al., using a combination of cell sorting and quantitative DNA PCR techniques, observed that in patients with AIDS, at least 1 percent of CD4-positive lymphocytes are infected with HIV-1.21 , 22 In asymptomatic persons seropositive for HIV-1, the range of CD4-positive lymphocytes harboring HIV-1 is broad — 1 in 100 to 1 in 100,000.22 Recently, Hsia and Spector,23 using a "booster" PCR method, calculated that at least 10 percent of CD4-positive lymphocytes carry HIV-1 provirus in AIDS and symptomatic HIV-1 infection, whereas relatively lower proportions of CD4-positive lymphocytes are positive for the provirus in asymptomatic HIV-1 infection.

A current limitation of PCR with isolated DNA is that the results of amplification cannot be directly associated with a specific cell type, nor can the percentage of cells that carry the target sequence be easily measured. For example, in cell culture the HIV-1 virus infects CD4-positive lymphocytes, CD8-positive lymphocytes, monocytes, B lymphocytes, fibroblasts, and glial cells.24 25 26 27 28 29 30 31 32 Although the CD4-positive lymphocyte may be the primary reservoir of HIV-1 in the bloodstream,21 and the monocyte—macrophage may be the principal reservoir in solid tissues,33 34 35 it is highly desirable to identify all cell types that carry the virus in vivo, as well as the cells that allow active replication of HIV-1. Recently, Haase et al.36 reported success in developing an in situ PCR method for visna virus, using cell suspensions. It can be hypothesized that an intact, fixed cell may function as a microscopic amplification vessel. It appears generally possible that once cells are fixed and made permeable by paraformaldehyde, PCR reagents, including Taq DNA polymerase and PCR primers, can diffuse into the cell. After amplification, most of the amplified PCR product remains within the nucleus of the cell — under certain favorable conditions, possibly bound to the nuclear double membranes and nuclear matrix — or within the cytoplasmic membrane.

To determine the precise levels of HIV-1—infected PBMC in HIV-1—seropositive patients in various stages of disease, we developed an in situ PCR technique for HIV-1 and used it to count the total number of PBMC infected with HIV-1, whether in a productive or latent state of replication.

Methods

Patients

Blood specimens were obtained from 56 HIV-1—seropositive adults who were under the care of physicians at the Division of Infectious Disease or the Division of Hematology, Jefferson Medical College, Thomas Jefferson University. All studies were conducted with the approval of the institutional review board. The patients had received no antiretroviral therapy for at least 30 days. Nineteen patients were asymptomatic, and 37 were symptomatic. Specimens of peripheral blood were obtained from each patient, treated with heparin, assigned a code number by the clinical nurse, and forwarded to our laboratory for analysis. Specimens were also obtained from 11 HIV-1—seronegative patients by the clinical staff and assigned a code. The patients' identity and serologic status for HIV-1 remained unknown to the laboratory investigators until the studies were completed, and thus all specimens were evaluated in a blinded fashion.

Blood samples were processed within four hours after venipuncture, and PBMC were isolated by Ficoll–Hypaque (Histopaque, Sigma Chemical, St. Louis) gradient centrifugation. Cells were washed twice with phosphate-buffered saline and placed on slides for in situ PCR as described below. The slides were evaluated by in situ PCR in batches of 10 to 15.

In Situ PCR

To perform in situ PCR to detect HIV-1 provirus, cells (1×106 cells per milliliter) were seeded into the wells (1 × 105 cells per well) of specially designed, heavy, polytetrafluoroethylene (Tefton)-coated slides (Cell-Line Associates, Newfield, N.J.; 14-mm wells), by sedimentation through gravity. The slides were air-dried and then placed sequentially, first on a heat block at 105°C for 90 seconds and then in 1 percent paraformaldehyde—phosphate-buffered saline solution (pH 7.4) for 1 hour. The paraformaldehyde was inactivated by washing the slides in 3× phosphate-buffered saline; the slides were then washed three times in 1 × phosphate-buffered saline. Endogenous peroxidase activity was abolished by quenching the specimens with a 3 percent solution of hydrogen peroxidase overnight at 37°C. The slides were then treated with proteinase K (60 μg per milliliter in phosphate-buffered saline) for two hours at 55°C. Proteinase K was inactivated by placing the slides on a heat block at 96°C for two minutes. Finally, the slides were washed in distilled water and air-dried.

The cells were then subjected to amplification. A primer pair, complementary to conserved regions of the HIV-1 gag gene (SK38, nucleotides 1551—1578; SK39, nucleotides 1638—1665; Synthetic Genetics, San Diego, Calif.), was used to amplify HIV-1 DNA. Fifteen microliters of a PCR reaction mixture containing 10 μM (each) deoxyadenosine triphosphate, deoxycytidine triphosphate, deoxyguanosine triphosphate, and deoxythymidine triphosphate, 20 pmol of each primer, 50 mM potassium chloride, 10 mM TRIS (pH 8.3), 2.5 mM magnesium chloride, and 1.0 μ1 of Taq polymerase (1 unit per microliter; Gene Amp, Cetus, Norwalk, Conn.) was added to the top two wells of each slide, and a PCR mixture lacking the primers was added to the bottom well. These slides were covered with coverslips (22 by 60 mm), which were sealed with a clear nail polish. The slides were placed on an automatic thermocycler (M.J. Research, Boston), and amplification was carried out at 94, 45, and 72°C for one minute at each temperature, for 30 cycles. The primers for HLA-DQα (HLA-DQ-GH-26/27, Synthetic Genetics), together with a biotinylated probe for HLA-DQα, were used as positive controls.

After amplification all the slides were washed in 2 × saline sodium citrate (SSC) buffer (0.3 M sodium chloride and 0.03 M sodium citrate), and amplification products were detected by a biotinylated oligonucleotide (SK19, nucleotides 1595—1635; Synthetic Genetics), according to the in situ hybridization method. The hybridization mixture contained 15 to 25 pg of biotin-labeled probe, 10 mM dithiothreitol, 2×SSC, fragmented salmon-sperm DNA (1 mg per milliliter), 50 percent formaldehyde, 2 percent bovine serum albumin, and Escherichia coli transfer RNA (1 mg per milliliter). The mixture was applied to each well of the slide. The slides were sealed with coverslips and incubated on a heat block at 92°C for five minutes. The slides were then transferred to another heated, humidified chamber and kept there for four hours at 48°C. These slides were thoroughly washed with phosphate-buffered saline and then incubated with streptavidin—peroxidase complex (100 μg per milliliter in phosphate-buffered saline, pH 7.2) for one hour at 37°C. After incubation, slides were thoroughly washed with phosphate-buffered saline. The color was developed with 3′-amino-9′-ethylene carbozone in the presence of 0.03 percent hydrogen peroxide in 50 mM acetate buffer (pH 5.0) for 10 minutes at 37°C. The slides were washed and coverslips were applied, with a 50 percent solution of glycerol—phosphate-buffered saline. They were then analyzed with an optical microscope. When detected with the biotinylated probes, positive cells stained brownish red. A total of 10,000 PBMC were counted in all preparations to derive the percentages of HIV-1—positive cells.

In all amplifications, one slide well was used as an internal control in which amplified cells were hybridized with an unrelated probe. In every case, hybridization with an unrelated probe (HLA-DQα) gave negative results. In addition, the use of an HIV-1—specific probe (tat gene probe) in a region of HIV-1 not amplified by the gag primers demonstrated extremely few positive cells (<10–5). It had been previously noted that other HIV-1—specific sets of primers and biotinylated probes (for the long terminal repeat and tat) and a 32P-labeled gag probe gave consistent results in this assay system (data not shown). When U1 and ACH-2 cells were evaluated with cytomegalovirus-specific primers and probes, no positively staining cells were detected.

Statistical Analysis

Student's t-test was used to compare differences in the number of HIV-1—infected PBMC among groups of patients.

Results

Validation of in Situ PCR

We examined the validity of the in situ PCR technique by mixing monocytoid cells with latent HIV-1 infection (the U1 cell line37) with monocytoid cells without HIV-1 infection (the U937 line38) in various proportions. In situ PCR with HIV-1—specific primers and probe demonstrated that all U1 cells were positive for the HIV-1 provirus (Fig. 1Figure 1Identification of HIV-1 in Cell Lines by in Situ PCR (All Panels ×200).A), whereas the same procedure did not show any U937 cells to be HIV-1—positive (Fig. 1B). PCR evaluation of U1 and U937 cells in a ratio of 1:10 (Fig. 1C) and in other proportions (1:1, 1:2, 1:100, and 1:1000 [data not shown]) gave results expected at these dilutions. These findings concurred with previous data that demonstrate that the U1 cells are a latently HIV-1—infected subclone of U937 cells, with two copies of the HIV-1 provirus per cell.37 In addition, U1l cells that underwent in situ hybridization with the gag probe but without the steps for amplification only rarely stained positive (<10–4 cell) (Fig. 1D). The rare cells staining positive on in situ hybridization showed mainly cytoplasmic staining, in contrast to the dramatic nuclear staining of cells positive on in situ PCR. As a positive control for in situ PCR, HLA-DQα primers were used; they demonstrated positive amplification in all U1 or U937 cells, after these cells had been hybridized with a biotinylated probe for HLA-DQα (Fig. 1E).

The sensitivity of the in situ PCR technique was further tested with ACH-2 cells, a latently HIV-1—infected subclone of the T-lymphocytic cell line, CEM, which contains only one copy of the HIV-1 provirus per cell.39 When ACH-2 cells were subjected to in situ PCR, all cells were positive at the same degree of intensity (data not shown). When these cells were mixed in varying proportions with uninfected CEM cells, the results were those expected (i.e., the same results as those with U1 cells).

In addition, experiments were conducted to evaluate the theoretical possibility that HIV-1 virions may encapsulate some proviral DNA, which could contaminate uninfected cells during in situ PCR. Cells from an HIV-1—infected T-lymphocytic cell line, SupT-1, were mixed in various ratios with uninfected cells from a T-lymphocytic cell line, H9,2 as the U1 cells and uninfected U937 cells had been mixed, and the predicted ratios of infected to uninfected cells were observed after in situ PCR (data not shown). Thus, if there was virion-associated proviral DNA, it did not contaminate HIV-1—negative cells during this procedure.

These experiments demonstrated that in situ amplification can be accomplished in cell populations known to carry one or two copies of the HIV-1 provirus per cell. This modification of gene amplification makes in situ PCR more sensitive than many standard PCR methods for examining DNA.16 17 18 19 20 21 22 In addition, these data showed that with this technique, amplified DNA does not leak out of infected cells and contaminate uninfected cells.

HIV-1 Provirus in PBMC

As shown in Table 1Table 1Quantitation of HIV-1 Provirus in HIV-1—Seropositive Patients, According to Stage of Infection. and Figure 2Figure 2Identification of PBMC Containing HIV-1 Provirus by in Situ PCR., the proportions of PBMC containing HIV-1 provirus as determined by the in situ PCR technique varied widely, from 0.1 percent to 13.5 percent. The range of positive cells was 0.1 percent to 3.6 percent in the 19 asymptomatic HIV-1—seropositive patients and 1.2 percent to 13.5 percent in the 13 HIV-1—infected patients with persistent generalized lymphadenopathy (Stages II and III, respectively, as categorized by the modified classification system of the Centers for Disease Control40). Four patients in the latter group (Table 1, Patients 26, 28, 30, and 31) later had an oral candidal infection (thrush), in addition to the persistent generalized lymphadenopathy. The percentages of PBMC positive for the HIV-1 provirus ranged from 0.1 percent to 11.8 percent in the 19 patients with AIDS in Stages IV-A to IV-C, but they were relatively lower — 0.8 percent to 2.0 percent — in the 5 patients with AIDS in Stage IV-D who had evidence of Kaposi's sarcoma. Thus, patients in Stage II (asymptomatic) had lower percentages of HIV-1—positive PBMC than the patients in Stages III or IV-A to IV-C (P<0.001 by Student's t-test). The patients in Stage IV-D (with Kaposi's sarcoma, without opportunistic infection) had a relatively lower percentage of cells infected with HIV-1 (P<0.08). There was no statistically significant difference between the patients in Stage III and those in Stages IV-A to IV-C in the level of HIV-1—positive PBMC. All 11 HIV-1—seronegative controls were consistently negative according to in situ PCR.

Evaluation of the same PBMC from HIV-1—seropositive patients by standard in situ hybridization revealed only 1 in 5000 to 1 in 100,000 PBMC positive for HIV-1—specific nucleic acids (data not shown). These results were consistently observed in experiments with gag, tat, and long-terminal-repeat biotinylated probes and primers and recently with a 32P-labeled nick-translated probe (data not shown). In vivo, the vast majority of HIV-1—infected PBMC do not express large quantities of HIV-1 RNA and do not actively produce high levels of virus. Cells producing small quantities of HIV-1 genomic RNA or solely spliced HIV-1 messenger RNA41 may be detected if an in situ PCR technique incorporating reverse transcriptase is developed.

Discussion

The most detrimental clinical consequence of infection with HIV-1 is the severe depletion of CD4-positive lymphocyctes.42 , 43 Initially, it was assumed that such depletion was the result of selective infection and destruction of CD4-positive lymphocytes by HIV-1.1 , 2 However, Harper et al.,4 using an in situ hybridization method, demonstrated HIV-1—specific RNA in only 1 in 10,000 to 1 in 100,000 PBMC or lymph-node cells from patients with AIDS or symptomatic HIV-1 infection. These studies did not discount the possibility that HIV-1 may be present in a latent, proviral form, with no expression of viral messenger RNA, or that it may selectively express only low levels of multiply spliced HIV-1 RNA, without unspliced RNA.41 Our study of PBMC from 56 HIV-1—seropositive patients, using in situ hybridization alone, also revealed only 1 in 5000 to 1 in 100,000 cells positive for HIV-1—specific nucleic acids (data not shown). The findings of Harper et al.4 and the low rates of isolation of HIV-1 from patients with the infection studied earlier by Salahuddin et al.3 suggested that indirect mechanisms might mediate HIV-1—induced destruction of CD4-positive lymphocytes. Several factors have been proposed to account for the severe depletion of CD4-positive lymphocytes, including a direct cytopathic effect of HIV-1 on CD4-positive cells; HIV-1—specific cytotoxic T lymphocytes or antibody-dependent cellular cytotoxicity, which destroy cells expressing surface HIV-1—specific proteins; the formation of giant-cell syncytia, secondary to an interaction of the CD4 receptor and a fusion domain of the HIV-1 envelope glycoproteins; and antibodies against T lymphocytes, bone marrow stem cells, or immature thymocytes.42 , 43 Our finding with the use of in situ PCR that large numbers of PBMC from HIV-1—seropositive patients contain the provirus suggests that direct cytopathic effects of the virus may be an important but not necessarily the sole cause of depletion of CD4-positive lymphocytes. Our data also argue strongly against the theory that HIV-1 is not the primary etiologic agent of AIDS.44

The ability to detect a significantly higher level of HIV-1—infected cells with in situ PCR than with some other techniques (e.g., viral culture or standard PCR for DNA6 , 22) is based on the exquisite sensitivity of this technique. The reason for the unusually high sensitivity of the in situ PCR method is not as yet clear. However, it appears that with the standard PCR for DNA, HIV-1 DNA is diluted among DNA not containing HIV-1, which may lower the sensitivity of the method, whereas with in situ PCR, a cell may act as a microscopic amplification container, in which a DNA segment can be amplified in a concentrated fashion and without dilution by other DNA. It is also possible that when DNA is diluted by DNA from various subgroups of T lymphocytes and monocytes, genes may interfere with the optimal amplification of a given gene segment. Recently, various poorly described factors and genetic elements have been noted; these may inhibit the amplification of HIV-1 DNA fragments.45 46 47

The relatively large numbers of provirus-positive PBMC in the blood of persons with HIV-1 infection suggest that some of these proviruses may be transcriptionally quiescent or latent in vivo. This apparent latency of the provirus in vivo is pertinent to the understanding of the pathogenesis of HIV-1. A molecular mechanism of HIV-1 proviral latency has recently been described,41 although latent infection may also precede proviral integration.48 , 49

Our observation that the numbers of PBMC harboring HIV-1 provirus are significantly higher than the levels of infectious HIV-1 cells per mononuclear cell in coculture assays6 suggests that some copies of the HIV-1 provirus may be either defective or maintained in cells that are not activated in cell cultures to produce virions. Defective copies of the provirus have recently been found in vivo.50 As such, the evaluation of proviral latency and defective viral genomes in vivo remains an important area in the study of the complex pathogenesis of HIV-1 infection. As the sensitivity to detect HIV-1 in vivo has improved, the understanding of its molecular pathogenesis has continued to evolve. The ability to measure precisely the load of the HIV-1 provirus in peripheral blood in vivo is also critical to evaluation of the clinical efficacy of therapeutic interventions and as a prognostic indicator of the progression of HIV-1 infection.19 , 22

Recent studies with a quantitative DNA PCR technique, unlike previous studies,51 have suggested that there is a correlation between the clinical state of HIV-1 infection and the level of HIV-1—specific PCR signals.22 In our studies using in situ PCR, we were able to quantitate the percentage of cells positive for HIV-1 provirus and show a relation between viral load and the stage of HIV-1 clinical infection. Patients in Stage II had a significantly lower percentage of HIV-1—positive PBMC than those in Stage III and Stages IV-A to IV-C. Patients in Stage IV-D (who had Kaposi's sarcoma only) had relatively low numbers of HIV-1—infected cells. This finding is rather surprising, and it may be one of the reasons that some investigations have failed to observe the correlation between the clinical stage of HIV-1 infection and the degree of DNA amplification by the PCR. This may also account for the longer life expectancy of patients with Kaposi's sarcoma as compared with other patients with AIDS.52 However, this observation requires further verification in a larger cohort of patients.

One of the main concerns of investigators about the standard DNA PCR method is false positive results due to contamination of samples by HIV-1—positive amplified genetic segments.53 However, with the use of in situ PCR, such concerns are greatly diminished since limited contamination of amplified genetic segments will potentially contaminate only a few cells, thus avoiding the totally false positive results that may be produced by the standard DNA PCR method, in which the results of amplification are measured in toto.

The technique of in situ PCR allows a specific DNA fragment to be amplified within an intact cell. This technique has great potential for determining the actual proviral load in peripheral blood at various stages of HIV-1 infection and for evaluating the efficacy of various therapeutic interventions. Currently, there is no reliable way to determine the state of HIV-1 infection in newborns of HIV-1—seropositive mothers.54 , 55 This new technique may prove useful in determining which newborns are infected with HIV-1.

We are indebted to Ms. Roberta Benjamin, R.N., Ms. Suzanne Bachman, Ms. Joann Stockman, and Ms. Lisa Creran, R.N., for assistance in obtaining blood samples from the patients; to Dr. T. Seshamma and Mr. Joseph W. Oakes for technical assistance; to Drs. Stephen Spector and Didier Trono for helpful discussions; to Ms. Rita Victor and Ms. Brenda Gordon for assistance in the preparation of the manuscript; and to Dr. Thomas Folks (AIDS Research and Reference Program, National Institute of Allergy and Infectious Diseases) for donating the U1 and ACH-2 cell lines.

Source Information

From the Infectious Disease Division (O.B., M.S., R.J.P.) and the Cardeza Foundation for Hematologic Research (S.P.H.), Jefferson Medical College, Thomas Jefferson University, and the Department of Pediatrics, St. Christopher's Hospital for Children and Temple University (H.W.L.), all in Philadelphia. Address reprint requests to Dr. Bagasra at the Department of Medicine, Jefferson Medical College, 1025 Walnut St., Suite 813, Philadelphia, PA 19107.

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