In situ hybridization in flow cytometry.

Molecular approaches to diagnostic questions in clinical medicine are greatly impacting the way researchers and clinicians investigate and treat disease. By combining molecular techniques with classical immunologic tools such as flow cytometry (FCM; 1-3), one can begin to more fully understand and appreciate the role of cellular heterogeneity in disease processes. The marriage of these two powerful techniques, termed molecular cytometry, will, in one instance, allow investigators to explore expression of nucleic acid sequences in subpopulations of cells defined by immunologic phenotype while, conversely, making it possible to examine the heterogeneity of cellular characteristics within populations identified by the presence of specific nucleic acid sequences or gene expression. Future developments may result in several advantages for the patient that may include, but are not limited to, earlier detection of viral infection, earlier and more sensitive detection of malignancy, and higher sensitivity and resolution of small populations of infected or aberrant cells. These developments may also assist in the identification of therapeutically resistant populations within a neoplasia, more effective and specific monitoring of therapy, and possibly the identification of new and disease-specific targeted therapies based on genetic information. The characterization and assessment of cellular heterogeneity is clearly key to understanding disease onset, progression, and therapeutic response in both infectious disease and in human malignancies.

Detection of HIV-RNA-positive monocytes in peripheral blood of HIV-positive patients by simultaneous flow cytometric analysis of intracellular HIV RNA and cellular immunophenotype.

Determinations of plasma HIV viral RNA copy numbers help to define the kinetics of HIV-1 infection in vivo and to monitor antiretroviral therapy. However, questions remain regarding the identity of various infected cell types contributing to this free virus pool and to the in vivo lifecycle of HIV during disease progression. Characterization of a novel fluorescence in situ hybridization (FISH) assay employing a pool of labeled oligonucleotide probes directed against HIV RNA was done followed by coupling of the FISH assay with simultaneous surface immunophenotyping to address these questions. In vitro characterizations of this assay using tumor necrosis factor-alpha stimulated and unstimulated ACH-2 cells demonstrated the ability to detect < 5% HIV RNA positive cells with a sensitivity of < 30 RNA copies per cell. Peripheral blood mononuclear cells from 39 HIV-seropositive patients on no, single, combination, or triple drug therapy and 8 HIV-seronegative patients were examined. The majority of HIV-positive patients (24/39) harbored monocytes positive for HIV RNA and a significantly higher fraction of patients with high plasma viral load carried positive monocytes (13/16) than did patients in the low plasma viral load group (11/23). These results demonstrate the effectiveness of a novel FISH assay for identifying and monitoring HIV-infected cell populations in the peripheral blood of HIV-positive patients. In addition, monocytes are a major source of cellular HIV virus in the peripheral blood of HIV patients, even with progression of disease.

Reducing cellular autofluorescence in flow cytometry: an in situ method.

Cellular autofluorescence affects the sensitivity of flow cytometric assays by interfering with detection of low level specific fluorescence. These detection limits increase with use of protocols, such as thermocycling and fluorescent in-situ hybridization (FISH), that can increase intrinsic cellular fluorescence to 5,000-20,000 fluorescein isothiocyanate (FITC) equivalents. In order to improve signal to noise ratios when using FITC labeled probes in these procedures, we employed a method using the polyanionic azo dye, trypan blue, to reduce intracellular autofluorescence. Dyes such as these are commonly used in immunofluorescent microscopy to reduce background fluorescence. By using this method, we realized an approximately 5-fold increase in signal to noise ratio (S/N) in the direct detection of RNA target probes using flow cytometry. Trypan blue aided in the resolution of dim surface antibodies, internal markers and probes, and functions to reduce background autofluorescence after thermocycling and hybridization. This technique is rapid and easily applicable for reducing intracellular autofluorescence, and can be used in single and dual color applications.