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Journal of Clinical Microbiology, July 2008, p. 2314-2319, Vol. 46, No. 7
0095-1137/08/$08.00+0 doi:10.1128/JCM.02197-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

University of Florida, College of Veterinary Medicine, Department of Infectious Diseases and Pathology, Gainesville, Florida 32610
Received 13 November 2007/ Returned for modification 26 December 2007/ Accepted 13 May 2008
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In situ rolling-circle amplification of padlock probes. In situ DNA target-primed rolling-circle amplification of padlock probes was performed with modifications of a previously described technique (11). All reactions were performed on microscope slides without coverslips. The final volume of all reaction mixtures was 40 µl. All heated reactions were performed in a 16/16 dual block slide chamber mounted on a DNA engine (PTC-200) Peltier thermal cycler (Bio-Rad Laboratories, Hercules, CA). Cytospin culture material on the microscope slides was uniformly treated as follows. The slides were washed twice in 1x phosphate-buffered saline (PBS) (pH 7.4, 2 min), fixed in 70% denatured ethanol (20 min), and subsequently washed twice in 1x PBS (2 min). The cells were permeabilized in HCl (pH 3.6, 37°C)—RF/6A endothelial cells for 3 min and HL-60 myeloblastic leukemia cells for 1.5 min. Afterward, the slides were washed three times in 1x PBS (2 min).
The bacterial genome was made irreversibly linear by the endonuclease digestion of A. phagocytophilum with AfeI (New England BioLabs, Ipswich, MA) and of A. marginale with ZraI (New England BioLabs, Ipswich, MA); each endonuclease was used at 0.5 U/µl in 1x supplied enzyme buffer plus 0.2 µg/µl bovine serum albumin (New England BioLabs, Ipswich, MA) (37°C, 30 min), followed by a brief rinse in buffer A (0.1 M Tris-HCl [pH 7.5], 0.15 M NaCl, and 0.05% Tween 20). The genomic DNA target was made single stranded by 5'-to-3' exonucleolysis (Lambda exonuclease; New England BioLabs, Ipswich, MA). The exonuclease was used at 0.2 U/µl in 1x supplied enzyme buffer plus 0.2 µg/µl bovine serum albumin and 10% glycerol (Sigma, St. Louis, MO) (37°C, 15 min), followed by a brief rinse in buffer A.
The genomic DNA target was detected by hybridization to a circularizable, linear, oligonucleotide padlock probe (Fig. 1). Either an A. phagocytophilum-specific probe, an A. marginale-specific probe, or a nonspecific probe was used at 0.10 µM in 2x SSC (pH 7.0) (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate)-20% formamide (Fisher Scientific, Pittsburg, PA), and 0.5 µg/µl sonicated fish sperm (DNA, MB-grade; Roche Applied Science, Indianapolis, IN) (37°C, 15 min). Subsequently, the slides were washed in prewarmed buffer B (2x SSC [pH 7.0] and 0.05% Tween 20; 37°C, 5 min) and rinsed briefly in buffer A.
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FIG. 1. Three padlock probes were used: AB1251 (A. phagocytophilum specific), AB1270 (A. marginale specific), and AB1253 (nonspecific). The genomic DNA target-specific sequences of AB1251 and AB1270 are within the underlined 5' and 3' arms of the padlock probes. When the single-stranded genomic complement of each probe's target-specific sequence is detected, the probe hybridizes as a nicked circle, which is subsequently locked in place by ligase as a partially double-helical, closed circle. The circularized padlock probe is the template for in situ DNA target-primed rolling-circle amplification. The 5' and 3' arms of the nonspecific probe, AB1253, had the same nucleotide composition as AB1251; however, the sequence of the nucleotides was randomized within the underlined regions. The 5' and 3' arms of the padlock probes were joined by identical intervening linker regions. The amplification product of the italicized portion of the probe linker region is the complement of the fluorescently labeled oligonucleotide tags, AB1252 and AB1279 (also known as Lin 33 [11]). All oligonucleotides contained a 5'-end modification, designated P (phosphate), FAM (phosphoramidite-coupled fluorescein), or Alexa 555 (Alexa Fluor 555; Invitrogen, Carlsbad, CA).
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After exonucleolysis of any remaining 3' single-stranded genomic DNA, the genomic DNA target was used to prime isothermal in situ rolling-circle amplification of the specifically bound padlock probe (phi29 DNA polymerase; New England BioLabs, Ipswich, MA). The polymerase was used at 1.0 U/µl in 1x supplied enzyme buffer plus 0.25 mM each deoxynucleoside triphosphate (deoxynucleotide solution mix; New England BioLabs, Ipswich, MA), 0.2 µg/µl bovine serum albumin, and 10% glycerol (37°C, 30 min). During the 30-min DNA polymerization, the slides were removed from the slide chamber every 10 min to gently agitate the reaction mixture. The slides were then rinsed briefly in buffer A before the single-stranded, loosely coiled, concatameric amplification product was hybridized to a fluorescently labeled, linear oligonucleotide tag (oligonucleotide AB1252 [green] or oligonucleotide AB1279 [red; also known as Lin 33 {11}]), used at 0.25 µM in 2x SSC, 20% formamide, and 0.5 µg/µl sonicated fish sperm (37°C, 15 min).
Afterward, the slides were rinsed briefly in buffer A, dehydrated in graded denatured ethanols (75%, 85%, 100%; 3 min each), and either immunofluorescently stained for von Willebrand factor or immediately air dried and coverslip mounted using Vectashield HardSet mounting medium with 1.5 µg/ml DAPI (4',6'-diamidino-2-phenylindole) (Vector Laboratories, Burlingame, CA). The slides were examined using a Leica DMI 3000B inverted microscope fitted for epifluorescence and equipped with a digital camera (MicroPublisher 3.3 RTV; QImaging Corporation, Surrey, BC, Canada) and then stored at 4°C. Digital images were collected using QCapture Pro 5.1.1.14 (QImaging Corporation, Surrey, BC, Canada) and uniformly processed using SPOT Advanced Windows version 4.0.9 (Diagnostic Instruments, Sterling Heights, MI) and Adobe Photoshop Elements 2.0 (Adobe Systems Incorporated, San Jose, CA).
Padlock probe design. Three circularizable, linear, oligonucleotide padlock probes were used (Fig. 1) (MWG Biotech, High Point, NC). The A. phagocytophilum-specific probe (AB1251) was designed to include an A. phagocytophilum genomic DNA target-specific sequence whose cognate is a conserved 5' region of msp2 (p44) that is present in the expression sites of three geographic isolates from the United States (HZ isolate) (5), Norway (1), and Sweden (1) and in 81 different pseudogenes of the HZ isolate (5). Of these target sequences within the A. phagocytophilum genome (HZ isolate), there are 29 potential targets (the expression site and 28 pseudogenes) that are associated with a 3' AfeI endonuclease recognition site within 100 bp of the genomic target and could, therefore, be detected by the technique described here.
The A. marginale-specific probe (AB1270) was designed to include an A. marginale genomic DNA target-specific sequence, whose cognate is orfY, which is repeated eight times in the genome (2). Of these target sequences within the A. marginale genome (St. Maries isolate), there are seven potential targets that are associated with a 3' ZraI endonuclease recognition site within 1 bp of the genomic target and could, therefore, be detected by the technique described here. The use of repetitive sequences [msp2 (p44) for A. phagocytophilum and orfY for A. marginale] as genomic DNA targets for padlock probe hybridization was expected to increase the sensitivity beyond that provided by rolling-circle amplification alone.
The target-specific sequence of the padlock probe is within the 5' and 3' arms of the probe, which are joined by an intervening linker region. The rolling-circle amplification product is detected by a fluorescently labeled oligonucleotide tag (AB1252 or AB1279; also known as Lin 33 [11]) that is the complement of the padlock probe linker region amplification product. The linker region of the nonspecific padlock probe (AB1253) was identical to those of the A. phagocytophilum-specific and A. marginale-specific padlock probes. The 5' and 3' arms of the nonspecific probe had the same nucleotide composition as that of the A. phagocytophilum-specific probe; however, the sequence of the nucleotides was randomized.
Indirect immunofluorescent staining of von Willebrand factor in cultured endothelial cells. After the final graded-alcohol dehydration of the in situ rolling-circle amplification procedure, slides that had been reacted with the A. phagocytophilum-specific padlock probe or the nonspecific padlock probe were immunofluorescently stained for von Willebrand factor. All reactions were performed on microscope slides without coverslips; the final volume of all reaction mixtures was 150 µl. The cytospin culture material was blocked with normal rabbit serum (X0902; Dako, Carpinteria, CA), 5% in 1x PBS (pH 7.4, 30 min), and subsequently washed once in 1x PBS (5 min). The cytospin culture material was then incubated with either antibody-free diluent or rabbit polyclonal anti-human von Willebrand factor antibody (N1505; Dako, Carpinteria, CA) diluted 1:1 in 0.05 M Tris-HCl (pH 7.5)-1% bovine serum albumin fraction V (Fisher Scientific, Pittsburg, PA) (30 min). The slides were washed twice in 1x PBS (5 min) prior to secondary antibody labeling. The cytospin culture material was subsequently incubated with a highly cross-adsorbed goat polyclonal anti-rabbit immunoglobulin G antibody-Alexa Fluor 568 conjugate (A11036; Invitrogen Molecular Probes, Carlsbad, CA) used at 2 µg/ml in 0.05 M Tris-HCl (pH 7.5)-1% bovine serum albumin fraction V (30 min). Afterward, the slides were washed twice in 1x PBS (5 min), air dried, coverslip mounted using Vectashield HardSet mounting medium with DAPI, and examined as described above.
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Cytospin preparations of uninfected or A. phagocytophilum HZ-infected human myeloblastic leukemia cell cultures and a padlock probe, either a nonspecific probe or an A. phagocytophilum-specific probe, were used for in situ DNA target-primed rolling-circle amplification. When A. phagocytophilum HZ-infected cytospin preparations were microscopically examined after in situ DNA target-primed rolling-circle amplification of an A. phagocytophilum-specific padlock probe, numerous stippled, green or red fluorescent aggregates, which represented the fluorescently labeled, localized amplification product, were frequently identified within intact cultured myeloblastic leukemia cells. The intracellular location of fluorescence correlated well with microscopic observations of A. phagocytophilum morulae within intact myeloblastic leukemia cells in a Wright-Giemsa-stained infected cytospin culture (Fig. 2A, B, and D). Similar fluorescence was not observed when either an uninfected cytospin culture (not shown) or a nonspecific padlock probe (Fig. 2C and E) was used. The results were confirmed in five independent experiments.
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FIG. 2. Numerous intracellular morulae were observed within heavily A. phagocytophilum HZ-infected, intact human myeloblasts in cytospin preparations stained with Wright-Giemsa (bright field) (A) or when detected as a stippled, green fluorescent product (B) or a stippled, red fluorescent product (D) by in situ DNA target-primed rolling-circle amplification of an A. phagocytophilum-specific padlock probe (63x objective; differential interference contrast with blue and green emissions [B] or with blue and red emissions [D]). Similar fluorescence was not detected when a nonspecific padlock probe was used in an otherwise identical procedure (C and E) (63x objective; differential interference contrast with blue and green emissions [C] or with blue and red emissions [E]).
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FIG. 3. Intracellular morulae were observed within A. marginale-infected, intact fetal rhesus monkey endothelial cells in cytospin preparations stained with Wright-Giemsa (bright field) (A) or when detected as a stippled, green fluorescent product (B) or a stippled, red fluorescent product (D) by in situ DNA target-primed rolling-circle amplification of an A. marginale-specific padlock probe (63x objective; differential interference contrast with blue and green emissions [B] or with blue and red emissions [D]). Similar fluorescence was not detected when a nonspecific padlock probe was used in an otherwise identical procedure (C and E) (63x objective; differential interference contrast with blue and green emissions [C] or with blue and red emissions [E]).
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When A. phagocytophilum NY18-infected cytospin cultures were microscopically examined after in situ DNA target-primed rolling-circle amplification of an A. phagocytophilum-specific padlock probe, stippled, green fluorescent focal aggregates, which represented the fluorescently labeled, localized amplification product, were often identified perinuclearly within intact cultured endothelial cells. The intracellular location of green fluorescence correlated well with microscopic observations of A. phagocytophilum morulae within intact endothelial cells in a Wright-Giemsa-stained infected cytospin culture (Fig. 4A and B). Similar green fluorescence was not observed when either an uninfected cytospin culture (not shown) or a nonspecific padlock probe (Fig. 4C) was used. The results were confirmed in five independent experiments.
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FIG. 4. A few perinuclear morulae were observed within intact A. phagocytophilum NY18-infected fetal rhesus monkey endothelial cells in cytospin preparations when stained with Wright-Giemsa (bright field) (A) or when detected as a stippled, green fluorescent product by in situ DNA target-primed rolling-circle amplification of an A. phagocytophilum-specific padlock probe (63x objective; phase contrast with blue and green emissions) (B). A similar green fluorescent product was not detected when a nonspecific padlock probe was used in the otherwise identical procedure (40x objective; phase contrast with blue and green emissions) (C). A. phagocytophilum-infected fetal rhesus monkey endothelial cells in cytospin preparations were subjected to combined in situ DNA target-primed rolling-circle amplification of an A. phagocytophilum-specific padlock probe and indirect immunofluorescent staining of von Willebrand factor. Stippled, green fluorescent focal aggregates were identified perinuclearly and juxtaposed with focal areas of red fluorescence, which represented the fluorescently labeled von Willebrand factor (D); similar green and red fluorescence was not observed when the combined procedure was performed using a nonspecific padlock probe and only the fluorescently labeled secondary antibody (40x objective; blue, red, and green emissions) (E).
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The specificity of this technique arises from the use of a padlock probe, which depends upon hybridization specific to the genomic DNA target sequence. The use of ligase allows interrogation of the hybridization quality between the target-specific sequence of the padlock probe and the genomic target. If the quality of the hybridization is not optimal, ligation of the padlock probe to form a closed, partially double-stranded circle involving the genomic target will not occur. The use of ligase in this procedure is the basis for the distinction of genomic single nucleotide polymorphisms based on the quality of hybridization with the 3' terminus of the padlock probe (9, 10, 11, 13, 14, 15). The exponential amplification of the bound padlock probe is one basis for the sensitivity of this technique (11, 15). The amplification product remains bound to the target sequence and is subsequently detected by the addition of a second fluorescently labeled oligonucleotide tag that specifically binds repeated linker sequences within the concatameric amplification product. The fact that the amplification product remains tightly bound as a 3' extension of the genomic target limits background fluorescence, which also contributes to the sensitivity and specificity of this technique and is another improvement over other in situ nucleotide detection techniques (11, 14).
An additional benefit of the in situ DNA amplification technique applied here over other methods of in situ DNA detection is that the reactions are isothermal, which preserves tissue architecture and allows subsequent immunostaining of host cell antigens, such as the endothelial cell antigen von Willebrand factor. This is of particular import, given the recently heightened interest in endothelial cells as a potential natural mammalian infection nidus in light of the ability to continuously cultivate A. phagocytophilum and A. marginale in fetal primate endothelial cells (12) and the preliminary immunofluorescent colocalization of A. phagocytophilum or A. marginale with endothelial cell antigens in vivo (3, 8).
Transformation of A. phagocytophilum that renders it able to express green fluorescent protein and subsequent experimental infection of mice with A. phagocytophilum transformants have been recently described (6). Such transformants may facilitate temporal tracking of organism tissue distribution during experimental infection, including host cellular binding, entry, and intracellular development; however, their use is dependent upon an experimental model of mammalian infection and the ability to maintain stable transformants in long-term culture and during the full course of acute and chronic infections. The fluorescence microscopy-based Anaplasma sp. detection method described here does not depend upon a genetic transformant that may be unstable or attenuated and could be applied to naturally or experimentally infected mammalian or arthropod host tissues to detect potentially cryptic sites of infection. Additionally, with the knowledge of variable Anaplasma genomic DNA sequences that may be present in host tissues during an infection, multiple padlock probes that bind to differentially labeled fluorescent oligonucleotide tags could be designed and used in a single isothermal reaction to provide information about Anaplasma nucleotide sequences in situ.
In summary, the observations presented here show that in situ DNA target-primed rolling-circle amplification of padlock probes can be used to detect Anaplasma spp. within intact cultured mammalian cells. This demonstrates that the amplification technique can be used for in situ detection of an intracellular microorganism. Also, this technique can be combined with immunofluorescent staining in order to identify a host cell antigen and the fluorescently labeled rolling-circle amplification product within a single cell. This work forms the foundation for future applications of this technique to detect, localize, and analyze Anaplasma nucleotide sequences in the tissues of infected hosts and in cell cultures. There is also the potential to apply the technique described here to investigate prospective cryptic host cellular localization of other microorganisms and to further elucidate the etiopathogenesis of disease associated with infection by other obligate or facultative intracellular microorganisms.
We thank Basima Al-Khedery and A. Rick Alleman for the provision of uninfected, A. phagocytophilum-infected, and A. marginale-infected cell cultures.
Published ahead of print on 21 May 2008. ![]()
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