Nested Primer Polymerase Chain Reaction Research Articles

Improved sizing of fragile X CCG repeats by nested polymerase chain reaction

We have developed an improved method for polymerase chain reaction (PCR)-based sizing of the CCG repeat region at the fragile X locus, FMR-1. This method is designed to optimize denaturation and replication of long repeats with high G + C content, which are otherwise refractory to amplification. The method utilizes nested PCR primers to increase sensitivity and specificity. Alkaline denaturation of the genomic template DNA, combined with addition of glycerol and deaza-dGTP, facilitates strand separation. Labeled PCR products are sized on denaturing polyacrylamide gels. For alleles in the normal-to-premutation size range, strong reproducible signals are routinely obtained from small amounts of rapidly prepared DNA. This allows precise determination of the CCG repeat number, providing data related to the expansion potential of the repetitive segment. Detection of large premutations and some full mutations is also enhanced by the improved procedure.

Development of a sensitive, highly controlled assay for molecular detection of the Philadelphia chromosome in patients with chronic myelogenous leukemia

The Philadelphia chromosome (Ph1), present in ⩾95% of chronic myelogenous leukemia (CML) patients, is a well-characterized translocation that results in a unique chimeric gene product ( BCR/ABL) with transforming capability. Molecular methods utilizing the polymerase chain reaction (PCR) to detect BCR/ABL mRNA transcripts has been useful for detecting minimal residual disease (MRD) after treatment, as well as for establishing the diagnosis of CML. Amplification-based assays for the BCR/ABL transcript, however, have shown variable reproducibility and sensitivity. This variability may be largely due to technical differences and insufficient controls. In this report, we describe the development of a highly controlled, reproducible, and sensitive PCR assay to detect Ph1 that is well suited to clinical and research applications. A validation study of 82 samples was performed consisting of 25 dilutions of K562 cells (Ph1+) into normal cultured B cells, 26 pre- and post-transplant peripheral blood samples from CML patients, 16 peripheral blood samples for diagnosis of CML, and 15 peripheral blood samples from healthy individuals. RNA isolated from 3 to 5 million leukocytes was reverse transcribed (RT) and amplified by nested primer PCR. The products were characterized using agarose gel electrophoresis. Approximately 1000 Ph1-positive cells admixed with 10 6 normal cells were detectable after one round of amplification. In 60% of assays where one Ph1-positive cell was admixed with 10 6 normal cells, a BCR/ABL product was detectable after nested primer PCR. Specific measures to ensure accurate results in routine testing included (a) assessing RNA integrity and adequate cDNA preparation by detection of the constitutively expressed ABL mRNA, (b) monitoring sensitivity with the addition and detection of K562 RNA mixed with RNA from unknown samples (failure to detect the “spiked” K562 RNA indicates the presence of inhibitors or ribonucleases within the unknown RNA sample), (c) detection of nucleic acid contaminants by using negative controls in every assay, and (d) duplicate analysis of all samples and controls. Internally, this assay was 100% reproducible. Our results verify that nested primer RT-PCR is a fast, sensitive alternative to cytogenetic or Southern blot analysis for monitoring MRD after treatment and for diagnosis of CML. In addition, the highly controlled detection scheme presented here can be used as a general model for the development of other amplification-based detection assays.

The detection of hepatitis C virus RNA in human breast milk using a nested primer polymerase chain reaction

The detection of hepatitis C virus RNA in human breast milk using a nested primer polymerase chain reaction

Sequential switching from mu to epsilon via gamma 4 in human B cells stimulated with IL-4 and hydrocortisone.

The molecular events leading to IgE synthesis in human B cells stimulated with IL-4 and hydrocortisone were analyzed. IL-4, but not hydrocortisone, induced C epsilon germ line transcription. However, hydrocortisone increased the levels of IL-4-induced germ line C epsilon transcripts by twofold and delivered the signal required for transcription of mature C epsilon mRNA. Nested primer polymerase chain reaction of high m.w. DNA revealed deletional switch recombination occurring in B cells sorted for lack of expression of surface IgE and stimulated with both IL-4 and hydrocortisone, but not in B cells stimulated with IL-4 alone or hydrocortisone alone. DNA sequence analysis of 10 switch fragments revealed direct joining of S mu to S epsilon in eight fragments, one of which exhibited an 876-bp deletion in S mu. The ninth fragment contained a 50-bp insertion at the S mu/S epsilon junction, which was likely to be derived from S gamma 4. The sequence of the 10th fragment was consistent with either a 17-bp insertion at the S mu/S epsilon junction derived from S gamma 4 or with a complex 38-bp deletion within S epsilon. Mapping of the switch junction sites showed "hot spots" for recombination within S mu but not within S epsilon. These findings indicate that hydrocortisone induces S mu-S epsilon deletional switch recombination in IL-4-treated B cells, and support a model of sequential isotype switching from IgM to IgE via IgG4.

Expression of platelet C1 inhibitor

AbstractHuman platelets contain a pool of C1 inhibitor (C1 INH) distinct from that in plasma. Twelve normal platelet samples washed by centrifugation had a mean platelet C1 INH antigen level of 19.3 +/- 2.8 ng (mean +/- SEM) per 10(8) platelets. These values contrast with the mean +/- SEM platelet C1 INH antigen level of 6.1 +/- 0.9 per 10(8) platelets from 12 C1 INH-deficient patients. The level of platelet C1 INH correlated (r = .7) with the level of plasma C1 INH in normal individuals and patients with classic hereditary angioedema. Platelet C1 INH, like plasma C1 INH, was a 105-Kd protein on immunoblots of solubilized platelets and in thrombin- or collagen-induced platelet releasates. On indirect immunofluorescence, morphologically and immunochemically identifiable elutriated human megakaryocytes had C1 INH antigen. Using nested primer polymerase chain reaction, C1 INH mRNA was detected in megakaryocytes. When activated, human platelets expressed a portion of their total pool of C1 INH antigen on their membrane. Using a competitive enzyme-linked immunosorbent assay for C1 INH as a quantitative, indirect antibody consumption assay, the surface of unstimulated platelets had 0.55 +/- 0.4 ng C1 INH/10(8) platelets (mean +/- SEM). When activated with thrombin, platelets secreted 7.37 +/- 2.2 ng C1 INH/10(8) platelets into the suspension buffer and simultaneously expressed 4.4 +/- 1.2 ng C1 INH/10(8) platelets on their external membrane. These studies showed that activated platelets secreted 38% of their C1 INH and externalized another 23% of the total platelet C1 INH on their membrane. Furthermore, in 125I-anti-C1 INH Fab' binding experiments to platelets, about 8 ng of the antibody fragment specifically bound to 10(8) activated platelets. These data suggest that level of platelet C1 INH packaged into platelet alpha-granules is modulated by the amount of protein produced in megakaryocytes. Platelet alpha-granule C1 INH can both be secreted from platelets and expressed on their activated membranes. The cell membrane expression of C1 INH may be important to modulate the activity of the proteases of the complement and contact systems of plasma proteolysis in the microenvironment of the inflammatory response.

Expression of platelet C1 inhibitor

Human platelets contain a pool of C1 inhibitor (C1 INH) distinct from that in plasma. Twelve normal platelet samples washed by centrifugation had a mean platelet C1 INH antigen level of 19.3 +/- 2.8 ng (mean +/- SEM) per 10(8) platelets. These values contrast with the mean +/- SEM platelet C1 INH antigen level of 6.1 +/- 0.9 per 10(8) platelets from 12 C1 INH-deficient patients. The level of platelet C1 INH correlated (r = .7) with the level of plasma C1 INH in normal individuals and patients with classic hereditary angioedema. Platelet C1 INH, like plasma C1 INH, was a 105-Kd protein on immunoblots of solubilized platelets and in thrombin- or collagen-induced platelet releasates. On indirect immunofluorescence, morphologically and immunochemically identifiable elutriated human megakaryocytes had C1 INH antigen. Using nested primer polymerase chain reaction, C1 INH mRNA was detected in megakaryocytes. When activated, human platelets expressed a portion of their total pool of C1 INH antigen on their membrane. Using a competitive enzyme-linked immunosorbent assay for C1 INH as a quantitative, indirect antibody consumption assay, the surface of unstimulated platelets had 0.55 +/- 0.4 ng C1 INH/10(8) platelets (mean +/- SEM). When activated with thrombin, platelets secreted 7.37 +/- 2.2 ng C1 INH/10(8) platelets into the suspension buffer and simultaneously expressed 4.4 +/- 1.2 ng C1 INH/10(8) platelets on their external membrane. These studies showed that activated platelets secreted 38% of their C1 INH and externalized another 23% of the total platelet C1 INH on their membrane. Furthermore, in 125I-anti-C1 INH Fab' binding experiments to platelets, about 8 ng of the antibody fragment specifically bound to 10(8) activated platelets. These data suggest that level of platelet C1 INH packaged into platelet alpha-granules is modulated by the amount of protein produced in megakaryocytes. Platelet alpha-granule C1 INH can both be secreted from platelets and expressed on their activated membranes. The cell membrane expression of C1 INH may be important to modulate the activity of the proteases of the complement and contact systems of plasma proteolysis in the microenvironment of the inflammatory response.

Search for Mycobacterium paratuberculosis DNA in tissue from patients with sarcoidosis by enzymatic gene amplification.

The etiology of sarcoidosis has not yet been established, but several mycobacterial species have been implicated in the pathogenesis of this disease. We have used a nested primer polymerase chain reaction (PCR) specific for the IS900 Mycobacterium paratuberculosis insertion element to analyse paraffin-embedded mediastinal lymphoid tissue from 18 patients with pulmonary sarcoidosis verified by mediastinoscopy. Only the positive control contained M. paratuberculosis-specific DNA. The present study does not support a role for M. paratuberculosis in the pathogenesis of sarcoidosis. However, further studies are needed in order to clarify the possible role of other mycobacteria in this disease.

Simultaneous Amplification of Multiple HIV-1 DNA Sequences from Clinical Specimens by Using Nested-Primer Polymerase Chain Reaction

A sensitive and specific polymerase chain reaction (PCR) protocol with nested primers was developed for simultaneous amplification of three independent human immunodeficiency virus type 1 (HIV-1) DNA sequences from clinical specimens. DNA samples were first amplified with gag, pol, and env outer primer pairs and then with the corresponding three inner primer pairs in the same two-step reaction. Detection of the different amplification products was readily accomplished by simple agarose gel electrophoresis of the reaction product, even when starting with a single copy of HIV-1 DNA. Equivalent amounts of the three PCR products were generated, provided that the relative concentrations of the inner primer pairs were optimized. In addition, a beta-globin control primer pair could be conveniently included in the internal amplification step to verify that the DNA sample was suitable for PCR analysis. One nested multiplex PCR test was sufficient to detect HIV-1 DNA in all of 80 HIV-1-seropositive individuals and none of 50 HIV-1-seronegative healthy blood donors. The nested multiplex PCR procedure provides an attractive means for simple, rapid, and cost-effective direct detection of HIV-1 DNA in patient samples.

Use of the polymerase chain reaction to detect spacer size heterogeneity in plant 5S-rRNA gene clusters and to locate such clusters in wheat (Triticum aestivum L.)

We have used the polymerase chain reaction to analyse variation in the size of individual 5S-ribosomal gene spacer sequences. This reaction can be used to demonstrate inter- and intraspecific variation in spacer size, and combined with DNA sequencing it may thus be a valuable taxonomic tool. Two sets of nested polymerase chain reaction primers were designed to amplify the nontranscribed spacer DNA between repeated 5S-rRNA genes. These "universal" primers were used to generate fragments from the genomic DNA from several unrelated monocotyledonous plants. Ribosomal RNA spacer sequences generated in these experiments could also be used to locate 5S-rRNA gene clusters on specific chromosomes in hexaploid wheat (Triticum aestivum). Three distinct spacer sizes were observed after amplification. These were assigned locations on chromosomes by analysing amplification products of genomic DNA from nullisomic/tetrasomic and ditelosomic wheat stocks. "Large" 508-bp 5S repeats are located on the short arm of chromosome 5B and "short" 416-bp and 425-bp repeat unit variants are located on the short arms of chromosomes 1B and 1D, respectively. No other loci were detected. The spacer fragments were cloned, sequenced, and shown to be homologous to wheat 5S-rRNA spacers previously identified. Spacers of uniform size but with some sequence heterogeneity were shown to be located at each locus.

Improved Detection of HIV-2 DNA in Clinical Samples Using a Nested Primer-Based Polymerase Chain Reaction

A two-step polymerase chain reaction (PCR), with four double (nested) primer pairs, used for the detection of HIV-2 in clinical samples is described. With these four nested primer pairs we could detect HIV-2 DNA in 17 of 17 virus isolates and in blood mononuclear cell samples from 31 of 37 (83.7%) seropositive individuals after ethidium bromide staining of the amplified DNA. The nested primer PCR was also compared with a single primer pair-based PCR followed by hybridization. The sensitivities of the two methods were almost equal, but the nested primer PCR offered obvious technical advantages.

Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro

Nested-primer polymerase chain reaction (PCR) has been applied to the molecular cloning of 4.6-kb half-genome fragments of human immunodeficiency virus type 1 (HIV-1) taken directly from the peripheral blood mononuclear cells (PBMC) of an individual with neurological symptoms of HIV-1 infection. In a similar manner, gp120-coding portions of the envelope gene were cloned after PBMC from the same blood sample were cocultivated with uninfected PBMC for 28 days. The complete 1.6-kb nucleotide sequence of the gp120 gene was determined from each of 35 clones examined. Two of 13 (15%) PBMC-derived gp120 genes and 3 of 22 (14%) coculture-derived gp120 genes were defective as a result of frameshifts and an in-frame stop codon(s). Mean diversity between individual gp120-coding sequences in PBMC was fivefold greater (3.24%) than after coculture (0.65%). A predominant sequence of "strain" was found after coculture that was distinct from the diverse viral genotypes detected in vivo and therefore was selectively amplified during in vitro propagation. Multiple distinct third variable (V3) regions encoding the principal neutralizing domain of the envelope protein were detected in PBMC-derived genes, suggesting the presence of immunologic diversity of HIV env genes in vivo not reflected in the cocultured virus sample. The large size of the HIV fragments generated in this study will permit analysis of the diversity of immunologic reactivity, gene function, and pathogenicity of HIV genomes present within infected individuals, including the functional significance of the loss of diversity that occurs upon coculture.

Prognostic Significance of Philadelphia Chromosome-Positive Cells Detected by the Polymerase Chain Reaction After Allogeneic Bone Marrow Transplant for Chronic Myelogenous Leukemia

Although rare cells expressing the bcr/abl fusion transcript can be detected by the polymerase chain reaction (PCR) in patient blood or marrow after allogeneic bone marrow transplant (BMT) for Philadelphia chromosome (Ph+)-positive chronic myelogenous leukemia (CML), the prognostic significance of this finding is unknown. This paper reports clinical, cytogenetic, and molecular data derived from 64 CML patients following allogeneic BMT. Nested primer PCR was performed on patient blood and bone marrow samples to detect the presence of residual bcr/abl (+) cells in CML patients considered to be in clinical remission at the time of study. Bcr/abl transcripts were detected in 37 of 64 patients for at least one timepoint post-BMT. Thirteen of these 37 bcr/abl (+) patients have subsequently relapsed, as defined by clinical and/or persistent cytogenetic findings, in contrast to 0 relapses among the 27 bcr/abl (-) patients (P = .0025). The median time from first (+) bcr/abl PCR signal to relapse was 150 days (range 90 to 832). Fifty-four patients were studied at two or more timepoints post-BMT: five of eight patients persistently bcr/abl (+) have relapsed; 5 of 23 patients with both bcr/abl (+) and (-) assays during follow-up have relapsed; and none of 23 patients persistently (-) have relapsed (cumulative actuarial relapse rates 77%, 20%, and 0%, respectively, P = .0017). These data indicate that among CML patients in apparent clinical remission after BMT, nested primer bcr/abl PCR can define subgroups with low, intermediate, and high risk of relapse. The pattern of bcr/abl PCR detection after transplant may aid in the development of trials designed to reduce the risk of relapse, or allow for early intervention in patients who fail to clear the malignant clone.

Prognostic significance of Philadelphia chromosome-positive cells detected by the polymerase chain reaction after allogeneic bone marrow transplant for chronic myelogenous leukemia

Although rare cells expressing the bcr/abl fusion transcript can be detected by the polymerase chain reaction (PCR) in patient blood or marrow after allogeneic bone marrow transplant (BMT) for Philadelphia chromosome (Ph+)-positive chronic myelogenous leukemia (CML), the prognostic significance of this finding is unknown. This paper reports clinical, cytogenetic, and molecular data derived from 64 CML patients following allogeneic BMT. Nested primer PCR was performed on patient blood and bone marrow samples to detect the presence of residual bcr/abl (+) cells in CML patients considered to be in clinical remission at the time of study. Bcr/abl transcripts were detected in 37 of 64 patients for at least one timepoint post-BMT. Thirteen of these 37 bcr/abl (+) patients have subsequently relapsed, as defined by clinical and/or persistent cytogenetic findings, in contrast to 0 relapses among the 27 bcr/abl (-) patients (P = .0025). The median time from first (+) bcr/abl PCR signal to relapse was 150 days (range 90 to 832). Fifty-four patients were studied at two or more timepoints post- BMT: five of eight patients persistently bcr/abl (+) have relapsed; 5 of 23 patients with both bcr/abl (+) and (-) assays during follow-up have relapsed; and none of 23 patients persistently (-) have relapsed (cumulative actuarial relapse rates 77%, 20%, and 0%, respectively, P = .0017). These data indicate that among CML patients in apparent clinical remission after BMT, nested primer bcr/abl PCR can define subgroups with low, intermediate, and high risk of relapse. The pattern of bcr/abl PCR detection after transplant may aid in the development of trials designed to reduce the risk of relapse, or allow for early intervention in patients who fail to clear the malignant clone.

Fibrinogen γ-Chain mRNA Is Not Detected In Human Megakaryocytes

Human megakaryocytes and platelets contain counterparts of several plasma proteins. The origin of most of these alpha-granule proteins is unclear. Fibrinogen represents one of those molecules, being essential in hemostasis, thrombosis, and platelet aggregation. To study whether fibrinogen is endocytosed by megakaryocytes and packaged into alpha-granules or newly synthesized by these cells, we established a highly sensitive nested primer polymerase chain reaction for the detection of human fibrinogen gamma-chain mRNA. In enriched megakaryocyte fractions, as well as fluorescence-activated cell sorter-purified megakaryocytes from bone marrow samples of healthy volunteers, no fibrinogen gamma-chain mRNA could be detected, despite the presence of the corresponding fibrinogen gamma-chain DNA. We conclude that fibrinogen gamma-chain mRNA, as detectable by our amplification system, is missing in megakaryocytes. This finding suggests that fibrinogen might be acquired from plasma by endocytosis and sequestered in alpha-granules before reentering the circulation after platelet activation.

Fibrinogen gamma-chain mRNA is not detected in human megakaryocytes

Human megakaryocytes and platelets contain counterparts of several plasma proteins. The origin of most of these alpha-granule proteins is unclear. Fibrinogen represents one of those molecules, being essential in hemostasis, thrombosis, and platelet aggregation. To study whether fibrinogen is endocytosed by megakaryocytes and packaged into alpha- granules or newly synthesized by these cells, we established a highly sensitive nested primer polymerase chain reaction for the detection of human fibrinogen gamma-chain mRNA. In enriched megakaryocyte fractions, as well as fluorescence-activated cell sorter-purified megakaryocytes from bone marrow samples of healthy volunteers, no fibrinogen gamma- chain mRNA could be detected, despite the presence of the corresponding fibrinogen gamma-chain DNA. We conclude that fibrinogen gamma-chain mRNA, as detectable by our amplification system, is missing in megakaryocytes. This finding suggests that fibrinogen might be acquired from plasma by endocytosis and sequestered in alpha-granules before reentering the circulation after platelet activation.