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Biomarkers for biological agents.

Biomarkers of exposure to biological agents have proved to be extremely useful in establishing causal associations between infections and human cancer, as well as in tracing the natural history of the relevant agents. This chapter will focus on biomarkers for biological agents currently recognized as causally associated with various human cancers after evaluation at the IARC. These are human papillomavirus (HPV), hepatitis B (HBV) and C virus (HCV) and Helicobacter pylori. A prototype of nucleic-acid-based biomarkers is detection of HPV DNA. It measures the presence of type-specific DNA at a given point in time. PCR-based assays are considered the method of choice for epidemiological investigations. The test requires collection of exfoliated cells or biopsies. Specimens can be kept stored at -20 degrees C for long periods of time. DNA degradation is low. Some of the limitations of the marker for cancer epidemiology lie in the fact that HPV DNA infections are often transient, especially in young women. In repeated measurements, HPV DNA may fluctuate, but the reasons for this are unknown. Antigens and antibodies from the HBV and HCV can be viewed as prototypes for serological biomarkers. For HBV, there are markers able to distinguish between past and persistent infections. HBV DNA detection in sera further refines the assessment of exposure. Standardized serological assays are available and widely used in developing countries. For HCV antibodies, serological assays are standardized and widely available. RNA detection in sera by PCR is under development. A limitation of the currently available assays is the type and subtype variation of HCV by geography, which requires further research and standardization. In low-risk populations, numerous false-positive results arise and confirmatory tests are required.

Biomarkers, Tumor↗

[Detection of the nucleic acids of hepatitis B and C viruses and human immunodeficiency virus for the biological screening of blood donations. Viral Hepatitis and Retrovirus Working Groups and Subgroup for Molecular Biology Applied to Transfusion Virology of the French Blood Transfusion Society].

Direct viral DNA or RNA detection by genomic amplification methods should contribute to the improvement of blood supply safety by reducing the pre-seroconversion window period. However, nucleic acid testing may not eliminate virus transmission from window period donations. Moreover, the virus subtype diversity has to be taken into account for the choice of nucleic amplification assays. Technology for nucleic acid testing has not been developed to be implemented in blood screening laboratories. The limitations of these procedures are mainly linked to the difficulties related to the automation of sample processing and to the possibilities of cross contamination of samples due to the high sensitivity of amplification methods. The extreme complexity of nucleic acid testing for single donation screening (development of an on-site automated high-throughput instrumentation, training, specialized facilities for sample processing, amplification and detection...) and its high cost mean that strategies using amplification testing of pooled samples should be developed.

AIDS Serodiagnosis↗

The origin of the polydispersity in sedimentation patterns of rapidly labelled nuclear ribonucleic acid.

1. A study was made of the sedimentation properties of purified preparations of the rapidly labelled RNA in the nucleus and the cytoplasm of the HeLa cell. The sedimentation of the rapidly labelled nuclear RNA was very sensitive to changes in ionic strength and bivalent cation concentration. Under the conditions usually used in sucrose-density-gradient centrifugation the rapidly labelled nuclear RNA showed extreme polydispersity, and much of it sedimented more rapidly than the 28s RNA. At low ionic strength and after removal of Mg(2+), however, the rapidly labelled nuclear RNA sedimented as a single peak at about 16s. The conversion of the polydisperse material into the 16s form did not involve degradation of the RNA, since the effect could be reversed by increasing the ionic strength of the solution. 2. The cytoplasm did not contain any RNA that showed polydisperse sedimentation under the usual conditions of sucrose-density-gradient centrifugation, or that had the same sensitivity as the rapidly labelled nuclear RNA to changes in ionic strength. All the radioactivity in the cytoplasmic RNA sedimented with the 28s, 16s and 4s components over a wide range of physical conditions, but these components did contain a labelled fraction with some of the features of the rapidly labelled nuclear RNA on columns of methylated albumin on kieselguhr. 3. In both nucleus and cytoplasm the RNA detected by ultraviolet absorption could also be converted into a 16s form by removal of bivalent cations at low ionic strength; this effect was again, within certain limits, reversible. The nuclear RNA as a whole was more susceptible to changes in ionic strength than the cytoplasmic RNA. 4. It thus appears that all the RNA in the cell, except the 4s RNA, can be prepared, without degradation, as a single peak sedimenting at about 16s. The relationship of these various 16s components to each other is discussed.

Albumins↗

Hepatitis C and risk of lymphoma: results of the European multicenter case-control study EPILYMPH.

BACKGROUND & AIMS: Increasing evidence points toward a role of hepatitis C virus (HCV) infection in the etiology of malignant lymphomas. However, previous epidemiologic studies were limited in size to establish an association between HCV infection and specific lymphoma subtypes. We performed a large, multicenter, case-control study to address this question. METHODS: The study comprised 5 European countries and included newly diagnosed cases of any lymphoid malignancy recruited between 1998 and 2004. Controls were matched to cases by 5-year age group, sex, and study center. In-person interviews were conducted to collect data on demographic, medical, and family history as well as environmental exposures. Serum samples of 1807 cases and 1788 controls (excluding human immunodeficiency virus-positive and organ-transplantation subjects) were screened for HCV infection using an enzyme immunoassay. Positive as well as randomly selected negative samples were subjected to HCV RNA detection and HCV genotyping. RESULTS: HCV infection was detected in 53 (2.9%) lymphoma cases and in 41 (2.3%) control subjects (odds ratio [OR], 1.42; 95% confidence interval [CI]: 0.93-2.15). Restricted to individuals who tested positive for HCV-RNA (indicating persistent infection and active viral replication), the OR was 1.82 (95% CI: 1.13-2.91). In subtype-specific analyses, HCV prevalence was associated with diffuse large B-cell lymphoma (OR, 2.19; 95% CI: 1.23-3.91) but not with chronic lymphocytic leukemia or follicular, Hodgkin's, or T-cell lymphoma. The sample size was not sufficient to derive any conclusions for rare lymphoma entities such as splenic marginal zone lymphoma. CONCLUSIONS: These results support a model that chronic HCV replication contributes to lymphomagenesis and establish a specific role of HCV infection in the pathogenesis of diffuse large B-cell lymphoma.

Adult↗

Persistence of viremia in patients with type-C chronic hepatitis during long-term follow-up.

To clarify the evolution of antibody to hepatitis C virus (anti-HCV) and of liver histologic findings during the natural course of type-C chronic hepatitis, 111 patients with biopsy-proven chronic hepatitis type C were consecutively enrolled in this study and were followed up biochemically, serologically, and histologically for more than 5 years. All were positive for the first- and second-generation antibody to HCV (anti-HCV-1 and anti-HCV-2). None received antiviral therapy during the follow-up period. At the end of follow-up, all remained positive for anti-HCV-2, but four patients turned negative for anti-HCV-1. HCV RNA, detected by the polymerase chain reaction method, was tested serially in 20 patients who persisted positive anti-HCV-1 and in 4 patients who lost anti-HCV-1. HCV RNA disappeared from only two patients, who lost anti-HCV-1 during the follow-up period. A normalization of the serum transaminase level was found in only two patients, who lost both anti-HCV-1 and HCV RNA. A repeat liver biopsy was performed in 62 patients with chronic hepatitis who were persistently positive for all HCV markers and in 4 patients who lost anti-HCV-1. Of the 62 patients who retained all HCV markers, 16 progressed to hepatocellular carcinoma, 6 to cirrhosis of the liver, and 1 had a normal liver, whereas the remaining 39 had chronic hepatitis. Two patients who lost both anti-HCV-1 and HCV RNA showed a normal liver. Of two patients who lost only anti-HCV-1 one progressed to hepatocellular carcinoma and one to chronic hepatitis.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

[Studies on the treatment of chronic hepatitis C with interferon. Assessment of treatment regimens and response to treatment].

The difference in response rate to interferon (IFN) among several treatment regimens was assessed retrospectively in 48 HCV-RNA positive patients with chronic hepatitis C. The study focused on patients' pretreatment profiles and response to treatment, histological findings before and after the treatment and the significance of HCV-RNA detection in evaluating the outcome. A complete response (CR) evaluated by the outcome of alanine aminotransferase (ALT) was obtained in 16 of 25 patients (64.0%) treated with IFN in doses of 3 to 6 million units daily for the first 4 or 8 wks and subsequent dosing twice or three times weekly for the following 8 to 146 wks. In contrast, CR was obtained in only 7 of 16 patients (43.8%) treated with the regimen in which patients received IFN in doses of 1 to 6 million units daily for 4 to 8 wks and no subsequent IFN. In comparing the responders to IFN (25 cases) and the non responders (19 cases), there were no significant differences regarding patients' age, sex, the presence or absence of history of blood transfusion, pretreatment ALT values or histological magnitude, or total doses of IFN administered. When the basal and final biopsy samples were compared, Knodell's index of histological activity had decreased significantly in the responders but not in the non responders. In 24 of the 25 responders, HCV-RNA had disappeared from their serum at the end of treatment, and in 23 it remained undetectable 6 months after treatment. In contrast, in 6 of the 19 non responders HCV-RNA had become negative at the end of treatment but was detectable in all cases 6 months after treatment. Thus, it is concluded that (1) a regimen of daily administration for the first 4 or 8 wks with subsequent dosing twice or three times weekly was preferable in terms of obtaining frequent CR, (2) response to IFN cannot be predicted by a patient's pretreatment profile, (3) in responders, histological activity decreases, and (4) in responders, HCV-RNA becomes undetectable not only at the end of treatment but also 6 months after treatment.

Adult↗

Membranoproliferative glomerulonephritis associated with hepatitis C virus infection.

BACKGROUND AND METHODS: Hepatitis C virus (HCV) infection causes both acute and chronic liver disease and is also associated with mixed cryoglobulinemia. Whether HCV is also associated with renal disease, as is the hepatitis B virus, is not known. We describe the clinical, pathologic, virologic, and immunologic features of eight patients with HCV infection who were referred to nephrologists for glomerulonephritis. Four patients were treated with interferon alfa. RESULTS: All eight patients had proteinuria, and seven had decreased renal function. Renal biopsy in all patients revealed membranoproliferative glomerulonephritis, characterized by the deposition of IgG, IgM, and C3 in glomeruli. Electron microscopy of the biopsy specimens showed cryoglobulin-like structures in three of four patients. All eight patients had HCV RNA detected in their serum, elevated serum aminotransferase concentrations, and hypocomplementemia, and the majority had cryoglobulins and circulating immune complexes in their serum. Cryoprecipitates from the three patients who were tested contained HCV RNA and IgG anti-HCV antibodies to the nucleocapsid core antigen (HCVc or c22-3). IgM rheumatoid factors, present in all patients, bound anti-HCV IgG in all six patients tested. Four patients received interferon alfa for 2 to 12 months; all had evidence of decreased HCV replication and improvement of their renal and liver disease. CONCLUSIONS: Chronic HCV infection is associated with cryoglobulinemia and membranoproliferative glomerulonephritis. The pathogenesis is unknown, but may relate to deposition within glomeruli of immune complexes containing HCV, anti-HCV IgG, and IgM rheumatoid factors.

Adult↗

Lack of persistence of influenza virus genetic information in ducks.

Clearance of infectious virus and RNA occurred concurrently after oral infection of ducks with influenza virus. There was no evidence from polymerase chain reaction (PCR) analysis of the hemagglutinin (HA) gene for persistence of viral genetic information. No detectable RNA was found in the spleen indicating processing of antigen near the site of replication.

Animals↗

Dynamics of a mobile RNA of potato involved in a long-distance signaling pathway.

BEL1-like transcription factors interact with Knotted1 types to regulate numerous developmental processes. In potato (Solanum tuberosum), the BEL1 transcription factor St BEL5 and its protein partner POTH1 regulate tuber formation by mediating hormone levels in the stolon tip. The accumulation of St BEL5 RNA increases in response to short-day photoperiods, inductive for tuber formation. RNA detection methods and heterografting experiments demonstrate that BEL5 transcripts are present in phloem cells and move across a graft union to localize in stolon tips, the site of tuber induction. This movement of RNA to stolon tips is correlated with enhanced tuber production. Overexpression of BEL5 transcripts that include the untranslated sequences of the BEL5 transcript endows transgenic lines with the capacity to overcome the inhibitory effects of long days on tuber formation. Addition of the untranslated regions leads to preferential accumulation of the BEL5 RNA in stolon tips under short-day conditions. Using a leaf-specific promoter, the movement of BEL5 RNA to stolon tips was facilitated by a short-day photoperiod, and this movement was correlated with enhanced tuber production. These results implicate the transcripts of St BEL5 in a long-distance signaling pathway that are delivered to the target organ via the phloem stream.

Gene Expression Regulation, Plant↗

A sensitive dot blot procedure for detecting mRNA in lymphoid cells grown in liquid culture.

A sensitive dot blot procedure for detecting RNA transcripts with radiolabelled cDNA probes in small numbers of cells in suspension culture is described. For a frequent mRNA species such as that for immunoglobulin in an IgM secretor hybridoma, as few as 30 cells can be detected using a C mu probe; for a less frequent mRNA species such as transcripts coding for alpha, beta or gamma genes of the T cell receptor in T cell tumors or CTL clones, as few as 3 X 10(3) to 10(4) cells can be detected using C alpha, C beta or C gamma probes. High sensitivity is achieved by confining the cells to a very small area on the filter on which they are probed, and by treating the filter with formaldehyde.

Animals↗

Evidence of non-A, non-B, non-C infection in chronic hepatitis by polymerase chain reaction testing for hepatitis B and C viruses.

BACKGROUND/AIMS: Although hepatitis C virus is clearly the major cause of non-A, non-B acute and chronic hepatitis, there is a group of patients with histologically documented chronic hepatitis with no serological marker of hepatitis B and C, nor any other risk factors for liver disease. METHODS: We have investigated 17 well-characterized patients with chronic active hepatitis. HBV-DNA and HCV-RNA were tested by polymerase chain reaction in 17 serum samples and in six liver biopsies. RESULTS: Four of the 17 patients had serum HCV-RNA detectable by polymerase chain reaction, while none had HBV-DNA detectable by polymerase chain reaction. Three of the six liver samples gave a positive signal by cyclin A and HLA, and only these were considered for the study. One of the three was HCV-RNA positive, while none was HBV-DNA positive. CONCLUSIONS: Our results, obtained through careful elimination of all known risk factors for liver disease, strongly suggest that non-A, non-B, non-C hepatotropic virus(es) could be involved in some cases of chronic active liver disease.

Adolescent↗

Astrocytes, not microglia, are the main cells responsible for viral persistence in Theiler's murine encephalomyelitis virus infection leading to demyelination.

The BeAn strain of Theiler's murine encephalomyelitis virus (TMEV) persists in the CNS and produces a chronic inflammatory demyelinating disease that is an animal model for human multiple sclerosis (MS). The mechanisms leading to TMEV-induced demyelination are still under study but most likely involve both immune-mediated and virus induced damage to cells in the CNS, both depending on viral persistence. It is therefore important to identify the cells in which continued virus production is permitted. In this study, we looked at virus infection in primary astrocytes, microglia and oligodendrocytes, derived from brains of neonatal susceptible SJL/J mice. As evidenced by Western blots and immunocytochemistry, we were able to detect viral antigens in all these brain-derived cells. In addition, we extended the study to spinal cord tissues from mice suffering TMEV-induced disease. Immunohistochemistry staining with anti-TMEV sera and antibodies to specific cell markers detected viral antigens in all these cells. We then asked the question whether viral antigen present in these cells, particularly in microglia/macrophages, represented true viral replication or not. By using different techniques, including immunoprecipitation experiments and the very sensitive method of negative RNA detection through RNase protection assay, we show that both astrocytes and oligodendroglia permit de novo viral replication and viral protein synthesis but with only minimal cytopathic effects. Of these two cell types, astrocytes carry the brunt of viral replication. In microglia, on the other hand, viral replication is restricted since only minimal amounts of negative RNA copies can be demonstrated, while there are clear signs that some of these cells undergo apoptosis. These findings show that the main cell for viral replication is the astrocyte, rather than the microglia/macrophage. Most of the viral antigen present in macrophages, therefore, is probably the result of phagocytosis, rather than actual viral replication. In view of the demonstrated presence of viral replication in astrocytes and of great amounts of viral antigens in microglia/macrophages, it is possible that both types of cells act as antigen presenting cells during this immunopathological disease.

Animals↗

Evaluation of real-time PCR versus PCR with liquid-phase hybridization for detection of enterovirus RNA in cerebrospinal fluid.

A LightCycler and two TaqMan real-time PCR assays were evaluated against an older PCR with liquid-phase hybridization method for the detection of enterovirus RNA in 74 patient samples. The two-step LightCycler and the two-step TaqMan formats correlated well with each other (r(2) = 0.90) and were equally sensitive compared to the liquid-phase hybridization method, whereas the one-step recombinant Tth DNA polymerase format was rather insensitive, detecting enterovirus RNA in only about one-half of those patient samples previously positive by liquid-phase hybridization. The two-step TaqMan method was optimized utilizing 10 micro l of cDNA and demonstrated the highest degree of analytical sensitivity among the methods evaluated in our study, being able to reproducibly quantify down to 510 copies of enteroviral RNA/ml of cerebrospinal fluid. This new assay can be performed in 4 h, is much less labor intensive, and showed less cross-reactivity with rhinovirus than the liquid-phase hybridization assay. Thus, the two-step TaqMan assay should prove useful in the diagnosis of enteroviral meningitis versus bacterial meningitis, thereby resulting in timely and appropriate clinical management that can amount to significant cost savings to the patient and health care system.

Computational Biology↗

Development, technical performance, and clinical evaluation of a NucliSens basic kit application for detection of enterovirus RNA in cerebrospinal fluid.

The combination of nucleic acid sequence-based amplification and electrochemiluminescence detection was used to develop an internally controlled, highly sensitive and specific assay for the detection of enterovirus (EV) RNA in cerebrospinal fluid (CSF). The analytical performance of the assay was determined using both in vitro-transcribed EV RNAs and viral culture isolates. The sensitivity of the assay was 10 EV RNA copies per amplification reaction. The assay detected all enteroviral isolates tested with no cross-reactivity to 21 nonenteroviral species, including rhinovirus and parechovirus. The clinical performance of the assay was evaluated by testing 992 CSF specimens collected from adult and pediatric patients. NucliSens EV results from a subset of 327 CSF samples were compared to viral culture of nasopharyngeal specimens and rectal swabs (n = 195) and/or CSF (n = 212). Of the 212 CSF samples, 96 samples were positive by either the NucliSens EV assay (94/96; 97.9%) or culture (63/96; 65.6%), and 61/96 (63.5%) were positive by both methods. The inclusion of an EV-specific internal control monitored the entire process, including the efficiency of nucleic acid extraction, amplification, and detection. In total, only five blood-clotted CSF samples (0.5%) were inhibited. The NucliSens EV assay demonstrated superior sensitivity over viral culture (P < 0.001), excellent specificity, clear delineation of positive samples, and minimal amplification inhibition.

Adolescent↗

Immunoelectron microscopic localization of RNA polymerase B on isolated polytene chromosomes of Chironomus tentans.

RNA polymerase B (or II) was localized by immunoelectron microscopy in ultrathin sections of polytene chromosomes isolated from larval salivary glands of Chironomus tentans. The enzyme was found at decondensed sites (puffs and interbands), whereas no detectable RNA polymerase B was present in condensed loci (bands). Within each of the large puffs the highest enzyme concentration was observed wherever the chromatin was in the most decondensed state. Otherwise the enzyme appeared homogeneously distributed within puffs and interbands. This immunoelectron microscopic study, along with the recently published immunofluorescent and autoradiographic analysis of isolated Chironomus chromosomes (Sass, 1982) unequivocally demonstrates that RNA polymerase B is present in most, if not all interbands.

Animals↗

Detection of enteroviral RNA and specific DNA of herpesviruses by multiplex genome amplification.

A reverse transcription (RT) multiplex polymerase chain reaction (PCR) assay was developed to allow rapid, sensitive and simultaneous detection of enteroviral RNA and herpesviral DNA specific sequences in a single tube. The method involves a reverse transcription step followed by a multiplex nested PCR in which the combination of primers amplifies cDNA from enteroviruses and specific herpesviruses DNA. Nested amplification utilises primers designed to anneal into the amplification product from the first reaction. Individual viruses were then detected and differentiated by the size of their PCR products determined using ethidium bromide stained agarose gels. To exclude false negatives due to sample inhibitors an internal amplification control, a cloned fragment of DNA from Pseudorabies virus (PRV DNA) was included in the reaction mixture. Detection levels between 0.01 and 0.001 TCID50 of prototype strains of Polio and Coxsackie type B viruses and between 1 and 100 molecules of cloned-DNA of herpesviruses prototype strains were achieved. The RT multiplex PCR method proved capable of detecting enteroviral RNA or herpesviral DNA in cerebro spinal fluid (CSF) samples from patients with aetiologically well characterized encephalitis or aseptic meningitis.

Child↗

Monitoring of inhibitors of enzymatic amplification in polymerase chain reaction and evaluation of efficacy of RNA extraction for the detection of hepatitis C virus using the internal control.

Inhibitors of enzymatic amplification in serum may cause false-negative results for direct detection of hepatitis C virus (HCV) by polymerase chain reaction (PCR). This study was undertaken to demonstrate the importance of the internal control in a PCR assay for detection of HCV-RNA to monitor false-negatives due to inhibitors. HCV-RNA was extracted using RNA extraction kit (SepaGene RV-R, Sanko Junyaku) and a prototype instrument for automated specific capture of HCV-RNA with probes and magnetic bead/fluid separation (Roche Molecular Systems). The extracted HCV-RNA and internal control were detected by an automated PCR machine (Cobas Amplicor, Roche Diagnostic Systems). Addition of hemoglobin (up to 4.5 g/l) to the sera followed by RNA extraction with SepaGene RV-R had no inhibitory effect on the detection of either HCV-RNA or the internal control. In contrast, addition of heparin to the sera showed an inhibitory effect with a dose-dependent manner on the detection of both HCV-RNA and the internal control, with a greater effect at lower copy number of HCV. When HCV-RNA was extracted by the automated system, the inhibitory effect of heparin was successfully eliminated. In the assays of 65 serum samples positive for anti-HCV antibodies, positivity for the internal control indicated efficient amplification and validated 14 negative and two equivocal results for detection of HCV-RNA. Detection of the internal control was negatively correlated with viral copy number in sera suggesting competitive inhibition of high viral copy number on amplification of the internal control. Extraction, co-amplification and detection of the internal control appears useful for estimating effects of inhibitors on amplification in each assay for the detection of HCV-RNA, and for evaluating efficacy of RNA extraction methods.

Enzyme Inhibitors↗

[Study on enhanced leukocyte antigen-related tyrosine phosphatase in keratoconus].

OBJECTIVE: To study the enhanced expression of leukocyte antigen-related tyrosine phosphatase (LAR) in human keratoconus cornea. METHODS: Corneal buttons of patients received keratoplasty in Eye Center of Beijing Tongren from December 2001 to March 2002 were collected. Total RNA was isolated from the buttons from keratoconus (15 eyes), normal cornea (7 eyes), bullous keratopathy (6 eyes), non-neovascular cornea scar (3 eyes) and corneal dystrophy (2 eyes). Polymerase chain reaction (RT-PCR) was performed in this group. The results were displayed by agarose gels electrophoresis. In another group of patients, the corneal buttons of patients received keratoplasty in Eye Center of Beijing Tongren from July 2002 to December 2002 were collected. Total protein was extracted from the buttons of keratoconus (6 eyes), normal cornea (3 eyes), bullous keratopathy (3 eyes), non-neovascular cornea scar (3 eyes) and corneal dystrophy (2 eyes). Western blot was performed in this group. The results were displayed by enhanced chemical illumination. Bands of LAR RNA and LAR protein from these two tests were analyzed quantitatively. RESULTS: In RT-PCR study using the same amount of total RNA, high signal of LAR RNA was detected in RNA from the keratoconus, whereas low or no signal was detected in normal cornea and other diseases. Sequence analysis of the product of amplified LAR fragment from keratoconus showed deletion of exon 13. In Western blot study using the same amount of total protein, high signal of LAR was detected in keratoconus by the LAR antibodies, while low or no signal was detected in normal cornea and other diseases. CONCLUSIONS: LAR mRNA and protein are enhanced in keratoconus, whereas there are low or no expression in normal cornea, bullous keratopathy, non-neovascular cornea scar and corneal dystrophy. Elevated LAR in keratoconus indicates that LAR plays an essential role in the occurrence of keratoconus. Deletion of exon 13 in keratoconus may play a potential role in the abnormal LAR function.

Humans↗