Glucocorticoid receptor polymorphisms and haplotypes associated with chronic fatigue syndrome.

Chronic fatigue syndrome (CFS) is a significant public health problem of unknown etiology, the pathophysiology has not been elucidated, and there are no characteristic physical signs or laboratory abnormalities. Some studies have indicated an association of CFS with deregulation of immune functions and hypothalamic-pituitary-adrenal (HPA) axis activity. In this study, we examined the association of sequence variations in the glucocorticoid receptor gene (NR3C1) with CFS because NR3C1 is a major effector of the HPA axis. There were 137 study participants (40 with CFS, 55 with insufficient symptoms or fatigue, termed as ISF, and 42 non-fatigued controls) who were clinically evaluated and identified from the general population of Wichita, KS. Nine single nucleotide polymorphisms (SNPs) in NR3C1 were tested for association of polymorphisms and haplotypes with CFS. We observed an association of multiple SNPs with chronic fatigue compared to non-fatigued (NF) subjects (P < 0.05) and found similar associations with quantitative assessments of functional impairment (by the SF-36), with fatigue (by the Multidimensional Fatigue Inventory) and with symptoms (assessed by the Centers for Disease Control Symptom Inventory). Subjects homozygous for the major allele of all associated SNPs were at increased risk for CFS with odds ratios ranging from 2.61 (CI 1.05-6.45) to 3.00 (CI 1.12-8.05). Five SNPs, covering a region of approximately 80 kb, demonstrated high linkage disequilibrium (LD) in CFS, but LD gradually declined in ISF to NF subjects. Furthermore, haplotype analysis of the region in LD identified two associated haplotypes with opposite alleles: one protective and the other conferring risk of CFS. These results demonstrate NR3C1 as a potential mediator of chronic fatigue, and implicate variations in the 5' region of NR3C1 as a possible mechanism through which the alterations in HPA axis regulation and behavioural characteristics of CFS may manifest.

Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR.

We evaluated real-time (kinetic) reverse transcription-polymerase chain reaction (RT-PCR) to validate differentially expressed genes identified by DNA arrays. Gene expression of two keratinocyte subclones differing in the physical state of human papillomavirus (episomal or integrated) was used as a model system. High-density filter arrays identified 444 of 588 genes as either negative or expressed with less than twofold difference, and the other 144 genes as expressed uniquely or with more than twofold difference between the two subclones. Real-time RT-PCR used LightCycler-based SYBR Green I dye detection and melting curve analysis to validate the relative change in gene expression. Real-time RT-PCR confirmed the change in expression of 17 of 24 (71%) genes identified by high-density filter arrays. Genes with strong hybridization signals and at least twofold difference were likely to be validated by real-time RT-PCR. This data suggests that (i) both hybridization intensity and the level of differential expression determine the likelihood of validating high-density filter array results and (ii) genes identified by DNA arrays with a two- to fourfold difference in expression cannot be eliminated as false nor be accepted as true without validation. Real-time RT-PCR based on LightCycler technology is well-suited to validate DNA array results because it is quantitative, rapid, and requires 1000-fold less RNA than conventional assays.

Detection of human papillomaviruses by polymerase chain reaction and in situ hybridization.

The clinical utility of human papillomavirus (HPV) testing continues to be the focus of much debate. The clear epidemiologic link of HPV infection with the development of cervical intraepithelial neoplasia and invasive cervical cancers.

Use of real-time quantitative PCR to validate the results of cDNA array and differential display PCR technologies.

Real-time reverse transcription polymerase chain reaction (RT-PCR) methods that monitor product accumulation were adapted for the validation of differentially expressed genes. We describe a real-time quantitative PCR assay that uses SYBR Green I dye-based detection and product melting curve analysis to validate differentially expressed genes identified by gene expression profiling technologies. Since SYBR Green I dye is a nonspecific intercalating dye, the reaction is made specific by using "hot-start" PCR and empirically determined annealing and signal acquisition temperatures for each gene-specific primer. Relative expression levels were quantified by constructing a standard curve using cDNA dilutions of a highly expressed gene. Using this approach, real-time PCR validated 17 of 21 (71%) genes identified by DNA arrays, and all but 1 of 13 (91%) genes identified by differential display PCR (DD-PCR). Validation of differentially expressed genes detected by array analysis was related to hybridization intensity. Real-time RT-PCR results suggest that genes identified by DNA arrays with a two to fourfold difference in expression cannot be accepted as true or false without validation. Validation of differentially expressed genes detected by DD-PCR was not affected by band intensities. Regardless of the gene expression profiling technology (microarrays, DD-PCR, serial analysis of gene expression and subtraction hybridization), once the sequence of gene of interest is known, the real-time RT-PCR approach is well suited for validation of differential expression since it is quantitative and rapid and requires 1000-fold less RNA than conventional assays.

Comparison of human papillomavirus detection and typing by cycle sequencing, line blotting, and hybrid capture.

We compared the results of human papillomavirus (HPV) detection and typing from 781 cervical samples assayed by three methods: L1 consensus PCR followed by cycle sequencing, L1 consensus PCR with biotinylated primers followed by hybridization to a line blot, and Hybrid Capture assay. Both PCR assays used L1 consensus PCR with primers MY09 and MY11. We evaluated the amplification efficiencies of both PCR assays and also compared the specific HPV types detected by each method. The samples positive by the Hybrid Capture assay were compared to the specific types detected by the PCR-based assays. The concordance between the two PCR assays in producing an HPV amplicon visible by gel electrophoresis or in detecting any HPV type was moderate: kappa values were 0.61 (95% confidence interval [CI] = 0.56 to 0.67) and 0.51 (95% CI = 0.46 to 0.58), respectively. The McNemar test for correlated proportions indicated that biotinylated PCR was less likely to produce a band (P = 0.001) and to detect an HPV type (P = 0.001) than the other PCR assay. In comparing the Hybrid Capture assay results with the HPV types detected by the PCR-based assays, we found that positivity by the Hybrid Capture assay for a number of samples may be due to cross-hybridization with HPV types not included in the Hybrid Capture assay probe cocktails.

Reproducibility of alternative probe synthesis approaches for gene expression profiling with arrays.

Before gene expression profiling with microarray technology can be transferred to the diagnostic setting, we must have alternative approaches for synthesizing probe from limited RNA samples, and we must understand the limits of reproducibility in interpreting gene expression results. The current gold standard of probes for use with both microarrays and high-density filter arrays are synthesized from 1 microg of purified poly(A)+ RNA. We evaluated two approaches for synthesizing cDNA probes from total RNA with subsequent hybridization to high-density filter arrays: 1) reverse transcription (RT) of 5 microg total RNA and 2) RT-polymerase chain reaction (RT-PCR) of 1 microg total RNA, using the SMART system. The reproducibility of these two approaches was compared to the current gold standard. All three methods were highly reproducible. Triplicate experiments resulted in the following concordance correlation coefficients to evaluate reproducibility: 0.88 for the gold standard, 0.86 for cDNA probe synthesized by RT from total RNA, and 0.96 for the SMART cDNA probe synthesized from total RNA. We also compared the expression profile of 588 genes for the total RNA methods to that obtained with the gold standard. Of 150 positive genes detected by the gold standard, 97 (65%) were detected by cDNA probe synthesized by RT of total RNA, and 122 (81%) were detected by the SMART cDNA probe. We conclude that SMART cDNA probe produces highly reproducible results and yields gene expression profiles that represent the majority of transcripts detected with the gold standard.

An unusual cervical carcinoma showing exception to epitheliotropism of human papillomavirus.

Human papillomaviruses (HPV) infect epithelial tissues but have not been previously detected within mesenchymal cells. During a systematic investigation of FIGO stage Ib cervical cancers with colorimetric in situ hybridization, we detected HPV 16 DNA within the stromal compartment of an unusual undifferentiated carcinoma. The mesenchymal nature of the HPV-containing cells was confirmed by immunohistochemistry and electron microscopy. No viral particles were identified. Sequencing the majority of the HPV 16 genome identified few changes from the revised reference clone; all previously reported in other HPV 16 variants. These viral changes are unlikely to explain the exceptional mesenchymal localization of the HPV 16 DNA in this case.

Chemiluminescent analysis of gene expression on high-density filter arrays.

We have optimized conditions for the chemiluminescent analysis of gene expression using high-density filter arrays (HDFAs). High sensitivity and specificity were achieved by optimizing cDNA probe synthesis, hybridization, and detection parameters. The chemiluminescent expression profile reflected expected differences in the transcripts isolated from different sources (placenta and keratinocytes). We estimated the detection limit for low-abundance message to be 1-15 transcripts per cell, a sensitivity rivaling that reported for microarray formats and exceeding that reported for autoradiographic HDFAs. The method allows for short exposure times and reuse of probe. It should be equally applicable to techniques such as differential screening of cDNA libraries and differential display PCR.

Association of human papillomavirus with HIV and CD4 cell count in women with high or low numbers of sex partners.

OBJECTIVE: To explore whether HIV serostatus (HIV-1, HIV-2, and dual (HIV-D) reactivity) and CD4 cell count affect human papillomavirus (HPV) in two groups of women from Côte d'Ivoire. METHODS: We conducted a cross sectional study of two groups of women. One group had low numbers of lifetime sex partners (maternal women, n = 258) and were enrolled based on HIV serostatus. The other group had high numbers of sex partners (female sex workers, n = 278) and all consenting self identified sex workers were admitted to this study. We collected epidemiological and clinical data, and cervicovaginal lavage for HPV testing. RESULTS: The groups had different distributions of HIV seroreactivity, but the rates of HPV DNA detection were similar. Most of the HPV DNAs detected in both groups were high risk types. A strong association of high risk HPV DNA and HIV-1 seropositivity was found in both maternal women (adjusted odds ratio (OR) 7.5 (95% CI 3.2-17.4)) and in sex workers (OR 5.0 (2.1-12.0)). The maternal group also showed an association of high risk HPV DNA detection with HIV-2 (OR 3.7 (1.6-8.5)) and HIV-D (OR 12.7 (4.3-37.5)) that was not observed in the sex workers. In addition, the association of high risk HPV DNA with HIV-1 in the maternal group was independent of low CD4 cell count, while in the sex workers the association depended on CD4 cell counts < or = 500 x 10(6)/l. CONCLUSIONS: We found that an association between HPV and HIV varied depending on the sexual behaviour and CD4 cell count of the population examined.

HIV and human papillomavirus as independent risk factors for cervical neoplasia in women with high or low numbers of sex partners.

OBJECTIVE: To explore whether HIV types 1 and 2 and CD4 cell count affect cervical neoplasia independent of human papillomavirus (HPV) in women with high or low numbers of sexual partners residing in Abidjan, Côte d'Ivoire. METHODS: The study population and methods are described in the companion paper. Additional methods include a Papanicolaou smear for cytological diagnosis and statistical analysis. RESULTS: In maternal women, both HIV-1 and high risk HPV were significant independent risk factors for squamous intraepithelial lesions (SIL) (adjusted odds ratio (OR) 11.0 (95% CI 1.1-112) and 5.4 (1.5-18.8), respectively). Only high levels of HPV DNA in the lavage were associated with SIL (OR 13.2 (3.6-47.8)) in the maternal group. In female sex workers, high risk HPV was significantly associated with SIL (OR 23.7 (4.4-126)); HIV seropositivity was not. Any positive level (high or low amounts) of HPV DNA was significantly associated with SIL in sex workers (ORs 15.9 (3.3-76) and 12.7 (3.6-44), respectively). There was no association of SIL with CD4 cell counts < or = 500 x 10(6)/l in HIV seropositive women from either group. CONCLUSION: HPV or HIV-1 infection independently affect cervical neoplasia in women with low numbers of sex partners.

Gynaecological conditions associated with HIV infection in women who are partners of HIV-positive Thai blood donors.

Women who were partners of HIV-positive blood donors were enrolled in a study of heterosexual HIV transmission between March 1992 and December 1996 and were interviewed and examined. Gynaecological conditions, including cervical dysplasia, human papillomavirus (HPV) infection, gonorrhoea, chlamydial infection, trichomoniasis, bacterial vaginosis, vaginal candidiasis and syphilis were assessed in addition to HIV status and CD4 level. Of 481 women enrolled, 224 (46.6%) were HIV seropositive. HIV-infected women were more likely to have abnormal vaginal discharge on physical examination (OR=2.6, P <0.01), HPV infection with a high-risk type (OR=6.9, P <0.01), and cervical dysplasia (OR=5.3, P <0.01). The prevalence of other gynaecological conditions detected at the enrolment visit did not differ by HIV status. History of prior STD (OR=2.0, P <0.01) was more common among HIV-infected women. The median CD4 count was 400 cells/microl among HIV-infected women. The prevalence of abnormal vaginal discharge and bacterial vaginosis increased significantly with decreasing CD4 count. The prevalence of ectopy, vaginal candidiasis, and cervical dysplasia increased with decreasing CD4 count, but these trends were not significant. We conclude that HIV-infected Thai women appear to have increased prevalences of abnormal vaginal discharge, squamous intraepithelial lesions and self-reported history of STD.

PIP: Gynecologic conditions associated with HIV infection were examined in 481 regular female sex partners of HIV-positive male blood donors enrolled in a study of heterosexual HIV transmission conducted at Chiang Mai University Hospital and Lampang Provincial Hospital in Thailand in 1992-96. Of these women, 224 (46.6%) were HIV-infected. HIV-positive and HIV-negative women were similar in terms of age, education, and age at first intercourse; however, a history of sexually transmitted disease was more common among the HIV-infected women (31.7%) than their uninfected counterparts (18.7%). HIV-infected women also were significantly more likely to have abnormal gynecologic conditions, including abnormal vaginal discharge at physical examination (odds ratio (OR), 2.6; 95% confidence interval (CI), 1.6-4.2) and cervical dysplasia (OR, 5.3; 95% CI, 2.0-15.2). Among HIV-positive women, the prevalence of abnormal vaginal discharge and bacterial vaginosis increased significantly with decreasing CD4 count. Syphilis, gonorrhea, chlamydia, and trichomoniasis rates were generally low and did not differ by HIV status. These findings suggest a need for further research on variations in gynecologic conditions associated with HIV infection in different countries.

Detection of human papillomavirus in archival tissues. Comparison of in situ hybridization and polymerase chain reaction.

Formalin-fixed, paraffin-embedded tissues in pathology archives are an important resource for molecular epidemiology studies. Use of these tissues requires that assays be optimized to account for inevitable variations in tissue fixation and processing that occur in the performance of routine histology. We compared results of colorimetric in situ hybridization (ISH) to L1 consensus polymerase chain reaction (PCR) for detection and typing of human papillomavirus (HPV) in 180 blocks of archival tissues (up to 9 years in storage) from cervical cancer patients. Fifteen samples could not be amplified by PCR, but assays were concordant in 75.1% (124/165) of samples that could be analyzed by both methods. Similar numbers of ISH+/PCR- (23) and ISH-/PCR+ (18) cases were found. Eight of the 18 ISH-/PCR+ cases were attributable to PCR detection of HPV types not included in the ISH assay. This degree of concordance required individual optimization of assay conditions for each block. ISH and PCR assays for HPV yield complementary results, and both can be successfully applied to archival tissues.

Human papillomavirus and disease status following therapy for cervical cancer.

We enrolled 85 patients with invasive cervical cancer and collected cervicovaginal lavage samples at each clinical visit for diagnosis, staging, treatment, and follow-up. Lavage samples were tested by L1 consensus polymerase chain reaction for human papillomavirus (HPV). Results were compared with HPV demonstrated in tumor tissue and the clinical status at time of sample collection. Sensitivity and specificity of the lavage for detection of tumor HPV, determined on the basis of results of tests on lavage samples collected prior to therapy, were found to be 56% and 76.9%, respectively. The proportion of lavage samples detecting tumor HPV decreased significantly with treatment, from 0.54 at diagnosis to 0.03 at complete response (P < .001). Local treatment failure was associated with increased detection of tumor HPV; however, no samples were positive prior to clinically detected treatment failure. These results suggest that cervicovaginal lavage is not an effective sampling method for epidemiological analysis of HPV in cervical tumors.

Human papillomavirus type in anal epithelial lesions is influenced by human immunodeficiency virus.

BACKGROUND AND OBJECTIVE: Infection with human immunodeficiency virus (HIV) increases the risk for human papillomavirus (HPV)-associated genital neoplasia. Human immunodeficiency virus-infected patients also have higher rates of treatment failure and more rapid neoplastic progression. Impaired immune function does not entirely explain these clinical observations. This pilot project was designed to investigate the hypothesis that HIV infection is associated with changes in HPV type and integration within anogenital lesions that could explain the increased risk of neoplastic progression. METHODS: Anal neoplastic lesions from patients with and without HIV infection were analyzed for the presence, type, and integration status of HPV by colorimetric in situ hybridization. Tissue localization of HIV was evaluated by p24 immunohistochemistry and HIV-1 DNA polymerase chain reaction. Results for matched histology were compared for the two patient groups. RESULTS: For all lesions, the presence of high-risk HPV types and multiple HPV types was strongly associated with HIV infection (P = .003 and .0003, respectively). For lesions with matched histology there was no association of HPV integration with HIV status. Tissue localization of HIV did not significantly influence HPV type or integration. CONCLUSIONS: The presence of high-risk HPV types and multiple types within low-grade lesions may explain the increased risk of neoplastic progression in HIV patients. Colocalization of HIV and HPV does not appear to be required for this effect. There is no evidence that HPV integration is influenced by HIV infection.

Association of human papillomavirus type 16 integration in the E2 gene with poor disease-free survival from cervical cancer.

To determine the clinical relevance of human papillomavirus (HPV) integration and E2 function suggested by in vitro studies, we investigated 50 patients with HPV 16-positive primary cervical carcinoma (stage Ib-IV) diagnosed and treated at one institution. The physical state of HPV was determined by colorimetric in situ hybridization and was not found to vary by stage. Overall, 62% of tumors had integrated HPV, 16% had episomal and 22% had both integrated and episomal. The E1/E2 region was evaluated by 8 separate polymerase chain reactions, which resulted in overlapping products. There was no significant variation in ability to amplify the E1/E2 region with stage. E1/E2 amplification correlated with physical state. Nearly all tumors with episomal or mixed HPV 16 DNA amplified all 8 E1/E2 fragments. Half of the tumors with integrated HPV 16 DNA failed to amplify one or more E1/E2 fragments. Disruptions were most frequent in the E2 region. For all 46 patients receiving curative therapy, the Kaplan-Meier estimate of disease-free survival was determined for those whose primary tumors had amplifiable E2 compared with those lacking one or more E2 DNA fragments. Disruption of E2 was associated with significantly shortened disease-free survival.

Cervical cancer survival in a high risk urban population.

BACKGROUND: Cervical cancer remains an important public health problem, particularly for the urban minority population. To the authors' knowledge, determinants of cervical cancer survival have not been studied in this high risk population. METHODS: This study included all 158 women diagnosed and treated for invasive cervical cancer from January 1, 1986, through December 31, 1992, at the Grady Memorial Hospital and Clinics (Atlanta, GA). Medical records were abstracted to determine age at diagnosis, race, International Federation of Gynecology and Obstetrics (FIGO) clinical stage, treatment, and survival. Pathologic material was reviewed to confirm the diagnosis. RESULTS: Most patients (80%) were African American, and the stage distribution was similar for African American and white patients. Sixty-six (42%) had FIGO Stage I disease; 50%, Stage II or III; and 8%, Stage IV. Four-year actuarial survival differed significantly according to clinical stage (Ia = 94%, Ib = 79%, II = 39%, III = 26%, IV = 0%). Overall survival was lower for patients with glandular carcinomas than for those with squamous cell carcinomas (26% vs. 55%, P = 0.09). This difference was almost entirely due to increased mortality in patients with Stage Ib adenocarcinomas (53% vs. 88% for squamous cell carcinoma, Stage Ib, P = 0.03). CONCLUSIONS: The major prognostic markers for cervical cancer survival in this high risk patient population were clinical stage and histology, factors identical to those identified for other populations.

Human papillomavirus and disease-free survival in FIGO stage Ib cervical cancer.

To determine if human papillomavirus (HPV) in the primary tumor was associated with disease-free survival of stage Ib cervical cancer patients, archival tissues from 47 patients were analyzed for HPV DNA by in situ hybridization (ISH) and polymerase chain reaction. HPV integration was determined by ISH signal pattern. Laboratory data were correlated with clinical parameters and disease-free survival. Kaplan-Meier estimates of 4-year disease-free survival were 56% in women with HPV detected in the primary tumor by ISH and 100% for women in whom HPV was not detected (P = .02). Four-year disease-free survival was 39% for patients with integrated HPV in the primary tumor (P = .005 vs. HPV-negative tumors and .05 vs. HPV episomal or episomal/integrated). HPV detection and integration state was not associated with any other clinical variable. Detection of integrated HPV DNA in the primary tumor was strongly associated with treatment failure.

Kaposi sarcoma presenting as a vulvar mass.

BACKGROUND: Kaposi sarcoma has become a common manifestation in people with AIDS, especially men. A few reports of Kaposi sarcoma in women with AIDS have involved nongenital areas. However, of the few patients with genital Kaposi sarcoma reported in the United States, none was believed to be human immunodeficiency virus (HIV)-positive. Genital Kaposi sarcoma associated with HIV has been reported in other parts of the world. CASE: A 29-year-old black woman presented with severe vulvar pain, vaginal discharge, and a vulvar mass. She had been diagnosed with AIDS 25 months earlier. Biopsy of the vulvar mass revealed Kaposi sarcoma; viral analysis of the tumor was positive for herpes simplex virus type 2. Sequencing of polymerase chain reaction product verified the presence of human papillomavirus 26. CONCLUSION: We report an HIV-associated Kaposi sarcoma presenting as a vulvar mass. This report should alert health care providers to include Kaposi sarcoma in the differential diagnosis of vulvar lesions.

Human papillomavirus infection and associated disease in persons infected with human immunodeficiency virus.

Genital infection with human papillomavirus (HPV) is the most common sexually transmitted infection in the United States. Genital or anal infection with oncogenic types of HPV, particularly types 16 and 18, can cause precancerous lesions of the squamous epithelium. Infection with human immunodeficiency virus (HIV) increases the risk for HPV-associated genital neoplasias in both women and men. Detectable cervical and anal HPV infection is more prevalent among women and men with HIV infection than among those who are HIV-seronegative, and the magnitude of the increase in prevalence is proportionate to the severity of immunosuppression. Coinfection with HIV and HPV increases the risk for genital intraepithelial neoplasia, and the increase in this risk also reflects the severity of immunosuppression. One difficulty complicating elucidation of the association between HIV and HPV infections is that the risk factors for acquisition and transmission of the two viruses are similar. The strength of this association represents a burgeoning health problem, yet there are no treatment guidelines aimed specifically at HIV-infected individuals with HPV-associated genital neoplasias. Treatment of HPV-associated cervical disease in HIV-infected women may be further complicated by a greater risk of treatment failure and recurrence than exists among HIV-seronegative women; it is not known whether dysplasia progresses to invasive disease more rapidly in women infected with HIV. A thorough understanding of the associations among HIV, HPV, and HPV-associated disease is essential to the development of effective strategies for intervention and prevention.