A11 Evaluation of phylogenetic inference methods to determine direction of HIV transmission

It has been postulated that the direction of HIV transmission between two individuals can be determined by phylogenetic analysis of HIV sequences. This approach may be problematic, since HIV sequences from newly infected individuals are often more similar to index sequences from samples collected years before transmission, compared to those from samples collected at the time of transmission. We evaluated the accuracy of phylogenetic methods for determining the direction of HIV transmission by analyzing next-generation sequencing (NGS) data from index–partner pairs enrolled in the HIV Prevention Trials Network (HPTN) 052 trial. HIV-infected index and HIV-uninfected partner participants were enrolled as serodiscordant couples; samples were analyzed from couples with index-to-partner HIV transmission that was confirmed by genetic linkage studies. NGS for HIV gp41 (HXB2 coordinates: 7691–8374) was performed using plasma samples from thirty-nine index–partner pairs (seventy-eight samples collected within 3 months of partner seroconversion). Maximum likelihood trees were generated using the entire dataset using FastTree v.2. Topological patterns of HIV from each index–partner pair were analyzed. The analysis included 9,368 consensus sequences and 521,145 total sequence reads for the seventy-eight samples analyzed. In 10 per cent (four out of thirty-nine) of couples, the phylogeny was inconsistent with the known direction of transmission. In 26 per cent (ten out of thirty-nine) of couples, the phylogeny results could not discern directionality. In 64 per cent (twenty-five out of thirty-nine) of couples, the results correctly indicated index-to-partner transmission; in two of these twenty-five cases, only one index sequence was closest to the most recent common ancestor. Phylogenetic analysis of NGS data obtained from samples collected within 3 months of transmission correctly determined the direction of transmission in 64 per cent of the cases analyzed. In 36 per cent of the cases, the phylogenetic topology did not support the known direction of infection, and in one-third of these cases the observed topology was opposite to the known direction of transmission. This demonstrates that phylogenetic topology alone may not be sufficient to accurately determine the direction of HIV transmission.

Age-Related Differences in Socio-demographic and Behavioral Determinants of HIV Testing and Counseling in HPTN 043/NIMH Project Accept

Youth represent a large proportion of new HIV infections worldwide, yet their utilization of HIV testing and counseling (HTC) remains low. Using the post-intervention, cross-sectional, population-based household survey done in 2011 as part of HPTN 043/NIMH Project Accept, a cluster-randomized trial of community mobilization and mobile HTC in South Africa (Soweto and KwaZulu Natal), Zimbabwe, Tanzania and Thailand, we evaluated age-related differences among socio-demographic and behavioral determinants of HTC in study participants by study arm, site, and gender. A multivariate logistic regression model was developed using complete individual data from 13,755 participants with recent HIV testing (prior 12 months) as the outcome. Youth (18-24 years) was not predictive of recent HTC, except for high-risk youth with multiple concurrent partners, who were less likely (aOR 0.75; 95% CI 0.61-0.92) to have recently been tested than youth reporting a single partner. Importantly, the intervention was successful in reaching men with site specific success ranging from aOR 1.27 (95% CI 1.05-1.53) in South Africa to aOR 2.30 in Thailand (95% CI 1.85-2.84). Finally, across a diverse range of settings, higher education (aOR 1.67; 95% CI 1.42, 1.96), higher socio-economic status (aOR 1.21; 95% CI 1.08-1.36), and marriage (aOR 1.55; 95% CI 1.37-1.75) were all predictive of recent HTC, which did not significantly vary across study arm, site, gender or age category (18-24 vs. 25-32 years).

Allelic loss on chromosome 5q34 is associated with poor prognosis in hepatocellular carcinoma

PURPOSE

To identify and characterize novel genetic alterations in hepatocellular carcinoma (HCC).

METHODS

DNA was extracted from 29 HCC and corresponding normal tissues and amplified with 59 different 10-base arbitrary primers. A 550 bp DNA fragment amplified using primer Q-9 and which was present in 19 of 29 cases (66%) was cloned, sequenced, and compared with known nucleotide sequences deposited in Genome database, and quantified by real-time PCR.

RESULTS

DNA alterations were found on chromosomes 5q34, 6p25.2 and 8q12.1 in 11 of 29 cases (38%), 7 of 29 cases (24%), and 12 of 29 cases (41%), respectively. Multivariate analysis showed that the allelic loss on chromosome 5q34 was an independent prognostic factor for poor survival of HCC patients, with the median survival time of 19 weeks for allelic loss versus 109 weeks for no allelic loss (P = 0.001).

CONCLUSIONS

This study indicates that allelic loss on chromosome 5q34 may be involved in the development of HCC and could be used as a prognostic indicator in HCC patients.

Novel DNA amplification on chromosomes 2p25.3 and 7q11.23 in cholangiocarcinoma identified by arbitrarily primed polymerase chain reaction

PURPOSE

To detect and characterize amplified DNA sequences in cholangiocarcinoma (CCA).

PATIENTS AND METHODS

We extracted DNA from tumor and corresponding normal tissues of 30 patients with CCA and amplified with 30 random ten-mer arbitrary primers by the arbitrarily primed polymerase chain reaction (AP-PCR) technique.

RESULTS

Our results showed gains of genomic sequences at high frequency. Using the AX-11 arbitrary primer, we determined an amplified DNA fragment occurred frequently in the tumors analyzed. The DNA fragment was isolated and identified as two sequences mapped to chromosomes 2p25.3 and 7q11.23. Specific primers were designed employing these sequences and used for detecting amplification by real-time quantitative PCR. The amplification of the DNA sequences on chromosomes 2p25.3 and 7q11.23 was detected in 10 (33%) and 6 (20%) cases, respectively. Thirteen (43%) cases showed amplification on both or one of the chromosomes. In addition, amplification of the DNA on chromosome 2p25.3 was predominantly observed in poorly differentiated tumors.

CONCLUSIONS

Our findings suggest that the novel amplified DNA on chromosomal regions at 2p25.3 and 7q11.23 might be involved in the development and progression of CCA.

Quality of life and functional status of patients with hip fractures in Thailand

Measurement of quality of life and functional status provides important additional information for priority setting in health policy formulation and resource allocation. Hip fracture has been a concern in health planning in developing countries due to an increasing trend, as reported in several studies. Ironically, in developing countries, studies of the impacts of hip fracture on quality of life and functional status are rare. This prompted our team to seek evidence of the impacts using a longitudinal follow-up approach in a Thai setting. In this study, health-related quality of life (HRQOL) before and after hip fractures was evaluated in 250 Thai patients. Measurement of HRQOL was based on a modified SF-12 questionnaire, which was developed with a realization of the following demands: 1) cultural sensitivity of measurement tools; 2) disease-specific HRQOL measurement and 3) feasibility of conducting field work. Functional status was measured using an adapted version of the Index of Activity of Daily Living (ADL), which was previously developed in another setting in Thailand. Mild, moderate and severe deficits in quality of life were found in 36%, 60%, and 4% respectively, of surviving patients. The number of patients with physical functioning dependency, as measured by the ADL, also increased significantly in all 10 activities assessed. Comorbidities were associated with deficits in health-related quality of life but age, sex, income, education level, and surgery were not. Our findings indicate that hip fracture could lead to crippling consequences, with a pronounced effect on the quality of life of Thai patients. Further studies using control groups and longitudinal design are needed to validate the results of this study.

Mortality after hip fractures in Thailand

Hip fractures have long been considered a major threat to the survival of elderly people. Most of the studies on survival following hip fractures have been reported from developed countries where orthopedic care is well distributed. This report describes the survival experience of 330 elderly hip fracture patients who were seen at hospitals in Chiang Mai, Thailand. The mortality rate during hospitalization was 2.1%. The 3-, 6-, and 12-month survival rates after hip fractures were 91%, 88% and 83%, respectively. The significant predictors of mortality were male sex, age over 80 years, presence of chronic illnesses, poor pre-fracture walking ability, and nonoperative treatment.

Clinical presentation and risk behaviors of patients with acquired immunodeficiency syndrome in Thailand, 1994--1998: regional variation and temporal trends

From 1994 through 1998, the clinical and demographic features and risk behaviors of 101,945 adolescent and adult patients with acquired immunodeficiency syndrome (AIDS) were reported to the Ministry of Public Health in Thailand. The number of reported cases of AIDS infection increased from 12,005 in 1994 to 24,722 in 1997. Nearly 40% of the cases were reported from the northern provinces, which contained only approximately 20% of the adult population. About 80% of cases were among male patients, and 87% had been acquired via sexual contact. Tuberculosis was the most commonly reported opportunistic infection, occurring in 28.9% of patients; it was more commonly reported among injection drug abusers, especially in Bangkok. Pneumocystis carinii pneumonia and cryptococcal meningitis each occurred in nearly 20% of patients and were more frequently reported in patients with risk factors related to sex than in injection drug abusers. Penicillium marneffei infections were reported in 6.8% of patients from the northern provinces but less frequently elsewhere. These data suggest that AIDS is common in Thailand, and human immunodeficiency virus-infected persons should be given prophylaxis for tuberculosis, fungal infections, and P. carinii pneumonia.

Aberrant cyclooxygenase isozyme expression in human intrahepatic cholangiocarcinoma

METHODS

Cellular localisation of the cyclooxygenase (COX) isozymes COX-1 and COX-2 was analysed in 24 cholangiocarcinomas, including 17 matched tissues originating from non-tumorous liver tissue adjacent to tumours and seven biopsies of normal human liver, by immunohistochemistry using isozyme selective antibodies.

RESULTS

In normal liver, constitutive expression of COX-2 protein was a characteristic feature of hepatocytes whereas no COX-2 immunosignal was detectable in normal bile duct epithelium, Kupffer, and endothelial cells. In cholangiocarcinoma cells, COX-2 protein was strongly expressed at high frequency. The intensity, percentage of positive cells, and pattern of COX-2 expression were found to be independent of the stage of tumour differentiation. In hepatocytes of matched non-tumorous tissue, COX-2 expression was unaltered. In contrast, strong COX-1 expression was frequently localised to Kupffer cells, endothelial cells, and occasionally to hepatocytes, but not to bile duct epithelial cells. In approximately half of moderately and poorly differentiated but not well differentiated cholangiocarcinomas, weak to moderate COX-1 staining was found in tumour cells while COX-1 expression in Kupffer cells was much more pronounced.

CONCLUSION

Aberrant COX-2 expression occurs during the early stage while COX-1 over expression seems to be related to later stages of cholangiocarcinogenesis.

Correlation between immunohistochemical and biochemical estrogen receptors in the prognosis of patients with breast cancer

To evaluate the reliability of immunohistochemical estrogen receptor (ER) in the prognosis of patients with breast cancer, 83 primary tumors from patients were studied. Immunohistochemical analysis (IHA) was performed using antibody ER 1D5 (Dako) together with microwave treatment for antigen retrieval. ER values obtained using the biochemical steroid binding assay (polyethyleneglycol method, PEG) were available for comparison. Of all tumors, ER positivity was detected in 44.6% by IHA and 36.1% by PEG method. The concordance between the two methods was 69%. No significant correlation was found between the ER status determined by both methods and clinical stage, tumor size, lymph node status or age of patient at diagnosis. However, we found that the immunohistochemical ER is a superior predictor of early recurrence in patients with primary breast cancer to biochemical ER. The findings in the present study emphasize the clinical benefit of the immunohistochemical ER assay as a measure for prognosis.

Immunohistochemical detection of estrogen and progesterone receptors in primary breast cancer

To evaluate the reliability of the immunohistochemical assay for estrogen receptor (ER) and progesterone receptor (PR) in the prognosis of patients with breast cancer, 83 primary tumors from the patients were studied. Immunohistochemical analysis was performed using antibody ER 1D5 for ER determination and antibody PR-ICA for PR determination. Of all tumors, ER and PR positivities were detected in 36.1% and 45.8% respectively. There was no significant relationship between ER, PR and age of the patients, tumor size or number of involved nodes. However, we found that only the immunohistochemical ER was a predictor of early recurrence in patients with primary breast cancer. In addition, there was no additive effect in recurrence-free survival when both receptor expressions were combined.

Prognostic importance of p53 and c-erbB-2 oncoproteins overexpression in patients with breast cancer

Using immunohistochemistry, 119 breast cancer tissues were examined for overexpression of p53 and c-erbB-2 oncogene proteins. In 46 (38.7%) of the cases p53 was overexpressed, while 35 (29.4%) demonstrated positive c-erbB-2 immunostaining. Expression of these two oncogene products was closely correlated (p < 0.01). There was no significant association between p53 protein expression and age of the patients, clinical stage, tumor size, number of involved nodes or estrogen receptor status. However, we found significant correlation between p53 protein expression and 5-year disease-free survival (p = 0.0113). In addition, the findings in this study clearly indicated that the co-overexpression of p53 and c-erbB-2 proteins was a powerful predictor for early recurrence in the patients with breast cancer.

Association of mdr1 gene expression with other prognostic factors and clinical outcome in human breast cancer

Multidrug resistance of cancer (CA) is one of a major problems in CA chemotherapy that is frequently associated with the expression of P-glycoprotein (P-gp) encoded by mdr1 genes. However, the controversial results exist regarding to the significance of mdr1 gene expression on clinical drug resistance to chemotherapy of breast CA cells. Recent evidence reported a strong correlation between the increased P-gp levels and the prognosis in advanced breast CA. The current study investigated whether mdr1 gene expression has any impact on prognosis and response to chemotherapy in breast CA patients. We determined mdr1 expression in 127 primary and 8 locally relapsed breast CA using a sensitive, specific and quantitative technique based on a RT-PCR and Southern blot hybridization detection by non-radioactive labelled-probe. In patients with primary breast CA, mdr1 expression were negative (mdr1-ve), low (< 10 units), high (> or = 10 units) in 63.8, 8.7 and 27.5 per cent of the patients, respectively. No differences in age, menopause status, tumor size, stage, lymph node involvement, estrogen receptor level and p53 level were observed between mdr1-ve and mdr1+ve expression patients. However, mdr1 gene expression is often associated with number of positive lymph nodes and negative estrogen receptors (p = 0.008 and 0.0007, respectively). In locally relapsed cases, mdr1-ve was 62.5 per cent whereas 37.5 per cent were mdr1+ve with high level of mdr1 RNA. No differences in other prognostic factors: lymph nodal involvement, estrogen receptor level and p53 level, were detected in both groups. Response to chemotherapy in primary and recurrent breast CA was not different in mdr1-ve and mdr1+ve patients. Finally, our results show that mdr1 gene expression is frequently present in breast CA both before and after chemotherapy. Association of mdr1 gene overexpression with other two prognostic factors suggests that they may confer a more aggressive nature of the tumor, drug resistance and poor prognosis. Evaluation of these factors may improve the ability to identify and select breast CA patients at high risk for poor prognosis for aggressive treatment. However, in this series response to CMF chemotherapy of primary and locally recurrent breast CA were not affected by the presence or absence of mdr1 gene product.

Case-control study of risk factors for Penicillium marneffei infection in human immunodeficiency virus-infected patients in northern Thailand

A case-control study was done in Chiang Mai, Thailand, comparing risk-related behavior and exposures in 80 incident cases of disseminated Penicillium marneffei infection in patients with AIDS and 160 control patients with AIDS who did not have P. marneffei infection. All subjects were admitted to Chiang Mai University Hospital between December 1993 and October 1995. Cases were younger than controls (16-30 years vs. > 30 years of age; odds ratio [OR] = 2.22; 95% CI, 1.22-4.07). Patients with a recent history of occupational or other exposure to soil, especially during the rainy season (May to October), were more likely to present with P. marneffei infection (OR = 1.91; 95% CI, 1.04-3.52). History of exposure to or consumption of bamboo rats, the only known nonhuman hosts of P. marneffei, was not a risk factor for infection. Our data suggest that recent exposure to a potential environmental reservoir of organisms in the soil may be associated with disseminated P. marneffei infections among patients with AIDS in Northern Thailand.

Immunohistochemical detection of c-erbB-2 oncoprotein in patients with breast cancer

Using a polyclonal antibody against the c-erbB-2 gene product, an immunohistochemical study on the expression of c-erbB-2 oncoprotein was performed in routine formalin-fixed, paraffin-embedded tissue sections from 119 patients with primary breast cancer. Overexpression of c-erbB-2 protein was detected in 35 cases (29%). There was a strongly negative association between c-erbB-2 protein overexpression and estrogen receptor status (p < 0.001). Expression of c-erbB-2 protein was found to be related to clinical stage and tumor size (p < 0.05) but not to the number of involved nodes or age of patients at diagnosis. In addition, this study demonstrated that the c-erbB-2 protein over-expression was an effective independent prognostic indicator in patients with breast cancer.

Restriction endonuclease analysis of Penicillium marneffei

Forty-six isolates of Penicillium marneffei were differentiated into two DNA types on the basis of their restriction fragment length polymorphisms. Of the 22 human isolates of P. marneffei, 16 (72.7%) were type I and 6 (27.3%) were type II. Of the 23 bamboo rat isolates, 20 from Rhizomys sumatrensis were type I and 3 from Cannomys badius were type II. The soil isolate was type II. These data represent the first molecular epidemiological study of this important emerging fungal pathogen.

Seasonal variation of disseminated Penicillium marneffei infections in northern Thailand: a clue to the reservoir?

Disseminated Penicillium marneffei infections are common AIDS-defining opportunistic infections among persons with human immunodeficiency virus (HIV) infection in northern Thailand. Penicilliosis due to P. marneffei is the third most frequent AIDS-defining infection in this population, after tuberculosis and cryptococcosis. Very little is known about the epidemiology and natural reservoir of P. marneffei. The seasonal distribution of two common AIDS-defining fungal infections was compared among patients diagnosed between 1991 and 1994 at Chiang Mai University Hospital. There were 550 cases (492 male, 58 female patients) of P. marneffei and 793 cases (685 male, 108 female patients) of Cryptococcus neoformans infection diagnosed. In each year, P. marneffei but not C. neoformans infections were more frequent in the rainy than the dry season. Seasonal variation of P. marneffei infections in AIDS patients in northern Thailand may provide valuable information in determining the important reservoirs and exposures to this organism that lead to disseminated disease in these patients.

Rhizomys sumatrensis and Cannomys badius, new natural animal hosts of Penicillium marneffei

The incidence of Penicillium marneffei infection has increased substantially, especially in persons with HIV infection. Very little is known about the natural reservoirs or animal hosts of P. marneffei. This pathogenic fungus was first isolated from a species of bamboo rat (Rhizomys sinensis) in Vietnam and later from another rodent species, R. pruinosus. We studied a total of 75 captured bamboo rats; P. marneffei could be isolated from the internal organs of 13 of 14 (92.8%) of large bamboo rats, R. sumatrensis, and of 3 of 10 reddish-brown small bay bamboo rats, Cannomys badius (30%). All 51 greyish-black C. badius were negative on culture. Among R. sumatrensis, P. marneffei were frequently recovered from the lungs (85.7%), spleen (50%) and liver (28.6%). Of the 28 soil samples collected from the bamboo rat burrows and the 67 from the residential areas of patients with P. marneffei infection, P. marneffei was isolated from one soil sample collected from a burrow of R. sumatrensis. The mycological characteristics of P. marneffei isolates from bamboo rats and humans were very similar. Our data indicate that R. sumatrensis and C. badius may be important animal hosts of P. marneffei in northern Thailand.

Comparison of c-erbB-2 oncoprotein expression in tissue and serum of patients with stomach cancer

Resected specimens of 288 primary stomach cancers (175 early cases and 113 advanced cases) and recurrent tumors or biopsy specimens of 21 recurrent or inoperable metastatic stomach cancers were examined immunohistochemically for expression of c-erbB-2 oncogene product. c-erbB-2 protein-positive staining was detected in 6.9, 15.9 and 28.6% of early, advanced and recurrent or inoperable metastatic stomach cancers, respectively, the difference being significant (p < 0.005). Four patients with advanced cancer showed positive staining in metastatic lymph nodes but not in the primary tumors. The results of tissue immunostaining were compared with c-erbB-2 protein levels in sera of the patients measured by an enzyme-linked immunosorbent assay. The levels of this oncogene product were consistently low in the sera of most of the patients with primary stomach cancers, regardless of whether or not c-erbB-2 protein was expressed in the tumor. However, in the recurrent or inoperable metastatic stomach cancers, 5 of 6 patients with c-erbB-2 protein-positive tumors showed elevated levels of c-erbB-2 protein in the serum. After following up c-erbB-2 protein levels in the sera of 3 patients during the period of chemotherapy against recurrent or inoperable metastatic disease, we found that the levels increased only in the late stage. These results suggest that, in stomach cancer, c-erbB-2 protein is likely to be excreted into the serum at a relatively late stage, reflecting systemic spread of the disease.