Haplotype analysis of HLA-A, -B antigens and -DRB1 alleles in south Indian HIV-1-infected patients with and without pulmonary tuberculosis

We have shown earlier the association of human leucocyte antigen (HLA)-A11 with resistance and HLA-B40 and -DR2 with susceptibility to HIV and HIV-TB. In the present study, we have attempted to find out the HLA-DR2 subtypes and the possible HLA-A/-B/-DRB1 haplotype combinations that are associated with susceptibility or resistance to HIV and HIV with pulmonary tuberculosis (HIV+PTB+). HLA-DR2 subtyping was carried out by polymerase chain reaction-based sequence-specific oligonucleotide probe method. Overrepresentation of HLA-DRB1*1501 in HIV-positive PTB-negative (HIV+PTB-) patients (P = 0.004, P(c) = 0.06) and -DRB1*1502 in HIV-positive PTB-positive (HIV+PTB+) patients (P = 0.019) was observed as compared to healthy controls. Haplotype analysis revealed an increased frequency of HLA-A2-DRB1*1501 haplotype in HIV+PTB- patients (P = 0.008) and HLA-A2-DRB1*1502 among HIV+PTB+ patients (P = 0.01) compared to healthy controls. The haplotypes B40-DRB1*1501 and B40-DRB1*04 were found to be moderately increased in HIV+PTB(-) and HIV+PTB+ patients (P < 0.05). The study suggests that HLA-A2-DRB1*1501 haplotype may be associated with HIV infection while HLA-A2-DRB1*1502 haplotype might be associated with susceptibility to PTB in HIV patients. Moreover, HLA-B40-DRB1*1501 and HLA-B40-DRB1*04 haplotypes may be associated with susceptibility to HIV infection and to PTB in HIV patients.

CD209 gene polymorphisms in South Indian HIV and HIV-TB patients

Dendritic-cell-specific intercellular adhesion molecule-3 (ICAM-3)-grabbing non-integrin (DC-SIGN), a pattern recognition receptor, is associated with immune functions and is also exploited by HIV-1 and Mycobacterium tuberculosis as a part of their immune evasion strategy. In the present study we investigated whether variants in the DC-SIGN encoding CD209 gene are associated with susceptibility to or protection against HIV-1 infection as well as development of tuberculosis (TB) among HIV-1 infected south Indian patients. CD209 gene variants in the promoter region (-336 and -139), in the intron and 3'-untranslated regions (In2+11 and 2281) were studied using polymerase chain reaction-based genotyping methods in 131 HIV patients without TB (HIV+TB-) and 107 HIV patients with TB (HIV+TB+), 107 HIV negative pulmonary TB patients (HIV-PTB+) and 157 healthy controls. Results revealed a decreased frequency of -336 G/G genotype among all HIV patients compared to healthy controls and -336 G/G genotype was not observed among HIV+TB- individuals (p=0.005; odds ratio (OR) 0 (95% confidence intervals (CI) 0-0.46); Peto's odds ratio 0.149 (95% CI 0.045-0.50)). Among HIV+ patients, those with TB had a significantly increased frequency of -336 G/G genotype (p=0.003; OR undefined; Peto's odds ratio 9.8 (95% CI 2.2-44.3)) compared to those without TB. Other polymorphisms were not significantly different between the various study groups. The results suggest that -336 G/G genotype while associated with protection against HIV-1 infection the same genotype is also associated with susceptibility to HIV-TB among south Indians.

Miliary tuberculosis in human immunodeficiency virus infected patients not on antiretroviral therapy: clinical profile and response to shortcourse chemotherapy

BACKGROUND

An increase in tuberculosis (TB) incidence has been associated with human immunodeficiency virus (HIV).

AIMS

To describe the clinical characteristics and treatment outcome of patients with HIV and miliary TB treated with short-course intermittent chemotherapy in the absence of access to highly active antiretroviral therapy (HAART).

SETTINGS AND DESIGN

Prospective study of HIV infected adults referred to a TB clinic between July 1999 and July 2004.

MATERIALS AND METHODS

On diagnosis of miliary TB, patients were treated with a standard regimen of two months of isoniazid, rifampicin, ethambutol and pyrazinamide followed by four months of isoniazid and rifampicin (2EHRZ 3 /4RH 3 ) thrice weekly and followed up for 24 months. Patients were reviewed clinically every month and two sputa were collected. Chest radiographs and blood investigations were done at two months, end of treatment and every six months thereafter.

RESULTS

Of 498 patients with HIV and tuberculosis, 31 (6%) were diagnosed as miliary tuberculosis. At diagnosis, sputum smear was positive for acid-fast bacilli (AFB) in 14 patients (45%) and Mycobacterium tuberculosis was isolated in 21 (68%). The mean CD4 cell count was 129 +/- 125 cells/mm3 . Twenty-five patients were declared cured at the end of treatment (81%) while one (3%) died and five (16%) failed. The recurrence rate was 19.4/100 person-years and the median survival was 17 months (95% CI 14 to 20). None of the patients received antiretroviral therapy.

CONCLUSIONS

Miliary TB tends to occur among HIV infected patients with severe immunosuppression. Though the initial response to short-course chemotherapy was encouraging, a high recurrence rate and mortality was observed indicating poor prognosis in HIV.

HLA-DQB1 and -DPB1 allele profile in HIV infected patients with and without pulmonary tuberculosis of south India

We made an attempt to find out whether Human Leucocyte Antigen (HLA)-DQB1 and -DPB1 alleles are associated with susceptibility or resistance to Human Immunodeficiency Virus (HIV) infection and development of pulmonary tuberculosis (PTB) in HIV infected patients. The allelic profile of HLA-DQB1 and -DPB1 was studied among HIV patients without pulmonary tuberculosis (HIV+PTB-) (n = 115), HIV patients with pulmonary TB (HIV+PTB+) (n = 59), HIV negative PTB patients (HIV-PTB+) (n = 110) and healthy controls (n=112) by polymerase chain reaction and sequence specific oligonucleotide probe method. Increased frequency of HLA-DQB1*050301 was observed in HIV+PTB- [p = 0.024, Odds Ratio (OR) 2.30, 95% Confidence Interval (CI) 1.11-4.90] and HIV+PTB+ patients (p = 0.044, OR 2.41, 95% CI 1.01-5.73) compared to healthy controls, suggesting that DQB1*050301 may be associated with susceptibility to HIV infection as well as development of PTB in HIV patients. Underrepresentation of HLA-DPB1*1501 was observed in HIV-PTB+ (p = 0.002, Pc = 0.034) and HIV+PTB+ (p = 0.036) patients compared to healthy controls, suggesting that DPB1*1501 may be associated with protection against PTB development both in HIV positive and negative subjects. Analysis on the amino acid variation in the peptide binding pocket at beta69 position of HLA-DPB1 molecules revealed that the beta69 arginine containing HLA-DPB1 alleles and the genotype lysine/arginine were underrepresented in HIV-PTB+ (allele: p = 0.003, Pc = 0.009; genotype: p = 0.0002, Pc = 0.001) and HIV+PTB+ (allele: p = 0.016, Pc = 0.048; genotype: p = 0.026). This suggests that HLA-DPB1 alleles with arginine may be associated with protection against development of PTB in both HIV infected as well as uninfected individuals. Further, the haplotypes HLA-DRB1*1502-DPB1*0201 and HLA-DQB1*0601-DPB1*0201 (Pc < 0.001) and HLA-DRB1*1502-DQB1*0601-DPB1*0201 (p = 0.006, OR 5.09, 95% CI 1.42-22.66) were significantly overrepresented in HIV+PTB+ patients compared to healthy controls suggesting that genetic susceptibility to PTB development in HIV patients may be modulated by interplay between HLA class II alleles, besides HLA class I alleles.

Modeling, analysis, and validation of a novel HIV integrase structure provide insights into the binding modes of potent integrase inhibitors

It has been shown that L-731988, a potent integrase inhibitor, targets a conformation of the integrase enzyme formed when complexed to viral DNA, with the 3'-end dinucleotide already cleaved. It has also been shown that diketo acid inhibitors bind to the strand transfer complex of integrase and are competitive with the host target DNA. However, published X-ray structures of HIV integrase do not include the DNA; thus, there is a need to develop a model representing the strand transfer complex. In this study, we have constructed an active-site model of the HIV-1 integrase complexed with viral DNA using the crystal structure of DNA-bound transposase and have identified a binding mode for inhibitors. This proposed binding mechanism for integrase inhibitors involves interaction with a specific Mg(2+) in the active site, accentuated by a hydrophobic interaction in a cavity formed by a flexible loop upon DNA binding. We further validated the integrase active-site model by selectively mutating key residues predicted to play an important role in the binding of inhibitors. Thus, we have a binding model that is applicable to a wide range of potent integrase inhibitors and is consistent with the available resistant mutation data.

Cardiac and vascular metal deposition with high mortality in nephrogenic systemic fibrosis

Nephrogenic systemic fibrosis is a severe disabling disease that can follow gadolinium-based contrast exposure. In this study we analyzed the clinical and laboratory records of patients with nephrogenic systemic fibrosis who had a history of exposure to gadolinium-based contrast media and identified their cardiac and vascular events. At autopsy, we found that the heart, blood vessels, and skin of three patients who died of cardiac and/or vascular complications had appreciable amounts of gadolinium, iron, and aluminum as measured by inductively coupled plasma-mass spectrometry and confirmed by x-ray fluorescence. Of the 32 patients with nephrogenic systemic fibrosis studied, 10 died at a median of 112 days after diagnosis. Cardiovascular events contributed to the mortality of 9 patients and included congestive heart failure, recurrent arrhythmias, hypotension, stroke, limb ischemia, posterior ischemic optic neuropathy and sudden death. Our results show that increased cardiac and vascular complications along with short survival in nephrogenic systemic fibrosis are associated with metal accumulation in the heart, blood vessels, and skin of these patients.

Tuberculin skin test results in HIV-infected patients in India: implications for latent tuberculosis treatment

OBJECTIVE

To evaluate the utility of the tuberculin skin test (TST) in detecting latent and active tuberculosis (TB) among human immunodeficiency virus (HIV) infected patients in South India.

DESIGN

TSTs and CD4 counts were collected from 631 HIV-infected individuals without active TB and 209 antiretroviral and anti-tuberculosis treatment-naïve HIV-infected patients with TB. We calculated the proportion of TST-positive individuals, as well as the sensitivity, specificity, positive predictive value (PPV) and negative predictive value of TST in the diagnosis of TB.

RESULTS

Among subjects without active TB, 28% with a CD4 count <100 cells/microl vs. 43% of the total cohort had a TST >5 mm (P = 0.14), while the proportions with induration >10 mm were 14% vs. 36%, respectively (P < 0.01). Among those with active TB, using a 5 mm cut-off, the sensitivity was 42% for those with CD4 counts <200 cells/mul compared to 70% for those with CD4 counts >or=200 cells/microl (P < 0.001). The PPV for detecting active TB was 29%.

CONCLUSIONS

TST is a poor predictor of both latent and active TB in HIV-infected individuals in TB endemic countries. Programmes offering treatment for latent TB should consider including all HIV-positive patients regardless of TST status, or use other indicators, such as CD4 count.

Structural genomics of protein phosphatases

The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.

Feasibility of routine HIV testing among TB patients through a voluntary counselling and testing centre

BACKGROUND

Despite the synergy between the human immunodeficiency virus (HIV) and tuberculosis (TB) epidemics, the public health responses have largely been separate. Detection of HIV among TB patients is crucial to the holistic management of HIV-TB co-infected patients.

OBJECTIVE

To assess the feasibility of screening all TB patients for HIV through referral to a voluntary counselling and testing centre.

DESIGN

This cross-sectional study of 4802 newly diagnosed TB patients between July 2005 and June 2006 was performed in Tamilnadu, India, at six sites.

RESULTS

Of 4802 patients invited, 69% were willing to participate in the test. The most significant variables that influenced willingness were sex, age and place of residence (P < 0.01). The other significant variables that influenced willingness to participate were higher education, being employed and being married (P < 0.05). The main reasons for refusal of HIV screening among the patients were 'no risk behaviour' (30%), followed by 'too old' (23%) and for reasons of privacy (12%).

CONCLUSIONS

The present study suggests that it is feasible to routinely test TB patients for HIV. However it is crucial for health providers to focus on an effective referral process keeping patient concerns in mind. Motivation strategies need to be sex-, age-, education- and residence-specific.

Single antigen detects both immunoglobulin M (IgM) and IgG antibodies elicited by all four dengue virus serotypes

The resurgence of dengue (DEN) virus infections in the last few decades coupled with the lack of a preventive vaccine and specific antiviral drugs has jointly contributed to making this a significant global public health problem. Currently, symptomatic supportive treatment and fluid replacement therapy are the only means available to minimize DEN-induced mortality. As the clinical symptoms associated with DEN virus infections are indistinguishable from those of many other viral, bacterial, and parasitic infections, specific diagnostic tests assume critical importance in the unequivocal identification of DEN virus infections. We have designed a novel chimeric antigen based on envelope domain III (EDIII), a critical antigenic region of the major structural protein of DEN viruses. We fused EDIIIs corresponding to each of the four DEN virus serotypes using pentaglycyl linkers, overexpressed the resultant tetravalent chimeric protein in Escherichia coli, and affinity purified it in high yields, obtaining approximately 30 mg protein of >95% purity per liter of culture. We show that this tetravalent antigen could specifically recognize anti-DEN virus antibodies of both the immunoglobulin M (IgM) and IgG classes. Using a large panel of IgM antibody capture-enzyme-linked immunosorbent assay- and hemagglutination inhibition-confirmed DEN virus-infected and uninfected patient sera (n = 289), we demonstrate that this tetravalent antigen can function as a diagnostic tool of high sensitivity and specificity.

Ex vivo expansion of umbilical cord blood stem cells using different combinations of cytokines and stromal cells

Umbilical cord blood is a promising source of hematopoietic stem cells (HSC) for allogeneic transplantation. However, graft rejection and delayed engraftment remain major limitations, both of which are related to a limited number of stem cells in the cord blood graft. Ex vivo expansion of HSC has been suggested as one of the ways of overcoming the challenges caused by a limited hematopoietic cell number from cord blood stem cell transplantation. In this study, we quantified and characterized an ex vivo expansion capacity of cord blood-derived HSC in a liquid culture system under different conditions. These conditions included: the combinations and concentrations of hematopoietic growth factors [stem cell factor (SCF), granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin (IL)-3, IL-6 and erythropoietin (EPO)], placental conditioning medium (PCM), and stromal cell support. During culture, the mean nucleated cell count, the mean CD34+ cell count, fold expansion, viability, clonogenic assays and immunophenotypic characterization were performed on day 0, day 7, day 12 and day 14 on the expanded cellular product. The maximum expansion was achieved using GF2 (SCF + IL-3 + GM-CSF) with stromal cell support. The mean CD34+ cell expansion on days 7 and 12 was 16.25- and 21.4-fold (5.2-32), respectively, and the mean nucleated cell expansion was 15.1- and 21-fold (18.1-23.2). The mean nucleated cell viability on day 12 was 87.9% (85.6-92.5). After 12 days, granulocyte-macrophage colony-forming units CFU-GEMM showed a 20.4-fold increase. A 21.4-fold increase in the CD34+ cells and a 20-fold increase in the CFU-GEMM should provide enough cells from a single cord blood unit to reduce the period of cytopenia after single unit cord blood transplantation. Even if there was some doubt about the long-term repopulating capacity of the expanded cells part of the collected umbilical cord cells (25%) could be expanded till day 12 after transplanting the major part (75%) of the collection.

Multi-step microfluidic device for studying cancer metastasis

This paper describes a multi-step microfluidic device for studying the deformation and extravasation of primary tumor cells. Prior to extravasation, primary tumor cells undergo sequential steps of deformation through the capillaries, before adhering and transmigrating through the endothelial lining and basement membrane. To study this cascade of events, we fabricated a multi-step microfluidic device whose microgaps were coated with Matrigel to mimic the basement membrane. The microchannel was lined with human microvascular endothelial cells (HMECs) to replicate the endothelial lining. Analysis of deformation, biological and migratory capabilities of various tumor cell lines viz. HepG2, HeLa, and MDA-MB 435S were quantified using the fabricated device. After deformation, the cells' viabilities were significantly reduced and their doubling times were simultaneously increased, indicating changes in their biological capability. However, cell deformation did not significantly reduce their cell motility. Cell motility was co-assessed using the cell's migration rate and the overall population's percentage migration under various conditions (no barrier, Matrigel and Matrigel-HMEC). The device was also used to quantify the effects of Matrigel and the endothelial lining on cell migration. Our results suggest that both played an independent role in inhibiting cell extravasation, with the Matrigel significantly slowing down cell movement and the endothelial lining reducing the total number of transmigrated cells.

Matrigel coated polydimethylsiloxane based microfluidic devices for studying metastatic and non-metastatic cancer cell invasion and migration

Three-dimensional (3-D) extracellular matrices (ECM) allow complex biochemical and biophysical interactions between cells and matrices. Unlike 2-D systems, 3-D models provide a better representation of the micro and local environments in living tissues for facilitating the physiological study of cell migration. Here, we report a microfluidic device based on polydimethylsiloxane (PDMS) for monitoring 3-D cell migration across ECM-coated microgaps with real-time light microscopy. We tracked the migration of the invasive MDA-MB-231 (mammary carcinoma) cells and mapped out their migration paths. It enabled us to quantify the percentage of migrated cells as well as migration information of individual cells. This wide spectrum of data acquisition is vital for elucidating the migration capabilities of different type of cells and to understand the basic mechanism involved in cancer metastasis.

Resident dendritic cells are the predominant TNF-secreting cell in early renal ischemia-reperfusion injury

Renal ischemia-reperfusion injury (IRI) rapidly induces production of inflammatory mediators including, and in particular, tumor necrosis factor (TNF). Possible sources include resident parenchymal and bone marrow-derived cells as well as recruited leukocytes. Cell suspensions from kidneys subjected to IRI were examined by cell separation followed by in vitro culture and enzyme-linked immunosorbent assay (ELISA), immunoperoxidase and immunofluorescence microscopy, and multicolor flow cytometry to determine the contribution of dendritic cells (DCs) to early production of TNF and other inflammatory mediators. Secretion of TNF, interleukin (IL-6), monocyte chemoattractant protein-1 (MCP-1), and regulated on activation normal T cell expressed and secreted (RANTES) was increased in cell suspensions from IRI compared with control kidneys and was higher in DC-enriched preparations. Immunostaining identified TNF(+ve) cells that coexpressed the DC marker CD11c. Flow cytometry of bone marrow-derived (CD45(+ve)) cell populations at 24 h post-IRI demonstrated that F4/80(+ve)/CD11c(+ve) DCs remained proportionately stable and exhibit higher levels of DC maturation markers, whereas the proportion of F4/80(-ve) DCs, monocytes, neutrophils, and T cells increased. Intracellular staining for TNF confirmed that F4/80(+ve) DCs were the predominant TNF(+ve) cell and expressed higher levels than other TNF(+ve) cells. In vivo depletion of DCs from the kidney substantially attenuated TNF secretion by total and CD45(+ve) cells following IRI. The results uncover a role for resident F4/80(+ve) DCs as the predominant secretors of TNF within 24 h of IRI.

How stigmatizing is Stigma in the life of people living with HIV: A study on HIV positive individuals from Chennai, South India

The nature and intensity of AIDS stigma are shaped by the social construction of the epidemic in different locales. Stigma therefore needs to be discussed in its cultural context. This clinic-based study aims at understanding stigma among 203 HIV positive individuals from Chennai, South India. The study throws light on the impact of stigma on the quality of life among these individuals. It also discusses the gender implications of stigma. This study brings out the findings that actual stigma experienced among those infected with HIV is much less (26%) as compared to the fear of being stigmatized or perceived stigma (97%). Internalizing of stigma was found to have a highly significant negative correlation with quality of life in the psychological domain and a significant negative correlation in the environmental domain. However individuals who did experience actual stigma seemed more determined to live and experience an above moderate quality of life. The implication of this study encourages HIV infected individuals to rise above stigma, avoid internalizing their stigmatized feelings and work toward a better quality of life. Health providers need to address these issues in their care for HIV infected individuals.

A quantitative observation and imaging of single tumor cell migration and deformation using a multi-gap microfluidic device representing the blood vessel

A microfluidic device was developed for quantifying the migratory and deformability capabilities of a single tumor cell using direct imaging. It was fabricated using photolithography and is made of polydimethysiloxane. Chemotaxis approach was used for directing cell movement, using 10 microm microgaps to restrict the migration to a single cell. Each cell's migration rate is quantified as a measure of its distance traveled over time taken. Real-time recording of cell deformation under physiological flow was performed, and the elongation index and surface area change of the cells were compared. Three human tumor cell lines viz. HepG2, HeLa and MDA-MB-435S were used to verify the operation and methodology of the device. Their migration rates ranged from 5 to 15 microm/h, consistent with other scientific reports. By reducing the microgap width to 3 microm, it was found that the cells moved along the row of microgaps but were unable to migrate across the microgaps. Subsequent deformation of the cells through the gaps further showed that their migratory capability might be governed by their deformation ability and the deformation stress on their membranes. The strategy of targeting cancer cell membrane for rupture may provide a therapy for metastasis. Being a valuable tool for rapid quantification of a single cell's migratory capability, this device should be helpful for pharmacologic and drug screening, investigation of factors that regulate cell migration and deformation.

Major antifungal activity from the bulbs of Indian squill Urginea indica is a chitinase

We have identified a chitinase with antifungal activity in the bulbs of the plant Urginea indica(Indian squill) and purified it about 26-fold. The purified preparation contained a Mr 29 kDa protein that was an active growth inhibitor of the fungal pathogens Fusarium oxysporum and Rhizoctonia solani in an in vitro assay. Amino acid sequence analysis of the Mr 29 kDa protein revealed it to be highly homologous to the family 19 glycoside hydrolases, which are known to possess chitinase activity. The U. indica chitinase lacked a cysteine-rich N-terminal domain (characteristic of class I chitinases) and contained a conserved motif indicative of the signature 1 of family 19 glycoside hydrolases. It shared a approximately 70% sequence identity with the 26 kDa endochitinase of Hordeum vulgare, a typical class II chitinase of family 19. The five cysteines in the partial sequence of the Mr 29 kDa chitinase were found to be identical in location to five of the seven cysteines present in the catalytic domain of the H. vulgare enzyme. The molecular weight, the lack of an N-terminal cysteine-rich sequence, and the striking identity to the H. vulgare endochitinase suggest that the Mr 29 kDa U. indica protein is a putative class II chitinase. The antifungal activity is presumably mediated through the chitinolytic activity of the Mr 29 kDa protein.