Dectin-1 stimulation promotes a distinct inflammatory signature in the setting of HIV-infection and aging.

Dectin-1 is an innate immune receptor that recognizes and binds ß-1, 3/1, 6 glucans on fungi. We evaluated Dectin-1 function in myeloid cells in a cohort of HIV-positive and HIV-negative young and older adults. Stimulation of monocytes with ß-D-glucans induced a pro-inflammatory phenotype in monocytes of HIV-infected individuals that was characterized by increased levels of IL-12, TNF-α, and IL-6, with some age-associated cytokine increases also noted. Dendritic cells showed a striking HIV-associated increase in IFN-α production. These increases in cytokine production paralleled increases in Dectin-1 surface expression in both monocytes and dendritic cells that were noted with both HIV and aging. Differential gene expression analysis showed that HIV-positive older adults had a distinct gene signature compared to other cohorts characterized by a robust TNF-α and coagulation response (increased at baseline), a persistent IFN-α and IFN-γ response, and an activated dendritic cell signature/M1 macrophage signature upon Dectin-1 stimulation. Dectin-1 stimulation induced a strong upregulation of MTORC1 signaling in all cohorts, although increased in the HIV-Older cohort (stimulation and baseline). Overall, our study demonstrates that the HIV Aging population has a distinct immune signature in response to Dectin-1 stimulation. This signature may contribute to the pro-inflammatory environment that is associated with HIV and aging.

IL-33 mediates Pseudomonas induced airway fibrogenesis and is associated with CLAD.

BACKGROUND: Long term outcomes of lung transplantation are impacted by the occurrence of chronic lung allograft dysfunction (CLAD). Recent evidence suggests a role for the lung microbiome in the occurrence of CLAD, but the exact mechanisms are not well defined. We hypothesize that the lung microbiome inhibits epithelial autophagic clearance of pro-fibrotic proteins in an IL-33 dependent manner, thereby augmenting fibrogenesis and risk for CLAD. METHODS: Autopsy derived CLAD and non-CLAD lungs were collected. IL-33, P62 and LC3 immunofluorescence was performed and assessed using confocal microscopy. Pseudomonas aeruginosa (PsA), Streptococcus Pneumoniae (SP), Prevotella Melaninogenica (PM), recombinant IL-33 or PsA-lipopolysaccharide was co-cultured with primary human bronchial epithelial cells (PBEC) and lung fibroblasts in the presence or absence of IL-33 blockade. Western blot analysis and quantitative reverse transcription (qRT) PCR was performed to evaluate IL-33 expression, autophagy, cytokines and fibroblast differentiation markers. These experiments were repeated after siRNA silencing and upregulation (plasmid vector) of Beclin-1. RESULTS: Human CLAD lungs demonstrated markedly increased expression of IL-33 and reduced basal autophagy compared to non-CLAD lungs. Exposure of co-cultured PBECs to PsA, SP induced IL-33, and inhibited PBEC autophagy, while PM elicited no significant response. Further, PsA exposure increased myofibroblast differentiation and collagen formation. IL-33 blockade in these co-cultures recovered Beclin-1, cellular autophagy and attenuated myofibroblast activation in a Beclin-1 dependent manner. CONCLUSION: CLAD is associated with increased airway IL-33 expression and reduced basal autophagy. PsA induces a fibrogenic response by inhibiting airway epithelial autophagy in an IL-33 dependent manner.

N-myc-interactor mediates microbiome induced epithelial to mesenchymal transition and is associated with chronic lung allograft dysfunction.

BACKGROUND: Recent evidence suggests a role for lung microbiome in occurrence of chronic lung allograft dysfunction (CLAD). However, the mechanisms linking the microbiome to CLAD are poorly delineated. We investigated a possible mechanism involved in microbial modulation of mucosal response leading to CLAD with the hypothesis that a Proteobacteria dominant lung microbiome would inhibit N-myc-interactor (NMI) expression and induce epithelial to mesenchymal transition (EMT). METHODS: Explant CLAD, non-CLAD, and healthy nontransplant lung tissue were collected, as well as bronchoalveolar lavage from 14 CLAD and matched non-CLAD subjects, which were followed by 16S rRNA amplicon sequencing and quantitative polymerase chain reaction (PCR) analysis. Pseudomonas aeruginosa (PsA) or PsA-lipopolysaccharide was cocultured with primary human bronchial epithelial cells (PBEC). Western blot analysis and quantitative reverse transcription (qRT) PCR was performed to evaluate NMI expression and EMT in explants and in PsA-exposed PBECs. These experiments were repeated after siRNA silencing and upregulation (plasmid vector) of EMT regulator NMI. RESULTS: 16S rRNA amplicon analyses revealed that CLAD patients have a higher abundance of phyla Proteobacteria and reduced abundance of the phyla Bacteroidetes. At the genera level, CLAD subjects had an increased abundance of genera Pseudomonas and reduced Prevotella. Human CLAD airway cells showed a downregulation of the N-myc-interactor gene and presence of EMT. Furthermore, exposure of human primary bronchial epithelial cells to PsA resulted in downregulation of NMI and induction of an EMT phenotype while NMI upregulation resulted in attenuation of this PsA-induced EMT response. CONCLUSIONS: CLAD is associated with increased bacterial biomass and a Proteobacteria enriched airway microbiome and EMT. Proteobacteria such as PsA induces EMT in human bronchial epithelial cells via NMI, demonstrating a newly uncovered mechanism by which the microbiome induces cellular metaplasia.

DrugRepV: a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses.

Viruses are responsible for causing various epidemics and pandemics with a high mortality rate e.g. ongoing SARS-CoronaVirus-2 crisis. The discovery of novel antivirals remains a challenge but drug repurposing is emerging as a potential solution to develop antivirals in a cost-effective manner. In this regard, we collated the information of repurposed drugs tested for antiviral activity from literature and presented it in the form of a user-friendly web server named 'DrugRepV'. The database contains 8485 entries (3448 unique) with biological, chemical, clinical and structural information of 23 viruses responsible to cause epidemics/pandemics. The database harbors browse and search options to explore the repurposed drug entries. The data can be explored by some important fields like drugs, viruses, drug targets, clinical trials, assays, etc. For summarizing the data, we provide overall statistics of the repurposed candidates. To make the database more informative, it is hyperlinked to various external repositories like DrugBank, PubChem, NCBI-Taxonomy, Clinicaltrials.gov, World Health Organization and many more. 'DrugRepV' database (https://bioinfo.imtech.res.in/manojk/drugrepv/) would be highly useful to the research community working to develop antivirals.

Distribution pattern of amino acid mutations in chloroquine and antifolate drug resistance associated genes in complicated and uncomplicated Plasmodium vivax isolates from Chandigarh, North India.

BACKGROUND: The increasing antimalarial drug resistance is a significant hindrance to malaria control and elimination programs. For the last six decades, chloroquine (CQ) plus pyrimethamine remains the first-line treatment for P. vivax malaria. Regions where both P. falciparum and P. vivax co-exist, P. vivax is exposed to antifolate drugs due to either misdiagnosis or improper treatment that causes selective drug pressure to evolve. Therefore, the present study aims to estimate antimalarial drug resistance among the complicated and uncomplicated P. vivax patients. METHODS: A total of 143 P. vivax malaria positive patients were enrolled in this study, and DNA was isolated from their blood samples. Pvcrt-o, Pvmdr-1, Pvdhps, and Pvdhfr genes were PCRs amplified, and drug resistance-associated gene mutations were analyzed. Statistical analysis of the drug resistance genes and population diversity was performed using MEGA vs. 7.0.21 and DnaSP v software. RESULTS: Among the CQ resistance marker gene Pvcrt-o, the prevalence of K10 insertion was 17.5% (7/40) and 9.5% (7/73) of complicated and uncomplicated P vivax group isolates respectively. In Pvmdr-1, double mutant haplotype (M958/L1076) was found in 99% of the clinical isolates. Among the pyrimethamine resistance-associated gene Pvdhfr, the double mutant haplotype I13P33F57R58T61N117I173 was detected in 23% (11/48) in complicated and 20% (17/85) in uncomplicated group isolates. In the sulphadoxine resistance-associated Pvdhps gene, limited polymorphism was observed with the presence of a single mutant (D459A) among 16 and 5% of the clinical isolates in the complicated and uncomplicated group respectively. CONCLUSION: The study presents the situations of polymorphism in the antimalarial drug resistance-associated genes and emphasizes the need for regular surveillance. It is imperative for the development of suitable antimalarial drug policy in India.

NipahVR: a resource of multi-targeted putative therapeutics and epitopes for the Nipah virus.

Nipah virus (NiV) is an emerging and priority pathogen from the Paramyxoviridae family with a high fatality rate. It causes various diseases such as respiratory ailments and encephalitis and poses a great threat to humans and livestock. Despite various efforts, there is no approved antiviral treatment available. Therefore, to expedite and assist the research, we have developed an integrative resource NipahVR (http://bioinfo.imtech.res.in/manojk/nipahvr/) for the multi-targeted putative therapeutics and epitopes for NiV. It is structured into different sections, i.e. genomes, codon usage, phylogenomics, molecular diagnostic primers, therapeutics (siRNAs, sgRNAs, miRNAs) and vaccine epitopes (B-cell, CTL, MHC-I and -II binders). Most decisively, potentially efficient therapeutic regimens targeting different NiV proteins and genes were anticipated and projected. We hope this computational resource would be helpful in developing combating strategies against this deadly pathogen. Database URL: http://bioinfo.imtech.res.in/manojk/nipahvr/.

Exploration of genetic diversity of Plasmodium vivax circumsporozoite protein (Pvcsp) and Plasmodium vivax sexual stage antigen (Pvs25) among North Indian isolates.

BACKGROUND: Malaria is one of the important vector-borne diseases with high fatality rates in tropical countries. The pattern of emergence and spread of novel antigenic variants, leading to escape of vaccine-induced immunity might be factors responsible for severe malaria. A high level of polymorphism has been reported among malarial antigens which are under selection pressure imposed by host immunity. There are limited reports available on comparative stage-specific genetic diversity among Plasmodium vivax candidate genes in complicated vivax malaria. The present study was planned to study genetic diversity (Pvcsp and Pvs25) among complicated and uncomplicated P. vivax isolates. METHODS: Pvcsp and Pvs2-specific PCRs and DNA sequencing were performed on P. vivax PCR positive samples. Genetic diversity was analysed using appropriate software. RESULTS: The present study was carried out on 143 P. vivax clinical isolates, collected from Postgraduate Institute of Medical Education and Research, Chandigarh. Among the classic and variant types of Pvcsp, the VK210 (99%; 115/116) was found to be predominant in both complicated and uncomplicated group isolates. Out of the various peptide repeat motifs (PRMs) observed, GDRADGQPA (PRM1) and GDRAAGQPA (PRM2) was the most widely distributed among the P. vivax isolates. Whereas among the Pvs25 isolates, 100% of double mutants (E97Q/I130T) in both the complicated (45/45) as well as in the uncomplicated (81/81) group was observed. CONCLUSION: An analysis of genetic variability enables an understanding of the role of genetic variants in severe vivax malaria.

Institutional outbreak of varicella in a child welfare institute in Chandigarh, North India.

Introduction: Varicella outbreaks are known to occur in developing nations as vaccine coverage is still low. Material and Methods: In the present study, an institutional outbreak from Chandigarh, India, is reported wherein the utility of non-invasive samples such as saliva and urine was studied for the molecular diagnosis of varicella by conventional polymerase chain reaction (PCR), real-time PCR and real-time loop-mediated isothermal amplification (real-time LAMP). Results: The results of the present study showed that saliva and urine samples can be used for outbreak investigation of varicella compared to varicella-zoster virus DNA in vesicular swab samples with reasonable sensitivity. Conclusion: Thus, molecular techniques may be useful in the early identification of the outbreak and timely isolation, and the treatment of cases can further prevent its spread.

Computational Identification of Inhibitors Using QSAR Approach Against Nipah Virus.

Nipah virus (NiV) caused several outbreaks in Asian countries including the latest one from Kerala state of India. There is no drug available against NiV till now, despite its urgent requirement. In the current study, we have provided a computational one-stop solution for NiV inhibitors. We have developed the first "anti-Nipah" web resource, which comprising of a data repository, prediction method, and data visualization module. The database contains of 313 (181 unique) chemicals extracted from research articles and patents, which were tested for different strains of NiV isolated from various outbreaks. Moreover, the quantitative structure-activity relationship (QSAR) based regression predictors were developed using chemicals having half maximal inhibitory concentration (IC50). Predictive models were accomplished using support vector machine employing 10-fold cross validation technique. The overall predictor showed the Pearson's correlation coefficient of 0.82 on training/testing dataset. Likewise, it also performed equally well on the independent validation dataset. The robustness of the predictive model was confirmed by applicability domain (William's plot) and scatter plot between actual and predicted efficiencies. Further, the data visualization module from chemical clustering analysis displayed the diversity in the NiV inhibitors. Therefore, this web platform would be of immense help to the researchers working in developing effective inhibitors against NiV. The user-friendly web server is freely available on URL: http://bioinfo.imtech.res.in/manojk/antinipah/.

Screening and identification of potential novel biomarker for diagnosis of complicated Plasmodium vivax malaria.

BACKGROUND: In the recent years Plasmodium vivax has been reported to cause severe infections associated with mortality. Clinical evaluation has limited accuracy for the early identification of the patients progressing towards the fatal condition. Researchers have tried to identify the serum and the plasma-based indicators of the severe malaria. Discovery of MicroRNA (miRNA) has opened up an era of identification of early biomarkers for various infectious and non-infectious diseases. MicroRNAs (miRNA) are the small non-coding RNA molecules of length 19-24 nts and are responsible for the regulation of the majority of human gene expressions at post transcriptional level. METHODS: We identified the differentially expressed miRNAs by microarray and validated the selected miRNAs by qRT-PCR. We assessed the diagnostic potential of these up-regulated miRNAs for complicated P. vivax malaria. Futher, the bioinformtic analysis was performed to construct protein-protein and mRNA-miRNA networks to identify highly regulated miRNA. RESULTS: In the present study, utility of miRNA as potential biomarker of complicated P. vivax malaria was explored. A total of 276 miRNAs were found to be differentially expressed by miRNA microarray and out of which 5 miRNAs (hsa-miR-7977, hsa-miR-28-3p, hsa-miR-378-5p, hsa-miR-194-5p and hsa-miR-3667-5p) were found to be significantly up-regulated in complicated P. vivax malaria patients using qRT-PCR. The diagnostic potential of these 5 miRNAs were found to be significant with sensitivity and specificity of 60-71% and 69-81% respectively and area under curve (AUC) of 0.7 (p < 0.05). Moreover, in silico analysis of the common targets of up-regulated miRNAs revealed UBA52 and hsa-miR-7977 as majorly regulated hubs in the PPI and mRNA-miRNA networks, suggesting their putative role in complicated P. vivax malaria. CONCLUSION: miR-7977 might act as a potential biomarker for differentiating complicated P. vivax malaria from uncomplicated type. The elevated levels of miR-7977 may have a role to play in the disease pathology through UBA52 or TGF-beta signalling pathway.

Molecular epidemiology of circulating human adenovirus types in acute conjunctivitis cases in Chandigarh, North India.

Human adenovirus (HAdV) is a major cause of viral conjunctivitis. The various serotypes implicated in the causation are 3, 4, 8, 19 and 37. The present study aimed to know the circulating types of HAdV causing acute conjunctivitis in North India. A total of 23 conjunctival swabs were collected from patients with clinically suspected acute viral conjunctivitis during 2014-2015. The HAdV was implicated in the etiology in 65.2% of cases. The sequencing of representative samples using hexon gene suggests the presence of serotype 8 and 4. The serotype eight sequences showed 99%-100% similarity with other Indian strains. The phylogenetic analysis showed that the current circulating serotypes, responsible for conjunctivitis, belonged to epidemic keratoconjunctivitis strains.

25-Hydroxyvitamin D3 and 1,25 Dihydroxyvitamin D3 as an Antiviral and Immunomodulator Against Herpes Simplex Virus-1 Infection in HeLa Cells.

The antiviral and immunomodulatory role of vitamin D has been shown in various viral infections. However, there is scanty literature available about the effect of vitamin D supplementation in herpes simplex virus-1 (HSV-1) infection. Therefore, the present study aimed to evaluate the role of two different forms of vitamin D: 25-hydroxyvitamin D3 (25D3) and 1,25-dihydroxyvitamin D3 (1,25D3) against HSV-1 in HeLa cells. The HeLa cells were supplemented with either 25D3 or 1,25D3 before HSV-1 infection and were studied after 6, 12, and 24 h postinfection (p.i.). The mRNA levels of toll-like receptors (TLRs), (2, 3, 4, 7, and 9), vitamin D signaling genes, and HSV-1 were studied using real-time PCR. The HSV-1 DNA load was estimated in culture supernatant. The supplementation of 25D3 and 1,25D3 significantly downregulated the mRNA levels of TLR2 (p < 0.0001) at 12 h p.i. The mRNA levels of TLR9 were found to be significantly downregulated in 1,25D3-supplemented cells at 12 h p.i. Furthermore, the significant downregulation was observed in HSV-1 titer in both 25D3- and 1,25D3-supplemented cells at 24 h p.i.(p < 0.0001). However, the effect of 25D3 supplementation persisted till 24 h p.i. with significant downregulation of TLR2 (p < 0.05) mRNA levels. The supplementation of both 25D3 and 1,25D3 before HSV-1 infection was found to downregulate the viral titer and TLR2 mRNA during the intial phase of infection. However, the effect of 25D3 supplementation was found to last for a longer duration compared with 1,25D3.

Ocular Pharmacokinetics of 25-Hydroxyvitamin D3 After Weekly Supplementation in Rabbits Using Ultra Performance Liquid Chromatography-Tandem Mass Spectrometer.

BACKGROUND AND OBJECTIVES: The protective role of vitamin D supplementation has recently been shown to be present in various ocular inflammatory diseases. The oral supplementation of vitamin D may take time to achieve adequate levels in intraocular fluids. Therefore, the present study was performed to understand the ocular pharmacokinetics of 25-hydroxyvitamin D3 (25D3) in aqueous humor after weekly supplementation of 25D3 in rabbits. METHODS: A total of 21 rabbits were fed orally with 25D3 (7.22 µg/kg/week) for 8 weeks and 9th dose was given at the end of 8 weeks. The blood and aqueous humor samples were collected from ear vein and though anterior chamber paracentesis, respectively. The serum and aqueous humor samples were spiked with deuterium labeled internal standard and were extracted using liquid extraction method. Furthermore, the samples were derivatized and 25D3 estimation was performed using ultra performance liquid chromatography-tandem mass spectrometer (UHPLC-MS/MS). RESULTS: The 25D3 supplementation significantly increased the 25D3 levels in serum (78.5 ± 21.6 ng/ml) (mean ± SD) (p < 0.0001) and in aqueous humor (991.3 ± 180.6 pg/ml) (mean ± SD) (p < 0.0001) compared to baseline levels. The maximum concentration was achieved in serum after the 10th hour of supplementation of 1st and 9th dose, while the same was observed at the 24th hour in aqueous humor. CONCLUSION: The oral supplementation of 25D3 was found to significantly increase 25D3 levels in aqueous humor; however, the time required to achieve 25D3 concentration in aqueous humor was higher as compared to that in serum. Therefore, weekly oral supplementation of 25D3 may have a beneficial role in ocular diseases.

Investigation of an outbreak of varicella in Chandigarh, North India, using a real-time polymerase chain reaction approach.

Outbreaks of varicella are reported when susceptible population accumulates. This study reports a chickenpox outbreak in Burail in August 2014, wherein 20 laboratory-confirmed cases were identified by the detection of varicella zoster virus (VZV) DNA and VZV IgM antibodies. The viral load between vesicular swabs and serum samples from 8 patients with active lesions was found to have good correlation and further also related with disease severity. Real-time polymerase chain reaction can be useful for early diagnosis of an outbreak and vesicular swab can be used as a less invasive sample for assessing the disease severity.

Development and evaluation of multiplex real-time PCR for diagnosis of HSV-1, VZV, CMV, and Toxoplasma gondii in patients with infectious uveitis.

Infectious uveitis is a vision threatening inflammatory ocular disease wherein early diagnosis may prevent the loss of vision. The purpose of this study was to develop a multiplex real-time PCR for the diagnosis of Herpes simplex virus-1, Varicella zoster virus, cytomegalovirus and Toxoplasma gondii in patients with suspected infectious uveitis. A total of 126 intraocular samples (aqueous and vitreous humor) were collected and subjected to multiplex real-time PCR. Overall 26.2% (33/126) patients were found to be positive for one or more of the pathogens tested. The overall positivity for VZV, HSV, CMV and T. gondii was found to be 16 (12.7%), 7 (5.6%), 5 (3.9%), and 9 (7.1%); with mean pathogen load of 5.07×105, 9.5×104, 1.08×104 and 394 (copies/µl) respectively. The development of highly sensitive and specific assay for early differentiation of pathogens is important for the early initiation of treatment thereby preventing irreversible damage to the ocular structures.

Quantitative nucleic acid amplification methods and their implications in clinical virology.

Recently, a number of techniques have been approved for quantification of viral nucleic acids in clinical samples. Viral load (VL) tests have considerable importance in the management of patients and are widely used in routine diagnosis. In clinical virology, VL testing are important to monitor the antiviral treatment, to initiate preemptive therapy, to understand pathogenesis, and to evaluate the infectivity. These tests have now become a part of many diagnostic and treatment guidelines. Considering the various challenges for in-house viral testing related to the standardization, validation, and precision; they are gradually being replaced by the United States Food and Drug Administration (US FDA) cleared tests. This review summarizes the various viral quantification methods and also discusses the clinical applicability of these in human immunodeficiency virus, Hepatitis B virus, Hepatitis C virus, Cytomegalovirus, and Epstein Barr virus infected patients. Further the challenges and future perspectives of VL testing have also been discussed.

Multiplex polymerase chain reaction for the detection of high-risk-human papillomavirus types in formalin-fixed paraffin-embedded cervical tissues.

Detecting high-risk-human papillomavirus (HPV) types has become an integral part of the cervical cancer screening programmes. This study aimed to develop a multiplex polymerase chain reaction (PCR) for identification of HPV types 16 and 18 along with the beta globin gene in formalin-fixed and paraffin-embedded cervical biopsy specimens. A total of 59 samples from patients with cervical abnormalities were tested. HPV 16 positivity was 50% in cervical cancers and 52.9% in cervical intraepithelial neoplasia. Our multiplex PCR protocol can be used as a simple and cost-effective tool for high-risk-HPV detection in cervical cancer screening programmes.

Infectious agents in congenital cataract in a tertiary care referral center in North India.

Congenital cataract has the potential for inhibiting early visual development. Intrauterine infections with Rubella virus, Herpes simplex virus (HSV) and Toxoplasma gondii plays an important role in the development of congenital cataract. The study included 120 children under the age of 6 years presenting with congenital cataract and diagnosed using serology and polymerase chain reaction (PCR). The IgM positivity for rubella, HSV, T. gondii was found to be 5.8%, 1.6% and 8.3% respectively. The overall PCR positivity was found to be 40(33.3%), 25 (20.8%) and 39 (32.5%) for rubella, HSV and T. gondii with mean copy number of 1599 copies/µL; 1716 copies/µL and 1503 copies/µL respectively. Infective etiology significantly contributes to the causation of congenital cataract particularly for rubella virus which is a potentially eradicable disease. This study provides an epidemiological data for rubella, HSV and T. gondii in children with congenital cataract and highlights the need to introduce rubella vaccine in the National Immunization Programme of India.