Ph.D., University of Calcutta, India, Bioinformatics (2019)
M.Sc., University of Calcutta, India, Biochemistry (2012)
B.Sc, University of Calcutta, India, Microbiology (2010)
Current Research and Scholarly Interests
My research involves studying the pathogenic mechanisms underlying the host-pathogen interaction in pulmonary diseases. I am particularly interested in exploring transcriptomic and proteomic changes in Cystic Fibrosis and Asthma patients who develop severe allergic inflammation due to fungal hypersensitivity. Complete understanding of these interaction will help us identify significant fungal virulence factors and help us define clinically relevant targets for therapeutic use.
The safety and tolerability of pirfenidone for bronchiolitis obliterans syndrome after hematopoietic cell transplant (STOP-BOS) trial.
Bone marrow transplantation
Bronchiolitis obliterans syndrome (BOS) is the most morbid form of chronic graft-versus-host disease (cGVHD) after hematopoietic cell transplantation (HCT). Progressive airway fibrosis leads to a 5-year survival of 40%. Treatment options for BOS are limited. A single arm, 52-week, Phase I study of pirfenidone was conducted. The primary outcome was tolerability defined as maintaining the recommended dose of pirfenidone (2403mg/day) without a dose reduction totaling more than 21 days, due to adverse events (AEs) or severe AEs (SAEs). Secondary outcomes included pulmonary function tests (PFTs) and patient reported outcomes (PROs). Among 22 participants treated for 1 year, 13 (59%) tolerated the recommended dose, with an average daily tolerated dose of 2325.6mg/day. Twenty-two SAEs were observed, with 90.9% related to infections, none were attributed to pirfenidone. There was an increase in the average percent predicted forced expiratory volume in 1s (FEV1%) of 7 percentage points annually and improvements in PROs related to symptoms of cGVHD. In this Phase I study, treatment with pirfenidone was safe. The stabilization in PFTs and improvements in PROs suggest the potential of pirfenidone for BOS treatment and support the value of a randomized controlled trial to evaluate the efficacy of pirfenidone in BOS after HCT. The study is registered in ClinicalTrials.gov (NCT03315741).
View details for DOI 10.1038/s41409-022-01716-4
View details for PubMedID 35641662
NIKKOMYCIN Z AGAINST DISSEMINATED COCCIDIOIDOMYCOSIS IN A MURINE MODEL OF SUSTAINED RELEASE DOSING.
Antimicrobial agents and chemotherapy
Introduction. Nikkomycin Z (nikZ) is a chitin synthase inhibitor. Efficacy against Coccidioides has been demonstrated in animal models of pulmonary or brain infection. Its short half-life, in mice and humans, would necessitate divided daily dosing. We assayed nikZ efficacy in disseminated coccidioidomycosis (in a reduction of CFU design), and whether sustained release might be useful. Methods. Mice were challenged intravenously, with low or high arthroconidial inocula. Fluconazole, clinically the most commonly used anti-coccidioidal drug, was compared (gavage) at high dose to a dose range of nikZ administered intraperitoneally or, to mimic sustained release, administered continuously in drinking water. Therapy was given for 5 days. Results. In vitro, both fluconazole and nikZ inhibited the isolate studied; nikZ was fungicidal. Oral nikZ therapy gave similar results to intraperitoneal nikZ, and sterilized infection in most animals after low inoculum challenge. In both challenges, oral nikZ produced greater reduction of CFU in organs (lung, liver, spleen) than fluconazole. Oral nikZ doses ≥200 mg/kg/day were particularly effective, in all organs, and were well tolerated. This efficacy occurred even though, after severe challenge, mice had reduced water intake, resulting in ingesting less than the desired dose, particularly initially after infection. Summary. This study shows, for the first time, efficacy of nikZ against disseminated coccidioidomycosis. Efficacy was shown after challenges producing different levels of severity of disease. This study also suggests the likely benefits of developing an extended release formulation, supplying continuous systemic concentrations of nikZ.
View details for DOI 10.1128/AAC.00285-21
View details for PubMedID 34252303
Altered Pseudomonas Strategies to Inhibit Surface Aspergillus Colonies.
Frontiers in cellular and infection microbiology
2021; 11: 734296
Pseudomonas aeruginosa and Aspergillus fumigatus infections frequently co-localize in lungs of immunocompromised patients and individuals with cystic fibrosis (CF). The antifungal activity of P. aeruginosa has been described for its filtrates. Pyoverdine and pyocyanin are the principal antifungal P. aeruginosa molecules active against A. fumigatus biofilm metabolism present in iron-limited or iron-replete planktonic P. aeruginosa culture filtrates, respectively. Using various P. aeruginosa laboratory wild-type strains (PA14, PAO1, PAK), we found antifungal activity against Aspergillus colonies on agar. Comparing 36 PA14 and 7 PAO1 mutants, we found that mutants lacking both major siderophores, pyoverdine and pyochelin, display higher antifungal activity on agar than their wild types, while quorum sensing mutants lost antifungal activity. Addition of ferric iron, but not calcium or magnesium, reduced the antifungal effects of P. aeruginosa on agar, whereas iron-poor agar enhanced antifungal effects. Antifungal activity on agar was mediated by PQS and HHQ, via MvfR. Among the MvfR downstream factors, rhamnolipids and elastase were produced in larger quantities by pyoverdine-pyochelin double mutants and showed antifungal activity on agar. In summary, antifungal factors produced by P.aeruginosa on agar differ from those produced by bacteria grown in liquid cultures, are dependent on quorum sensing, and are downregulated by the availability of ferric iron. Rhamnolipids and elastase seem to be major mediators of Pseudomonas' antifungal activity on a solid surface.
View details for DOI 10.3389/fcimb.2021.734296
View details for PubMedID 34746024
Under nonlimiting iron conditions pyocyanin is a major antifungal molecule, and differences between prototypic Pseudomonas aeruginosa strains.
Airways of immunocompromised patients, or individuals with cystic fibrosis (CF), are common ground for Pseudomonas aeruginosa and Aspergillus fumigatus infections. Hence, in such a microenvironment both pathogens compete for resources. While under limiting iron conditions the siderophore pyoverdine is the most effective antifungal P. aeruginosa product, we now provide evidence that under nonlimiting iron conditions P. aeruginosa supernatants lack pyoverdine but still possess considerable antifungal activity. Spectrometric analyses of P. aeruginosa supernatants revealed the presence of phenazines, such as pyocyanin, only under nonlimiting iron conditions. Supernatants of quorum sensing mutants of strain PA14, defective in phenazine production, as well as supernatants of the P. aeruginosa strain PAO1, lacked pyocyanin, and were less inhibitory toward A. fumigatus biofilms under nonlimiting iron conditions. When blood as a natural source of iron was present during P. aeruginosa supernatant production, pyoverdine was absent, and phenazines, including pyocyanin, appeared, resulting in an antifungal effect on A. fumigatus biofilms. Pure pyocyanin reduced A. fumigatus biofilm metabolism. In summary, P. aeruginosa has mechanisms to compete with A. fumigatus under limiting and non-limiting iron conditions, and can switch from iron-denial-based to toxin-based antifungal activity. This has implications for the evolution of the microbiome in clinical settings where the two pathogens co-exist. Important differences in the iron response of P. aeruginosa laboratory strains PA14 and PAO1 were also uncovered.LAY SUMMARY: P. aeruginosa (Pa) and A. fumigatus (Af) form biofilms in lungs of persons with cystic fibrosis and interact via virulence factors. Pa inhibits Af via different factors, depending on the availability of iron from blood. Low iron favors the use of pyoverdine, high iron the use of the toxin pyocyanin.
View details for DOI 10.1093/mmy/myaa066
View details for PubMedID 32827431
Review of Potential Pseudomonas Weaponry, Relevant to the Pseudomonas-Aspergillus Interplay, for the Mycology Community.
Journal of fungi (Basel, Switzerland)
2020; 6 (2)
Pseudomonas aeruginosa is one of the most prominent opportunistic bacteria in airways of cystic fibrosis patients and in immunocompromised patients. These bacteria share the same polymicrobial niche with other microbes, such as the opportunistic fungus Aspergillus fumigatus. Their inter-kingdom interactions and diverse exchange of secreted metabolites are responsible for how they both fare in competition for ecological niches. The outcomes of their contests likely determine persistent damage and degeneration of lung function. With a myriad of virulence factors and metabolites of promising antifungal activity, P. aeruginosa products or their derivatives may prove useful in prophylaxis and therapy against A. fumigatus. Quorum sensing underlies the primary virulence strategy of P. aeruginosa, which serves as cell-cell communication and ultimately leads to the production of multiple virulence factors. Understanding the quorum-sensing-related pathogenic mechanisms of P. aeruginosa is a first step for understanding intermicrobial competition. In this review, we provide a basic overview of some of the central virulence factors of P. aeruginosa that are regulated by quorum-sensing response pathways and briefly discuss the hitherto known antifungal properties of these virulence factors. This review also addresses the role of the bacterial secretion machinery regarding virulence factor secretion and maintenance of cell-cell communication.
View details for DOI 10.3390/jof6020081
View details for PubMedID 32517271
Epigenetic Drug Repositioning for Alzheimer's Disease Based on Epigenetic Targets in Human Interactome.
Journal of Alzheimer's disease : JAD
2018; 61 (1): 53-65
Epigenetics has emerged as an important field in drug discovery. Alzheimer's disease (AD), the leading neurodegenerative disorder throughout the world, is shown to have an epigenetic basis. Currently, there are very few effective epigenetic drugs available for AD.In this work, for the first time we have proposed 14 AD repositioning epigenetic drugs and identified their targets from extensive human interactome.Interacting partners of the AD epigenetic proteins were identified from the extensive human interactome to construct Epigenetic Protein-Protein Interaction Network (EP-PPIN). Epigenetic Drug-Target Network (EP-DTN) was constructed with the drugs associated with the proteins of EP-PPIN. Regulation of non-coding RNAs associated with the target proteins of these drugs was also studied. AD related target proteins, epigenetic targets, enriched pathways, and functional categories of the proposed repositioning drugs were also studied.The proposed 14 AD epigenetic repositioning drugs have overlapping targets and miRs with known AD epigenetic targets and miRs. Furthermore, several shared functional categories and enriched pathways were obtained for these drugs with FDA approved epigenetic drugs and known AD drugs.The findings of our work might provide insight into future AD epigenetic-therapeutics.
View details for DOI 10.3233/JAD-161104
View details for PubMedID 29199645
Biological networks in Parkinson's disease: an insight into the epigenetic mechanisms associated with this disease.
2017; 18 (1): 721
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease.We have studied gene co-expression network obtained from a PD-specific microarray data. The co-expression network identified 11 hub genes, of which eight genes are not previously known to be associated with PD. Further study on the functionality of these eight novel hub genes revealed that these genes play important roles in several neurodegenerative diseases. Furthermore, we have studied the tissue-specific expression and histone modification patterns of the novel hub genes. Most of these genes possess several histone modification sites those are already known to be associated with neurodegenerative diseases. Regulatory network namely mTF-miRNA-gene-gTF involves microRNA Transcription Factor (mTF), microRNA (miRNA), gene and gene Transcription Factor (gTF). Whereas long noncoding RNA (lncRNA) mediated regulatory network involves miRNA, gene, mTF and lncRNA. mTF-miRNA-gene-gTF regulatory network identified a novel feed-forward loop. lncRNA-mediated regulatory network identified novel lncRNAs of PD and revealed the two-way regulatory pattern of PD-specific miRNAs where miRNAs can be regulated by both the TFs and lncRNAs. SNP analysis of the most significant genes of the co-expression network identified 20 SNPs. These SNPs are present in the 3' UTR of known PD genes and are controlled by those miRNAs which are also involved in PD.Our study identified eight novel hub genes which can be considered as possible candidates for future biomarker identification studies for PD. The two regulatory networks studied in our work provide a detailed overview of the cellular regulatory mechanisms where the non-coding RNAs namely miRNA and lncRNA, can act as epigenetic regulators of PD. SNPs identified in our study can be helpful for identifying PD at an earlier stage. Overall, this study may impart a better comprehension of the complex molecular interactions associated with PD from systems biology perspective.
View details for DOI 10.1186/s12864-017-4098-3
View details for PubMedID 28899360
View details for PubMedCentralID PMC5596942
Structural insight into GRIP1-PDZ6 in Alzheimer's disease: study from protein expression data to molecular dynamics simulations.
Journal of biomolecular structure & dynamics
2017; 35 (10): 2235-2247
Protein-protein interaction domain, PDZ, plays a critical role in efficient synaptic transmission in brain. Dysfunction of synaptic transmission is thought to be the underlying basis of many neuropsychiatric and neurodegenerative disorders including Alzheimer's disease (AD). In this study, Glutamate Receptor Interacting Protein1 (GRIP1) was identified as one of the most important differentially expressed, topologically significant proteins in the protein-protein interaction network. To date, very few studies have analyzed the detailed structural basis of PDZ-mediated protein interaction of GRIP1. In order to gain better understanding of structural and dynamic basis of these interactions, we employed molecular dynamics (MD) simulations of GRIP1-PDZ6 dimer bound with Liprin-alpha and GRIP1-PDZ6 dimer alone each with 100 ns simulations. The analyses of MD simulations of Liprin-alpha bound GRIP1-PDZ6 dimer show considerable conformational differences than that of peptide-free dimer in terms of SASA, hydrogen bonding patterns, and along principal component 1 (PC1). Our study also furnishes insight into the structural attunement of the PDZ6 domains of Liprin-alpha bound GRIP1 that is attributed by significant shift of the Liprin-alpha recognition helix in the simulated peptide-bound dimer compared to the crystal structure and simulated peptide-free dimer. It is evident that PDZ6 domains of peptide-bound dimer show differential movements along PC1 than that of peptide-free dimers. Thus, Liprin-alpha also serves an important role in conferring conformational changes along the dimeric interface of the peptide-bound dimer. Results reported here provide information that may lead to novel therapeutic approaches in AD.
View details for DOI 10.1080/07391102.2016.1214085
View details for PubMedID 27425598
Comparative analysis of RNA-Seq data from brain and blood samples of Parkinson's disease.
Biochemical and biophysical research communications
2017; 484 (3): 557-564
Parkinson's disease (PD) is the second most common neurodegenerative disorders throughout the world. In order to search for PD biomarkers, we performed a system-level study of RNA-Seq data from PD brain and blood samples. Differentially expressed miRs of RNA-Seq data were subjected to generate the Co-expression networks. Three highly co-expressed clusters were identified based on their correlation coefficient values and fold change ratio. SM2miR drugs of the miRs contained in the three highly co-expressed clusters were identified, and drugs common among these clusters were selected. Co-expressed miRs not previously known to be associated with PD were identified from both the samples. Functional enrichment analyses of these miR targets were done, and the pathways common and unique to both the samples were identified. Thus, our study presents a comparative analysis of miRs, their associated pathways, and drugs from brain and blood samples of PD that may help in system level understanding of this disease. miRs identified from our study may serve as biomarkers for PD.
View details for DOI 10.1016/j.bbrc.2017.01.121
View details for PubMedID 28131841
Insight into the Epigenetics of Alzheimer's Disease: A Computational Study from Human Interactome.
Current Alzheimer research
2016; 13 (12): 1385-1396
Alzheimer's disease (AD) is the most prevalent neurodegenerative disease throughout the world. Most of the clinical symptoms of AD appear at a very later stage, therefore, the identification of disease markers is essential which can help proper detection of AD at an earlier stage and slow down its progression. Studies have implicated that epigenetic biomarkers, such as DNA methylation, histone modification and non coding RNA mediated regulation serve crucial roles in several disease progression including AD.The aim of our study was to identify the topologically significant AD-related proteins from experimentally validated human protein-protein interaction database, HPRD (interactome) and find out novel epigenetic biomarkers.In this computational work, we constructed AD specific diseasome from AD genelist and interactome. Using this diseasome we screened the interactome with the help of novel parameters namely degree band and similarity index and identified AD related proteins. Regulatory network involving AD related proteins, not previously known to be associated with AD was constructed. Several network motifs and epigenetic modification patterns of regulators of these motifs were studied.Our study identified computationally predicted 22 epigenetic genes and 11 epigenetic miRs, not previously known to be associated with AD, from the network motifs. Most of these genes and miRs show brain specific expression. Further study on the epigenetic modification patterns of these regulators regarding histone modification, CpG island and lncRNAs strengthened their association in AD.Computationally predicted genes and miRs identified in our study might provide insight into new epigenetic AD therapeutic targets.
View details for DOI 10.2174/1567205013666160803151101
View details for PubMedID 27492077
A bidirectional drug repositioning approach for Parkinson's disease through network-based inference.
Biochemical and biophysical research communications
2015; 457 (3): 280-7
Parkinson's Disease (PD) is one of the most prevailing neurodegenerative disorders. Novel computational approaches are required to find new ways of using the existing drugs or drug repositioning, as currently there exists no cure for PD. We proposed a new bidirectional drug repositioning method that consists of Top-down and Bottom-up approaches and finally gives information about significant repositioning drug candidates. This method takes into account of the topological significance of drugs in the tripartite Indication-drug-target network (IDTN) as well the significance of their targets in the PD-specific protein-protein interaction network (PPIN). 9 non-Parkinsonian drugs have been proposed as the significant repositioning candidates for PD. In order to find out the efficiency of the repositioning candidates we introduced a parameter called the On-target ratio (OTR). The average OTR value of final repositioning candidates has been found to be higher than that of known PD specific drugs.
View details for DOI 10.1016/j.bbrc.2014.12.101
View details for PubMedID 25576361
Studying the system-level involvement of microRNAs in Parkinson's disease.
2014; 9 (4): e93751
Parkinson's Disease (PD) is a progressive neurologic disorder that affects movement and balance. Recent studies have revealed the importance of microRNA (miR) in PD. However, the detailed role of miR and its regulation by Transcription Factor (TF) remain unexplored. In this work for the first time we have studied TF-miR-mRNA regulatory network as well as miR co-expression network in PD.We compared the 204 differentially expressed miRs from microarray data with 73 PD related miRs obtained from literature, Human MicroRNA Disease Database and found a significant overlap of 47 PD related miRs (p-value<0.05). Functional enrichment analyses of these 47 common (Group1) miRs and the remaining 157 (Group2) miRs revealed similar kinds of over-representative GO Biological Processes and KEGG pathways. This strengthens the possibility that some of the Group 2 miRs can have functional roles in PD progression, hitherto unidentified in any study. In order to explore the cross talk between TF, miR and target mRNA, regulatory networks were constructed. Study of these networks resulted in 14 Inter-Regulatory hub miRs whereas miR co-expression network revealed 18 co-expressed hub miRs. Of these 32 hub miRs, 23 miRs were previously unidentified with respect to their association with PD. Hierarchical clustering analysis further strengthens the roles of these novel miRs in different PD pathways. Furthermore hsa-miR-92a appeared as novel hub miR in both regulatory and co-expression network indicating its strong functional role in PD. High conservation patterns were observed for most of these 23 novel hub miRs across different species including human. Thus these 23 novel hub miRs can be considered as potential biomarkers for PD.Our study identified 23 novel miR markers which can open up new avenues for future studies and shed lights on potential therapeutic targets for PD.
View details for DOI 10.1371/journal.pone.0093751
View details for PubMedID 24690883
View details for PubMedCentralID PMC3972105