Kanury Rao

Translational Health Science and Technology Institute | THSTI · Drug Discovery Research Center (DDRC)

Apart from being preventable and treatable, tuberculosis is the deadliest bacterial disease afflicting humankind owing to its ability to evade host defence responses, many of which are controlled by epigenetic mechanisms. Here, we report the temporal dynamics of the proteome of macro-phage-like host cells after infecting them for 6, 18, 30, and 42...

Growth factor receptor-bound protein 2 (Grb2) is an adaptor protein involved in the signal transduction pathways. This dataset enlists proteins which interact with Grb2 in the presence and absence of a mitogenic stimulus. Grb2 expressing HEK293 cells were cultured in light and heavy labeled SILAC media. Normal lysine and arginine were incorporated...

Objective: Signal transduction not only initiates entry into the cell cycle, but also reprograms the cell's metabolism. To control abnormalities in cell proliferation, both the aspects should be taken care of, thus pleiotropic signaling molecules are considered as crucial modulators. Considering this, we investigated the role of AKT1 in central ca...

Cell growth and proliferation are two diverse processes yet always linked. Akt1, a serine/threonine kinase, is a multi-functional protein implicated in regulation of cell growth, survival and proliferation. Though it has a role in G1/S progression, the manner by which Akt1 controls cell cycle and blends cell growth with proliferation is not well ex...

Akt1 is a multi-functional protein, implicated in multiple human solid tumors. Pertaining to its key role in cell survival, Akt1 is under focus for development of targeted therapies. Functional diversity of Akt1 is a result of its interactions with other proteins; which changes with changing context. This investigation was designed to capture the d...

Modulation of host metabolic machinery by Mycobacterium tuberculosis is a well established phenomenon. In our earlier study Mehrotra et al. (2014), we observed a marked increase in acetyl-CoA levels in cells bearing virulent Mycobacterium tuberculosis infections compared to host cells harbouring avirulent infections. The difference was observed ins...

Akt1 is a multi-functional protein implicated in key cellular processes including regulation of proliferation, survival, metabolism and protein synthesis. Its functional diversity results through interactions with other proteins which change with changing context. This study was designed to capture proteins, which interact with Akt1 as the cell cyc...

Here we provide data for SILAC and iTRAQ based hyperplexing combined with BONCAT based click chemistry for selective enrichment of newly synthesized proteins secreted by THP1 macrophages at various time points after infection with four different strains of Mycobacterium tuberculosis. The macrophages were infected with H37Ra, H37Rv, BND433 and JAL22...

Here we provide data for SILAC and iTRAQ based hyperplexing combined with BONCAT based click chemistry for selective enrichment of newly synthesized proteins secreted by THP1 macrophages at various time points after infection with four different strains of Mycobacterium tuberculosis. The macrophages were infected with H37Ra, H37Rv, BND433 and JAL22...

Incomplete understanding of mechanisms involved in the host–pathogen interactions constrains our efforts to eliminate tuberculosis. In many individuals, resulting from immune response to mycobacterial infection organised structures called granulomas are formed. To identify host responses that may control at least the early stages of infection, we e...

Mycobacterium tuberculosis (Mtb) is an adaptable intracellular pathogen, existing in both dormant as well as active disease-causing states. Here we report systematic proteomic analyses of four strains - H37Ra, H37Rv, and clinical isolates BND and JAL, to determine the differences in protein expression patterns that contribute to their virulence and...

Survival of Mycobacterium tuberculosis (Mtb) within the host macrophage is mediated through pathogen-dependent inhibition of phagosome-lysosome fusion, which enables bacteria to persist within the immature phagosomal compartment. By employing ultrastructural examination of different field isolates supported by biochemical analysis, we found that so...

Cloud-based, fast, interactive data visualization of major Protein-Protein Interaction databases, including DIP, MINT, BioGrid, HHPID and more at http://www.gpsprot.org Data Visualization for Human Interactions (~236K PPIs) and HIV-Human Interactions (~7K PPIs) and HIV Genetic Screens (~2K Genetic interactions)

Infection of humans with Mycobacterium tuberculosis (Mtb) results in diverse outcomes that range from acute disease to establishment of persistence and to even clearance of the pathogen. These different outcomes represent the combined result of host heterogeneity on the one hand, and virulence properties of the infecting strain of pathogen on the o...

Upon infection, Mycobacterium tuberculosis (Mtb) deploys specialized secretion machinery to deliver virulent proteins with the capacity to modulate a variety of host-cellular pathways. Studies on the identification of intra-macrophage Mtb proteins, however, are constricted by an inability to selectively enrich these virulent effectors against overw...

The Foamy Macrophage (FM) differentiation forms a major component of the host dependent survival axis of M. tuberculosis. The FM which are characterized by the intracellular accumulation of lipid bodies (LBs), ensure a privileged existence for the bacilli through ready provision of nutrients and by conferring protection against bactericidal pathway...

Obesity is a metabolic state associated with excess of positive energy balance. While adipose tissues are considered the major contributor for complications associated with obesity, they influence a variety of tissues and inflict significant metabolic and inflammatory alterations. Unfortunately, the communication network between different cell-type...

Unsatisfactory performance of the existing BCG vaccines, especially against the adult pulmonary disease, has urged the need for an effective vaccine against tuberculosis (TB). In this study, we employed differential proteomics to obtain a list of antigens as potential vaccine candidates. Bacterial epitopes being presented at early stages on MHC cla...

] Fluctuations in metabolite levels in mammalian cells are the most direct form of readout of the cellular metabolic state. The current protocol describes a method for pulse labeling and subsequent isolation of metabolites from adherent mammalian cells. The isolated metabolites can be identified and quantified by mass-spectrometry, allowing for est...

Despite extensive studies on the interactions between Mycobacterium tuberculosis (M.tb) and macrophages, the mechanism by which pathogen evades anti-microbial responses and establishes persistence within the host cell remains unknown. In this study, we developed a four-dimensional ODE model to describe the dynamics of host-pathogen interactions in...

Background Obesity is now a worldwide epidemic disease and poses a major risk for diet related diseases like type 2 diabetes, cardiovascular disease, stroke and fatty liver among others. In the present study we employed the murine model of diet-induced obesity to determine the early, tissue-specific, gene expression signatures that characterized pr...

Author Summary Mycobacterium tuberculosis (Mtb) is a highly successful human pathogen, representing the leading bacterial cause of death worldwide. Mtb infects macrophages and it adapts to the hostile intracellular milieu of this cell by exploiting the plasticity of its central carbon metabolism machinery. While several studies have detailed the ba...

Given the pivotal role that macrophages play in determining the outcome of infection, it is now becoming apparent that a better understanding of the molecular interplay between the pathogen and this host cell type will be crucial for developing more effective strategies for tuberculosis therapy. In this context the need to capture the dynamic featu...

M. tuberculosis, the causative agent of tuberculosis, has persisted inthe human population despite decades of intervention strategies. While our knowledge about the pathogen and the disease process it causes have grown substantially over the years, we are still grap-pling with devising strategies for its control. This arti-cle attempts to understan...

Activation of the antigen receptors on the surface of B cells in response to their cognate ligands is tightly controlled by feedback mechanisms. Apart from ligand induced signaling, B cell receptors (BCRs) emanate ligand independent tonic signaling crucial for B cell survival and development. In the absence of a ligand, BCR tonic signaling is contr...

To probe how the pathogen Mycobacterium tuberculosis controls host cellular death pathways, we compared mitochondrial responses in human macrophages infected either with the avirulent mycobacterial strain H37Ra, or its virulent counterpart H37Rv. Following H37Ra infection, induction of the apoptotic response was foreshadowed by the early suppressio...

Supplementary Table 2

Supplementary Table 1

Supplementary Figure 1

Kal-1 is a polyherbal decoction of seven different natural ingredients, traditionally used in controlling sugar levels, inflammatory conditions particularly regulating metabolic and immunoinflammatory balance which are the major factors involved in obesity and related diseases. In the present study, we aimed to investigate the effect of Kal-1 (an a...

[This corrects the article DOI: 10.1038/srep00464.].

The differentiation of human primary T helper 1 (Th1) cells from naïve precursor cells is regulated by a complex, interrelated signaling network. The identification of factors regulating the early steps of Th1 cell polarization can provide important insight in the development of therapeutics for many inflammatory and autoimmune diseases. The serine...

Upon infection, Mycobacterium tuberculosis (Mtb) metabolically alters the macrophage to create a niche that is ideally suited to its persistent lifestyle. Infected macrophages acquire a "foamy" phenotype characterized by the accumulation of lipid bodies (LBs), which serve as both a source of nutrients and a secure niche for the bacterium. While the...

Molecular mechanism governing biological processes leading to dietary obesity and diabetes are largely unknown. Here we study the liver proteome differentially expressed in a long-term high-fat and high sucrose diet (HFHSD)-induced obesity and diabetes mouse model. Changes in mouse liver proteins were identified using iTRAQ, offline 2D LC (SCX and...

In this study we show that IL-4 is crucial during reinforcement window of human Th2 differentiation for optimal Th2 development. We have also shown here that during this stage, IL-4 helps in cellular decision-making process of differentiation versus proliferation. We have combined computational and experimental methods to analyze Th2 transcription...

Supplimentary Data

We demonstrate that the mitogen-activated protein kinases extracellular signal-regulated kinase (ERK)-1 and ERK-2 have a central role in mediating T-cell receptor-dependent induction of IL4 expression in human CD4(+) T cells. Significantly, this involved a novel mechanism wherein receptor cross-linking induced activated ERK to physically associate...

Drug development efforts against cancer are often hampered by the complex properties of signaling networks. Here we combined the results of an RNAi screen targeting the cellular signaling machinery, with graph theoretical analysis to extract the core modules that process both mitogenic and oncogenic signals to drive cell cycle progression. These mo...

Complexes and subunits identified by proteomic profiling studies.

Dataset of 222 human complexes derived from CORUM by clustering and details of manual refinement of complexes.

Comparison of broad expression level of Mtb and HIV screens.

RNAi-mediated depletion of MED30 blocks early steps of replication of a VSV-G pseudotyped HIV luciferase virus.

Published and converted identifiers for all seven HIV screens.

Complexes and subunits identified by RNAi studies.

The increasing availability of HIV-host interaction datasets, including both physical and genetic interactions, has created a need for software tools to integrate and visualize the data. Because these host-pathogen interactions are extensive and interactions between human proteins are found within many different databases, it is difficult to genera...

Development of noninvasive methods for tuberculosis (TB) diagnosis, with the potential to be administered in field situations, remains as an unmet challenge. A wide array of molecules are present in urine and reflect the pathophysiological condition of a subject. With infection, an alteration in the molecular constituents is anticipated, characteri...

Systems biology seeks to study biological systems as a whole, by adopting an integrated approach to study and understand the function of biological systems, particularly, the response of such systems to various perturbations. In this article, we focus on the Indian efforts towards systems-level studies of Mycobacterium tuberculosis and its interact...

Coordinated coupling of biochemical reactions involving protein phosphorylation and dephosphorylation represents the hallmark of the intracellular signal transduction machinery. Distinct classes of enzymes known as kinases and phosphatases respectively drive these reactions. Alterations in activity of such signaling intermediates, either due to mut...

Engagement of the antigen receptor on immature B-lymphocytes leads to cell cycle arrest, and subsequent apoptosis. This is an essential process for eliminating self reactive B cells during its different stages of development. However, the mechanism by which it is achieved is not completely understood. Here we employed a systems biology approach tha...

This contains the complete List of Additional Files including tables, figures and additional methods.

This file contains the complete information of the RT-PCR data and analysis.

This contains the list of TFs probed by the combo array and their corresponding activation pattern. This file also contains the information regarding the Entrez Gene IDs of the TFs shown in Figure 2.

This review elaborates on recent insights gained on the dynamic aspects of interactions between pathogen and the host intracellular machinery in tuberculosis infection. In addition we will also discuss the utility of adopting a systems biology approach, both for a better understanding of TB biology, and for the development of more effective ways fo...

Dissecting the molecular mechanisms by which T helper (Th) cells differentiate to effector Th2 cells is important for understanding the pathogenesis of immune-mediated diseases, such as asthma and allergy. Because the STAT6 transcription factor is an upstream mediator required for interleukin-4 (IL-4)-induced Th2 cell differentiation, its targets i...

Infection of J774.1 cells infected with H37Rv. J774.1 cells were infected with H37Rv labelled with PKH67 at an MOI of 10 as described in Methods). Panels A, B and C show confocal image of J774.1 cells after 24, 36, and 72 hours of infection respectively. Serial confocal sections (0.5 µm thick) within a z-stack spanning a total thickness of 10–12 µm...

Efficiency of siRNA transfection and the resultant silencing of expression of target proteins in J774.1 cells. J774.1 cells were transfected with AllStars Negative Control siRNA, Alexa Fluor 488 Labeled (RNAi Human/Mouse starter kit, Qiagen) at a 10nM concentration using hiperfect transfection reagent (according to manufacturer's protocol). Cells w...

Supplementary Methods (0.05 MB DOC)

Effect of D4476 on the intracellular growth of mycobacteria in primary mouse macrophages. Panel A shows the growth profiles of the indicated strains of Mtb in peritoneal mouse macrophages. The protocol employed here was identical to that described for Figure 3C in the main text. For the experiment in Panel B, macrophages independently infected with...

Screening Data for Kinase-Phosphatase siRNA Library. Primary screening data for H37Rv survival in J774.1 cells is presented in sheet 1 of Table S1. siRNA against each target gene was tested in duplicate, and data readings were obtained at two different dilutions for each. Here, we took care to ensure that both sets of the duplicate were not placed...

Cell Viability by MTT assay. Viability of H37Rv-infected and uninfected J774.1 cells was assessed at 90 hours after treatment with the siRNA pools for the 41 validated targets by the MTT assay (detail protocol in Methods). The average value for the MTT assay (mean of three) along with fold SD deviation from the control mean is shown for both infect...

Functional Class and disease association of ‘Hits’. ‘Hits’ identified in this study were searched extensively for their various GO class association, thereby summarizing the potential set of biological functions that they may be involved in regulating. We also examined for any known disease association for these ‘hits’ and this information is inclu...

Gene expression data for the validated targets. Hits filtered out after validation was checked for their expression level in J774.1 cells using one-color microarray-based gene expression analysis performed by hybridizing against a mouse whole genome array consisting of probes for 44,000 genes (Agilent). Values equal to or above 100 are considered a...

The stable infection of host macrophages by Mycobacterium tuberculosis (Mtb) involves, and depends on, the attenuation of the diverse microbicidal responses mounted by the host cell. This is primarily achieved through targeted perturbations of the host cellular signaling machinery. Therefore, in view of the dependency of the pathogen on host molecu...