Identification and differential expression of serotransferrin and apolipoprotein A-I in the plasma of HIV-1 patients treated with first-line antiretroviral therapy.

BACKGROUND: Plasma proteins are known to interfere the drug metabolism during therapy. As limited information is available regarding the role of plasma proteins in HIV drug resistance during ART in HIV/AIDS patients, the present study aimed to identify and characterize the differentially expressed plasma proteins in the drug resistant and drug respondent groups of HIV-1 infected patients with > 6 years of first line ART. METHODS: Four-drug resistant (treatment failure) and four-drug respondent (treatment responder) patients were selected for plasma proteomic analysis based on viral load and drug resistance associated mutations from a cohort study designed on the first line ART patients who were enrolled in the antiretroviral therapy center, Sarojini Naidu Medical College, Agra, India from December 2009 to November 2016. After depleting high abundant proteins, plasma proteins were resolved using two-dimensional gel electrophoresis on IPG strips, pH range of 3-10. Spots were selected in the gel based on the density of staining which was common in the drug resistant and drug respondent groups separately. The fold change of each spot was calculated using image-J. Each protein spot was identified using the matrix assisted laser desorption/ionization-time of flight/time of flight (MALDI-TOF/TOF) after tryptic digestion. Peptide peaks were identified through flex analysis version 3.3, and a search against a protein data base using the internal Mascot. Gene ontology study was completed through STRING v.11 and Panther15.0. RESULTS: Out of eight spots from 2D gel samples analyzed by MALDITOF/TOF, two proteins were found to have significant score (> 56) after Flex analysis. These two proteins were identified to be apolipoprotein A1 and serotransferrin. The fold change expression of these two proteins were analyzed in drug resistant and drug respondent group. Apolipoprotein-A1 and serotransferrin were observed to be expressed 1.76 and 1.13-fold more respectively in drug respondent group compared to drug resistant group. The gene ontology analysis revealed the involvement of these two proteins in various important physiological processes. CONCLUSION: Apolipoprotein A-I and serotransferrin were found to be expressed more in drug respondent group compared to drug resistant group.

Recent insights into Mycobacterium tuberculosis through proteomics and implications for the clinic.

INTRODUCTION: This review aimed at providing an update on the application of proteomics-based approaches to gain recent insights of Mycobacterium tuberculosis (M.tb) and its relevance to clinic. Proteomics and bioinformatics approaches helped in the identification and characterization of novel proteins. Studying M.tb, causative agent of tuberculosis (TB), at the proteomic level can contribute to the identification of proteins which can be considered as potential targets for developed drugs and can help us in better understanding the pathogen physiology. Areas covered: In this review we have presented a comprehensive literature pertaining to role of proteomics in understanding M.tb. We have also focused on how the development and advancement in technology in the field of proteomics has augmented the research and played a pivotal role in answering many unexplored questions. Lastly, the application of proteomics to clinic has also been discussed. Expert commentary: We envisage that proteomics has gained remarkable momentum over the years. Proteomics can play an important role in the discovery of biomarkers for TB and other diseases. Also, it can aid in development of effective vaccines and simple, rapid and cost-effective test for the diagnosis of TB which is crucial for the management and control of the disease.

Interactome analysis of Rv0148 to predict potential targets and their pathways linked to aminoglycosides drug resistance: An insilico approach.

Failure of multi drug resistant tuberculosis (MDR-TB) treatment has increased the risk of aminoglycosides resistance, disease transmission, morbidity and mortality. Aminoglycosides are commonly used in multi drug resistant tuberculosis (MDR-TB) treatment. They inhibit protein synthesis by interacting with translationary steps. Apart from gene mutations various mechanisms of aminoglycosides resistance have been reported but still our knowledge regarding aminoglycosides resistance is fragmentary. Proteomics and bioinformatics approaches are the most accepted approaches to explore the unrevealed mechanisms of aminoglycosides resistance. Our previous studies suggested that over expression of Rv0148 in aminoglycosides resistant M. tuberculosis clinical isolates potentially leads to aminoglycosides resistance. In this study we have analyzed the protein-protein interactions of putative short-chain type dehydrogenase/reductase (Rv0148) and predicted the proteins target linked to the aminoglycosides drug resistance. Interactome predicted that fatty acid synthase (fas), dehydrogenase (htdY), dehydrogenase (MT3642), quinine oxidoreductase (MT0157), phenyloxazoline synthase (mbtB), hypothetical protein (Rv0130), 3-oxoacyl-ACP synthase (kasA), 3-oxoacyl-ACP synthase (kasB) aldehyde dehydrogenase (MT0155) and hypothetical protein (Rv1867) were the interactive partners of Rv0148. We have suggested that Rv0148, its predictive interactive protein partners and their pathways (via lipid metabolism as well as intermediary metabolism and respiration) cumulatively unlock the mystery of aminoglycosides resistance in M. tuberculosis.

Cytosolic Proteome Profiling of Aminoglycosides Resistant Mycobacterium tuberculosis Clinical Isolates Using MALDI-TOF/MS.

Emergence of extensively drug resistant tuberculosis (XDR-TB) is the consequence of the failure of second line TB treatment. Aminoglycosides are the important second line anti-TB drugs used to treat the multi drug resistant tuberculosis (MDR-TB). Main known mechanism of action of aminoglycosides is to inhibit the protein synthesis by inhibiting the normal functioning of ribosome. Primary target of aminoglycosides are the ribosomal RNA and its associated proteins. Various mechanisms have been proposed for aminoglycosides resistance but still some are unsolved. As proteins are involved in most of the biological processes, these act as a potential diagnostic markers and drug targets. In the present study we analyzed the purely cytosolic proteome of amikacin (AK) and kanamycin (KM) resistant Mycobacterium tuberculosis isolates by proteomic and bioinformatic approaches. Twenty protein spots were found to have over expressed in resistant isolates and were identified. Among these Rv3208A, Rv2623, Rv1360, Rv2140c, Rv1636, and Rv2185c are six proteins with unknown functions or undefined role. Docking results showed that AK and KM binds to the conserved domain (DUF, USP-A, Luciferase, PEBP and Polyketidecyclase/dehydrase domain) of these hypothetical proteins and over expression of these proteins might neutralize/modulate the effect of drug molecules. TBPred and GPS-PUP predicted cytoplasmic nature and potential pupylation sites within these identified proteins, respectively. String analysis also suggested that over expressed proteins along with their interactive partners might be involved in aminoglycosides resistance. Cumulative effect of these over expressed proteins could be involved in AK and KM resistance by mitigating the toxicity, repression of drug target and neutralizing affect. These findings need further exploitation for the expansion of newer therapeutics or diagnostic markers against AK and KM resistance so that an extreme condition like XDR-TB can be prevented.