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Quantitative proteomics for identifying biomarkers for tuberculous meningitis

Ghantasala S Sameer Kumar12, Abhilash K Venugopal1234, Anita Mahadevan5, Santosh Renuse1346, H C Harsha1, Nandini A Sahasrabuddhe17, Harsh Pawar18, Rakesh Sharma9, Praveen Kumar1, Sudha Rajagopalan10, Keith Waddell11, Yarappa L Ramachandra2, Parthasarathy Satishchandra12, Raghothama Chaerkady1234, T S Keshava Prasad11367, K Shankar5* and Akhilesh Pandey1141534*

Author Affiliations

1 Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India

2 Department of Biotechnology, Kuvempu University, Shimoga, 577451, India

3 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, 733 N. Broadway, BRB 527, Baltimore, MD, 21205, USA

4 Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA

5 Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, 560029, India

6 Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690525, India

7 Manipal University, Madhav Nagar, Manipal, 576104, India

8 Rajiv Gandhi University of Health Sciences, Bangalore, 560041, India

9 Department of Neurochemistry, National Institute of Mental Health and Neurosciences, Bangalore, 560029, India

10 Agilent Technologies India Pvt. Ltd, Bangalore, 560048, India

11 Agilent Technologies, Santa Clara, CA, USA

12 Department of Neurology, National Institute of Mental Health and Neurosciences, Bangalore, 560029, India

13 Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014, India

14 Pathology Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA

15 Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA

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Clinical Proteomics 2012, 9:12  doi:10.1186/1559-0275-9-12

Published: 30 November 2012

Abstract

Introduction

Tuberculous meningitis is a frequent extrapulmonary disease caused by Mycobacterium tuberculosis and is associated with high mortality rates and severe neurological sequelae. In an earlier study employing DNA microarrays, we had identified genes that were differentially expressed at the transcript level in human brain tissue from cases of tuberculous meningitis. In the current study, we used a quantitative proteomics approach to discover protein biomarkers for tuberculous meningitis.

Methods

To compare brain tissues from confirmed cased of tuberculous meningitis with uninfected brain tissue, we carried out quantitative protein expression profiling using iTRAQ labeling and LC-MS/MS analysis of SCX fractionated peptides on Agilent’s accurate mass QTOF mass spectrometer.

Results and conclusions

Through this approach, we identified both known and novel differentially regulated molecules. Those described previously included signal-regulatory protein alpha (SIRPA) and protein disulfide isomerase family A, member 6 (PDIA6), which have been shown to be overexpressed at the mRNA level in tuberculous meningitis. The novel overexpressed proteins identified in our study included amphiphysin (AMPH) and neurofascin (NFASC) while ferritin light chain (FTL) was found to be downregulated in TBM. We validated amphiphysin, neurofascin and ferritin light chain using immunohistochemistry which confirmed their differential expression in tuberculous meningitis. Overall, our data provides insights into the host response in tuberculous meningitis at the molecular level in addition to providing candidate diagnostic biomarkers for tuberculous meningitis.

Keywords:
Relative quantitation; Cerebrospinal fluid; Histopathology; Early diagnosis; Tuberculosis