1
|
Dey G, Mohanty AK, Sreenivasamurthy SK, Kumar M, Kumar A, Prasad TSK. Proteomics dataset of adult Anopheles Stephensi female brain. Data Brief 2020; 32:106243. [PMID: 32984457 PMCID: PMC7495016 DOI: 10.1016/j.dib.2020.106243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/11/2020] [Accepted: 08/25/2020] [Indexed: 11/27/2022] Open
Abstract
Mosquitoes with their ability to transmit several pathogens of human disease pose a serious threat to healthcare worldwide. Although much has been done to prevent the disease transmission by mosqitos. The rising rate of resistance in mosquitos towards conventionally used control strategies necessitates developing of novel strategies to counter disease transmission. The mosquito brain plays a key role in host-seeking, finding mates and selection of oviposition sites. However, not much is know about the underlying physiological processes in mosquito brain. The data presented in this study describes the proteins that have been identified in the brain tissue of adult female Anopheles stephensi and their associated processes. Interpretation of the data can be related to the previously published article “Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes” [1].
Collapse
Affiliation(s)
- Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Ajeet Kumar Mohanty
- ICMR-National Institute of Malaria Research, Field Station, Campal, Panaji, Goa 403001, India
| | | | - Manish Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
| | - Ashwani Kumar
- ICMR-Vector Control Research Centre, Indira Nagar, Puducherry-605 006, UT, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Deralakatte, Mangalore-575018, India
| |
Collapse
|
2
|
Pandey A, Stawiski EW, Durinck S, Gowda H, Goldstein LD, Barbhuiya MA, Schröder MS, Sreenivasamurthy SK, Kim SW, Phalke S, Suryamohan K, Lee K, Chakraborty P, Kode V, Shi X, Chatterjee A, Datta K, Khan AA, Subbannayya T, Wang J, Chaudhuri S, Gupta S, Shrivastav BR, Jaiswal BS, Poojary SS, Bhunia S, Garcia P, Bizama C, Rosa L, Kwon W, Kim H, Han Y, Yadav TD, Ramprasad VL, Chaudhuri A, Modrusan Z, Roa JC, Tiwari PK, Jang JY, Seshagiri S. Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate. Nat Commun 2020; 11:4225. [PMID: 32839463 PMCID: PMC7445288 DOI: 10.1038/s41467-020-17880-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 07/23/2020] [Indexed: 02/08/2023] Open
Abstract
Gallbladder cancer (GBC) is an aggressive gastrointestinal malignancy with no approved targeted therapy. Here, we analyze exomes (n = 160), transcriptomes (n = 115), and low pass whole genomes (n = 146) from 167 gallbladder cancers (GBCs) from patients in Korea, India and Chile. In addition, we also sequence samples from 39 GBC high-risk patients and detect evidence of early cancer-related genomic lesions. Among the several significantly mutated genes not previously linked to GBC are ETS domain genes ELF3 and EHF, CTNNB1, APC, NSD1, KAT8, STK11 and NFE2L2. A majority of ELF3 alterations are frame-shift mutations that result in several cancer-specific neoantigens that activate T-cells indicating that they are cancer vaccine candidates. In addition, we identify recurrent alterations in KEAP1/NFE2L2 and WNT pathway in GBC. Taken together, these define multiple targetable therapeutic interventions opportunities for GBC treatment and management.
Collapse
Affiliation(s)
- Akhilesh Pandey
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India.
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
- Center for Individualized Medicine and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Eric W Stawiski
- Bioinformatics and Computational Biology Department, Genentech Inc, South San Francisco, CA, 94080, USA.
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA.
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA.
| | - Steffen Durinck
- Bioinformatics and Computational Biology Department, Genentech Inc, South San Francisco, CA, 94080, USA
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Harsha Gowda
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Leonard D Goldstein
- Bioinformatics and Computational Biology Department, Genentech Inc, South San Francisco, CA, 94080, USA
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Mustafa A Barbhuiya
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Markus S Schröder
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
- SciGenom Labs, Cochin, Kerala, 682037, India
| | | | - Sun-Whe Kim
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea
| | - Sameer Phalke
- Research and Development Department, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka, 560099, India
| | - Kushal Suryamohan
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Kayla Lee
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Papia Chakraborty
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Vasumathi Kode
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Xiaoshan Shi
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Aditi Chatterjee
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
| | - Keshava Datta
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
| | - Aafaque A Khan
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
| | | | - Jing Wang
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Sanjiv Gupta
- Department of Pathology, Cancer Hospital and Research Institute, Gwalior, Madhya Pradesh, 474009, India
| | - Braj Raj Shrivastav
- Department of Surgical Oncology, Cancer Hospital and Research Institute, Gwalior, Madhya Pradesh, 474009, India
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | | | | | - Patricia Garcia
- Department of Pathology, Millennium Institute on Immunology and Immunotherapy, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Bizama
- Department of Pathology, Millennium Institute on Immunology and Immunotherapy, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Rosa
- Applied Molecular and Cellular Biology PhD Program Universidad De la Frontera, Temuco, Chile
| | - Wooil Kwon
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea
| | - Hongbeom Kim
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea
| | - Youngmin Han
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea
| | - Thakur Deen Yadav
- Department of Surgery, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Vedam L Ramprasad
- Research and Development Department, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka, 560099, India
| | - Amitabha Chaudhuri
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Juan Carlos Roa
- Department of Pathology, Millennium Institute on Immunology and Immunotherapy, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Jin-Young Jang
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea.
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA.
- SciGenom Research Foundation, 3rd Floor, Narayana Nethralaya Building, Narayana Health City, #258/A, Bommasandra, Hosur Road, Bangalore, Karnataka, 560099, India.
| |
Collapse
|
3
|
Sinha S, Ray A, Abhilash L, Kumar M, Sreenivasamurthy SK, Keshava Prasad TS, Inamdar MS. Proteomics of Asrij Perturbation in Drosophila Lymph Glands for Identification of New Regulators of Hematopoiesis. Mol Cell Proteomics 2019; 18:1171-1182. [PMID: 30923041 PMCID: PMC6553936 DOI: 10.1074/mcp.ra119.001299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/07/2019] [Indexed: 11/06/2022] Open
Abstract
Hematopoiesis is the process of differentiation of precursor blood cells into mature blood cells that is controlled by a complex set of molecular interactions. Understanding hematopoiesis is important for the study of hematological disorders. However, a comprehensive understanding of how physiological and genetic mechanisms regulate blood cell precursor maintenance and differentiation is lacking. Owing to simplicity and ease of genetic analysis, the Drosophila melanogaster lymph gland (LG) is an excellent model to study hematopoiesis. Here, we quantitatively analyzed the LG proteome under genetic conditions that either maintain precursors or promote their differentiation in vivo, by perturbing expression of Asrij, a conserved endosomal regulator of hematopoiesis. Using iTRAQ-based quantitative proteomics, we determined the relative expression levels of proteins in Asrij-knockout and overexpressing LGs from 1500 larval dissections compared with wild type. Our data showed that at least 6.5% of the Drosophila proteome is expressed in wild type LGs. Of the 2133 proteins identified, 780 and 208 proteins were common to previously reported cardiac tube and hemolymph proteomes, respectively, resulting in the identification of 1238 proteins exclusive to the LG. Perturbation of Asrij levels led to differential expression of 619 proteins, of which 27% have human homologs implicated in various diseases. Proteins regulating metabolism, immune system, signal transduction and vesicle-mediated transport were significantly enriched. Immunostaining of representative candidates from the enriched categories and previous reports confirmed 73% of our results, indicating the validity of our LG proteome. Our study provides, for the first time, an in vivo proteomics resource for identifying novel regulators of hematopoiesis that will also be applicable to understanding vertebrate blood cell development.
Collapse
Affiliation(s)
- Saloni Sinha
- From the ‡Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Arindam Ray
- From the ‡Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Lakshman Abhilash
- From the ‡Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Manish Kumar
- §Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- ¶Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sreelakshmi K Sreenivasamurthy
- §Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- ‖NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - T S Keshava Prasad
- §Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- **Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore-575018, India
| | - Maneesha S Inamdar
- From the ‡Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India;
- ‡‡Institute for Stem Cell Biology and Regenerative Medicine, GKVK, Bellary Road, Bangalore 560065, India
| |
Collapse
|
4
|
Mohanty AK, Dey G, Kumar M, Sreenivasamurthy SK, Garg S, Prasad TSK, Kumar A. Proteome data of female Anopheles stephensi antennae. Data Brief 2019; 24:103911. [PMID: 31049374 PMCID: PMC6479098 DOI: 10.1016/j.dib.2019.103911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/26/2019] [Accepted: 04/02/2019] [Indexed: 11/27/2022] Open
Abstract
Antennae of female Anopheles stephensi mosquitoes were dissected and lysed with 1% SDS. Proteins were extracted using ultra sonication and analyzed on high resolution mass spectrometer. Proteomic data was analyzed using two search algorithms SEQUEST and Mascot, resulting in the identification of 22,729 peptides corresponding to 3262 proteins. These proteins were characterized using different bioinformatics tools. VectorBase resource was used to assign Gene Ontology (GO) terms. Using Biomart tool ortholog information was fetched from the VectorBase database. Raw mass spectrometric data was deposited in ProteomeXchange Consortium via PRIDE partner repository in the public dataset PXD001128. Proteins involved in insecticide resistance and odorant binding were the most abundant in the antennae. The proteins identified in this study could be targeted for developing novel vector control strategy.
Collapse
Affiliation(s)
- Ajeet Kumar Mohanty
- ICMR - National Institute of Malaria Research, Field Unit, Campal, Panaji, Goa 403001, India
| | - Gourav Dey
- Institute of Bioinformatics, Discoverer Building, International Tech Park, Bangalore 560 066, India
| | - Manish Kumar
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Sandeep Garg
- Department of Microbiology, Goa University, Taleigao Plateau, Goa Pin - 403206, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya University, Mangalore 575018, India
| | - Ashwani Kumar
- ICMR - National Institute of Malaria Research, Field Unit, Campal, Panaji, Goa 403001, India
| |
Collapse
|
5
|
Madugundu AK, Muthusamy B, Sreenivasamurthy SK, Bhavani C, Sharma J, Kumar B, Murthy KR, Ravikumar R, Pandey A. A Next-Generation Sequencing-Based Molecular Approach to Characterize a Tick Vector in Lyme Disease. OMICS 2019; 22:565-574. [PMID: 30106352 DOI: 10.1089/omi.2018.0089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Next-generation sequencing approaches have revolutionized genomic medicine and enabled rapid diagnosis for several diseases. These approaches are widely used for pathogen detection in several infectious diseases. Lyme disease is a tick-borne infectious disease, which affects multiple organs. The causative organism is a spirochete, Borrelia burgdorferi, which is transmitted by ticks. Lyme disease can be treated easily if detected early, but its diagnosis is often delayed or is incorrect leading to a chronic debilitating condition. Current confirmatory diagnostic tests for Lyme disease rely on detection of antigens derived from B. burgdorferi, which are prone to both false positives and false negatives. Instead of focusing only on the human host for the diagnosis of Lyme disease, one could also attempt to identify the vector (tick) and the causative organism carried by the tick. Since all ticks do not transmit Lyme disease, it can be informative to accurately identify the tick from the site of bite, which is often observed by the patient and discarded. However, identifying ticks based on morphology alone requires a trained operator and can still be incorrect. Thus, we decided to take a molecular approach by sequencing DNA and RNA from a tick collected from an individual bitten by the tick. Using next-generation sequencing, we confirmed the identity of the tick as a dog tick, Dermacentor variabilis, and did not identify any pathogenic bacterial sequences, including Borrelia species. Despite the limited availability of nucleotide sequences for many types of ticks, our approach correctly identified the tick species. This proof-of-principle study demonstrates the potential of next-generation sequencing in the diagnosis of tick-borne infections, which can also be extended to other zoonotic diseases.
Collapse
Affiliation(s)
- Anil K Madugundu
- 1 Manipal Academy of Higher Education (MAHE) , Manipal, Karnataka, India .,2 Institute of Bioinformatics , International Technology Park, Bangalore, Karnataka, India .,3 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Babylakshmi Muthusamy
- 1 Manipal Academy of Higher Education (MAHE) , Manipal, Karnataka, India .,2 Institute of Bioinformatics , International Technology Park, Bangalore, Karnataka, India
| | - Sreelakshmi K Sreenivasamurthy
- 1 Manipal Academy of Higher Education (MAHE) , Manipal, Karnataka, India .,2 Institute of Bioinformatics , International Technology Park, Bangalore, Karnataka, India .,3 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland.,4 National Institute of Mental Health and Neurosciences , Bangalore, Karnataka, India
| | - Chandra Bhavani
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, Karnataka, India
| | - Jyoti Sharma
- 1 Manipal Academy of Higher Education (MAHE) , Manipal, Karnataka, India .,2 Institute of Bioinformatics , International Technology Park, Bangalore, Karnataka, India
| | - Bankatesh Kumar
- 4 National Institute of Mental Health and Neurosciences , Bangalore, Karnataka, India
| | - Krishna R Murthy
- 1 Manipal Academy of Higher Education (MAHE) , Manipal, Karnataka, India .,2 Institute of Bioinformatics , International Technology Park, Bangalore, Karnataka, India .,5 Vittala International Institute of Ophthalmology , Bangalore, Karnataka, India
| | - Raju Ravikumar
- 4 National Institute of Mental Health and Neurosciences , Bangalore, Karnataka, India
| | - Akhilesh Pandey
- 3 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland.,6 Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland.,7 Department of Oncology, Johns Hopkins University School of Medicine , Baltimore, Maryland.,8 Department of Pathology, Johns Hopkins University School of Medicine , Baltimore, Maryland
| |
Collapse
|
6
|
Dey G, Mohanty AK, Sreenivasamurthy SK, Kumar M, Keshava Prasad TS, Kumar A. Proteome data of Anopheles stephensi salivary glands using high-resolution mass spectrometry analysis. Data Brief 2019; 21:2554-2561. [PMID: 30761337 PMCID: PMC6288417 DOI: 10.1016/j.dib.2018.11.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/14/2018] [Indexed: 10/29/2022] Open
Abstract
The data article reports data of the proteins expressed in female Anopheles stephensi salivary glands. Proteomic data were acquired using high-resolution mass spectrometers - Orbitrap-Velos and Orbitrap-Elite. Samples derived from adult female A. stephensi salivary glands led to the identification of 4390 proteins. Mass spectrometry data were analyzed on Proteome Discoverer (Version 2.1) platform with Sequest and Mascot search engines. The identified proteins were analyzed for their Gene Ontology annotation, interaction network and their possible roles in vector-parasite interaction. The data provided here are related to our published article "Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes" (Prasad et al., 2017) [1].
Collapse
Affiliation(s)
- Gourav Dey
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.,Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Ajeet Kumar Mohanty
- ICMR-National Institute of Malaria Research, Field Unit, Campal, Panaji, Goa 403001, India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Manish Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.,Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Ashwani Kumar
- ICMR-National Institute of Malaria Research, Field Unit, Campal, Panaji, Goa 403001, India
| |
Collapse
|
7
|
Dey G, Mohanty AK, Kumar M, Sreenivasamurthy SK, Patil AH, Keshava Prasad TS, Kumar A. Proteome data of Anopheles stephensi ovary using high-resolution mass spectrometry. Data Brief 2018; 20:723-731. [PMID: 30211266 PMCID: PMC6129740 DOI: 10.1016/j.dib.2018.08.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/10/2018] [Accepted: 08/21/2018] [Indexed: 11/20/2022] Open
Abstract
This article contains data on the proteins expressed in the ovaries of Anopheles stephensi, a major vector of malaria in India. Data acquisition was performed using a high-resolution Orbitrap-Velos mass spectrometer. The acquired MS/MS data was searched against An. stephensi protein database comprising of 11,789 sequences. Overall, 4407 proteins were identified, functional analysis was performed for the identified proteins and a protein-protein interaction map predicted. The data provided here is also related to a published article - “Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes” (Prasad et al., 2017) [1].
Collapse
Affiliation(s)
- Gourav Dey
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore 575018, India.,Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India
| | - Ajeet Kumar Mohanty
- ICMR-National Institute of Malaria Research, Field Unit, Campal, Panaji, Goa 403001, India
| | - Manish Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India
| | - Arun H Patil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore 575018, India.,Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore 575018, India.,Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - Ashwani Kumar
- ICMR-National Institute of Malaria Research, Field Unit, Campal, Panaji, Goa 403001, India
| |
Collapse
|
8
|
Mohanty AK, Dey G, Kumar M, Sreenivasamurthy SK, Garg S, Prasad TSK, Kumar A. Mapping Anopheles stephensi midgut proteome using high-resolution mass spectrometry. Data Brief 2018; 17:1295-1303. [PMID: 29845101 PMCID: PMC5966514 DOI: 10.1016/j.dib.2018.02.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/16/2018] [Accepted: 02/12/2018] [Indexed: 11/24/2022] Open
Abstract
Anopheles stephensi Liston is one of the major vectors of malaria in urban areas of India. Midgut plays a central role in the vector life cycle and transmission of malaria. Because gene expression of An. stephensi midgut has not been investigated at protein level, an unbiased mass spectrometry-based proteomic analysis of midgut tissue was carried out. Midgut tissue proteins from female An. stephensi mosquitoes were extracted using 0.5% SDS and digested with trypsin using two complementary approaches, in-gel and in-solution digestion. Fractions were analysed on high-resolution mass spectrometer, which resulted in acquisition of 494,960 MS/MS spectra. The MS/MS spectra were searched against protein database comprising of known and predicted proteins reported in An. stephensi using Sequest and Mascot software. In all, 47,438 peptides were identified corresponding to 5,709 An. stephensi proteins. The identified proteins were functionally categorized based on their cellular localization, biological processes and molecular functions using Gene Ontology (GO) annotation. Several proteins identified in this data are known to mediate the interaction of the Plasmodium with vector midgut and also regulate parasite maturation inside the vector host. This study provides information about the protein composition in midgut tissue of female An. stephensi, which would be useful in understanding vector parasite interaction at molecular level and besides being useful in devising malaria transmission blocking strategies. The data of this study is related to the research article “Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes”.
Collapse
Affiliation(s)
- Ajeet Kumar Mohanty
- ICMR-National Institute of Malaria Research, Field Unit, Campal, Panaji, Goa 403001, India
| | - Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore 575018, India.,Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, India
| | - Manish Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, India
| | - Sandeep Garg
- Department of Microbiology, Goa University, Taleigao Plateau, Goa 403206, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Ashwani Kumar
- ICMR-National Institute of Malaria Research, Field Unit, Campal, Panaji, Goa 403001, India
| |
Collapse
|
9
|
Dey G, Mohanty AK, Kumar M, Sreenivasamurthy SK, Kumar A, Prasad TSK. Proteome data of Anopheles stephensi hemolymph using high resolution mass spectrometry. Data Brief 2018; 18:1441-1447. [PMID: 29900324 PMCID: PMC5997892 DOI: 10.1016/j.dib.2018.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/10/2018] [Indexed: 11/29/2022] Open
Abstract
The article provides insights into the protein expression in Anopheles stephensi hemolymph. We carried out data acquisition using a high-resolution LTQ-Orbitrap Velos mass spectrometer to identify the hemolymph proteins of An. stephensi. Experimentally derived mass spectrometry data was analyzed using Proteome Discoverer 2.1 software using two different search algorithms SEQUEST and MASCOT. A total of 1091 proteins were identified from the hemolymph. The identified proteins were categorized for their role in biological processes and molecular functions. The interactions between these proteins were predicted using STRING online tool. Relation can be drawn between the data provided in this study to the already published article “Integrating transcriptomics and proteomics data for accurate assembly and annotation of genomes” (Prasad et al., 2017) [1].
Collapse
Affiliation(s)
- Gourav Dey
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.,Institute of Bioinformatics, Discoverer Building, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Ajeet Kumar Mohanty
- National Institute of Malaria Research, Field Station, Campal, Panaji, Goa 403001, India
| | - Manish Kumar
- Institute of Bioinformatics, Discoverer Building, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, Discoverer Building, International Tech Park, Bangalore 560066, India.,Manipal Academy of Higher Education, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Ashwani Kumar
- National Institute of Malaria Research, Field Station, Campal, Panaji, Goa 403001, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.,Institute of Bioinformatics, Discoverer Building, International Tech Park, Bangalore 560066, India
| |
Collapse
|
10
|
Kumar M, Mohanty AK, Sreenivasamurthy SK, Dey G, Advani J, Pinto SM, Kumar A, Prasad TSK. Response to Blood Meal in the Fat Body of Anopheles stephensi Using Quantitative Proteomics: Toward New Vector Control Strategies Against Malaria. OMICS 2017; 21:520-530. [PMID: 28873011 DOI: 10.1089/omi.2017.0092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Malaria remains a grand challenge for disruptive innovation in global health therapeutics and diagnostics. Anopheles stephensi is one of the major vectors of malaria in Asia. Vector and transmission control are key focus areas in the fight against malaria, a field of postgenomics research where proteomics can play a substantive role. Moreover, to identify novel strategies to control the vector population, it is necessary to understand the vector life processes at a global and molecular scale. In this context, fat body is a vital organ required for vitellogenesis, vector immunity, vector physiology, and vector-parasite interaction. Given its central role in energy metabolism, vitellogenesis, and immune function, the proteome profile of the fat body and the impact of blood meal (BM) ingestion on the protein abundances of this vital organ have not been investigated so far. Therefore, using a proteomics approach, we identified the proteins expressed in the fat body of An. stephensi and their differential expression in response to BM ingestion. In all, we identified 3,218 proteins in the fat body using high-resolution mass spectrometry, of which 483 were found to be differentially expressed in response to the BM ingestion. Bioinformatics analysis of these proteins underscored their role in amino acid metabolism, vitellogenesis, lipid transport, signal peptide processing, mosquito immunity, and oxidation-reduction processes. Interestingly, we identified five novel genes, which were found to be differentially expressed upon BM ingestion. Proteins that exhibited altered expression in the present study are potential targets for vector control strategies and development of transmission blocking vaccines in the fight against malaria.
Collapse
Affiliation(s)
- Manish Kumar
- 1 Institute of Bioinformatics , Bangalore, India .,2 Manipal University , Manipal, India
| | | | | | - Gourav Dey
- 1 Institute of Bioinformatics , Bangalore, India .,2 Manipal University , Manipal, India
| | - Jayshree Advani
- 1 Institute of Bioinformatics , Bangalore, India .,2 Manipal University , Manipal, India
| | - Sneha M Pinto
- 4 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India
| | - Ashwani Kumar
- 3 National Institute of Malaria Research (ICMR) , Panjim, India
| | - Thottethodi Subrahmanya Keshava Prasad
- 1 Institute of Bioinformatics , Bangalore, India .,4 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India .,5 NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences , Bangalore, India
| |
Collapse
|
11
|
Sreenivasamurthy SK, Madugundu AK, Patil AH, Dey G, Mohanty AK, Kumar M, Patel K, Wang C, Kumar A, Pandey A, Prasad TSK. Mosquito-Borne Diseases and Omics: Tissue-Restricted Expression and Alternative Splicing Revealed by Transcriptome Profiling of Anopheles stephensi. OMICS 2017; 21:488-497. [PMID: 28708456 DOI: 10.1089/omi.2017.0073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Malaria is one of the most debilitating mosquito-borne diseases with high global health burdens. While much of the research on malaria and mosquito-borne diseases is focused on Africa, Southeast Asia accounts for a sizable portion of the global burden of malaria. Moreover, about 50% of the Asian malaria incidence and deaths have been from India. A promising development in this context is that the completion of genome sequence of Anopheles stephensi, a major malaria vector in Asia, offers new opportunities for global health innovation, including the progress in deciphering the vectorial ability of this mosquito species at a molecular level. Moving forward, tissue-based expression profiling would be the next obvious step in understanding gene functions of An. stephensi. We report in this article, to the best of our knowledge, the first in-depth study on tissue-based transcriptomic profile of four important organs (midgut, Malpighian tubules, fat body, and ovary) of adult female An. stephensi mosquitoes. In all, we identified over 20,000 transcripts corresponding to more than 12,000 gene loci from these four tissues. We present and discuss the tissue-based expression profiles of majority of annotated transcripts in An. stephensi genome, and the dynamics of their alternative splicing in these tissues, in this study. The domain-based Gene Ontology analysis of the differentially expressed transcripts in each of the mosquito tissue indicated enrichment of transcripts with proteolytic activity in midgut; transporter activity in Malpighian tubules; cell cycle, DNA replication, and repair activities in ovaries; and oxidoreductase activities in fat body. Tissue-based study of transcript expression and gene functions markedly enhances our understanding of this important malaria vector, and in turn, offers rationales for further studies on vectorial ability and identification of novel molecular targets to intercept malaria transmission.
Collapse
Affiliation(s)
| | - Anil K Madugundu
- 1 Institute of Bioinformatics , Bangalore, India .,3 Centre for Bioinformatics, Pondicherry University , Kalapet, India
| | - Arun H Patil
- 1 Institute of Bioinformatics , Bangalore, India .,4 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India .,5 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Gourav Dey
- 1 Institute of Bioinformatics , Bangalore, India .,2 Manipal University , Manipal, India
| | - Ajeet Kumar Mohanty
- 6 National Institute of Malaria Research , Field Station, Panjim, India .,7 Department of Zoology, Goa University , Taleigao Plateau, India
| | - Manish Kumar
- 1 Institute of Bioinformatics , Bangalore, India .,2 Manipal University , Manipal, India
| | - Krishna Patel
- 1 Institute of Bioinformatics , Bangalore, India .,8 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Charles Wang
- 9 Center for Genomics and Department of Basic Sciences, School of Medicine, Loma Linda University , Loma Linda, California
| | - Ashwani Kumar
- 6 National Institute of Malaria Research , Field Station, Panjim, India
| | - Akhilesh Pandey
- 1 Institute of Bioinformatics , Bangalore, India .,10 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland.,11 Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland.,12 Department of Oncology, Johns Hopkins University School of Medicine , Baltimore, Maryland.,13 Department of Pathology, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | | |
Collapse
|
12
|
Cutler JA, Tahir R, Sreenivasamurthy SK, Mitchell C, Renuse S, Nirujogi RS, Patil AH, Heydarian M, Wong X, Wu X, Huang TC, Kim MS, Reddy KL, Pandey A. Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis. Leukemia 2017; 31:1513-1524. [DOI: 10.1038/leu.2017.61] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/04/2017] [Accepted: 01/11/2017] [Indexed: 12/15/2022]
|
13
|
Prasad TSK, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G, Nirujogi RS, Pinto SM, Madugundu AK, Patil AH, Advani J, Manda SS, Gupta MK, Dwivedi SB, Kelkar DS, Hall B, Jiang X, Peery A, Rajagopalan P, Yelamanchi SD, Solanki HS, Raja R, Sathe GJ, Chavan S, Verma R, Patel KM, Jain AP, Syed N, Datta KK, Khan AA, Dammalli M, Jayaram S, Radhakrishnan A, Mitchell CJ, Na CH, Kumar N, Sinnis P, Sharakhov IV, Wang C, Gowda H, Tu Z, Kumar A, Pandey A. Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Res 2016; 27:133-144. [PMID: 28003436 PMCID: PMC5204337 DOI: 10.1101/gr.201368.115] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/10/2016] [Indexed: 01/05/2023]
Abstract
Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.
Collapse
Affiliation(s)
- T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India
| | - Ajeet Kumar Mohanty
- National Institute of Malaria Research, Field Station, Goa 403001, India.,Department of Zoology, Goa University, Taleigao Plateau, Goa 403206, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Srikanth S Manda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Manoj Kumar Gupta
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sutopa B Dwivedi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Dhanashree S Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Brantley Hall
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Xiaofang Jiang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Ashley Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Soujanya D Yelamanchi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Hitendra S Solanki
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Krishna M Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Ankit P Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Keshava K Datta
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Aafaque Ahmed Khan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Manjunath Dammalli
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka 572103, India
| | - Savita Jayaram
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Aneesha Radhakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Christopher J Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Chan-Hyun Na
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Nirbhay Kumar
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana 70112, USA
| | - Photini Sinnis
- Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Charles Wang
- Center for Genomics and Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Zhijian Tu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Ashwani Kumar
- National Institute of Malaria Research, Field Station, Goa 403001, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| |
Collapse
|
14
|
Selvan LDN, Sreenivasamurthy SK, Kumar S, Yelamanchi SD, Madugundu AK, Anil AK, Renuse S, Nair BG, Gowda H, Mathur PP, Satishchandra P, Shankar SK, Mahadevan A, Keshava Prasad TS. Characterization of host response to Cryptococcus neoformans through quantitative proteomic analysis of cryptococcal meningitis co-infected with HIV. Mol Biosyst 2016; 11:2529-40. [PMID: 26181685 DOI: 10.1039/c5mb00187k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cryptococcal meningitis is the most common opportunistic fungal infection causing morbidity and mortality (>60%) in HIV-associated immunocompromised individuals caused by Cryptococcus neoformans. Molecular mechanisms of cryptococcal infection in brain have been studied using experimental animal models and cell lines. There are limited studies for the molecular understanding of cryptococcal meningitis in human brain. The proteins involved in the process of invasion and infection in human brain still remains obscure. To this end we carried out mass spectrometry-based quantitative proteomics of frontal lobe brain tissues from cryptococcal meningitis patients and controls to identify host proteins that are associated with the pathogenesis of cryptococcal meningitis. We identified 317 proteins to be differentially expressed (≥2-fold) from a total of 3423 human proteins. We found proteins involved in immune response and signal transduction to be differentially expressed in response to cryptococcal infection in human brain. Immune response proteins including complement factors, major histocompatibility proteins, proteins previously known to be involved in fungal invasion to brain such as caveolin 1 and actin were identified to be differentially expressed in cryptococcal meningitis brain tissues co-infected with HIV. We also validated the expression status of 5 proteins using immunohistochemistry. Overexpression of major histocompatibility complexes, class I, B (HLA-B), actin alpha 2 smooth muscle aorta (ACTA2) and caveolin 1 (CAV1) and downregulation of peripheral myelin protein 2 (PMP2) and alpha crystallin B chain (CRYAB) in cryptococcal meningitis were confirmed by IHC-based validation experiments. This study provides the brain proteome profile of cryptococcal meningitis co-infected with HIV for a better understanding of the host response associated with the disease.
Collapse
|
15
|
Harish G, Mahadevan A, Pruthi N, Sreenivasamurthy SK, Puttamallesh VN, Keshava Prasad TS, Shankar SK, Srinivas Bharath MM. Characterization of traumatic brain injury in human brains reveals distinct cellular and molecular changes in contusion and pericontusion. J Neurochem 2015; 134:156-72. [PMID: 25712633 DOI: 10.1111/jnc.13082] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 01/07/2015] [Accepted: 02/19/2015] [Indexed: 12/22/2022]
Abstract
Traumatic brain injury (TBI) contributes to fatalities and neurological disabilities worldwide. While primary injury causes immediate damage, secondary events contribute to long-term neurological defects. Contusions (Ct) are primary injuries correlated with poor clinical prognosis, and can expand leading to delayed neurological deterioration. Pericontusion (PC) (penumbra), the region surrounding Ct, can also expand with edema, increased intracranial pressure, ischemia, and poor clinical outcome. Analysis of Ct and PC can therefore assist in understanding the pathobiology of TBI and its management. This study on human TBI brains noted extensive neuronal, astroglial and inflammatory changes, alterations in mitochondrial, synaptic and oxidative markers, and associated proteomic profile, with distinct differences in Ct and PC. While Ct displayed petechial hemorrhages, thrombosis, inflammation, neuronal pyknosis, and astrogliosis, PC revealed edema, vacuolation of neuropil, axonal loss, and dystrophic changes. Proteomic analysis demonstrated altered immune response, synaptic, and mitochondrial dysfunction, among others, in Ct, while PC displayed altered regulation of neurogenesis and cytoskeletal architecture, among others. TBI brains displayed oxidative damage, glutathione depletion, mitochondrial dysfunction, and loss of synaptic proteins, with these changes being more profound in Ct. We suggest that analysis of markers specific to Ct and PC may be valuable in the evaluation of TBI pathobiology and therapeutics. We have characterized the primary injury in human traumatic brain injury (TBI). Contusions (Ct) - the injury core displayed hemorrhages, inflammation, and astrogliosis, while the surrounding pericontusion (PC) revealed edema, vacuolation, microglial activation, axonal loss, and dystrophy. Proteomic analysis demonstrated altered immune response, synaptic and mitochondrial dysfunction in Ct, and altered regulation of neurogenesis and cytoskeletal architecture in PC. Ct displayed more oxidative damage, mitochondrial, and synaptic dysfunction compared to PC.
Collapse
Affiliation(s)
- Gangadharappa Harish
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India
| | - Nupur Pruthi
- Department of Neurosurgery, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India
| | | | | | | | - Susarla Krishna Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India
| | | |
Collapse
|
16
|
Sahu A, Kumar S, Sreenivasamurthy SK, Selvan LDN, Madugundu AK, Yelamanchi SD, Puttamallesh VN, Dey G, Anil AK, Srinivasan A, Mukherjee KK, Gowda H, Satishchandra P, Mahadevan A, Pandey A, Prasad TSK, Shankar SK. Host response profile of human brain proteome in toxoplasma encephalitis co-infected with HIV. Clin Proteomics 2014; 11:39. [PMID: 25404878 PMCID: PMC4232683 DOI: 10.1186/1559-0275-11-39] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 09/02/2014] [Indexed: 01/27/2023] Open
Abstract
Background Toxoplasma encephalitis is caused by the opportunistic protozoan parasite Toxoplasma gondii. Primary infection with T. gondii in immunocompetent individuals remains largely asymptomatic. In contrast, in immunocompromised individuals, reactivation of the parasite results in severe complications and mortality. Molecular changes at the protein level in the host central nervous system and proteins associated with pathogenesis of toxoplasma encephalitis are largely unexplored. We used a global quantitative proteomic strategy to identify differentially regulated proteins and affected molecular networks in the human host during T. gondii infection with HIV co-infection. Results We identified 3,496 proteins out of which 607 proteins were differentially expressed (≥1.5-fold) when frontal lobe of the brain from patients diagnosed with toxoplasma encephalitis was compared to control brain tissues. We validated differential expression of 3 proteins through immunohistochemistry, which was confirmed to be consistent with mass spectrometry analysis. Pathway analysis of differentially expressed proteins indicated deregulation of several pathways involved in antigen processing, immune response, neuronal growth, neurotransmitter transport and energy metabolism. Conclusions Global quantitative proteomic approach adopted in this study generated a comparative proteome profile of brain tissues from toxoplasma encephalitis patients co-infected with HIV. Differentially expressed proteins include previously reported and several new proteins in the context of T. gondii and HIV infection, which can be further investigated. Molecular pathways identified to be associated with the disease should enhance our understanding of pathogenesis in toxoplasma encephalitis. Electronic supplementary material The online version of this article (doi:10.1186/1559-0275-11-39) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Apeksha Sahu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry, 605014 India
| | - Satwant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Manipal University, Madhav Nagar, Manipal, 576104 India
| | - Lakshmi Dhevi N Selvan
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry, 605014 India
| | - Soujanya D Yelamanchi
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; School of Biotechnology, KIIT University, Bhubaneswar, 751024 India
| | | | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Manipal University, Madhav Nagar, Manipal, 576104 India
| | | | - Anand Srinivasan
- Department of Pharmacology, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012 India
| | - Kanchan K Mukherjee
- Department of Neurosurgery, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012 India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | | | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India ; Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 1205 USA ; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ; The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry, 605014 India ; Manipal University, Madhav Nagar, Manipal, 576104 India ; Amrita School of Biotechnology, Amrita University, Kollam, 690525 India ; NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India
| | - Susarla Krishna Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India ; Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India
| |
Collapse
|
17
|
Puttamallesh VN, Sreenivasamurthy SK, Singh PK, Harsha HC, Ganjiwale A, Broor S, Pandey A, Narayana J, Prasad TSK. Proteomic profiling of serum samples from chikungunya-infected patients provides insights into host response. Clin Proteomics 2013; 10:14. [PMID: 24124767 PMCID: PMC3879382 DOI: 10.1186/1559-0275-10-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/17/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chikungunya is a highly debilitating febrile illness caused by Chikungunya virus, a single-stranded RNA virus, which is transmitted by Aedes aegypti or Aedes albopictus mosquito species. The pathogenesis and host responses in individuals infected with the chikungunya virus are not well understood at the molecular level. We carried out proteomic profiling of serum samples from chikungunya patients in order to identify molecules associated with the host response to infection by this virus. RESULTS Proteomic profiling of serum obtained from the infected individuals resulted in identification of 569 proteins. Of these, 63 proteins were found to be differentially expressed (≥ 2-fold) in patient as compared to control sera. These differentially expressed proteins were involved in various processes such as lipid metabolism, immune response, transport, signal transduction and apoptosis. CONCLUSIONS This is the first report providing a global proteomic profile of serum samples from individuals infected with the chikungunya virus. Our data provide an insight into the proteins that are involved as host response factors during an infection. These proteins include clusterin, apolipoproteins and S100A family of proteins.
Collapse
Affiliation(s)
- Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | | | - Pradeep Kumar Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Anjali Ganjiwale
- Microtest Innovations Pvt. Limited, International Technology Park, Bangalore 560 066, India
| | - Shobha Broor
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
| | - Jayasuryan Narayana
- Microtest Innovations Pvt. Limited, International Technology Park, Bangalore 560 066, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| |
Collapse
|
18
|
Sreenivasamurthy SK, Dey G, Ramu M, Kumar M, Gupta MK, Mohanty AK, Harsha HC, Sharma P, Kumar N, Pandey A, Kumar A, Prasad TSK. A compendium of molecules involved in vector-pathogen interactions pertaining to malaria. Malar J 2013; 12:216. [PMID: 23802619 PMCID: PMC3734095 DOI: 10.1186/1475-2875-12-216] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 06/24/2013] [Indexed: 02/06/2023] Open
Abstract
Malaria is a vector-borne disease causing extensive morbidity, debility and mortality. Development of resistance to drugs among parasites and to conventional insecticides among vector-mosquitoes necessitates innovative measures to combat this disease. Identification of molecules involved in the maintenance of complex developmental cycles of the parasites within the vector and the host can provide attractive targets to intervene in the disease transmission. In the last decade, several efforts have been made in identifying such molecules involved in mosquito-parasite interactions and, subsequently, validating their role in the development of parasites within the vector. In this study, a list of mosquito proteins, which facilitate or inhibit the development of malaria parasites in the midgut, haemolymph and salivary glands of mosquitoes, is compiled. A total of 94 molecules have been reported and validated for their role in the development of malaria parasites inside the vector. This compendium of molecules will serve as a centralized resource to biomedical researchers investigating vector-pathogen interactions and malaria transmission.
Collapse
|