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Gupta P, Goswami SG, Kumari G, Saravanakumar V, Bhargava N, Rai AB, Singh P, Bhoyar RC, Arvinden VR, Gunda P, Jain S, Narayana VK, Deolankar SC, Prasad TSK, Natarajan VT, Scaria V, Singh S, Ramalingam S. Development of pathophysiologically relevant models of sickle cell disease and β-thalassemia for therapeutic studies. Nat Commun 2024; 15:1794. [PMID: 38413594 PMCID: PMC10899644 DOI: 10.1038/s41467-024-46036-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Ex vivo cellular system that accurately replicates sickle cell disease and β-thalassemia characteristics is a highly sought-after goal in the field of erythroid biology. In this study, we present the generation of erythroid progenitor lines with sickle cell disease and β-thalassemia mutation using CRISPR/Cas9. The disease cellular models exhibit similar differentiation profiles, globin expression and proteome dynamics as patient-derived hematopoietic stem/progenitor cells. Additionally, these cellular models recapitulate pathological conditions associated with both the diseases. Hydroxyurea and pomalidomide treatment enhanced fetal hemoglobin levels. Notably, we introduce a therapeutic strategy for the above diseases by recapitulating the HPFH3 genotype, which reactivates fetal hemoglobin levels and rescues the disease phenotypes, thus making these lines a valuable platform for studying and developing new therapeutic strategies. Altogether, we demonstrate our disease cellular systems are physiologically relevant and could prove to be indispensable tools for disease modeling, drug screenings and cell and gene therapy-based applications.
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Affiliation(s)
- Pragya Gupta
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sangam Giri Goswami
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geeta Kumari
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Vinodh Saravanakumar
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
| | - Nupur Bhargava
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
| | - Akhila Balakrishna Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Praveen Singh
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rahul C Bhoyar
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
| | - V R Arvinden
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Padma Gunda
- Thalassemia and Sickle Cell Society- Kamala Hospital and Research Centre, Shivarampally, Hyderabad, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society- Kamala Hospital and Research Centre, Shivarampally, Hyderabad, India
| | - Vanya Kadla Narayana
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Sayali C Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Vivek T Natarajan
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinod Scaria
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shailja Singh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
| | - Sivaprakash Ramalingam
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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2
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Mehdiratta K, Nain S, Sharma M, Singh S, Srivastava S, Dhamale BD, Mohanty D, Kamat SS, Natarajan VT, Sharma R, Gokhale RS. Respiratory Quinone Switches from Menaquinone to Polyketide Quinone during the Development Cycle in Streptomyces sp. Strain MNU77. Microbiol Spectr 2023; 11:e0259722. [PMID: 36507669 PMCID: PMC9927152 DOI: 10.1128/spectrum.02597-22] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Type III polyketide synthases (PKSs) found across Streptomyces species are primarily known for synthesis of a vast repertoire of clinically and industrially relevant secondary metabolites. However, our understanding of the functional relevance of these bioactive metabolites in Streptomyces physiology is still limited. Recently, a role of type III PKS harboring gene cluster in producing alternate electron carrier, polyketide quinone (PkQ) was established in a related member of the Actinobacteria, Mycobacteria, highlighting the critical role these secondary metabolites play in primary cellular metabolism of the producer organism. Here, we report the developmental stage-specific transcriptional regulation of homologous type III PKS containing gene cluster in freshwater Streptomyces sp. strain MNU77. Gene expression analysis revealed the type III PKS gene cluster to be stringently regulated, with significant upregulation observed during the dormant sporulation stage of Streptomyces sp. MNU77. In contrast, the expression levels of only known electron carrier, menaquinone biosynthetic genes were interestingly found to be downregulated. Our liquid chromatography-high-resolution mass spectrometry (LC-HRMS) analysis of a metabolite extract from the Streptomyces sp. MNU77 spores also showed 10 times more metabolic abundance of PkQs than menaquinones. Furthermore, through heterologous complementation studies, we demonstrate that Streptomyces sp. MNU77 type III PKS rescues a respiratory defect of the Mycobacterium smegmatis type III PKS deletion mutant. Together, our studies reveal that freshwater Streptomyces sp. MNU77 robustly produces novel PkQs during the sporulation stage, suggesting utilization of PkQs as alternate electron carriers across Actinobacteria during dormant hypoxic conditions. IMPORTANCE The complex developmental life cycle of Streptomyces sp. mandates efficient cellular respiratory reconfiguration for a smooth transition from aerated nutrient-rich vegetative hyphal growth to the hypoxic-dormant sporulation stage. Polyketide quinones (PkQs) have recently been identified as a class of alternate electron carriers from a related member of the Actinobacteria, Mycobacteria, that facilitates maintenance of membrane potential in oxygen-deficient niches. Our studies with the newly identified freshwater Streptomyces sp. strain MNU77 show conditional transcriptional upregulation and metabolic abundance of PkQs in the spore state of the Streptomyces life cycle. In parallel, the levels of menaquinones, the only known Streptomyces electron carrier, were downregulated, suggesting deployment of PkQs as universal electron carriers in low-oxygen, unfavorable conditions across the Actinobacteria family.
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Affiliation(s)
- Kritee Mehdiratta
- National Institute of Immunology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sonam Nain
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Meenakshi Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shubham Singh
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | | | | | | | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Vivek T. Natarajan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rakesh Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rajesh S. Gokhale
- National Institute of Immunology, New Delhi, India
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
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3
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Gupta I, Shankrit S, Narta K, Ghazi M, Grover R, Pandey R, Kar HK, Menon SM, Gupta A, Yenamandra VK, Singh A, Mukerji M, Mukhopadhyay A, Rani R, Gokhale RS, Dash D, Natarajan VT. Whole-Exome Sequencing of Vitiligo Lesions Indicates Lower Burden of Somatic Variations: Implications in Risk for Nonmelanoma Skin Cancers. J Invest Dermatol 2022; 143:1111-1114.e8. [PMID: 36535361 DOI: 10.1016/j.jid.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Iti Gupta
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shambhavi Shankrit
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Kiran Narta
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Madeeha Ghazi
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ritika Grover
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Pandey
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Hemanta Kumar Kar
- Department of Dermatology, PGIMER Dr. Ram Manohar Lohia Hospital, New Delhi, India; Department of Dermatology, Kalinga Institute of Medical Sciences, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha
| | - Shruti M Menon
- Department of Dermatology, Dr. D.Y. Patil Medical College, Hospital & Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Hospital & Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, India
| | - Vamsi K Yenamandra
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Archana Singh
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mitali Mukerji
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Arijit Mukhopadhyay
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India; Translational Medicine Unit, Biomedical Research Centre, University of Salford, Manchester, United Kingdom
| | - Rajni Rani
- National Institute of Immunology, New Delhi, India
| | - Rajesh S Gokhale
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; National Institute of Immunology, New Delhi, India
| | - Debasis Dash
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vivek T Natarajan
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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4
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Sultan F, Basu R, Murthy D, Kochar M, Attri KS, Aggarwal A, Kumari P, Dnyane P, Tanwar J, Motiani RK, Singh A, Gadgil C, Bhavesh NS, Singh PK, Natarajan VT, Gokhale RS. Temporal analysis of melanogenesis identifies fatty acid metabolism as key skin pigment regulator. PLoS Biol 2022; 20:e3001634. [PMID: 35584084 PMCID: PMC9116682 DOI: 10.1371/journal.pbio.3001634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/19/2022] [Indexed: 11/19/2022] Open
Abstract
Therapeutic methods to modulate skin pigmentation has important implications for skin cancer prevention and for treating cutaneous hyperpigmentary conditions. Towards defining new potential targets, we followed temporal dynamics of melanogenesis using a cell-autonomous pigmentation model. Our study elucidates 3 dominant phases of synchronized metabolic and transcriptional reprogramming. The melanogenic trigger is associated with high MITF levels along with rapid uptake of glucose. The transition to pigmented state is accompanied by increased glucose channelisation to anabolic pathways that support melanosome biogenesis. SREBF1-mediated up-regulation of fatty acid synthesis results in a transient accumulation of lipid droplets and enhancement of fatty acids oxidation through mitochondrial respiration. While this heightened bioenergetic activity is important to sustain melanogenesis, it impairs mitochondria lately, shifting the metabolism towards glycolysis. This recovery phase is accompanied by activation of the NRF2 detoxication pathway. Finally, we show that inhibitors of lipid metabolism can resolve hyperpigmentary conditions in a guinea pig UV-tanning model. Our study reveals rewiring of the metabolic circuit during melanogenesis, and fatty acid metabolism as a potential therapeutic target in a variety of cutaneous diseases manifesting hyperpigmentary phenotype. Temporal analysis of melanogenesis, based on transcriptomic and metabolomic signatures, reveals fatty acid metabolism as a crucial mediator of the transition between pigmentation phases. Inhibitors of the fatty acid pathway could represent a new target for modulating pigmentation.
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Affiliation(s)
- Farina Sultan
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
| | - Reelina Basu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Divya Murthy
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Manisha Kochar
- Immunometabolism Laboratory, National Institute of Immunology, New Delhi, India
| | - Kuldeep S. Attri
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Ayush Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
| | - Pooja Kumari
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Pooja Dnyane
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
- CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Jyoti Tanwar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
- Laboratory of Calciomics and Systemic Pathophysiology, Regional Centre of Biotechnology (RCB), Faridabad, Haryana, India
| | - Rajender K. Motiani
- Laboratory of Calciomics and Systemic Pathophysiology, Regional Centre of Biotechnology (RCB), Faridabad, Haryana, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
| | - Chetan Gadgil
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
- CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Neel Sarovar Bhavesh
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Pankaj K. Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Vivek T. Natarajan
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, UP, India
- * E-mail: (VTN); (RSG)
| | - Rajesh S. Gokhale
- Immunometabolism Laboratory, National Institute of Immunology, New Delhi, India
- * E-mail: (VTN); (RSG)
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5
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Sharma B, Subramaniam YJ, Ayyappa Raja D, Aggarwal A, Sivasubbu S, Natarajan VT. Reverse Genetic Approach to Identify Regulators of Pigmentation using Zebrafish. J Vis Exp 2022. [DOI: 10.3791/62955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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6
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Chakraborty S, Singhmar S, Singh D, Maulik M, Patil R, Agrawal SK, Mishra A, Ghazi M, Vats A, Natarajan VT, Juvekar S, Prasher B, Mukerji M. Baseline cell proliferation rates and response to UV differ in lymphoblastoid cell lines derived from healthy individuals of extreme constitution types. Cell Cycle 2021; 20:903-913. [PMID: 33870855 DOI: 10.1080/15384101.2021.1909884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Differences in human phenotypes and susceptibility to complex diseases are an outcome of genetic and environmental interactions. This is evident in diseases that progress through a common set of intermediate patho-endophenotypes. Precision medicine aims to delineate molecular players for individualized and early interventions. Functional studies of lymphoblastoid cell line (LCL) model of phenotypically well-characterized healthy individuals can help deconvolute and validate these molecular mechanisms. In this study, LCLs are developed from eight healthy individuals belonging to three extreme constitution types, deep phenotyped on the basis of Ayurveda. LCLs were characterized by karyotyping and immunophenotyping. Growth characteristics and response to UV were studied in these LCLs. Significant differences in cell proliferation rates were observed between the contrasting groups such that one type (Kapha) proliferates significantly slower than the other two (Vata, Pitta). In response to UV, one of the fast growing groups (Vata) shows higher cell death but recovers its numbers due to an inherent higher rates of proliferation. This study reveals that baseline differences in cell proliferation could be a key to understanding the survivability of cells under UV stress. Variability in baseline cellular phenotypes not only explains the cellular basis of different constitution types but can also help set priors during the design of an individualized therapy with DNA damaging agents. This is the first study of its kind that shows variability of intermediate patho-phenotypes among healthy individuals with potential implications in precision medicine.
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Affiliation(s)
- Sumita Chakraborty
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sunanda Singhmar
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dayanidhi Singh
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mahua Maulik
- CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Department of Biological Sciences, Indian Institute of Science Education & Research, IISER Kolkata, Mohanpur, Nadia, West Bengal, India
| | - Rutuja Patil
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, Maharashtra, India
| | - Satyam Kumar Agrawal
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,School of Pharmacy and Emerging Sciences (SPES), Baddi University of Emerging Science and Technology (BUEST), Baddi, Himachal Pradesh, India
| | - Anushree Mishra
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Madeeha Ghazi
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Archana Vats
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Vivek T Natarajan
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Juvekar
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, Maharashtra, India
| | - Bhavana Prasher
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mitali Mukerji
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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7
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Raja DA, Subramaniam Y, Aggarwal A, Gotherwal V, Babu A, Tanwar J, Motiani RK, Sivasubbu S, Gokhale RS, Natarajan VT. Histone variant dictates fate biasing of neural crest cells to melanocyte lineage. Development 2020; 147:dev.182576. [PMID: 32098766 DOI: 10.1242/dev.182576] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022]
Abstract
In the neural crest lineage, progressive fate restriction and stem cell assignment are crucial for both development and regeneration. Whereas fate commitment events have distinct transcriptional footprints, fate biasing is often transitory and metastable, and is thought to be moulded by epigenetic programmes. Therefore, the molecular basis of specification is difficult to define. In this study, we established a role for a histone variant, H2a.z.2, in specification of the melanocyte lineage from multipotent neural crest cells. H2a.z.2 silencing reduces the number of melanocyte precursors in developing zebrafish embryos and from mouse embryonic stem cells in vitro We demonstrate that this histone variant occupies nucleosomes in the promoter of the key melanocyte determinant mitf, and enhances its induction. CRISPR/Cas9-based targeted mutagenesis of this gene in zebrafish drastically reduces adult melanocytes, as well as their regeneration. Thereby, our study establishes the role of a histone variant upstream of the core gene regulatory network in the neural crest lineage. This epigenetic mark is a key determinant of cell fate and facilitates gene activation by external instructive signals, thereby establishing melanocyte fate identity.
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Affiliation(s)
- Desingu Ayyappa Raja
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Yogaspoorthi Subramaniam
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Ayush Aggarwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishvabandhu Gotherwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Aswini Babu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Jyoti Tanwar
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Rajender K Motiani
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Sridhar Sivasubbu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Rajesh S Gokhale
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Vivek T Natarajan
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India .,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
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8
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Vaish U, Kumar AA, Varshney S, Ghosh S, Sengupta S, Sood C, Kar HK, Sharma P, Natarajan VT, Gokhale RS, Rani R. Author Correction: Micro RNAs upregulated in Vitiligo skin play an important role in its aetiopathogenesis by altering TRP1 expression and keratinocyte-melanocytes cross-talk. Sci Rep 2020; 10:2166. [PMID: 32015404 PMCID: PMC6997451 DOI: 10.1038/s41598-020-58949-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | - Swati Varshney
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Shreya Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Chandni Sood
- National Institute of Immunology, New Delhi, 110067, India
| | - Hemanta K Kar
- Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - Pankaj Sharma
- Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Rajesh S Gokhale
- National Institute of Immunology, New Delhi, 110067, India.,CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Rajni Rani
- National Institute of Immunology, New Delhi, 110067, India.
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9
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Raja DA, Gotherwal V, Burse SA, Subramaniam YJ, Sultan F, Vats A, Gautam H, Sharma B, Sharma S, Singh A, Sivasubbu S, Gokhale RS, Natarajan VT. pH-controlled histone acetylation amplifies melanocyte differentiation downstream of MITF. EMBO Rep 2020; 21:e48333. [PMID: 31709752 PMCID: PMC6945066 DOI: 10.15252/embr.201948333] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 10/04/2019] [Accepted: 10/15/2019] [Indexed: 12/20/2022] Open
Abstract
Tanning response and melanocyte differentiation are mediated by the central transcription factor MITF. This involves the rapid and selective induction of melanocyte maturation genes, while concomitantly the expression of other effector genes is maintained. In this study, using cell-based and zebrafish model systems, we report on a pH-mediated feed-forward mechanism of epigenetic regulation that enables selective amplification of the melanocyte maturation program. We demonstrate that MITF activation directly elevates the expression of the enzyme carbonic anhydrase 14 (CA14). Nuclear localization of CA14 leads to an increase of the intracellular pH, resulting in the activation of the histone acetyl transferase p300/CBP. In turn, enhanced H3K27 histone acetylation at selected differentiation genes facilitates their amplified expression via MITF. CRISPR-mediated targeted missense mutation of CA14 in zebrafish results in the formation of immature acidic melanocytes with decreased pigmentation, establishing a central role for this mechanism during melanocyte differentiation in vivo. Thus, we describe an epigenetic control system via pH modulation that reinforces cell fate determination by altering chromatin dynamics.
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Affiliation(s)
- Desingu Ayyappa Raja
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Vishvabandhu Gotherwal
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Shaunak A Burse
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Yogaspoorthi J Subramaniam
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Farina Sultan
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Archana Vats
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
| | - Hemlata Gautam
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
| | - Babita Sharma
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Sachin Sharma
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
- Present address:
National Institute of ImmunologyNew DelhiIndia
| | - Archana Singh
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | | | - Rajesh S Gokhale
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Present address:
National Institute of ImmunologyNew DelhiIndia
| | - Vivek T Natarajan
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
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10
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Grover R, Burse SA, Shankrit S, Aggarwal A, Kirty K, Narta K, Srivastav R, Ray AK, Malik G, Vats A, Motiani RK, Thukral L, Roy SS, Bhattacharya S, Sharma R, Natarajan K, Mukerji M, Pandey R, Gokhale RS, Natarajan VT. Myg1 exonuclease couples the nuclear and mitochondrial translational programs through RNA processing. Nucleic Acids Res 2019; 47:5852-5866. [PMID: 31081026 PMCID: PMC6582341 DOI: 10.1093/nar/gkz371] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 09/12/2018] [Revised: 04/12/2019] [Accepted: 04/30/2019] [Indexed: 01/25/2023] Open
Abstract
Semi-autonomous functioning of mitochondria in eukaryotic cell necessitates coordination with nucleus. Several RNA species fine-tune mitochondrial processes by synchronizing with the nuclear program, however the involved components remain enigmatic. In this study, we identify a widely conserved dually localized protein Myg1, and establish its role as a 3′-5′ RNA exonuclease. We employ mouse melanoma cells, and knockout of the Myg1 ortholog in Saccharomyces cerevisiae with complementation using human Myg1 to decipher the conserved role of Myg1 in selective RNA processing. Localization of Myg1 to nucleolus and mitochondrial matrix was studied through imaging and confirmed by sub-cellular fractionation studies. We developed Silexoseqencing, a methodology to map the RNAse trail at single-nucleotide resolution, and identified in situ cleavage by Myg1 on specific transcripts in the two organelles. In nucleolus, Myg1 processes pre-ribosomal RNA involved in ribosome assembly and alters cytoplasmic translation. In mitochondrial matrix, Myg1 processes 3′-termini of the mito-ribosomal and messenger RNAs and controls translation of mitochondrial proteins. We provide a molecular link to the possible involvement of Myg1 in chronic depigmenting disorder vitiligo. Our study identifies a key component involved in regulating spatially segregated organellar RNA processing and establishes the evolutionarily conserved ribonuclease as a coordinator of nucleo-mitochondrial crosstalk.
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Affiliation(s)
- Ritika Grover
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shaunak A Burse
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shambhavi Shankrit
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ayush Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Kritika Kirty
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kiran Narta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajpal Srivastav
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ashwini Kumar Ray
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Garima Malik
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Archana Vats
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajender K Motiani
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Soumya Sinha Roy
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Sudha Bhattacharya
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | | | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
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11
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Vaish U, Kumar AA, Varshney S, Ghosh S, Sengupta S, Sood C, Kar HK, Sharma P, Natarajan VT, Gokhale RS, Rani R. Micro RNAs upregulated in Vitiligo skin play an important role in its aetiopathogenesis by altering TRP1 expression and keratinocyte-melanocytes cross-talk. Sci Rep 2019; 9:10079. [PMID: 31300697 PMCID: PMC6625998 DOI: 10.1038/s41598-019-46529-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 11/30/2018] [Accepted: 07/01/2019] [Indexed: 01/20/2023] Open
Abstract
Translation of genes is regulated by many factors including microRNAs (miRNAs). miRNA profiling of lesional and non-lesional epidermal RNA from 18 vitiligo patients revealed significant upregulation of 29 miRNAs in the lesional epidermis, of which 6 miRNAs were transfected in normal human epidermal keratinocytes (NHEKs) to study their downstream effects using quantitative proteomics. Many proteins involved in oxidative stress, Vesicle trafficking, Cellular apoptosis, Mitochondrial proteins and Keratins were regulated after miRNA transfections in the keratinocytes. However, tyrosinase related protein-1 (TRP1/TYRP1), a melanogenesis protein, was consistently downregulated in NHEKs by all the six miRNAs tested, which was quite intriguing. TRP1 was also downregulated in lesional epidermis compared with non-lesional epidermis. Since melanocytes synthesize and transfer melanosomes to the surrounding keratinocytes, we hypothesized that downregulation of TRP1 in NHEKs may have a role in melanosome transfer, which was confirmed by our co-culture experiments. Downregulation of TRP1 in keratinocytes negatively affected the melanosome transfer from melanocytes to keratinocytes resulting in melanin accumulation which may be leading to melanin induced cytotoxicity in melanocytes. Regulation of key processes involved in aetiopathogenesis of vitiligo along with TRP1 suggests that miRNAs act in an integrated manner which may be detrimental for the loss of melanocytes in vitiligo.
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Affiliation(s)
| | | | - Swati Varshney
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Shreya Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Chandni Sood
- National Institute of Immunology, New Delhi, 110067, India
| | - Hemanta K Kar
- Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - Pankaj Sharma
- Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Rajesh S Gokhale
- National Institute of Immunology, New Delhi, 110067, India.,CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Rajni Rani
- National Institute of Immunology, New Delhi, 110067, India.
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12
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Gupta I, Narang A, Singh P, Manchanda V, Khanna S, Mukerji M, Natarajan VT, Dash D. VitiVar: A locus specific database of vitiligo associated genes and variations. Gene 2019; 721S:100018. [PMID: 32550548 PMCID: PMC7286000 DOI: 10.1016/j.gene.2019.100018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 12/31/2018] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 12/17/2022]
Abstract
Vitiligo is the most common skin pigmentation disorder which affects around 1% of the population worldwide. The disease has complex pathogenesis and is of multifactorial etiology, that finally culminates in patchy depigmentation of skin. Genetic contribution to the disease is well studied, however the information about multiple associated genes and contributing variations are scattered across the literature. To address this complex disorder affecting the skin, we systematically cataloged the genes and variations by creating a Locus Specific Database for vitiligo called, “VitiVar”. This comprehensive resource houses manually curated 322 genes and 254 variations, from 202 articles indexed in PubMed. We applied an integrative approach to stratify genes and variations to facilitate dissection of vitiligo pathogenesis by layering it with expression status in specific constituent cell types of skin and in-house vitiligo expression data. Finally, we were able to demonstrate the utility of VitiVar by generating a vitiligo interactome using GeneMANIA and overlaying the vitiligo and cell type specific information. This interaction network yielded 20 new genes (apart from 322 VitiVar genes) of which we were able to prioritize IFI27 and IFI6 for further validation. This, thereby makes VitiVar a comprehensive integrative platform in unravelling disease biology by providing meaningful leads for functional interrogation. VitiVar is freely accessible to the research community for prioritizing and validating the candidate genes and variations (http://vitivar.igib.res.in/). We developed a Vitiligo centric web resource cataloguing the associated genes and variations Overlaid the information of cell type specificity and expression status in Vitiliginous skin Utilizing the network approach, we prioritized IFI6 & IFI27 which could be functionally interrogated in disease pathology
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Affiliation(s)
- Iti Gupta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR Campus, CSIR Road, Chennai, India
| | - Ankita Narang
- CSIR's Ayurgenomics Unit - TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-IGIB, Mathura Road, Delhi, India
| | - Prateek Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR Campus, CSIR Road, Chennai, India
| | - Vijeta Manchanda
- CSIR's Ayurgenomics Unit - TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-IGIB, Mathura Road, Delhi, India
| | - Sangeeta Khanna
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
| | | | - Mitali Mukerji
- CSIR's Ayurgenomics Unit - TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-IGIB, Mathura Road, Delhi, India
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
| | - Vivek T. Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR Campus, CSIR Road, Chennai, India
- Correspondence to: V. T Natarajan, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India.
| | - Debasis Dash
- CSIR's Ayurgenomics Unit - TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-IGIB, Mathura Road, Delhi, India
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR Campus, CSIR Road, Chennai, India
- Correspondence to: D. Dash, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India.
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13
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Motiani RK, Tanwar J, Raja DA, Vashisht A, Khanna S, Sharma S, Srivastava S, Sivasubbu S, Natarajan VT, Gokhale RS. STIM1 activation of adenylyl cyclase 6 connects Ca 2+ and cAMP signaling during melanogenesis. EMBO J 2018; 37:embj.201797597. [PMID: 29311116 DOI: 10.15252/embj.201797597] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/29/2017] [Accepted: 12/06/2017] [Indexed: 11/09/2022] Open
Abstract
Endoplasmic reticulum (ER)-plasma membrane (PM) junctions form functionally active microdomains that connect intracellular and extracellular environments. While the key role of these interfaces in maintenance of intracellular Ca2+ levels has been uncovered in recent years, the functional significance of ER-PM junctions in non-excitable cells has remained unclear. Here, we show that the ER calcium sensor protein STIM1 (stromal interaction molecule 1) interacts with the plasma membrane-localized adenylyl cyclase 6 (ADCY6) to govern melanogenesis. The physiological stimulus α-melanocyte-stimulating hormone (αMSH) depletes ER Ca2+ stores, thus recruiting STIM1 to ER-PM junctions, which in turn activates ADCY6. Using zebrafish as a model system, we further established STIM1's significance in regulating pigmentation in vivo STIM1 domain deletion studies reveal the importance of Ser/Pro-rich C-terminal region in this interaction. This mechanism of cAMP generation creates a positive feedback loop, controlling the output of the classical αMSH-cAMP-MITF axis in melanocytes. Our study thus delineates a signaling module that couples two fundamental secondary messengers to drive pigmentation. Given the central role of calcium and cAMP signaling pathways, this module may be operative during various other physiological processes and pathological conditions.
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Affiliation(s)
- Rajender K Motiani
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Jyoti Tanwar
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Desingu Ayyappa Raja
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Ayushi Vashisht
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shivangi Khanna
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Sachin Sharma
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Sonali Srivastava
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sridhar Sivasubbu
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Vivek T Natarajan
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Rajesh S Gokhale
- Systems Biology Group, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
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14
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Dani P, Patnaik N, Singh A, Jaiswal A, Agrawal B, Kumar AA, Varkhande SR, Sharma A, Vaish U, Ghosh P, Sharma VK, Sharma P, Verma G, Kar HK, Gupta S, Natarajan VT, Gokhale RS, Rani R. Association and expression of the antigen-processing gene PSMB8, coding for low-molecular-mass protease 7, with vitiligo in North India: case-control study. Br J Dermatol 2017; 178:482-491. [PMID: 28207947 DOI: 10.1111/bjd.15391] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND Vitiligo is a multifactorial, autoimmune, depigmenting disorder of the skin where aberrant presentation of autoantigens may have a role. OBJECTIVES To study the association of two antigen-processing genes, PSMB8 and PSMB9, with vitiligo. METHODS In total 1320 cases of vitiligo (1050 generalized and 270 localized) and 752 healthy controls were studied for the PSMB9 exon 3 G/A single-nucleotide polymorphism (SNP), PSMB8 exon 2 C/A SNP and PSMB8 intron 6 G/T SNP at site 37 360 using polymerase chain reaction (PCR)-restriction fragment length polymorphism. Real-time PCR was used for transcriptional expression of PSMB8 and cytokines. Expression of ubiquitinated proteins and phosphorylated-p38 (P-p38) was studied by Western blotting. RESULTS Significant increases in PSMB8 exon 2 allele A (P < 2.07 × 10-6 , odds ratio 1·93) and genotypes AA (P < 1.03 × 10-6 , odds ratio 2·51) and AC (P < 1.29 × 10-6 , odds ratio 1·63) were observed in patients with vitiligo. Interferon-γ stimulation induced lower expression of PSMB8 in peripheral blood mononuclear cells of cases compared with controls, suggesting impaired antigen processing, which was confirmed by accumulation of ubiquitinated proteins in both lesional and nonlesional skin of patients with vitiligo. Expression of proinflammatory cytokines - interleukin (IL)-6, IL-1β and IL-8 - was higher in the lesional skin. P-p38 expression was variable but correlated with the amount of ubiquitinated proteins in the lesional and nonlesional skin, suggesting that the inflammatory cytokine responses in lesional skin could be a result of both P-p38-dependent and -independent pathways. CONCLUSIONS The PSMB8 exon 2 SNP is significantly associated with vitiligo. Accumulation of ubiquitinated proteins in skin of cases of vitiligo suggests their aberrant processing, which may promote the development of the disease.
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Affiliation(s)
- P Dani
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India
| | - N Patnaik
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India
| | - A Singh
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India.,Systems Biology Group, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - A Jaiswal
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India
| | - B Agrawal
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India
| | - A A Kumar
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India
| | - S R Varkhande
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India
| | - A Sharma
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India
| | - U Vaish
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India
| | - P Ghosh
- Systems Biology Group, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - V K Sharma
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - P Sharma
- Department of Dermatology, PGIMER, Dr Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - G Verma
- Department of Dermatology, PGIMER, Dr Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - H K Kar
- Department of Dermatology, PGIMER, Dr Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - S Gupta
- Department of Dermatology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - V T Natarajan
- Systems Biology Group, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - R S Gokhale
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India.,Systems Biology Group, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - R Rani
- Molecular Immunogenetics Group, National Institute of Immunology, New Delhi, 110067, India.,Systems Biology Group, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110025, India
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15
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Singh A, Gotherwal V, Junni P, Vijayan V, Tiwari M, Ganju P, Kumar A, Sharma P, Fatima T, Gupta A, Holla A, Kar HK, Khanna S, Thukral L, Malik G, Natarajan K, Gadgil CJ, Lahesmaa R, Natarajan VT, Rani R, Gokhale RS. Mapping architectural and transcriptional alterations in non-lesional and lesional epidermis in vitiligo. Sci Rep 2017; 7:9860. [PMID: 28852211 PMCID: PMC5575244 DOI: 10.1038/s41598-017-10253-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 04/19/2017] [Accepted: 08/08/2017] [Indexed: 01/31/2023] Open
Abstract
In vitiligo, chronic loss of melanocytes and consequent absence of melanin from the epidermis presents a challenge for long-term tissue maintenance. The stable vitiligo patches are known to attain an irreversible depigmented state. However, the molecular and cellular processes resulting in this remodeled tissue homeostasis is unclear. To investigate the complex interplay of inductive signals and cell intrinsic factors that support the new acquired state, we compared the matched lesional and non-lesional epidermis obtained from stable non-segmental vitiligo subjects. Hierarchical clustering of genome-wide expression of transcripts surprisingly segregated lesional and non-lesional samples in two distinct clades, despite the apparent heterogeneity in the lesions of different vitiligo subjects. Pathway enrichment showed the expected downregulation of melanogenic pathway and a significant downregulation of cornification and keratinocyte differentiation processes. These perturbations could indeed be recapitulated in the lesional epidermal tissue, including blunting of rete-ridges, thickening of stratum corneum and increase in the size of corneocytes. In addition, we identify marked increase in the putrescine levels due to the elevated expression of spermine/spermidine acetyl transferase. Our study provides insights into the intrinsic self-renewing ability of damaged lesional tissue to restore epidermal functionality in vitiligo.
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Affiliation(s)
- Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Vishvabandhu Gotherwal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Päivi Junni
- Turku Centre for Biotechnology, University of Turku and ÅboAkademi University, Turku, Finland
| | - Vinaya Vijayan
- CSIR-National Chemical Laboratory, Chemical Engineering Division, Pune, India
| | - Manisha Tiwari
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Parul Ganju
- National Institute of Immunology, ArunaAsaf Ali Marg, New Delhi, India
| | - Avinash Kumar
- National Institute of Immunology, ArunaAsaf Ali Marg, New Delhi, India
| | - Pankaj Sharma
- Department of Dermatology, Post Graduate Institute for Medical Education and Research (PGIMER), Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Tanveer Fatima
- Department of Dermatology, Post Graduate Institute for Medical Education and Research (PGIMER), Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D. Y. Patil Medical College, Pimpri, Pune, India
| | - Ananthaprasad Holla
- MelanoSite, Center for Advanced Vitiligo Treatment and Collaborative Pigment Cell Research, New Delhi, India
| | - Hemanta K Kar
- Department of Dermatology, Post Graduate Institute for Medical Education and Research (PGIMER), Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Sangeeta Khanna
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Garima Malik
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | | | - Chetan J Gadgil
- CSIR-National Chemical Laboratory, Chemical Engineering Division, Pune, India
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and ÅboAkademi University, Turku, Finland
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India. .,Academy of Scientific and Innovative Research, New Delhi, India.
| | - Rajni Rani
- National Institute of Immunology, ArunaAsaf Ali Marg, New Delhi, India.
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India. .,National Institute of Immunology, ArunaAsaf Ali Marg, New Delhi, India. .,CSIR-National Chemical Laboratory, Chemical Engineering Division, Pune, India. .,Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India.
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Ramkumar A, Murthy D, Raja DA, Singh A, Krishnan A, Khanna S, Vats A, Thukral L, Sharma P, Sivasubbu S, Rani R, Natarajan VT, Gokhale RS. Classical autophagy proteins LC3B and ATG4B facilitate melanosome movement on cytoskeletal tracks. Autophagy 2017; 13:1331-1347. [PMID: 28598240 DOI: 10.1080/15548627.2017.1327509] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macroautophagy/autophagy is a dynamic and inducible catabolic process that responds to a variety of hormonal and environmental cues. Recent studies highlight the interplay of this central pathway in a variety of pathophysiological diseases. Although defective autophagy is implicated in melanocyte proliferation and pigmentary disorders, the mechanistic relationship between the 2 pathways has not been elucidated. In this study, we show that autophagic proteins LC3B and ATG4B mediate melanosome trafficking on cytoskeletal tracks. While studying melanogenesis, we observed spatial segregation of LC3B-labeled melanosomes with preferential absence at the dendritic ends of melanocytes. This LC3B labeling of melanosomes did not impact the steady-state levels of these organelles but instead facilitated their intracellular positioning. Melanosomes primarily traverse on microtubule and actin cytoskeletal tracks and our studies reveal that LC3B enables the assembly of microtubule translocon complex. At the microtubule-actin crossover junction, ATG4B detaches LC3B from melanosomal membranes by enzymatic delipidation. Further, by live-imaging we show that melanosomes transferred to keratinocytes lack melanocyte-specific LC3B. Our study thus elucidates a new role for autophagy proteins in directing melanosome movement and reveal the unconventional use of these proteins in cellular trafficking pathways. Such crosstalk between the central cellular function and housekeeping pathway may be a crucial mechanism to balance melanocyte bioenergetics and homeostasis.
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Affiliation(s)
- Amrita Ramkumar
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India.,b Academy of Scientific and Innovative Research , Rafi Marg, New Delhi , India
| | - Divya Murthy
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India
| | - Desingu Ayyappa Raja
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India.,b Academy of Scientific and Innovative Research , Rafi Marg, New Delhi , India
| | - Archana Singh
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India
| | - Anusha Krishnan
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India.,b Academy of Scientific and Innovative Research , Rafi Marg, New Delhi , India
| | - Sangeeta Khanna
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India
| | - Archana Vats
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India
| | - Lipi Thukral
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India
| | - Pushkar Sharma
- c National Institute of Immunology , Aruna Asaf Ali Marg, New Delhi , India
| | - Sridhar Sivasubbu
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India
| | - Rajni Rani
- c National Institute of Immunology , Aruna Asaf Ali Marg, New Delhi , India
| | - Vivek T Natarajan
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India.,b Academy of Scientific and Innovative Research , Rafi Marg, New Delhi , India
| | - Rajesh S Gokhale
- a CSIR- Institute of Genomics and Integrative Biology , Mathura Road, New Delhi , India.,b Academy of Scientific and Innovative Research , Rafi Marg, New Delhi , India.,c National Institute of Immunology , Aruna Asaf Ali Marg, New Delhi , India.,d Jawaharlal Nehru Center for Advanced Scientific Research , Jakkur, Bangalore , India
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Vij M, Alam S, Gupta N, Gotherwal V, Gautam H, Ansari KM, Santhiya D, Natarajan VT, Ganguli M. Non-invasive Oil-Based Method to Increase Topical Delivery of Nucleic Acids to Skin. Mol Ther 2017; 25:1342-1352. [PMID: 28366765 DOI: 10.1016/j.ymthe.2017.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 06/07/2016] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 10/19/2022] Open
Abstract
Topical delivery of nucleic acids to skin has huge prospects in developing therapeutic interventions for cutaneous disorders. In spite of initial success, clinical translation is vastly impeded by the constraints of bioavailability as well as stability in metabolically active environment of skin. Various physical and chemical methods used to overcome these limitations involve invasive procedures or compounds that compromise skin integrity. Hence, there is an increasing demand for developing safe skin penetration enhancers for efficient nucleic acid delivery to skin. Here, we demonstrate that pretreatment of skin with silicone oil can increase the transfection efficiency of non-covalently associated peptide-plasmid DNA nanocomplexes in skin ex vivo and in vivo. The method does not compromise skin integrity, as indicated by microscopic evaluation of cellular differentiation, tissue architecture, enzyme activity assessment, dye penetration tests using Franz assay, and cytotoxicity and immunogenicity analyses. Stability of nanocomplexes is not hampered on pretreatment, thereby avoiding nuclease-mediated degradation. The mechanistic insights through Fourier transform infrared (FTIR) spectroscopy reveal some alterations in the skin hydration status owing to possible occlusion effects of the enhancer. Overall, we describe a topical, non-invasive, efficient, and safe method that can be used to increase the penetration and delivery of plasmid DNA to skin for possible therapeutic applications.
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Affiliation(s)
- Manika Vij
- CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Shamshad Alam
- CSIR-Indian Institute of Toxicology Research, Post Box 80, Mahatma Gandhi Marg, Lucknow (Uttar Pradesh) 226001, India
| | - Nidhi Gupta
- Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, New Delhi 110042, India
| | - Vishvabandhu Gotherwal
- CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Hemlata Gautam
- CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India
| | - Kausar M Ansari
- CSIR-Indian Institute of Toxicology Research, Post Box 80, Mahatma Gandhi Marg, Lucknow (Uttar Pradesh) 226001, India
| | - Deenan Santhiya
- Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, New Delhi 110042, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Munia Ganguli
- CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India.
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Singh J, Joshi S, Mumtaz S, Maurya N, Ghosh I, Khanna S, Natarajan VT, Mukhopadhyay K. Enhanced Cationic Charge is a Key Factor in Promoting Staphylocidal Activity of α-Melanocyte Stimulating Hormone via Selective Lipid Affinity. Sci Rep 2016; 6:31492. [PMID: 27526963 PMCID: PMC4985751 DOI: 10.1038/srep31492] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 03/23/2016] [Accepted: 07/20/2016] [Indexed: 02/07/2023] Open
Abstract
The steady rise in antimicrobial resistance poses a severe threat to global public health by hindering treatment of an escalating spectrum of infections. We have previously established the potent activity of α-MSH, a 13 residue antimicrobial peptide, against the opportunistic pathogen Staphylococcus aureus. Here, we sought to determine whether an increase in cationic charge in α-MSH could contribute towards improving its staphylocidal potential by increasing its interaction with anionic bacterial membranes. For this we designed novel α-MSH analogues by replacing polar uncharged residues with lysine and alanine. Similar to α-MSH, the designed peptides preserved turn/random coil conformation in artificial bacterial mimic 1,2-dimyristoyl-sn-glycero-3-phosphocholine:1,2-dimyristoyl-sn-glycero-3-phospho-rac-(1-glycerol) (7:3, w/w) vesicles and showed preferential insertion in the hydrophobic core of anionic membranes. Increased cationic charge resulted in considerable augmentation of antibacterial potency against MSSA and MRSA. With ~18-fold better binding than α-MSH to bacterial mimic vesicles, the most charged peptide KKK-MSH showed enhanced membrane permeabilization and depolarization activity against intact S. aureus. Scanning electron microscopy confirmed a membrane disruptive mode of action for KKK-MSH. Overall, increasing the cationic charge improved the staphylocidal activity of α-MSH without compromising its cell selectivity. The present study would help in designing more effective α-MSH-based peptides to combat clinically relevant staphylococcal infections.
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Affiliation(s)
- Jyotsna Singh
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Seema Joshi
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Sana Mumtaz
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Nancy Maurya
- Biochemistry and Environmental Toxicology Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Ilora Ghosh
- Biochemistry and Environmental Toxicology Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Shivangi Khanna
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110020, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110020, India
| | - Kasturi Mukhopadhyay
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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Vij M, Grover R, Gotherwal V, Wani NA, Joshi P, Gautam H, Sharma K, Chandna S, Gokhale RS, Rai R, Ganguli M, Natarajan VT. Bioinspired Functionalized Melanin Nanovariants with a Range of Properties Provide Effective Color Matched Photoprotection in Skin. Biomacromolecules 2016; 17:2912-9. [DOI: 10.1021/acs.biomac.6b00740] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Manika Vij
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 020, India
- Academy of Scientific and Innovative research, CSIR campus, CSIR Road, Chennai 600113, India
| | - Ritika Grover
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 020, India
- Academy of Scientific and Innovative research, CSIR campus, CSIR Road, Chennai 600113, India
| | - Vishvabandhu Gotherwal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 020, India
- Academy of Scientific and Innovative research, CSIR campus, CSIR Road, Chennai 600113, India
| | - Naiem Ahmad Wani
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Prashant Joshi
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Hemlata Gautam
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 020, India
| | - Kanupriya Sharma
- Institute of Nuclear Medicine and Allied Sciences, Brig. SK Mazumdar Road, Delhi 110054, India
| | - Sudhir Chandna
- Institute of Nuclear Medicine and Allied Sciences, Brig. SK Mazumdar Road, Delhi 110054, India
| | - Rajesh S. Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 020, India
- Academy of Scientific and Innovative research, CSIR campus, CSIR Road, Chennai 600113, India
- National Institute of Immunology, Aruna Asaf Ali Marg, Delhi 110067, India
| | - Rajkishor Rai
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Munia Ganguli
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 020, India
- Academy of Scientific and Innovative research, CSIR campus, CSIR Road, Chennai 600113, India
| | - Vivek T. Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 020, India
- Academy of Scientific and Innovative research, CSIR campus, CSIR Road, Chennai 600113, India
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20
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Singh VP, Motiani RK, Singh A, Malik G, Aggarwal R, Pratap K, Wani MR, Gokhale SB, Natarajan VT, Gokhale RS. Water Buffalo (Bubalus bubalis) as a spontaneous animal model of Vitiligo. Pigment Cell Melanoma Res 2016; 29:465-9. [DOI: 10.1111/pcmr.12485] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 04/21/2016] [Indexed: 01/20/2023]
Affiliation(s)
- Vijay Pal Singh
- Systems Biology Group; CSIR-Institute of Genomics and Integrative Biology; New Delhi India
| | - Rajender K. Motiani
- Systems Biology Group; CSIR-Institute of Genomics and Integrative Biology; New Delhi India
| | - Archana Singh
- Systems Biology Group; CSIR-Institute of Genomics and Integrative Biology; New Delhi India
| | - Garima Malik
- Systems Biology Group; CSIR-Institute of Genomics and Integrative Biology; New Delhi India
| | - Rangoli Aggarwal
- Systems Biology Group; CSIR-Institute of Genomics and Integrative Biology; New Delhi India
| | - Kunal Pratap
- Systems Biology Group; CSIR-Institute of Genomics and Integrative Biology; New Delhi India
| | | | | | - Vivek T. Natarajan
- Systems Biology Group; CSIR-Institute of Genomics and Integrative Biology; New Delhi India
- Academy of Scientific and Innovative Research; New Delhi India
| | - Rajesh S. Gokhale
- Systems Biology Group; CSIR-Institute of Genomics and Integrative Biology; New Delhi India
- Academy of Scientific and Innovative Research; New Delhi India
- National Institute of Immunology; New Delhi India
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21
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Vij M, Natarajan P, Pattnaik BR, Alam S, Gupta N, Santhiya D, Sharma R, Singh A, Ansari KM, Gokhale RS, Natarajan VT, Ganguli M. Non-invasive topical delivery of plasmid DNA to the skin using a peptide carrier. J Control Release 2016; 222:159-68. [DOI: 10.1016/j.jconrel.2015.12.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/25/2015] [Accepted: 12/12/2015] [Indexed: 01/18/2023]
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Anand A, Verma P, Singh AK, Kaushik S, Pandey R, Shi C, Kaur H, Chawla M, Elechalawar CK, Kumar D, Yang Y, Bhavesh NS, Banerjee R, Dash D, Singh A, Natarajan VT, Ojha AK, Aldrich CC, Gokhale RS. Polyketide Quinones Are Alternate Intermediate Electron Carriers during Mycobacterial Respiration in Oxygen-Deficient Niches. Mol Cell 2015; 60:637-50. [PMID: 26585386 DOI: 10.1016/j.molcel.2015.10.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 08/24/2015] [Accepted: 10/08/2015] [Indexed: 11/16/2022]
Abstract
Mycobacterium tuberculosis (Mtb) adaptation to hypoxia is considered crucial to its prolonged latent persistence in humans. Mtb lesions are known to contain physiologically heterogeneous microenvironments that bring about differential responses from bacteria. Here we exploit metabolic variability within biofilm cells to identify alternate respiratory polyketide quinones (PkQs) from both Mycobacterium smegmatis (Msmeg) and Mtb. PkQs are specifically expressed in biofilms and other oxygen-deficient niches to maintain cellular bioenergetics. Under such conditions, these metabolites function as mobile electron carriers in the respiratory electron transport chain. In the absence of PkQs, mycobacteria escape from the hypoxic core of biofilms and prefer oxygen-rich conditions. Unlike the ubiquitous isoprenoid pathway for the biosynthesis of respiratory quinones, PkQs are produced by type III polyketide synthases using fatty acyl-CoA precursors. The biosynthetic pathway is conserved in several other bacterial genomes, and our study reveals a redox-balancing chemicocellular process in microbial physiology.
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Affiliation(s)
- Amitesh Anand
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India
| | - Priyanka Verma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anil Kumar Singh
- CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Sandeep Kaushik
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Ce Shi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Harneet Kaur
- Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA
| | - Manbeena Chawla
- Department of Microbiology and Cell Biology, Centre for Infectious Disease and Research, Indian Institute of Science, Bangalore 560012, India
| | - Chandra Kumar Elechalawar
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India; CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Dhirendra Kumar
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Yong Yang
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Neel S Bhavesh
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Rajkumar Banerjee
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India; CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease and Research, Indian Institute of Science, Bangalore 560012, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Anil K Ojha
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India; National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Gupta A, Sharma Y, Dash KN, Verma S, Natarajan VT, Singh A. Ultrastructural Investigations in an Autosomal Recessively Inherited Case of Dyschromatosis Universalis Hereditaria. Acta Derm Venereol 2015; 95:738-40. [PMID: 25474346 DOI: 10.2340/00015555-2030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Aayush Gupta
- Department Of Dermatology, Leprology and Venereology, Dr. D.Y. Patil Medical College, Pimpri, Pune, India
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Gautam P, Chaurasia A, Bhattacharya A, Grover R, Mukerji M, Natarajan VT. Population diversity and adaptive evolution in keratinization genes: impact of environment in shaping skin phenotypes. Mol Biol Evol 2014; 32:555-73. [PMID: 25534032 DOI: 10.1093/molbev/msu342] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations.
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Affiliation(s)
- Pramod Gautam
- Genomics and Molecular Medicine, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Amit Chaurasia
- Genomics and Molecular Medicine, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Aniket Bhattacharya
- Genomics and Molecular Medicine, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India Academy of Scientific and Innovative Research, Delhi, India
| | - Ritika Grover
- Academy of Scientific and Innovative Research, Delhi, India Systems Biology Group, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Mitali Mukerji
- Genomics and Molecular Medicine, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India Academy of Scientific and Innovative Research, Delhi, India
| | - Vivek T Natarajan
- Academy of Scientific and Innovative Research, Delhi, India Systems Biology Group, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
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Natarajan VT, Ganju P, Ramkumar A, Grover R, Gokhale RS. Multifaceted pathways protect human skin from UV radiation. Nat Chem Biol 2014; 10:542-51. [DOI: 10.1038/nchembio.1548] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/02/2014] [Indexed: 02/07/2023]
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26
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Natarajan VT, Singh A, Kumar AA, Sharma P, Kar HK, Marrot L, Meunier JR, Natarajan K, Rani R, Gokhale RS. Transcriptional Upregulation of Nrf2-Dependent Phase II Detoxification Genes in the Involved Epidermis of Vitiligo Vulgaris. J Invest Dermatol 2010; 130:2781-9. [DOI: 10.1038/jid.2010.201] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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Arora P, Goyal A, Natarajan VT, Rajakumara E, Verma P, Gupta R, Yousuf M, Trivedi OA, Mohanty D, Tyagi A, Sankaranarayanan R, Gokhale RS. Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis. Nat Chem Biol 2009; 5:166-73. [PMID: 19182784 PMCID: PMC2644305 DOI: 10.1038/nchembio.143] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [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: 07/29/2008] [Accepted: 01/02/2009] [Indexed: 11/29/2022]
Abstract
The recent discovery of fatty acyl-AMP ligases (FAALs) in Mycobacterium tuberculosis (Mtb) provided a new perspective to fatty acid activation dogma. These proteins convert fatty acids to corresponding adenylates, which is an intermediate of acyl-CoA-synthesizing fatty acyl-CoA ligases (FACLs). Presently, it is not evident how obligate pathogens like Mtb have evolved such new themes of functional versatility and whether the activation of fatty acids to acyl-adenylates could indeed be a general mechanism. Here, based on elucidation of the first structure of a FAAL protein and by generating loss- as well as gain-of-function mutants that interconvert FAAL and FACL activities, we demonstrate that an insertion motif dictates formation of acyl-adenylate. Since FAALs in Mtb are crucial nodes in biosynthetic network of virulent lipids, inhibitors directed against these proteins provide a unique multi-pronged approach of simultaneously disrupting several pathways.
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Affiliation(s)
- Pooja Arora
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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