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Agrawal P, Tiwari A, Chowdhury SK, Vohra M, Gour A, Waghmare N, Bhutani U, Kamalnath S, Sangwan B, Rajput J, Raj R, Rajendran NP, Kamath AV, Haddadin R, Chandru A, Sangwan VS, Bhowmick T. Kuragel: A biomimetic hydrogel scaffold designed to promote corneal regeneration. iScience 2024; 27:109641. [PMID: 38646166 PMCID: PMC11031829 DOI: 10.1016/j.isci.2024.109641] [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: 09/07/2023] [Revised: 01/30/2024] [Accepted: 03/26/2024] [Indexed: 04/23/2024] Open
Abstract
Cornea-related injuries are the most common cause of blindness worldwide. Transplantation remains the primary approach for addressing corneal blindness, though the demand for donor corneas outmatches the supply by millions. Tissue adhesives employed to seal corneal wounds have shown inefficient healing and incomplete vision restoration. We have developed a biodegradable hydrogel - Kuragel, with the ability to promote corneal regeneration. Functionalized gelatin and hyaluronic acid form photo-crosslinkable hydrogel with transparency and compressive modulus similar to healthy human cornea. Kuragel composition was tuned to achieve sufficient adhesive strength for sutureless integration to host tissue, with minimal swelling post-administration. Studies in the New Zealand rabbit mechanical injury model affecting corneal epithelium and stroma demonstrate that Kuragel efficiently promotes re-epithelialization within 1 month of administration, while stroma and sub-basal nerve plexus regenerate within 3 months. We propose Kuragel as a regenerative treatment for patients suffering from corneal defects including thinning, by restoration of transparency and thickness.
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Affiliation(s)
| | - Anil Tiwari
- Pandorum Technologies Pvt., Ltd, Bangalore, India
- Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | | | - Mehak Vohra
- Pandorum Technologies Pvt., Ltd, Bangalore, India
| | - Abha Gour
- Pandorum Technologies Pvt., Ltd, Bangalore, India
- Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | | | | | - S. Kamalnath
- Pandorum Technologies Pvt., Ltd, Bangalore, India
| | | | - Jyoti Rajput
- Pandorum Technologies Pvt., Ltd, Bangalore, India
| | - Ritu Raj
- Pandorum Technologies Pvt., Ltd, Bangalore, India
| | | | | | - Ramez Haddadin
- Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Arun Chandru
- Pandorum Technologies Pvt., Ltd, Bangalore, India
| | | | - Tuhin Bhowmick
- Pandorum Technologies Pvt., Ltd, Bangalore, India
- Pandorum International Inc, San Francisco, CA, USA
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2
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Raj R, Agrawal P, Bhutani U, Bhowmick T, Chandru A. Spinning with exosomes: electrospun nanofibers for efficient targeting of stem cell-derived exosomes in tissue regeneration. Biomed Mater 2024; 19:032004. [PMID: 38593835 DOI: 10.1088/1748-605x/ad3cab] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 04/09/2024] [Indexed: 04/11/2024]
Abstract
Electrospinning technique converts polymeric solutions into nanoscale fibers using an electric field and can be used for various biomedical and clinical applications. Extracellular vesicles (EVs) are cell-derived small lipid vesicles enriched with biological cargo (proteins and nucleic acids) potential therapeutic applications. In this review, we discuss extending the scope of electrospinning by incorporating stem cell-derived EVs, particularly exosomes, into nanofibers for their effective delivery to target tissues. The parameters used during the electrospinning of biopolymers limit the stability and functional properties of cellular products. However, with careful consideration of process requirements, these can significantly improve stability, leading to longevity, effectiveness, and sustained and localized release. Electrospun nanofibers are known to encapsulate or surface-adsorb biological payloads such as therapeutic EVs, proteins, enzymes, and nucleic acids. Small EVs, specifically exosomes, have recently attracted the attention of researchers working on regeneration and tissue engineering because of their broad distribution and enormous potential as therapeutic agents. This review focuses on current developments in nanofibers for delivering therapeutic cargo molecules, with a special emphasis on exosomes. It also suggests prospective approaches that can be adapted to safely combine these two nanoscale systems and exponentially enhance their benefits in tissue engineering, medical device coating, and drug delivery applications.
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Affiliation(s)
- Ritu Raj
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, Karnataka, India
| | - Parinita Agrawal
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, Karnataka, India
| | - Utkarsh Bhutani
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, Karnataka, India
| | - Tuhin Bhowmick
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, Karnataka, India
| | - Arun Chandru
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, Karnataka, India
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3
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Bhutani U, Dey N, Chowdhury SK, Waghmare N, Mahapatra RD, Selvakumar K, Chandru A, Bhowmick T, Agrawal P. Biopolymeric corneal lenticules by digital light processing based bioprinting: a dynamic substitute for corneal transplant. Biomed Mater 2024; 19:035017. [PMID: 38471165 DOI: 10.1088/1748-605x/ad3312] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/12/2024] [Indexed: 03/14/2024]
Abstract
Digital light processing (DLP) technology has gained significant attention for its ability to construct intricate structures for various applications in tissue modeling and regeneration. In this study, we aimed to design corneal lenticules using DLP bioprinting technology, utilizing dual network bioinks to mimic the characteristics of the human cornea. The bioink was prepared using methacrylated hyaluronic acid and methacrylated gelatin, where ruthenium salt and sodium persulfate were included for mediating photo-crosslinking while tartrazine was used as a photoabsorber. The bioprinted lenticules were optically transparent (85.45% ± 0.14%), exhibited adhesive strength (58.67 ± 17.5 kPa), and compressive modulus (535.42 ± 29.05 kPa) sufficient for supporting corneal tissue integration and regeneration. Puncture resistance tests and drag force analysis further confirmed the excellent mechanical performance of the lenticules enabling their application as potential corneal implants. Additionally, the lenticules demonstrated outstanding support for re-epithelialization and stromal regeneration when assessed with human corneal stromal cells. We generated implant ready corneal lenticules while optimizing bioink and bioprinting parameters, providing valuable solution for individuals suffering from various corneal defects and waiting for corneal transplants.
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Affiliation(s)
- Utkarsh Bhutani
- Pandorum Technologies Private Limited, Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City, Phase 1, Bengaluru 560100, India
| | - Namit Dey
- Pandorum Technologies Private Limited, Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City, Phase 1, Bengaluru 560100, India
| | - Suvro Kanti Chowdhury
- Pandorum Technologies Private Limited, Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City, Phase 1, Bengaluru 560100, India
| | - Neha Waghmare
- Pandorum Technologies Private Limited, Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City, Phase 1, Bengaluru 560100, India
| | - Rita Das Mahapatra
- Pandorum Technologies Private Limited, Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City, Phase 1, Bengaluru 560100, India
| | - Kamalnath Selvakumar
- Pandorum Technologies Private Limited, Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City, Phase 1, Bengaluru 560100, India
| | - Arun Chandru
- Pandorum Technologies Private Limited, Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City, Phase 1, Bengaluru 560100, India
| | - Tuhin Bhowmick
- Pandorum Technologies Private Limited, Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City, Phase 1, Bengaluru 560100, India
- Pandorum International Inc., San Francisco, CA, United States of America
| | - Parinita Agrawal
- Pandorum Technologies Private Limited, Bangalore Bioinnovation Centre, Helix Biotech Park, Electronic City, Phase 1, Bengaluru 560100, India
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4
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Vohra M, Gour A, Rajput J, Sangwan B, Chauhan M, Goel K, Kamath A, Mathur U, Chandru A, Sangwan VS, Bhowmick T, Tiwari A. Chemical (Alkali) Burn-Induced Neurotrophic Keratitis Model in New Zealand Rabbit Investigated Using Medical Clinical Readouts and In Vivo Confocal Microscopy (IVCM). Cells 2024; 13:379. [PMID: 38474343 DOI: 10.3390/cells13050379] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 03/14/2024] Open
Abstract
PURPOSE Chemical eye injury is an acute emergency that can result in vision loss. Neurotrophic keratitis (NK) is the most common long-term manifestation of chemical injury. NK due to alkali burn affects ocular surface health and is one of its most common causes. Here, we established a rabbit model of corneal alkali burns to evaluate the severity of NK-associated changes. MATERIAL METHODS Alkali burns were induced in NZ rabbits by treating the cornea with (i) a 5 mm circular filter paper soaked in 0.75 N NaOH for 10 s (Mild NK) and (ii) trephination using a guarded trephine (5 mm diameter and 150-micron depth), followed by alkali burn, with a 5 mm circular filter paper soaked in 0.75 N NaOH for 10 s (a severe form of NK). Immediately after, the cornea was rinsed with 10 mL of normal saline to remove traces of NaOH. Clinical features were evaluated on Day 0, Day 1, Day 7, Day 15, and Day 21 post-alkali burn using a slit lamp, Pentacam, and anterior segment optical coherence tomography (AS-OCT). NK-like changes in epithelium, sub-basal nerve plexus, and stroma were observed using in vivo confocal microscopy (IVCM), and corneal sensation were measured using an aesthesiometer post alkali injury. After 21 days, pro-inflammatory cytokines were evaluated for inflammation through ELISA. RESULTS Trephination followed by alkali burn resulted in the loss of epithelial layers (manifested using fluorescein stain), extensive edema, and increased corneal thickness (550 µm compared to 380 µm thickness of control) evaluated through AS-OCT and increased opacity score in alkali-treated rabbit (80 compared to 16 controls). IVCM images showed complete loss of nerve fibers, which failed to regenerate over 30 days, and loss of corneal sensation-conditions associated with NK. Cytokines evaluation of IL6, VEGF, and MMP9 indicated an increased angiogenic and pro-inflammatory milieu compared to the milder form of NK and the control. DISCUSSION Using clinical parameters, we demonstrated that the alkali-treated rabbit model depicts features of NK. Using IVCM in the NaOH burn animal model, we demonstrated a complete loss of nerve fibers with poor self-healing capability associated with sub-basal nerve degeneration and compromised corneal sensation. This pre-clinical rabbit model has implications for future pre-clinical research in neurotrophic keratitis.
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Affiliation(s)
- Mehak Vohra
- Shroff-Pandorum Center for Ocular Regeneration, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, India
| | - Abha Gour
- Shroff-Pandorum Center for Ocular Regeneration, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
| | - Jyoti Rajput
- Shroff-Pandorum Center for Ocular Regeneration, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, India
| | - Bharti Sangwan
- Shroff-Pandorum Center for Ocular Regeneration, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, India
| | - Monika Chauhan
- Shroff-Pandorum Center for Ocular Regeneration, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, India
| | - Kartik Goel
- Shroff-Pandorum Center for Ocular Regeneration, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, India
| | - Ajith Kamath
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, India
| | - Umang Mathur
- Shroff-Pandorum Center for Ocular Regeneration, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
| | - Arun Chandru
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, India
| | - Virender Singh Sangwan
- Shroff-Pandorum Center for Ocular Regeneration, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
| | - Tuhin Bhowmick
- Pandorum Technologies Pvt. Ltd., Bangalore 560100, India
| | - Anil Tiwari
- Shroff-Pandorum Center for Ocular Regeneration, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
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5
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Bhowmick T, Seesing J, Gustavsson K, Guettler J, Wang Y, Pumir A, Mehlig B, Bagheri G. Inertia Induces Strong Orientation Fluctuations of Nonspherical Atmospheric Particles. Phys Rev Lett 2024; 132:034101. [PMID: 38307048 DOI: 10.1103/physrevlett.132.034101] [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] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/28/2023] [Accepted: 11/22/2023] [Indexed: 02/04/2024]
Abstract
The orientation of nonspherical particles in the atmosphere, such as volcanic ash and ice crystals, influences their residence times and the radiative properties of the atmosphere. Here, we demonstrate experimentally that the orientation of heavy submillimeter spheroids settling in still air exhibits decaying oscillations, whereas it relaxes monotonically in liquids. Theoretical analysis shows that these oscillations are due to particle inertia, caused by the large particle-fluid mass-density ratio. This effect must be accounted for to model solid particles in the atmosphere.
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Affiliation(s)
- T Bhowmick
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, D-37077 Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Friedrich-Hund-Platz 1, Göttingen, D-37077 Germany
| | - J Seesing
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, D-37077 Germany
| | - K Gustavsson
- Department of Physics, Gothenburg University, Gothenburg, SE-40530 Sweden
| | - J Guettler
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, D-37077 Germany
| | - Y Wang
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, D-37077 Germany
| | - A Pumir
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, D-37077 Germany
- Laboratoire de Physique, ENS de Lyon, Université de Lyon 1 and CNRS, Lyon, F-69007 France
| | - B Mehlig
- Department of Physics, Gothenburg University, Gothenburg, SE-40530 Sweden
| | - G Bagheri
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, D-37077 Germany
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6
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Mondal M, Vohra M, Sangwan J, Verma S, Coulson-Thomas VJ, Chandru A, Bhowmick T, Sangwan VS, Acharya M, Tiwari A. In vitro Assay to Examine the Function of Tears on Corneal Epithelial Cells. Bio Protoc 2024; 14:e4910. [PMID: 38213327 PMCID: PMC10777051 DOI: 10.21769/bioprotoc.4910] [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: 04/21/2023] [Revised: 10/23/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024] Open
Abstract
Tears contain numerous secreted factors, enzymes, and proteins that help in maintaining the homeostatic condition of the eye and also protect it from the external environment. However, alterations to these enzymes and/or proteins during pathologies such as mechanical injury and viral or fungal infections can disrupt the normal ocular homeostasis, further contributing to disease development. Several tear film components have a significant role in curbing disease progression and promoting corneal regeneration. Additionally, several factors related to disease progression are secreted into the tear film, thereby serving as a valuable reservoir of biomarkers. Tears are readily available and can be collected via non-invasive techniques or simply from contact lenses. Tears can thus serve as a valuable and easy source for studying disease-specific biomarkers. Significant advancements have been made in recent years in the field of tear film proteomics, lipidomics, and transcriptomics to allow a better understanding of how tears can be utilized to gain insight into the etiology of diseases. These advancements have enabled us to study the pathophysiology of various disease states using tear samples. However, the mechanisms by which tears help to maintain corneal homeostasis and how they are able to form the first line of defense against pathogens remain poorly understood and warrant detailed in vitro studies. Herein, we have developed an in vitro assay to characterize the functional importance of patient isolated tears and their components on corneal epithelial cells. This novel approach closely mimics real physiological conditions and could help the researchers gain insight into the underlying mechanisms of ocular pathologies and develop new treatments. Key features • This method provides a new technique for analyzing the effect of tear components on human corneal epithelial cells. • The components of the tears that are altered in response to diseases can be used as a biomarker for detecting ocular complications. • This procedure can be further employed as an in vitro model for assessing the efficacy of drugs and discover potential therapeutic interventions.
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Affiliation(s)
- Moumita Mondal
- Eicher-Shroff Center for Stem Cell Research, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Mehak Vohra
- Pandorum technologies Pvt. Ltd., Bangalore, India
| | - Jyoti Sangwan
- Eicher-Shroff Center for Stem Cell Research, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Sudhir Verma
- Department of Zoology, Deen Dayal Upadhyaya College, New Delhi, India
- College of Optometry, University of Houston, Houston, TX, USA
| | | | - Arun Chandru
- Pandorum technologies Pvt. Ltd., Bangalore, India
| | | | - Virender S. Sangwan
- Eicher-Shroff Center for Stem Cell Research, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
- Department of Cornea, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Manisha Acharya
- Department of Cornea, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Anil Tiwari
- Eicher-Shroff Center for Stem Cell Research, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
- Department of Cornea, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
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7
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Tare P, Bhowmick T, Katagi G, China A, Nagaraja V. Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time. ACS Omega 2023; 8:47510-47519. [PMID: 38144119 PMCID: PMC10733919 DOI: 10.1021/acsomega.3c04754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/11/2023] [Indexed: 12/26/2023]
Abstract
RNA polymerases (RNAPs) across the bacterial kingdom have retained a conserved structure and function. In spite of the remarkable similarity of the enzyme in different bacteria, a wide variation is found in the promoter-polymerase interaction, transcription initiation, and termination. However, the transcription elongation was considered to be a monotonic process, although the rate of elongation could vary in different bacteria. Such variations in RNAP elongation rates could be important to fine-tune the transcription, which in turn would influence cellular metabolism and growth rates. Here, we describe a quantitative study to measure the transcription rates for the RNAPs from three bacteria, namely, Mycobacterium tuberculosis, Mycobacterium smegmatis, and Escherichia coli, which exhibit different growth kinetics. The RNA synthesis rates of the RNAPs were calculated from the real-time elongation kinetic profile using surface plasmon resonance through a computational flux flow model. The computational model revealed the modular process of elongation, with different rate profiles for the three RNAPs. Notably, the transcription elongation rates of these RNAPs followed the trend in the growth rates of these bacteria.
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Affiliation(s)
- Priyanka Tare
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Tuhin Bhowmick
- Department
of Physics, Indian Institute of Science, Bangalore 560012, India
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Gurunath Katagi
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Arnab China
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
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8
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Selvam S, Ben Thomas M, Bhowmick T, Chandru A. Bioprinting of exosomes: Prospects and challenges for clinical applications. Int J Bioprint 2023; 9:690. [DOI: 10.18063/ijb.690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/17/2022] [Indexed: 03/06/2023] Open
Abstract
Three-dimensional bioprinting (3DBP) is an additive manufacturing technique that has emerged as a promising strategy for the fabrication of scaffolds, which can suc¬cessfully recapitulate the architectural, biochemical, and physical cues of target tis¬sues. More importantly, 3DBP offers fine spatiotemporal control and high submicron scale resolution, which can be leveraged for the incorporation and directional gra¬dient release of single or multiple biomimetic cues, including cell-derived exosomes (EXOs). EXOs are extracellular vesicles that originate from the endosomal compart¬ment of various cell types, with sizes ranging from 30 to120 nm. They act as cell medi¬ators and contain discrete cell constituents, including growth factors, cytokines, lipid moieties, nucleic acids, metabolites, and cell surface markers, depending on the cell type. Essentially, owing to their therapeutic potential, EXOs derived from mesenchy¬mal stem cells (MSCs) have been recently investigated in several clinical trials for the treatment of various conditions, including cancer, diabetes, dry eyes, periodontitis, and acute ischemic stroke. The 3DBP strategy of EXOs is especially useful in tissue engineering and regenerative medicine applications, as tissues can be biofabricat¬ed to closely mimic the complex microarchitecture and developmental profiles of native heterogeneous tissues for restoring biological functions. Moreover, EXOs can be manipulated to carry exogenous cargo such as genes or proteins of therapeutic interest, confer multifunctional attributes, and further enhance their tissue regenera¬tive potential. However, significant challenges, including the selection of appropriate bioink, pattern resolution, engineering-defined exosomal gradient, spatial presen¬tation and modulation of EXO release kinetics, as well as EXO stability and storage conditions, must be addressed for the successful translation of therapeutic grade EXOs to clinical settings. In this review, we highlight the recent advances and offer future perspectives on the bioprinting of EXOs as regenerative biotherapeutics for the fabrication of complex heterogeneous tissues that are suitable for clinical trans¬plantation.
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9
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Dutta T, Sangwan J, Mondal M, Vohra M, Nidhi V, Gour A, Kapur N, Gupta N, Bhowmick T, Chandru A, Mathur U, Sangwan VS, Acharya M, Tiwari A. Prolonged Inflammation and Infectious Changes in the Corneal Epithelium Are Associated with Persistent Epithelial Defect (PED). Pathogens 2023; 12:pathogens12020261. [PMID: 36839533 PMCID: PMC9960897 DOI: 10.3390/pathogens12020261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/07/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Purpose: Failure of rapid re-epithelialization within 10-14 days after corneal injury, even with standard supportive treatment, is referred to as persistent corneal epithelial (CE) defect (PED). Though an array of genes regulates reepithelization, their mechanisms are poorly understood. We sought to understand the network of genes driving the re-epithelialization in PED. Method: After obtaining informed consent, patients underwent an ophthalmic examination. Epithelial scrapes and tears samples of six PED patients and six individuals (control) undergoing photorefractive keratectomy (PRK) were collected. RNA isolation and quantification were performed using either the epithelial scrape taken from PED patients or from HCLE cells treated with control tears or tears of PED patients. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect the expression of a few important genes in CE homeostasis, inflammation, and cell-cell communication, viz., Kruppel-like factor 4 (KLF4), GPX4, IL6, TNFα, STING, IL8, desmoglein, and E-cadherin, among others. Their expressions were normalized with their respective housekeeping genes and fold changes were recorded. KLF4 localization and MMPs activity was carried out via immunofluorescence and zymography, respectively. Results: KLF4, a transcription factor important for CE homeostasis, was upregulated in tears-treated HCLE cells and downregulated in PED patients compared to the healthy PRK group. Cell-cell communication genes were also upregulated in tears-treated cells, whereas they were downregulated in the PED tissue group. Genes involved in proinflammation (IL6, 282-fold; TNFα, 43-fold; IL8, 4.2-fold) were highly upregulated in both conditions. MMP9 activity increased upon tears treatment. Conclusions: This study suggests that tears create an acute proinflammatory milieu driving the PED disease pathology, whereas the PED patients scrapes are an indicator of the chronic stage of the disease. Interferons, pro-inflammatory genes, and their pathways are involved in PED, which can be a potential target for inducing epithelialization of the cornea.
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Affiliation(s)
- Tanmoy Dutta
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
- Institute of Medicine, Sahlgrenska Academy, Gothenburg University, 41345 Gothenburg, Sweden
| | - Jyoti Sangwan
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Moumita Mondal
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Mehak Vohra
- Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Vatsala Nidhi
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Abha Gour
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Neha Kapur
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Nidhi Gupta
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Tuhin Bhowmick
- Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Arun Chandru
- Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Umang Mathur
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | | | - Manisha Acharya
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Anil Tiwari
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
- Correspondence: or
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10
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Verma S, Singh A, Varshney A, Chandru RA, Acharya M, Rajput J, Sangwan VS, Tiwari AK, Bhowmick T, Tiwari A. Infectious Keratitis: An Update on Role of Epigenetics. Front Immunol 2021; 12:765890. [PMID: 34917084 PMCID: PMC8669721 DOI: 10.3389/fimmu.2021.765890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022] Open
Abstract
Epigenetic mechanisms modulate gene expression and function without altering the base sequence of DNA. These reversible, heritable, and environment-influenced mechanisms generate various cell types during development and orchestrate the cellular responses to external stimuli by regulating the expression of genome. Also, the epigenetic modifications influence common pathological and physiological responses including inflammation, ischemia, neoplasia, aging and neurodegeneration etc. In recent past, the field of epigenetics has gained momentum and become an increasingly important area of biomedical research As far as eye is concerned, epigenetic mechanisms may play an important role in many complex diseases such as corneal dystrophy, cataract, glaucoma, diabetic retinopathy, ocular neoplasia, uveitis, and age-related macular degeneration. Focusing on the epigenetic mechanisms in ocular diseases may provide new understanding and insights into the pathogenesis of complex eye diseases and thus can aid in the development of novel treatments for these diseases. In the present review, we summarize the clinical perspective of infectious keratitis, role of epigenetics in infectious keratitis, therapeutic potential of epigenetic modifiers and the future perspective.
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Affiliation(s)
- Sudhir Verma
- Department of Zoology, Deen Dayal Upadhyaya College (University of Delhi), New Delhi, India
| | - Aastha Singh
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - Akhil Varshney
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - R Arun Chandru
- Pandorum Technologies Ltd., Bangalore Bioinnovation Centre, Bangalore, India
| | - Manisha Acharya
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - Jyoti Rajput
- Pandorum Technologies Ltd., Bangalore Bioinnovation Centre, Bangalore, India
| | | | - Amit K Tiwari
- Department of Pharmacology and Experimental Therapeutics, The University of Toledo, Toledo, OH, United States
| | - Tuhin Bhowmick
- Pandorum Technologies Ltd., Bangalore Bioinnovation Centre, Bangalore, India
| | - Anil Tiwari
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
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Tiwari A, Singh A, Verma S, Stephenson S, Bhowmick T, Sangwan VS. Mini Review: Current Trends and Understanding of Exosome Therapeutic Potential in Corneal Diseases. Front Pharmacol 2021; 12:684712. [PMID: 34489693 PMCID: PMC8417240 DOI: 10.3389/fphar.2021.684712] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
Exosomes are a subset of extracellular vesicles (EVs) that are secreted by most cell types. They are nanosized EVs ranging from 30 to 150 nm. The membrane-enclosed bodies originate by the process of endocytosis and mainly comprise DNA, RNA, protein, and lipids. Exosomes not only act as cell-to-cell communication signaling mediators but also have the potential to act as biomarkers for clinical application and as a promising carrier for drug delivery. Unfortunately, the purification methods for exosomes remain an obstacle. While most of the exosome researches are mainly focused on cancer, there are limited studies highlighting the importance of exosomes in ocular biology, specifically cornea-associated pathologies. Here, we summarize a brief description of exosome biogenesis, roles of exosomes and exosome-based therapies in corneal pathologies, and exosome bioengineering for tissue-specific therapy.
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Affiliation(s)
- Anil Tiwari
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - Aastha Singh
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - Sudhir Verma
- Department of Zoology, Deen Dayal Upadhyaya College (University of Delhi), New Delhi, India
| | - Sarah Stephenson
- Pandorum Technologies Ltd., Bangalore Bioinnovation Centre, Bangalore, India.,Department of Surgery/Division of Transplant Surgery, The Medical University of South Carolina, Charleston, SC, United States
| | - Tuhin Bhowmick
- Pandorum Technologies Ltd., Bangalore Bioinnovation Centre, Bangalore, India
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Chandru A, Agrawal P, Ojha SK, Selvakumar K, Shiva VK, Gharat T, Selvam S, Thomas MB, Damala M, Prasad D, Basu S, Bhowmick T, Sangwan VS, Singh V. Human Cadaveric Donor Cornea Derived Extra Cellular Matrix Microparticles for Minimally Invasive Healing/Regeneration of Corneal Wounds. Biomolecules 2021; 11:532. [PMID: 33918484 PMCID: PMC8066719 DOI: 10.3390/biom11040532] [Citation(s) in RCA: 3] [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: 03/02/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/10/2023] Open
Abstract
Biological materials derived from extracellular matrix (ECM) proteins have garnered interest as their composition is very similar to that of native tissue. Herein, we report the use of human cornea derived decellularized ECM (dECM) microparticles dispersed in human fibrin sealant as an accessible therapeutic alternative for corneal anterior stromal reconstruction. dECM microparticles had good particle size distribution (≤10 µm) and retained the majority of corneal ECM components found in native tissue. Fibrin-dECM hydrogels exhibited compressive modulus of 70.83 ± 9.17 kPa matching that of native tissue, maximum burst pressure of 34.3 ± 3.7 kPa, and demonstrated a short crosslinking time of ~17 min. The fibrin-dECM hydrogels were found to be biodegradable, cytocompatible, non-mutagenic, non-sensitive, non-irritant, and supported the growth and maintained the phenotype of encapsulated human corneal stem cells (hCSCs) in vitro. In a rabbit model of anterior lamellar keratectomy, fibrin-dECM bio-adhesives promoted corneal re-epithelialization within 14 days, induced stromal tissue repair, and displayed integration with corneal tissues in vivo. Overall, our results suggest that the incorporation of cornea tissue-derived ECM microparticles in fibrin hydrogels is non-toxic, safe, and shows tremendous promise as a minimally invasive therapeutic approach for the treatment of superficial corneal epithelial wounds and anterior stromal injuries.
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Affiliation(s)
- Arun Chandru
- Pandorum Technologies Private Limited, Bangalore, Karnataka 560100, India; (P.A.); (S.K.O.); (K.S.); (V.K.S.); (T.G.); (S.S.); (M.B.T.)
| | - Parinita Agrawal
- Pandorum Technologies Private Limited, Bangalore, Karnataka 560100, India; (P.A.); (S.K.O.); (K.S.); (V.K.S.); (T.G.); (S.S.); (M.B.T.)
| | - Sanjay Kumar Ojha
- Pandorum Technologies Private Limited, Bangalore, Karnataka 560100, India; (P.A.); (S.K.O.); (K.S.); (V.K.S.); (T.G.); (S.S.); (M.B.T.)
| | - Kamalnath Selvakumar
- Pandorum Technologies Private Limited, Bangalore, Karnataka 560100, India; (P.A.); (S.K.O.); (K.S.); (V.K.S.); (T.G.); (S.S.); (M.B.T.)
| | - Vaishnavi K. Shiva
- Pandorum Technologies Private Limited, Bangalore, Karnataka 560100, India; (P.A.); (S.K.O.); (K.S.); (V.K.S.); (T.G.); (S.S.); (M.B.T.)
| | - Tanmay Gharat
- Pandorum Technologies Private Limited, Bangalore, Karnataka 560100, India; (P.A.); (S.K.O.); (K.S.); (V.K.S.); (T.G.); (S.S.); (M.B.T.)
| | - Shivaram Selvam
- Pandorum Technologies Private Limited, Bangalore, Karnataka 560100, India; (P.A.); (S.K.O.); (K.S.); (V.K.S.); (T.G.); (S.S.); (M.B.T.)
| | - Midhun Ben Thomas
- Pandorum Technologies Private Limited, Bangalore, Karnataka 560100, India; (P.A.); (S.K.O.); (K.S.); (V.K.S.); (T.G.); (S.S.); (M.B.T.)
| | - Mukesh Damala
- Brien Holden Eye Research Center, LV Prasad Eye Institute, Hyderabad, Telangana 500034, India; (M.D.); (D.P.); (S.B.); (V.S.S.)
| | - Deeksha Prasad
- Brien Holden Eye Research Center, LV Prasad Eye Institute, Hyderabad, Telangana 500034, India; (M.D.); (D.P.); (S.B.); (V.S.S.)
| | - Sayan Basu
- Brien Holden Eye Research Center, LV Prasad Eye Institute, Hyderabad, Telangana 500034, India; (M.D.); (D.P.); (S.B.); (V.S.S.)
- Center for Ocular Regeneration (CORE), LV Prasad Eye Institute, Hyderabad, Telangana 500034, India
| | - Tuhin Bhowmick
- Pandorum Technologies Private Limited, Bangalore, Karnataka 560100, India; (P.A.); (S.K.O.); (K.S.); (V.K.S.); (T.G.); (S.S.); (M.B.T.)
| | - Virender Singh Sangwan
- Brien Holden Eye Research Center, LV Prasad Eye Institute, Hyderabad, Telangana 500034, India; (M.D.); (D.P.); (S.B.); (V.S.S.)
- Center for Ocular Regeneration (CORE), LV Prasad Eye Institute, Hyderabad, Telangana 500034, India
| | - Vivek Singh
- Brien Holden Eye Research Center, LV Prasad Eye Institute, Hyderabad, Telangana 500034, India; (M.D.); (D.P.); (S.B.); (V.S.S.)
- Center for Ocular Regeneration (CORE), LV Prasad Eye Institute, Hyderabad, Telangana 500034, India
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Patra AK, Bhowmick T, Roy S, Ramakumar S, Chakravarty AR. Correction to Copper(II) Complexes of l-Arginine as Netropsin Mimics Showing DNA Cleavage Activity in Red Light. Inorg Chem 2019; 58:13502-13503. [DOI: 10.1021/acs.inorgchem.9b02484] [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: 11/29/2022]
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Patra AK, Bhowmick T, Ramakumar S, Chakravarty AR. Correction to Metal-Based Netropsin Mimics Showing AT-Selective DNA Binding and DNA Cleavage Activity at Red Light. Inorg Chem 2019; 58:9514. [DOI: 10.1021/acs.inorgchem.9b01731] [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: 11/28/2022]
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Lahiri D, Bhowmick T, Pathak B, Shameema O, Patra AK, Ramakumar S, Chakravarty AR. Correction to Anaerobic Photocleavage of DNA in Red Light by Dicopper(II) Complexes of 3,3′-Dithiodipropionic Acid. Inorg Chem 2019; 58:8892. [DOI: 10.1021/acs.inorgchem.9b00930] [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: 11/29/2022]
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Liu Y, Bhowmick T, Liu Y, Gao X, Mertens HDT, Svergun DI, Xiao J, Zhang Y, Wang JH, Meijers R. Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC. Neuron 2018; 97:1261-1267.e4. [PMID: 29503192 PMCID: PMC5871715 DOI: 10.1016/j.neuron.2018.02.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/19/2017] [Accepted: 02/05/2018] [Indexed: 11/25/2022]
Abstract
Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue that binds to deleted in colorectal cancer (DCC), and it has been proposed that the guidance cue Draxin modulates this interaction. Here, we present structural snapshots of Draxin/DCC and Draxin/Netrin-1 complexes, revealing a triangular relationship that affects Netrin-mediated haptotaxis and fasciculation. Draxin interacts with DCC through the N-terminal four immunoglobulin domains, and Netrin-1 through the EGF-3 domain, in the same region where DCC binds. Netrin-1 and DCC bind to adjacent sites on Draxin, which appears to capture Netrin-1 and tether it to the DCC receptor. We propose the conformational flexibility of the single-pass membrane receptor DCC is used to promote fasciculation and regulate axon guidance through concerted Netrin-1/Draxin binding. Video Abstract
Crystal structure of cysteine knot domain of Draxin in complex with DCC Crystal structure of Netrin-1 in complex with a Draxin fragment Netrin-1 contains a competing binding site for DCC and Draxin on the EGF-3 domain Draxin tethers Netrin-1 and DCC together to promote fasciculation
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Tuhin Bhowmick
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Yiqiong Liu
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871 Beijing, China
| | - Xuefan Gao
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Science and Peking-Tsinghua Centre for Life Sciences, Peking University, 100871 Beijing, China.
| | - Yan Zhang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871 Beijing, China.
| | - Jia-Huai Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China; Department of Medical Oncology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany.
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Bhowmick T, Ghosh S, Dixit K, Ganesan V, Ramagopal UA, Dey D, Sarma SP, Ramakumar S, Nagaraja V. Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors. Nat Commun 2014; 5:4124. [PMID: 24916461 DOI: 10.1038/ncomms5124] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 05/15/2014] [Indexed: 01/03/2023] Open
Abstract
The nucleoid-associated protein HU plays an important role in maintenance of chromosomal architecture and in global regulation of DNA transactions in bacteria. Although HU is essential for growth in Mycobacterium tuberculosis (Mtb), there have been no reported attempts to perturb HU function with small molecules. Here we report the crystal structure of the N-terminal domain of HU from Mtb. We identify a core region within the HU-DNA interface that can be targeted using stilbene derivatives. These small molecules specifically inhibit HU-DNA binding, disrupt nucleoid architecture and reduce Mtb growth. The stilbene inhibitors induce gene expression changes in Mtb that resemble those induced by HU deficiency. Our results indicate that HU is a potential target for the development of therapies against tuberculosis.
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Affiliation(s)
- Tuhin Bhowmick
- 1] Department of Physics, Indian Institute of Science, Bangalore 560012, India [2]
| | - Soumitra Ghosh
- 1] Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560012, India [2]
| | - Karuna Dixit
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Varsha Ganesan
- Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560012, India
| | - Udupi A Ramagopal
- 1] Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Ullmann Building, Room 409, Bronx, New York 10461, USA [2] Biological Sciences Division, Poornaprajna Institute of Scientific Research, Bangalore 562110, India
| | - Debayan Dey
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Siddhartha P Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Valakunja Nagaraja
- 1] Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560012, India [2] Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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Kundu PP, Bhowmick T, Swapna G, Pavan Kumar GV, Nagaraja V, Narayana C. Allosteric transition induced by Mg²⁺ ion in a transactivator monitored by SERS. J Phys Chem B 2014; 118:5322-30. [PMID: 24783979 DOI: 10.1021/jp5000733] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate the utility of the surface-enhanced Raman spectroscopy (SERS) to monitor conformational transitions in protein upon ligand binding. The changes in protein's secondary and tertiary structures were monitored using amide and aliphatic/aromatic side chain vibrations. Changes in these bands are suggestive of the stabilization of the secondary and tertiary structure of transcription activator protein C in the presence of Mg(2+) ion, whereas the spectral fingerprint remained unaltered in the case of a mutant protein, defective in Mg(2+) binding. The importance of the acidic residues in Mg(2+) binding, which triggers an overall allosteric transition in the protein, is visualized in the molecular model. The present study thus opens up avenues toward the application of SERS as a potential tool for gaining structural insights into the changes occurring during conformational transitions in proteins.
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Affiliation(s)
- Partha P Kundu
- Light Scattering Laboratory, Chemistry and Physics of Material Unit, Jawaharlal Nehru Center for Advanced Scientific Research , Jakkur, Bangalore 560064, India
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Lahiri D, Bhowmick T, Banik B, Railkar R, Ramakumar S, Dighe RR, Chakravarty AR. Photocytotoxic and anaerobic DNA cleavage activity of binuclear 3,3′-dithiodipropionic acid cobalt(II) complexes having phenanthroline bases. Polyhedron 2010. [DOI: 10.1016/j.poly.2010.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Patra AK, Bhowmick T, Roy S, Ramakumar S, Chakravarty AR. Copper(II) Complexes of l-Arginine as Netropsin Mimics Showing DNA Cleavage Activity in Red Light. Inorg Chem 2009; 48:2932-43. [PMID: 19254037 DOI: 10.1021/ic8017425] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ashis K. Patra
- Department of Inorganic and Physical Chemistry and Bioinformatics Center, Department of Physics, Indian Institute of Science, Bangalore 560 012, India
| | - Tuhin Bhowmick
- Department of Inorganic and Physical Chemistry and Bioinformatics Center, Department of Physics, Indian Institute of Science, Bangalore 560 012, India
| | - Sovan Roy
- Department of Inorganic and Physical Chemistry and Bioinformatics Center, Department of Physics, Indian Institute of Science, Bangalore 560 012, India
| | - Suryanarayanarao Ramakumar
- Department of Inorganic and Physical Chemistry and Bioinformatics Center, Department of Physics, Indian Institute of Science, Bangalore 560 012, India
| | - Akhil R. Chakravarty
- Department of Inorganic and Physical Chemistry and Bioinformatics Center, Department of Physics, Indian Institute of Science, Bangalore 560 012, India
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Lahiri D, Bhowmick T, Pathak B, Shameema O, Patra AK, Ramakumar S, Chakravarty AR. Anaerobic photocleavage of DNA in red light by dicopper(II) complexes of 3,3'-dithiodipropionic acid. Inorg Chem 2009; 48:339-49. [PMID: 19055345 DOI: 10.1021/ic800806j] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binuclear copper(II) complexes [{(phen)Cu(II)}(2)(mu-dtdp)(2)] (1), [{(dpq)Cu(II)}(2)(mu-dtdp)(2)] (2), [{(phen)Cu(II)}(2)(mu-az)(2)] (3), and [{(dpq)Cu(II)}(2)(mu-az)(2)] (4) and a zinc(II) complex [{(phen)Zn(II)}(2)(mu-dtdp)(2)] (5), having 3,3'-dithiodipropionic acid (H(2)dtdp), azelaic acid (nonanedioic acid), 1,10-phenanthroline (phen), and dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), were prepared and characterized by physicochemical methods. Complex 1 has been structurally characterized by X-ray crystallography. The complexes have each metal center bound to a chelating phenanthroline base and two bridging carboxylate ligands giving a square-planar MN(2)O(2) coordination geometry. The molecular structure of complex 1 shows two sterically constrained disulfide moieties of the dtdp ligands. The complexes show good binding propensity to calf thymus DNA in the major groove. The photoinduced DNA cleavage activity of the complexes has been studied using 365 nm UV light and 647.1 nm and >750 nm red light under both aerobic and anaerobic conditions. The phen complex 1, having dtdp ligand, cleaves supercoiled (SC) DNA to its nicked circular (NC) form. The dpq analogue 2 shows formation of a significant quantity of linear DNA resulting from double-strand breaks (dsb) in air. Mechanistic studies reveal the involvement of HO(*) and (1)O(2) as the reactive species under an aerobic medium. The dsb of DNA is rationalized from the docking studies on 2, showing a close proximity of two photosensitizers, namely, the disulfide moiety of dtdp and the quinoxaline ring of dpq to the complementary strands of DNA. The copper(II) complexes of the dtdp ligand cleave SC DNA to its NC form upon exposure to UV or red light under an argon atmosphere. An enhancement of the DNA cleavage activity under argon has been observed upon increasing the concentration of the DMF solvent in the DMF-Tris buffer medium. Theoretical studies suggest the possibility of sulfide anion radical formation from a copper(II)-bound dtdp ligand in >750 nm red light, which further cleaves the DNA. The copper(II) azelate complexes are inactive under similar reaction conditions. The azelate complex of the dpq ligand cleaves DNA in air following the (1)O(2) pathway. The zinc(II) complex of the dtdp ligand (5) does not show any photoinduced DNA cleavage activity in red light.
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Affiliation(s)
- Debojyoti Lahiri
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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Roy M, Bhowmick T, Santhanagopal R, Ramakumar S, Chakravarty AR. Photo-induced double-strand DNA and site-specific protein cleavage activity of l-histidine (μ-oxo)diiron(iii) complexes of heterocyclic bases. Dalton Trans 2009:4671-82. [DOI: 10.1039/b901337g] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Suryanarayanarao R, Bhowmick T, Ghosh S, Udupi R, Valakunja N. Crystal structure and structure-based drug design of HU (histone-like protein) from M. tuberculosis. Acta Crystallogr A 2008. [DOI: 10.1107/s010876730808906x] [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: 11/10/2022] Open
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Patra AK, Bhowmick T, Ramakumar S, Nethaji M, Chakravarty AR. DNA cleavage in red light promoted by copper(ii) complexes of α-amino acids and photoactive phenanthroline bases. Dalton Trans 2008:6966-76. [DOI: 10.1039/b802948b] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Roy M, Bhowmick T, Ramakumar S, Nethaji M, Chakravarty AR. Double-strand DNA cleavage from photodecarboxylation of (μ-oxo)diiron(iii) l-histidine complex in visible light. Dalton Trans 2008:3542-5. [DOI: 10.1039/b802533a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Patra AK, Bhowmick T, Ramakumar S, Chakravarty AR. Metal-Based Netropsin Mimics Showing AT-Selective DNA Binding and DNA Cleavage Activity at Red Light. Inorg Chem 2007; 46:9030-2. [PMID: 17880211 DOI: 10.1021/ic701326z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Copper(II) bis-arginate [Cu(l-arg)2](NO3)2 (1) and [Cu(l-arg)(phen)Cl]Cl (2) as mimics of the minor-groove-binding natural antibiotic netropsin show preferential binding to the AT-rich region of double-stranded DNA. The complexes with a d-d band near 600 nm display oxidative DNA cleavage activity on photoirradiation at UV-A light of 365 nm and at red light of 647.1 nm (Ar-Kr laser) in a metal-assisted photoexcitation process forming singlet oxygen (1O2) species in a type-2 pathway.
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Affiliation(s)
- Ashis K Patra
- Department of Inorganic and Physical Chemistry, and Bioinformatics Center, Department of Physics, Indian Institute of Science, Bangalore, India
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