1
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Hussain N, Apotikar A, Pidathala S, Mukherjee S, Burada AP, Sikdar SK, Vinothkumar KR, Penmatsa A. Cryo-EM structures of pannexin 1 and 3 reveal differences among pannexin isoforms. Nat Commun 2024; 15:2942. [PMID: 38580658 PMCID: PMC10997603 DOI: 10.1038/s41467-024-47142-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Pannexins are single-membrane large-pore channels that release ions and ATP upon activation. Three isoforms of pannexins 1, 2, and 3, perform diverse cellular roles and differ in their pore lining residues. In this study, we report the cryo-EM structure of pannexin 3 at 3.9 Å and analyze its structural differences with pannexin isoforms 1 and 2. The pannexin 3 vestibule has two distinct chambers and a wider pore radius in comparison to pannexins 1 and 2. We further report two cryo-EM structures of pannexin 1, with pore substitutions W74R/R75D that mimic the pore lining residues of pannexin 2 and a germline mutant of pannexin 1, R217H at resolutions of 3.2 Å and 3.9 Å, respectively. Substitution of cationic residues in the vestibule of pannexin 1 results in reduced ATP interaction propensities to the channel. The germline mutant R217H in transmembrane helix 3 (TM3), leads to a partially constricted pore, reduced ATP interaction and weakened voltage sensitivity. The study compares the three pannexin isoform structures, the effects of substitutions of pore and vestibule-lining residues and allosteric effects of a pathological substitution on channel structure and function thereby enhancing our understanding of this vital group of ATP-release channels.
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Affiliation(s)
- Nazia Hussain
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Ashish Apotikar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Shabareesh Pidathala
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sourajit Mukherjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
- Department of Chemistry, The University of Chicago, Chicago, USA
| | - Ananth Prasad Burada
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Sujit Kumar Sikdar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Kutti R Vinothkumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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2
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Sinha RA, Yen PM. Metabolic Messengers: Thyroid Hormones. Nat Metab 2024; 6:639-650. [PMID: 38671149 DOI: 10.1038/s42255-024-00986-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 01/15/2024] [Indexed: 04/28/2024]
Abstract
Thyroid hormones (THs) are key hormones that regulate development and metabolism in mammals. In man, the major target tissues for TH action are the brain, liver, muscle, heart, and adipose tissue. Defects in TH synthesis, transport, metabolism, and nuclear action have been associated with genetic and endocrine diseases in man. Over the past few years, there has been renewed interest in TH action and the therapeutic potential of THs and thyromimetics to treat several metabolic disorders such as hypercholesterolemia, dyslipidaemia, non-alcoholic fatty liver disease (NAFLD), and TH transporter defects. Recent advances in the development of tissue and TH receptor isoform-targeted thyromimetics have kindled new hope for translating our fundamental understanding of TH action into an effective therapy. This review provides a concise overview of the historical development of our understanding of TH action, its physiological and pathophysiological effects on metabolism, and future therapeutic applications to treat metabolic dysfunction.
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Affiliation(s)
- Rohit A Sinha
- Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India.
| | - Paul M Yen
- Laboratory of Hormonal Regulation, Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore.
- Div. Endocrinology, Metabolism, and Nutrition, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA.
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3
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Adaikkan C, Joseph J, Foustoukos G, Wang J, Polygalov D, Boehringer R, Middleton SJ, Huang AJY, Tsai LH, McHugh TJ. Silencing CA1 pyramidal cells output reveals the role of feedback inhibition in hippocampal oscillations. Nat Commun 2024; 15:2190. [PMID: 38467602 PMCID: PMC10928166 DOI: 10.1038/s41467-024-46478-3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The precise temporal coordination of neural activity is crucial for brain function. In the hippocampus, this precision is reflected in the oscillatory rhythms observed in CA1. While it is known that a balance between excitatory and inhibitory activity is necessary to generate and maintain these oscillations, the differential contribution of feedforward and feedback inhibition remains ambiguous. Here we use conditional genetics to chronically silence CA1 pyramidal cell transmission, ablating the ability of these neurons to recruit feedback inhibition in the local circuit, while recording physiological activity in mice. We find that this intervention leads to local pathophysiological events, with ripple amplitude and intrinsic frequency becoming significantly larger and spatially triggered local population spikes locked to the trough of the theta oscillation appearing during movement. These phenotypes demonstrate that feedback inhibition is crucial in maintaining local sparsity of activation and reveal the key role of lateral inhibition in CA1 in shaping circuit function.
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Affiliation(s)
| | - Justin Joseph
- Centre for Brain Research, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Georgios Foustoukos
- Laboratory for Circuit and Behavioral Physiology, RIKEN Center for Brain Science, Wakoshi, Saitama, Japan
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Jun Wang
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Denis Polygalov
- Laboratory for Circuit and Behavioral Physiology, RIKEN Center for Brain Science, Wakoshi, Saitama, Japan
| | - Roman Boehringer
- Laboratory for Circuit and Behavioral Physiology, RIKEN Center for Brain Science, Wakoshi, Saitama, Japan
| | - Steven J Middleton
- Laboratory for Circuit and Behavioral Physiology, RIKEN Center for Brain Science, Wakoshi, Saitama, Japan
| | - Arthur J Y Huang
- Laboratory for Circuit and Behavioral Physiology, RIKEN Center for Brain Science, Wakoshi, Saitama, Japan
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas J McHugh
- Laboratory for Circuit and Behavioral Physiology, RIKEN Center for Brain Science, Wakoshi, Saitama, Japan.
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
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4
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Foss S, Sakya SA, Aguinagalde L, Lustig M, Shaughnessy J, Cruz AR, Scheepmaker L, Mathiesen L, Ruso-Julve F, Anthi AK, Gjølberg TT, Mester S, Bern M, Evers M, Bratlie DB, Michaelsen TE, Schlothauer T, Sok D, Bhattacharya J, Leusen J, Valerius T, Ram S, Rooijakkers SHM, Sandlie I, Andersen JT. Human IgG Fc-engineering for enhanced plasma half-life, mucosal distribution and killing of cancer cells and bacteria. Nat Commun 2024; 15:2007. [PMID: 38453922 PMCID: PMC10920689 DOI: 10.1038/s41467-024-46321-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Monoclonal IgG antibodies constitute the fastest growing class of therapeutics. Thus, there is an intense interest to design more potent antibody formats, where long plasma half-life is a commercially competitive differentiator affecting dosing, frequency of administration and thereby potentially patient compliance. Here, we report on an Fc-engineered variant with three amino acid substitutions Q311R/M428E/N434W (REW), that enhances plasma half-life and mucosal distribution, as well as allows for needle-free delivery across respiratory epithelial barriers in human FcRn transgenic mice. In addition, the Fc-engineered variant improves on-target complement-mediated killing of cancer cells as well as both gram-positive and gram-negative bacteria. Hence, this versatile Fc technology should be broadly applicable in antibody design aiming for long-acting prophylactic or therapeutic interventions.
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Affiliation(s)
- Stian Foss
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Siri A Sakya
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Leire Aguinagalde
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Marta Lustig
- Section for Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jutamas Shaughnessy
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ana Rita Cruz
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lisette Scheepmaker
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Line Mathiesen
- Department of Public Health, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fulgencio Ruso-Julve
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Aina Karen Anthi
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Torleif Tollefsrud Gjølberg
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Simone Mester
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Malin Bern
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Mitchell Evers
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Diane B Bratlie
- Infection Immunology, Norwegian Institute of Public Health, Oslo, Norway
| | - Terje E Michaelsen
- Infection Immunology, Norwegian Institute of Public Health, Oslo, Norway
- Department of Chemical Pharmacy, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Tilman Schlothauer
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Munich, Germany
| | - Devin Sok
- International AIDS Vaccine Initiative (IAVI), New York, NY, USA
| | - Jayanta Bhattacharya
- Antibody Translational Research Program, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Jeanette Leusen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Thomas Valerius
- Section for Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Sanjay Ram
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Inger Sandlie
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway.
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway.
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5
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Walia K, Sharma A, Paul S, Chouhan P, Kumar G, Ringe R, Sharma M, Tuli A. SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle. Nat Commun 2024; 15:2053. [PMID: 38448435 PMCID: PMC10918171 DOI: 10.1038/s41467-024-46417-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, uses the host endolysosomal system for entry, replication, and egress. Previous studies have shown that the SARS-CoV-2 virulence factor ORF3a interacts with the lysosomal tethering factor HOPS complex and blocks HOPS-mediated late endosome and autophagosome fusion with lysosomes. Here, we report that SARS-CoV-2 infection leads to hyperactivation of the late endosomal and lysosomal small GTP-binding protein Rab7, which is dependent on ORF3a expression. We also observed Rab7 hyperactivation in naturally occurring ORF3a variants encoded by distinct SARS-CoV-2 variants. We found that ORF3a, in complex with Vps39, sequesters the Rab7 GAP TBC1D5 and displaces Rab7 from this complex. Thus, ORF3a disrupts the GTP hydrolysis cycle of Rab7, which is beneficial for viral production, whereas the Rab7 GDP-locked mutant strongly reduces viral replication. Hyperactivation of Rab7 in ORF3a-expressing cells impaired CI-M6PR retrieval from late endosomes to the trans-Golgi network, disrupting the biosynthetic transport of newly synthesized hydrolases to lysosomes. Furthermore, the tethering of the Rab7- and Arl8b-positive compartments was strikingly reduced upon ORF3a expression. As SARS-CoV-2 egress requires Arl8b, these findings suggest that ORF3a-mediated hyperactivation of Rab7 serves a multitude of functions, including blocking endolysosome formation, interrupting the transport of lysosomal hydrolases, and promoting viral egress.
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Affiliation(s)
- Kshitiz Walia
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Abhishek Sharma
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Sankalita Paul
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Priya Chouhan
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gaurav Kumar
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Rajesh Ringe
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Amit Tuli
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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6
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Dharavath B, Butle A, Chaudhary A, Pal A, Desai S, Chowdhury A, Thorat R, Upadhyay P, Nair S, Dutt A. Recurrent UBE3C-LRP5 translocations in head and neck cancer with therapeutic implications. NPJ Precis Oncol 2024; 8:63. [PMID: 38438481 PMCID: PMC10912599 DOI: 10.1038/s41698-024-00555-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
Head and neck cancer is a major cause of morbidity and mortality worldwide. The identification of genetic alterations in head and neck cancer may improve diagnosis and treatment outcomes. In this study, we report the identification and functional characterization of UBE3C-LRP5 translocation in head and neck cancer. Our whole transcriptome sequencing and RT-PCR analysis of 151 head and neck cancer tumor samples identified the LRP5-UBE3C and UBE3C-LRP5 fusion transcripts in 5.3% of patients of Indian origin (n = 151), and UBE3C-LRP5 fusion transcripts in 1.2% of TCGA-HNSC patients (n = 502). Further, whole genome sequencing identified the breakpoint of UBE3C-LRP5 translocation. We demonstrate that UBE3C-LRP5 fusion is activating in vitro and in vivo, and promotes the proliferation, migration, and invasion of head and neck cancer cells. In contrast, depletion of UBE3C-LRP5 fusion suppresses the clonogenic, migratory, and invasive potential of the cells. The UBE3C-LRP5 fusion activates the Wnt/β-catenin signaling by promoting nuclear accumulation of β-catenin, leading to upregulation of Wnt/β-catenin target genes, MYC, CCND1, TCF4, and LEF1. Consistently, treatment with the FDA-approved drug, pyrvinium pamoate, significantly reduced the transforming ability of cells expressing the fusion protein and improved survival in mice bearing tumors of fusion-overexpressing cells. Interestingly, fusion-expressing cells upon knockdown of CTNNB1, or LEF1 show reduced proliferation, clonogenic abilities, and reduced sensitivity to pyrvinium pamoate. Overall, our study suggests that the UBE3C-LRP5 fusion is a promising therapeutic target for head and neck cancer and that pyrvinium pamoate may be a potential drug candidate for treating head and neck cancer harboring this translocation.
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Affiliation(s)
- Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Department of Biochemistry, All India Institute of Medical Sciences, Nagpur, Maharashtra, 441108, India
| | - Akshita Chaudhary
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Ankita Pal
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Aniket Chowdhury
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Rahul Thorat
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Pawan Upadhyay
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sudhir Nair
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India.
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7
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Aggarwal C, Ahmed H, Sharma P, Reddy ES, Nayak K, Singla M, Maheshwari D, Chawla YM, Panda H, Rai RC, Gunisetty S, Priyamvada L, Bhaumik SK, Ahamed SF, Vivek R, Bhatnagar P, Singh P, Kaur M, Dixit K, Kumar S, Gottimukkala K, Saini K, Bajpai P, Sreekanth GP, Mammen S, Rajan A, Verghese VP, Abraham AM, Shah P, Alagarasu K, Yu T, Davis CW, Wrammert J, Ansari A, Antia R, Kabra SK, Medigeshi GR, Ahmed R, Lodha R, Shet A, Chandele A, Murali-Krishna K. Severe disease during both primary and secondary dengue virus infections in pediatric populations. Nat Med 2024; 30:670-674. [PMID: 38321219 DOI: 10.1038/s41591-024-02798-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: 11/02/2020] [Accepted: 01/02/2024] [Indexed: 02/08/2024]
Abstract
Dengue is a global epidemic causing over 100 million cases annually. The clinical symptoms range from mild fever to severe hemorrhage and shock, including some fatalities. The current paradigm is that these severe dengue cases occur mostly during secondary infections due to antibody-dependent enhancement after infection with a different dengue virus serotype. India has the highest dengue burden worldwide, but little is known about disease severity and its association with primary and secondary dengue infections. To address this issue, we examined 619 children with febrile dengue-confirmed infection from three hospitals in different regions of India. We classified primary and secondary infections based on IgM:IgG ratios using a dengue-specific enzyme-linked immunosorbent assay according to the World Health Organization guidelines. We found that primary dengue infections accounted for more than half of total clinical cases (344 of 619), severe dengue cases (112 of 202) and fatalities (5 of 7). Consistent with the classification based on binding antibody data, dengue neutralizing antibody titers were also significantly lower in primary infections compared to secondary infections (P ≤ 0.0001). Our findings question the currently widely held belief that severe dengue is associated predominantly with secondary infections and emphasizes the importance of developing vaccines or treatments to protect dengue-naive populations.
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Affiliation(s)
- Charu Aggarwal
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Pragati Sharma
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Elluri Seetharami Reddy
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Kaustuv Nayak
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mohit Singla
- Division of Pediatric Pulmonology and Intensive Care, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Deepti Maheshwari
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Yadya M Chawla
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Harekrushna Panda
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ramesh Chandra Rai
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sivaram Gunisetty
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Lalita Priyamvada
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Siddhartha Kumar Bhaumik
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Syed Fazil Ahamed
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bengaluru, India
| | - Rosario Vivek
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bengaluru, India
- The University of Trans-Disciplinary Health Sciences & Technology, Bengaluru, India
| | - Priya Bhatnagar
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- TERI school of advanced studies, New Delhi, India
| | - Prabhat Singh
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Manpreet Kaur
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kritika Dixit
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sanjeev Kumar
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kamal Gottimukkala
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Keshav Saini
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Prashant Bajpai
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Gopinathan Pillai Sreekanth
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shobha Mammen
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Anand Rajan
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Valsan Philip Verghese
- Pediatric Infectious Diseases, Department of Pediatrics, Christian Medical College, Vellore, India
| | - Asha Mary Abraham
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Paresh Shah
- Department of Molecular Virology, National Institute of Virology, Pune, India
| | - Kalichamy Alagarasu
- Department of Molecular Virology, National Institute of Virology, Pune, India
| | - Tianwei Yu
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Shenzhen Research Institute of Big Data, School of Data Science, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Carl W Davis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Aftab Ansari
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sushil Kumar Kabra
- Division of Pediatric Pulmonology and Intensive Care, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Guruprasad R Medigeshi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Rakesh Lodha
- Division of Pediatric Pulmonology and Intensive Care, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India.
| | - Anita Shet
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bengaluru, India.
- International Vaccine Access Centre, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Anmol Chandele
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Kaja Murali-Krishna
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
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8
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Kalita B, Sahu S, Bharadwaj A, Panneerselvam L, Martinez-Cebrian G, Agarwal M, Mathew SJ. The Wnt-pathway corepressor TLE3 interacts with the histone methyltransferase KMT1A to inhibit differentiation in Rhabdomyosarcoma. Oncogene 2024; 43:524-538. [PMID: 38177411 DOI: 10.1038/s41388-023-02911-3] [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: 07/05/2022] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Rhabdomyosarcoma tumor cells resemble differentiating skeletal muscle cells, which unlike normal muscle cells, fail to undergo terminal differentiation, underlying their proliferative and metastatic properties. We identify the corepressor TLE3 as a key regulator of rhabdomyosarcoma tumorigenesis by inhibiting the Wnt-pathway. Loss of TLE3 function leads to Wnt-pathway activation, reduced proliferation, decreased migration, and enhanced differentiation in rhabdomyosarcoma cells. Muscle-specific TLE3-knockout results in enhanced expression of terminal myogenic differentiation markers during normal mouse development. TLE3-knockout rhabdomyosarcoma cell xenografts result in significantly smaller tumors characterized by reduced proliferation, increased apoptosis and enhanced differentiation. We demonstrate that TLE3 interacts with and recruits the histone methyltransferase KMT1A, leading to repression of target gene activation and inhibition of differentiation in rhabdomyosarcoma. A combination drug therapy regime to promote Wnt-pathway activation by the small molecule BIO and inhibit KMT1A by the drug chaetocin led to significantly reduced tumor volume, decreased proliferation, increased expression of differentiation markers and increased survival in rhabdomyosarcoma tumor-bearing mice. Thus, TLE3, the Wnt-pathway and KMT1A are excellent drug targets which can be exploited for treating rhabdomyosarcoma tumors.
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Affiliation(s)
- Bhargab Kalita
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Subhashni Sahu
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Anushree Bharadwaj
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Lakshmikanthan Panneerselvam
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | | | - Megha Agarwal
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Affiliated to Manipal University, Manipal, Karnataka, 576104, India
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sam J Mathew
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India.
- Affiliated to Manipal University, Manipal, Karnataka, 576104, India.
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9
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Lin QXX, Rajagopalan D, Gamage AM, Tan LM, Venkatesh PN, Chan WOY, Kumar D, Agrawal R, Chen Y, Fong SW, Singh A, Sun LJ, Tan SY, Chai LYA, Somani J, Lee B, Renia L, Ng LFP, Ramanathan K, Wang LF, Young B, Lye D, Singhal A, Prabhakar S. Longitudinal single cell atlas identifies complex temporal relationship between type I interferon response and COVID-19 severity. Nat Commun 2024; 15:567. [PMID: 38238298 PMCID: PMC10796319 DOI: 10.1038/s41467-023-44524-0] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
Due to the paucity of longitudinal molecular studies of COVID-19, particularly those covering the early stages of infection (Days 1-8 symptom onset), our understanding of host response over the disease course is limited. We perform longitudinal single cell RNA-seq on 286 blood samples from 108 age- and sex-matched COVID-19 patients, including 73 with early samples. We examine discrete cell subtypes and continuous cell states longitudinally, and we identify upregulation of type I IFN-stimulated genes (ISGs) as the predominant early signature of subsequent worsening of symptoms, which we validate in an independent cohort and corroborate by plasma markers. However, ISG expression is dynamic in progressors, spiking early and then rapidly receding to the level of severity-matched non-progressors. In contrast, cross-sectional analysis shows that ISG expression is deficient and IFN suppressors such as SOCS3 are upregulated in severe and critical COVID-19. We validate the latter in four independent cohorts, and SOCS3 inhibition reduces SARS-CoV-2 replication in vitro. In summary, we identify complexity in type I IFN response to COVID-19, as well as a potential avenue for host-directed therapy.
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Affiliation(s)
- Quy Xiao Xuan Lin
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Deepa Rajagopalan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Akshamal M Gamage
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Le Min Tan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Prasanna Nori Venkatesh
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Wharton O Y Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Dilip Kumar
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
| | - Ragini Agrawal
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Yao Chen
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Louisa J Sun
- Alexandra Hospital, Singapore, 159964, Singapore
| | - Seow-Yen Tan
- Changi General Hospital, Singapore, 529889, Singapore
| | - Louis Yi Ann Chai
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jyoti Somani
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Bernett Lee
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Kollengode Ramanathan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- National University Hospital, Singapore, 119074, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, 168753, Singapore
| | - Barnaby Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - David Lye
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Amit Singhal
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore.
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore.
| | - Shyam Prabhakar
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore.
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10
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Venkataraman P, Saini S. Ecological disruptive selection acting on quantitative loci can drive sympatric speciation. NPJ Syst Biol Appl 2024; 10:6. [PMID: 38225420 PMCID: PMC10789801 DOI: 10.1038/s41540-024-00332-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024] Open
Abstract
The process of speciation generates biodiversity. According to the null model of speciation, barriers between populations arise in allopatry, where, prior to biology, geography imposes barriers to gene flow. On the other hand, sympatric speciation requires that the process of speciation happen in the absence of a geographical barrier, where the members of the population have no spatial, temporal barriers. Several attempts have been made to theoretically identify the conditions in which speciation can occur in sympatry. However, these efforts suffer from several limitations. We propose a model for sympatric speciation based on adaptation for resource utilization. We use a genetics-based model to investigate the relative roles of prezygotic and postzygotic barriers, from the context of ecological disruptive selection, sexual selection, and genetic architecture, in causing and maintaining sympatric speciation. Our results show that sexual selection that acts on secondary sexual traits does not play any role in the process of speciation in sympatry and that assortative mating based on an ecologically relevant trait forces the population to show an adaptive response. We also demonstrate that understanding the genetic architecture of the trait under ecological selection is very important and that it is not required for the strength of ecological disruptive selection to be very high in order for speciation to occur in sympatry. Our results provide an insight into the kind of scenarios in which sympatric speciation can be demonstrated in the lab.
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Affiliation(s)
- Pavithra Venkataraman
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400 076, India.
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400 076, India
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11
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Srinivasan S, Sivaprasad S, Rajalakshmi R, Anjana RM, Malik RA, Kulothungan V, Raman R, Bhende M. Association of OCT and OCT angiography measures with the development and worsening of diabetic retinopathy in type 2 diabetes. Eye (Lond) 2023; 37:3781-3786. [PMID: 37280352 PMCID: PMC10698183 DOI: 10.1038/s41433-023-02605-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/30/2023] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
OBJECTIVE To assess if optical coherence tomography (OCT) and OCT angiography (OCTA) measures are associated with the development and worsening of diabetic retinopathy (DR) over four years. METHODS 280 participants with type 2 diabetes underwent ultra-wide field fundus photography, OCT and OCTA. OCT-derived macular thickness measures, retinal nerve fibre layer and ganglion cell-inner plexiform layer thickness and OCTA-derived foveal avascular zone area, perimeter, circularity, vessel density (VD) and macular perfusion (MP) were examined in relation to the development and worsening of DR over four years. RESULTS After four years, 206 eyes of 219 participants were eligible for analysis. 27 of the 161 eyes (16.7%) with no DR at baseline developed new DR, which was associated with a higher baseline HbA1c and longer diabetes duration. Of the 45 eyes with non-proliferative DR (NPDR) at baseline, 17 (37.7%) showed DR progression. Baseline VD (12.90 vs. 14.90 mm/mm2, p = 0.032) and MP (31.79% vs. 36.96%, p = 0.043) were significantly lower in progressors compared to non-progressors. Progression of DR was inversely related to VD ((hazard ratio [HR] = 0.825) and to MP (HR = 0.936). The area under the receiver operating characteristic curves for VD was AUC = 0.643, with 77.4% sensitivity and 41.8% specificity for a cut-off of 15.85 mm/mm2 and for MP it was AUC = 0.635, with 77.4% sensitivity and 25.5% specificity for a cut-off of 40.8%. CONCLUSIONS OCTA metrics have utility in predicting progression rather than the development of DR in individuals with type 2 diabetes.
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Affiliation(s)
| | | | | | - Ranjit Mohan Anjana
- Dr. Mohan's Diabetes Specialties Centre and Madras Diabetes Research Foundation, Chennai, India
| | - Rayaz A Malik
- Weill Cornell Medicine-Qatar, Education City, Doha, Qatar & Central Manchester University Hospitals Foundation Trust, Manchester, UK
| | - Vaitheeswaran Kulothungan
- National Centre for Disease Informatics and Research (NCDIR) & Indian Council of Medical Research (ICMR), Bangalore, India
| | - Rajiv Raman
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, India
| | - Muna Bhende
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, India.
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12
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Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. Nat Nanotechnol 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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13
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Jacob P, Lindelöf H, Rustad CF, Sutton VR, Moosa S, Udupa P, Hammarsjö A, Bhavani GS, Batkovskyte D, Tveten K, Dalal A, Horemuzova E, Nordgren A, Tham E, Shah H, Merckoll E, Orellana L, Nishimura G, Girisha KM, Grigelioniene G. Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13. NPJ Genom Med 2023; 8:39. [PMID: 37993442 PMCID: PMC10665555 DOI: 10.1038/s41525-023-00380-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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023] Open
Abstract
Spondyloepimetaphyseal dysplasia with severe short stature, RPL13-related (SEMD-RPL13), MIM#618728), is a rare autosomal dominant disorder characterized by short stature and skeletal changes such as mild spondylar and epimetaphyseal dysplasia affecting primarily the lower limbs. The genetic cause was first reported in 2019 by Le Caignec et al., and six disease-causing variants in the gene coding for a ribosomal protein, RPL13 (NM_000977.3) have been identified to date. This study presents clinical and radiographic data from 12 affected individuals aged 2-64 years from seven unrelated families, showing highly variable manifestations. The affected individuals showed a range from mild to severe short stature, retaining the same radiographic pattern of spondylar- and epi-metaphyseal dysplasia, but with varying severity of the hip and knee deformities. Two new missense variants, c.548 G>A, p.(Arg183His) and c.569 G>T, p.(Arg190Leu), and a previously known splice variant c.477+1G>A were identified, confirming mutational clustering in a highly specific RNA binding motif. Structural analysis and interpretation of the variants' impact on the protein suggests that disruption of extra-ribosomal functions of the protein through binding of mRNA may play a role in the skeletal phenotype of SEMD-RPL13. In addition, we present gonadal and somatic mosaicism for the condition.
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Affiliation(s)
- Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hillevi Lindelöf
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilie F Rustad
- Department of Medial Genetics, Oslo University Hospital, Oslo, Norway
| | - Vernon Reid Sutton
- Department of Molecular & Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Cape Town, South Africa
| | - Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Eva Horemuzova
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Else Merckoll
- Department of Radiology, Oslo University Hospital, Oslo, Norway
| | - Laura Orellana
- Protein Dynamics and Mutation lab, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gen Nishimura
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Radiology, Musashino-Yowakai Hospital, Tokyo, Japan
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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14
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Pardasani M, Ramakrishnan AM, Mahajan S, Kantroo M, McGowan E, Das S, Srikanth P, Pandey S, Abraham NM. Perceptual learning deficits mediated by somatostatin releasing inhibitory interneurons of olfactory bulb in an early life stress mouse model. Mol Psychiatry 2023; 28:4693-4706. [PMID: 37726451 PMCID: PMC10914616 DOI: 10.1038/s41380-023-02244-3] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/21/2023]
Abstract
Early life adversity (ELA) causes aberrant functioning of neural circuits affecting the health of an individual. While ELA-induced behavioural disorders resulting from sensory and cognitive disabilities can be assessed clinically, the neural mechanisms need to be probed using animal models by employing multi-pronged experimental approaches. As ELA can alter sensory perception, we investigated the effect of early weaning on murine olfaction. By implementing go/no-go odour discrimination paradigm, we observed olfactory learning and memory impairments in early life stressed (ELS) male mice. As olfactory bulb (OB) circuitry plays a critical role in odour learning, we studied the plausible changes in the OB of ELS mice. Lowered c-Fos activity in the external plexiform layer and a reduction in the number of dendritic processes of somatostatin-releasing, GABAergic interneurons (SOM-INs) in the ELS mice led us to hypothesise the underlying circuit. We recorded reduced synaptic inhibitory feedback on mitral/tufted (M/T) cells, in the OB slices from ELS mice, explaining the learning deficiency caused by compromised refinement of OB output. The reduction in synaptic inhibition was nullified by the photo-activation of ChR2-expressing SOM-INs in ELS mice. The role of SOM-INs was revealed by learning-dependent refinement of Ca2+dynamics quantified by GCaMP6f signals, which was absent in ELS mice. Further, the causal role of SOM-INs involving circuitry was investigated by optogenetic modulation during the odour discrimination learning. Photo-activating these neurons rescued the ELA-induced learning deficits. Conversely, photo-inhibition caused learning deficiency in control animals, while it completely abolished the learning in ELS mice, confirming the adverse effects mediated by SOM-INs. Our results thus establish the role of specific inhibitory circuit in pre-cortical sensory area in orchestrating ELA-dependent changes.
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Affiliation(s)
- Meenakshi Pardasani
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Anantha Maharasi Ramakrishnan
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Sarang Mahajan
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Meher Kantroo
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Eleanor McGowan
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Susobhan Das
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Priyadharshini Srikanth
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Sanyukta Pandey
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Nixon M Abraham
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India.
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15
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Lathia R, Nagpal S, Modak CD, Mishra S, Sharma D, Reddy BS, Nukala P, Bhat R, Sen P. Tunable encapsulation of sessile droplets with solid and liquid shells. Nat Commun 2023; 14:6445. [PMID: 37833273 PMCID: PMC10575970 DOI: 10.1038/s41467-023-41977-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Droplet encapsulations using liquid or solid shells are of significant interest in microreactors, drug delivery, crystallization, and cell growth applications. Despite progress in droplet-related technologies, tuning micron-scale shell thickness over a large range of droplet sizes is still a major challenge. In this work, we report capillary force assisted cloaking using hydrophobic colloidal particles and liquid-infused surfaces. The technique produces uniform solid and liquid shell encapsulations over a broad range (5-200 μm shell thickness for droplet volume spanning over four orders of magnitude). Tunable liquid encapsulation is shown to reduce the evaporation rate of droplets by up to 200 times with a wide tunability in lifetime (1.5 h to 12 days). Further, we propose using the technique for single crystals and cell/spheroid culture platforms. Stimuli-responsive solid shells show hermetic encapsulation with tunable strength and dissolution time. Moreover, scalability, and versatility of the technique is demonstrated for on-chip applications.
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Affiliation(s)
- Rutvik Lathia
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Satchit Nagpal
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Chandantaru Dey Modak
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Satyarthi Mishra
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Deepak Sharma
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Bheema Sankar Reddy
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Pavan Nukala
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Ramray Bhat
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
- Department of BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Prosenjit Sen
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
- Department of BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
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16
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Panwar V, Singh A, Bhatt M, Tonk RK, Azizov S, Raza AS, Sengupta S, Kumar D, Garg M. Multifaceted role of mTOR (mammalian target of rapamycin) signaling pathway in human health and disease. Signal Transduct Target Ther 2023; 8:375. [PMID: 37779156 PMCID: PMC10543444 DOI: 10.1038/s41392-023-01608-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [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: 05/12/2023] [Revised: 07/25/2023] [Accepted: 08/14/2023] [Indexed: 10/03/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) is a protein kinase that controls cellular metabolism, catabolism, immune responses, autophagy, survival, proliferation, and migration, to maintain cellular homeostasis. The mTOR signaling cascade consists of two distinct multi-subunit complexes named mTOR complex 1/2 (mTORC1/2). mTOR catalyzes the phosphorylation of several critical proteins like AKT, protein kinase C, insulin growth factor receptor (IGF-1R), 4E binding protein 1 (4E-BP1), ribosomal protein S6 kinase (S6K), transcription factor EB (TFEB), sterol-responsive element-binding proteins (SREBPs), Lipin-1, and Unc-51-like autophagy-activating kinases. mTOR signaling plays a central role in regulating translation, lipid synthesis, nucleotide synthesis, biogenesis of lysosomes, nutrient sensing, and growth factor signaling. The emerging pieces of evidence have revealed that the constitutive activation of the mTOR pathway due to mutations/amplification/deletion in either mTOR and its complexes (mTORC1 and mTORC2) or upstream targets is responsible for aging, neurological diseases, and human malignancies. Here, we provide the detailed structure of mTOR, its complexes, and the comprehensive role of upstream regulators, as well as downstream effectors of mTOR signaling cascades in the metabolism, biogenesis of biomolecules, immune responses, and autophagy. Additionally, we summarize the potential of long noncoding RNAs (lncRNAs) as an important modulator of mTOR signaling. Importantly, we have highlighted the potential of mTOR signaling in aging, neurological disorders, human cancers, cancer stem cells, and drug resistance. Here, we discuss the developments for the therapeutic targeting of mTOR signaling with improved anticancer efficacy for the benefit of cancer patients in clinics.
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Affiliation(s)
- Vivek Panwar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Aishwarya Singh
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh, 201313, India
| | - Manini Bhatt
- Department of Biomedical Engineering, Indian Institute of Technology, Ropar, Punjab, 140001, India
| | - Rajiv K Tonk
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Shavkatjon Azizov
- Laboratory of Biological Active Macromolecular Systems, Institute of Bioorganic Chemistry, Academy of Sciences Uzbekistan, Tashkent, 100125, Uzbekistan
- Faculty of Life Sciences, Pharmaceutical Technical University, 100084, Tashkent, Uzbekistan
| | - Agha Saquib Raza
- Rajive Gandhi Super Speciality Hospital, Tahirpur, New Delhi, 110093, India
| | - Shinjinee Sengupta
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh, 201313, India.
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India.
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh, 201313, India.
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17
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Rakshit S, Babji S, Parthiban C, Madhavan R, Adiga V, J SE, Chetan Kumar N, Ahmed A, Shivalingaiah S, Shashikumar N, V M, Johnson AR, Ramesh N, B RG, Asokan M, Mayor S, Kang G, D'souza G, Dias M, Vyakarnam A. Polyfunctional CD4 T-cells correlating with neutralising antibody is a hallmark of COVISHIELD TM and COVAXIN ® induced immunity in COVID-19 exposed Indians. NPJ Vaccines 2023; 8:134. [PMID: 37709772 PMCID: PMC10502007 DOI: 10.1038/s41541-023-00731-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Detailed characterisation of immune responses induced by COVID-19 vaccines rolled out in India: COVISHIELDTM (CS) and COVAXIN® (CO) in a pre-exposed population is only recently being discovered. We addressed this issue in subjects who received their primary series of vaccination between November 2021 and January 2022. Both vaccines are capable of strongly boosting Wuhan Spike-specific neutralising antibody, polyfunctional Th1 cytokine producing CD4+ T-cells and single IFN-γ + CD8+ T-cells. Consistent with inherent differences in vaccine platform, the vector-based CS vaccine-induced immunity was of greater magnitude, breadth, targeting Delta and Omicron variants compared to the whole-virion inactivated vaccine CO, with CS vaccinees showing persistent CD8+ T-cells responses until 3 months post primary vaccination. This study provides detailed evidence on the magnitude and quality of CS and CO vaccine induced responses in subjects with pre-existing SARS-CoV-2 immunity in India, thereby mitigating vaccine hesitancy arguments in such a population, which remains a global health challenge.
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Affiliation(s)
- Srabanti Rakshit
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Sudhir Babji
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
| | - Chaitra Parthiban
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Ramya Madhavan
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
| | - Vasista Adiga
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
- Department of Biotechnology, PES University, Bangalore, Karnataka, India
| | - Sharon Eveline J
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Nirutha Chetan Kumar
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Asma Ahmed
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | | | - Nandini Shashikumar
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
| | - Mamatha V
- St. John's Medical College, Bangalore, Karnataka, India
| | | | - Naveen Ramesh
- St. John's Medical College, Bangalore, Karnataka, India
| | | | | | - Satyajit Mayor
- National Centre for Biological Sciences, Bengaluru, Karnataka, India
| | - Gagandeep Kang
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, Tamil Nadu, India
| | - George D'souza
- Department of Pulmonary Medicine, St. John's Medical College, Bangalore, Karnataka, India
| | - Mary Dias
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India
- St. John's Medical College, Bangalore, Karnataka, India
| | - Annapurna Vyakarnam
- Division of Infectious Diseases, St. John's Research Institute, Bangalore, Karnataka, India.
- Department of Immunobiology, School of Immunology & Microbial Sciences, Faculty of Life Science & Medicine, King's College, London, UK.
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18
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Issarapu P, Arumalla M, Elliott HR, Nongmaithem SS, Sankareswaran A, Betts M, Sajjadi S, Kessler NJ, Bayyana S, Mansuri SR, Derakhshan M, Krishnaveni GV, Shrestha S, Kumaran K, Di Gravio C, Sahariah SA, Sanderson E, Relton CL, Ward KA, Moore SE, Prentice AM, Lillycrop KA, Fall CHD, Silver MJ, Chandak GR. DNA methylation at the suppressor of cytokine signaling 3 (SOCS3) gene influences height in childhood. Nat Commun 2023; 14:5200. [PMID: 37626025 PMCID: PMC10457295 DOI: 10.1038/s41467-023-40607-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Human height is strongly influenced by genetics but the contribution of modifiable epigenetic factors is under-explored, particularly in low and middle-income countries (LMIC). We investigate links between blood DNA methylation and child height in four LMIC cohorts (n = 1927) and identify a robust association at three CpGs in the suppressor of cytokine signaling 3 (SOCS3) gene which replicates in a high-income country cohort (n = 879). SOCS3 methylation (SOCS3m)-height associations are independent of genetic effects. Mendelian randomization analysis confirms a causal effect of SOCS3m on height. In longitudinal analysis, SOCS3m explains a maximum 9.5% of height variance in mid-childhood while the variance explained by height polygenic risk score increases from birth to 21 years. Children's SOCS3m is associated with prenatal maternal folate and socio-economic status. In-vitro characterization confirms a regulatory effect of SOCS3m on gene expression. Our findings suggest epigenetic modifications may play an important role in driving child height in LMIC.
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Affiliation(s)
- Prachand Issarapu
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Manisha Arumalla
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Suraj S Nongmaithem
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Alagu Sankareswaran
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India
| | - Modupeh Betts
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Sara Sajjadi
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India
| | - Noah J Kessler
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Swati Bayyana
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India
| | - Sohail R Mansuri
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India
| | - Maria Derakhshan
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - G V Krishnaveni
- Epidemiology Research Unit, CSI Holdsworth Memorial Hospital, Mysore, Karnataka, India
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Kalyanaraman Kumaran
- Epidemiology Research Unit, CSI Holdsworth Memorial Hospital, Mysore, Karnataka, India
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Chiara Di Gravio
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Eleanor Sanderson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kate A Ward
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
- Department of Women & Children's Health, King's College London, London, UK
| | - Sophie E Moore
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
- Department of Women & Children's Health, King's College London, London, UK
| | - Andrew M Prentice
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Karen A Lillycrop
- School of Medicine, University of Southampton, Southampton, UK
- Biological Sciences, University of Southampton, Southampton, UK
| | - Caroline H D Fall
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Matt J Silver
- MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine (LSHTM), London, UK.
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India.
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, India.
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19
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Sarma P, Carino CMC, Seetharama D, Pandey S, Dwivedi-Agnihotri H, Rui X, Cao Y, Kawakami K, Kumari P, Chen YC, Luker KE, Yadav PN, Luker GD, Laporte SA, Chen X, Inoue A, Shukla AK. Molecular insights into intrinsic transducer-coupling bias in the CXCR4-CXCR7 system. Nat Commun 2023; 14:4808. [PMID: 37558722 PMCID: PMC10412580 DOI: 10.1038/s41467-023-40482-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
Chemokine receptors constitute an important subfamily of G protein-coupled receptors (GPCRs), and they are critically involved in a broad range of immune response mechanisms. Ligand promiscuity among these receptors makes them an interesting target to explore multiple aspects of biased agonism. Here, we comprehensively characterize two chemokine receptors namely, CXCR4 and CXCR7, in terms of their transducer-coupling and downstream signaling upon their stimulation by a common chemokine agonist, CXCL12, and a small molecule agonist, VUF11207. We observe that CXCR7 lacks G-protein-coupling while maintaining robust βarr recruitment with a major contribution of GRK5/6. On the other hand, CXCR4 displays robust G-protein activation as expected but exhibits significantly reduced βarr-coupling compared to CXCR7. These two receptors induce distinct βarr conformations even when activated by the same agonist, and CXCR7, unlike CXCR4, fails to activate ERK1/2 MAP kinase. We also identify a key contribution of a single phosphorylation site in CXCR7 for βarr recruitment and endosomal localization. Our study provides molecular insights into intrinsic-bias encoded in the CXCR4-CXCR7 system with broad implications for drug discovery.
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Affiliation(s)
- Parishmita Sarma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 208016, India
| | - Carlo Marion C Carino
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Deeksha Seetharama
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 208016, India
| | - Shubhi Pandey
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 208016, India
| | - Hemlata Dwivedi-Agnihotri
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 208016, India
| | - Xue Rui
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Yubo Cao
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, H3G 1Y6, Canada
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Poonam Kumari
- Neuroscience and Ageing Biology Division, CSIR-Central Drug Research Institute Sector 10, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Yu-Chih Chen
- Department of Computational and Systems Biology, Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kathryn E Luker
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI, USA
| | - Prem N Yadav
- Neuroscience and Ageing Biology Division, CSIR-Central Drug Research Institute Sector 10, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Gary D Luker
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Stéphane A Laporte
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, H3G 1Y6, Canada
- Department of Medicine, McGill University Health Center, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Xin Chen
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 208016, India.
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20
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Sankhe GD, Raja R, Singh DP, Bheemireddy S, Rana S, Athira PJ, Dixit NM, Saini DK. Sequestration of histidine kinases by non-cognate response regulators establishes a threshold level of stimulation for bacterial two-component signaling. Nat Commun 2023; 14:4483. [PMID: 37491529 PMCID: PMC10368727 DOI: 10.1038/s41467-023-40095-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
Bacterial two-component systems (TCSs) consist of a sensor histidine kinase (HK) that perceives a specific signal, and a cognate response regulator (RR) that modulates the expression of target genes. Positive autoregulation improves TCS sensitivity to stimuli, but may trigger disproportionately large responses to weak signals, compromising bacterial fitness. Here, we combine experiments and mathematical modelling to reveal a general design that prevents such disproportionate responses: phosphorylated HKs (HK~Ps) can be sequestered by non-cognate RRs. We study five TCSs of Mycobacterium tuberculosis and find, for all of them, non-cognate RRs that show higher affinity than cognate RRs for HK~Ps. Indeed, in vitro assays show that HK~Ps preferentially bind higher affinity non-cognate RRs and get sequestered. Mathematical modelling indicates that this sequestration would introduce a 'threshold' stimulus strength for eliciting responses, thereby preventing responses to weak signals. Finally, we construct tunable expression systems in Mycobacterium bovis BCG to show that higher affinity non-cognate RRs suppress responses in vivo.
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Affiliation(s)
- Gaurav D Sankhe
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Rubesh Raja
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Devendra Pratap Singh
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Sneha Bheemireddy
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Subinoy Rana
- Materials Research Centre, Indian Institute of Science, Bengaluru, India
| | - P J Athira
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Narendra M Dixit
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India.
| | - Deepak Kumar Saini
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India.
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21
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Kulkarni UP, Selvarajan S, Fouzia NA, Lionel S, Nair SC, Balasubramanian P, Mani T, Abraham A, George B, Mathews V. Intracranial bleeding in acute promyelocytic leukemia treated with arsenic trioxide based regimens is associated with induction mortality but not with relapse. Blood Cancer J 2023; 13:94. [PMID: 37349334 PMCID: PMC10287743 DOI: 10.1038/s41408-023-00873-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Affiliation(s)
| | - Sushil Selvarajan
- Department of Haematology, Christian Medical College, Vellore, India
| | - N A Fouzia
- Department of Haematology, Christian Medical College, Vellore, India
| | - Sharon Lionel
- Department of Haematology, Christian Medical College, Vellore, India
| | - Sukesh Chandran Nair
- Department of Transfusion Medicine and Immunohaematology, Christian Medical College, Vellore, India
| | | | - Thenmozhi Mani
- Department of Biostatistics, Christian Medical College, Vellore, India
| | - Aby Abraham
- Department of Haematology, Christian Medical College, Vellore, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, India
| | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, India
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22
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Singh P, Goyal S, Gupta S, Garg S, Tiwari A, Rajput V, Bates AS, Gupta AK, Gupta N. Combinatorial encoding of odors in the mosquito antennal lobe. Nat Commun 2023; 14:3539. [PMID: 37322224 PMCID: PMC10272161 DOI: 10.1038/s41467-023-39303-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
Among the cues that a mosquito uses to find a host for blood-feeding, the smell of the host plays an important role. Previous studies have shown that host odors contain hundreds of chemical odorants, which are detected by different receptors on the peripheral sensory organs of mosquitoes. But how individual odorants are encoded by downstream neurons in the mosquito brain is not known. We developed an in vivo preparation for patch-clamp electrophysiology to record from projection neurons and local neurons in the antennal lobe of Aedes aegypti. Combining intracellular recordings with dye-fills, morphological reconstructions, and immunohistochemistry, we identify different sub-classes of antennal lobe neurons and their putative interactions. Our recordings show that an odorant can activate multiple neurons innervating different glomeruli, and that the stimulus identity and its behavioral preference are represented in the population activity of the projection neurons. Our results provide a detailed description of the second-order olfactory neurons in the central nervous system of mosquitoes and lay a foundation for understanding the neural basis of their olfactory behaviors.
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Affiliation(s)
- Pranjul Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India
| | - Shefali Goyal
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India
| | - Smith Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India
| | - Sanket Garg
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India
- Department of Economic Sciences, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India
| | - Abhinav Tiwari
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India
| | - Varad Rajput
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India
| | - Alexander Shakeel Bates
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Arjit Kant Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India
| | - Nitin Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India.
- Mehta Family Center for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India.
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23
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Marmamula S, Barrenkala NR, Kumbham TR, Modepalli SB, Yellapragada R, Khanna RC, Friedman DS. Impact of an intervention for avoidable vision loss on visual function in the elderly-The Hyderabad Ocular Morbidity in Elderly Study (HOMES). Eye (Lond) 2023; 37:1725-1731. [PMID: 36104520 PMCID: PMC10220055 DOI: 10.1038/s41433-022-02229-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/08/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND/OBJECTIVES To report the impact of interventions for avoidable vision impairment (VI) on the visual function of elderly residents in 'homes for the aged' in India. METHODS Participants aged ≥60 years were recruited. A comprehensive eye examination was conducted by trained examiners and interventions were provided. Trained social investigators administered the Indian Vision Function questionnaire (INDVFQ) to assess visual function before and after the intervention (spectacles, cataract surgery or laser capsulotomy). Lower scores on IVFQ imply better visual function. VI was defined as presenting visual acuity worse than 6/18 in the better eye. VI due to cataract, uncorrected refractive errors, and posterior capsular opacification after cataract surgery were considered avoidable VI. RESULTS The mean age of the participants (n = 613) was 73.8 years (standard deviation: 8.1 years) and 378 (62.2%) were women. 64/103 (62.1%) participants who had avoidable VI at baseline were evaluated after the intervention. Significant gains were observed in all four domains of visual function. There was a 14.9% improvement in mobility scores (33.8 versus 28.8; p = 0.03), a 19.9% improvement in the activity limitations score (36.8 versus 29.5; p < 0.01), a 10.9% improvement in the psychosocial impact score (41.1 versus 36.6; p < 0.01) and a 13.6% improvement in the visual symptoms score (49.2 versus 42.5 p < 0.01). Overall, the mean IVFQ score improved by 16.4% (47.6 versus 39.8; p < 0.01). CONCLUSION Elderly individuals in residential care with avoidable VI had a significant improvement in visual function after relatively low-cost interventions such as spectacles and cataract surgery. Strategies are needed to provide these interventions for the elderly in 'homes for the aged' in India.
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Affiliation(s)
- Srinivas Marmamula
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India.
- Brien Holden Institute of Optometry and Vision Science, L V Prasad Eye Institute, Hyderabad, India.
- Department of Biotechnology / Wellcome Trust India Alliance, L V Prasad Eye Institute, Hyderabad, India.
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW, Australia.
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Harvard Medical School, Boston, MA, USA.
| | - Navya Rekha Barrenkala
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
- Brien Holden Institute of Optometry and Vision Science, L V Prasad Eye Institute, Hyderabad, India
| | - Thirupathi Reddy Kumbham
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
| | - Satya Brahmanandam Modepalli
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
| | - Ratnakar Yellapragada
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
- Brien Holden Institute of Optometry and Vision Science, L V Prasad Eye Institute, Hyderabad, India
| | - Rohit C Khanna
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW, Australia
| | - David S Friedman
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Harvard Medical School, Boston, MA, USA
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Udupa P, Ghosh DK, Kausthubham N, Shah H, Bartakke S, Dalal A, Girisha KM, Bhavani GS. Genome sequencing identifies a large non-coding region deletion of SNX10 causing autosomal recessive osteopetrosis. J Hum Genet 2023; 68:287-290. [PMID: 36526684 PMCID: PMC10040338 DOI: 10.1038/s10038-022-01104-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Autosomal recessive osteopetrosis (ARO) is a rare genetic disorder caused by impaired osteoclast activity. In this study, we describe a 4-year-old boy with increased bone density due to osteopetrosis, autosomal recessive 8. Using genome sequencing, we identified a large deletion in the 5'-untranslated region (UTR) of SNX10 (sorting nexin 10), where the regulatory region of this gene is located. This large deletion resulted in the absence of the SNX10 transcript and led to abnormal osteoclast activity. SNX10 is one of the nine genes known to cause ARO, shown to interact with V-ATPase (vacuolar type H( + )-ATPase), as it plays an important role in bone resorption. Our study highlights the importance of regulatory regions in the 5'-UTR of SNX10 for its expression while also demonstrating the importance of genome sequencing for detecting large deletion of the regulatory region of SNX10.
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Affiliation(s)
- Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Debasish Kumar Ghosh
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sandip Bartakke
- Department of Clinical Hematology, Aditya Birla Memorial Hospital, Pune, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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25
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Ren B, Liang X, Brouwers JF, Miron RC, Shen B, Gupta N. Synthesis vs. salvage of ester- and ether-linked phosphatidylethanolamine in the intracellular protozoan pathogen Toxoplasma gondii. Commun Biol 2023; 6:306. [PMID: 36949328 PMCID: PMC10033509 DOI: 10.1038/s42003-023-04664-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Toxoplasma gondii is a prevalent zoonotic pathogen infecting livestock as well as humans. The exceptional ability of this parasite to reproduce in several types of nucleated host cells necessitates a coordinated usage of endogenous and host-derived nutritional resources for membrane biogenesis. Phosphatidylethanolamine is the second most common glycerophospholipid in T. gondii, but how its requirement in the acutely-infectious fast-dividing tachyzoite stage is satisfied remains enigmatic. This work reveals that the parasite deploys de novo synthesis and salvage pathways to meet its demand for ester- and ether-linked PtdEtn. Auxin-mediated depletion of the phosphoethanolamine cytidylyltransferase (ECT) caused a lethal phenotype in tachyzoites due to impaired invasion and cell division, disclosing a vital role of the CDP-ethanolamine pathway during the lytic cycle. In accord, the inner membrane complex appeared disrupted concurrent with a decline in its length, parasite width and major phospholipids. Integrated lipidomics and isotope analyses of the TgECT mutant unveiled the endogenous synthesis of ester-PtdEtn, and salvage of ether-linked lipids from host cells. In brief, this study demonstrates how T. gondii operates various means to produce distinct forms of PtdEtn while featuring the therapeutic relevance of its de novo synthesis.
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Affiliation(s)
- Bingjian Ren
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Xiaohan Liang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jos F Brouwers
- Research Group for Analysis Techniques in the Life Sciences, School of Life Sciences and Technology, Avans University of Applied Sciences, Breda, The Netherlands
| | - Rosalba Cruz Miron
- Intracellular Parasite Education and Research Labs (iPEARL), Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS-P), Hyderabad, India
| | - Bang Shen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
| | - Nishith Gupta
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany.
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
- Intracellular Parasite Education and Research Labs (iPEARL), Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS-P), Hyderabad, India.
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26
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Dharavath B, Butle A, Pal A, Desai S, Upadhyay P, Rane A, Khandelwal R, Manavalan S, Thorat R, Sonawane K, Vaish R, Gera P, Bal M, D'Cruz AK, Nair S, Dutt A. Role of miR-944/MMP10/AXL- axis in lymph node metastasis in tongue cancer. Commun Biol 2023; 6:57. [PMID: 36650344 PMCID: PMC9845355 DOI: 10.1038/s42003-023-04437-6] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Occult lymph-node metastasis is a crucial predictor of tongue cancer mortality, with an unmet need to understand the underlying mechanism. Our immunohistochemical and real-time PCR analysis of 208 tongue tumors show overexpression of Matrix Metalloproteinase, MMP10, in 86% of node-positive tongue tumors (n = 79; p < 0.00001). Additionally, global profiling for non-coding RNAs associated with node-positive tumors reveals that of the 11 significantly de-regulated miRNAs, miR-944 negatively regulates MMP10 by targeting its 3'-UTR. We demonstrate that proliferation, migration, and invasion of tongue cancer cells are suppressed by MMP10 knockdown or miR-944 overexpression. Further, we show that depletion of MMP10 prevents nodal metastases using an orthotopic tongue cancer mice model. In contrast, overexpression of MMP10 leads to opposite effects upregulating epithelial-mesenchymal-transition, mediated by a tyrosine kinase gene, AXL, to promote nodal and distant metastasis in vivo. Strikingly, AXL expression is essential and sufficient to mediate the functional consequence of MMP10 overexpression. Consistent with our findings, TCGA-HNSC data suggests overexpression of MMP10 or AXL positively correlates with poor survival of the patients. In conclusion, our results establish that the miR-944/MMP10/AXL- axis underlies lymph node metastases with potential therapeutic intervention and prediction of nodal metastases in tongue cancer patients.
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Affiliation(s)
- Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Ankita Pal
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Pawan Upadhyay
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Aishwarya Rane
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Risha Khandelwal
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sujith Manavalan
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Rahul Thorat
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Kavita Sonawane
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Richa Vaish
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Poonam Gera
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Tissue Biorepository, Advanced Centre for Treatment Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Munita Bal
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Anil K D'Cruz
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
- Apollo Cancer Center, Apollo Hospitals, CBD Belapur, Navi Mumbai, 400614, India
| | - Sudhir Nair
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India.
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
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Srinivasan S, Sobha Sivaprasad, Rajalakshmi R, Anjana RM, Malik RA, Kulothungan V, Raman R, Muna Bhende. Retinal structure-function correlation in type 2 diabetes. Eye (Lond) 2022; 36:1865-1871. [PMID: 34462581 PMCID: PMC9500073 DOI: 10.1038/s41433-021-01761-1] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/16/2021] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVE To examine the relationship of visual function as assessed by visual acuity, contrast sensitivity, and multifocal electroretinography (mfERG) to macular structural and microvascular measures on optical coherence tomography (OCT) and angiography (OCTA) in individuals with diabetes. METHODS This is a prospective observational study conducted at a tertiary eye care centre in India. Right eyes of 121 adults with type 2 diabetes with no diabetic retinopathy (DR), mild or moderate nonproliferative DR (NPDR) were examined. Severe NPDR, proliferative DR and diabetic macular oedema were excluded. Participants underwent assessment of glycated haemoglobin (HbA1C), blood pressure, best corrected visual acuity (LogMAR), contrast sensitivity (CS), mfERG, ultrawide field fundus photography, OCT and OCTA. Correlations were assessed by Spearman's rank correlation (rho). RESULTS Of the total of 121 eyes, 89 had No DR, 32 had mild to moderate NPDR. In the No DR group, the LogMAR acuity was significantly and negatively correlated to central subfoveal thickness (CST) (rho = -0.420), macular vessel density (rho = -0.270) and perfusion (rho = -0.270). (ii) Contrast sensitivity correlated to foveal avascular zone circularity (rho = 0.297); (iii) mfERG P1 response densities were better with higher macular perfusion index (rho = 0.240). In the NPDR group, the LogMAR acuity also showed a significant negative correlation to CST (rho = -0.379). Other correlations were not significant. CONCLUSION Retinal and visual functional changes are evident in diabetic patients with No DR and are correlated to subclinical retinal structural changes detectable using multimodal imaging.
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Affiliation(s)
| | | | | | - Ranjit Mohan Anjana
- Dr. Mohan's Diabetes Specialties Centre and Madras Diabetes Research Foundation, Chennai, India
| | - Rayaz A Malik
- Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
- Institute of Cardiovascular Medicine, University of Manchester, Manchester, UK
| | - Vaitheeswaran Kulothungan
- National Centre for Disease Informatics and Research (NCDIR) & Indian Council of Medical Research (ICMR), Bangalore, India
| | - Rajiv Raman
- Shri Bhagwan Mahavir Vitreoretinal Services, SankaraNethralaya, Chennai, India
| | - Muna Bhende
- Shri Bhagwan Mahavir Vitreoretinal Services, SankaraNethralaya, Chennai, India.
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28
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Sreenivasan V, Kumar S, Pestilli F, Talukdar P, Sridharan D. GPU-accelerated connectome discovery at scale. Nat Comput Sci 2022; 2:298-306. [PMID: 38177824 PMCID: PMC10766542 DOI: 10.1038/s43588-022-00250-z] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 04/21/2022] [Indexed: 01/06/2024]
Abstract
Diffusion magnetic resonance imaging and tractography enable the estimation of anatomical connectivity in the human brain, in vivo. Yet, without ground-truth validation, different tractography algorithms can yield widely varying connectivity estimates. Although streamline pruning techniques mitigate this challenge, slow compute times preclude their use in big-data applications. We present 'Regularized, Accelerated, Linear Fascicle Evaluation' (ReAl-LiFE), a GPU-based implementation of a state-of-the-art streamline pruning algorithm (LiFE), which achieves >100× speedups over previous CPU-based implementations. Leveraging these speedups, we overcome key limitations with LiFE's algorithm to generate sparser and more accurate connectomes. We showcase ReAl-LiFE's ability to estimate connections with superlative test-retest reliability, while outperforming competing approaches. Moreover, we predicted inter-individual variations in multiple cognitive scores with ReAl-LiFE connectome features. We propose ReAl-LiFE as a timely tool, surpassing the state of the art, for accurate discovery of individualized brain connectomes at scale. Finally, our GPU-accelerated implementation of a popular non-negative least-squares optimization algorithm is widely applicable to many real-world problems.
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Affiliation(s)
| | - Sawan Kumar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| | - Franco Pestilli
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
| | - Partha Talukdar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India
| | - Devarajan Sridharan
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India.
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India.
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29
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De M, Bhushan A, Grubbe WS, Roy S, Mendoza JL, Chinnaswamy S. Distinct molecular phenotypes involving several human diseases are induced by IFN-λ3 and IFN-λ4 in monocyte-derived macrophages. Genes Immun 2022; 23:73-84. [PMID: 35115664 PMCID: PMC9042695 DOI: 10.1038/s41435-022-00164-w] [Citation(s) in RCA: 2] [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: 10/07/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/23/2022]
Abstract
Human Interferon (IFN) lambda 3 (IFN-λ3) and IFN-λ4 are closely linked at the IFNL locus and show association with several diseases in genetic studies. Since they are only ~30% identical to each other, to better understand their roles in disease phenotypes, comparative studies are needed. Monocytes are precursors to macrophages (monocyte-derived macrophages; MDMs) that get differentiated under the influence of various immune factors, including IFNs. In a recent study, we characterized lipopolysaccharide-activated M1 and M2-MDMs that were differentiated in presence of IFN-λ3 or IFN-λ4. In this study, we performed transcriptomics on these M1 and M2-MDMs to further understand their molecular phenotypes. We identified over 760 genes that were reciprocally regulated by IFN-λ3 and IFN-λ4, additionally we identified over 240 genes that are significantly affected by IFN-λ4 but not IFN-λ3. We observed that IFN-λ3 was more active in M2-MDMs while IFN-λ4 showed superior response in M1-MDMs. Providing a structural explanation for these functional differences, molecular modeling showed differences in expected interactions of IFN-λ3 and IFN-λ4 with the extracellular domain of IFN-λR1. Further, pathway analysis showed several human infectious diseases and even cancer-related pathways being significantly affected by IFN-λ3 and/or IFN-λ4 in both M1 and M2-MDMs.
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Affiliation(s)
- Manjarika De
- National Institute of Biomedical Genomics, Kalyani, West Bengal, 741251, India
| | - Anand Bhushan
- National Institute of Biomedical Genomics, Kalyani, West Bengal, 741251, India
- Cleveland Clinic Cole Eye Institute & Lerner Research Institute, Cleveland, OH, 44195, USA
| | - William S Grubbe
- Pritzker School of Molecular Engineering and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Subhajit Roy
- National Institute of Biomedical Genomics, Kalyani, West Bengal, 741251, India
| | - Juan L Mendoza
- Pritzker School of Molecular Engineering and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
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Kumar G, Chawla P, Dhiman N, Chadha S, Sharma S, Sethi K, Sharma M, Tuli A. RUFY3 links Arl8b and JIP4-Dynein complex to regulate lysosome size and positioning. Nat Commun 2022; 13:1540. [PMID: 35314681 PMCID: PMC8938454 DOI: 10.1038/s41467-022-29077-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 03/19/2021] [Accepted: 02/24/2022] [Indexed: 02/08/2023] Open
Abstract
The bidirectional movement of lysosomes on microtubule tracks regulates their whole-cell spatial arrangement. Arl8b, a small GTP-binding (G) protein, promotes lysosome anterograde trafficking mediated by kinesin-1. Herein, we report an Arl8b effector, RUFY3, which regulates the retrograde transport of lysosomes. We show that RUFY3 interacts with the JIP4-dynein-dynactin complex and facilitates Arl8b association with the retrograde motor complex. Accordingly, RUFY3 knockdown disrupts the positioning of Arl8b-positive endosomes and reduces Arl8b colocalization with Rab7-marked late endosomal compartments. Moreover, we find that RUFY3 regulates nutrient-dependent lysosome distribution, although autophagosome-lysosome fusion and autophagic cargo degradation are not impaired upon RUFY3 depletion. Interestingly, lysosome size is significantly reduced in RUFY3 depleted cells, which could be rescued by inhibition of the lysosome reformation regulatory factor PIKFYVE. These findings suggest a model in which the perinuclear cloud arrangement of lysosomes regulates both the positioning and size of these proteolytic compartments.
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Affiliation(s)
- Gaurav Kumar
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Prateek Chawla
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Neha Dhiman
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Sanya Chadha
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Sheetal Sharma
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Kanupriya Sethi
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Amit Tuli
- Divison of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India.
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Lesurf R, Said A, Akinrinade O, Breckpot J, Delfosse K, Liu T, Yao R, Persad G, McKenna F, Noche RR, Oliveros W, Mattioli K, Shah S, Miron A, Yang Q, Meng G, Yue MCS, Sung WWL, Thiruvahindrapuram B, Lougheed J, Oechslin E, Mondal T, Bergin L, Smythe J, Jayappa S, Rao VJ, Shenthar J, Dhandapany PS, Semsarian C, Weintraub RG, Bagnall RD, Ingles J, Melé M, Maass PG, Ellis J, Scherer SW, Mital S. Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. NPJ Genom Med 2022; 7:18. [PMID: 35288587 PMCID: PMC8921194 DOI: 10.1038/s41525-022-00288-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/04/2022] [Indexed: 11/08/2022] Open
Abstract
Cardiomyopathy (CMP) is a heritable disorder. Over 50% of cases are gene-elusive on clinical gene panel testing. The contribution of variants in non-coding DNA elements that result in cryptic splicing and regulate gene expression has not been explored. We analyzed whole-genome sequencing (WGS) data in a discovery cohort of 209 pediatric CMP patients and 1953 independent replication genomes and exomes. We searched for protein-coding variants, and non-coding variants predicted to affect the function or expression of genes. Thirty-nine percent of cases harbored pathogenic coding variants in known CMP genes, and 5% harbored high-risk loss-of-function (LoF) variants in additional candidate CMP genes. Fifteen percent harbored high-risk regulatory variants in promoters and enhancers of CMP genes (odds ratio 2.25, p = 6.70 × 10-7 versus controls). Genes involved in α-dystroglycan glycosylation (FKTN, DTNA) and desmosomal signaling (DSC2, DSG2) were most highly enriched for regulatory variants (odds ratio 6.7-58.1). Functional effects were confirmed in patient myocardium and reporter assays in human cardiomyocytes, and in zebrafish CRISPR knockouts. We provide strong evidence for the genomic contribution of functionally active variants in new genes and in regulatory elements of known CMP genes to early onset CMP.
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Affiliation(s)
- Robert Lesurf
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Abdelrahman Said
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Oyediran Akinrinade
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- St. George's University School of Medicine, Grenada, Grenada
| | | | - Kathleen Delfosse
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ting Liu
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Roderick Yao
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gabrielle Persad
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Fintan McKenna
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ramil R Noche
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Zebrafish Genetics and Disease Models Core, The Hospital for Sick Children, Toronto, ON, Canada
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shreya Shah
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anastasia Miron
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Qian Yang
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Guoliang Meng
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jane Lougheed
- Division of Cardiology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Erwin Oechslin
- Peter Munk Cardiac Centre, Division of Cardiology, Toronto General Hospital, University of Toronto, Toronto, ON, Canada
| | - Tapas Mondal
- Department of Pediatrics, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Lynn Bergin
- Division of Cardiology, London Health Sciences Centre, London, ON, Canada
| | - John Smythe
- Department of Pediatrics, Kingston General Hospital, Kingston, ON, Canada
| | - Shashank Jayappa
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Vinay J Rao
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Jayaprakash Shenthar
- Department of Cardiology, Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bengaluru, India
| | - Perundurai S Dhandapany
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Robert G Weintraub
- Cardiology Department, Royal Children's Hospital, Melbourne, Australia
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard D Bagnall
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Cardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Philipp G Maass
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Seema Mital
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.
- Ted Rogers Centre for Heart Research, Toronto, ON, Canada.
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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Padmanabhan P, Desikan R, Dixit NM. Modeling how antibody responses may determine the efficacy of COVID-19 vaccines. Nat Comput Sci 2022; 2:123-131. [PMID: 38177523 DOI: 10.1038/s43588-022-00198-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 01/20/2022] [Indexed: 01/06/2024]
Abstract
Predicting the efficacy of COVID-19 vaccines would aid vaccine development and usage strategies, which is of importance given their limited supplies. Here we develop a multiscale mathematical model that proposes mechanistic links between COVID-19 vaccine efficacies and the neutralizing antibody (NAb) responses they elicit. We hypothesized that the collection of all NAbs would constitute a shape space and that responses of individuals are random samples from this space. We constructed the shape space by analyzing reported in vitro dose-response curves of ~80 NAbs. Sampling NAb subsets from the space, we recapitulated the responses of convalescent patients. We assumed that vaccination would elicit similar NAb responses. We developed a model of within-host SARS-CoV-2 dynamics, applied it to virtual patient populations and, invoking the NAb responses above, predicted vaccine efficacies. Our predictions quantitatively captured the efficacies from clinical trials. Our study thus suggests plausible mechanistic underpinnings of COVID-19 vaccines and generates testable hypotheses for establishing them.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.
| | - Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
- Certara QSP, Certara UK Limited, Sheffield, UK
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India.
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India.
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33
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Marmamula S, Barrenkala NR, Khanna RC, Challa R, Bhakki M, Kumbham TR, Modepalli SB, Yellapragada R, Friedman DS. Near vision impairment among the elderly in residential care-the Hyderabad Ocular Morbidity in Elderly Study (HOMES). Eye (Lond) 2021; 35:2310-2315. [PMID: 33159176 PMCID: PMC8302663 DOI: 10.1038/s41433-020-01243-w] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/10/2020] [Accepted: 10/16/2020] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND/OBJECTIVE To report on the prevalence and risk factors for near vision impairment (NVI) among the elderly in residential care in Telangana State in India. METHODS Individuals aged ≥60 years were recruited from 41 'home for the aged' centres in Hyderabad, India. All participants had complete eye examinations including presenting and best-corrected visual acuity assessment for distance and near. NVI was defined as binocular presenting near vision worse than N8 (6/15) among those who had a normal presenting distance visual acuity of 6/18 in the better eye. RESULTS Of the 826 participants, the mean age was 74.4 years (standard deviation-8.4 years), 525 (63.6%) were women, 715 (86.6%) had at least school education. The prevalence of NVI was 51.2% (95% CI: 47.7-54.7) based on presenting vision. On applying multiple logistic regression analysis, the odds of NVI were higher in 80 years and older age (OR: 2.17; 95% CI: 3.44-13.6). Those with school education (OR: 0.58: 95% CI: 0.36-0.94) and higher education (OR: 0.38; 95% CI: 0.21-0.69) had lower odds for NVI. Similarly, those with self-reported diabetes (OR: 0.69; 95% CI: 0.49-0.97), those using spectacles (OR: 0.09; 95% CI: 0.05-0.16), and those who had undergone cataract surgery (OR: 0.51; 95% CI: 0.36-0.74) had lower odds for NVI. CONCLUSIONS NVI was common among the elderly in residential care in homes for the aged in Hyderabad, India. As most of this NVI is correctable, a routine screening programme and dispensing of spectacles can be undertaken to address this vision loss.
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Affiliation(s)
- Srinivas Marmamula
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India.
- Brien Holden Institute of Optometry and Vision Science, L V Prasad Eye Institute, Hyderabad, India.
- Wellcome Trust/Department of Biotechnology India Alliance, L V Prasad Eye Institute, Hyderabad, India.
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW, Australia.
| | - Navya Rekha Barrenkala
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
| | - Rohit C Khanna
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW, Australia
| | - Rajesh Challa
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
| | - Madhuri Bhakki
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
| | - Thirupathi Reddy Kumbham
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
| | - Satya Brahmanandam Modepalli
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
| | - Ratnakar Yellapragada
- Allen Foster Community Eye Health Research Centre, Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye care, L V Prasad Eye Institute, Hyderabad, India
| | - David S Friedman
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
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34
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Arora N, Hazra JP, Rakshit S. Anisotropy in mechanical unfolding of protein upon partner-assisted pulling and handle-assisted pulling. Commun Biol 2021; 4:925. [PMID: 34326473 PMCID: PMC8322310 DOI: 10.1038/s42003-021-02445-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 02/10/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
Proteins as force-sensors respond to mechanical cues and regulate signaling in physiology. Proteins commonly connect the source and response points of mechanical cues in two conformations, independent proteins in end-to-end geometry and protein complexes in handshake geometry. The force-responsive property of independent proteins in end-to-end geometry is studied extensively using single-molecule force spectroscopy (SMFS). The physiological significance of the complex conformations in force-sensing is often disregarded as mere surge protectors. However, with the potential of force-steering, protein complexes possess a distinct mechano-responsive property over individual force-sensors. To decipher, we choose a force-sensing protein, cadherin-23, from tip-link complex and perform SMFS using end-to-end geometry and handshake complex geometry. We measure higher force-resilience of cadherin-23 with preferential shorter extensions in handshake mode of pulling over the direct mode. The handshake geometry drives the force-response of cadherin-23 through different potential-energy landscapes than direct pulling. Analysis of the dynamic network structure of cadherin-23 under tension indicates narrow force-distributions among residues in cadherin-23 in direct pulling, resulting in low force-dissipation paths and low resilience to force. Overall, the distinct and superior mechanical responses of cadherin-23 in handshake geometry than single protein geometry highlight a probable evolutionary drive of protein-protein complexes as force-conveyors over independent ones.
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Affiliation(s)
- Nisha Arora
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
| | - Sabyasachi Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
- Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
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35
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Kumar S, Athreya A, Gulati A, Nair RM, Mahendran I, Ranjan R, Penmatsa A. Structural basis of inhibition of a transporter from Staphylococcus aureus, NorC, through a single-domain camelid antibody. Commun Biol 2021; 4:836. [PMID: 34226658 PMCID: PMC8257674 DOI: 10.1038/s42003-021-02357-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 10/26/2020] [Accepted: 06/10/2021] [Indexed: 12/11/2022] Open
Abstract
Transporters play vital roles in acquiring antimicrobial resistance among pathogenic bacteria. In this study, we report the X-ray structure of NorC, a 14-transmembrane major facilitator superfamily member that is implicated in fluoroquinolone resistance in drug-resistant Staphylococcus aureus strains, at a resolution of 3.6 Å. The NorC structure was determined in complex with a single-domain camelid antibody that interacts at the extracellular face of the transporter and stabilizes it in an outward-open conformation. The complementarity determining regions of the antibody enter and block solvent access to the interior of the vestibule, thereby inhibiting alternating-access. NorC specifically interacts with an organic cation, tetraphenylphosphonium, although it does not demonstrate an ability to transport it. The interaction is compromised in the presence of NorC-antibody complex, consequently establishing a strategy to detect and block NorC and related transporters through the use of single-domain camelid antibodies.
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Affiliation(s)
- Sushant Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Van Andel Institute, Grand Rapids, MI, USA
| | - Arunabh Athreya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Ashutosh Gulati
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rahul Mony Nair
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Ithayaraja Mahendran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Structural Parasitology Lab, International Centre for Genetic engineering and Biotechnology, New Delhi, India
| | - Rakesh Ranjan
- Principal Scientist, ICAR-National Research Centre of Camel (NRCC), Bikaner, India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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36
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Pidathala S, Mallela AK, Joseph D, Penmatsa A. Structural basis of norepinephrine recognition and transport inhibition in neurotransmitter transporters. Nat Commun 2021; 12:2199. [PMID: 33850134 PMCID: PMC8044178 DOI: 10.1038/s41467-021-22385-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 08/18/2020] [Accepted: 03/01/2021] [Indexed: 12/23/2022] Open
Abstract
Norepinephrine is a biogenic amine neurotransmitter that has widespread effects on alertness, arousal and pain sensation. Consequently, blockers of norepinephrine uptake have served as vital tools to treat depression and chronic pain. Here, we employ the Drosophila melanogaster dopamine transporter as a surrogate for the norepinephrine transporter and determine X-ray structures of the transporter in its substrate-free and norepinephrine-bound forms. We also report structures of the transporter in complex with inhibitors of chronic pain including duloxetine, milnacipran and a synthetic opioid, tramadol. When compared to dopamine, we observe that norepinephrine binds in a different pose, in the vicinity of subsite C within the primary binding site. Our experiments reveal that this region is the binding site for chronic pain inhibitors and a determinant for norepinephrine-specific reuptake inhibition, thereby providing a paradigm for the design of specific inhibitors for catecholamine neurotransmitter transporters.
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Affiliation(s)
| | | | - Deepthi Joseph
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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37
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George B, Assaiya A, Roy RJ, Kembhavi A, Chauhan R, Paul G, Kumar J, Philip NS. CASSPER is a semantic segmentation-based particle picking algorithm for single-particle cryo-electron microscopy. Commun Biol 2021; 4:200. [PMID: 33589717 PMCID: PMC7884729 DOI: 10.1038/s42003-021-01721-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 01/19/2021] [Indexed: 11/27/2022] Open
Abstract
Particle identification and selection, which is a prerequisite for high-resolution structure determination of biological macromolecules via single-particle cryo-electron microscopy poses a major bottleneck for automating the steps of structure determination. Here, we present a generalized deep learning tool, CASSPER, for the automated detection and isolation of protein particles in transmission microscope images. This deep learning tool uses Semantic Segmentation and a collection of visually prepared training samples to capture the differences in the transmission intensities of protein, ice, carbon, and other impurities found in the micrograph. CASSPER is a semantic segmentation based method that does pixel-level classification and completely eliminates the need for manual particle picking. Integration of Contrast Limited Adaptive Histogram Equalization (CLAHE) in CASSPER enables high-fidelity particle detection in micrographs with variable ice thickness and contrast. A generalized CASSPER model works with high efficiency on unseen datasets and can potentially pick particles on-the-fly, enabling data processing automation.
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Affiliation(s)
- Blesson George
- Artificial Intelligence Research and Intelligent Systems (airis4D), Thelliyoor, Kerala, India
- Department of Physics, CMS College, Kottayam, Kerala, India
| | - Anshul Assaiya
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, S. P. Pune University Campus, Pune, India
| | - Robin J Roy
- Artificial Intelligence Research and Intelligent Systems (airis4D), Thelliyoor, Kerala, India
| | - Ajit Kembhavi
- Inter-University Centre for Astronomy and Astrophysics (IUCAA), S. P. Pune University Campus, Pune, India
| | - Radha Chauhan
- Laboratory of Structural Biology, National Centre for Cell Science, S. P. Pune University Campus, Pune, India
| | - Geetha Paul
- Artificial Intelligence Research and Intelligent Systems (airis4D), Thelliyoor, Kerala, India
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, S. P. Pune University Campus, Pune, India.
| | - Ninan S Philip
- Artificial Intelligence Research and Intelligent Systems (airis4D), Thelliyoor, Kerala, India.
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38
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Appadurai R, Nagesh J, Srivastava A. High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme. Nat Commun 2021; 12:958. [PMID: 33574233 PMCID: PMC7878814 DOI: 10.1038/s41467-021-21105-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [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: 06/15/2020] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
Mapping free energy landscapes of complex multi-funneled metamorphic proteins and weakly-funneled intrinsically disordered proteins (IDPs) remains challenging. While rare-event sampling molecular dynamics simulations can be useful, they often need to either impose restraints or reweigh the generated data to match experiments. Here, we present a parallel-tempering method that takes advantage of accelerated water dynamics and allows efficient and accurate conformational sampling across a wide variety of proteins. We demonstrate the improved sampling efficiency by benchmarking against standard model systems such as alanine di-peptide, TRP-cage and β-hairpin. The method successfully scales to large metamorphic proteins such as RFA-H and to highly disordered IDPs such as Histatin-5. Across the diverse proteins, the calculated ensemble averages match well with the NMR, SAXS and other biophysical experiments without the need to reweigh. By allowing accurate sampling across different landscapes, the method opens doors for sampling free energy landscape of complex uncharted proteins.
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Affiliation(s)
- Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Jayashree Nagesh
- Solid State & Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India.
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39
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Bruin WB, Taylor L, Thomas RM, Shock JP, Zhutovsky P, Abe Y, Alonso P, Ameis SH, Anticevic A, Arnold PD, Assogna F, Benedetti F, Beucke JC, Boedhoe PSW, Bollettini I, Bose A, Brem S, Brennan BP, Buitelaar JK, Calvo R, Cheng Y, Cho KIK, Dallaspezia S, Denys D, Ely BA, Feusner JD, Fitzgerald KD, Fouche JP, Fridgeirsson EA, Gruner P, Gürsel DA, Hauser TU, Hirano Y, Hoexter MQ, Hu H, Huyser C, Ivanov I, James A, Jaspers-Fayer F, Kathmann N, Kaufmann C, Koch K, Kuno M, Kvale G, Kwon JS, Liu Y, Lochner C, Lázaro L, Marques P, Marsh R, Martínez-Zalacaín I, Mataix-Cols D, Menchón JM, Minuzzi L, Moreira PS, Morer A, Morgado P, Nakagawa A, Nakamae T, Nakao T, Narayanaswamy JC, Nurmi EL, O'Neill J, Pariente JC, Perriello C, Piacentini J, Piras F, Piras F, Reddy YCJ, Rus-Oswald OG, Sakai Y, Sato JR, Schmaal L, Shimizu E, Simpson HB, Soreni N, Soriano-Mas C, Spalletta G, Stern ER, Stevens MC, Stewart SE, Szeszko PR, Tolin DF, Venkatasubramanian G, Wang Z, Yun JY, van Rooij D, Thompson PM, van den Heuvel OA, Stein DJ, van Wingen GA. Structural neuroimaging biomarkers for obsessive-compulsive disorder in the ENIGMA-OCD consortium: medication matters. Transl Psychiatry 2020; 10:342. [PMID: 33033241 PMCID: PMC7598942 DOI: 10.1038/s41398-020-01013-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/09/2020] [Accepted: 09/14/2020] [Indexed: 11/08/2022] Open
Abstract
No diagnostic biomarkers are available for obsessive-compulsive disorder (OCD). Here, we aimed to identify magnetic resonance imaging (MRI) biomarkers for OCD, using 46 data sets with 2304 OCD patients and 2068 healthy controls from the ENIGMA consortium. We performed machine learning analysis of regional measures of cortical thickness, surface area and subcortical volume and tested classification performance using cross-validation. Classification performance for OCD vs. controls using the complete sample with different classifiers and cross-validation strategies was poor. When models were validated on data from other sites, model performance did not exceed chance-level. In contrast, fair classification performance was achieved when patients were grouped according to their medication status. These results indicate that medication use is associated with substantial differences in brain anatomy that are widely distributed, and indicate that clinical heterogeneity contributes to the poor performance of structural MRI as a disease marker.
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Affiliation(s)
- Willem B Bruin
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, Amsterdam, Netherlands.
| | - Luke Taylor
- Department of Physiology, Anatomy and Genetics, Oxford, UK
| | - Rajat M Thomas
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Jonathan P Shock
- Department of mathematics and applied mathematics, University of Cape Town, Cape Town, South Africa
| | - Paul Zhutovsky
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Yoshinari Abe
- Department of Psychiatry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Pino Alonso
- Department of Psychiatry, Bellvitge University Hospital, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomèdica en Red de Salud Mental-CIBERSAM, Barcelona, Spain
- Department of Clinical Sciences, University of Barcelona, Barcelona, Spain
| | - Stephanie H Ameis
- The Margaret and Wallace McCain Centre for Child, Youth and Family Mental Health, Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health, Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Canada
- Centre for Brain and Mental Health, The Hospital for Sick Children, Toronto, Canada
| | - Alan Anticevic
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Paul D Arnold
- Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Francesca Assogna
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Francesco Benedetti
- Psychiatry and Clinical Psychobiology, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
| | - Jan C Beucke
- Department of Psychology, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Clinical Neuroscience, Centre for Psychiatric Research and Education, Karolinska Institutet, Stockholm, Sweden
| | - Premika S W Boedhoe
- Amsterdam UMC, Vrije Universteit Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Irene Bollettini
- Psychiatry and Clinical Psychobiology, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
| | - Anushree Bose
- Obsessive-Compulsive Disorder (OCD) Clinic Department of Psychiatry National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Silvia Brem
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric Hospital, University of Zurich, Zurich, Switzerland
- University of Zurich and ETH Zurich, Neuroscience Center Zurich, Zurich, Switzerland
| | - Brian P Brennan
- McLean Hospital, Harvard Medical School, Belmont, MA, 02115, USA
| | - Jan K Buitelaar
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
- Karakter Child and Adolescent Psychiatry University Center, Nijmegen, The Netherlands
| | - Rosa Calvo
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clínic Universitari, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en red de Salud Mental (CIBERSAM), Barcelona, Spain
| | - Yuqi Cheng
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Kang Ik K Cho
- Institute of Human Behavioral Medicine, SNU-MRC, Seoul, Republic of Korea
| | - Sara Dallaspezia
- Psychiatry and Clinical Psychobiology, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
| | - Damiaan Denys
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, Amsterdam, Netherlands
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Benjamin A Ely
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jamie D Feusner
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, 94612, USA
| | - Kate D Fitzgerald
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jean-Paul Fouche
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Egill A Fridgeirsson
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Patricia Gruner
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Deniz A Gürsel
- Department of Neuroradiology, Klinikum rechts der Isar, Technische Universität München, München, Germany
- TUM-Neuroimaging Center (TUM-NIC) of Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Tobias U Hauser
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric Hospital, University of Zurich, Zurich, Switzerland
- Max Planck UCL Centre for Computational Psychiatry and Ageing Research, London, UK
- Wellcome Centre for Human Neuroimaging, University College London, London, UK
| | - Yoshiyuki Hirano
- Research Center for Child Mental Development, Chiba University, Chiba, Japan
| | - Marcelo Q Hoexter
- Departamento e Instituto de Psiquiatria do Hospital das Clinicas, IPQ HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brasil
| | - Hao Hu
- Shanghai Mental Health Center Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaim Huyser
- De Bascule, Academic Center for Child and Adolescent Psychiatry, Amsterdam, The Netherlands
- Department of child and adolescent psychiatry Amsterdam UMC, Amsterdam, The Netherlands
| | - Iliyan Ivanov
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anthony James
- Department of Psychiatry, , Oxford University, Oxford, UK
| | | | - Norbert Kathmann
- Department of Psychology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Kaufmann
- Department of Psychology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kathrin Koch
- Department of Neuroradiology, Klinikum rechts der Isar, Technische Universität München, München, Germany
- TUM-Neuroimaging Center (TUM-NIC) of Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Masaru Kuno
- Research Center for Child Mental Development, Chiba University, Chiba, Japan
| | - Gerd Kvale
- Bergen Center for Brain Plasticity, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Psychology, University of Bergen, Bergen, Norway
| | - Jun Soo Kwon
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Brain and Cognitive Sciences, Seoul National University College of Natural Sciences, Seoul, Korea
| | - Yanni Liu
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christine Lochner
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, Stellenbosch University, Stellenbosch, South Africa
| | - Luisa Lázaro
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clínic Universitari, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en red de Salud Mental (CIBERSAM), Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Paulo Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Clinical Academic Center-Braga, Braga, Portugal
| | - Rachel Marsh
- Columbia University Irving Medical Center, Columbia University, New York, NY, 10027, USA
- The Division of Child and Adolescent Psychiatry, New York State Psychiatric Institute, Columbia University, New York, NY, 10027, USA
| | - Ignacio Martínez-Zalacaín
- Department of Psychiatry, Bellvitge University Hospital, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, University of Barcelona, Barcelona, Spain
| | - David Mataix-Cols
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
| | - José M Menchón
- Department of Psychiatry, Bellvitge University Hospital, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomèdica en Red de Salud Mental-CIBERSAM, Barcelona, Spain
- Department of Clinical Sciences, University of Barcelona, Barcelona, Spain
| | - Luciano Minuzzi
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Pedro S Moreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Clinical Academic Center-Braga, Braga, Portugal
| | - Astrid Morer
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clínic Universitari, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en red de Salud Mental (CIBERSAM), Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pedro Morgado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Clinical Academic Center-Braga, Braga, Portugal
| | - Akiko Nakagawa
- Research Center for Child Mental Development, Chiba University, Chiba, Japan
| | - Takashi Nakamae
- Department of Psychiatry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomohiro Nakao
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Janardhanan C Narayanaswamy
- Obsessive-Compulsive Disorder (OCD) Clinic Department of Psychiatry National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Erika L Nurmi
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, 94612, USA
| | - Joseph O'Neill
- Division of Child and Adolescent Psychiatry, Jane and Terry Semel Institute For Neurosciences, University of California, Los Angeles, CA, 94612, USA
| | - Jose C Pariente
- Magnetic Resonance Image Core Facility, IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain
| | - Chris Perriello
- McLean Hospital, Harvard Medical School, Belmont, MA, 02115, USA
- University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
| | - John Piacentini
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, 94612, USA
| | - Fabrizio Piras
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Federica Piras
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Y C Janardhan Reddy
- Obsessive-Compulsive Disorder (OCD) Clinic Department of Psychiatry National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Oana G Rus-Oswald
- University of Zürich, University Hospital Zürich, Dept. Neuroradiology, Zürich, Switzerland
- University Department of Geriatric Medicine Felix Platter, Basel, Switzerland
| | - Yuki Sakai
- Department of Psychiatry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- ATR Brain Information Communication Research Laboratory Group, Kyoto, Japan
| | - João R Sato
- Center of Mathematics, Computing and Cognition, Universidade Federal do ABC, Santo Andre, Brazil
| | - Lianne Schmaal
- Orygen, Parkville, VIC, Australia
- Centre for Youth Mental Health, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Eiji Shimizu
- Research Center for Child Mental Development, Chiba University, Chiba, Japan
- Department of Cognitive Behavioral Physiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - H Blair Simpson
- Columbia University Irving Medical Center, Columbia University, New York, NY, 10027, USA
- Center for OCD and Related Disorders, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Noam Soreni
- Pediatric OCD Consultation service, Anxiety Treatment and Research Center, St. Joseph's HealthCare, Hamilton, ON, L9C 0E3, Canada
- Offord Child Center, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Carles Soriano-Mas
- Department of Psychiatry, Bellvitge University Hospital, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomèdica en Red de Salud Mental-CIBERSAM, Barcelona, Spain
- Department of Psychobiology and Methodology of Health Sciences, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Gianfranco Spalletta
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
- Beth K. and Stuart C. Yudofsky Division of Neuropsychiatry, Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Emily R Stern
- Department of Psychiatry, New York University Langone School of Medicine, New York, NY, 10016, USA
- Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, 10962, USA
| | - Michael C Stevens
- Olin Neuropsychiatry Research Center, Hartford Hospital, Hartford, CT, 06106, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, 06510, USA
| | - S Evelyn Stewart
- University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- British Columbia Children's Hospital, Vancouver, BC, V6H 3N1, Canada
- British Columbia Mental Health and Addictions Research Institute, Vancouver, BC, V6H 3N1, Canada
| | - Philip R Szeszko
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J. Peters VA Medical Center, Bronx, New York, NY, 10468, USA
| | - David F Tolin
- Institute of Living/Hartford Hospital, Hartford, CT, 06119, USA
- Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ganesan Venkatasubramanian
- Obsessive-Compulsive Disorder (OCD) Clinic Department of Psychiatry National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Zhen Wang
- Shanghai Mental Health Center Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Je-Yeon Yun
- Seoul National University Hospital, Seoul, Republic of Korea
- Yeongeon Student Support Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Daan van Rooij
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Donders Centre for Cognitive Neuroimaging, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90007, USA
| | - Odile A van den Heuvel
- Amsterdam UMC, Vrije Universteit Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Dan J Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Guido A van Wingen
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, Amsterdam, Netherlands.
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Walavalkar K, Saravanan B, Singh AK, Jayani RS, Nair A, Farooq U, Islam Z, Soota D, Mann R, Shivaprasad PV, Freedman ML, Sabarinathan R, Haiman CA, Notani D. A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer. Nat Commun 2020; 11:3598. [PMID: 32680982 PMCID: PMC7368061 DOI: 10.1038/s41467-020-17325-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 10/28/2019] [Accepted: 06/24/2020] [Indexed: 11/18/2022] Open
Abstract
Genetic variation at the 8q24 locus is linked with the greater susceptibility to prostate cancer in men of African ancestry. One such African ancestry specific rare variant, rs72725854 (A>G/T) (~6% allele frequency) has been associated with a ~2-fold increase in prostate cancer risk. However, the functional relevance of this variant is unknown. Here we show that the variant rs72725854 is present in a prostate cancer-specific enhancer at 8q24 locus. Chromatin-conformation capture and dCas9 mediated enhancer blocking establish a direct regulatory link between this enhancer and lncRNAs PCAT1, PRNCR1 and PVT1. The risk allele ('T') is associated with higher expression of PCAT1, PVT1 and c-myc in prostate tumors. Further, enhancer with the risk allele gains response to androgen stimulation by recruiting the transcription factor SPDEF whereas, non-risk alleles remain non-responsive. Elevated expression of these lncRNAs and c-myc in risk allele carriers may explain their greater susceptibility to prostate cancer.
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Affiliation(s)
- Kaivalya Walavalkar
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Bharath Saravanan
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
- Sastra Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Anurag Kumar Singh
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Ranveer Singh Jayani
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Ashwin Nair
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
- Sastra Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Umer Farooq
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
- Trans-Disciplinary University, IVRI road, Bangalore, Tamil Nadu, 560064, Karnataka, India
| | - Zubairul Islam
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
- Sastra Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Deepanshu Soota
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Rajat Mann
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Padubidri V Shivaprasad
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
- Centre for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Radhakrishnan Sabarinathan
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90007, USA
| | - Dimple Notani
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.
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Goutham S, Kumari I, Pally D, Singh A, Ghosh S, Akhter Y, Bhat R. Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins. Sci Rep 2020; 10:6040. [PMID: 32269229 PMCID: PMC7142085 DOI: 10.1038/s41598-020-61427-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 06/20/2019] [Accepted: 01/30/2020] [Indexed: 11/08/2022] Open
Abstract
Several post-translational protein modifications lie predominantly within regions of disorder: the biased localization has been proposed to expand the binding versatility of disordered regions. However, investigating a representative dataset of 500 human N-glycoproteins, we observed the sites of N-linked glycosylations or N-glycosites, to be predominantly present in the regions of predicted order. When compared with disordered stretches, ordered regions were not found to be enriched for asparagines, serines and threonines, residues that constitute the sequon signature for conjugation of N-glycans. We then investigated the basis of mutual exclusivity between disorder and N-glycosites on the basis of amino acid distribution: when compared with control ordered residue stretches without any N-glycosites, residue neighborhoods surrounding N-glycosites showed a depletion of bulky, hydrophobic and disorder-promoting amino acids and an enrichment for flexible and accessible residues that are frequently found in coiled structures. When compared with control disordered residue stretches without any N-glycosites, N-glycosite neighborhoods were depleted of charged, polar, hydrophobic and flexible residues and enriched for aromatic, accessible and order-promoting residues with a tendency to be part of coiled and β structures. N-glycosite neighborhoods also showed greater phylogenetic conservation among amniotes, compared with control ordered regions, which in turn were more conserved than disordered control regions. Our results lead us to propose that unique primary structural compositions and differential propensities for evolvability allowed for the mutual spatial exclusion of N-glycosite neighborhoods and disordered stretches.
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Affiliation(s)
- Shyamili Goutham
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Indu Kumari
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, District-Kangra, Shahpur, Himachal Pradesh, 176206, India
| | - Dharma Pally
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Alvina Singh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Sujasha Ghosh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Ramray Bhat
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India.
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42
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Abstract
Imagine smelling a novel perfume with only one nostril and then smelling it again with the other nostril. Clearly, you can tell that it is the same perfume both times. This simple experiment demonstrates that odor information is shared across both hemispheres to enable perceptual unity. In many sensory systems, perceptual unity is believed to be mediated by inter-hemispheric connections between iso-functional cortical regions. However, in the olfactory system, the underlying neural mechanisms that enable this coordination are unclear because the two olfactory cortices are not topographically organized and do not seem to have homotypic inter-hemispheric mapping. This review presents recent advances in determining which aspects of odor information are processed unilaterally or bilaterally, and how odor information is shared across the two hemispheres. We argue that understanding the mechanisms of inter-hemispheric coordination can provide valuable insights that are hard to achieve when focusing on one hemisphere alone.
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Affiliation(s)
- Tal Dalal
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Nitin Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, 208016, India
| | - Rafi Haddad
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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43
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Dubey A, Ray S. Comparison of tuning properties of gamma and high-gamma power in local field potential (LFP) versus electrocorticogram (ECoG) in visual cortex. Sci Rep 2020; 10:5422. [PMID: 32214127 PMCID: PMC7096473 DOI: 10.1038/s41598-020-61961-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 06/11/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022] Open
Abstract
Electrocorticogram (ECoG), obtained from macroelectrodes placed on the cortex, is typically used in drug-resistant epilepsy patients, and is increasingly being used to study cognition in humans. These studies often use power in gamma (30-70 Hz) or high-gamma (>80 Hz) ranges to make inferences about neural processing. However, while the stimulus tuning properties of gamma/high-gamma power have been well characterized in local field potential (LFP; obtained from microelectrodes), analogous characterization has not been done for ECoG. Using a hybrid array containing both micro and ECoG electrodes implanted in the primary visual cortex of two female macaques (for some stimulus conditions, separate ECoG and microelectrode arrays in two additional male macaques were also used), we compared the stimulus tuning preferences of gamma/high-gamma power in LFP versus ECoG in up to four monkeys, and found them to be surprisingly similar. High-gamma power, thought to index the average firing rate around the electrode, was highest for the smallest stimulus (0.3° radius), and decreased with increasing size in both LFP and ECoG, suggesting local origins of both signals. Further, gamma oscillations were similarly tuned in LFP and ECoG to stimulus orientation, contrast and spatial frequency. This tuning was significantly weaker in electroencephalogram (EEG), suggesting that ECoG is more like LFP than EEG. Overall, our results validate the use of ECoG in clinical and basic cognitive research.
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Affiliation(s)
- Agrita Dubey
- Centre for Neuroscience, Indian Institute of Science, Bangalore, 560012, India
- Center for Neural Science, New York University, New York, 10003, USA
| | - Supratim Ray
- Centre for Neuroscience, Indian Institute of Science, Bangalore, 560012, India.
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44
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Tiwari R, Manzar N, Bhatia V, Yadav A, Nengroo MA, Datta D, Carskadon S, Gupta N, Sigouros M, Khani F, Poutanen M, Zoubeidi A, Beltran H, Palanisamy N, Ateeq B. Androgen deprivation upregulates SPINK1 expression and potentiates cellular plasticity in prostate cancer. Nat Commun 2020; 11:384. [PMID: 31959826 PMCID: PMC6971084 DOI: 10.1038/s41467-019-14184-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 03/07/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
Emergence of an aggressive androgen receptor (AR)-independent neuroendocrine prostate cancer (NEPC) after androgen-deprivation therapy (ADT) is well-known. Nevertheless, the majority of advanced-stage prostate cancer patients, including those with SPINK1-positive subtype, are treated with AR-antagonists. Here, we show AR and its corepressor, REST, function as transcriptional-repressors of SPINK1, and AR-antagonists alleviate this repression leading to SPINK1 upregulation. Increased SOX2 expression during NE-transdifferentiation transactivates SPINK1, a critical-player for maintenance of NE-phenotype. SPINK1 elicits epithelial-mesenchymal-transition, stemness and cellular-plasticity. Conversely, pharmacological Casein Kinase-1 inhibition stabilizes REST, which in cooperation with AR causes SPINK1 transcriptional-repression and impedes SPINK1-mediated oncogenesis. Elevated levels of SPINK1 and NEPC markers are observed in the tumors of AR-antagonists treated mice, and in a subset of NEPC patients, implicating a plausible role of SPINK1 in treatment-related NEPC. Collectively, our findings provide an explanation for the paradoxical clinical-outcomes after ADT, possibly due to SPINK1 upregulation, and offers a strategy for adjuvant therapies.
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Affiliation(s)
- Ritika Tiwari
- Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, UP, 208016, India
| | - Nishat Manzar
- Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, UP, 208016, India
| | - Vipul Bhatia
- Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, UP, 208016, India
| | - Anjali Yadav
- Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, UP, 208016, India
| | - Mushtaq A Nengroo
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, UP, 226031, India
| | - Dipak Datta
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, UP, 226031, India
| | - Shannon Carskadon
- Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Nilesh Gupta
- Department of Pathology, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Michael Sigouros
- Division of Medical Oncology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Francesca Khani
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
| | - Amina Zoubeidi
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Himisha Beltran
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Nallasivam Palanisamy
- Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Bushra Ateeq
- Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, UP, 208016, India.
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45
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Reddy PC, Gungi A, Ubhe S, Pradhan SJ, Kolte A, Galande S. Molecular signature of an ancient organizer regulated by Wnt/β-catenin signalling during primary body axis patterning in Hydra. Commun Biol 2019; 2:434. [PMID: 31799436 PMCID: PMC6879750 DOI: 10.1038/s42003-019-0680-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 11/06/2019] [Indexed: 11/20/2022] Open
Abstract
Wnt/β-catenin signalling has been shown to play a critical role during head organizer formation in Hydra. Here, we characterized the Wnt signalling regulatory network involved in formation of the head organizer. We found that Wnt signalling regulates genes that are important in tissue morphogenesis. We identified that majority of transcription factors (TFs) regulated by Wnt/β-catenin signalling belong to the homeodomain and forkhead families. Silencing of Margin, one of the Wnt regulated homeodomain TFs, results in loss of the ectopic tentacle phenotype typically seen upon activation of Wnt signalling. Furthermore, we show that the Margin promoter is directly bound and regulated by β-catenin. Ectopic expression of Margin in zebrafish embryos results in body axis abnormalities suggesting that Margin plays a role in axis patterning. Our findings suggest that homeobox TFs came under the regulatory umbrella of Wnt/β-catenin signalling presumably resulting in the evolution of primary body axis in animal phyla.
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Affiliation(s)
- Puli Chandramouli Reddy
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Akhila Gungi
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Suyog Ubhe
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Saurabh J. Pradhan
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Amol Kolte
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, 411008 India
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Tiwari HK, Robertson ID, O'Dea M, Vanak AT. Demographic characteristics of free-roaming dogs (FRD) in rural and urban India following a photographic sight-resight survey. Sci Rep 2019; 9:16562. [PMID: 31719565 PMCID: PMC6851138 DOI: 10.1038/s41598-019-52992-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/24/2019] [Indexed: 11/08/2022] Open
Abstract
An understanding of the core demographic characteristics of the sub-populations of FRD is essential to effectively implement both rabies control interventions through mass vaccination of FRD, and dog population control programmes. This study compares the data obtained following photographic sight-resight surveys in rural (Shirsuphal village in west India) and urban (Municipal Corporation Panchkula in north India) locations . A total of 263 and 1408 FRD were seen at least once through 617 and 3465 sightings in the rural and urban sites, respectively. The rural location had a lower proportion of females (OR 0.5, 95% CI 0.4-0.7) and a higher proportion of poor and fair conditioned dogs (OR 1.8, 95% CI 1.3-2.3) compared to the urban setting. The rural site also had fewer active FRD (OR 0.6, 95% CI 0.5-0.7) and FRD were less likely to be sighted within 20 m of garbage points (OR 0.3, 95% CI 0.2-0.3) compared to the urban site. The demographic composition of the FRD population was found to vary within the urban location, with the odds of sighting a de-sexed dog being significantly higher in residential areas compared to other areas. The study underlines the importance of knowing the demographic composition of FRD for implementation of effective interventions against rabies. Fewer female dogs in the rural location indicate that spaying could be an effective tool for dog population management in this setting, while presence of dogs within 20 m of garbage points in urban settings highlights that an improved garbage management may reduce the carrying capacity of the urban locality resulting in smaller FRD population. It is concluded that quick and low cost surveys can generate useful demographic data for FRD in urban and rural settings which can be useful to understand the epidemiology of rabies and its control.
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Affiliation(s)
- Harish Kumar Tiwari
- College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia.
- Ashoka Trust for Research on Ecology and the Environment (ATREE), Bangalore, India.
- AUSVET, 5 Shuffrey Street, Fremantle, Perth, Western Australia, Australia.
| | - Ian D Robertson
- College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
- China-Australia Joint Research and Training Center for Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mark O'Dea
- College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Abi Tamim Vanak
- Ashoka Trust for Research on Ecology and the Environment (ATREE), Bangalore, India
- Wellcome Trust/DBT India-Alliance Fellow, Hyderabad, India
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
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Ganesan S, Palani HK, Lakshmanan V, Balasundaram N, Alex AA, David S, Venkatraman A, Korula A, George B, Balasubramanian P, Palakodeti D, Vyas N, Mathews V. Stromal cells downregulate miR-23a-5p to activate protective autophagy in acute myeloid leukemia. Cell Death Dis 2019; 10:736. [PMID: 31570693 PMCID: PMC6769009 DOI: 10.1038/s41419-019-1964-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 04/03/2019] [Revised: 08/08/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022]
Abstract
Complex molecular cross talk between stromal cells and the leukemic cells in bone marrow is known to contribute significantly towards drug-resistance. Here, we have identified the molecular events that lead to stromal cells mediated therapy-resistance in acute myeloid leukemia (AML). Our work demonstrates that stromal cells downregulate miR-23a-5p levels in leukemic cells to protect them from the chemotherapy induced apoptosis. Downregulation of miR-23a-5p in leukemic cells leads to upregulation of protective autophagy by targeting TLR2 expression. Further, autophagy inhibitors when used as adjuvants along with conventional drugs can improve drug sensitivity in vitro as well in vivo in a mouse model of leukemia. Our work also demonstrates that this mechanism of bone marrow stromal cell mediated regulation of miR-23a-5p levels and subsequent molecular events are relevant predominantly in myeloid leukemia. Our results illustrate the critical and dynamic role of the bone marrow microenvironment in modulating miRNA expression in leukemic cells which could contribute significantly to drug resistance and subsequent relapse, possibly through persistence of minimal residual disease in this environment.
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Affiliation(s)
- Saravanan Ganesan
- Department of Haematology, Christian Medical College, Vellore, India
| | | | - Vairavan Lakshmanan
- Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | | | - Ansu Abu Alex
- Department of Haematology, Christian Medical College, Vellore, India
| | - Sachin David
- Department of Haematology, Christian Medical College, Vellore, India
| | | | - Anu Korula
- Department of Haematology, Christian Medical College, Vellore, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, India
| | | | - Dasaradhi Palakodeti
- Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | - Neha Vyas
- Molecular Medicine Department, St. John's Research Institute, St. John's National Academy of Health Sciences, Bengaluru, India.
| | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, India.
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Abstract
GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better understanding of structural changes that underlie receptor functions, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. While the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a resting state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using structures as a guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. The mutational analysis also identified putative N-glycan interacting residues. Our results provide a molecular framework for understanding gating properties unique to GluK3 and exploring the role of N-linked glycosylation in their modulation.
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Affiliation(s)
- Jyoti Kumari
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Maharashtra, Pune, 411007, India
| | - Rajesh Vinnakota
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Maharashtra, Pune, 411007, India
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Maharashtra, Pune, 411007, India.
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