1
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Paramore SV, Trenado-Yuste C, Sharan R, Nelson CM, Devenport D. Vangl-dependent mesenchymal thinning shapes the distal lung during murine sacculation. Dev Cell 2024:S1534-5807(24)00178-3. [PMID: 38569553 DOI: 10.1016/j.devcel.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 10/18/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
The planar cell polarity (PCP) complex is speculated to function in murine lung development, where branching morphogenesis generates an epithelial tree whose distal tips expand dramatically during sacculation. Here, we show that PCP is dispensable in the airway epithelium for sacculation. Rather, we find a Celsr1-independent role for the PCP component Vangl in the pulmonary mesenchyme: loss of Vangl1/2 inhibits mesenchymal thinning and expansion of the saccular epithelium. Further, loss of mesenchymal Wnt5a mimics sacculation defects observed in Vangl2-mutant lungs, implicating mesenchymal Wnt5a/Vangl signaling as a key regulator of late lung morphogenesis. A computational model predicts that sacculation requires a fluid mesenchymal compartment. Lineage-tracing and cell-shape analyses are consistent with the mesenchyme acting as a fluid tissue, suggesting that loss of Vangl1/2 impacts the ability of mesenchymal cells to exchange neighbors. Our data thus identify an explicit function for Vangl and the pulmonary mesenchyme in actively shaping the saccular epithelium.
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Affiliation(s)
- Sarah V Paramore
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Carolina Trenado-Yuste
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Rishabh Sharan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Celeste M Nelson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
| | - Danelle Devenport
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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2
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Cetera M, Sharan R, Hayward-Lara G, Phillips B, Biswas A, Halley M, Beall E, vonHoldt B, Devenport D. Region-specific reversal of epidermal planar polarity in the rosette fancy mouse. Development 2023; 150:dev202078. [PMID: 37622728 PMCID: PMC10499026 DOI: 10.1242/dev.202078] [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: 06/13/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
The planar cell polarity (PCP) pathway collectively orients cells with respect to a body axis. Hair follicles of the murine epidermis provide a striking readout of PCP activity in their uniform alignment across the skin. Here, we characterize, from the molecular to tissue-scale, PCP establishment in the rosette fancy mouse, a natural variant with posterior-specific whorls in its fur, to understand how epidermal polarity is coordinated across the tissue. We find that rosette hair follicles emerge with reversed orientations specifically in the posterior region, creating a mirror image of epidermal polarity. The rosette trait is associated with a missense mutation in the core PCP gene Fzd6, which alters a consensus site for N-linked glycosylation, inhibiting its membrane localization. Unexpectedly, the Fzd6 trafficking defect does not block asymmetric localization of the other PCP proteins. Rather, the normally uniform axis of PCP asymmetry rotates where the PCP-directed cell movements that orient follicles are reversed, suggesting the PCP axis rotates 180°. Collectively, our multiscale analysis of epidermal polarity reveals PCP patterning can be regionally decoupled to produce posterior whorls in the rosette fancy mouse.
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Affiliation(s)
- Maureen Cetera
- Department of Genetics, Cell Biology and Development, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Rishabh Sharan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | | | - Brooke Phillips
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Abhishek Biswas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Research Computing, Office of Information Technology, Princeton University, Princeton, NJ 08540, USA
| | - Madalene Halley
- Department of Genetics, Cell Biology and Development, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Evalyn Beall
- Department of Genetics, Cell Biology and Development, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
| | - Danelle Devenport
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
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3
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Cetera M, Sharan R, Hayward-Lara G, Phillips B, Biswas A, Halley M, Beall E, vonHoldt B, Devenport D. Region-specific reversal of epidermal planar polarity in the fancy rosette mouse. bioRxiv 2023:2023.07.27.550849. [PMID: 37546950 PMCID: PMC10402159 DOI: 10.1101/2023.07.27.550849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The planar cell polarity (PCP) pathway collectively orients thousands of cells with respect to a body axis to direct cellular behaviors that are essential for embryonic morphogenesis. Hair follicles of the murine epidermis provide a striking readout of PCP activity in their uniform alignment along the entire skin surface. Here, we characterize, from the molecular to tissue-scale, PCP establishment in the rosette fancy mouse, a natural variant with posterior-specific whorls in its fur, to understand how epidermal polarity is coordinated across the tissue. We find that embryonic hair follicles of rosette mutants emerge with reversed orientations specifically in the posterior region, creating a mirror image of epidermal polarity. The rosette trait is associated with a missense mutation in the core PCP gene Fzd6 , which alters a consensus site for N-linked glycosylation and inhibits its membrane localization. Unexpectedly, this defect in Fzd6 trafficking, observed across the entire dorsal epidermis, does not interfere with the ability of other core PCP proteins to localize asymmetrically. Rather, the normally uniform axis of PCP asymmetry is disrupted and rotated in the posterior region such that polarity is reflected on either side of a transition zone. The result is a reversal of polarized cell movements that orient nascent follicles, specifically in the posterior of the embryo. Collectively, our multiscale analysis of epidermal polarity reveals PCP patterning can be regionally decoupled to produce the unique posterior whorls of the fancy rosette mouse. Summary Region-specific rotation of the Planar Cell Polarity axis reverses posterior hair follicles in the fancy rosette mouse.
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4
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Manikantan K, Jain PV, Sharan R, Arun P. Feasibility of a truncated surveillance schedule for patients following curative intent treatment for carcinoma of the oral cavity. Int J Oral Maxillofac Surg 2021; 51:987-991. [PMID: 34772601 DOI: 10.1016/j.ijom.2021.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/24/2022]
Abstract
The purpose of this study was to determine whether a regular follow-up schedule with examination by clinicians results in a better detection rate of disease recurrence and eventual better clinical outcomes when compared to patients who present with symptoms to the clinic and are subsequently detected to have a recurrence of oral squamous cell carcinoma. Retrospective data from 642 patients who underwent treatment for oral squamous cell carcinoma at a tertiary level cancer centre were analysed. Of the 642 patients, 197 had recurrences of which 108 were detected on regular follow-up and 87 were detected in patients presenting out of schedule with symptoms; two patients were detected to have recurrence at another centre, but their mode of detection could not be ascertained. There was no difference in the loco-regional recurrence-free survival or disease-free survival between the two groups. A strict follow-up schedule in the first year followed by a more flexible symptom-based schedule in the subsequent years, with supplementation of imaging if clinically indicated, should be an adequate surveillance plan for oral cancer patients.
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Affiliation(s)
- K Manikantan
- Department of Head and Neck Surgery, Tata Medical Center, New Town, Kolkata, India.
| | - P V Jain
- Department of Head and Neck Surgery, Tata Medical Center, New Town, Kolkata, India
| | - R Sharan
- Department of Head and Neck Surgery, Tata Medical Center, New Town, Kolkata, India
| | - P Arun
- Department of Head and Neck Surgery, Tata Medical Center, New Town, Kolkata, India
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5
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Signorini LF, Almozlino T, Sharan R. ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. BMC Bioinformatics 2021; 22:526. [PMID: 34706638 PMCID: PMC8555137 DOI: 10.1186/s12859-021-04449-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/13/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND ANAT is a Cytoscape plugin for the inference of functional protein-protein interaction networks in yeast and human. It is a flexible graphical tool for scientists to explore and elucidate the protein-protein interaction pathways of a process under study. RESULTS Here we present ANAT3.0, which comes with updated PPI network databases of 544,455 (human) and 155,504 (yeast) interactions, and a new machine-learning layer for refined network elucidation. Together they improve network reconstruction to more than twofold increase in the quality of reconstructing known signaling pathways from KEGG. CONCLUSIONS ANAT3.0 includes improved network reconstruction algorithms and more comprehensive protein-protein interaction networks than previous versions. ANAT is available for download on the Cytoscape Appstore and at https://www.cs.tau.ac.il/~bnet/ANAT/ .
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Affiliation(s)
- L F Signorini
- Blavatnik School of Computer Science, Tel Aviv University, 6997801, Tel Aviv, Israel.,Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - T Almozlino
- Blavatnik School of Computer Science, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - R Sharan
- Blavatnik School of Computer Science, Tel Aviv University, 6997801, Tel Aviv, Israel.
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6
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Basta LP, Hill-Oliva M, Paramore SV, Sharan R, Goh A, Biswas A, Cortez M, Little KA, Posfai E, Devenport D. New mouse models for high resolution and live imaging of planar cell polarity proteins in vivo. Development 2021; 148:271988. [PMID: 34463728 DOI: 10.1242/dev.199695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/24/2021] [Indexed: 01/10/2023]
Abstract
The collective polarization of cellular structures and behaviors across a tissue plane is a near universal feature of epithelia known as planar cell polarity (PCP). This property is controlled by the core PCP pathway, which consists of highly conserved membrane-associated protein complexes that localize asymmetrically at cell junctions. Here, we introduce three new mouse models for investigating the localization and dynamics of transmembrane PCP proteins: Celsr1, Fz6 and Vangl2. Using the skin epidermis as a model, we characterize and verify the expression, localization and function of endogenously tagged Celsr1-3xGFP, Fz6-3xGFP and tdTomato-Vangl2 fusion proteins. Live imaging of Fz6-3xGFP in basal epidermal progenitors reveals that the polarity of the tissue is not fixed through time. Rather, asymmetry dynamically shifts during cell rearrangements and divisions, while global, average polarity of the tissue is preserved. We show using super-resolution STED imaging that Fz6-3xGFP and tdTomato-Vangl2 can be resolved, enabling us to observe their complex localization along junctions. We further explore PCP fusion protein localization in the trachea and neural tube, and discover new patterns of PCP expression and localization throughout the mouse embryo.
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Affiliation(s)
- Lena P Basta
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA
| | - Michael Hill-Oliva
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA.,Department of Medicine, Columbia University, New York, NY 10032USA
| | - Sarah V Paramore
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA
| | - Rishabh Sharan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA
| | - Audrey Goh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA
| | - Abhishek Biswas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA.,Research Computing, Office of Information Technology, Princeton University, Princeton, NJ 08544, USA
| | - Marvin Cortez
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA
| | - Katherine A Little
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA
| | - Eszter Posfai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA
| | - Danelle Devenport
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544USA
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7
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Mallick I, Roy P, Saha S, Arun I, Arun P, Sharan R, Manikantan K, Jain P, Zameer L, Chatterjee S. PO-0952 A dynamically updating individualized survival prediction modelling tool for oral cancer. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)07403-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Stahley SN, Basta LP, Sharan R, Devenport D. Celsr1 adhesive interactions mediate the asymmetric organization of planar polarity complexes. eLife 2021; 10:62097. [PMID: 33529151 PMCID: PMC7857726 DOI: 10.7554/elife.62097] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/23/2021] [Indexed: 12/31/2022] Open
Abstract
To orchestrate collective polarization across tissues, planar cell polarity (PCP) proteins localize asymmetrically to cell junctions, a conserved feature of PCP that requires the atypical cadherin Celsr1. We report that mouse Celsr1 engages in both trans- and cis-interactions, and organizes into dense and highly stable punctate assemblies. We provide evidence suggesting that PCP-mutant variant of Celsr1, Celsr1Crsh, selectively impairs lateral cis-interactions. Although Celsr1Crsh mediates cell adhesion in trans, it displays increased mobility, diminishes junctional enrichment, and fails to engage in homophilic adhesion with the wild-type protein, phenotypes that can be rescued by ectopic cis-dimerization. Using biochemical and super-resolution microscopy approaches, we show that although Celsr1Crsh physically interacts with PCP proteins Frizzled6 and Vangl2, it fails to organize these proteins into asymmetric junctional complexes. Our results suggest mammalian Celsr1 functions not only as a trans-adhesive homodimeric bridge, but also as an organizer of intercellular Frizzled6 and Vangl2 asymmetry through lateral, cis-interactions.
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Affiliation(s)
- Sara N Stahley
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Lena P Basta
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Rishabh Sharan
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Danelle Devenport
- Department of Molecular Biology, Princeton University, Princeton, United States
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9
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Gallagher R, Pattatheyil A, Pantvaidya G, Panizza B, Sharan R, Deshmukh A, Barnett C, Swart D, Mynott T, Cleal A, Gordon V, Prawira A. 974TiP Exploratory phase Ib/IIa study of intratumorally administered tigilanol tiglate to assess safety, tolerability and tumour response in patients with head and neck squamous cell carcinoma. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.1089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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10
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Manickam A, Nallathambi C, Sharan R, Manikantan K, Chatterjee S, Mallick I, Roy P, Zameer M, Arun I, Pattetheyil A. EP-1145: Does Carcinoma Tongue Differ From Gingivobuccal Sulcus? Analysis of Clinicopathology and Outcomes. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)31455-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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11
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Chanet S, Sharan R, Khan Z, Martin AC. Myosin 2-Induced Mitotic Rounding Enables Columnar Epithelial Cells to Interpret Cortical Spindle Positioning Cues. Curr Biol 2017; 27:3350-3358.e3. [DOI: 10.1016/j.cub.2017.09.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/29/2017] [Accepted: 09/19/2017] [Indexed: 01/27/2023]
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12
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Sharan R, Perez-Cruz M, Kervoaze G, Gosset P, Weynants V, Godfroid F, Hermand P, Trottein F, Pichavant M, Gosset P. Interleukin-22 protects against non-typeable Haemophilus influenzae infection: alteration during chronic obstructive pulmonary disease. Mucosal Immunol 2017; 10:139-149. [PMID: 27143304 DOI: 10.1038/mi.2016.40] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 03/24/2016] [Indexed: 02/04/2023]
Abstract
Chronic obstructive pulmonary disease is a major health problem becoming a leading cause of morbidity and mortality worldwide. A large part of these disorders is associated with acute exacerbations resulting from infection by bacteria, such as non-typeable Haemophilus influenzae (NTHi). Our understanding of the pathogenesis of these exacerbations is still elusive. We demonstrate herein that NTHi infection of mice chronically exposed to cigarette smoke (CS), an experimental model of chronic obstructive pulmonary disease (COPD), not only causes acute pulmonary inflammation but also impairs the production of interleukin (IL)-22, a cytokine with potential anti-bacterial activities. We also report that mice lacking IL-22, as well as mice exposed to CS, have a delayed clearance of NTHi bacteria and display enhanced alveolar wall thickening and airway remodeling compared with controls. Supplementation with IL-22 not only boosted bacterial clearance and the production of anti-microbial peptides but also limited lung damages induced by infection both in IL-22-/- and CS-exposed mice. In vitro exposure to CS extract altered the NTHi-induced IL-22 production by spleen cells. This study shows for the first time that a defect in IL-22 is involved in the acute exacerbation induced by NTHi infection during experimental COPD and opens the way to innovative therapeutic strategies.
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Affiliation(s)
- R Sharan
- Université Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- CNRS, UMR 8204, Lille, France
- Inserm, U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - M Perez-Cruz
- Université Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- CNRS, UMR 8204, Lille, France
- Inserm, U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - G Kervoaze
- Université Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- CNRS, UMR 8204, Lille, France
- Inserm, U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Pierre Gosset
- Service d'Anatomo-pathologie, Hôpital Saint Vincent de Paul, Lille, France
| | | | | | | | - F Trottein
- Université Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- CNRS, UMR 8204, Lille, France
- Inserm, U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - M Pichavant
- Université Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- CNRS, UMR 8204, Lille, France
- Inserm, U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - P Gosset
- Université Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- CNRS, UMR 8204, Lille, France
- Inserm, U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
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Abstract
A variety of designed RNA ring structures (ranging from triangles to hexagonal rings) have been reported in the scientific literature. Designing self-assembling RNA ring structures from structural motifs is, however, a nontrivial problem as there are many combinations of motifs and linking helices. Moreover, most combinations of motifs and linker helices will not lead to ring closure. A solution to this problem was recently published using a "design-by-catalog" approach where motif combinations that lead to rings are precomputed and tabulated. Here we present a web-browser based workflow for creating RNA rings using Galaxy, a web-based platform that can be used for workflow management. An example of how these RNA rings are generated and processed to create a 3D model of the ring is discussed.
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Affiliation(s)
- Rishabh Sharan
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Eckart Bindewald
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, USA
| | - Wojciech K Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Bruce A Shapiro
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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14
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Parlea L, Bindewald E, Sharan R, Bartlett N, Moriarty D, Oliver J, Afonin KA, Shapiro BA. Ring Catalog: A resource for designing self-assembling RNA nanostructures. Methods 2016; 103:128-37. [PMID: 27090005 PMCID: PMC6319925 DOI: 10.1016/j.ymeth.2016.04.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 01/21/2016] [Revised: 04/14/2016] [Accepted: 04/14/2016] [Indexed: 01/02/2023] Open
Abstract
Designing self-assembling RNA ring structures based on known 3D structural elements connected via linker helices is a challenging task due to the immense number of motif combinations, many of which do not lead to ring-closure. We describe an in silico solution to this design problem by combinatorial assembly of RNA 3-way junctions, bulges, and kissing loops, and tabulating the cases that lead to ring formation. The solutions found are made available in the form of a web-accessible Ring Catalog. As an example of a potential use of this resource, we chose a predicted RNA square structure consisting of five RNA strands and demonstrate experimentally that the self-assembly of those five strands leads to the formation of a square-like complex. This is a demonstration of a novel "design by catalog" approach to RNA nano-structure generation. The URL https://rnajunction.ncifcrf.gov/ringdb can be used to access the resource.
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Affiliation(s)
- Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Rishabh Sharan
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Nathan Bartlett
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Daniel Moriarty
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Jerome Oliver
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Bruce A Shapiro
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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15
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Manikantan K, Bang B, Sharan R, Mallick I, Chatterjee S, Arun P. Therapeutic Neck Dissection in Oral Squamous Cell Carcinoma: Is Selective Neck Dissection the Way Ahead? Kathmandu Univ Med J (KUMJ) 2016; 14:221-225. [PMID: 28814682] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Background Selective neck dissection in multimodality treatment protocols is slowly being accepted for the management of N+ neck in many centers. This is because the functional disability is lower than modified radical neck dissection. Objective This study compares the regional recurrence rates between patients who underwent selective neck dissection and patients underwent comprehensive neck dissection for node positive oral squamous cell carcinoma. Method A retrospective study comparing patients with node positive oral squamous cell carcinoma who underwent either selective neck dissection or comprehensive neck dissection between August 2011 and January 2014 was done, with a mean follow up period of 12 months. Regional failures were assessed to whether they were isolated neck failures or associated with a local or distant failure. Result A total of 131 neck dissections were performed which included 93 selective neck dissections and 38 comprehensive neck dissections. A total of 17 patients developed regional recurrence, of which 11 patients had ipsilateral neck recurrence. Of the 11 patients with ipsilateral neck recurrence one patient also had contralateral neck nodes and in two patients there was associated distant metastasis. Conclusion Selective neck dissection for management of node positive neck disease is based on sound scientific principles and a randomised controlled trial comparing it with modified radical neck dissection would probably give the answer regarding the optimal procedure for these patients.
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Affiliation(s)
- K Manikantan
- Department of Head and Neck Surgery, Tata Medical Center, Newtown Kolkata 700156, India
| | - B Bang
- Department of Head and Neck Surgery, Tata Medical Center, Newtown Kolkata 700156, India
| | - R Sharan
- Department of Head and Neck Surgery, Tata Medical Center, Newtown Kolkata 700156, India
| | - I Mallick
- Department of Radiation Oncology, Tata Medical Center, Newtown, Kolkata 700156, India
| | - S Chatterjee
- Department of Radiation Oncology, Tata Medical Center, Newtown, Kolkata 700156, India
| | - P Arun
- Department of Head and Neck Surgery, Tata Medical Center, Newtown, Kolkata 700156, India
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Sharma A, Sane H, Gokulchandra N, Sharan R, Paranjape A, Kulkarni P, Yadav J, Badhe P. Effect of Cellular Therapy in Progression of Becker's Muscular Dystrophy: A Case Study. Eur J Transl Myol 2016; 26:5522. [PMID: 27054018 PMCID: PMC4821220 DOI: 10.4081/ejtm.2016.5522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Becker muscular dystrophy (BMD) is an inherited disorder due to deletions of the dystrophin gene that leads to muscle weakness. Effects of bone marrow mononuclear cell (BMMNC) transplantation in Muscular Dystrophy have shown to be safe and beneficial. We treated a 20-year-old male suffering from BMD with autologous BMMNC transplantation followed by multidisciplinary rehabilitation. He presented with muscle weakness and had difficulty in performing his activities. The BMMNCs were transplanted via intrathecal and intramuscular routes. The effects were measured on clinical and functional changes. Over 9 months, gradual improvement was noticed in muscle strength, respiratory functions and North Star Ambulatory Assessment Scale. Functional Independence Measure, Berg Balance Score, Brooke and Vignos Scale remained stable indicating halting of the progression. The case report suggests that cellular therapy combined with rehabilitation may have possibility of repairing and regenerating muscle fibers and decreasing the rate of progression of BMD.
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Affiliation(s)
- Alok Sharma
- Department of Medical Services and Clinical Research, NeuroGen Brain and Spine Institute , Mumbai, India
| | - Hemangi Sane
- Department of Research and Development, NeuroGen Brain and Spine Institute , Mumbai, India
| | - Nandini Gokulchandra
- Department of Medical Services and Clinical Research, NeuroGen Brain and Spine Institute , Mumbai, India
| | - Rishabh Sharan
- Department of Research and Development, NeuroGen Brain and Spine Institute , Mumbai, India
| | - Amruta Paranjape
- Department of Neuro-Rehabilitation, NeuroGen Brain and Spine Institute , Mumbai, India
| | - Pooja Kulkarni
- Department of Research and Development, NeuroGen Brain and Spine Institute , Mumbai, India
| | - Jayanti Yadav
- Department of Neuro-Rehabilitation, NeuroGen Brain and Spine Institute , Mumbai, India
| | - Prerna Badhe
- Department of Medical Services and Clinical Research, NeuroGen Brain and Spine Institute , Mumbai, India
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Uziel O, Yosef N, Sharan R, Ruppin E, Kupiec M, Kushnir M, Beery E, Cohen-Diker T, Nordenberg J, Lahav M. The effects of telomere shortening on cancer cells: a network model of proteomic and microRNA analysis. Genomics 2014; 105:5-16. [PMID: 25451739 DOI: 10.1016/j.ygeno.2014.10.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 10/08/2014] [Accepted: 10/27/2014] [Indexed: 12/21/2022]
Abstract
Previously, we have shown that shortening of telomeres by telomerase inhibition sensitized cancer cells to cisplatinum, slowed their migration, increased DNA damage and impaired DNA repair. The mechanism behind these effects is not fully characterized. Its clarification could facilitate novel therapeutics development and may obviate the time consuming process of telomere shortening achieved by telomerase inhibition. Here we aimed to decipher the microRNA and proteomic profiling of cancer cells with shortened telomeres and identify the key mediators in telomere shortening-induced damage to those cells. Of 870 identified proteins, 98 were differentially expressed in shortened-telomere cells. 47 microRNAs were differentially expressed in these cells; some are implicated in growth arrest or act as oncogene repressors. The obtained data was used for a network construction, which provided us with nodal candidates that may mediate the shortened-telomere dependent features. These proteins' expression was experimentally validated, supporting their potential central role in this system.
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Affiliation(s)
- O Uziel
- FMRC, RMC, Sackler School of Medicine, Tel Aviv University, Israel.
| | - N Yosef
- School of Computer Science, Tel Aviv University, Israel
| | - R Sharan
- School of Computer Science, Tel Aviv University, Israel
| | - E Ruppin
- School of Computer Science, Tel Aviv University, Israel
| | - M Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Israel
| | | | - E Beery
- FMRC, RMC, Sackler School of Medicine, Tel Aviv University, Israel
| | - T Cohen-Diker
- FMRC, RMC, Sackler School of Medicine, Tel Aviv University, Israel
| | - J Nordenberg
- FMRC, RMC, Sackler School of Medicine, Tel Aviv University, Israel
| | - M Lahav
- FMRC, RMC, Sackler School of Medicine, Tel Aviv University, Israel
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18
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Rosa CL, Longmate J, Lacey SF, Kaltcheva T, Sharan R, Marsano D, Kwon P, Drake J, Williams B, Denison S, Broyer S, Couture L, Nakamura R, Dadwal S, Kelsey MI, Krieg AM, Diamond DJ, Zaia JA. La Rosa C et al (J Infect Dis 2012; 205:1294-304). J Infect Dis 2013. [DOI: 10.1093/infdis/jit282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Chatterjee S, Sarkar S, Bang B, Sharan R, Pattatheyil A, Prasath S, Mallick I. EP-1023: Challenges in treatment of oral cavity squamous cell carcinoma in a tertiary care centre in India. Radiother Oncol 2013. [DOI: 10.1016/s0167-8140(15)33329-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Sharma M, Iyer S, Kuriakose M, Vijayaraghavan S, Arun P, Sudhir V, Chatni S, Sharan R. Functional reconstruction of near total glossectomy defects using composite gastro omental-dynamic gracilis flaps. J Plast Reconstr Aesthet Surg 2009; 62:1277-80. [DOI: 10.1016/j.bjps.2007.10.092] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Revised: 08/22/2007] [Accepted: 10/30/2007] [Indexed: 10/21/2022]
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21
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Abstract
MOTIVATION A central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering gene expression data into homogeneous groups was shown to be instrumental in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on clustering algorithms for gene expression analysis, very few works addressed the systematic comparison and evaluation of clustering results. Typically, different clustering algorithms yield different clustering solutions on the same data, and there is no agreed upon guideline for choosing among them. RESULTS We developed a novel statistically based method for assessing a clustering solution according to prior biological knowledge. Our method can be used to compare different clustering solutions or to optimize the parameters of a clustering algorithm. The method is based on projecting vectors of biological attributes of the clustered elements onto the real line, such that the ratio of between-groups and within-group variance estimators is maximized. The projected data are then scored using a non-parametric analysis of variance test, and the score's confidence is evaluated. We validate our approach using simulated data and show that our scoring method outperforms several extant methods, including the separation to homogeneity ratio and the silhouette measure. We apply our method to evaluate results of several clustering methods on yeast cell-cycle gene expression data. AVAILABILITY The software is available from the authors upon request.
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Affiliation(s)
- I Gat-Viks
- School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
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Gat-Viks I, Shamir R, Karp RM, Sharan R. Reconstructing chain functions in genetic networks. Pac Symp Biocomput 2004:498-509. [PMID: 14992528 DOI: 10.1142/9789812704856_0047] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Deciphering the mechanisms that control gene expression in the cell is a fundamental question in molecular biology. This task is complicated by the large number of possible regulation relations in the cell, and the relatively small amount of available experimental data. Recently, a new class of regulation functions called chain functions was suggested. Many signal transduction pathways can be accurately modeled by chain functions, and the restriction to chain functions greatly reduces the vast search space of regulation relations. In this paper we study the computational problem of reconstructing a chain function using a minimum number of experiments, in each of which only few genes are perturbed. We give optimal reconstruction schemes for several scenarios and show their application in reconstructing the regulation of galactose utilization in yeast.
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Affiliation(s)
- I Gat-Viks
- School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel.
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Sharan R, Ben-Dor A, Yakhini Z. Multiplexing schemes for generic SNP genotyping assays. Pac Symp Biocomput 2004:140-51. [PMID: 14992499 DOI: 10.1142/9789812704856_0014] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
A generic genotyping assay utilizes a fixed set of reagents, which is independent of the actual target sample, to determine all present alleles. An example is the interrogation of several amplicons spanning polymorphic sites using an all k-mer array. Due to the high cost associated with a genotyping experiment, it is desirable to design a set of experiments, which maximizes the number of SNPs that can be genotyped in parallel per assay. In this study we investigate algorithmic approaches for optimally multiplexing SNP genotyping using generic assays. We devise a graph theoretic formulation of the problem and use it to derive an approximation algorithm for the problem, and several practical heuristics. We apply our methods to simulated and real data, for evaluating the multiplexing rates afforded by generic techniques. The results on real human data show the practicality of generic approaches for genotyping, allowing, e.g., the genotyping of 5000 SNPs using four all 7-mer arrays.
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Affiliation(s)
- R Sharan
- International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA.
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24
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Affiliation(s)
- R Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
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25
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Abstract
In sequencing by hybridization (SBH), one has to reconstruct a sequence from its l-long substrings. SBH was proposed as an alternative to gel-based DNA sequencing approaches, but in its original form the method is not competitive. Positional SBH (PSBH) is a recently proposed enhancement of SBH in which one has additional information about the possible positions of each substring along the target sequence. We give a linear time algorithm for solving PSBH when each substring has at most two possible positions. On the other hand, we prove that the problem is NP-complete if each substring has at most three possible positions. We also show that PSBH is NP-complete if the set of allowed positions for each substring is an interval of length k and provide a fast algorithm for the latter problem when k is bounded.
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26
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Sharan R, Shamir R. CLICK: a clustering algorithm with applications to gene expression analysis. Proc Int Conf Intell Syst Mol Biol 2001; 8:307-16. [PMID: 10977092] [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] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Novel DNA microarray technologies enable the monitoring of expression levels of thousands of genes simultaneously. This allows a global view on the transcription levels of many (or all) genes when the cell undergoes specific conditions or processes. Analyzing gene expression data requires the clustering of genes into groups with similar expression patterns. We have developed a novel clustering algorithm, called CLICK, which is applicable to gene expression analysis as well as to other biological applications. No prior assumptions are made on the structure or the number of the clusters. The algorithm utilizes graph-theoretic and statistical techniques to identify tight groups of highly similar elements (kernels), which are likely to belong to the same true cluster. Several heuristic procedures are then used to expand the kernels into the full clustering. CLICK has been implemented and tested on a variety of biological datasets, ranging from gene expression, cDNA oligo-fingerprinting to protein sequence similarity. In all those applications it outperformed extant algorithms according to several common figures of merit. CLICK is also very fast, allowing clustering of thousands of elements in minutes, and over 100,000 elements in a couple of hours on a regular workstation.
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Affiliation(s)
- R Sharan
- Department of Computer Science, Tel-Aviv University, Israel.
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27
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Ghandehari H, Sharan R, Rubas W, Killing WM. Molecular modeling of arginine-glycine-aspartic acid (RGD) analogs: relevance to transepithelial transport. J Pharm Pharm Sci 2001; 4:32-41. [PMID: 11302788] [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] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
PURPOSE The aim of this research is to model the effect of methylation on hydrogen bonding ability, surface area, polar surface area, volume, lipophilicity, charge, and cross-sectional diameters of a series of mono-, di-, and tri- methyl substituted analogs of arginine-glycine-aspartic acid (RGD) and compare these parameters to in vitro transport properties across Caco-2 monolayers. METHODS Molecular modeling was used to investigate the structural parameters that may influence the transport properties of RGD and its methyl analogs at pH 7.4. Log P was experimentally determined using a potentiometric method and compared to cLogP. Transport studies were carried out using Caco-2 cell monolayers. RESULTS Parameters such as polar and total surface area, volume, and Log P were found to vary with both the number and the sites of methyl substitution on the RGD molecule. The calculated as well as the experimental Log P values were found to be less than minus 2. The calculated maximum cross-sectional diameters ranged from 9 to 12 A. No detectable transport was noted. CONCLUSIONS Results of our study indicate that in the design considerations for the development of new peptidomimetic RGD analogs with enhanced oral bioavailability, an important parameter to consider is the three dimensional conformation of the peptides which influences their hydrogen bonding ability, polarity and molecular geometry.
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Affiliation(s)
- H Ghandehari
- Department of Pharmaceutics, and Thad Cochran Center for the Development of Natural Products, University of Mississippi, University, Mississippi, USA
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28
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Zawia NH, Sharan R, Brydie M, Oyama T, Crumpton T. Sp1 as a target site for metal-induced perturbations of transcriptional regulation of developmental brain gene expression. Brain Res Dev Brain Res 1998; 107:291-8. [PMID: 9593950 DOI: 10.1016/s0165-3806(98)00023-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Differential gene expression is partially regulated by zinc finger proteins (ZFP) such as Sp1, which may be potential targets for perturbations by environmental metals. In this paper, we discuss the selective effects of lead (Pb) and other heavy metals on the in vitro and in vivo DNA-binding of Sp1, and the developmental expression of its target genes. We have found that the presence of Pb, Zn and Cd in a DNA-binding assay differentially modulated the binding of Sp1 to its specific DNA sequence, while Ca, Mg and Ba, did not. In PC12 cells, cultured in the presence of low concentrations of Pb, a premature enhancement of Sp1 DNA-binding was observed. Similarly, Sp1 DNA-binding in the cerebellum of Pb-exposed animals was shifted to the first week after birth, while the developmental profile of a non-ZFP, NFkB, was not. Furthermore, selective premature peaks of myelin basic protein and proteolipid protein mRNA expression were observed to occur in a manner relative to the changes in Sp1 DNA-binding. Since these genes are high targets for Sp1, these data suggest that exposure to heavy metals may alter developmental gene expression and brain development through selective modulation of the transcriptional activity of Sp1.
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Affiliation(s)
- N H Zawia
- Department of Pharmacology and Environmental Health Division, Meharry Medical College, 1005 D.B. Todd Blvd., Nashville, TN 37208, USA. zawian33ccvax.mmc.edu
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29
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Bajpai K, Singh VK, Sharan R, Yadav VS, Haq W, Mathur KB, Agarwal SS. Immunomodulating activity of analogs of noninflammatory fragment 163-171 of human interleukin-1beta. Immunopharmacology 1998; 38:237-45. [PMID: 9506823 DOI: 10.1016/s0162-3109(97)00070-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The synthetic nonapeptide Val-Gln-Gly-Glu-Glu-Ser-Asn-Asp-Lys corresponding to the amino acid sequence 163-171 of human interleukin-1beta (IL-1beta) has been reported to retain considerable immunostimulatory activity of the native protein without the induction of the inflammatory or pyrogenic responses. Two lipophilic derivatives of this nonapeptide, one having a lauroyl residue (1) and the other having a palmitoyl residue (2) at the N-terminus of the peptide, and a more stable analog carrying D-Val residue at position 1 of the peptide (3) were synthesized with a view to find out if these structural modifications had a favorable effect on in vitro mouse thymocyte proliferation and IL-1 dependent inhibition of A375 cells. We have found that analogs (1) and (2) are active in both the tests like the parent nonapeptide. The lipophilic analog (2) is in fact, effective at a lower dose as compared to the parent nonapeptide in mouse thymocyte proliferation assay. Although the analog (3) has the ability to inhibit A375 cells, it does not stimulate mouse thymocyte proliferation in vitro. The IL-1beta fragment (163-171) and the analog (2) were further compared for their effects on pyrogenicity, blood glucose level, acute phase response and radioprotection. Unlike IL-1beta, its fragment (163-171) and the analog (2) do not induce pyrogenicity and any of the acute phase related changes such as the increase in C-reactive protein and hypoglycemia following their administration in Balb/c mice. We have found that 40% of animals treated with analog (2) survive more than 21 days after lethal irradiation as compared to 20% survivors in groups treated with recombinant IL-1beta or its nonapeptide fragment (163-171), under conditions when all the control animals died within 10 days. This study may help in designing small peptides which may be more effective and stable.
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Affiliation(s)
- K Bajpai
- Department of Immunology, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, India
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30
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Biswas S, Singh VK, Rastogi A, Sharan R, Haq W, Mathur KB, Agarwal SS. Stimulation of IL-2 production and CD2R expression by splenopentin analogs. Int J Immunopharmacol 1997; 19:341-5. [PMID: 9467753 DOI: 10.1016/s0192-0561(97)00032-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Splenopentin (SP-5), is a pentapeptide corresponding to the amino acid sequence 32-36 (Arg-Lys-Glu-Val-Tyr) of the splenic hormone splenin. Its synthetic analogs: Lys-Lys-Glu-Val-Tyr(1) and D-Lys-Lys-Glu-Val-Tyr (2) have been evaluated for active T-cell rosette (CD2R), total T-cell rosette (CD2), interleukin-2 (IL-2) stimulation and effect on antibody production. SP-5 as well as both the analogs stimulated CD2R. Analogs (1) and (2) were also found to stimulate IL-2 production. These observations suggest that in vitro human NK cell augmentation with analogs (1) and (2) reported earlier may be due to enhanced IL-2 production.
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Affiliation(s)
- S Biswas
- Department of Immunology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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31
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Sharma P, Anuradha, Sharan R, Haq W, Kundu B, Katiyar J, Mathur K. Stimulation of Non-Specific Resistance by Human Casein Fragment (54-59) and its Synthetic Analogues against Leishmania Donovani Infection+. Protein Pept Lett 1996. [DOI: 10.2174/092986650304220615155913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
The prophylactic effect of human β casein fragment (54-59) and its synthetic congeners has been studied against L. donovani infection in hamsters. Maximum parasite inhibition (84%) was observed with compound 4. The activity of this compound was further confirmed in vitro
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Affiliation(s)
- P. Sharma
- Divisions of Parasitology, Central Drug Research Institute, Post Box 173, Lucknow-226 001, India
| | - Anuradha
- Divisions of Parasitology, Central Drug Research Institute, Post Box 173, Lucknow-226 001, India
| | - R. Sharan
- Divisions of Biopolymers , Central Drug Research Institute, Post Box 173, Lucknow-226 001, India
| | - W. Haq
- Divisions of Biopolymers , Central Drug Research Institute, Post Box 173, Lucknow-226 001, India
| | - B. Kundu
- Divisions of Biopolymers , Central Drug Research Institute, Post Box 173, Lucknow-226 001, India
| | - J.C. Katiyar
- Divisions of Parasitology, Central Drug Research Institute, Post Box 173, Lucknow-226 001, India
| | - K.B. Mathur
- Divisions of Biopolymers , Central Drug Research Institute, Post Box 173, Lucknow-226 001, India
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Chandra R, Srivastava AK, Mishra PC, Rahman H, Sharan R. Cerebral palsy. J Indian Med Assoc 1993; 91:236-7. [PMID: 8263349] [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] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In a prospective study it was found that cerebral palsy constituted 0.29% of total paediatric outdoor cases during the study period of 1988-1990. Seventy-five children suffering from cerebral palsy were studied at SN Children Hospital, Allahabad. Male to female ratio was 1:2. There were 42.8% cases who belonged to the age between one and 2 years. Hypertonic cases were predominant over hypotonic cases (3:1). Hemiplegia was commonest (68%) while triplegia was least common (2.7%). There were 24.5% cases who were mentally retarded. Hypertonic cases improved more frequently than hypotonic cases. An early management by paediatric physiotherapy may play an important role in the treatment of cerebral palsy.
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Affiliation(s)
- R Chandra
- Department of Paediatrics, SN Children Hospital, MLN Medical College, Allahabad
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Sharan R, Chaterjee S, Janakiramaiah N, Gangadhar BN. Familial and sporadic schizophrenics: a study of pursuit eye movements. Indian J Psychiatry 1992; 34:245-52. [PMID: 21776127 PMCID: PMC2982077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
15 familial schizophrenics, 15 sporadic schizophrenics, 15 normal sibs of familial schizophrenic probands, 15 normal sibs of sporadic schizophrenic probands and 15 normal subjects were examined by electro-oculogram (EOG) for the quality of their smooth pursuit eye movements. Results confirm the previous findings of SPEM dysfunction among schizophrenics as a group, but the trait-marker status of SPEM impairment of schizophrenia has been questioned and discussed. It has been suggested that the increased prevalence of impaired pursuit eye movement among sporadic schizophrenics may be due to the environmental factors of specific or non-specific nature. SPEM dysfunction could also be of pathoplastic significance in the manifestation of psychosis.
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Affiliation(s)
- R Sharan
- Ram Sharan, Assistant Professor, Department of Psychiatry, Dr. T.M.A. Pai Rotary Hospital, Bejai, Mangalore - 575 004
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Rahman H, Pandey S, Mishra PC, Sharan R, Srivastava AK, Agarwal VK. Surgical manifestations of ascariasis in childhood. J Indian Med Assoc 1992; 90:37-9. [PMID: 1588117] [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] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Amongst 50 patients with surgical complications of Ascaris lumbricoides 35 patients (70%) were treated conservatively and 15 patients (30%) required surgical intervention which included squeezing of worms to distal colon, resection and anastomosis of ileum, appendicectomy and peritoneal lavage. Intestinal perforation was observed in 3 cases. Two patients (4%) died because of postoperative complications. Those presenting with subacute intestinal obstruction had no mortality or morbidity. Although a large number of roundworms were seen in the jejunum, the obstruction was generally observed in the distal ileum.
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Affiliation(s)
- H Rahman
- Department of Paediatrics, MLN Medical College, Allahabad
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35
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Sharan R, Chaterjee S, Janakiramaiah N, Gangadhar BN. Eye movements and schizophrenia. Indian J Psychiatry 1990; 32:72-6. [PMID: 21927431 PMCID: PMC2989574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Smooth pursuit eye movements (SPEM) has been reported to be abnormal in schizophrenic patients. 30 schizophrenic patients and 15 normal subjects were examined for the quality of their smooth pursuit performance. 73.33% of the schizophrenics and 40% of the normal subjects had 'impaired' pursuit performance. The significance of the findings has been discussed.
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Affiliation(s)
- R Sharan
- Senior Resident, Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore - 560 029
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Hajailay R, Sharan R, Agarwal VK, Srivastava AK. Pyridoxine therapy in tetanus neonatorum. Indian Pediatr 1983; 20:935-9. [PMID: 6676307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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37
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Agarwal VK, Sharan R, Srivastava AK, Kumar P, Pandey CM. Blood pressure profile in children of age 3-15 years. Indian Pediatr 1983; 20:921-5. [PMID: 6676304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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39
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Srivastava AK, Kumar R, Rahman H, Sharan R, Agarwal VK. A clinical profile of paralytic poliomyelitis with special emphasis on physical therapy and rehabilitation. Indian Pediatr 1983; 20:415-9. [PMID: 6642613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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40
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Agarwal VK, Gupta SC, Chowdhary SR, Narula RK, Sharan R, Pande RC, Pachuari M. Some observations on perinatal mortality. Indian Pediatr 1982; 19:233-8. [PMID: 7141631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Sharan R. Neostigmine in the management of snakebite. J Indian Med Assoc 1982; 78:61-3. [PMID: 7108242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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42
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Sharan R. Primary tuberculosis of the nose. Practitioner 1981; 225:1506-7. [PMID: 7329938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Abstract
AbstractAN unusual case of otalgia with severe, piercing, almost constant, shock-like pain localized deep in the ear of a girl of 12 years is described. Clinical examination and investigations failed to demonstrate any organic pathology in the ear, nose, para-nasal sinuses, fauces, pharynx, larynx, teeth, jaws, temporomandibular joint, salivary glands, neck or posterior cranial fossa. Medical treatment and infiltration of local analgesics around the cutaneous nerves brought no relief. The pain was relieved temporarily by chorda tympani neurectomy and permanently by section of the nervus intermedius, thus leading to a diagnosis of nervus intermedius neuralgia.Pain is a warning signal against potential or actual damage to tissue cells. The middle ear is one of those areas which is sensitive to pricking, scratching, cutting, pressure or extremes of heat and cold.Earache is a very common complaint. Pain may be felt in the ear but the cause may lie elsewhere. Such patients with referred otalgia often present to the otologist; rarely, they present with otalgia of neuralgic quality, with piercing, shock-like pain, without any demonstrable or detectable cause in the distribution of the cranial nerves supplying the ear. One such condition is the otological type of geniculate neuralgia, in which the pain is centered within the ear and may radiate to the deeper structures of the face; the attack may be paroxysmal or continuous.The following case of otalgia is reported because of its rarity, its juvenile age of onset, and the problem posed in treatment. The patient was relieved only by surgical treatment.
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Sharan R, Kashyap AN. Atypical unilateral Treacher Collins syndrome. J Indian Med Assoc 1980; 74:76. [PMID: 7400595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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46
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Sharan R, Kashyap AN. Multilobed antrochoanal polyp. J Indian Med Assoc 1979; 73:96-7. [PMID: 541516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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47
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Abstract
A dentigerous cyst of the upper jaw is a common disease, forming 3 per cent of all alveolar cysts. However, its association with an oro-antral fistula is extremely rare and only a few cases have been reported so far.
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Sharan R. Recurrent nasopharyngeal sporidiosis. J Indian Med Assoc 1979; 72:168-9. [PMID: 512395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Sharan R, Akhtar MP. Extra-nasal glioma. Indian J Otolaryngol Head Neck Surg 1979. [DOI: 10.1007/bf02992248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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50
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Sharan R, Isser DK. Primary tuberculosis of the middle ear cleft. Practitioner 1979; 222:93-5. [PMID: 419055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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