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Uwaydat S, Chauhan MZ. Re: Perez et al.: Improved visual outcomes after severe open-globe injuries associated with perioperative vitreoretinal evaluation (Ophthalmol Retina. 2023;7:771-778). Ophthalmol Retina 2024; 8:e11-e12. [PMID: 38206239 DOI: 10.1016/j.oret.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024]
Affiliation(s)
- Sami Uwaydat
- Ophthalmology Department, University of Arkansas for Medical Sciences, Little Rock, Arkansas.
| | - Muhammad Zain Chauhan
- Ophthalmology Department, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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Collao V, Morris J, Zain Chauhan M, Abdelrahman L, Martίnez-de-la-Casa JM, Vidal-Villegas B, Burgos-Blasco B, Bhattacharya SK. Analyses of Pseudoexfoliation aqueous humor lipidome. Mol Omics 2022; 18:387-396. [DOI: 10.1039/d1mo00495f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pseudoexfoliation syndrome (PEX) is a systemic disorder that manifests as fluffy, proteinaceous fibrillar material throughout the body. In the eye such deposits result in glaucoma (PEXG), due to impeding aqueous...
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Affiliation(s)
| | - Sanjoy K Bhattacharya
- Miami Integrative Metabolomics Research Center, Bascom Palmer Eye Institute; Program In Biomedical Sciences and Neuroscience Graduate Program, University of Miami, Miami, FL, USA
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Zafar M, Hazeslip L, Chauhan MZ, Byrd AK. The Expression of Human DNA Helicase B Is Affected by G-Quadruplexes in the Promoter. Biochemistry 2020; 59:2401-2409. [PMID: 32478505 PMCID: PMC7346868 DOI: 10.1021/acs.biochem.0c00218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/26/2020] [Indexed: 12/25/2022]
Abstract
G-Quadruplexes are secondary structures that can form in guanine-rich DNA and RNA that have been implicated in regulating multiple biological processes, including transcription. G-Quadruplex-forming sequences are prevalent in promoter regions of proto-oncogenes and DNA repair proteins. HELB is a human helicase involved in DNA replication and repair with 12 runs of three to four guanines in the proximal promoter. This sequence has the potential to form three canonical three-tetrad G-quadruplexes. Our results show that although all three G-quadruplexes can form, a structure containing two noncanonical G-quadruplexes with longer loops containing runs of three to four guanines is the most prevalent. These HELB G-quadruplexes are stable under physiological conditions. In cells, stabilization of the G-quadruplexes results in a decrease in the level of HELB expression, suggesting that the G-quadruplexes in the HELB promoter serve as transcriptional repressors.
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Affiliation(s)
- Maroof
Khan Zafar
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Lindsey Hazeslip
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Muhammad Zain Chauhan
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Alicia K. Byrd
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Winthrop
P. Rockefeller Cancer Institute, Little Rock, Arkansas 72205, United States
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Abstract
DNA Helicase B (HELB) is a conserved helicase in higher eukaryotes with roles in the initiation of DNA replication and in the DNA damage and replication stress responses. HELB is a predominately nuclear protein in G1 phase where it is involved in initiation of DNA replication through interactions with DNA topoisomerase 2-binding protein 1 (TOPBP1), cell division control protein 45 (CDC45), and DNA polymerase α-primase. HELB also inhibits homologous recombination by reducing long-range end resection. After phosphorylation by cyclin-dependent kinase 2 (CDK2) at the G1 to S transition, HELB is predominately localized to the cytosol. However, this cytosolic localization in S phase is not exclusive. HELB has been reported to localize to chromatin in response to replication stress and to localize to the common fragile sites 16D (FRA16D) and 3B (FRA3B) and the rare fragile site XA (FRAXA) in S phase. In addition, HELB is phosphorylated in response to ionizing radiation and has been shown to localize to chromatin in response to various types of DNA damage, suggesting it has a role in the DNA damage response.
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Affiliation(s)
- Lindsey Hazeslip
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (L.H.); (M.K.Z.); (M.Z.C.)
| | - Maroof Khan Zafar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (L.H.); (M.K.Z.); (M.Z.C.)
| | - Muhammad Zain Chauhan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (L.H.); (M.K.Z.); (M.Z.C.)
| | - Alicia K. Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (L.H.); (M.K.Z.); (M.Z.C.)
- Winthrop P. Rockefeller Cancer Institute, Little Rock, AR 72205, USA
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Chauhan MZ, Arcuri J, Park KK, Zafar MK, Fatmi R, Hackam AS, Yin Y, Benowitz L, Goldberg JL, Samarah M, Bhattacharya SK. Multi-Omic Analyses of Growth Cones at Different Developmental Stages Provides Insight into Pathways in Adult Neuroregeneration. iScience 2020; 23:100836. [PMID: 32058951 PMCID: PMC6997871 DOI: 10.1016/j.isci.2020.100836] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 07/30/2019] [Revised: 01/05/2020] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
Growth cones (GCs) are structures associated with growing neurons. GC membrane expansion, which necessitates protein-lipid interactions, is critical to axonal elongation in development and in adult neuritogenesis. We present a multi-omic analysis that integrates proteomics and lipidomics data for the identification of GC pathways, cell phenotypes, and lipid-protein interactions, with an analytic platform to facilitate the visualization of these data. We combine lipidomic data from GC and adult axonal regeneration following optic nerve crush. Our results reveal significant molecular variability in GCs across developmental ages that aligns with the upregulation and downregulation of lipid metabolic processes and correlates with distinct changes in the lipid composition of GC plasmalemma. We find that these processes also define the transition into a growth-permissive state in the adult central nervous system. The insight derived from these analyses will aid in promoting adult regeneration and functional innervation in devastating neurodegenerative diseases. Simultaneous proteomics and lipidomics analyses of developmental growth cones Combined multi-omics analyses of regenerating optic nerves and growth cones Integrating protein-protein with protein-lipid interactions in growth cones
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Affiliation(s)
- Muhammad Zain Chauhan
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Miami Integrative Metabolomics Research Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jennifer Arcuri
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Miami Integrative Metabolomics Research Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Biomedical Sciences & Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Kevin K Park
- Miami Integrative Metabolomics Research Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Biomedical Sciences & Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Maroof Khan Zafar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Rabeet Fatmi
- Department of Computer Science, Florida Polytechnic University, Lakeland, FL 33805, USA
| | - Abigail S Hackam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Miami Integrative Metabolomics Research Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Biomedical Sciences & Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yuqin Yin
- Department of Neurosurgery, Harvard Medical School, Boston, MA 02115, USA; Department of Neurosurgery and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Larry Benowitz
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA; Department of Neurosurgery and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jeffrey L Goldberg
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mohammad Samarah
- Department of Computer Science, Florida Polytechnic University, Lakeland, FL 33805, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Miami Integrative Metabolomics Research Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Biomedical Sciences & Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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Chauhan MZ, Valencia AK, Piqueras MC, Enriquez-Algeciras M, Bhattacharya SK. Optic Nerve Lipidomics Reveal Impaired Glucosylsphingosine Lipids Pathway in Glaucoma. Invest Ophthalmol Vis Sci 2019; 60:1789-1798. [PMID: 31022733 PMCID: PMC6485987 DOI: 10.1167/iovs.18-25802] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Purpose To determine major differences in lipid profile between human control and glaucomatous optic nerve. To assess major enzymes in lipid pathway if aberration is revealed for a lipid class by profiling. Methods Optic nerve (ON) samples were obtained from human cadaveric donors [control (n = 11) and primary open-angle glaucoma (POAG; n = 12)]; the lipids were extracted using Bligh and Dyer methods. Control and glaucoma donors were all Caucasians age 72.3 ± 5.9 and 70.3 ± 10.5 (inclusive of both sexes), respectively. Lipids were extracted after weighing the tissue; the protein amounts in the corresponding aqueous phase of organic solvent extraction were recorded. High-resolution mass spectrometry was performed using a Q-exactive mass spectrometer coupled with an EASY-nLC 1000 liquid chromatograph instrument. Bioinformatics and statistical analysis were performed using LipidSearch v.4.1 and MetaboAnalyst 4.0/STATA 14.2. Protein amounts were determined using Bradford's method. Western blot, ELISA, and immunohistochemistry utilized established protocols and were performed for protein quantification and localization, respectively. Additional donor tissues were utilized for Western blot, ELISA, and immunohistochemistry. Results Principal component analysis (PCA) placed control and glaucomatous ONs in two distinct groups based on analysis of lipid profiles. Total lipid, total phospholipids, total ceramide, and total sphingolipids were similar (without significant difference) between control and glaucoma. However, we found a significant increase in glucosylsphingosine in glaucoma compared to control samples. We found similar levels of glucocerebrosidase (GBA), ceramide glucosyltransferase (UGCG), decreased nonlysosomal glucocerebrosidase (GBA2), and increased lysosomal and nonlysosomal acylsphingosine amidohydrolase (ASAH1 and ASAH2) levels in glaucomatous ON compared to control. Conclusions We found significant differences in glucosylsphingosine lipids, consistent with decreased GBA and GBA2 and increased ASAH1 and ASAH2 immunoreactivity in glaucoma, suggesting the potential impairment of sphingolipid enzymatic pathways in lysosomal and nonlysosomal cellular compartments.
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Affiliation(s)
- Muhammad Zain Chauhan
- Department of Ophthalmology & Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Ann-Katrin Valencia
- Department of Ophthalmology & Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Maria Carmen Piqueras
- Department of Ophthalmology & Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Mabel Enriquez-Algeciras
- Department of Ophthalmology & Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Sanjoy K Bhattacharya
- Department of Ophthalmology & Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
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