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Karisola P, Nikkola V, Joronen H, Ylianttila L, Grönroos M, Partonen T, Snellman E, Alenius H. Narrow-band UVB radiation triggers diverse changes in the gene expression and induces the accumulation of M1 macrophages in human skin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 253:112887. [PMID: 38460430 DOI: 10.1016/j.jphotobiol.2024.112887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND The underlying molecular mechanisms that determine the biological effects of UVB radiation exposure on human skin are still only partially comprehended. OBJECTIVES Our goal is to examine the human skin transcriptome and related molecular mechanisms following a single exposure to UVB in the morning versus evening. METHODS We exposed 20 volunteer females to four-fold standard erythema doses (SED4) of narrow-band UVB (309-313 nm) in the morning or evening and studied skin transcriptome 24 h after the exposure. We performed enrichment analyses of gene pathways, predicted changes in skin cell composition using cellular deconvolution, and correlated cell proportions with gene expression. RESULTS In the skin transcriptome, UVB exposure yielded 1384 differentially expressed genes (DEGs) in the morning and 1295 DEGs in the evening, of which the most statistically significant DEGs enhanced proteasome and spliceosome pathways. Unexposed control samples showed difference by 321 DEGs in the morning vs evening, which was related to differences in genes associated with the circadian rhythm. After the UVB exposure, the fraction of proinflammatory M1 macrophages was significantly increased at both timepoints, and this increase was positively correlated with pathways on Myc targets and mTORC1 signaling. In the evening, the skin clinical erythema was more severe and had stronger positive correlation with the number of M1 macrophages than in the morning after UVB exposure. The fractions of myeloid and plasmacytoid dendritic cells and CD8 T cells were significantly decreased in the morning but not in the evening. CONCLUSIONS NB-UVB-exposure causes changes in skin transcriptome, inhibiting cell division, and promoting proteasome activity and repair responses, both in the morning and in the evening. Inflammatory M1 macrophages may drive the UV-induced skin responses by exacerbating inflammation and erythema. These findings highlight how the same UVB exposure influences skin responses differently in morning versus evening and presents a possible explanation to the differences in gene expression in the skin after UVB irradiation at these two timepoints.
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Affiliation(s)
- Piia Karisola
- Faculty of Medicine, Human Microbiome Research Program, University of Helsinki, Finland.
| | - Veera Nikkola
- Tampere University, Faculty of Medicine and Health Technology, Department of Dermatology and Venereology, Tampere, Finland
| | - Heli Joronen
- Tampere University, Faculty of Medicine and Health Technology, Department of Dermatology and Venereology, Tampere, Finland; Päijät-Häme Social and Health Care Group, Department of Dermatology and Allergology, Lahti, Finland.
| | - Lasse Ylianttila
- Radiation and Nuclear Safety Authority (STUK), Helsinki, Finland.
| | - Mari Grönroos
- Päijät-Häme Social and Health Care Group, Department of Dermatology and Allergology, Lahti, Finland.
| | - Timo Partonen
- Finnish Institute for Health and Welfare, Department of Public Health and Welfare, Finland.
| | - Erna Snellman
- Tampere University, Faculty of Medicine and Health Technology, Department of Dermatology and Venereology, Tampere, Finland.
| | - Harri Alenius
- Faculty of Medicine, Human Microbiome Research Program, University of Helsinki, Finland; Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden.
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2
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Muhie S, Gautam A, Misganaw B, Yang R, Mellon SH, Hoke A, Flory J, Daigle B, Swift K, Hood L, Doyle FJ, Wolkowitz OM, Marmar CR, Ressler K, Yehuda R, Hammamieh R, Jett M. Integrated analysis of proteomics, epigenomics and metabolomics data revealed divergent pathway activation patterns in the recent versus chronic post-traumatic stress disorder. Brain Behav Immun 2023; 113:303-316. [PMID: 37516387 DOI: 10.1016/j.bbi.2023.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/16/2023] [Accepted: 07/22/2023] [Indexed: 07/31/2023] Open
Abstract
Metabolomics, proteomics and DNA methylome assays, when done in tandem from the same blood sample and analyzed together, offer an opportunity to evaluate the molecular basis of post-traumatic stress disorder (PTSD) course and pathogenesis. We performed separate metabolomics, proteomics, and DNA methylome assays on blood samples from two well-characterized cohorts of 159 active duty male participants with relatively recent onset PTSD (<1.5 years) and 300 male veterans with chronic PTSD (>7 years). Analyses of the multi-omics datasets from these two independent cohorts were used to identify convergent and distinct molecular profiles that might constitute potential signatures of severity and progression of PTSD and its comorbid conditions. Molecular signatures indicative of homeostatic processes such as signaling and metabolic pathways involved in cellular remodeling, neurogenesis, molecular safeguards against oxidative stress, metabolism of polyunsaturated fatty acids, regulation of normal immune response, post-transcriptional regulation, cellular maintenance and markers of longevity were significantly activated in the active duty participants with recent PTSD. In contrast, we observed significantly altered multimodal molecular signatures associated with chronic inflammation, neurodegeneration, cardiovascular and metabolic disorders, and cellular attritions in the veterans with chronic PTSD. Activation status of signaling and metabolic pathways at the early and late timepoints of PTSD demonstrated the differential molecular changes related to homeostatic processes at its recent and multi-system syndromes at its chronic phase. Molecular alterations in the recent PTSD seem to indicate some sort of recalibration or compensatory response, possibly directed in mitigating the pathological trajectory of the disorder.
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Affiliation(s)
- Seid Muhie
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; The Geneva Foundation, Silver Spring, MD 20910, USA.
| | - Aarti Gautam
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Burook Misganaw
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Vysnova Inc. Landover, MD 20785, USA
| | - Ruoting Yang
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Synthia H Mellon
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Allison Hoke
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Janine Flory
- Department of Psychiatry, James J. Peters VA Medical Center, Bronx, NY 10468, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10468, USA
| | - Bernie Daigle
- Departments of Biological Sciences and Computer Science, The University of Memphis, Memphis, TN 38152, USA
| | - Kevin Swift
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Francis J Doyle
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02134, USA
| | - Owen M Wolkowitz
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
| | - Charles R Marmar
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kerry Ressler
- McLean Hospital, Belmont, MA 02478, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Rachel Yehuda
- Department of Psychiatry, James J. Peters VA Medical Center, Bronx, NY 10468, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10468, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Marti Jett
- US Army Medical Research and Development Command, HQ, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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3
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Liang M, Hody C, Yammine V, Soin R, Sun Y, Lin X, Tian X, Meurs R, Perdrau C, Delacourt N, Oumalis M, Andris F, Conrard L, Kruys V, Gueydan C. eIF4EHP promotes Ldh mRNA translation in and fruit fly adaptation to hypoxia. EMBO Rep 2023; 24:e56460. [PMID: 37144276 PMCID: PMC10328074 DOI: 10.15252/embr.202256460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Hypoxia induces profound modifications in the gene expression program of eukaryotic cells due to lowered ATP supply resulting from the blockade of oxidative phosphorylation. One significant consequence of oxygen deprivation is the massive repression of protein synthesis, leaving a limited set of mRNAs to be translated. Drosophila melanogaster is strongly resistant to oxygen fluctuations; however, the mechanisms allowing specific mRNA to be translated into hypoxia are still unknown. Here, we show that Ldh mRNA encoding lactate dehydrogenase is highly translated into hypoxia by a mechanism involving a CA-rich motif present in its 3' untranslated region. Furthermore, we identified the cap-binding protein eIF4EHP as a main factor involved in 3'UTR-dependent translation under hypoxia. In accordance with this observation, we show that eIF4EHP is necessary for Drosophila development under low oxygen concentrations and contributes to Drosophila mobility after hypoxic challenge. Altogether, our data bring new insight into mechanisms contributing to LDH production and Drosophila adaptation to oxygen variations.
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Affiliation(s)
- Manfei Liang
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
- Present address:
Medical Science and Technology Innovation CenterShandong First Medical UniversityJinanChina
| | - Clara Hody
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Vanessa Yammine
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Romuald Soin
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Yuqiu Sun
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Xing Lin
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Xiaoying Tian
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Romane Meurs
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Camille Perdrau
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Nadège Delacourt
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Marina Oumalis
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Fabienne Andris
- Laboratoire d'Immunobiologie, Faculté des SciencesUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Louise Conrard
- Center of Microscopy and Molecular Imaging (CMMI)Université libre de Bruxelles (ULB)GosseliesBelgium
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
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4
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Ferrucci L, Candia J, Ubaida-Mohien C, Lyaskov A, Banskota N, Leeuwenburgh C, Wohlgemuth S, Guralnik JM, Kaileh M, Zhang D, Sufit R, De S, Gorospe M, Munk R, Peterson CA, McDermott MM. Transcriptomic and Proteomic of Gastrocnemius Muscle in Peripheral Artery Disease. Circ Res 2023; 132:1428-1443. [PMID: 37154037 PMCID: PMC10213145 DOI: 10.1161/circresaha.122.322325] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Few effective therapies exist to improve lower extremity muscle pathology and mobility loss due to peripheral artery disease (PAD), in part because mechanisms associated with functional impairment remain unclear. METHODS To better understand mechanisms of muscle impairment in PAD, we performed in-depth transcriptomic and proteomic analyses on gastrocnemius muscle biopsies from 31 PAD participants (mean age, 69.9 years) and 29 age- and sex-matched non-PAD controls (mean age, 70.0 years) free of diabetes or limb-threatening ischemia. RESULTS Transcriptomic and proteomic analyses suggested activation of hypoxia-compensatory mechanisms in PAD muscle, including inflammation, fibrosis, apoptosis, angiogenesis, unfolded protein response, and nerve and muscle repair. Stoichiometric proportions of mitochondrial respiratory proteins were aberrant in PAD compared to non-PAD, suggesting that respiratory proteins not in complete functional units are not removed by mitophagy, likely contributing to abnormal mitochondrial activity. Supporting this hypothesis, greater mitochondrial respiratory protein abundance was significantly associated with greater complex II and complex IV respiratory activity in non-PAD but not in PAD. Rate-limiting glycolytic enzymes, such as hexokinase and pyruvate kinase, were less abundant in muscle of people with PAD compared with non-PAD participants, suggesting diminished glucose metabolism. CONCLUSIONS In PAD muscle, hypoxia induces accumulation of mitochondria respiratory proteins, reduced activity of rate-limiting glycolytic enzymes, and an enhanced integrated stress response that modulates protein translation. These mechanisms may serve as targets for disease modification.
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Affiliation(s)
- Luigi Ferrucci
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Julián Candia
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | | | - Alexey Lyaskov
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Nirad Banskota
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Christiaan Leeuwenburgh
- University of Florida, Institute on Aging, Department of Physiology and Aging, Gainesville, FL, USA
| | - Stephanie Wohlgemuth
- University of Florida, Institute on Aging, Department of Physiology and Aging, Gainesville, FL, USA
| | - Jack M. Guralnik
- University of Maryland School of Medicine, Department of Epidemiology and Public Health, Baltimore, MD, USA
| | - Mary Kaileh
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Dongxue Zhang
- Northwestern University Feinberg School of Medicine, Department of Neurology, Chicago, IL, USA
| | - Robert Sufit
- Northwestern University Feinberg School of Medicine, Department of Neurology, Chicago, IL, USA
| | - Supriyo De
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Myriam Gorospe
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Rachel Munk
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Charlotte A. Peterson
- Center for Muscle Biology. College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Mary M. McDermott
- Northwestern University Feinberg School of Medicine, Department of Medicine, Chicago, IL, USA
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5
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Puzio M, Moreton N, Sullivan M, Scaife C, Glennon JC, O'Connor JJ. An Electrophysiological and Proteomic Analysis of the Effects of the Superoxide Dismutase Mimetic, MnTMPyP, on Synaptic Signalling Post-Ischemia in Isolated Rat Hippocampal Slices. Antioxidants (Basel) 2023; 12:antiox12040792. [PMID: 37107167 PMCID: PMC10135248 DOI: 10.3390/antiox12040792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Metabolic stress and the increased production of reactive oxygen species (ROS) are two main contributors to neuronal damage and synaptic plasticity in acute ischemic stroke. The superoxide scavenger MnTMPyP has been previously reported to have a neuroprotective effect in organotypic hippocampal slices and to modulate synaptic transmission after in vitro hypoxia and oxygen-glucose deprivation (OGD). However, the mechanisms involved in the effect of this scavenger remain elusive. In this study, two concentrations of MnTMPyP were evaluated on synaptic transmission during ischemia and post-ischemic synaptic potentiation. The complex molecular changes supporting cellular adaptation to metabolic stress, and how these are modulated by MnTMPyP, were also investigated. Electrophysiological data showed that MnTMPyP causes a decrease in baseline synaptic transmission and impairment of synaptic potentiation. Proteomic analysis performed on MnTMPyP and hypoxia-treated tissue indicated an impairment in vesicular trafficking mechanisms, including reduced expression of Hsp90 and actin signalling. Alterations of vesicular trafficking may lead to reduced probability of neurotransmitter release and AMPA receptor activity, resulting in the observed modulatory effect of MnTMPyP. In OGD, protein enrichment analysis highlighted impairments in cell proliferation and differentiation, such as TGFβ1 and CDKN1B signalling, in addition to downregulation of mitochondrial dysfunction and an increased expression of CAMKII. Taken together, our results may indicate modulation of neuronal sensitivity to the ischemic insult, and a complex role for MnTMPyP in synaptic transmission and plasticity, potentially providing molecular insights into the mechanisms mediating the effects of MnTMPyP during ischemia.
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Affiliation(s)
- Martina Puzio
- UCD School of Biomolecular & Biomedical Science, University College Dublin, Dublin 4, Ireland
- Mass Spectrometry Core Facility, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Niamh Moreton
- UCD School of Biomolecular & Biomedical Science, University College Dublin, Dublin 4, Ireland
- Mass Spectrometry Core Facility, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Mairéad Sullivan
- Mass Spectrometry Core Facility, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Caitriona Scaife
- Mass Spectrometry Core Facility, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Jeffrey C Glennon
- Mass Spectrometry Core Facility, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
| | - John J O'Connor
- UCD School of Biomolecular & Biomedical Science, University College Dublin, Dublin 4, Ireland
- Mass Spectrometry Core Facility, UCD Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
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6
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Sher S, Whipp E, Walker J, Zhang P, Beaver L, Williams K, Orwick S, Ravikrishnan J, Walker B, Perry E, Gregory C, Purcell M, Pan A, Yan P, Alinari L, Johnson AJ, Frigault MM, Greer JM, Hamdy A, Izumi R, Mo X, Sampath D, Woyach J, Blachly J, Byrd JC, Lapalombella R. VIP152 is a selective CDK9 inhibitor with pre-clinical in vitro and in vivo efficacy in chronic lymphocytic leukemia. Leukemia 2023; 37:326-338. [PMID: 36376377 PMCID: PMC9898036 DOI: 10.1038/s41375-022-01758-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/25/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is effectively treated with targeted therapies including Bruton tyrosine kinase inhibitors and BCL2 antagonists. When these become ineffective, treatment options are limited. Positive transcription elongation factor complex (P-TEFb), a heterodimeric protein complex composed of cyclin dependent kinase 9 (CDK9) and cyclin T1, functions to regulate short half-life transcripts by phosphorylation of RNA Polymerase II (POLII). These transcripts are frequently dysregulated in hematologic malignancies; however, therapies targeting inhibition of P-TEFb have not yet achieved approval for cancer treatment. VIP152 kinome profiling revealed CDK9 as the main enzyme inhibited at 100 nM, with over a 10-fold increase in potency compared with other inhibitors currently in development for this target. VIP152 induced cell death in CLL cell lines and primary patient samples. Transcriptome analysis revealed inhibition of RNA degradation through the AU-Rich Element (ARE) dysregulation. Mechanistically, VIP152 inhibits the assembly of P-TEFb onto the transcription machinery and disturbs binding partners. Finally, immune competent mice engrafted with CLL-like cells of Eµ-MTCP1 over-expressing mice and treated with VIP152 demonstrated reduced disease burden and improvement in overall survival compared to vehicle-treated mice. These data suggest that VIP152 is a highly selective inhibitor of CDK9 that represents an attractive new therapy for CLL.
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Affiliation(s)
- Steven Sher
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Ethan Whipp
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Janek Walker
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Pu Zhang
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Larry Beaver
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Katie Williams
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Shelley Orwick
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Janani Ravikrishnan
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Brandi Walker
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Elizabeth Perry
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Charles Gregory
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Matthew Purcell
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Alexander Pan
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Pearlly Yan
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | | | | | | | | | | | - Xiaokui Mo
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Deepa Sampath
- Department of Hematopoietic Biology & Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Woyach
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - James Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - John C Byrd
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Rosa Lapalombella
- Division of Hematology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA.
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7
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Zhang L, Wang D, Zhang L, Fu J, Yan P, Ge S, Li Z, Ahammed GJ, Han W, Li X. Expression and functional analysis of CsA-IPT5 splice variants during shoot branching in Camellia sinensis. FRONTIERS IN PLANT SCIENCE 2022; 13:977086. [PMID: 36072311 PMCID: PMC9444062 DOI: 10.3389/fpls.2022.977086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Alternative splicing (AS) is a process by which several functional splice variants are generated from the same precursor mRNA. In our recent study, five CsA-IPT5 splice variants with various numbers of ATTTA motifs in the untranslated regions (UTRs) were cloned. Meanwhile, their transient expression, as well as the expression and functional analysis in the two shoot branching processes were studied. Here, we examined how these splice variants regulate the other three important shoot branching processes, including the spring tea development, the distal branching of new shoots, and the shoot branching induced by 2,3,5-triiodobenzoic acid (TIBA) spraying, and thus unraveling the key CsA-IPT5 transcripts which play the most important roles in the shoot branching of tea plants. The results showed that the increased expression of 5' UTR AS3, 3' UTR AS1 and 3' UTR AS2 could contribute to the increased synthesis of tZ/iP-type cytokinins (CKs), thus promoting the spring tea development. Meanwhile, in the TIBA-induced shoot branching or in the distal branching of the new shoots, CsA-IPT5 transcripts regulated the synthesis of CsA-IPT5 protein and CKs through transcriptional regulation of the ratios of its splice variants. Moreover, 3' UTR AS1 and 3' UTR AS2 both play key roles in these two processes. In summary, it is revealed that 3' UTR AS1 and 3' UTR AS2 of CsA-IPT5 might act as the predominant splice variants in shoot branching of the tea plant, and they both can serve as gene resources for tea plant breeding.
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Affiliation(s)
- Liping Zhang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Donghui Wang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Lan Zhang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jianyu Fu
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Peng Yan
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Shibei Ge
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Zhengzhen Li
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Golam Jalal Ahammed
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Wenyan Han
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xin Li
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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8
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Abstract
RNA-binding proteins (RBPs) are of fundamental importance for post-transcriptional gene regulation and protein synthesis. They are required for pre-mRNA processing and for RNA transport, degradation and translation into protein, and can regulate every step in the life cycle of their RNA targets. In addition, RBP function can be modulated by RNA binding. RBPs also participate in the formation of ribonucleoprotein complexes that build up macromolecular machineries such as the ribosome and spliceosome. Although most research has focused on mRNA-binding proteins, non-coding RNAs are also regulated and sequestered by RBPs. Functional defects and changes in the expression levels of RBPs have been implicated in numerous diseases, including neurological disorders, muscular atrophy and cancers. RBPs also contribute to a wide spectrum of kidney disorders. For example, human antigen R has been reported to have a renoprotective function in acute kidney injury (AKI) but might also contribute to the development of glomerulosclerosis, tubulointerstitial fibrosis and diabetic kidney disease (DKD), loss of bicaudal C is associated with cystic kidney diseases and Y-box binding protein 1 has been implicated in the pathogenesis of AKI, DKD and glomerular disorders. Increasing data suggest that the modulation of RBPs and their interactions with RNA targets could be promising therapeutic strategies for kidney diseases.
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Zhang L, Li M, Yan P, Fu J, Zhang L, Li X, Han W. A novel adenylate isopentenyltransferase 5 regulates shoot branching via the ATTTA motif in Camellia sinensis. BMC PLANT BIOLOGY 2021; 21:521. [PMID: 34753426 PMCID: PMC8577036 DOI: 10.1186/s12870-021-03254-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/23/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Shoot branching is one of the important agronomic traits affecting yields and quality of tea plant (Camellia sinensis). Cytokinins (CTKs) play critical roles in regulating shoot branching. However, whether and how differently alternative splicing (AS) variant of CTKs-related genes can influence shoot branching of tea plant is still not fully elucidated. RESULTS In this study, five AS variants of CTK biosynthetic gene adenylate isopentenyltransferase (CsA-IPT5) with different 3' untranslated region (3' UTR) and 5' UTR from tea plant were cloned and investigated for their regulatory effects. Transient expression assays showed that there were significant negative correlations between CsA-IPT5 protein expression, mRNA expression of CsA-IPT5 AS variants and the number of ATTTA motifs, respectively. Shoot branching processes induced by exogenous 6-BA or pruning were studied, where CsA-IPT5 was demonstrated to regulate protein synthesis of CsA-IPT5, as well as the biosynthesis of trans-zeatin (tZ)- and isopentenyladenine (iP)-CTKs, through transcriptionally changing ratios of its five AS variants in these processes. Furthermore, the 3' UTR AS variant 2 (3AS2) might act as the predominant AS transcript. CONCLUSIONS Together, our results indicate that 3AS2 of the CsA-IPT5 gene is potential in regulating shoot branching of tea plant and provides a gene resource for improving the plant-type of woody plants.
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Affiliation(s)
- Liping Zhang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Menghan Li
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Peng Yan
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Jianyu Fu
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Lan Zhang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Xin Li
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Wenyan Han
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
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Teafatiller T, Agrawal S, De Robles G, Rahmatpanah F, Subramanian VS, Agrawal A. Vitamin C Enhances Antiviral Functions of Lung Epithelial Cells. Biomolecules 2021; 11:1148. [PMID: 34439814 PMCID: PMC8394979 DOI: 10.3390/biom11081148] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Vitamin C is well documented to have antiviral functions; however, there is limited information about its effect on airway epithelial cells-the first cells to encounter infections. Here, we examined the effect of vitamin C on human bronchial epithelium transformed with Ad12-SV40 2B (BEAS-2B) cells, and observed that sodium-dependent vitamin C transporter 2 (SVCT2) was the primary vitamin C transporter. Transcriptomic analysis revealed that treating BEAS-2B cells with vitamin C led to a significant upregulation of several metabolic pathways and interferon-stimulated genes (ISGs) along with a downregulation of pathways involved in lung injury and inflammation. Remarkably, vitamin C also enhanced the expression of the viral-sensing receptors retinoic acid-inducible gene 1 (RIG-1) and melanoma differentiation-associated protein 5 (MDA-5), which was confirmed at the protein and functional levels. In addition, the lungs of l-gulono-γ-lactone oxidase knockout (GULO-KO) mice also displayed a marked decrease in these genes compared to wild-type controls. Collectively, our findings indicate that vitamin C acts at multiple levels to exert its antiviral and protective functions in the lungs.
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Affiliation(s)
- Trevor Teafatiller
- Division of Gastroenterology, Department of Medicine, University of California, Irvine, CA 92697, USA;
| | - Sudhanshu Agrawal
- Division of Basic and Clinical Immunology, Department of Medicine, University of California, Irvine, CA 92697, USA;
| | - Gabriela De Robles
- Department of Pathology, University of California, Irvine, CA 92697, USA; (G.D.R.); (F.R.)
| | - Farah Rahmatpanah
- Department of Pathology, University of California, Irvine, CA 92697, USA; (G.D.R.); (F.R.)
| | - Veedamali S. Subramanian
- Division of Gastroenterology, Department of Medicine, University of California, Irvine, CA 92697, USA;
| | - Anshu Agrawal
- Division of Basic and Clinical Immunology, Department of Medicine, University of California, Irvine, CA 92697, USA;
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