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Li W, Gao G, Pan Y, Wang Z, Ruan J, Fan L, Shen Y, Wang H, Li M, Zhang P, Fang L, Fu J, Liu J. Integration of RNA-seq and ATAC-seq analyzes the effect of low dose neutron-γ radiation on gene expression of lymphocytes from oilfield logging workers. Front Chem 2023; 11:1269911. [PMID: 38099192 PMCID: PMC10720751 DOI: 10.3389/fchem.2023.1269911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Objective: Although radiation workers are exposed to much lower doses of neutron-γ rays than those suffered in nuclear explosions and accidents, it does not mean that their health is not affected by radiation. Lower doses of radiation do not always cause morphological aberrations in chromosomes, so more sophisticated tests must be sought to specific alterations in the exposed cells. Our goal was to characterize the specific gene expression in lymphocytes from logging workers who were continuously exposed to low doses of neutron-γ radiation. We hypothesized that the combination of cell type-specific transcriptomes and open chromatin profiles would identify lymphocyte-specific gene alterations induced by long-term radiation with low-dose neutron-γ-rays and discover new regulatory pathways and transcriptional regulatory elements. Methods: Lymphocytes were extracted from workers who have been occupationally exposed to neutron-γ and workers unexposed to radiation in the same company. mRNA-seq and ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) were performed, followed integrative analysis to identify specific gene regulatory regions induced by neutron-γ radiation. A qPCR assay was then performed to verify the downregulation of RNA coding for ribosomal proteins and flow cytometry was used to detect ribosomal protein expression and cell cycle alterations. Results: We identified transcripts that were specifically induced by neutron-γ radiation and discovered differential open chromatin regions that correlated with these gene activation patterns. Notably, we observed a downward trend in the expression of both differentially expressed genes and open chromatin peaks. Our most significant finding was that the differential peak upregulated in ATAC-seq, while the differential gene was downregulated in the ribosome pathway. We confirmed that neutron-γ radiation leads to transcriptional inhibition by analyzing the most enriched promoters, examining RPS18 and RPS27A expression by qPCR, and analyzing protein-protein interactions of the differential genes. Ribosomal protein expression and cell cycle were also affected by neutron-γ as detected by flow cytometry. Conclusion: We have comprehensively analyzed the genetic landscape of human lymphocytes based on chromatin accessibility and transcript levels, enabling the identification of novel neutron-γ induced signature genes not previously known. By comparing fine-mapping of open chromatin and RNA reads, we have determined that neutron-γ specifically leads to downregulation of genes in the ribosome pathway, with pseudogenes potentially playing a crucial role.
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Affiliation(s)
- Weiguo Li
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Gang Gao
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Yan Pan
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Ziqiang Wang
- School of Biomedical Sciences, Shandong First Medical University, Jinan, Shandong, China
| | - Jianlei Ruan
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Li Fan
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Yingjie Shen
- Safety and Environmental Protection Department, Shengli Logging Company, Sinopec Jingwei Co., LTD., Dongying, Shandong, China
| | - Haiqing Wang
- Dongying Center for Disease Control and Prevention, Dongying, Shandong, China
| | - Mian Li
- School of Biomedical Sciences, Shandong First Medical University, Jinan, Shandong, China
| | - Pinhua Zhang
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
| | - Lianying Fang
- School of Preventive Medicine, Shandong First Medical University Institute of Radiation Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jinghong Fu
- School of Preventive Medicine, Shandong First Medical University Institute of Radiation Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jianxiang Liu
- China CDC Key Laboratory of Radiological Protection and Nuclear Emergency, Chinese Center for Disease Control and Prevention, National Institute for Radiological Protection, Beijing, China
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I.M.H. Abdulrahman Y, Zaki M, Alhaddad MR, Hairat S, Akhtar K. Structural elucidation of new ferrocene appended scaffold and their metal complexes: Comparative in vitroDNA/BSA Binding and antibacterial assay. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Alanazi RLB, Zaki M, Bawazir WA. Synthesis and characterization of the new ligand, 1,2,4-triazino[5,6-b]indol-3-ylimino methyl naphthalene-2-ol and its Ni(II) and Cu(II) complexes: comparative studies of their in vitro DNA and HSA Binding. Biometals 2022; 35:1199-1223. [PMID: 36074281 DOI: 10.1007/s10534-022-00437-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 08/16/2022] [Indexed: 12/14/2022]
Abstract
A new ligand 1,2,4-triazino[5,6-b]indol-3-ylimino methyl naphthalene-2-ol (HL) was derived from 5H-[1,2,4]triazino[5,6-b]indol-3-amine and 2-hydroxy-1-naphthaldehyde. The metal complexes of the type [Ni(L)(Bipy)]1/2SO4 (1), [Cu(L)(Bipy)(H2O)2]1/2SO4 (2), [Ni(L)(Phen)]1/2SO4 (3) and [Cu(L)(Phen)(H2O)2]1/2SO4 (4) were synthesized. The ligand (HL) and complexes 1-4 were thoroughly characterized by elemental analysis and spectroscopic methods (FT-IR, ToF-MS, 1H NMR, 13C NMR), molar conductance and magnetic moment determination. The Ni(II) complexes 1 and 3 adopt the square planar geometry and Cu(II) complexes 2 and 4 acquire distorted octahedral arrangement. In vitro DNA binding behavior of ligand (HL) and metal complexes 1-4 was explored by fluorescence spectral and ethidium bromide studies. The outcomes reveal that the complexes interact with DNA via non-covalent groove binding and electrostatic interactions. The higher binding constant (K) values of 4.35 × 104 and 9.12 × 104 M-1 for complexes 2 and 4 indicate stronger binding ability with DNA. Moreover, in vitro human serum albumin (HSA) binding experiment with HL and complexes 1-4 reveals conformational modulations in the Trp-214 microenvironments in the subdomain IIA pocket.
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Affiliation(s)
- Reem L B Alanazi
- Department of Chemistry, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
| | - Mehvash Zaki
- Department of Chemistry, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia.
| | - Wafa A Bawazir
- Department of Chemistry, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
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Wang R, Li J, Niu DB, Xu FY, Zeng XA. Protective effect of baicalein on DNA oxidative damage and its binding mechanism with DNA: An in vitro and molecular docking study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 253:119605. [PMID: 33667888 DOI: 10.1016/j.saa.2021.119605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/31/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
In this work, the protective effect of baicalein on DNA oxidative damage and its possible protection mechanisms were investigated. 2-thiobarbituric acid (TBA) colorimetry and agarose gel electrophoresis study found that baicalein protected the deoxyribose residue and double-stranded backbone of DNA from the damage of hydroxyl radicals. Antioxidant analysis results showed that baicalein has excellent radicals scavenging effects and Fe2+ chelating ability, which might be the mechanism of baicalein protecting DNA. DNA binding studies indicated that baicalein bound to the minor groove of DNA with moderate binding affinity (K = (7.35 ± 0.91) × 103 M-1). Hydrogen bonding and van der Waals forces played a major role in driving the binding process. Molecular docking further confirmed the experimental results. This binding could stabilize DNA double helix structure, thereby protecting DNA from oxidative damage. This study may provide theoretical basis for designing new functional foods of baicalein for DNA damage protection.
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Affiliation(s)
- Rui Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
| | - Jian Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
| | - De-Bao Niu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
| | - Fei-Yue Xu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
| | - Xin-An Zeng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China.
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Pursuwani BH, Bhatt BS, Vaidya FU, Pathak C, Patel MN. Synthesis, Characterization, and Biological Evaluation of Osmium(IV) Pyrazole Carbothioamide Complexes. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1852581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Bharat H. Pursuwani
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Bhupesh S. Bhatt
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Foram U. Vaidya
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Chandramani Pathak
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Mohan N. Patel
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
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