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Rothschild D, Susanto TT, Sui X, Spence JP, Rangan R, Genuth NR, Sinnott-Armstrong N, Wang X, Pritchard JK, Barna M. Diversity of ribosomes at the level of rRNA variation associated with human health and disease. CELL GENOMICS 2024; 4:100629. [PMID: 39111318 DOI: 10.1016/j.xgen.2024.100629] [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: 01/18/2024] [Revised: 05/07/2024] [Accepted: 07/14/2024] [Indexed: 09/14/2024]
Abstract
With hundreds of copies of rDNA, it is unknown whether they possess sequence variations that form different types of ribosomes. Here, we developed an algorithm for long-read variant calling, termed RGA, which revealed that variations in human rDNA loci are predominantly insertion-deletion (indel) variants. We developed full-length rRNA sequencing (RIBO-RT) and in situ sequencing (SWITCH-seq), which showed that translating ribosomes possess variation in rRNA. Over 1,000 variants are lowly expressed. However, tens of variants are abundant and form distinct rRNA subtypes with different structures near indels as revealed by long-read rRNA structure probing coupled to dimethyl sulfate sequencing. rRNA subtypes show differential expression in endoderm/ectoderm-derived tissues, and in cancer, low-abundance rRNA variants can become highly expressed. Together, this study identifies the diversity of ribosomes at the level of rRNA variants, their chromosomal location, and unique structure as well as the association of ribosome variation with tissue-specific biology and cancer.
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Affiliation(s)
- Daphna Rothschild
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Xin Sui
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey P Spence
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Naomi R Genuth
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Maria Barna
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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Xu H, Wu F, Ding C, Qin Y, Sun W, Feng L, Chen J, Jiang Z, Li Y, Xia H, Lou J. The effect of the nucleolar protein ZNF385A on the ribosomal DNA copy number variation in response to Cr(VI)-induced DNA damage. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:117018. [PMID: 39260214 DOI: 10.1016/j.ecoenv.2024.117018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/26/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024]
Abstract
Hexavalent chromium [Cr(VI)] is a widely distributed carcinogen in industrial contexts and general environmental contexts. Emerging research highlights the central role of ribosomal DNA (rDNA) in DNA Damage Responses (DDRs). However, there remains a lack of investigation into the potential dose-dependent relationship between exposure to Cr(VI) and alterations in rDNA copy number (CN), as well as the related mechanisms underlying these effects. A molecular epidemiological investigation involving 67 workers exposed to Cr(VI) and 75 unexposed controls was conducted. There was a notable increase in ZNF385A expression, variations in rDNA CN, and elevated γH2AX levels in the peripheral blood of Cr(VI)-exposed workers. Restricted cubic spline (RCS) models showed that blood Cr levels in the exposed population exhibited non-linear dose-dependent relationships with γH2AX, rDNA CN, and ZNF385A. Of considerable interest, there were robust and positive associations between ZNF385A and both γH2AX and rDNA CN. Further in vitro experiments provided concrete evidence that Cr(VI) simultaneously caused an increase in ZNF385A expression and variations in rDNA CN. ZNF385A-depleted cells showed increased sensitivity to Cr(VI)-mediated DDRs and alterations in rDNA CN. This study indicated that ZNF385A played a highly significant role in the rDNA CN variation in response to Cr(VI)-induced DNA damage.
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Affiliation(s)
- Huadong Xu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Fan Wu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, Zhejiang 310015, China
| | - Chan Ding
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Yao Qin
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Wen Sun
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Junfei Chen
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Zhaoqiang Jiang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Yongxin Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Hailing Xia
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Jianlin Lou
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China; Huzhou Key Laboratory of Precise Prevention and Control of Major Chronic Diseases, School of Medicine, and the First Affiliated Hospital, Huzhou University, Huzhou, Zhejiang 313000, China.
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Huang J, Jiang Z, Ruan Z, Sheng H, Liu S, Dong X, Su X, Feng L, Li Y, Xu H, Chen J, Xia H, Li T, Li J, Xu L, Lou J. Cr (VI)-induced ribosomal DNA copy number variation is associated with semen quality impairment: Evidence from human to animal study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116700. [PMID: 38981392 DOI: 10.1016/j.ecoenv.2024.116700] [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: 03/22/2024] [Revised: 06/27/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
OBJECTIVES This study aimed to analyze the possible role of rDNA copy number variation in the association between hexavalent chromium [Cr (VI)] exposure and semen quality in semen donors and further confirm this association in mice. METHODS In this cross-sectional study, whole blood and semen samples were collected from 155 semen donors in the Zhejiang Human Sperm Bank from January 1st to April 31st, 2021. Adult C57BL/6 J male mice were treated with different doses of Cr (VI) (0, 10, or 15 mg/kg b.w./day). Semen quality, including semen volume, total spermatozoa count, sperm concentration, progressive motility, and total motility, were analyzed according to the WHO laboratory manual. Cr concentration was detected using inductively coupled plasma mass spectrometry. The rDNA copy number was measured using qPCR. RESULTS In semen donors, whole blood Cr concentration was negatively associated with semen concentration and total sperm counts. Semen 5 S and 45 S rDNA copy numbers were negatively associated with whole blood Cr concentration and whole blood 5.8 S rDNA copy number was negatively associated with semen Cr concentration. In mice, Cr (VI) damaged testicular tissue, decreased semen quality, and caused rDNA copy number variation. Semen quality was related to the rDNA copy number in whole blood, testicular tissue, and semen samples in mice. CONCLUSION Cr (VI) was associated with decreased semen quality in semen donors and mice. Our findings suggest an in-depth analysis of the role of the rDNA copy number variation in the Cr (VI)-induced impairment of semen quality.
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Affiliation(s)
- Jing Huang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Zhaoqiang Jiang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Zheng Ruan
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Huiqiang Sheng
- Zhejiang Mater Child and Reproductive Health Center, Hangzhou, Zhejiang Province, China
| | - Shuang Liu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Xiaowen Dong
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Xin Su
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Yongxin Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Huadong Xu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Junfei Chen
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Hailing Xia
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Tao Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Jiaping Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Ling Xu
- Zhejiang Mater Child and Reproductive Health Center, Hangzhou, Zhejiang Province, China.
| | - Jianlin Lou
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China; School of Medicine, and The First Affiliated Hospital, Huzhou University, Huzhou, Zhejiang Province, China.
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Godwin JS, Michel JM, Ludlow AT, Frugé AD, Mobley CB, Nader GA, Roberts MD. Relative rDNA copy number is not associated with resistance training-induced skeletal muscle hypertrophy and does not affect myotube anabolism in vitro. Am J Physiol Regul Integr Comp Physiol 2024; 327:R338-R348. [PMID: 39005083 DOI: 10.1152/ajpregu.00131.2024] [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: 05/16/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024]
Abstract
Ribosomal DNA (rDNA) copies exist across multiple chromosomes, and interindividual variation in copy number is speculated to influence the hypertrophic response to resistance training. Thus, we examined if rDNA copy number was associated with resistance training-induced skeletal muscle hypertrophy. Participants (n = 53 male, 21 ± 1 yr old; n = 29 female, 21 ± 2 yr old) performed 10-12 wk of full-body resistance training. Hypertrophy outcomes were determined, as was relative rDNA copy number from preintervention vastus lateralis (VL) biopsies. Pre- and postintervention VL biopsy total RNA was assayed in all participants, and mRNA/rRNA markers of ribosome content and biogenesis were also assayed in the 29 female participants before training, 24 h following training bout 1, and in the basal state after 10 wk of training. Across all participants, no significant associations were evident between relative rDNA copy number and training-induced changes in whole body lean mass (r = -0.034, P = 0.764), vastus lateralis thickness (r = 0.093, P = 0.408), mean myofiber cross-sectional area (r = -0.128, P = 0.259), or changes in muscle RNA concentrations (r = 0.026, P = 0.818), and these trends were similar when examining each gender. However, all Pol-I regulon mRNAs as well as 45S pre-rRNA, 28S rRNA, and 18S rRNA increased 24 h following the first training bout in female participants. Follow-up studies using LHCN-M2 myotubes demonstrated that a reduction in relative rDNA copy number induced by bisphenol A did not significantly affect insulin-like-growth factor-induced myotube hypertrophy. These findings suggest that relative rDNA copy number is not associated with myofiber hypertrophy.NEW & NOTEWORTHY We examined ribosomal DNA (rDNA) copy numbers in men and women who resistance trained for 10-12 wk and found no significant associations with skeletal muscle hypertrophy outcomes. These data, along with in vitro data in immortalized human myotubes whereby rDNA copy number was reduced, provide strong evidence that relative rDNA copy number is not associated with anabolism.
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Affiliation(s)
- Joshua S Godwin
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
| | - J Max Michel
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
| | - Andrew T Ludlow
- School of Kinesiology, University of Michigan, Ann Arbor, Michigan, United States
| | - Andrew D Frugé
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
- College of Nursing, Auburn University, Auburn, Alabama, United States
| | - C Brooks Mobley
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
| | - Gustavo A Nader
- Department of Kinesiology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States
| | - Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
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Coradduzza D, Congiargiu A, Azara E, Mammani IMA, De Miglio MR, Zinellu A, Carru C, Medici S. Heavy metals in biological samples of cancer patients: a systematic literature review. Biometals 2024; 37:803-817. [PMID: 38347295 PMCID: PMC11254964 DOI: 10.1007/s10534-024-00583-4] [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: 03/24/2023] [Accepted: 01/07/2024] [Indexed: 07/18/2024]
Abstract
The majority of the so-called heavy metals are suspected to be involved in a number of pathologies and play a role in human carcinogenesis. Some of them (i.e. arsenic (As), cadmium (Cd), chromium (Cr), lead (Pb), mercury (Hg) and nickel (Ni)) have been defined as carcinogens, increasing the susceptibility of tumor development and progression in humans. Moreover, Ni, Cr, Cd, Hg, and Pb together with zinc (Zn) and iron (Fe), may be capable of stimulating the progression of breast cancer and reducing a patient's sensitivity to treatment through alterations to DNA methylation. In patients with gastric cancers, levels of various heavy metals are augmented and hypothesized to amplify the expression of the human epidermal growth factor receptor type 2 gene. Cd may increase the risk of lung cancer development and have a negative impact on the overall survival of lung cancer patients. To investigate the relation between heavy metals in biological samples and risk, occurrence and survival cancer individuals, a comprehensive review work was performed, with a focus on breast, lung, prostate and gastric cancers. An extensive search strategy was devised to ensure relevant literature could be identified, with the PECO framework being adopted to facilitate this and identify key search terms. As evidenced in this review, there is substantial data to support the hypothesis that heavy metals influence tumor development and progression. Unluckily the number of papers dealing with the determination of metals directly in samples from cancer tissues is still rather limited, so we decided to expand the scope of this review also to analyses carried out on other biological samples, as urine, plasma, hair, nail, etc. The studies reviewed showed that several limitations and current knowledge gaps are present in the literature that require further investigation to improve our comprehension of the impact of different heavy metals on tumorigenesis.
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Affiliation(s)
- Donatella Coradduzza
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100, Sassari, Italy.
| | - Antonella Congiargiu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100, Sassari, Italy
| | - Emanuela Azara
- Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy
| | | | - Maria Rosaria De Miglio
- Department of Medical, Surgery and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100, Sassari, Italy
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100, Sassari, Italy.
| | - Serenella Medici
- Department of Chemistry and Pharmacy, University of Sassari, Vienna 2, 07100, Sassari, Italy
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Chen Y, Liu Y, Zhao P, Liang Y, Ma Y, Liu H, Hou J, Hou C, Huo D. Sulfhydryl-functionalized 3D MXene-AuNPs enabled electrochemical sensors for the selective determination of Pb 2+, Cu 2+ and Hg 2+ in grain. Food Chem 2024; 446:138770. [PMID: 38428079 DOI: 10.1016/j.foodchem.2024.138770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/08/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Herein, we made 3D MXene-AuNPs by in situ growth of gold nanoparticles (AuNPs) on the surface of MXene by chemical reduction method, and then introduced three sulfhydryl (-SH) compounds as functionalized modifiers attached to the AuNPs to form a highly selective composite material for the detection of Pb2+, Cu2+, and Hg2+, respectively. The doping of AuNPs changes the microstructure of 2D MXene and generates more active sites. On a sensing platform based on ITO array electrodes, the detection system was optimised with sensitivities up to 1.157, 0.846 and 0.799 μA·μg-1Lcm-2 (Pb2+, Cu2+, and Hg2+). The selectivity of MXene@AuNPs was effectively improved by sulfhydryl group modification. In the range of 1-1300 μg L-1, the detection limits of three ions were 0.07, 0.13 and 0.21 μg L-1. In addition, this method can efficiently and accurately detect heavy metal ions in four cereal samples with consistent results with inductively coupled plasma mass spectrometry.
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Affiliation(s)
- Yuanyuan Chen
- Key Laboratory for Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China
| | - Yiyi Liu
- Key Laboratory for Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China
| | - Peng Zhao
- Key Laboratory for Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China
| | - Yi Liang
- Key Laboratory for Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China
| | - Yi Ma
- Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, 188 University Town, Yibin 644000, PR China
| | - Huan Liu
- Chongqing Institute for Food and Drug Control, Chongqing 401121, PR China
| | - Jingzhou Hou
- Key Laboratory for Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China; Postdoctoral Research Station, Chongqing University, Bioengineering College of Chongqing University, Chongqing 400044, PR China; Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing 401331, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China; Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, 188 University Town, Yibin 644000, PR China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
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Chen C, Feng L, Chen J, Shen J, Lin L. Ribosomal DNA copy number alteration in blood sample from gastric cancer patients. Mol Biol Rep 2023; 50:7155-7160. [PMID: 37407803 DOI: 10.1007/s11033-023-08630-y] [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: 05/04/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Ribosomal DNA (rDNA) is the most abundant and important housekeeping gene in the cell. It usually acted as DNA damage sensor in DNA damage reaction. Gastric cancer (GC) as a tumor with high morbidity and mortality, it is hard to diagnosis in an early stage. METHODS In this study, we collected and test the copy number of rDNA in blood sample of 42 GC patients and 56 healthy controls (HC) to explore the relationship between rDNA and GC. Besides, we make a correlation between the copy number of rDNA and ten biomarkers (CYFR21-1, CA15-3, CA72-4, NSE, CEA, CA125, ProGRP, AFP, SCC, CA19-9). RESULTS The copy number of 18 S, 5.8 S, 28 S rDNA in GC is less than HC and 5 S is more than HC in their blood sample. And the expression of H-cox-1 and ND1 in GC is higher than HC in blood sample. it shows the expression of CA15-3 is related to ND1 and H-cox-1. CONCLUSION We found for the first time the changes of rDNA and mtDNA expression in the blood of patients with gastric cancer. All these finding suggests rDNA may have potential in diagnosing GC.
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Affiliation(s)
- Changchang Chen
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Junfei Chen
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jian Shen
- Department of Medical Administration, Affiliated People's Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Lijun Lin
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China.
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Zhao T, Sun D, Long K, Lemos B, Zhang Q, Man J, Zhao M, Zhang Z. N 6-methyladenosine upregulates ribosome biogenesis in environmental carcinogenesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163428. [PMID: 37061066 DOI: 10.1016/j.scitotenv.2023.163428] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/20/2023] [Accepted: 04/06/2023] [Indexed: 06/01/2023]
Abstract
Many trace metal pollutants in surface water, the atmosphere, and soil are carcinogenic, and ribosome biogenesis plays an important role in the carcinogenicity of heavy metals. However, the contradiction between upregulated ribosome biogenesis and decreased ribosomal DNA copy number in environmental carcinogenesis is not fully understood. Here, from a perspective of the most predominant and abundant RNA epigenetic modification, N6-methyladenosine (m6A), we explored the reason behind this contradiction at the post-transcriptional level using arsenite-induced skin carcinogenesis models both in vitro and in vivo. Based on the m6A microarray assay and a series of experiments, we found for the first time that the elevated m6A in arsenite-induced transformation is mainly enriched in the genes regulating ribosome biogenesis. m6A upregulates ribosome biogenesis post-transcriptionally by stabilizing ribosomal proteins and modulating non-coding RNAs targeting ribosomal RNAs and proteins, leading to arsenite-induced skin carcinogenesis. Using multi-omics analysis of human subjects and experimental validation, we identified an unconventional role of a well-known key proliferative signaling node AKT1 as a vital mediator between m6A and ribosome biogenesis in arsenic carcinogenesis. m6A activates AKT1 and transmits proliferative signals to ribosome biogenesis, exacerbating the upregulation of ribosome biogenesis in arsenite-transformed keratinocytes. Similarly, m6A promotes cell proliferation by upregulating ribosome biogenesis in cell transformation induced by carcinogenic heavy metals (chromium and nickel). Importantly, inhibiting m6A reduces ribosome biogenesis. Targeted inhibition of m6A-upregulated ribosome biogenesis effectively prevents cell transformation induced by trace metals (arsenic, chromium, and nickel). Our results reveal the mechanism of ribosome biogenesis upregulated by m6A in the carcinogenesis of trace metal pollutants. From the perspective of RNA epigenetics, our study improves our understanding of the contradiction between upregulated ribosome biogenesis and decreased ribosomal DNA copy number in the carcinogenesis of environmental carcinogens.
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Affiliation(s)
- Tianhe Zhao
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Donglei Sun
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Keyan Long
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Bernardo Lemos
- Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston 02108, MA, USA
| | - Qian Zhang
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Jin Man
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Manyu Zhao
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Zunzhen Zhang
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China.
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9
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Xu H, Shi L, Feng L, Wu F, Chen J, Qin Y, Dong X, Jiang Z, Li Y, Xia H, Lou J. Hexavalent chromium [Cr(VI)]-induced ribosomal DNA copy number variation and DNA damage responses and their associations with nucleolar protein HRAS in humans and cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023:121816. [PMID: 37182578 DOI: 10.1016/j.envpol.2023.121816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/06/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023]
Abstract
The carcinogenicity of hexavalent chromium [Cr(VI)] and its compounds has been widely recognized, yet the mechanism of genetic damage is still not fully understood. The ribosomal DNA (rDNA) copy number is recently considered a potential marker of cancer-associated stress. To investigate the roles of rDNA copy number variation (CNV) in DNA damage responses (DDRs) induced by Cr(VI) and the potential mechanism from nucleolar protein HRAS, a cross-sectional study in Cr(Ⅵ)-exposed workers and an in vitro experiment using HeLa cells were conducted. Our results showed increased levels of rDNA CNV, DDRs, and HRAS expression in Cr(VI)-exposed workers. Generalized linear regression analyses showed that Cr(VI) exposure was significantly positively associated with increased levels of rDNA CNV, DDRs, and HRAS expression in Cr(VI)-exposed workers. Moreover, there were pairwise associations between rDNA CNV, DDRs, and HRAS levels. Mediation analyses found that rDNA CNV significantly mediated the association between Cr(VI) exposure and DDRs. The in vitro experiments further confirmed that Cr(VI) treatment induced increased levels of rDNA CNV, DDRs, and HRAS expression in HeLa cells. Cr(VI)-induced rDNA CNV, ATM activation, and apoptosis damage were then strongly enhanced by HRAS depletion with siRNA in vitro, suggesting the important role of HRAS in CNV and DDRs caused by Cr(VI). The combined results of the human and cell line studies indicated that Cr(VI) exposure might enhance rDNA CNV by regulation of HRAS expression, which leads to Cr(VI)-induced genetic damage.
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Affiliation(s)
- Huadong Xu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Li Shi
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Fan Wu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Junfei Chen
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Yao Qin
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Xiaowen Dong
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Zhaoqiang Jiang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Yongxin Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Hailing Xia
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China
| | - Jianlin Lou
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China; School of Medicine, and the First Affiliated Hospital, Huzhou University, Huzhou, Zhejiang, 313000, China.
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10
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Morton EA, Hall AN, Cuperus JT, Queitsch C. Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans. Genetics 2023; 224:iyad039. [PMID: 36919976 PMCID: PMC10474940 DOI: 10.1093/genetics/iyad039] [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] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
The genes that encode ribosomal RNAs are present in several hundred copies in most eukaryotes. These vast arrays of repetitive ribosomal DNA (rDNA) have been implicated not just in ribosome biogenesis, but also aging, cancer, genome stability, and global gene expression. rDNA copy number is highly variable among and within species; this variability is thought to associate with traits relevant to human health and disease. Here we investigate the phenotypic consequences of multicellular life at the lower bounds of rDNA copy number. We use the model Caenorhabditis elegans, which has previously been found to complete embryogenesis using only maternally provided ribosomes. We find that individuals with rDNA copy number reduced to ∼5% of wild type are capable of further development with variable penetrance. Such individuals are sterile and exhibit severe morphological defects, particularly in post-embryonically dividing tissues such as germline and vulva. Developmental completion and fertility are supported by an rDNA copy number ∼10% of wild type, with substantially delayed development. Worms with rDNA copy number reduced to ∼33% of wild type display a subtle developmental timing defect that was absent in worms with higher copy numbers. Our results support the hypothesis that rDNA requirements vary across tissues and indicate that the minimum rDNA copy number for fertile adulthood is substantially less than the lowest naturally observed total copy number. The phenotype of individuals with severely reduced rDNA copy number is highly variable in penetrance and presentation, highlighting the need for continued investigation into the biological consequences of rDNA copy number variation.
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Affiliation(s)
| | - Ashley N Hall
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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11
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Wang Y, Meng T, Zhang L, Lin Y, Wu N, Yuan H, He Z, Niu Y, Dai Y, Zhao X, Duan H. Inhalable mixture of polycyclic aromatic hydrocarbons and metals, DNA oxidative stress and nasal ribosomal DNA copy number amplification: Direct and indirect effect analyses among population. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131538. [PMID: 37156045 DOI: 10.1016/j.jhazmat.2023.131538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/09/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023]
Abstract
The ribosomal DNA (rDNA) plays a crucial role in maintaining genome stability. So far, alterations of rDNA from airborne pollutants exposure remain unclear. Nasal epithelial cells are the earliest respiratory barrier, which has an accessible surrogate for evaluating respiratory impairment. We developed a mixture-centered biomarkers study integrated epidemiological and biological evidence among 768 subjects, a mixture of polycyclic aromatic hydrocarbons (PAHs) and metals. We identified the mixed exposure of PAHs and metals by environmental and biological monitoring, selected urinary 8-hydroxy-2'-deoxyguanosine as DNA oxidative stress marker, and measured their rDNA copy number (rDNA CN) in nasal epithelial cells. We performed linear regression, adaptive elastic net regression, BKMR, and mediation analyses to assess the direct and indirect effects. We found a 10% elevation in urinary 1-hydroxypyrene was correlated with a separate 0.31% and 0.82% amplification of nasal 5S and 45S rDNA CN, respectively (all P < 0.05). A 10% increment of urine nickel was associated with a separate 0.37% and 1.18% elevation of nasal 5S and 45S rDNA CN, respectively (all P < 0.05). BKMR results also confirmed our findings of PAHs and nickel. Our findings suggested that DNA oxidative stress might trigger rDNA instability induced by inhaled PAHs and metals.
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Affiliation(s)
- Yanhua Wang
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tao Meng
- Institute of Brain Science, Shanxi Datong University, Datong, Shanxi, China
| | - Liya Zhang
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Lin
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China; Center for Disease Control and Prevention of Chaoyang District of Beijing, Beijing, China
| | - Nan Wu
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China; China National Center for Food Safety Risk Assessment, Beijing, China
| | - Huige Yuan
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhizhou He
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yong Niu
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yufei Dai
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xing Zhao
- West China school of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Huawei Duan
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China.
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12
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Sun Y, Hu X, Qiu D, Zhang Z, Lei L. rDNA Transcription in Developmental Diseases and Stem Cells. Stem Cell Rev Rep 2023; 19:839-852. [PMID: 36633782 DOI: 10.1007/s12015-023-10504-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/01/2023] [Indexed: 01/13/2023]
Abstract
As the first and rate-limiting step in ribosome biogenesis, rDNA transcription undergoes significant dynamic changes during cell pluripotency alteration. Over the past decades, rDNA activity has demonstrated dynamic changes, but most people view it as passive compliance with cellular needs. The evidence for rDNA transcriptional activity determining stem cell pluripotency is growing as research advances, resulting in the arrest of embryonic development and impairment of stem cell lines stemness by rDNA transcription inhibition. The exact mechanism by which rDNA activation influences pluripotency remains unknown. The first objective of this opinion article is to describe rDNA changes in the pathological and physiological course of life, including developmental diseases, tumor genesis, and stem cell differentiation. After that, we propose three hypotheses regarding rDNA regulation of pluripotency: 1) Specialized ribosomes synthesized from rDNA variant, 2) Nucleolar stress induced by the drop of rDNA transcription, 3) Interchromosomal interactions between rDNA and other genes. The pluripotency regulatory center is expected to focus strongly on rDNA. A small molecule inhibitor of rDNA is used to treat tumors caused by abnormal pluripotency activation. By understanding how rDNA regulates pluripotency, we hope to treat developmental diseases and safely apply somatic cell reprogramming in clinical settings.
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Affiliation(s)
- Yuchen Sun
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Xinglin Hu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Dan Qiu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Zhijing Zhang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Lei Lei
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081.
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13
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Xu P, Feng L, Xu D, Wu L, Chen Y, Xiang J, Cheng P, Wang X, Lou J, Tang J, Lou X, Chen Z. Ribosomal DNA copy number associated with blood metal levels in school-age children: A follow-up study on a municipal waste incinerator in Zhejiang, China. CHEMOSPHERE 2022; 307:135676. [PMID: 35842053 DOI: 10.1016/j.chemosphere.2022.135676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/15/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
To evaluate the body burdens of heavy metals and explore the impact of environmental metal exposure on ribosomal DNA (rDNA) or mitochondrial DNA (mtDNA) copy number (CN) variation in school-age children living near a municipal waste incinerator (MWI), we conducted a follow-up study in 2019. A total of 146 sixth-grade children from a primary school located 1.2 km away from the MWI were recruited for our study. Metals, including vanadium (V), chromium (Cr), manganese (Mn), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), selenium (Se), cadmium (Cd), stannum (Sn), stibium (Sb), thallium (Tl), and lead (Pb), were determined by an inductively coupled plasma mass spectrometer method. Real-time qPCR was used to measure the rDNA and mtDNA CN. The blood metal levels followed this order: Zn > Cu > Se > Pb > Mn > Sb > As > Ni > Cd > Co > Cr > Sn > V > Tl. Blood Cr level was significantly correlated with 18 S, 2.5 S, and 45 S CN (β = -0.25, -0.22, -0.26, p < 0.05); Ni was correlated with 5 S (β = -0.36, p < 0.01); Cu was correlated with 28 S, 18 S, and 5.8 S (β = -0.24, -0.24, -0.23, p < 0.05); while Zn was correlated with 18 S, 5.8 S, and 45 S (β = -0.28, -0.32, -0.26, p < 0.05). In conclusion, school-age children living near the MWI had lower blood metal levels compared to children recruited in 2013, while rDNA CN loss was found to be correlated to several heavy metals in these children.
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Affiliation(s)
- Peiwei Xu
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, 8 Yi Kang Street, Lin'an District, 311399, Hangzhou, Zhejiang, China
| | - Dandan Xu
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China
| | - Lizhi Wu
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China
| | - Yuan Chen
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China
| | - Jie Xiang
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China
| | - Ping Cheng
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China
| | - Xiaofeng Wang
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China
| | - Jianlin Lou
- School of Public Health, Hangzhou Medical College, 8 Yi Kang Street, Lin'an District, 311399, Hangzhou, Zhejiang, China
| | - Jun Tang
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China
| | - Xiaoming Lou
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China
| | - Zhijian Chen
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Bin Sheng Road, Binjiang District, Hangzhou 310051, China.
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14
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Sharma D, Denmat SHL, Matzke NJ, Hannan K, Hannan RD, O'Sullivan JM, Ganley ARD. A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations. Genomics 2022; 114:110430. [PMID: 35830947 DOI: 10.1016/j.ygeno.2022.110430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/23/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
Abstract
Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs and in eukaryotes typically form tandem repeat arrays. Species have characteristic rDNA copy numbers, but there is substantial intra-species variation in copy number that results from frequent rDNA recombination. Copy number differences can have phenotypic consequences, however difficulties in quantifying copy number mean we lack a comprehensive understanding of how copy number evolves and the consequences. Here we present a genomic sequence read approach to estimate rDNA copy number based on modal coverage to help overcome limitations with existing mean coverage-based approaches. We validated our method using Saccharomyces cerevisiae strains with known rDNA copy numbers. Application of our pipeline to a global sample of S. cerevisiae isolates showed that different populations have different rDNA copy numbers. Our results demonstrate the utility of the modal coverage method, and highlight the high level of rDNA copy number variation within and between populations.
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Affiliation(s)
- Diksha Sharma
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sylvie Hermann-Le Denmat
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Katherine Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross D Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3168, Australia
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand; Maurice Wilkins Center, University of Auckland, New Zealand; MRC Lifecourse Unit, University of Southampton, United Kingdom; Brain Research New Zealand, The University of Auckland, Auckland, New Zealand
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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15
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Estimation of Children's Soil and Dust Ingestion Rates and Health Risk at E-Waste Dismantling Area. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19127332. [PMID: 35742584 PMCID: PMC9224165 DOI: 10.3390/ijerph19127332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 12/04/2022]
Abstract
Due to environmental health concerns, exposure to heavy metals and related adverse effects in electronic waste (e-waste) dismantling areas have attracted considerable interest in the recent years. However, little information is available about the Soil/Dust Ingestion Rates (SIR) of heavy metals for children living in such sites. This study estimated the soil ingestion of 66 children from e-waste disassembly areas by collecting and analyzing selected tracer elements in matched samples of their consumed food, feces, and urine, as well as soil samples from their play areas. The concentrations of tracer elements (including Al, Ba, Ce, Mn, Sc, Ti, Y, and V) in these samples were analyzed. The SIR was estimated to be 148.3 mg/day (median) and 383.3 mg/day (95th percentile) based on the Best Tracer Method (BTM). These values are somewhat higher than those observed in America, Canada, and other parts of China. Health risk assessments showed that Cr presented the greatest carcinogenic risk, at more than 10-6 in this typical polluted area, while As was second. These findings provide important insights into the exposure risks of heavy metals in e-waste dismantling sites and emphasize the health risk caused by Cr and As.
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16
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Hall AN, Morton E, Queitsch C. First discovered, long out of sight, finally visible: ribosomal DNA. Trends Genet 2022; 38:587-597. [PMID: 35272860 PMCID: PMC10132741 DOI: 10.1016/j.tig.2022.02.005] [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: 11/23/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 10/18/2022]
Abstract
With the advent of long-read sequencing, previously unresolvable genomic elements are being revisited in an effort to generate fully complete reference genomes. One such element is ribosomal DNA (rDNA), the highly conserved genomic region that encodes rRNAs. Genomic structure and content of the rDNA are variable in both prokarya and eukarya, posing interesting questions about the biology of rDNA. Here, we consider the types of variation observed in rDNA - including locus structure and number, copy number, and sequence variation - and their known phenotypic consequences. With recent advances in long-read sequencing technology, incorporating the full rDNA sequence into reference genomes is within reach. This knowledge will have important implications for understanding rDNA biology within the context of cell physiology and whole-organism phenotypes.
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Affiliation(s)
- Ashley N Hall
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Elizabeth Morton
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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17
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The Influence of Heavy Metals on Gastric Tumorigenesis. JOURNAL OF ONCOLOGY 2022; 2022:6425133. [PMID: 35669240 PMCID: PMC9167133 DOI: 10.1155/2022/6425133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/01/2022] [Accepted: 05/12/2022] [Indexed: 12/24/2022]
Abstract
Objectives This study aimed to observe the relationship among heavy metals concentration, microsatellite instability (MSI), and human epidermal growth factor receptor type 2 (HER2) gene amplification in gastric cancer (GC) patients. Methods The concentrations of 18 heavy metals in the plasma of GC patients and healthy controls were measured by inductive coupled plasma emission spectrometry (ICP-MS). MSI detection was conducted by detecting 5 microsatellite repeat markers by PCR analysis. HER2 gene amplification was detected by fluorescence in situ hybridization (FISH). The relationship among heavy metal elements, tumor biomarkers, HER2 amplification, and MSI status was analyzed by Pearson correlation analysis. Results A total of 105 GC patients and 62 healthy controls were recruited in this study. The concentration of arsenic (As), chromium (Cr), cuprum (Cu), mercury (Hg), manganese (Mn), lead (Pb), stibium (Sb), selenium (Se), stannum (Sn), strontium (Sr), thallium (Tl), vanadium (V), and zinc (Zn) were significantly different between GC patients and controls. Among 105 GC patients, including 87 microsatellite-stable (MSS) samples and 18 MSI samples, the concentration of Ga is significantly higher in the MSI group than that in the MSS group. Meanwhile, in 97 GC patients having detected HER2 gene amplification, 69 of 97 had negative HER2 gene amplification and the rest 28 GC patients had positive HER2 gene amplification. The concentration of Hg, Sn, and Tl is noticeably higher in the HER2 positive group than in the HER2 negative group. Only Sb was positively correlated with MSI, but none of these heavy metals was correlated with HER2 gene amplification. Conclusions The results indicated that Sb has significant positive correlation with the MSI status, which suggests that Sb may cause MSI in GC. However, further research studies are required to elucidate the mechanisms in the near feature.
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18
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Brown IN, Lafita-Navarro MC, Conacci-Sorrell M. Regulation of Nucleolar Activity by MYC. Cells 2022; 11:cells11030574. [PMID: 35159381 PMCID: PMC8834138 DOI: 10.3390/cells11030574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 01/20/2023] Open
Abstract
The nucleolus harbors the machinery necessary to produce new ribosomes which are critical for protein synthesis. Nucleolar size, shape, and density are highly dynamic and can be adjusted to accommodate ribosome biogenesis according to the needs for protein synthesis. In cancer, cells undergo continuous proliferation; therefore, nucleolar activity is elevated due to their high demand for protein synthesis. The transcription factor and universal oncogene MYC promotes nucleolar activity by enhancing the transcription of ribosomal DNA (rDNA) and ribosomal proteins. This review summarizes the importance of nucleolar activity in mammalian cells, MYC’s role in nucleolar regulation in cancer, and discusses how a better understanding (and the potential inhibition) of aberrant nucleolar activity in cancer cells could lead to novel therapeutics.
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Affiliation(s)
- Isabella N. Brown
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - M. Carmen Lafita-Navarro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Correspondence: (M.C.L.-N.); (M.C.-S.)
| | - Maralice Conacci-Sorrell
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence: (M.C.L.-N.); (M.C.-S.)
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19
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Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications. Pharmacol Ther 2021; 232:107995. [PMID: 34592204 DOI: 10.1016/j.pharmthera.2021.107995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 -- 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should improve future clinical applications of mCN measurements.
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20
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Danes JM, Palma FR, Bonini MG. Arsenic and other metals as phenotype driving electrophiles in carcinogenesis. Semin Cancer Biol 2021; 76:287-291. [PMID: 34563651 DOI: 10.1016/j.semcancer.2021.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022]
Abstract
There are several sources of heavy metal exposures whether occupational or environmental. These are connected both with the existence of natural reservoirs of metal toxicants or human activity such as mining, welding and construction. In general, exposure to heavy metals, such as cadmium (Cd), mercury (Hg), nickel (Ni), lead (Pb) and metalloids, such as arsenic (As), has been associated with diseases including neurodegenerative diseases, diabetes and cancer. Common to these diseases is the loss of cellular physiologic performance and phenotype required for proper function. On the metal side, electrophilic behavior that disrupts the electronic (or redox) state of cells is a common feature. This suggests that there may be a connection between changes to the redox equilibrium of cells caused by environmental exposures to heavy metals and the pathogenic effects of such exposures. In this mini-review, we will focus on two environmental contaminants cadmium (a metal) and arsenic (a metalloid) and explore their interactions with living organisms from the perspective of their electrophilic chemical reactivity that underlies both their potential as carcinogens and as drivers of more aggressive tumor phenotypes.
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Affiliation(s)
- Jeanne M Danes
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, United States
| | - Flavio R Palma
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, United States
| | - Marcelo G Bonini
- Department of Medicine, Division of Hematology Oncology, Northwestern University Feinberg School of Medicine and the Robert H. Lurie Comprehensive Cancer Center of Chicago, United States.
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21
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Xuan J, Gitareja K, Brajanovski N, Sanij E. Harnessing the Nucleolar DNA Damage Response in Cancer Therapy. Genes (Basel) 2021; 12:genes12081156. [PMID: 34440328 PMCID: PMC8393943 DOI: 10.3390/genes12081156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
The nucleoli are subdomains of the nucleus that form around actively transcribed ribosomal RNA (rRNA) genes. They serve as the site of rRNA synthesis and processing, and ribosome assembly. There are 400-600 copies of rRNA genes (rDNA) in human cells and their highly repetitive and transcribed nature poses a challenge for DNA repair and replication machineries. It is only in the last 7 years that the DNA damage response and processes of DNA repair at the rDNA repeats have been recognized to be unique and distinct from the classic response to DNA damage in the nucleoplasm. In the last decade, the nucleolus has also emerged as a central hub for coordinating responses to stress via sequestering tumor suppressors, DNA repair and cell cycle factors until they are required for their functional role in the nucleoplasm. In this review, we focus on features of the rDNA repeats that make them highly vulnerable to DNA damage and the mechanisms by which rDNA damage is repaired. We highlight the molecular consequences of rDNA damage including activation of the nucleolar DNA damage response, which is emerging as a unique response that can be exploited in anti-cancer therapy. In this review, we focus on CX-5461, a novel inhibitor of Pol I transcription that induces the nucleolar DNA damage response and is showing increasing promise in clinical investigations.
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Affiliation(s)
- Jiachen Xuan
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.X.); (K.G.); (N.B.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kezia Gitareja
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.X.); (K.G.); (N.B.)
| | - Natalie Brajanovski
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.X.); (K.G.); (N.B.)
| | - Elaine Sanij
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.X.); (K.G.); (N.B.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia
- St Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Department of Medicine -St Vincent’s Hospital, University of Melbourne, Melbourne, VIC 3010, Australia
- Correspondence: ; Tel.: +61-3-8559-5279
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22
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Jia J, Li T, Yao C, Chen J, Feng L, Jiang Z, Shi L, Liu J, Chen J, Lou J. Circulating differential miRNAs profiling and expression in hexavalent chromium exposed electroplating workers. CHEMOSPHERE 2020; 260:127546. [PMID: 32758765 DOI: 10.1016/j.chemosphere.2020.127546] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Hexavalent chromium [Cr (Ⅵ)] has extensive applications in industries, and long-term occupational exposure to Cr (Ⅵ) may lead to lung carcinoma and other cancers. While microRNA (miRNA) can take part in carcinogenesis, little is known about its expression profile in the population with Cr (Ⅵ) exposure. Thus, this study aimed to explore miRNA expression profiles in Cr (Ⅵ) exposed workers and to identify the potential biological function of differentially expressed miRNAs. A total of 45 significant differentially expressed miRNAs were identified by the miRNA array. The results of validation showed that miR-19a-3p, miR-19b-3p, and miR-142-3p were downregulated and miR-590-3p and miR-941 were upregulated in the exposure group. Multivariate analysis demonstrated that age, exposure duration and urinary chromium level were associated with one or more miRNAs expression. Target gene analysis indicated that these miRNAs might participate in the regulation of DNA damage-related signaling pathways. Taken together, Cr (Ⅵ) exposure can result in differential expression of miRNAs in occupational workers, and the expression of these miRNAs is correlated with the level and duration of Cr (Ⅵ) exposure, and the differentially expressed miRNAs may participate in DNA damage response.
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Affiliation(s)
- Junlin Jia
- Hangzhou Medical College, Hangzhou, 310053, China
| | - Tao Li
- Hangzhou Medical College, Hangzhou, 310053, China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China
| | - Chunji Yao
- Hangzhou Medical College, Hangzhou, 310053, China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China
| | - Junfei Chen
- Hangzhou Medical College, Hangzhou, 310053, China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China
| | - Lingfang Feng
- Hangzhou Medical College, Hangzhou, 310053, China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China
| | - Zhaoqiang Jiang
- Hangzhou Medical College, Hangzhou, 310053, China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China
| | - Li Shi
- Hangzhou Medical College, Hangzhou, 310053, China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China
| | - Jiaqi Liu
- Hangzhou Medical College, Hangzhou, 310053, China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China
| | - Junqiang Chen
- Hangzhou Medical College, Hangzhou, 310053, China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China
| | - Jianlin Lou
- Hangzhou Medical College, Hangzhou, 310053, China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China.
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