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Anjum F, Kaushik K, Salam A, Yadav A, Nandi CK. Super-Resolution Microscopy Unveils Synergistic Structural Changes of Organelles Upon Point Mutation. Adv Biol (Weinh) 2024; 8:e2300399. [PMID: 38053236 DOI: 10.1002/adbi.202300399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/02/2023] [Indexed: 12/07/2023]
Abstract
Ethyl methanesulphonate (EMS), is a widely used chemical mutagen that causes high-frequency germline null mutation by inserting an alkyl group into the nucleotide guanine in eukaryotic cells. The effect of EMS on the dynamics of the aneuploid genome, increased cellular instability, and carcinogenicity in relation to benign and malignant tumors are reported, but the molecular level understanding of morphological changes of higher-order chromatin structure has poorly been understood. This is due to a lack of sufficient resolution in conventional microscopic techniques to see small structures below the diffraction limit. Here, using super-resolution radial fluctuation, a largely fragmented, decompaction, and less dense heterochromatin structure upon EMS treatment to HEK 293A cells without any change in nuclear DNA domains is observed. This result suggests an early stage of carcinogenicity happened due to the point mutation. In addition, the distinct structural changes with an elongated morphology of lysosomes are also observed. On the other hand, fragmented and increased heterogeneous populations with an increased cytoplasmic occupancy of mitochondria are observed.
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Affiliation(s)
- Farhan Anjum
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Kush Kaushik
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Abdul Salam
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Aditya Yadav
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Chayan Kanti Nandi
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
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Sisdelli L, Cordioli MIV, Vaisman F, Monte O, Longui CA, Cury AN, Freitas MO, Rangel-Pozzo A, Mai S, Cerutti JM. A Multifocal Pediatric Papillary Thyroid Carcinoma (PTC) Harboring the AGK-BRAF and RET/PTC3 Fusion in a Mutually Exclusive Pattern Reveals Distinct Levels of Genomic Instability and Nuclear Organization. Biology (Basel) 2021; 10:biology10020125. [PMID: 33562578 PMCID: PMC7914679 DOI: 10.3390/biology10020125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/11/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
Simple Summary Genetic alterations, such as RET/PTC and AGK-BRAF fusions, are frequent events in pediatric papillary thyroid carcinoma (PTC). However, their role as prognostic markers in pediatric PTC is still under investigation. In this study, we present a patient harboring three tumor foci with distinct genetic alterations (AGK-BRAF, RET/PTC3 and an absence of canonical alterations) that were investigated for DNA structure and telomere-related genomic instability. These preliminary results highlight that AGK-BRAF fusion likely affects nuclear architecture, which might explain a more aggressive disease outcome observed in pediatric PTC cases with AGK-BRAF fusion. Abstract The spectrum and incidence of gene fusions in papillary thyroid carcinoma (PTC) can differ significantly depending on the age of onset, histological subtype or radiation exposure history. In sporadic pediatric PTC, RET/PTC1-3 and AGK-BRAF fusions are common genetic alterations. The role of RET/PTC as a prognostic marker in pediatric PTC is still under investigation. We recently showed that AGK-BRAF fusion is prevalent in young patients (mean 10 years) and associated with specific and aggressive pathological features such as multifocality and lung metastasis. In this pilot study, we report a unique patient harboring three different foci: the first was positive for AGK-BRAF fusion, the second was positive for just RET/PTC3 fusion and the third was negative for both rearrangements. To investigate whether AGK-BRAF and RET/PTC3 are associated with genomic instability and chromatin modifications, we performed quantitative fluorescence in situ hybridization (Q-FISH) of telomere repeats followed by 3D imaging analysis and 3D super-resolution Structured Illumination Microscopy (3D-SIM) to analyze the DNA structure from the foci. We demonstrated in this preliminary study that AGK-BRAF is likely associated with higher levels of telomere-related genomic instability and chromatin remodeling in comparison with RET/PTC3 foci. Our results suggest a progressive disruption in chromatin structure in AGK-BRAF-positive cells, which might explain a more aggressive disease outcome in patients harboring this rearrangement.
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Affiliation(s)
- Luiza Sisdelli
- The Genetic Basis of Thyroid Tumors Lab, Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil; (L.S.); (M.I.V.C.)
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (A.R.-P.); (S.M.)
| | - Maria Isabel V. Cordioli
- The Genetic Basis of Thyroid Tumors Lab, Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil; (L.S.); (M.I.V.C.)
| | | | - Osmar Monte
- Department of Pediatrics, Irmandade da Santa Casa de Misericórdia de São Paulo, São Paulo 01221-010, Brazil; (O.M.); (C.A.L.)
| | - Carlos A. Longui
- Department of Pediatrics, Irmandade da Santa Casa de Misericórdia de São Paulo, São Paulo 01221-010, Brazil; (O.M.); (C.A.L.)
| | - Adriano N. Cury
- Department of Medicine, Irmandade da Santa Casa de Misericórdia de São Paulo, São Paulo 01221-010, Brazil;
| | - Monique O. Freitas
- Medical Genetics Service of the Martagão Gesteira Childcare and Pediatrics Institute (IPPMG), Medical School, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil;
| | - Aline Rangel-Pozzo
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (A.R.-P.); (S.M.)
| | - Sabine Mai
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (A.R.-P.); (S.M.)
| | - Janete M. Cerutti
- The Genetic Basis of Thyroid Tumors Lab, Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil; (L.S.); (M.I.V.C.)
- Correspondence: ; Tel.: +55-11-5576-4979
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Nakagawa S, Yamazaki T, Hirose T. Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu. Open Biol 2018; 8:rsob.180150. [PMID: 30355755 PMCID: PMC6223218 DOI: 10.1098/rsob.180150] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/27/2018] [Indexed: 02/06/2023] Open
Abstract
Paraspeckles are nuclear bodies built on an architectural long noncoding RNA, NEAT1, and a series of studies have revealed their molecular components, fine internal structures and cellular and physiological functions. Emerging lines of evidence suggest that paraspeckle formation is elicited by phase separation of associating RNA-binding proteins containing intrinsically disordered regions, which induce ordered arrangement of paraspeckle components along NEAT1. In this review, we will summarize the history of paraspeckle research over the last couple of decades, especially focusing on the function and structure of the nuclear bodies. We also discuss the future directions of research on long noncoding RNAs that form ‘RNP milieux’, large and flexible phase-separated ribonucleoprotein complexes.
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Affiliation(s)
- Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
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Fukuta M, Ono A, Nawa Y, Inami W, Shen L, Kawata Y, Terekawa S. Cell structure imaging with bright and homogeneous nanometric light source. J Biophotonics 2017; 10:503-510. [PMID: 27274004 DOI: 10.1002/jbio.201500308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/19/2016] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
Label-free optical nano-imaging of dendritic structures and intracellular granules in biological cells is demonstrated using a bright and homogeneous nanometric light source. The optical nanometric light source is excited using a focused electron beam. A zinc oxide (ZnO) luminescent thin film was fabricated by atomic layer deposition (ALD) to produce the nanoscale light source. The ZnO film formed by ALD emitted the bright, homogeneous light, unlike that deposited by another method. The dendritic structures of label-free macrophage receptor with collagenous structure-expressing CHO cells were clearly visualized below the diffraction limit. The inner fiber structure was observed with 120 nm spatial resolution. Because the bright homogeneous emission from the ZnO film suppresses the background noise, the signal-to-noise ratio (SNR) for the imaging results was greater than 10. The ALD method helps achieve an electron beam excitation assisted microscope with high spatial resolution and high SNR.
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Affiliation(s)
- Masahiro Fukuta
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
| | - Atsushi Ono
- Research Institute of Electronics, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
| | - Yasunori Nawa
- Research Institute of Electronics, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
| | - Wataru Inami
- Research Institute of Electronics, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
| | - Lin Shen
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
| | - Yoshimasa Kawata
- Research Institute of Electronics, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
| | - Susumu Terekawa
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
- Photon Medical Research Center, Hamamatsu University School of Medicine, 1-20-1 Hondayama, Higashi, Hamamatsu, 431-3192, Japan
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