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Sehgal M, Nayak SP, Sahoo S, Somarelli JA, Jolly MK. Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma. Cancer Biol Ther 2024; 25:2301802. [PMID: 38230570 PMCID: PMC10795782 DOI: 10.1080/15384047.2024.2301802] [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: 09/08/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Neuroblastoma is the most frequent extracranial pediatric tumor and leads to 15% of all cancer-related deaths in children. Tumor relapse and therapy resistance in neuroblastoma are driven by phenotypic plasticity and heterogeneity between noradrenergic (NOR) and mesenchymal (MES) cell states. Despite the importance of this phenotypic plasticity, the dynamics and molecular patterns associated with these bidirectional cell-state transitions remain relatively poorly understood. Here, we analyze multiple RNA-seq datasets at both bulk and single-cell resolution, to understand the association between NOR- and MES-specific factors. We observed that NOR-specific and MES-specific expression patterns are largely mutually exclusive, exhibiting a "teams-like" behavior among the genes involved, reminiscent of our earlier observations in lung cancer and melanoma. This antagonism between NOR and MES phenotypes was also associated with metabolic reprogramming and with immunotherapy targets PD-L1 and GD2 as well as with experimental perturbations driving the NOR-MES and/or MES-NOR transition. Further, these "teams-like" patterns were seen only among the NOR- and MES-specific genes, but not in housekeeping genes, possibly highlighting a hallmark of network topology enabling cancer cell plasticity.
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Affiliation(s)
- Manas Sehgal
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Sonali Priyadarshini Nayak
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
- Max Planck School Matter to Life, University of Göttingen, Göttingen, Germany
| | - Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
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2
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Fanari O, Tavakoli S, Akeson S, Makhamreh A, Nian K, McCormick CA, Qiu Y, Bloch D, Jain M, Wanunu M, Rouhanifard SH. Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity. bioRxiv 2024:2024.03.26.586895. [PMID: 38585714 PMCID: PMC10996719 DOI: 10.1101/2024.03.26.586895] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Chemical modifications in mRNAs such as pseudouridine (psi) can regulate gene expression, although our understanding of the functional impact of individual psi modifications, especially in neuronal cells, is limited. We apply nanopore direct RNA sequencing to investigate psi dynamics under cellular perturbations in SH-SY5Y cells. We assign sites to psi synthases using siRNA-based knockdown. A steady-state enzyme-substrate model reveals a strong correlation between psi synthase and mRNA substrate levels and psi modification frequencies. Next, we performed either differentiation or lead-exposure to SH-SY5Y cells and found that, upon lead exposure, not differentiation, the modification frequency is less dependent on enzyme levels suggesting translational control. Finally, we compared the plasticity of psi sites across cellular states and found that plastic sites can be condition-dependent or condition-independent; several of these sites fall within transcripts encoding proteins involved in neuronal processes. Our psi analysis and validation enable investigations into the dynamics and plasticity of RNA modifications.
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Affiliation(s)
- Oleksandra Fanari
- Dept. of Bioengineering, Northeastern University, Boston, MA
- These authors contributed equally
| | - Sepideh Tavakoli
- Dept. of Bioengineering, Northeastern University, Boston, MA
- These authors contributed equally
| | - Stuart Akeson
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Amr Makhamreh
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Keqing Nian
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | | | - Yuchen Qiu
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Dylan Bloch
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Miten Jain
- Dept. of Bioengineering, Northeastern University, Boston, MA
- Dept. of Physics, Northeastern University, Boston, MA
| | - Meni Wanunu
- Dept. of Bioengineering, Northeastern University, Boston, MA
- Dept. of Physics, Northeastern University, Boston, MA
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Keresteš V, Kubeš J, Applová L, Kollárová P, Lenčová-Popelová O, Melnikova I, Karabanovich G, Khazeem MM, Bavlovič-Piskáčková H, Štěrbová-Kovaříková P, Austin CA, Roh J, Štěrba M, Šimůnek T, Jirkovská A. Exploring the effects of topoisomerase II inhibitor XK469 on anthracycline cardiotoxicity and DNA damage. Toxicol Sci 2024; 198:288-302. [PMID: 38290791 PMCID: PMC10964739 DOI: 10.1093/toxsci/kfae008] [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] [Indexed: 02/01/2024] Open
Abstract
Anthracyclines, such as doxorubicin (adriamycin), daunorubicin, or epirubicin, rank among the most effective agents in classical anticancer chemotherapy. However, cardiotoxicity remains the main limitation of their clinical use. Topoisomerase IIβ has recently been identified as a plausible target of anthracyclines in cardiomyocytes. We examined the putative topoisomerase IIβ selective agent XK469 as a potential cardioprotective and designed several new analogs. In our experiments, XK469 inhibited both topoisomerase isoforms (α and β) and did not induce topoisomerase II covalent complexes in isolated cardiomyocytes and HL-60, but induced proteasomal degradation of topoisomerase II in these cell types. The cardioprotective potential of XK469 was studied on rat neonatal cardiomyocytes, where dexrazoxane (ICRF-187), the only clinically approved cardioprotective, was effective. Initially, XK469 prevented daunorubicin-induced toxicity and p53 phosphorylation in cardiomyocytes. However, it only partially prevented the phosphorylation of H2AX and did not affect DNA damage measured by Comet Assay. It also did not compromise the daunorubicin antiproliferative effect in HL-60 leukemic cells. When administered to rabbits to evaluate its cardioprotective potential in vivo, XK469 failed to prevent the daunorubicin-induced cardiac toxicity in either acute or chronic settings. In the following in vitro analysis, we found that prolonged and continuous exposure of rat neonatal cardiomyocytes to XK469 led to significant toxicity. In conclusion, this study provides important evidence on the effects of XK469 and its combination with daunorubicin in clinically relevant doses in cardiomyocytes. Despite its promising characteristics, long-term treatments and in vivo experiments have not confirmed its cardioprotective potential.
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Affiliation(s)
- Veronika Keresteš
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
| | - Jan Kubeš
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
| | - Lenka Applová
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
| | - Petra Kollárová
- Department of Pharmacology, Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove 500 03, Czech Republic
| | - Olga Lenčová-Popelová
- Department of Pharmacology, Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove 500 03, Czech Republic
| | - Iuliia Melnikova
- Department of Organic and Bioorganic chemistry, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
| | - Galina Karabanovich
- Department of Organic and Bioorganic chemistry, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
| | - Mushtaq M Khazeem
- National Center of Hematology, Mustansiriyah University, Baghdad, Baghdad Governorate 79R2+RXM, Iraq
| | - Hana Bavlovič-Piskáčková
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
| | - Petra Štěrbová-Kovaříková
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
| | - Caroline A Austin
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jaroslav Roh
- Department of Organic and Bioorganic chemistry, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
| | - Martin Štěrba
- Department of Pharmacology, Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove 500 03, Czech Republic
| | - Tomáš Šimůnek
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
| | - Anna Jirkovská
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove 500 05, Czech Republic
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Zhang X, Haeri M, Swerdlow RH, Wang N. Loss of Adaptive DNA Breaks in Alzheimer's Disease Brains. J Alzheimers Dis 2024; 97:1861-1875. [PMID: 38306051 PMCID: PMC10894583 DOI: 10.3233/jad-231303] [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] [Accepted: 12/16/2023] [Indexed: 02/03/2024]
Abstract
Background DNA breaks accumulate in Alzheimer's disease (AD) brains. While their role as true genomic lesions is recognized, DNA breaks also support cognitive function by facilitating the expression of activity-dependent immediate early genes. This process involves TOP2B, a DNA topoisomerase that catalyzes the formation of DNA double-strand breaks. Objective To characterize how AD impacts adaptive DNA breaks at nervous system genes. Methods We leveraged the ability of DNA single- and double-strand breaks to activate poly(ADP-ribose) polymerases (PARPs) that conjugate poly(ADP-ribose) (PAR) to adjacent proteins. To characterize the genomic sites harboring DNA breaks in AD brains, nuclei extracted from 3 AD and 3 non-demented autopsy brains (frontal cortex, all male donors, age 78 to 91 years of age) were analyzed through CUT&RUN in which we targeted PAR with subsequent DNA sequencing. Results Although the AD brains contained 19.9 times more PAR peaks than the non-demented brains, PAR peaks at nervous system genes were profoundly lost in AD brains, and the expression of these genes was downregulated. This result is consistent with our previous CUT&RUN targeting γH2AX, which marks DNA double-strand breaks. In addition, TOP2B expression was significantly decreased in the AD brains. Conclusions Although AD brains contain a net increase in DNA breaks, adaptive DNA breaks at nervous system genes are lost in AD brains. This could potentially reflect diminished TOP2B expression and contribute to impaired neuron function and cognition in AD patients.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- Institute of Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | - Mohammad Haeri
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Russell H. Swerdlow
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ning Wang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- Institute of Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
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5
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Zhang X, Haeri M, Swerdlow RH, Wang N. Loss of Adaptive DNA Breaks in Alzheimer's Disease Brains. bioRxiv 2023:2023.12.11.566423. [PMID: 38168316 PMCID: PMC10760021 DOI: 10.1101/2023.12.11.566423] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background DNA breaks accumulate in Alzheimer's disease (AD) brains. While their role as true genomic lesions is recognized, DNA breaks also support cognitive function by facilitating the expression of activity-dependent immediate early genes (IEGs). This process involves TOP2B, a DNA topoisomerase that catalyzes the formation of DNA double-strand breaks (DSBs). Objective To characterize how AD impacts adaptive DNA breaks at nervous system genes. Methods We leveraged the ability of DNA single- and double-strand breaks to activate poly(ADP-ribose) polymerases (PARPs) that conjugate poly(ADP-ribose) (PAR) to adjacent proteins. To characterize the genomic sites harboring DNA breaks in AD brains, nuclei extracted from 3 AD and 3 non-demented (ND) autopsy brains (frontal cortex, all male donors, age 78 to 91 years of age) were analyzed through CUT&RUN in which we targeted PAR with subsequent DNA sequencing. Results Although the AD brains contained 19.9 times more PAR peaks than the ND brains, PAR peaks at nervous system genes were profoundly lost in AD brains, and the expression of these genes was downregulated. This result is consistent with our previous CUT&RUN targeting γH2AX, which marks DNA double-strand breaks (DSBs). In addition, TOP2B expression was significantly decreased in the AD brains. Conclusion Although AD brains contain a net increase in DNA breaks, adaptive DNA breaks at nervous system genes are lost in AD brains. This could potentially reflect diminished TOP2B expression and contribute to impaired neuron function and cognition in AD patients.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- Institute of Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | - Mohammad Haeri
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Russell H. Swerdlow
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ning Wang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- Institute of Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
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D’Amico S, Tempora P, Gragera P, Król K, Melaiu O, De Ioris MA, Locatelli F, Fruci D. Two bullets in the gun: combining immunotherapy with chemotherapy to defeat neuroblastoma by targeting adrenergic-mesenchymal plasticity. Front Immunol 2023; 14:1268645. [PMID: 37849756 PMCID: PMC10577183 DOI: 10.3389/fimmu.2023.1268645] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
Neuroblastoma (NB) is a childhood tumor that originates in the peripheral sympathetic nervous system and is responsible for 15% of cancer-related deaths in the pediatric population. Despite intensive multimodal treatment, many patients with high-risk NB relapse and develop a therapy-resistant tumor. One of the phenomena related to therapeutic resistance is intratumor heterogeneity resulting from the adaptation of tumor cells in response to different selective environmental pressures. The transcriptional and epigenetic profiling of NB tissue has recently revealed the existence of two distinct cellular identities in the NB, termed adrenergic (ADRN) and mesenchymal (MES), which can spontaneously interconvert through epigenetic regulation. This phenomenon, known as tumor plasticity, has a major impact on cancer pathogenesis. The aim of this review is to describe the peculiarities of these two cell states, and how their plasticity affects the response to current therapeutic treatments, with special focus on the immunogenic potential of MES cells. Furthermore, we will discuss the opportunity to combine immunotherapy with chemotherapy to counteract NB phenotypic interconversion.
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Affiliation(s)
- Silvia D’Amico
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Patrizia Tempora
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Paula Gragera
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Kamila Król
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Ombretta Melaiu
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Maria Antonietta De Ioris
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Pediatrics, Catholic University of the Sacred Heart, Rome, Italy
| | - Doriana Fruci
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
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7
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Cowell IG, Casement JW, Austin CA. To Break or Not to Break: The Role of TOP2B in Transcription. Int J Mol Sci 2023; 24:14806. [PMID: 37834253 PMCID: PMC10573011 DOI: 10.3390/ijms241914806] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Transcription and its regulation pose challenges related to DNA torsion and supercoiling of the DNA template. RNA polymerase tracking the helical groove of the DNA introduces positive helical torsion and supercoiling upstream and negative torsion and supercoiling behind its direction of travel. This can inhibit transcriptional elongation and other processes essential to transcription. In addition, chromatin remodeling associated with gene activation can generate or be hindered by excess DNA torsional stress in gene regulatory regions. These topological challenges are solved by DNA topoisomerases via a strand-passage reaction which involves transiently breaking and re-joining of one (type I topoisomerases) or both (type II topoisomerases) strands of the phosphodiester backbone. This review will focus on one of the two mammalian type II DNA topoisomerase enzymes, DNA topoisomerase II beta (TOP2B), that have been implicated in correct execution of developmental transcriptional programs and in signal-induced transcription, including transcriptional activation by nuclear hormone ligands. Surprisingly, several lines of evidence indicate that TOP2B-mediated protein-free DNA double-strand breaks are involved in signal-induced transcription. We discuss the possible significance and origins of these DSBs along with a network of protein interaction data supporting a variety of roles for TOP2B in transcriptional regulation.
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Affiliation(s)
- Ian G. Cowell
- Biosciences Institute, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - John W. Casement
- Bioinformatics Support Unit, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Caroline A. Austin
- Biosciences Institute, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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8
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Su S, Xue Y, Lee SK, Zhang Y, Fan J, De S, Sharov A, Wang W. A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation. Nucleic Acids Res 2023; 51:2415-2433. [PMID: 36794732 PMCID: PMC10018333 DOI: 10.1093/nar/gkad086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Topoisomerases are required to release topological stress generated by RNA polymerase II (RNAPII) during transcription. Here, we show that in response to starvation, the complex of topoisomerase 3b (TOP3B) and TDRD3 can enhance not only transcriptional activation, but also repression, which mimics other topoisomerases that can also alter transcription in both directions. The genes enhanced by TOP3B-TDRD3 are enriched with long and highly-expressed ones, which are also preferentially stimulated by other topoisomerases, suggesting that different topoisomerases may recognize their targets through a similar mechanism. Specifically, human HCT116 cells individually inactivated for TOP3B, TDRD3 or TOP3B topoisomerase activity, exhibit similarly disrupted transcription for both starvation-activated genes (SAGs) and starvation-repressed genes (SRGs). Responding to starvation, both TOP3B-TDRD3 and the elongating form of RNAPII exhibit concomitantly increased binding to TOP3B-dependent SAGs, at binding sites that overlap. Notably, TOP3B inactivation decreases the binding of elongating RNAPII to TOP3B-dependent SAGs while increased it to SRGs. Furthermore, TOP3B-ablated cells display reduced transcription of several autophagy-associated genes and autophagy per se. Our data suggest that TOP3B-TDRD3 can promote both transcriptional activation and repression by regulating RNAPII distribution. In addition, the findings that it can facilitate autophagy may account for the shortened lifespan of Top3b-KO mice.
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Affiliation(s)
- Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jinshui Fan
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alexei Sharov
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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9
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Menger KE, Chapman J, Díaz-Maldonado H, Khazeem M, Deen D, Erdinc D, Casement JW, Di Leo V, Pyle A, Rodríguez-Luis A, Cowell I, Falkenberg M, Austin C, Nicholls T. Two type I topoisomerases maintain DNA topology in human mitochondria. Nucleic Acids Res 2022; 50:11154-11174. [PMID: 36215039 PMCID: PMC9638942 DOI: 10.1093/nar/gkac857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/03/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Genetic processes require the activity of multiple topoisomerases, essential enzymes that remove topological tension and intermolecular linkages in DNA. We have investigated the subcellular localisation and activity of the six human topoisomerases with a view to understanding the topological maintenance of human mitochondrial DNA. Our results indicate that mitochondria contain two topoisomerases, TOP1MT and TOP3A. Using molecular, genomic and biochemical methods we find that both proteins contribute to mtDNA replication, in addition to the decatenation role of TOP3A, and that TOP1MT is stimulated by mtSSB. Loss of TOP3A or TOP1MT also dysregulates mitochondrial gene expression, and both proteins promote transcription elongation in vitro. We find no evidence for TOP2 localisation to mitochondria, and TOP2B knockout does not affect mtDNA maintenance or expression. Our results suggest a division of labour between TOP3A and TOP1MT in mtDNA topology control that is required for the proper maintenance and expression of human mtDNA.
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Affiliation(s)
- Katja E Menger
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - James Chapman
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Héctor Díaz-Maldonado
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Mushtaq M Khazeem
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dasha Deen
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Direnis Erdinc
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - John W Casement
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Valeria Di Leo
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alejandro Rodríguez-Luis
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ian G Cowell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Caroline A Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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