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Favasuli VK, Ronchetti D, Silvestris I, Puccio N, Fabbiano G, Traini V, Todoerti K, Erratico S, Ciarrocchi A, Fragliasso V, Giannandrea D, Tumiatti F, Chiaramonte R, Torrente Y, Finelli P, Morelli E, Munshi NC, Bolli N, Neri A, Taìana E. DIS3 depletion in multiple myeloma causes extensive perturbation in cell cycle progression and centrosome amplification. Haematologica 2024; 109:231-244. [PMID: 37439377 PMCID: PMC10772536 DOI: 10.3324/haematol.2023.283274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
DIS3 gene mutations occur in approximately 10% of patients with multiple myeloma (MM); furthermore, DIS3 expression can be affected by monosomy 13 and del(13q), found in roughly 40% of MM cases. Despite the high incidence of DIS3 mutations and deletions, the biological significance of DIS3 and its contribution to MM pathogenesis remain poorly understood. In this study we investigated the functional role of DIS3 in MM, by exploiting a loss-of-function approach in human MM cell lines. We found that DIS3 knockdown inhibits proliferation in MM cell lines and largely affects cell cycle progression of MM plasma cells, ultimately inducing a significant increase in the percentage of cells in the G0/G1 phase and a decrease in the S and G2/M phases. DIS3 plays an important role not only in the control of the MM plasma cell cycle, but also in the centrosome duplication cycle, which are strictly co-regulated in physiological conditions in the G1 phase. Indeed, DIS3 silencing leads to the formation of supernumerary centrosomes accompanied by the assembly of multipolar spindles during mitosis. In MM, centrosome amplification is present in about a third of patients and may represent a mechanism leading to genomic instability. These findings strongly prompt further studies investigating the relevance of DIS3 in the centrosome duplication process. Indeed, a combination of DIS3 defects and deficient spindle-assembly checkpoint can allow cells to progress through the cell cycle without proper chromosome segregation, generating aneuploid cells which ultimately lead to the development of MM.
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Affiliation(s)
- Vanessa K Favasuli
- Department of Oncology and Hemato-oncology, University of Milan, Italy; Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Noemi Puccio
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, 42123 Reggio Emilia, Italy; Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, 41121
| | - Giuseppina Fabbiano
- Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
| | - Valentina Traini
- Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
| | - Katia Todoerti
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan
| | - Silvia Erratico
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, University of Milan, Centro Dino Ferrari, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; Novystem Spa, Milan
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, 42123 Reggio Emilia
| | - Valentina Fragliasso
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, 42123 Reggio Emilia
| | | | - Francesca Tumiatti
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
| | | | - Yvan Torrente
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, University of Milan, Centro Dino Ferrari, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan
| | - Palma Finelli
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, 20090 Milan
| | - Eugenio Morelli
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
| | - Nikhil C Munshi
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
| | - Niccolò Bolli
- Department of Oncology and Hemato-oncology, University of Milan, Italy; Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
| | - Antonino Neri
- Scientific Directorate, Azienda USL-IRCCS Reggio Emilia, 42123 Reggio Emilia.
| | - Elisa Taìana
- Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
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Murphy JJ, Surendranath K, Kanagaraj R. RNA-Binding Proteins and Their Emerging Roles in Cancer: Beyond the Tip of the Iceberg. Int J Mol Sci 2023; 24:ijms24119612. [PMID: 37298567 DOI: 10.3390/ijms24119612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
RNA-binding proteins (RBPs) represent a large family of proteins with an extensive array of roles that contribute to coordinating and directing multiple functions in RNA metabolism and transcription [...].
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Affiliation(s)
- John J Murphy
- Genome Engineering Laboratory, School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK
| | - Kalpana Surendranath
- Genome Engineering Laboratory, School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK
| | - Radhakrishnan Kanagaraj
- Genome Engineering Laboratory, School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK
- School of Life Sciences, University of Bedfordshire, Park Square, Luton LU1 3JU, UK
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600119, India
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Thomas M, Dubacq C, Rabut E, Lopez BS, Guirouilh-Barbat J. Noncanonical Roles of RAD51. Cells 2023; 12:cells12081169. [PMID: 37190078 DOI: 10.3390/cells12081169] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Homologous recombination (HR), an evolutionary conserved pathway, plays a paramount role(s) in genome plasticity. The pivotal HR step is the strand invasion/exchange of double-stranded DNA by a homologous single-stranded DNA (ssDNA) covered by RAD51. Thus, RAD51 plays a prime role in HR through this canonical catalytic strand invasion/exchange activity. The mutations in many HR genes cause oncogenesis. Surprisingly, despite its central role in HR, the invalidation of RAD51 is not classified as being cancer prone, constituting the "RAD51 paradox". This suggests that RAD51 exercises other noncanonical roles that are independent of its catalytic strand invasion/exchange function. For example, the binding of RAD51 on ssDNA prevents nonconservative mutagenic DNA repair, which is independent of its strand exchange activity but relies on its ssDNA occupancy. At the arrested replication forks, RAD51 plays several noncanonical roles in the formation, protection, and management of fork reversal, allowing for the resumption of replication. RAD51 also exhibits noncanonical roles in RNA-mediated processes. Finally, RAD51 pathogenic variants have been described in the congenital mirror movement syndrome, revealing an unexpected role in brain development. In this review, we present and discuss the different noncanonical roles of RAD51, whose presence does not automatically result in an HR event, revealing the multiple faces of this prominent actor in genomic plasticity.
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Affiliation(s)
- Mélissa Thomas
- INSERM U1016, UMR 8104 CNRS, Institut Cochin, Université de Paris Cité, 24 rue du Faubourg St. Jacques, F-75014 Paris, France
| | - Caroline Dubacq
- Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, INSERM, CNRS, Sorbonne Université, F-75005 Paris, France
| | - Elise Rabut
- INSERM U1016, UMR 8104 CNRS, Institut Cochin, Université de Paris Cité, 24 rue du Faubourg St. Jacques, F-75014 Paris, France
| | - Bernard S Lopez
- INSERM U1016, UMR 8104 CNRS, Institut Cochin, Université de Paris Cité, 24 rue du Faubourg St. Jacques, F-75014 Paris, France
| | - Josée Guirouilh-Barbat
- INSERM U1016, UMR 8104 CNRS, Institut Cochin, Université de Paris Cité, 24 rue du Faubourg St. Jacques, F-75014 Paris, France
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Targeting DNA repair pathways with B02 and Nocodazole small molecules to improve CRIS-PITCh mediated cassette integration in CHO-K1 cells. Sci Rep 2023; 13:3116. [PMID: 36813818 PMCID: PMC9947112 DOI: 10.1038/s41598-023-29863-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/11/2023] [Indexed: 02/24/2023] Open
Abstract
CRISPR-mediated integration could be used to develop the recombinant CHO (rCHO) cells by knock-in into the hotspot loci. However, low HDR efficiency besides the complex donor design is the main barrier for achieving so. The recently introduced MMEJ-mediated CRISPR system (CRIS-PITCh) uses a donor with short homology arms, being linearized in the cells via two sgRNAs. In this paper, a new approach to improve CRIS-PITCh knock-in efficiency by employing small molecules was investigated. Two small molecules, B02, a Rad51 inhibitor, and Nocodazole, a G2/M cell cycle synchronizer, were used to target the S100A hotspot site using a bxb1 recombinase comprised landing pad in CHO-K1 cells. Following transfection, the CHO-K1 cells were treated with the optimum concentration of one or combination of small molecules, being determined by the cell viability or flow cytometric cell cycle assay. Stable cell lines were generated and the single-cell clones were achieved by the clonal selection procedure. The finding showed that B02 improved the PITCh-mediated integration approximately twofold. In the case of Nocodazole treatment, the improvement was even more significant, up to 2.4-fold. However, the combinatorial effects of both molecules were not substantial. Moreover, according to the copy number and out-out PCR analyses, 5 and 6 of 20 clonal cells exhibited mono-allelic integration in Nocodazole and B02 groups, respectively. The results of the present study as the first attempt to enhance the CHO platform generation by exploiting two small molecules in the CRIS-PITCh system could be used in future researches to establish rCHO clones.
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Boleslavska B, Oravetzova A, Shukla K, Nascakova Z, Ibini O, Hasanova Z, Andrs M, Kanagaraj R, Dobrovolna J, Janscak P. DDX17 helicase promotes resolution of R-loop-mediated transcription-replication conflicts in human cells. Nucleic Acids Res 2022; 50:12274-12290. [PMID: 36453994 PMCID: PMC9757067 DOI: 10.1093/nar/gkac1116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures composed of an RNA:DNA hybrid and displaced DNA strand. These structures can halt DNA replication when formed co-transcriptionally in the opposite orientation to replication fork progression. A recent study has shown that replication forks stalled by co-transcriptional R-loops can be restarted by a mechanism involving fork cleavage by MUS81 endonuclease, followed by ELL-dependent reactivation of transcription, and fork religation by the DNA ligase IV (LIG4)/XRCC4 complex. However, how R-loops are eliminated to allow the sequential restart of transcription and replication in this pathway remains elusive. Here, we identified the human DDX17 helicase as a factor that associates with R-loops and counteracts R-loop-mediated replication stress to preserve genome stability. We show that DDX17 unwinds R-loops in vitro and promotes MUS81-dependent restart of R-loop-stalled forks in human cells in a manner dependent on its helicase activity. Loss of DDX17 helicase induces accumulation of R-loops and the formation of R-loop-dependent anaphase bridges and micronuclei. These findings establish DDX17 as a component of the MUS81-LIG4-ELL pathway for resolution of R-loop-mediated transcription-replication conflicts, which may be involved in R-loop unwinding.
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Affiliation(s)
- Barbora Boleslavska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic,Faculty of Science, Charles University in Prague, Albertov 6, 128 00 Prague 2, Czech Republic
| | - Anna Oravetzova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic,Faculty of Science, Charles University in Prague, Albertov 6, 128 00 Prague 2, Czech Republic
| | - Kaustubh Shukla
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Zuzana Nascakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | | | - Zdenka Hasanova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Martin Andrs
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Radhakrishnan Kanagaraj
- School of Life Sciences, University of Bedfordshire, Park Square, Luton LU1 3JU, UK,School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK,Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600119, India
| | - Jana Dobrovolna
- Correspondence may also be addressed to Jana Dobrovolna. Tel: +420 241063127;
| | - Pavel Janscak
- To whom correspondence should be addressed. Tel: +41 44 6353470;
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Lee H, You SY, Han DW, La H, Park C, Yoo S, Kang K, Kang MH, Choi Y, Hong K. Dynamic Change of R-Loop Implicates in the Regulation of Zygotic Genome Activation in Mouse. Int J Mol Sci 2022; 23:ijms232214345. [PMID: 36430821 PMCID: PMC9699122 DOI: 10.3390/ijms232214345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
In mice, zygotic genome activation (ZGA) occurs in two steps: minor ZGA at the one-cell stage and major ZGA at the two-cell stage. Regarding the regulation of gene transcription, minor ZGA is known to have unique features, including a transcriptionally permissive state of chromatin and insufficient splicing processes. The molecular characteristics may originate from extremely open chromatin states in the one-cell stage zygotes, yet the precise underlying mechanism has not been well studied. Recently, the R-loop, a triple-stranded nucleic acid structure of the DNA/RNA hybrid, has been implicated in gene transcription and DNA replication. Therefore, in the present study, we examined the changes in R-loop dynamics during mouse zygotic development, and its roles in zygotic transcription or DNA replication. Our analysis revealed that R-loops persist in the genome of metaphase II oocytes and preimplantation embryos from the zygote to the blastocyst stage. In particular, zygotic R-loop levels dynamically change as development proceeds, showing that R-loop levels decrease as pronucleus maturation occurs. Mechanistically, R-loop dynamics are likely linked to ZGA, as inhibition of either DNA replication or transcription at the time of minor ZGA decreases R-loop levels in the pronuclei of zygotes. However, the induction of DNA damage by treatment with anticancer agents, including cisplatin or doxorubicin, does not elicit genome-wide changes in zygotic R-loop levels. Therefore, our study suggests that R-loop formation is mechanistically associated with the regulation of mouse ZGA, especially minor ZGA, by modulating gene transcription and DNA replication.
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Affiliation(s)
- Hyeonji Lee
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Seong-Yeob You
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Dong Wook Han
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Seonho Yoo
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Kiye Kang
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Min-Hee Kang
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea
- Correspondence:
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