Targeting DNA2 overcomes metabolic reprogramming in multiple myeloma.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
08 Feb 2024
Historique:
received: 29 07 2022
accepted: 18 01 2024
medline: 9 2 2024
pubmed: 9 2 2024
entrez: 8 2 2024
Statut: epublish

Résumé

DNA damage resistance is a major barrier to effective DNA-damaging therapy in multiple myeloma (MM). To discover mechanisms through which MM cells overcome DNA damage, we investigate how MM cells become resistant to antisense oligonucleotide (ASO) therapy targeting Interleukin enhancer binding factor 2 (ILF2), a DNA damage regulator that is overexpressed in 70% of MM patients whose disease has progressed after standard therapies have failed. Here, we show that MM cells undergo adaptive metabolic rewiring to restore energy balance and promote survival in response to DNA damage activation. Using a CRISPR/Cas9 screening strategy, we identify the mitochondrial DNA repair protein DNA2, whose loss of function suppresses MM cells' ability to overcome ILF2 ASO-induced DNA damage, as being essential to counteracting oxidative DNA damage. Our study reveals a mechanism of vulnerability of MM cells that have an increased demand for mitochondrial metabolism upon DNA damage activation.

Identifiants

pubmed: 38331987
doi: 10.1038/s41467-024-45350-8
pii: 10.1038/s41467-024-45350-8
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

1203

Subventions

Organisme : U.S. Department of Health & Human Services | NIH | Center for Scientific Review (NIH Center for Scientific Review)
ID : R01CA222253

Informations de copyright

© 2024. The Author(s).

Références

Shapiro, Y. N. et al. Lifestyle considerations in multiple myeloma. Blood Cancer J. 11, 172 (2021).
doi: 10.1038/s41408-021-00560-x pubmed: 34702799 pmcid: 8548591
Goldman-Mazur, S. & Kumar, S. K. Current approaches to management of high-risk multiple myeloma. Am. J. Hematol 96, 854–871 (2021).
doi: 10.1002/ajh.26161 pubmed: 33725367
Pawlyn, C. & Morgan, G. J. Evolutionary biology of high-risk multiple myeloma. Nat. Rev. Cancer 17, 543–556 (2017).
doi: 10.1038/nrc.2017.63 pubmed: 28835722
Kumar, S. K. et al. Risk of progression and survival in multiple myeloma relapsing after therapy with IMiDs and bortezomib: a multicenter international myeloma working group study. Leukemia 26, 149–157 (2012).
doi: 10.1038/leu.2011.196 pubmed: 21799510
Shah, V. et al. Prediction of outcome in newly diagnosed myeloma: a meta-analysis of the molecular profiles of 1905 trial patients. Leukemia 32, 102–110 (2018).
doi: 10.1038/leu.2017.179 pubmed: 28584253
Pawlyn, C. & Davies, F. E. Toward personalized treatment in multiple myeloma based on molecular characteristics. Blood 133, 660–675 (2019).
doi: 10.1182/blood-2018-09-825331 pubmed: 30587529 pmcid: 6384187
Walker, B. A. et al. A high-risk, double-Hit, group of newly diagnosed myeloma identified by genomic analysis. Leukemia 33, 159–170 (2019).
doi: 10.1038/s41375-018-0196-8 pubmed: 29967379
Marchesini, M. et al. ILF2 is a regulator of RNA splicing and DNA damage response in 1q21-amplified multiple myeloma. Cancer cell 32, 88–100.e106 (2017).
doi: 10.1016/j.ccell.2017.05.011 pubmed: 28669490 pmcid: 5593798
Marchesini, M., Fiorini, E. & Colla, S. RNA processing: a new player of genomic instability in multiple myeloma. Oncoscience 4, 73–74 (2017).
doi: 10.18632/oncoscience.361 pubmed: 28966938 pmcid: 5616198
MacLeod, A. R. & Crooke, S. T. RNA therapeutics in oncology: Advances, challenges, and future directions. J. Clin. Pharmacol. 57, S43–S59 (2017).
doi: 10.1002/jcph.957 pubmed: 28921648
Hong, D. et al. AZD9150, a next-generation antisense oligonucleotide inhibitor of STAT3 with early evidence of clinical activity in lymphoma and lung cancer. Sci. Transl. Med. 7, 314ra185 (2015).
doi: 10.1126/scitranslmed.aac5272 pubmed: 26582900 pmcid: 5279222
Hanamura, I. et al. Frequent gain of chromosome band 1q21 in plasma-cell dyscrasias detected by fluorescence in situ hybridization: incidence increases from MGUS to relapsed myeloma and is related to prognosis and disease progression following tandem stem-cell transplantation. Blood 108, 1724–1732 (2006).
doi: 10.1182/blood-2006-03-009910 pubmed: 16705089 pmcid: 1895503
Neri, P. et al. Bortezomib-induced “BRCAness” sensitizes multiple myeloma cells to PARP inhibitors. Blood 118, 6368–6379 (2011).
doi: 10.1182/blood-2011-06-363911 pubmed: 21917757 pmcid: 4348156
Molina, J. R. et al. An inhibitor of oxidative phosphorylation exploits cancer vulnerability. Nat. Med. 24, 1036–1046 (2018).
doi: 10.1038/s41591-018-0052-4 pubmed: 29892070
Zuo, Z. et al. Bifunctional Naphtho[2,3-d][1,2,3]triazole-4,9-dione compounds exhibit antitumor effects in vitro and in vivo by inhibiting dihydroorotate dehydrogenase and inducing reactive oxygen species production. J. Med. Chem. 63, 7633–7652 (2020).
doi: 10.1021/acs.jmedchem.0c00512 pubmed: 32496056
Colic, M. et al. Identifying chemogenetic interactions from CRISPR screens with drugZ. Genome Med. 11, 52 (2019).
doi: 10.1186/s13073-019-0665-3 pubmed: 31439014 pmcid: 6706933
Duxin, J. P. et al. Human Dna2 is a nuclear and mitochondrial DNA maintenance protein. Mol Cellular Biol. 29, 4274–4282 (2009).
doi: 10.1128/MCB.01834-08
Kumar, S. et al. Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells. Oncogenesis 6, e319 (2017).
doi: 10.1038/oncsis.2017.15 pubmed: 28414320 pmcid: 5520492
Liu, W. et al. A selective small molecule DNA2 inhibitor for sensitization of human cancer cells to chemotherapy. EBioMedicine 6, 73–86 (2016).
doi: 10.1016/j.ebiom.2016.02.043 pubmed: 27211550 pmcid: 4856754
Kopek, B. G., Shtengel, G., Xu, C. S., Clayton, D. A. & Hess, H. F. Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes. Proc. Natl. Acad. Sci. USA 109, 6136–6141 (2012).
doi: 10.1073/pnas.1121558109 pubmed: 22474357 pmcid: 3341004
Cogliati, S., Enriquez, J. A. & Scorrano, L. Mitochondrial cristae: where beauty meets functionality. Trends Biochem. Sci. 41, 261–273 (2016).
doi: 10.1016/j.tibs.2016.01.001 pubmed: 26857402
Kondadi, A. K., Anand, R. & Reichert, A. S. Functional interplay between cristae biogenesis, mitochondrial dynamics and mitochondrial DNA integrity. Int. J. Mol. Sci. 20 https://doi.org/10.3390/ijms20174311 (2019).
Ronchi, D. et al. Mutations in DNA2 link progressive myopathy to mitochondrial DNA instability. Am. J. Human Genet. 92, 293–300 (2013).
doi: 10.1016/j.ajhg.2012.12.014
Gonzalez-Del Angel, A. et al. Novel phenotypes and cardiac involvement associated with DNA2 genetic variants. Front Neurol 10, 1049 (2019).
doi: 10.3389/fneur.2019.01049 pubmed: 31636600 pmcid: 6787284
Tsvetkov, P. et al. Mitochondrial metabolism promotes adaptation to proteotoxic stress. Nat. Chem. Biol. 15, 681–689 (2019).
doi: 10.1038/s41589-019-0291-9 pubmed: 31133756 pmcid: 8183600
Peng, G. et al. Human nuclease/helicase DNA2 alleviates replication stress by promoting DNA end resection. Cancer Res. 72, 2802–2813 (2012).
doi: 10.1158/0008-5472.CAN-11-3152 pubmed: 22491672 pmcid: 3367086
Zheng, L., Meng, Y., Campbell, J. L. & Shen, B. Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases. Nucleic Acids Res. 48, 16–35 (2020).
doi: 10.1093/nar/gkz1101 pubmed: 31754720
Ronchi, D. et al. Novel mutations in DNA2 associated with myopathy and mtDNA instability. Ann. Clin. Transl. Neurol. 6, 1893–1899 (2019).
doi: 10.1002/acn3.50888 pubmed: 31478350 pmcid: 6764641
Notta, F., Doulatov, S. & Dick, J. E. Engraftment of human hematopoietic stem cells is more efficient in female NOD/SCID/IL-2Rgc-null recipients. Blood 115, 3704–3707 (2010).
doi: 10.1182/blood-2009-10-249326 pubmed: 20207983
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34, 525–527 (2016).
doi: 10.1038/nbt.3519 pubmed: 27043002
Cunningham, F. et al. Ensembl 2019. Nucleic Acids Res. 47, D745–D751 (2019).
doi: 10.1093/nar/gky1113 pubmed: 30407521
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
doi: 10.1186/s13059-014-0550-8 pubmed: 25516281 pmcid: 4302049
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).
doi: 10.1073/pnas.0506580102 pubmed: 16199517 pmcid: 1239896
Barlogie, B. et al. Total therapy 2 without thalidomide in comparison with total therapy 1: Role of intensified induction and posttransplantation consolidation therapies. Blood 107, 2633–2638 (2006).
doi: 10.1182/blood-2005-10-4084 pubmed: 16322468
Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 10, 1523 (2019).
doi: 10.1038/s41467-019-09234-6 pubmed: 30944313 pmcid: 6447622

Auteurs

Natthakan Thongon (N)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Feiyang Ma (F)

Division of Rheumatology, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA.

Natalia Baran (N)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Pamela Lockyer (P)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Jintan Liu (J)

Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Christopher Jackson (C)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Ashley Rose (A)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Ken Furudate (K)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Bethany Wildeman (B)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Matteo Marchesini (M)

IRCCS Instituto Romagnolo per lo Studio dei Tumori (IRST) Dino Amadori, Meldola, Italy.

Valentina Marchica (V)

Department of Medicine and Surgery, University of Parma, Parma, Italy.

Paola Storti (P)

Department of Medicine and Surgery, University of Parma, Parma, Italy.

Giannalisa Todaro (G)

Department of Medicine and Surgery, University of Parma, Parma, Italy.

Irene Ganan-Gomez (I)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Vera Adema (V)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Juan Jose Rodriguez-Sevilla (JJ)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Yun Qing (Y)

Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Min Jin Ha (MJ)

Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Rodrigo Fonseca (R)

Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA.

Caleb Stein (C)

Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA.

Caleb Class (C)

Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University, Indianapolis, IN, USA.

Lin Tan (L)

Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Sergio Attanasio (S)

Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Guillermo Garcia-Manero (G)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Nicola Giuliani (N)

Department of Medicine and Surgery, University of Parma, Parma, Italy.

David Berrios Nolasco (D)

Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Andrea Santoni (A)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Claudio Cerchione (C)

IRCCS Instituto Romagnolo per lo Studio dei Tumori (IRST) Dino Amadori, Meldola, Italy.

Carlos Bueso-Ramos (C)

Department of Hemopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Marina Konopleva (M)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Philip Lorenzi (P)

Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Koichi Takahashi (K)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Elisabet Manasanch (E)

Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Gabriella Sammarelli (G)

Department of Medicine and Surgery, University of Parma, Parma, Italy.

Rashmi Kanagal-Shamanna (R)

Department of Hemopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Andrea Viale (A)

Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Marta Chesi (M)

Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA.

Simona Colla (S)

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. scolla@mdanderson.org.

Classifications MeSH