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Landscape of G-quadruplex DNA structural regions in breast cancer
Open accessAbstract
Response and resistance to anticancer therapies vary due to intertumor and intratumor heterogeneity 1. Here, we map differentially enriched G-quadruplex (G4) DNA structure-forming regions (∆G4Rs) in 22 breast cancer patient-derived tumor xenograft (PDTX) models. ∆G4Rs are associated with the promoters of highly amplified genes showing high expression, and with somatic single-nucleotide variants. Differences in ΔG4R landscapes reveal seven transcription factor programs across PDTXs. ∆G4R abundance and locations stratify PDTXs into at least three G4-based subtypes. ∆G4Rs in most PDTXs (14 of 22) were found to associate with more than one breast cancer subtype, which we also call an integrative cluster (IC)2. This suggests the frequent coexistence of multiple breast cancer states within a PDTX model, the majority of which display aggressive triple-negative IC10 gene activity. Short-term cultures of PDTX models with increased ∆G4R levels are more sensitive to small molecules targeting G4 DNA. Thus, G4 landscapes reveal additional IC-related intratumor heterogeneity in PDTX biopsies, improving breast cancer stratification and potentially identifying new treatment strategies.
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“as a recent study revealed G4-associated intratumor heterogeneity in breast cancer patient-derived tumor xenografts beyond current classifications (90).”
From G-quadruplex-mediated genomic instability drives SNVs in cancer (2024) · cites this paper as [90]
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Cites
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
METABRIC Group, Curtis, C., Shah, S. P., Chin, S.-F., Turashvili, G., Rueda, O. M., Dunning, M. J., Speed, D., Lynch, A. G., Samarajiwa, S., et al. (2012) · Nature · doi:10.1038/nature10983 · Cited by 6,097
Self-citationQuantitative visualization of DNA G-quadruplex structures in human cells
Biffi, G., Tannahill, D., McCafferty, J., & Balasubramanian, S. (2013) · Nature Chemistry · doi:10.1038/nchem.1548 · Cited by 2,173
Self-citationPereira, B., Chin, S., Rueda, O. M., Vollan, H. K. M., Provenzano, E., Bardwell, H. A., Pugh, M., Jones, L. R., Russell, R., Sammut, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms11479 · Cited by 1,752
Self-citationPioneer transcription factors: establishing competence for gene expression
Zaret, K. S., & Carroll, J. S. (2011) · Genes & Development · doi:10.1101/gad.176826.111 · Cited by 1,589
G-quadruplexes and their regulatory roles in biology
Rhodes, D., & Lipps, H. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv862 · Cited by 1,537
Epigenetic plasticity and the hallmarks of cancer
Flavahan, W. A., Gaskell, E., & Bernstein, B. E. (2017) · Science · doi:10.1126/science.aal2380 · Cited by 1,340
The regulation and functions of DNA and RNA G-quadruplexes
Varshney, D., Spiegel, J., Zyner, K. G., Tannahill, D., & Balasubramanian, S. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0236-x · Cited by 1,292
Self-citationHigh-throughput sequencing of DNA G-quadruplex structures in the human genome
Chambers, V. S., Marsico, G., Boutell, J. M., Antonio, M. D., Smith, G. P., & Balasubramanian, S. (2015) · Nature Biotechnology · doi:10.1038/nbt.3295 · Cited by 1,261
Self-citationG-quadruplex structures mark human regulatory chromatin
Hänsel-Hertsch, R., Beraldi, D., Lensing, S. V., Marsico, G., Zyner, K., Parry, A., Di Antonio, M., Pike, J., Kimura, H., Narita, M., et al. (2016) · Nature Genetics · doi:10.1038/ng.3662 · Cited by 964
Self-citationDNA G-quadruplexes in the human genome: detection, functions and therapeutic potential
Hänsel‐Hertsch, R., Antonio, M. D., & Balasubramanian, S. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.3 · Cited by 882
Self-citationChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
Oki, S., Ohta, T., Shioi, G., Hatanaka, H., Ogasawara, O., Okuda, Y., Kawaji, H., Nakaki, R., Sese, J., & Meno, C. (2018) · The EMBO Reports · doi:10.15252/embr.201846255 · Cited by 763
CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours
Xu, H., Antonio, M. D., McKinney, S. E., Mathew, V., Ho, B., O’Neil, N. J., Santos, N. D., Silvester, J., Wei, V., Garcia, J., et al. (2017) · Nature Communications · doi:10.1038/ncomms14432 · Cited by 601
Self-citationPaeschke, K., Capra, J. A., & Zakian, V. A. (2011) · Cell · doi:10.1016/j.cell.2011.04.015 · Cited by 566
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
Khan, A., & Mathelier, A. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1708-7 · Cited by 537
ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions
Schmidt, D., Wilson, M. D., Spyrou, C., Brown, G. D., Hadfield, J., & Odom, D. T. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.001 · Cited by 530
Rodriguez, R., Müller, S., Yeoman, J. A., Trentesaux, C., Riou, J.-F., & Balasubramanian, S. (2008) · Journal of the American Chemical Society · doi:10.1021/ja805615w · Cited by 517
Self-citationQuantitative ChIP-Seq normalization reveals global modulation of the epigenome
Orlando, D. A., Chen, M. W., Brown, V. E., Solanki, S., Choi, Y. J., Olson, E. R., Fritz, C. C., Bradner, J. E., & Guenther, M. G. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.10.018 · Cited by 503
Scheinin, I., Sie, D., Bengtsson, H. L., van de Wiel, M. A., Olshen, A. B., van Thuijl, H. F., Essen, H. F. H. V., Eijk, P. P., Rustenburg, F., Meijer, G. A., et al. (2014) · Genome Research · doi:10.1101/gr.175141.114 · Cited by 497
Bruna, A., Rueda, O. M., Greenwood, W., Batra, A. S., Callari, M., Batra, R. N., McNamara, K. L., Sandoval, J. L., Cassidy, J. W., Vidaković, A. T., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.041 · Cited by 442
Self-citationWhole genome experimental maps of DNA G-quadruplexes in multiple species
Marsico, G., Chambers, V. S., Sahakyan, A. B., McCauley, P., Boutell, J. M., Antonio, M. D., & Balasubramanian, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz179 · Cited by 435
Self-citationDynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups
Rueda, O. M., Sammut, S., Seoane, J. A., Chin, S., Caswell-Jin, J. L., Callari, M., Batra, R. N., Pereira, B., Bruna, A., Ali, H. R., et al. (2019) · Nature · doi:10.1038/s41586-019-1007-8 · Cited by 423
Self-citationDistinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites
Gertz, J., Savic, D., Varley, K. E., Partridge, E. C., Safi, A., Jain, P., Cooper, G. M., Reddy, T. E., Crawford, G. E., & Myers, R. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.08.037 · Cited by 369
Hänsel‐Hertsch, R., Spiegel, J., Marsico, G., Tannahill, D., & Balasubramanian, S. (2018) · Nature Protocols · doi:10.1038/nprot.2017.150 · Cited by 334
Self-citationDNA G-quadruplex structures mold the DNA methylome
Mao, S.-Q., Ghanbarian, A. T., Spiegel, J., Cuesta, S. M., Beraldi, D., Antonio, M. D., Marsico, G., Hänsel‐Hertsch, R., Tannahill, D., & Balasubramanian, S. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0131-8 · Cited by 274
Self-citationDisruption of dog-1 in Caenorhabditis elegans triggers deletions upstream of guanine-rich DNA
Cheung, I. K., Schertzer, M. J., Rose, A. M., & Lansdorp, P. M. (2002) · Nature Genetics · doi:10.1038/ng928 · Cited by 270
Targeting BRCA1 and BRCA2 Deficiencies with G-Quadruplex-Interacting Compounds
Zimmer, J., Tacconi, E. M. C., Folio, C., Badie, S., Porru, M., Klare, K., Tumiati, M., Markkanen, E., Halder, S., Ryan, A., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2015.12.004 · Cited by 261
DNA secondary structures and epigenetic determinants of cancer genome evolution
De, S., & Michor, F. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2089 · Cited by 252
Elevated Levels of G-Quadruplex Formation in Human Stomach and Liver Cancer Tissues
Biffi, G., Tannahill, D., Miller, J., Howat, W. J., & Balasubramanian, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0102711 · Cited by 223
Self-citationG-Quadruplex DNA as a Molecular Target for Induced Synthetic Lethality in Cancer Cells
McLuckie, K. I. E., Antonio, M. D., Zecchini, H. I., Xian, J., Caldas, C., Krippendorff, B., Tannahill, D., Lowe, C., & Balasubramanian, S. (2013) · Journal of the American Chemical Society · doi:10.1021/ja404868t · Cited by 177
Self-citationPAVIS: a tool for Peak Annotation and Visualization
Huang, W., Loganantharaj, R., Schroeder, B., Fargo, D. C., & Li, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt520 · Cited by 157
DSBCapture: in situ capture and sequencing of DNA breaks
Lensing, S. V., Marsico, G., Hänsel‐Hertsch, R., Lam, E. Y. N., Tannahill, D., & Balasubramanian, S. (2016) · Nature Methods · doi:10.1038/nmeth.3960 · Cited by 155
Self-citationNoncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis
Georgakopoulos-Soares, I., Morganella, S., Jain, N., Hemberg, M., & Nik-Zainal, S. (2018) · Genome Research · doi:10.1101/gr.231688.117 · Cited by 146
G-quadruplex ligands exhibit differential G-tetrad selectivity
Le, D. D., Antonio, M. D., Chan, L. K. M., & Balasubramanian, S. (2015) · Chemical Communications · doi:10.1039/c5cc02252e · Cited by 120
Self-citationBouwman, B. A. M., & Crosetto, N. (2018) · Genes · doi:10.3390/genes9120632 · Cited by 65
Chin, S., Santonja, Á., Grzelak, M., Ahn, S., Sammut, S., Clifford, H., Rueda, O. M., Pugh, M., Goldgraben, M. A., Bardwell, H. A., et al. (2018) · Experimental and Molecular Pathology · doi:10.1016/j.yexmp.2018.03.006 · Cited by 31
Self-citation
Research works printed but not linked: 1
- Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013). · arXiv
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Kosiol, N., Juranek, S., Brossart, P., Heine, A., & Paeschke, K. (2021) · Molecular Cancer · doi:10.1186/s12943-021-01328-4 · Cited by 561
Aggregation-Induced Emission (AIE), Life and Health
Wang, H., Li, Q., Alam, P., Bai, H., Bhalla, V., Bryce, M. R., Cao, M., Chen, C., Chen, S., Chen, X., et al. (2023) · ACS Nano · doi:10.1021/acsnano.3c03925 · Cited by 404
Self-citationZou, Z., Ohta, T., Miura, F., & Oki, S. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac199 · Cited by 358
DNA G-quadruplex structures: more than simple roadblocks to transcription?
Robinson, J., Raguseo, F., Nuccio, S. P., Liano, D., & Antonio, M. D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab609 · Cited by 321
G-quadruplexes are transcription factor binding hubs in human chromatin
Spiegel, J., Cuesta, S. M., Adhikari, S., Hänsel‐Hertsch, R., Tannahill, D., & Balasubramanian, S. (2021) · Genome biology · doi:10.1186/s13059-021-02324-z · Cited by 279
Self-citation
Metadata
- Authors
- Hänsel-Hertsch, R., Simeone, A., Shea, A., Hui, W. W. I., Zyner, K. G., Marsico, G., Rueda, O. M., Bruna, A., Martin, A., Zhang, X., Adhikari, S., Tannahill, D., Caldas, C., & Balasubramanian, S.
- Affiliations
- University of Cambridge (GB)
- Institute of Cancer Research (GB)
- Corresponding author
- Balasubramanian, Shankar
- ORCID
- Venue
- Nature Genetics
- Published
- 2020-08-03
- Volume
- 52
- Issue
- 9
- Pages
- 878-883
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W3047068833
- Cited by
- 223
- References
- 37
- Citations by year
- 2026: 24 · 2025: 35 · 2024: 42 · 2023: 39 · 2022: 27 · 2021: 48 · 2020: 8
- FWCI
- 9.97
- Type
- journal article
- Language
- en
- Open access
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Cancer Research UK (C9681/A18618, C9681/A29214, C14303/A17197)
- Wellcome Trust (209441/z/17/z)
- University of Cologne | Center for Molecular Medicine Cologne, University of Cologne (2635020301)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- G-quadruplex, breast cancer, patient-derived xenografts, intratumoral heterogeneity, triple-negative breast cancer, gene amplification, somatic single nucleotide variants, tumor stratification, drug sensitivity
- MeSH terms
- Breast Neoplasms, DNA, Female, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Transcription Factors, G-Quadruplexes
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