Miller, K. D. et al. Brain and other central nervous system tumor statistics, 2021. CA Cancer J. Clin. 71, 381–406 (2021).
Aldape, K. et al. Challenges to curing primary brain tumours. Nat. Rev. Clin. Oncol. 16, 509–520 (2019).
Article CAS PubMed PubMed Central Google Scholar
Prager, B. C., Xie, Q., Bao, S. & Rich, J. N. Cancer stem cells: the architects of the tumor ecosystem. Cell Stem Cell 24, 41–53 (2019).
Article CAS PubMed PubMed Central Google Scholar
Hambardzumyan, D. & Bergers, G. Glioblastoma: defining tumor niches. Trends Cancer 1, 252–265 (2015).
Article PubMed PubMed Central Google Scholar
Terekhanova, N. V. et al. Epigenetic regulation during cancer transitions across 11 tumour types. Nature 623, 432–441 (2023).
Article CAS PubMed PubMed Central Google Scholar
Karimi, E. et al. Single-cell spatial immune landscapes of primary and metastatic brain tumours. Nature 614, 555–563 (2023).
Article CAS PubMed PubMed Central Google Scholar
Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013).
Article CAS PubMed Google Scholar
Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).
Article CAS PubMed PubMed Central Google Scholar
Nguyen, T. T. T. et al. HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models. J. Clin. Invest. 130, 3699–3716 (2020).
Article CAS PubMed PubMed Central Google Scholar
Lu, B. et al. Pharmacological inhibition of core regulatory circuitry liquid-liquid phase separation suppresses metastasis and chemoresistance in osteosarcoma. Adv. Sci. 8, e2101895 (2021).
Blayney, J. W. et al. Super-enhancers include classical enhancers and facilitators to fully activate gene expression. Cell 186, 5826–5839.e5818 (2023).
Article CAS PubMed PubMed Central Google Scholar
Dębek, S. & Juszczyński, P. Super enhancers as master gene regulators in the pathogenesis of hematologic malignancies. Biochim. Biophys. Acta Rev. Cancer 1877, 188697 (2022).
Wu, S. J. et al. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. Nat. Biotechnol. 39, 819–824 (2021).
Article CAS PubMed PubMed Central Google Scholar
Bartosovic, M., Kabbe, M. & Castelo-Branco, G. Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues. Nat. Biotechnol. 39, 825–835 (2021).
Article CAS PubMed PubMed Central Google Scholar
Shi, B. et al. UTX condensation underlies its tumour-suppressive activity. Nature 597, 726–731 (2021).
Article CAS PubMed PubMed Central Google Scholar
Lee, K. H. et al. C9orf72 dipeptide repeats impair the assembly, dynamics, and function of membrane-less organelles. Cell 167, 774–788.e717 (2016).
Article CAS PubMed PubMed Central Google Scholar
White, M. R. et al. C9orf72 poly(PR) dipeptide repeats disturb biomolecular phase separation and disrupt nucleolar function. Mol. Cell 74, 713–728.e716 (2019).
Article CAS PubMed PubMed Central Google Scholar
Morgan, R. et al. Antagonism of HOX/PBX dimer formation blocks the in vivo proliferation of melanoma. Cancer Res. 67, 5806–5813 (2007).
Article CAS PubMed Google Scholar
Shah, N. & Sukumar, S. The Hox genes and their roles in oncogenesis. Nat. Rev. Cancer 10, 361–371 (2010).
Article CAS PubMed Google Scholar
Wilmerding, A. et al. HoxB genes regulate neuronal delamination in the trunk neural tube by controlling the expression of Lzts1. Development 148, dev195404 (2021).
Article CAS PubMed Google Scholar
Afzal, Z. et al. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 150, dev201259 (2023).
Article CAS PubMed PubMed Central Google Scholar
Okuda, T., Nishimura, M., Nakao, M. & Fujita, Y. RUNX1/AML1: a central player in hematopoiesis. Int J. Hematol. 74, 252–257 (2001).
Article CAS PubMed Google Scholar
Carro, M. S. et al. The transcriptional network for mesenchymal transformation of brain tumours. Nature 463, 318–325 (2010).
Article CAS PubMed Google Scholar
Lovén, J. et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013).
Article PubMed PubMed Central Google Scholar
Kwiatkowski, N. et al. Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Nature 511, 616–620 (2014).
Article CAS PubMed PubMed Central Google Scholar
Eid, A., Alshareef, S. & Mahfouz, M. M. CRISPR base editors: genome editing without double-stranded breaks. Biochem. J. 475, 1955–1964 (2018).
Article CAS PubMed Google Scholar
Mill, C. P. et al. RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1. Blood 134, 59–73 (2019).
Article CAS PubMed PubMed Central Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Article CAS PubMed PubMed Central Google Scholar
Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).
Article CAS PubMed Google Scholar
Zheng, W. et al. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science 376, eabm1483 (2022).
Article CAS PubMed Google Scholar
Granja, J. M. et al. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat. Genet. 53, 403–411 (2021).
Comments (0)