Mesin, L., Ersching, J. & Victora, G. D. Germinal center B cell dynamics. Immunity 45, 471–482 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Muramatsu, M. et al. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 102, 553–563 (2000).

Article 
CAS 
PubMed 

Google Scholar
 

Liu, M. et al. Two levels of protection for the B cell genome during somatic hypermutation. Nature 451, 841–845 (2008).

Article 
CAS 
PubMed 

Google Scholar
 

Pasqualucci, L. et al. Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas. Nature 412, 341–346 (2001).

Article 
CAS 
PubMed 

Google Scholar
 

Shen, H. M., Peters, A., Baron, B., Zhu, X. & Storb, U. Mutation of BCL-6 gene in normal B cells by the process of somatic hypermutation of Ig genes. Science 280, 1750–1752 (1998).

Article 
CAS 
PubMed 

Google Scholar
 

Bal, E. et al. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature 607, 808–815 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ma, C. S., Deenick, E. K., Batten, M. & Tangye, S. G. The origins, function and regulation of T follicular helper cells. J. Exp. Med. 209, 1241–1253 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Suzuki, K., Grigorova, I., Phan, T. G., Kelly, L. M. & Cyster, J. G. Visualizing B cell capture of cognate antigen from follicular dendritic cells. J. Exp. Med. 206, 1485–1493 (2009).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Wang, X. et al. Follicular dendritic cells help establish follicle identity and promote B cell retention in germinal centers. J. Exp. Med. 208, 2497–2510 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bannard, O. et al. Ubiquitin-mediated fluctuations in MHC class II facilitate efficient germinal center B cell responses. J. Exp. Med. 213, 993–1009 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ise, W. et al. T follicular helper cell-germinal center B cell interaction strength regulates entry into plasma cell or recycling germinal center cell fate. Immunity 48, 702–715 e704 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Calado, D. P. et al. The cell-cycle regulator c-Myc is essential for the formation and maintenance of germinal centers. Nat. Immunol. 13, 1092–1100 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Dominguez-Sola, D. et al. The proto-oncogene MYC is required for selection in the germinal center and cyclic reentry. Nat. Immunol. 13, 1083–1091 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ersching, J. et al. Germinal center selection and affinity maturation require dynamic regulation of mTORC1 kinase. Immunity 46, 1045–1058 e1046 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Pae, J. et al. Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells. J. Exp. Med. 218, e20201699 (2021).

Article 
CAS 
PubMed 

Google Scholar
 

Victora, G. D. et al. Germinal center dynamics revealed by multiphoton microscopy with a photoactivatable fluorescent reporter. Cell 143, 592–605 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Gitlin, A. D. et al. T cell help controls the speed of the cell cycle in germinal center B cells. Science 349, 643–646 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Gitlin, A. D., Shulman, Z. & Nussenzweig, M. C. Clonal selection in the germinal centre by regulated proliferation and hypermutation. Nature 509, 637–640 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Dominguez, P. M. et al. TET2 deficiency causes germinal center hyperplasia, impairs plasma cell differentiation, and promotes B-cell lymphomagenesis. Cancer Discov. 8, 1632–1653 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Dominguez, P. M. et al. DNA methylation dynamics of germinal center B cells are mediated by AID. Cell Rep. 12, 2086–2098 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Rosikiewicz, W. et al. TET2 deficiency reprograms the germinal center B cell epigenome and silences genes linked to lymphomagenesis. Sci. Adv. 6, eaay5872 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Shaknovich, R. et al. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood 118, 3559–3569 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ortega-Molina, A. et al. The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development. Nat. Med. 21, 1199–1208 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Velichutina, I. et al. EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood 116, 5247–5255 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Beguelin, W. et al. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell 23, 677–692 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Hatzi, K. et al. Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis. Nat. Immunol. 20, 86–96 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Leung, W. et al. SETD2 haploinsufficiency enhances germinal center-associated AICDA somatic hypermutation to drive B-cell lymphomagenesis. Cancer Discov. 12, 1782–1803 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Li, J. et al. Loss of CREBBP and KMT2D cooperate to accelerate lymphomagenesis and shape the lymphoma immune microenvironment. Nat. Commun. 15, 2879 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Barisic, D. et al. ARID1A orchestrates SWI/SNF-mediated sequential binding of transcription factors with ARID1A loss driving pre-memory B cell fate and lymphomagenesis. Cancer Cell 42, 583–604 e511 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Doane, A. S. et al. OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity. Nat. Immunol. 22, 1327–1340 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bunting, K. L. et al. Multi-tiered reorganization of the genome during B cell affinity maturation anchored by a germinal center-specific locus control region. Immunity 45, 497–512 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Chu, C. S. et al. Unique immune cell coactivators specify locus control region function and cell stage. Mol. Cell 80, 845–861 e810 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Vilarrasa-Blasi, R. et al. Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation. Nat. Commun. 12, 651 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Gorelov, R. & Hochedlinger, K. A cellular identity crisis? Plasticity changes during aging and rejuvenation. Genes Dev. 38, 823–842 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Tata, P. R. & Rajagopal, J. Cellular plasticity: 1712 to the present day. Curr. Opin. Cell Biol. 43, 46–54 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Waddington, C. H. The Strategy of the Genes (Routledge, 2014).

Stadtfeld, M. & Hochedlinger, K. Induced pluripotency: history, mechanisms and applications. Genes Dev. 24, 2239–2263 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).

Article 
CAS 
PubMed 

Google Scholar
 

Di Stefano, B. et al. C/EBPalpha poises B cells for rapid reprogramming into induced pluripotent stem cells. Nature 506, 235–239 (2014).

Article 
PubMed 

Google Scholar
 

Eminli, S. et al. Differentiation stage determines potential of hematopoietic cells for reprogramming into induced pluripotent stem cells. Nat. Genet. 41, 968–976 (2009).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Hanna, J. et al. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462, 595–601 (2009).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bar-Nur, O., Russ, H. A., Efrat, S. & Benvenisty, N. Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells. Cell Stem Cell 9, 17–23 (2011).

Article 
CAS 
PubMed 

Google Scholar
 

Kim, K. et al. Epigenetic memory in induced pluripotent stem cells. Nature 467, 285–290 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ohi, Y. et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat. Cell Biol. 13, 541–549 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Polo, J. M. et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 151, 1617–1632 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Schmidt, R. & Plath, K. The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation. Genome Biol. 13, 251 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Vierbuchen, T. & Wernig, M. Molecular roadblocks for cellular reprogramming. Mol. Cell 47, 827–838 (2012).

Article 
CAS 
PubMed 

Google Scholar
 

Apostolou, E. & Hochedlinger, K. Chromatin dynamics during cellular reprogramming. Nature 502, 462–471 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Huyghe, A. et al. Comparative roadmaps of reprogramming and oncogenic transformation identify Bcl11b and Atoh8 as broad regulators of cellular plasticity. Nat. Cell Biol. 24, 1350–1363 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Stadtfeld, M., Maherali, N., Borkent, M. & Hochedlinger, K. A reprogrammable mouse strain from gene-targeted embryonic stem cells. Nat. Methods 7, 53–55 (2010).

Article 
CAS 
PubMed 

Google Scholar
 

Bar-Nur, O. et al. Small molecules facilitate rapid and synchronous iPSC generation. Nat. Methods 11, 1170–1176 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Lengner, C. J. et al. Oct4 expression is not required for mouse somatic stem cell self-renewal. Cell Stem Cell 1, 403–415 (2007).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Wernig, M. et al. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 448, 318–324 (2007).

Article 
CAS 
PubMed 

Google Scholar
 

Polo, J. M. et al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat. Biotechnol. 28, 848–855 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Di Giammartino, D. C. et al. KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks. Nat. Cell Biol. 21, 1179–1190 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Gaspar, J. A. et al. Gene expression signatures defining fundamental biological processes in pluripotent, early and late differentiated embryonic stem cells. Stem. Cells Dev. 21, 2471–2484 (2012).

Article 
CAS 
PubMed 

Google Scholar
 

Glover, C. H. et al. Meta-analysis of differentiating mouse embryonic stem cell gene expression kinetics reveals early change of a small gene set. PLoS Comput. Biol. 2, e158 (2006).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Ivanova, N. B. et al. A stem cell molecular signature. Science 298, 601–604 (2002).

Article 
CAS 
PubMed 

Google Scholar
 

Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49–55 (2008).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ramalho-Santos, M., Yoon, S., Matsuzaki, Y., Mulligan, R. C. & Melton, D. A. ‘Stemness’: transcriptional profiling of embryonic and adult stem cells. Science 298, 597–600 (2002).

Article 
CAS 
PubMed 

Google Scholar
 

Wong, D. J. et al. Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell 2, 333–344 (2008).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Yoshida, H. et al. The cis-regulatory atlas of the mouse immune system. Cell 176, 897–912 e820 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Kim, J. et al. A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell 143, 313–324 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Beguelin, W. et al. Mutant EZH2 induces a pre-malignant lymphoma niche by reprogramming the immune response. Cancer Cell 37, 655–673 e611 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Rivas, M. A. et al. Cohesin core complex gene dosage contributes to germinal center derived lymphoma phenotypes and outcomes. Front. Immunol. 12, 688493 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Yusufova, N. et al. Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture. Nature 589, 299–305 (2021).

Article 
CAS 
PubMed 

Google Scholar
 

Victora, G. D. & Nussenzweig, M. C. Germinal centers. Annu. Rev. Immunol. 40, 413–442 (2022).

Article 
CAS 
PubMed 

Google Scholar
 

Francesconi, M. et al. Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming. Elife 8, e41627 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Morin, R. D. et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat. Genet. 42, 181–185 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Beguelin, W. et al. EZH2 and BCL6 cooperate to assemble CBX8-BCOR complex to repress bivalent promoters, mediate germinal center formation and lymphomagenesis. Cancer Cell 30, 197–213 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Mlynarczyk, C. et al. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science 379, eabj7412 (2023).

Article 
CAS 
PubMed 
PubMed Central 

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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Guo, M. et al. A monoclonal antibody to the DEC-205 endocytosis receptor on human dendritic cells. Hum. Immunol. 61, 729–738 (2000).

Article 
CAS 
PubMed 

Google Scholar
 

Victora, G. D. et al. Identification of human germinal center light and dark zone cells and their relationship to human B-cell lymphomas. Blood 120, 2240–2248 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Cobaleda, C., Schebesta, A., Delogu, A. & Busslinger, M. Pax5: the guardian of B cell identity and function. Nat. Immunol. 8, 463–470 (2007).

Article 
CAS 
PubMed 

Google Scholar
 

Dominguez-Sola, D. et al. The FOXO1 transcription factor instructs the germinal center dark zone program. Immunity 43, 1064–1074 (2015).

Article 
CAS 
PubMed 

Google Scholar
 

Inoue, T. et al. The transcription factor Foxo1 controls germinal center B cell proliferation in response to T cell help. J. Exp. Med. 214, 1181–1198 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sander, S. et al. PI3 Kinase and FOXO1 transcription factor activity differentially control B cells in the germinal center light and dark zones. Immunity 43, 1075–1086 (2015).

Article 
CAS 
PubMed 

Google Scholar
 

Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Grosveld, F., van Staalduinen, J. & Stadhouders, R. Transcriptional regulation by (super)enhancers: from discovery to mechanisms. Annu. Rev. Genomics Hum. Genet. 22, 127–146 (2021).

Article 
PubMed 

Google Scholar
 

Schep, A. N., Wu, B., Buenrostro, J. D. & Greenleaf, W. J. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat. Methods 14, 975–978 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Koike, T., Harada, K., Horiuchi, S. & Kitamura, D. The quantity of CD40 signaling determines the differentiation of B cells into functionally distinct memory cell subsets. eLife 8, e44245 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Jang, J. Y. et al. A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas. J. Clin. Invest. 132, e160767 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Langlet, F. et al. Selective inhibition of FOXO1 activator/repressor balance modulates hepatic glucose handling. Cell 171, 824–835 e818 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Willcockson, M. A. et al. H1 histones control the epigenetic landscape by local chromatin compaction. Nature 589, 293–298 (2021).

Article 
CAS 
PubMed 

Google Scholar
 

Fan, Y. et al. H1 linker histones are essential for mouse development and affect nucleosome spacing in vivo. Mol. Cell. Biol. 23, 4559–4572 (2003).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Perez-Gonzalez, A., Bevant, K. & Blanpain, C. Cancer cell plasticity during tumor progression, metastasis and response to therapy. Nat. Cancer 4, 1063–1082 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Donati, G. & Amati, B. MYC and therapy resistance in cancer: risks and opportunities. Mol. Oncol. 16, 3828–3854 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Jakobsen, S. T. et al. MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch. Nat. Genet. 56, 663–674 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Petrich, A. M., Nabhan, C. & Smith, S. M. MYC-associated and double-hit lymphomas: a review of pathobiology, prognosis, and therapeutic approaches. Cancer 120, 3884–3895 (2014).

Article 
PubMed 

Google Scholar
 

Agirre, X. et al. Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response. Nat. Commun. 10, 821 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ennishi, D. et al. TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma. Nat. Med. 26, 577–588 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Reddy, A. et al. Genetic and functional drivers of diffuse large B cell lymphoma. Cell 171, 481–494 e415 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Schmitz, R. et al. Genetics and pathogenesis of diffuse large B-cell lymphoma. N. Engl. J. Med. 378, 1396–1407 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Alizadeh, A. A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503–511 (2000).

Article 
CAS 
PubMed 

Google Scholar
 

Wright, G. W. et al. A probabilistic classification tool for genetic subtypes of diffuse large B cell lymphoma with therapeutic implications. Cancer Cell 37, 551–568 e514 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

DuPage, M. & Bluestone, J. A. Harnessing the plasticity of CD4+ T cells to treat immune-mediated disease. Nat. Rev. Immunol. 16, 149–163 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Sica, A. & Mantovani, A. Macrophage plasticity and polarization: in vivo veritas. J. Clin. Invest. 122, 787–795 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ge, Y. & Fuchs, E. Stretching the limits: from homeostasis to stem cell plasticity in wound healing and cancer. Nat. Rev. Genet. 19, 311–325 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Flavahan, W. A., Gaskell, E. & Bernstein, B. E. Epigenetic plasticity and the hallmarks of cancer. Science 357, eaal2380 (2017).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Pitarresi, J. R. & Stanger, B. Z. Cellular origins and lineage plasticity in cancer. Cold Spring Harb. Perspect. Med. https://doi.org/10.1101/cshperspect.a041389 (2023).

Article 

Google Scholar
 

Yuan, S., Norgard, R. J. & Stanger, B. Z. Cellular plasticity in cancer. Cancer Discov. 9, 837–851 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Herrera, E., Martinez, A. C. & Blasco, M. A. Impaired germinal center reaction in mice with short telomeres. EMBO J. 19, 472–481 (2000).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Hu, B. T., Lee, S. C., Marin, E., Ryan, D. H. & Insel, R. A. Telomerase is up-regulated in human germinal center B cells in vivo and can be re-expressed in memory B cells activated in vitro. J. Immunol. 159, 1068–1071 (1997).

Article 
CAS 
PubMed 

Google Scholar
 

Hanahan, D. Hallmarks of cancer: new dimensions. Cancer Discov. 12, 31–46 (2022).

Article 
CAS 
PubMed 

Google Scholar
 

Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646–674 (2011).

Article 
CAS 
PubMed 

Google Scholar
 

Guldenpfennig, C., Teixeiro, E. & Daniels, M. NF-kB’s contribution to B cell fate decisions. Front. Immunol. 14, 1214095 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Pelzer, C. & Thome, M. IKKα takes control of canonical NF-kB activation. Nat. Immunol. 12, 815–816 (2011).

Article 
CAS 
PubMed 

Google Scholar
 

Cao, Y., Yi, Y., Han, C. & Shi, B. NF-kB signaling pathway in tumor microenvironment. Front. Immunol. 15, 1476030 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Jiang, C. et al. Innate immunity and the NF-κB pathway control prostate stem cell plasticity, reprogramming and tumor initiation. Nat. Cancer 6, 1537–1558 (2025).

Article 
CAS 
PubMed 

Google Scholar
 

Sardina, J. L. et al. Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate. Cell Stem Cell 23, 905–906 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Boller, S. et al. Pioneering activity of the C-terminal domain of EBF1 shapes the chromatin landscape for B cell programming. Immunity 44, 527–541 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Apostolou, E. & Stadtfeld, M. Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr. Opin. Genet. Dev. 52, 77–85 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Cyster, J. G. Germinal centers: gaining strength from the dark side. Immunity 43, 1026–1028 (2015).

Article 
CAS 
PubMed 

Google Scholar
 

Rais, Y. et al. Deterministic direct reprogramming of somatic cells to pluripotency. Nature 502, 65–70 (2013).

Article 
CAS 
PubMed 

Google Scholar
 

Esteller, M. et al. The epigenetic hallmarks of cancer. Cancer Discov. 14, 1783–1809 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Loh, J. J. & Ma, S. Hallmarks of cancer stemness. Cell Stem Cell 31, 617–639 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Weinberg, O. K. & Arber, D. A. Mixed-phenotype acute leukemia: historical overview and a new definition. Leukemia 24, 1844–1851 (2010).

Article 
CAS 
PubMed 

Google Scholar
 

Chang, K. C. et al. Stem cell characteristics promote aggressiveness of diffuse large B-cell lymphoma. Sci. Rep. 10, 21342 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Martinez-Climent, J. A., Fontan, L., Gascoyne, R. D., Siebert, R. & Prosper, F. Lymphoma stem cells: enough evidence to support their existence? Haematologica 95, 293–302 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Mlynarczyk, C., Fontan, L. & Melnick, A. Germinal center-derived lymphomas: the darkest side of humoral immunity. Immunol. Rev. 288, 214–239 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Hu, F. et al. Degree of stemness predicts micro-environmental response and clinical outcomes of diffuse large B-cell lymphoma and identifies a potential targeted therapy. Front. Immunol. 13, 1012242 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

in Guide for the Care and Use of Laboratory Animals The National Academies Collection: Reports funded by National Institutes of Health (National Academies Press, 2011).

Xia, M. et al. BCL10 mutations define distinct dependencies guiding precision therapy for DLBCL. Cancer Discov. 12, 1922–1941 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Craig, R. et al. IL-1β stimulates a novel axis within the NFkB pathway in endothelial cells regulated by IKKα and TAK-1. Biochem. Pharmacol. 232, 116736 (2025).

Article 
CAS 
PubMed 

Google Scholar
 

Riley, C. et al. Design and synthesis of novel aminoindazole-pyrrolo[2,3-b]pyridine inhibitors of IKKα that selectively perturb cellular non-canonical NF-kB signalling. Molecules https://doi.org/10.3390/molecules29153515 (2024).

Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 e3529 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

Article 
CAS 
PubMed 

Google Scholar
 

Liao, Y., Smyth, G. K. & Shi, W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res. 47, e47 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Hanzelmann, S., Castelo, R. & Guinney, J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 14, 7 (2013).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Pelham-Webb, B. et al. H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization. Mol. Cell 81, 1732–1748 e1738 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar