Our main goal is to unravel the nuclear events that drive peripheral activation of B lymphocytes. From genome-wide changes in epigenetics, chromatin architecture, and transcriptional activation, to recombination and hypermutation of antibody genes. Another major interest is to understand how deregulation of these mechanisms leads to B cell tumorigenesis. To achieve these goals, our team combines a wide range of cutting-edge technologies, including genome editing, nanoscopy, in situ Hi-C, cryo-EM, and bioinformatic tools.

Activation of naive B cells leads to amplification of the transcriptome.
Figure 1: Activation of G0 naïve B cells leads to a ~10 fold amplification of the transcriptome.  mRNA-Seq samples are normalized on a per cell basis using synthesized spike-in RNA controls (red rots).

B lymphocytes in higher organisms are born in the bone marrow, where they expand and undergo V(D)J recombination to assemble their cell surface antibody receptors. The newly generated B cells then migrate to the periphery as quiescent G0 lymphocytes. In this metabolically inert state, B cells can live for up to 4 months. If during their lifespan they encounter foreign antigens, naïve B cells become activated and enter the cell cycle in less than 24h. How B lymphocytes are able to respond so rapidly to infection has been a mystery. In the past 5 years, we have resolved this puzzle by showing that the genome of naïve B cells is poised. RNA polymerases, transcription factors, chromatin remodelers, histone acetyl and methyltransferases, and nuclear architectural proteins are all recruited to G0 chromatin in a manner nearly identical to that seen in activated counterparts. In naïve cells, the preloaded enzymes only display basal activity until an optimal concentration of their catalytic substrates or cofactors is reached during activation. Taking transcription as an example, a comparative analysis between G0 and cycling cells shows that expression of all genes is proportionally amplified ~10 fold (Figure 1). We have dubbed this new biological phenomenon (so far unique to lymphocytes) transcriptome, epigenome, or architectural amplification.


Activation of B cells also initiates a second round of antibody gene alterations. First, the Ch genes recombine to change the antibody isotype class, from IgM to IgG, IgE, or IgA. This process is known as class switch recombination and is mediated by the AID cytidine deaminase. In addition, the V domain of antibody genes is hypermutated, a process that couple to selection enhances the affinity of antibodies for the immunogen. Like switch recombination, somatic hypermutation is driven by AID.

RAGs, and most particularly AID, can be promiscuous in nature, and the proclivity of B cells towards lymphomagenesis stems largely from AID-mediated lesions across the genome which can create chromosomal translocations between oncogenes (e.g. MYC, PIM1, MIR142) and antibody gene loci. In a series of key studies also in the past 5 years our laboratory has identified the molecular basis for AID promiscuity. We have found that AID is recruited by super-enhancers owing to their heightened accessibility, topological complexity, and superior transcriptional activity relative to other loci (Figure 2).

AID recruitment in activated B cells.
Figure 2: In activated B cells, AID is preferentially recruited by highly transcribed genes regulated by H3K27Ac+ super-enhancers, such as Nfkbia.  AID-mediated damage is detected in 53BP1-/- B cells, where DNA breaks are processed by homologous recombination.  In this process, the single stranded-DNA binding protein RPA associates with resected DNA (sense (red) strand upstream of the break, antisense (grey) strand downstream). Nfkbia is embedded within a stripe contact domain, which in turn is embedded within H3K27Ac+ euchromatin in mouse chromosome 12.

Current topics of interest in our laboratory include:

1.  The impact of nuclear architecture on gene expression.

2.  The role of the Mediator complex on B cell transcriptional regulation.

3.  The generation of new mouse models expressing antibodies of clinical interest


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Scientific Publications

Khattabi LE, Zhao H, Kalchschmidt J, Young N, Jung S, Blerkom P, Kieffer-Kwon P, Kieffer-Kwon K, Park S, Wang X, Krebs J, Tripathi S, Sakabe N, Sobreira DR, Huang S, Rao SSP, Pruett N, Chauss D, Sadler E, Lopez A, Nobrega MA, Aiden EL, Asturias FJ, Casellas R. A pliable mediator acts as a functional, rather than an architectural bridge, between promoters and enhancers. Cell. 2019 Aug 8. pii: S0092-8674(19)30776-7. doi: 10.1016/j.cell.2019.07.011.

Shastri N, Tsai YC, Hile S, Jordan D, Powell B, Chen J, Maloney D, Dose M, Lo Y, Anastassiadis T, Rivera O, Kim T, Shah S,Borole P, Asija K, Wang X, Smith KD, Finn D, Schug J, Casellas R, Yatsunyk LA, Eckert KA, Brown EJ. Genome-wide identification of structure-forming repeats as principal sites of fork collapse upon ATR inhibitionMol Cell. 2018 Oct 4. pii:S1097-2765(18)30739-1. doi: 10.1016/j.molcel.2018.08.047.

Delgado-Benito V, Rosen DB, Wang Q, Gazumyan A, Pai J, Oliveira TY, Sundaravinayagam D, Zhang W, Andreani M, Keller L, Kieffer-Kwon K, Pekowska A, Jung S, Driesner M, Subbotin RI, Casellas R, Chait BT, Nussenzweig MC, Virgilio MD. The chromatin reader ZMYND8 regulates Igh enhancers to promote immunoglobulin class switch recombination. Mol Cell. 2018 Sep 26. pii: S1097-2765(18)30702-0. doi: 10.1016/j.molcel.2018.08.042.

Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R. The energetics and physiological impact of cohesin extrusion. Cell. 2018 May 17;173(5):1165-1178.e20. doi: 10.1016/j.cell.2018.03.072

Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL.  Cohesin loss eliminates all loop domainsCell. 2017 Oct 5;171(2):305-320.e24. doi: 10.1016/j.cell.2017.09.026.

Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network.  The 4D nucleome project. Nature. 2017 Sep 13;549(7671):219-226. doi: 10.1038/nature23884. Erratum in: Nature. 2017 Nov 22;:.

Kieffer-Kwon KR, Nimura K, Rao SSP, Xu J, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, Huang SC, Ricci MA, Baranello L, Zheng Y, Tomassoni Ardori F, Resch W, Stavreva D, Nelson S, McAndrew M, Casellas A, Finn E, Gregory C, St Hilaire BG, Johnson SM, Dubois W, Cosma MP, Batchelor E, Levens D, Phair RD, Misteli T, Tessarollo L, Hager G, Lakadamyali M, Liu Z, Floer M, Shroff H, Aiden EL, Casellas R.  Myc regulates chromatin decompaction and nuclear architecture during B cell activationMol Cell. 2017 Aug 17;67(4):566-578.e10. doi: 10.1016/j.molcel.2017.07.013. Epub 2017 Aug 10.

Canela A, Maman Y, Jung S, Wong N, Callen E, Day A, Kieffer-Kwon KR, Pekowska A, Zhang H, Rao SSP, Huang SC, Mckinnon PJ, Aplan PD, Pommier Y, Aiden EL, Casellas R, Nussenzweig A.  Genome organization drives chromosome fragilityCell. 2017 Jul 27;170(3):507-521.e18. doi: 10.1016/j.cell.2017.06.034. Epub 2017 Jul 20. 

Casellas R, Basu U, Yewdell WT, Chaudhuri J, Robbiani DF, Di Noia JM.  Mutations, kataegis and translocations in B cells: understanding AID promiscuous activityNat Rev Immunol. 2016 Mar;16(3):164-76. doi: 10.1038/nri.2016.2. Epub 2016 Feb 22. Review.

Aiden EL, Casellas R.  Somatic Rearrangement in B Cells: It's (Mostly) Nuclear PhysicsCell. 2015 Aug 13;162(4):708-11. doi: 10.1016/j.cell.2015.07.034. Review.

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Last Updated: August 2019