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

Image & Media Gallery

Scientific Publications

Fundamental roles of chromatin loop extrusion in antibody class switching.

Zhang X, Zhang Y, Ba Z, Kyritsis N, Casellas R, Alt FW
2019 Nov;
doi: 10.1038/s41586-019-1723-0
PMID: 31666703

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers.

El Khattabi L, Zhao H, Kalchschmidt J, Young N, Jung S, Van Blerkom P, Kieffer-Kwon P, Kieffer-Kwon KR, Park S, Wang X, Krebs J, Tripathi S, Sakabe N, Sobreira DR, Huang SC, Rao SSP, Pruett N, Chauss D, Sadler E, Lopez A, Nóbrega MA, Aiden EL, Asturias FJ, Casellas R
2019 Aug 22;
doi: 10.1016/j.cell.2019.07.011
PMID: 31402173

Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition.

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
Molecular cell.
2018 Oct 18;
doi: 10.1016/j.molcel.2018.08.047
PMID: 30293786

The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination.

Delgado-Benito V, Rosen DB, Wang Q, Gazumyan A, Pai JA, Oliveira TY, Sundaravinayagam D, Zhang W, Andreani M, Keller L, Kieffer-Kwon KR, Pękowska A, Jung S, Driesner M, Subbotin RI, Casellas R, Chait BT, Nussenzweig MC, Di Virgilio M
Molecular cell.
2018 Nov 15;
doi: 10.1016/j.molcel.2018.08.042
PMID: 30293785

The Energetics and Physiological Impact of Cohesin Extrusion.

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
2018 May 17;
doi: 10.1016/j.cell.2018.03.072
PMID: 29706548

Cohesin Loss Eliminates All Loop Domains.

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
2017 Oct 5;
doi: 10.1016/j.cell.2017.09.026
PMID: 28985562

The 4D nucleome project.

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.
2017 Sep 13;
doi: 10.1038/nature23884
PMID: 28905911

Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.

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
Molecular cell.
2017 Aug 17;
doi: 10.1016/j.molcel.2017.07.013
PMID: 28803781

Genome Organization Drives Chromosome Fragility.

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
2017 Jul 27;
doi: 10.1016/j.cell.2017.06.034
PMID: 28735753

Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity.

Casellas R, Basu U, Yewdell WT, Chaudhuri J, Robbiani DF, Di Noia JM
Nature reviews. Immunology.
2016 Mar;
doi: 10.1038/nri.2016.2
PMID: 26898111

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Last Updated: May 2020