Advances in chromosomal conformation capture technologies and next-generation sequencing (NGS) have revealed that mammalian genomes are structured into 3D structures like topologically associating domains (TADs), promoter-enhancer loops, chromosome territories, and nuclear compartments. Structural variations (SVs) disrupt the linear genomic continuity and reconfigure 3D nuclear design, which affects gene regulation and leads to cancer development. Initially, SVs were believed to be fusion proteins, but recent studies found that they also affect long-range interactions, chromatin folding, and nuclear positioning.
Mantle cell lymphoma (MCL) is a non-Hodgkin lymphoma subtype. It is an excellent model to study these effects because of its distinctive hallmark t(11;14)(q13;q32) translocation. This rearrangement juxtaposes the immunoglobulin heavy-chain (IGH) enhancer with Cyclin D1 (CCND1), which leads to overexpression of CCND1. The aim of this study is to understand how IGH translocation transforms genome organization, changes long-range chromatin interaction, and drives the transcriptional deregulation in entire chromosome arms with a focus on the role of pre-existing epigenetic state.
The study integrated reanalysis of published RNA-seq and Hi-C datasets with newly generated data from the MCL cell line Z-138. Additional B-cell malignancy lines and the reference lymphoblastoid cell line GM12878 were included for comparison. Chromosomes 9 -12 and derivative chromosome 11 were isolated, sequenced, and structurally defined by flow karyotyping. High-resolution Tiled-C and Hi-C methods identified chromatic interactions with nucleotide-level accuracy. Hi-C libraries were sequenced and processed by TADbit to achieve complete coverage and define TAD borders, compartments, and interchromosomal interactions.
Breakpoints were mapped using contact drops and allele-specific Hi-C based on heterozygous single-nucleotide polymorphisms (SNPs). Complementary assays, such as Chrom3D modelling, clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) genome editing to introduce de novo t(11;14) translocations in GM12878, and 3D fluorescence in situ hybridization (FISH), confirmed nuclear relocation and chromatin folding alterations. Transcriptomic profiling was carried out by bulk RNS-seq in patient samples and engineered cell models, with differential expression analysis conducted using DESeq2. Single-cell RNA-seq was performed with MART-seq2 and the droplet-based Singleron platform to detect cellular heterogeneity and allele-specific effects.
Results revealed that the MCL-linked translocation significantly reshapes nuclear architecture. Derivative chromosome 11 (der11) relocated in the nuclear interior, corresponding to its smaller size and higher gene density, while der14 shifted outward. These alterations were linked to disrupted intrachromosomal folding specifically near breakpoints and broad abnormalities in interchromosomal contacts, separating MCL from healthy B cells and chronic lymphocytic leukemia. High-resolution Tiled-C showed that the IGH enhancer on der14 was involved in pre-existing ultra-long-range interaction in more than 50 Mb on chromosome 11. This hijacked conserved 3D loops to create a de novo regulatory landscape.
Transcriptomic analysis showed massive upregulation of genes within the distal chr11q region, with expression hotspots at 106–108 Mb and 118–120 Mb. These included T-cell receptor CD3 genes and signaling-related loci.
Enhancer hijacking in breast cancer cells activates transcriptionally active genes. Silent promoters remained unaffected. Single-cell RNA-seq showed heterogeneity in these effects, with some cells displaying chromosome arm-wide upregulation, while others exhibited more localized effects. Maternal alleles were strongly affected because of parent-of-origin effects associated with 3D chromatic folding. The oncogenic effects of translocations were affected by the epigenetic state of originating cells, specifically in MCL. Translocation-induced deregulation occurs in entire chromosome arms. Translocations may abnormally activate T-cell pathways, which explain the atypical immunophenotypes in some MCL cases.
The findings indicate that the oncogenic effects of translocations depend strongly on the epigenetic state of the originating cell, particularly in MCL. By incorporating an in vitro model, patient sample, and single-cell analysis, the study provides strong evidence that oncogenic effects of SVs are context-dependent and rely on nuclear position, allele-specific folding, and chromatin state. These findings advance current knowledge of how genome integrity protects against malignant transformation and identify translocations as strong reprogrammers of 3D nuclear architecture.
This work also opens avenues for more accurate pre-clinical modeling. These improved diagnostics incorporate 3D genome context, and novel therapeutic strategies targeting enhancer hijacking and chromatin architecture in MCL and other cancers.
Reference: Oncins A, Zaurin R, Toukabri H, et al. Translocations can drive expression changes of multiple genes in regulons covering entire chromosome arms. Nucleic Acids Res. 2025;53(15):gkaf677. doi:10.1093/nar/gkaf677
