Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies

Wu, J.; Chu, S.-C. A.; Cho, J. W.; Movahed-Ezazi, M.; Galbraith, K.; Fang, C. S.; Yang, Y.; Schroff, C.; Sikkink, K.; Perez-Arreola, M.; Van Meter, L.; Gemus, S.; Belton, J.-M.; Nardi, V.; Louissant, A.; Shasha, D.; Tsirigos, A.; Brown, N.; Gindin, T.; Cieslik, M. P.; Kim, M.; Schmitt, A. D.; Snuderl, M.; Ryan, R. J. H.

doi:10.1101/2025.03.15.643352

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bioRxiv · 10.1101/2025.03.15.643352

Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies

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Abstract

Standard techniques for detecting genomic rearrangements in formalin-fixed paraffin-embedded (FFPE) biopsies have important limitations. We performed FFPE-compatible Hi-C on 44 clinical biopsies comprising large B-cell lymphomas (n=18), plasma cell neoplasms (n=14), and other diverse lymphoid cancers, identifying consistent topological differences between malignant B cell and plasma cell states. Hi-C detected expected oncogene rearrangements at high concordance with fluorescence in-situ hybridization (FISH) and supported enhancer-hijacking in recurrent rearrangements of BCL2, CCND1, and MYC, plus unanticipated variants involving homologous loci. Hi-C identified unanticipated non-coding rearrangements involving PD-1 ligand genes and other loci of potential therapeutic relevance, distinguished between functionally divergent classes of BCL6 rearrangements, and provided topological information supporting the interpretation of atypical MYC rearrangements. In biopsies lacking MYC-activating rearrangements, Hi-C revealed differential interactions with functionally-validated disease-specific native MYC locus enhancers. FFPE-compatible Hi-C detects oncogene rearrangements and their topological consequences at genome-wide scale, finding clinically-relevant drivers that are missed by standard approaches.

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Wu, J., Chu, S.-C. A., Cho, J. W., Movahed-Ezazi, M., Galbraith, K., Fang, C. S., Yang, Y., Schroff, C., Sikkink, K., Perez-Arreola, M., Van Meter, L., Gemus, S., Belton, J.-M., Nardi, V., Louissant, A., Shasha, D., Tsirigos, A., Brown, N., Gindin, T., Cieslik, M. P., Kim, M., Schmitt, A. D., Snuderl, M., Ryan, R. J. H.. 2025-03-18. Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies. https://doi.org/10.1101/2025.03.15.643352

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