Kristan V. Piroeva1, Charlotte McDonald2, Charalampos Xanthopoulos2, Chelsea Fox1, Christopher T. Clarkson1,9, Jan-Philipp Mallm3,4,5, Yevhen Vainshtein6, Luminita Ruje1, Lara C. Klett4,5, Stephan Stilgenbauer7, Daniel Mertens7,8, Efterpi Kostareli2, Karsten Rippe4,5 and Vladimir B. Teif1 1School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom; 2Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom; 3German Cancer Research Center (DKFZ) Heidelberg, Single Cell Open Lab, 69120 Heidelberg, Germany; 4German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany; 5Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany; 6Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB, 70569 Stuttgart, Germany; 7Division of CLL, University Hospital Ulm, Department of Internal Medicine III, 89081 Ulm, Germany; 8German Cancer Research Center (DKFZ) Heidelberg, Cooperation Unit Mechanisms of Leukemogenesis, 69120 Heidelberg, Germany

↵9 Present address: University College London, London WC1E 6BT, UK

Corresponding authors: vteifessex.ac.uk, karsten.rippedkfz.de, e.kostareliqub.ac.uk Abstract

The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral blood B cells from patients with chronic lymphocytic leukemia (CLL) and healthy individuals at single-base-pair resolution. Our investigation uncovered significant changes of nucleosome positioning in CLL. Globally, the spacing between nucleosomes—the nucleosome repeat length (NRL)—is shortened in CLL. This effect is stronger in the more aggressive IGHV-unmutated CLL subtype than in the IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites are linked to active chromatin remodeling and reduced DNA methylation. Nucleosomes lost or gained in CLL marks differential binding of 3D chromatin organizers such as CTCF as well as immune response–related transcription factors and delineated mechanisms of epigenetic deregulation. The principal component analysis of nucleosome occupancy in cancer-specific regions allowed the classification of samples between cancer subtypes and normal controls. Furthermore, patients could be better assigned to CLL subtypes according to differential nucleosome occupancy than based on DNA methylation or gene expression. Thus, nucleosome positioning constitutes a novel readout to dissect molecular mechanisms of disease progression and to stratify patients. Furthermore, we anticipate that the global nucleosome repositioning detected in our study, such as changes in the NRL, can be exploited for liquid biopsy applications based on cell-free DNA to stratify patients and monitor disease progression.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.277298.122.

Freely available online through the Genome Research Open Access option.

Received September 8, 2022. Accepted September 7, 2023.