Functional analysis of structural variants in single cells using Strand-seq PMID: 36424487

ADC Targets in Oncology

2026-04-10

Functional analysis of structural variants in single cells using Strand-seq

Nat Biotechnol. 2022 Nov 24. doi: 10.1038/s41587-022-01551-4.

Hyobin Jeong ^# ¹ ² , Karen Grimes ^# ¹ ³ , Kerstin K Rauwolf ⁴ , Peter-Martin Bruch ⁵ ⁶ ⁷ , Tobias Rausch ¹ ⁶ , Patrick Hasenfeld ¹ , Eva Benito ¹ , Tobias Roider ¹ ⁵ ⁶ , Radhakrishnan Sabarinathan ⁸ , David Porubsky ⁹ ¹⁰ ¹¹ , Sophie A Herbst ⁵ ⁶ , Büşra Erarslan-Uysal ⁶ ¹² , Johann-Christoph Jann ¹³ , Tobias Marschall ¹⁴ , Daniel Nowak ¹³ , Jean-Pierre Bourquin ⁴ , Andreas E Kulozik ⁶ ¹² , Sascha Dietrich ⁵ ⁶ ⁷ ¹⁵ , Beat Bornhauser ⁴ , Ashley D Sanders ¹⁶ ¹⁷ ¹⁸ ¹⁹ , Jan O Korbel ²⁰ ²¹ ²²

Affiliations

1. Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
2. Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea.
3. Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany.
4. Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland.
5. Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.
6. Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.
7. Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany.
8. National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
9. Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
10. Max Planck Institute for Informatics, Saarbrücken, Germany.
11. Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
12. Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany.
13. Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Heidelberg, Germany.
14. Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
15. Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.
16. Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. [email protected].
17. Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. [email protected].
18. Berlin Institute of Health (BIH), Berlin, Germany. [email protected].
19. Charité-Universitätsmedizin, Berlin, Germany. [email protected].
20. Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. [email protected].
21. Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany. [email protected].
22. Bridging Research Division on Mechanisms of Genomic Variation and Data Science, German Cancer Research Center (DKFZ), Heidelberg, Germany. [email protected].
# Contributed equally.

Abstract

Somatic structural variants (SVs) are widespread in Cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in Cell Culture, using a Notch Inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations.