Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations

Tyler E Miller; Caleb A Lareau; Julia A Verga; Erica A K DePasquale; Vincent Liu; Daniel Ssozi; Katalin Sandor; Yajie Yin; Leif S Ludwig; Chadi A El Farran; Duncan M Morgan; Ansuman T Satpathy; Gabriel K Griffin; Andrew A Lane; J Christopher Love; Bradley E Bernstein; Vijay G Sankaran; Peter van Galen

doi:10.1038/s41587-022-01210-8

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations

Nat Biotechnol. 2022 Jul;40(7):1030-1034. doi: 10.1038/s41587-022-01210-8. Epub 2022 Feb 24.

Authors

Tyler E Miller^{1

2

3}, Caleb A Lareau^{2

4

5

6}, Julia A Verga^{2

3}, Erica A K DePasquale^{2

7}, Vincent Liu^{4

5}, Daniel Ssozi^{2

7}, Katalin Sandor⁴, Yajie Yin⁴, Leif S Ludwig^{2

6

8}, Chadi A El Farran^{2

3}, Duncan M Morgan^{9

10}, Ansuman T Satpathy⁴, Gabriel K Griffin^{2

11}, Andrew A Lane^{2

12

13}, J Christopher Love^{2

9

10}, Bradley E Bernstein^{2

3

13

14}, Vijay G Sankaran^{2

6}, Peter van Galen^{15

16

17}

Affiliations

¹ Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
² Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³ Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁴ Department of Pathology, Stanford University, Stanford, CA, USA.
⁵ Department of Genetics, Stanford University, Stanford, CA, USA.
⁶ Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
⁷ Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA.
⁸ Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
⁹ Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁰ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹¹ Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
¹² Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
¹³ Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
¹⁴ Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA.
¹⁵ Broad Institute of MIT and Harvard, Cambridge, MA, USA. pvangalen@bwh.harvard.edu.
¹⁶ Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA. pvangalen@bwh.harvard.edu.
¹⁷ Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA. pvangalen@bwh.harvard.edu.

Abstract

The combination of single-cell transcriptomics with mitochondrial DNA variant detection can be used to establish lineage relationships in primary human cells, but current methods are not scalable to interrogate complex tissues. Here, we combine common 3' single-cell RNA-sequencing protocols with mitochondrial transcriptome enrichment to increase coverage by more than 50-fold, enabling high-confidence mutation detection. The method successfully identifies skewed immune-cell expansions in primary human clonal hematopoiesis.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

DNA, Mitochondrial* / genetics
High-Throughput Nucleotide Sequencing* / methods
Humans
Mitochondria / genetics
Mutation
Sequence Analysis, RNA
Single-Cell Analysis

Substances

DNA, Mitochondrial

Abstract

Publication types

MeSH terms

Substances

Grants and funding