Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

Leif S Ludwig; Caleb A Lareau; Jacob C Ulirsch; Elena Christian; Christoph Muus; Lauren H Li; Karin Pelka; Will Ge; Yaara Oren; Alison Brack; Travis Law; Christopher Rodman; Jonathan H Chen; Genevieve M Boland; Nir Hacohen; Orit Rozenblatt-Rosen; Martin J Aryee; Jason D Buenrostro; Aviv Regev; Vijay G Sankaran

doi:10.1016/j.cell.2019.01.022

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

Cell. 2019 Mar 7;176(6):1325-1339.e22. doi: 10.1016/j.cell.2019.01.022. Epub 2019 Feb 28.

Authors

Leif S Ludwig¹, Caleb A Lareau², Jacob C Ulirsch³, Elena Christian⁴, Christoph Muus⁵, Lauren H Li⁶, Karin Pelka⁷, Will Ge⁴, Yaara Oren⁸, Alison Brack⁴, Travis Law⁴, Christopher Rodman⁴, Jonathan H Chen⁹, Genevieve M Boland¹⁰, Nir Hacohen⁷, Orit Rozenblatt-Rosen⁴, Martin J Aryee¹¹, Jason D Buenrostro¹², Aviv Regev¹³, Vijay G Sankaran¹⁴

Affiliations

¹ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: ludwig@broadinstitute.org.
² Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.
³ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁵ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
⁶ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
⁷ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
⁸ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
⁹ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.
¹⁰ Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
¹¹ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
¹² Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Society of Fellows, Harvard University, Cambridge, MA 02138, USA.
¹³ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology and Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: aregev@broadinstitute.org.
¹⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address: sankaran@broadinstitute.org.

Abstract

Lineage tracing provides key insights into the fate of individual cells in complex organisms. Although effective genetic labeling approaches are available in model systems, in humans, most approaches require detection of nuclear somatic mutations, which have high error rates, limited scale, and do not capture cell state information. Here, we show that somatic mutations in mtDNA can be tracked by single-cell RNA or assay for transposase accessible chromatin (ATAC) sequencing. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their utility as highly accurate clonal markers to infer cellular relationships. We track native human cells both in vitro and in vivo and relate clonal dynamics to gene expression and chromatin accessibility. Our approach should allow clonal tracking at a 1,000-fold greater scale than with nuclear genome sequencing, with simultaneous information on cell state, opening the way to chart cellular dynamics in human health and disease.

Keywords: chronic myeloid leukemia; colon cancer; hematopoiesis; lineage tracing; mitochondrial DNA; mtDNA; sequencing; single cell genomics; somatic mutations.

Publication types

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

MeSH terms

Base Sequence
Cell Lineage
Chromatin
Colorectal Neoplasms / genetics
Colorectal Neoplasms / pathology
DNA, Mitochondrial / genetics*
Genomics / methods
HEK293 Cells
Hematopoietic Stem Cells / physiology
High-Throughput Nucleotide Sequencing / methods
Humans
Mitochondria / genetics*
Mutation
Single-Cell Analysis
Transposases

Substances

Chromatin
DNA, Mitochondrial
Transposases

Abstract

Publication types

MeSH terms

Substances

Grants and funding