1. Cancer Biology
  2. Genetics and Genomics
Download icon

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

  1. Jin Xu
  2. Kevin Nuno
  3. Ulrike M Litzenburger
  4. Yanyan Qi
  5. M Ryan Corces  Is a corresponding author
  6. Ravindra Majeti  Is a corresponding author
  7. Howard Y Chang  Is a corresponding author
  1. Stanford University, United States
Short Report
  • Cited 28
  • Views 7,226
  • Annotations
Cite this article as: eLife 2019;8:e45105 doi: 10.7554/eLife.45105

Abstract

Simultaneous measurement of cell lineage and cell fates is a longstanding goal in biomedicine. Here we describe EMBLEM, a strategy to track cell lineage using endogenous mitochondrial DNA variants in ATAC-seq data. We show that somatic mutations in mitochondrial DNA can reconstruct cell lineage relationships at single cell resolution with high sensitivity and specificity. Using EMBLEM, we define the genetic and epigenomic clonal evolution of hematopoietic stem cells and their progenies in patients with acute myeloid leukemia. EMBLEM extends lineage tracing to any eukaryotic organism without genetic engineering.

Article and author information

Author details

  1. Jin Xu

    Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0944-9835

  2. Kevin Nuno

    Department of Medicine, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  3. Ulrike M Litzenburger

    Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  4. Yanyan Qi

    Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

  5. M Ryan Corces

    Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
    For correspondence
    rcorces@stanford.edu
    Competing interests
    No competing interests declared.

  6. Ravindra Majeti

    Department of Medicine, Stanford University, Stanford, United States
    For correspondence
    rmajeti@stanford.edu
    Competing interests
    Ravindra Majeti, Reviewing editor, eLife.

  7. Howard Y Chang

    Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
    For correspondence
    howchang@stanford.edu
    Competing interests
    Howard Y Chang, is a co-founder of Accent Therapeutics and an advisor for 10x Genomics and Spring Discovery. Stanford University has filed a patent on ATAC-seq(US20160060691A1), on which HYC is named as an inventor..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9459-4393

Funding

National Human Genome Research Institute (P50-HG007735)

  • Howard Y Chang

Howard Hughes Medical Institute

  • Howard Y Chang

National Cancer Institute (R01HL142637)

  • Ravindra Majeti

National Cancer Institute (R01CA188055)

  • Ravindra Majeti

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: AML samples were obtained from patients at the Stanford Medical Center with informed consent, according to institutional review board (IRB)-approved protocols (Stanford IRB, 18329 and 6453).

Reviewing Editor

  1. Ross L Levine, Memorial Sloan Kettering Cancer Center, United States

Publication history

  1. Received: January 12, 2019
  2. Accepted: April 7, 2019
  3. Accepted Manuscript published: April 8, 2019 (version 1)
  4. Accepted Manuscript updated: April 9, 2019 (version 2)
  5. Version of Record published: April 17, 2019 (version 3)

Copyright

© 2019, Xu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 7,226
    Page views
  • 1,014
    Downloads
  • 28
    Citations

Article citation count generated by polling the highest count across the following sources: Scopus, Crossref, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Categories and tags

Research organism

Further reading

    1. Cancer Biology
    2. Genetics and Genomics

    MITF reprograms the extracellular matrix and focal adhesion in melanoma

    Ramile Dilshat et al.
    Research Article

    The microphthalmia associated transcription factor (MITF) is a critical regulator of melanocyte development and differentiation. It also plays an important role in melanoma where it has been described as a molecular rheostat that, depending on activity levels, allows reversible switching between different cellular states. Here we show that MITF directly represses the expression of genes associated with the extracellular matrix (ECM) and focal adhesion pathways in human melanoma cells as well as of regulators of epithelial to mesenchymal transition (EMT) such as CDH2, thus affecting cell morphology and cell-matrix interactions. Importantly, we show that these effects of MITF are reversible, as expected from the rheostat model. The number of focal adhesion points increased upon MITF knockdown, a feature observed in drug resistant melanomas. Cells lacking MITF are similar to the cells of minimal residual disease observed in both human and zebrafish melanomas. Our results suggest that MITF plays a critical role as a repressor of gene expression and is actively involved in shaping the microenvironment of melanoma cells in a cell-autonomous manner.

    1. Cancer Biology

    Visualization of stem cell activity in pancreatic cancer expansion by direct lineage tracing with live imaging

    Takahisa Maruno et al.
    Research Article Updated

    Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease. Although rigorous efforts identified the presence of ‘cancer stem cells (CSCs)’ in PDAC and molecular markers for them, stem cell dynamics in vivo have not been clearly demonstrated. Here we focused on Doublecortin-like kinase 1 (Dclk1), known as a CSC marker of PDAC. Using genetic lineage tracing with a dual-recombinase system and live imaging, we showed that Dclk1+ tumor cells continuously provided progeny cells within pancreatic intraepithelial neoplasia, primary and metastatic PDAC, and PDAC-derived spheroids in vivo and in vitro. Furthermore, genes associated with CSC and epithelial mesenchymal transition were enriched in mouse Dclk1+ and human DCLK1-high PDAC cells. Thus, we provided direct functional evidence for the stem cell activity of Dclk1+ cells in vivo, revealing the essential roles of Dclk1+ cells in expansion of pancreatic neoplasia in all progressive stages.

    1. Cancer Biology

    Use of signals of positive and negative selection to distinguish cancer genes and passenger genes

    László Bányai et al.
    Research Article

    A major goal of cancer genomics is to identify all genes that play critical roles in carcinogenesis. Most approaches focused on genes positively selected for mutations that drive carcinogenesis and neglected the role of negative selection. Some studies have actually concluded that negative selection has no role in cancer evolution. We have re-examined the role of negative selection in tumor evolution through the analysis of the patterns of somatic mutations affecting the coding sequences of human genes. Our analyses have confirmed that tumor suppressor genes are positively selected for inactivating mutations, oncogenes, however, were found to display signals of both negative selection for inactivating mutations and positive selection for activating mutations. Significantly, we have identified numerous human genes that show signs of strong negative selection during tumor evolution, suggesting that their functional integrity is essential for the growth and survival of tumor cells.