Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA
- Stanford University, United States
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.
Data availability
Sequencing data have been deposited in GEO under accession codes GSE122576 and GSE122577.
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Single cell lineage tracing by endogenous mitochondrial DNA mutations in ATAC-seq dataNCBI Gene Expression Omnibus, GSE122576.
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Single cell lineage tracing by endogenous mitochondrial DNA mutations in ATAC-seq dataNCBI Gene Expression Omnibus, GSE122577.
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Single-cell chromatin accessibility data using scATAC-seqNCBI Gene Expression Omnibus, GSE65360.
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ATAC-seq dataNCBI Gene Expression Omnibus, GSE74912.
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Single-cell chromatin accessibility data using scATAC-seqNCBI Gene Expression Omnibus, GSE74310.
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Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiationNCBI Gene Expression Omnibus, GSE96772.
Article and author information
Author details
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).
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.
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Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA
eLife 8:e45105.
https://doi.org/10.7554/eLife.45105
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Metastasis is the leading cause of cancer-related mortality. Paneth cells provide stem cell niche factors in homeostatic conditions, but the underlying mechanisms of cancer stem cell niche development are unclear. Here, we report that Dickkopf-2 (DKK2) is essential for the generation of cancer cells with Paneth cell properties during colon cancer metastasis. Splenic injection of Dkk2 knockout (KO) cancer organoids into C57BL/6 mice resulted in a significant reduction of liver metastases. Transcriptome analysis showed reduction of Paneth cell markers such as lysozymes in KO organoids. Single-cell RNA sequencing analyses of murine metastasized colon cancer cells and patient samples identified the presence of lysozyme positive cells with Paneth cell properties including enhanced glycolysis. Further analyses of transcriptome and chromatin accessibility suggested hepatocyte nuclear factor 4 alpha (HNF4A) as a downstream target of DKK2. Chromatin immunoprecipitation followed by sequencing analysis revealed that HNF4A binds to the promoter region of Sox9, a well-known transcription factor for Paneth cell differentiation. In the liver metastatic foci, DKK2 knockout rescued HNF4A protein levels followed by reduction of lysozyme positive cancer cells. Taken together, DKK2-mediated reduction of HNF4A protein promotes the generation of lysozyme positive cancer cells with Paneth cell properties in the metastasized colon cancers.
