Cell-free DNA as a potential biomarker of differentiation and toxicity in cardiac organoids
- Mechanistic Toxicology Branch, DNTP, United States
- Molecular Genomics Core, DIR NIEHS, United States
Figures
Figure 1
Cardiac organoids derived from H9 embryonic stem cells exhibit characteristic morphological changes and express markers of differentiation.
(A) Brightfield images of cardiac organoids during growth and differentiation. Scale bars represent 100 µm. (B) Quantification of beats per minute across three separate biological replicates for …
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Figure 1—source data 1
Cardiac organoids derived from H9 embryonic stem cells exhibit characteristic morphological changes and express markers of differentiation.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig1-data1-v2.zip
Figure 2 with 1 supplement
Cardiac organoids release cfDNA during their development.
(A) Schematic illustrating timepoints of cfDNA collection in cardiac organoids. (B) Shown are cfDNA concentrations taken from n = 3 biological replicates during cardiac organoid differentiation. …
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Figure 2—source data 1
Electropherogram showing fragment lengths of cfDNA derived from cardiac organoids at different time points during development.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig2-data1-v2.zip
Figure 2—figure supplement 1
Overlay of representative electropherograms showing fragment sizes of cfDNA derived from cardiac organoids on different growth days.
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Figure 2—figure supplement 1—source data 1
Electropherogram showing fragment lengths of cfDNA derived from cardiac organoids at different time points during development.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig2-figsupp1-data1-v2.zip
Figure 3
Cardiac organoids exhibit a time-dependent decrease in cell-free mitochondrial DNA abundance during growth.
(A) Schematic showing the location of markers examined on the mitochondrial genome, adapted from Figure 1 of Uhler and Falkenberg, 2015. (B) Relative abundance of mitochondrial markers ND1, ND4, …
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Figure 3—source data 1
Cardiac organoids exhibit a time-dependent decrease in cell-free mitochondrial DNA abundance during growth.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig3-data1-v2.zip
Figure 4 with 1 supplement
Abundance of specific gDNA sequences is reflective of tissue-level changes in marker expression.
(A) Immunofluorescence staining of Nkx2.5 in cardiac organoids during differentiation. Scale bars represent 200 μm. (B) Nkx2.5 copies/μl in 1 ng of cardiac organoid-derived cfDNA at different time …
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Figure 4—source data 1
Copy number of Sox17 or Oct3/4 in cfDNA derived from cardiac organoids on different growth days during development.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig4-data1-v2.zip
Figure 4—figure supplement 1
Abundance of specific gDNA sequences is reflective of tissue-level changes in marker expression.
Sox17 (A) or Oct3/4 (B) copies/μl in 1 ng of cardiac organoid-derived cfDNA at different time points during differentiation obtained using ddPCR, taken from n = 3 biological replicates. Graphs show …
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Figure 4—figure supplement 1—source data 1
Copy number of Sox17 or Oct3/4 in cfDNA derived from cardiac organoids on different growth days during development.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig4-figsupp1-data1-v2.zip
Figure 5 with 1 supplement
Doxorubicin (DOX) causes severe cardiac organoid malformation in comparison to CPI.
(A) Schematic showing drug treatment and collection times of cfDNA during cardiac organoid growth. Representative images of tissues on day 6: control (B), DOX-treated (C), and CPI-treated (D). …
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Figure 5—source data 1
Doxorubicin causes severe cardiac organoid malformation in comparison to CPI-203.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig5-data1-v2.zip
Figure 5—figure supplement 1
Toxicity of DOX and CPI-203 in cardiac organoids is impacted by time of exposure.
(A) Schematic showing treatment and cfDNA collection times during the growth of cardiac organoids. Representative images of mature cardiac organoids on day 9 treated with doxorubicin (DOX) (B) or …
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Figure 5—figure supplement 1—source data 1
Toxicity of DOX and CPI-203 in cardiac organoids is impacted by time of exposure.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig5-figsupp1-data1-v2.zip
Figure 6 with 1 supplement
Specific cfDNA sequences may be predictive of toxicity in cardiac organoids.
Abundance of ND1 (A), mtCOX2 (B), Nkx2.5 (C), or p53 (D) in 0.5 ng cfDNA collected from cardiac organoids on growth day 6 treated with doxorubicin (DOX) or CPI, obtained using ddPCR. Graphs show …
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Figure 6—source data 1
Specific sequences of cfDNA may be predictive of toxicity in cardiac organoids.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig6-data1-v2.zip
Figure 6—figure supplement 1
Concentration of cfDNA in response to early or late exposure to DOX or CPI-203.
(A) cfDNA concentrations from cardiac organoids on day 6 treated with either doxorubicin (DOX) or CPI. (B) cfDNA concentrations from cardiac organoids on day 9 treated with either DOX or CPI on …
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Figure 6—figure supplement 1—source data 1
Concentration of cfDNA in response to early or late exposure to DOX or CPI-203.
- https://cdn.elifesciences.org/articles/83532/elife-83532-fig6-figsupp1-data1-v2.zip
