Kameneva et al. (2021) — Human sympathoadrenal development¶

Dataset: Kameneva P, Artemov AV, Kastriti ME, Faure L, Olsen TK, Otte J, et al. Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin. Nature Genetics 2021; 53:694–706.
Preprocessing: Gandrillon O. Inferring and simulating a gene regulatory network for the sympathoadrenal differentiation from single-cell transcriptomics in human. F1000 Research 2025; 14:910. This reference preprocessing selects 97 genes and orders cells by pseudo-timepoints.
Organism / tissue: Human embryonic adrenal gland (sympathoadrenal progenitors).
Time points: 4 developmental stages (Carnegie stages 15–21), cells ordered by pseudo-timepoints.
Genes analysed: 97 genes selected in the Gandrillon 2025 preprocessing.

Biological context¶

The sympathoadrenal lineage arises from neural crest cells that migrate to the adrenal gland and differentiate into sympathoblasts, chromaffin cells, and Schwann cell precursors. Aberrant differentiation in this lineage is implicated in neuroblastoma. This dataset challenges CardamomOT with multi-branch topology and a relatively small number of time points.

CardamomOT configuration¶

cardamomot pipeline \
    -i experimental_datasets/Kameneva \
    -s full \
    -r 0.7 \
    -c 0 \
    --mean-forcing 0.5 \
    --stimulus 1.0 \
    --prior 1.0 \
    --force-basins 1.0 \
    --temporal-basins 1

Multiple --stimulus values (0.2, 0.3, 0.5, 1.0) were explored to assess sensitivity to the stimulus-edge penalisation, as reflected in the pre-computed outputs.

Results¶

Inferred network¶

The regulatory network captures the transition from multipotent progenitors (SOX10+, TFAP2A+) to committed sympathoblasts (PHOX2B+, HAND2+) and chromaffin precursors (CHGA+, STMN2+).

In-silico perturbations¶

KO experiments targeting CHGA with over-expression of STMN2 test the role of chromaffin-to-sympathoblast reversibility. Pre-computed results for several --stimulus values are stored in experimental_datasets/Kameneva/cardamomOT/ and visualised with utils/plot_data_to_sim_KOV.ipynb.

Sensitivity to the stimulus parameter¶

A sweep over --stimulus values 0.2, 0.3, 0.5 and 1.0 demonstrates that the core regulatory topology is robust while precise edge weights vary. The pre-computed outputs for each value are available in experimental_datasets/Kameneva/cardamomOT/.

Post-analysis notebooks¶

Notebook	Content
`plot_networks.ipynb`	Inferred GRN across stimulus values
`plot_data_to_sim.ipynb`	Data vs simulation comparison (UMAP, marginals)
`plot_data_to_sim_KOV.ipynb`	`KO_CHGA_OV_none`, `KO_none_OV_STMN2`, and combined perturbations
`compare_cell_types.ipynb`	Sympathoblast/chromaffin proportions in data vs simulation