Abstract B78: Role of noradrenergic core regulatory circuitry transcription factors in neuroblastoma cell identity
Bibliographic record
Abstract
Abstract Introduction: The heterogeneity of neuroblastoma cell identity has been recently revealed with the characterization of noradrenergic and NCC (neural crest cell)-like/mesenchymal cells, each cell type being governed by a core regulatory circuitry (CRC) of specific transcription factors (Boeva et al., 2017; van Groningen et al., 2017). Whereas the noradrenergic CRC includes the PHOX2B, HAND2, and GATA3 transcription factors, the CRC associated to the NCC-like/mesenchymal identity is composed of AP-1 transcription factors among others. The present study aims at deciphering the role of the identity-related transcription factors, PHOX2B and GATA3, in the establishment and maintenance of the noradrenergic identity. Experimental Procedures: Using the CRISPR-Cas9 gene editing approach, we performed the knockout of PHOX2B and GATA3 genes in the SH-SY5Y neuroblastoma cell line. The obtained clones were characterized in terms of growth, phenotype, and identity, using in particular transcriptomic (RNA-seq) and epigenomic (H3K27ac ChIP-seq) analysis. Results: PHOX2B knockout in the SH-SY5Y cell line did not change its identity. PHOX2B−/− cells keep their noradrenergic phenotype, demonstrating that PHOX2B expression is not essential for the maintenance of the noradrenergic CRC. Nevertheless, the absence of PHOX2B expression in these cells decreased their proliferation both in vitro and in vivo, after mouse xenografts. In contrast to PHOX2B knockout cells, GATA3 knockout cells exhibit a mesenchymal phenotype: GATA3−/− cells harbor actin stress fibers and display migration and invasion capacities. Compared to the parental cells, they exhibit a higher resistance to chemotherapy in vitro. In a hierarchical unsupervised clustering, GATA3−/− cells show a transcriptomic profile close to neuroblastoma mesenchymal cell lines, with a weak expression of the noradrenergic set of transcription factors, including PHOX2B, and a high expression of factors related to the mesenchymal identity. Consistently with their transcriptomic profile, GATA3−/− cells are characterized by a super-enhancer landscape close to that of the SH-EP mesenchymal cell line. Finally, GATA3 knockout cells exhibit a decreased proliferation both in vitro and in vivo in xenograft experiments. Further experiments are ongoing to explore cell identity in the obtained tumors. Conclusions: PHOX2B and GATA3, which are two members of the noradrenergic CRC, play different roles in the maintenance of the noradrenergic identity in neuroblastoma cells. We hypothesize that PHOX2A could compensate for the absence of PHOX2B, thus explaining why PHOX2B knockout cells maintain their noradrenergic identity. In contrast, GATA3 knockout cells exhibit a mesenchymal identity. Bioinformatics analyses are ongoing to decipher the reprogramming process of these cells. Citation Format: Agathe Peltier, Caroline Louis-Brennetot, Cécile Pierre-Eugène, Cécile Thirant, Simon Durand, Divya Sahu, Sandrine Grossetête-Lalami, Virginie Raynal, Sylvain Baulande, Olivier Delattre, Valentina Boeva, Isabelle Janoueix-Lerosey. Role of noradrenergic core regulatory circuitry transcription factors in neuroblastoma cell identity [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B78.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.008 | 0.003 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".