Abstract B074: Clonal decomposition and DNA replication states defined by scaled single-cell DNA and RNA sequencing suggest clone-specific therapeutic vulnerabilities in neuroblastoma
Bibliographic record
Abstract
Abstract Background: In neuroblastoma (NB), intratumor heterogeneity (ITH) is frequently observed, but the role of cell-to-cell allele-specific copy number alterations in phenotypic variation, clonal evolution and treatment response remains to be determined. Here we investigate ITH, timing of specific genomic aberrations, single-cell replication timing and the co-evolution of the genome and transcriptome in NB tumors at single-cell resolution, with an aim to analyse subclonal dynamics and clone-specific response or resistance under targeted therapeutic pressure. Methods: In addition to germline/tumor bulk whole exome sequencing (WES), ultra-low depth (0.25x) single-cell whole-genome DNA sequencing (scDNAseq) was performed using 10x genomics Chromium single-cell CNV (scCNV) kit and 9410 tumor cells were characterized from 14 patient-derived xenografts (PDX) NB-models and 4 tumor biopsies from NB-patients, either at diagnosis (n=7), progression (n=3) or relapse (n=8). Single-cell RNA sequencing (scRNAseq) data was obtained from the same PDX and patient tumor samples (Thirant et al, 2023). 6/14 PDX models were subjected to different treatment combinations (targeted treatment with/without chemotherapy) and bulk WES was performed at two time-points, pre- and post-treatment. Results: Both monoclonal (n=7) and polyclonal (n=11) genomes were determined by allele and haplotype specific copy number (CN) alteration using both scDNAseq and scRNAseq data analysis, with 2 to 11 clones observed per polyclonal NB tumor. Whole genome duplication events (n=7) were observed in both polyclonal and monoclonal genomes. Known driver CN (segmental loss in chr1p and chr11q and gain at chr17q, or MYCN/ALK amplification) or somatic mutations (ALK/ATRX/TP53/NF1) were early clonal events.Study of replication timing (RT) based on scDNAseq revealed significant differences in RT between the MYCN amplified (n=7) and non-amplified groups (n=5), with NB tumors without MYCN amplification (no MNA) characterized by a predominance of late replicating domains, in contrast to MYCN amplified (MNA) tumors, which are enriched in early replicating domains In a PDX model of interest, scDNAseq analysis showed parallel copy number evolution of two distinct clones, subclone s1/s2. Data integration of clonal mutational profiles with pre- and post-targeted therapy (Lorlatinib) revealed clone-specific treatment response. Subclone s2 was partially responding with extinction of a sub-set of somatic alterations, whereas no change was observed in subclone s1. The replication timing (RT) profile of these two clones, subclone s1 (early-RT) and s2 (late-RT) were mutually exclusive. Genotype to phenotype analysis revealed subclone s1 genotype was preferentially expressed at transcriptomic level. Conclusion: Together, these results determine the evolutionary trajectories of NB tumors, linked to distinct replication timing and highlight opportunities for targetable early clonal alteration detection. Citation Format: Jaydutt Bhalshankar, Angela Bellini, Irene Jimenez, Cécile Thirant, Elnaz Saberi-Ansari, Yasmine Iddir, Alexandra Saint Charles, Charlotte Butterworth, Amira Kramdi, Virginie Raynal, Sylvain Baulande, Didier Surdez, Sakina Zaidi, Gaelle Pierron, Angel Montero Carcaboso, Birgit Geoerger, Andrei Zinovyev, Olivier Delattre, Isabelle Janoueix-lerosey, Gudrun Schleiermacher. Clonal decomposition and DNA replication states defined by scaled single-cell DNA and RNA sequencing suggest clone-specific therapeutic vulnerabilities in neuroblastoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr B074.
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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 | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
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".