Single cell multi-omics analysis of chromothriptic medulloblastoma highlights genomic and transcriptomic consequences of genome instability

Abstract

Chromothripsis is a form of genome instability, whereby a presumably single catastrophic event generates extensive genomic rearrangements of one or few chromosome(s). However, little is known about the heterogeneity of chromothripsis across different clones from the same tumor, as well as changes in response to treatment. We analyzed single-cell genomic and transcriptomic alterations linked with chromothripsis in human p53-deficient medulloblastoma (n=7). We reconstructed the order of somatic events, identified early alterations likely linked to chromothripsis and depicted the contribution of chromothripsis to malignancy. We characterized subclonal variation of chromothripsis and its effects on double-minute chromosomes, cancer drivers and putatively druggable targets. Furthermore, we highlighted the causative role and the fitness consequences of specific rearrangements in neural progenitors.

Single-cell DNA sequencing identifies risk-associated clonal complexity and evolutionary trajectories in childhood medulloblastoma development

“…Independent inspection of single-cell WGS data reported for 2 Li-Fraumeni-associated primary MB SHH Fig. 7 A model of risk-associated clonal evolution in medulloblastoma tumours with TP53 mutations [35] revealed evolutionary trajectories closely similar to the gradual trajectories we observed for our MB SHH -TP53 mutated tumours, providing important validation of our findings for this tumour group. Thirdly, we also characterised an intermediate group of medulloblastomas with a moderate clonal composition, which were sampled from multiple non-VHR risk-groups.…”

“…Second, MBs with an extensive clonal landscape, characterised by multiple events at initiation, followed by the gradual evolution of subclones with unique genetic composition, resulting in the most diverse clonal substructures observed. These trajectories were only found in very highrisk tumours-their clonal diversity and clinical behaviour being consistent with the involvement of initiating events previously associated with genomic instability (TP53 mutation and/or MYC(N) amplification [31,35,37]); and the presence of aggressive large-cell/anaplastic histology [11]. Independent inspection of single-cell WGS data reported for 2 Li-Fraumeni-associated primary MB SHH Fig.…”

“…These trajectories were only found in very high-risk tumours—their clonal diversity and clinical behaviour being consistent with the involvement of initiating events previously associated with genomic instability ( TP53 mutation and/or MYC(N) amplification [ 31 , 35 , 37 ]) ; and the presence of aggressive large-cell/anaplastic histology [ 11 ]. Independent inspection of single-cell WGS data reported for 2 Li–Fraumeni-associated primary MB SHH tumours with TP53 mutations [ 35 ] revealed evolutionary trajectories closely similar to the gradual trajectories we observed for our MB SHH - TP53 mutated tumours, providing important validation of our findings for this tumour group. Thirdly, we also characterised an intermediate group of medulloblastomas with a moderate clonal composition, which were sampled from multiple non-VHR risk-groups.…”

“…Systematic single-cell studies of MB are essential to further explore these issues. Studies to date have, however, focussed on intra-tumoural transcriptional variability and its relationship to cellular origins and cerebellar development [ 15 , 32 , 46 , 49 ], with only one specific study analysing genetic heterogeneity within two Li–Fraumeni-associated MBs [ 35 ]. The cellular genetic constituency of the major MB sub-classes, and its relationship to disease initiation, clonal and temporal evolution, thus remains poorly understood [ 8 ].…”

“…Here, we report the application of sc-WGS to reconstruct the development and clonal evolution of 14 MBs, encompassing sampling of two spatially distinct regions of each tumour. Unlike previous single-cell MB transcriptomic studies predicated on fresh tumour material [ 15 , 32 , 35 , 46 , 49 ], our use of fresh-frozen tumours enabled specific selection of molecularly and clinically phenotyped tumours representative of the major MB sub-classes and risk groups. Using these data, we derive a clinically focussed understanding of MB intra-tumoural heterogeneity, providing critical insights into differences in initiation, drivers, clonal evolution trajectories and spatial impact.…”