4 research outputs found
Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma
Neuroblastomas are childhood tumors with frequent fatal relapses after induction treatment, which is related to tumor evolution with additional genomic events. Our whole-genome sequencing data analysis revealed a high frequency of somatic cytosine > adenine (C > A) substitutions in primary neuroblastoma tumors, which was associated with poor survival. We showed that increased levels of C > A substitutions correlate with copy number loss (CNL) of OGG1 or MUTYH. Both genes encode DNA glycosylases that recognize 8-oxo-guanine (8-oxoG) lesions as a first step of 8-oxoG repair. Tumor organoid models with CNL of OGG1 or MUTYH show increased 8-oxoG levels compared to wild-type cells. We used CRISPR-Cas9 genome editing to create knockout clones of MUTYH and OGG1 in neuroblastoma cells. Whole-genome sequencing of single-cell OGG1 and MUTYH knockout clones identified an increased accumulation of C > A substitutions. Mutational signature analysis of these OGG1 and MUTYH knockout clones revealed enrichment for C > A signatures 18 and 36, respectively. Clustering analysis showed that the knockout clones group together with tumors containing OGG1 or MUTYH CNL. In conclusion, we demonstrate that defects in 8-oxoG repair cause accumulation of C > A substitutions in neuroblastoma, which contributes to mutagenesis and tumor evolution
Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes
Neuroblastoma is a childhood tumour of the peripheral sympathetic nervous system. The pathogenesis has for a long time been quite enigmatic, as only very few gene defects were identified in this often lethal tumour. Frequently detected gene alterations are limited to MYCN amplification (20%) and ALK activations (7%). Here we present a whole-genome sequence analysis of 87 neuroblastoma of all stages. Few recurrent amino-acid-changing mutations were found. In contrast, analysis of structural defects identified a local shredding of chromosomes, known as chromothripsis, in 18% of high-stage neuroblastoma. These tumours are associated with a poor outcome. Structural alterations recurrently affected ODZ3, PTPRD and CSMD1, which are involved in neuronal growth cone stabilization. In addition, ATRX, TIAM1 and a series of regulators of the Rac/Rho pathway were mutated, further implicating defects in neuritogenesis in neuroblastoma. Most tumours with defects in these genes were aggressive high-stage neuroblastomas, but did not carry MYCN amplifications. The genomic landscape of neuroblastoma therefore reveals two novel molecular defects, chromothripsis and neuritogenesis gene alterations, which frequently occur in high-risk tumours
Differential mRNA expression of Ara-C-metabolizing enzymes explains Ara-C sensitivity in MLL gene-rearranged infant acute lymphoblastic leukemia
Infant acute lymphoblastic leukemia (ALL) is characterized by a high
incidence of mixed lineage leukemia (MLL) gene rearrangements, a poor
outcome, and resistance to chemotherapeutic drugs. One exception is
cytosine arabinoside (Ara-C), to which infant ALL cells are highly
sensitive. To investigate the mechanism underlying Ara-C sensitivity in
infants with ALL, mRNA levels of Ara-C-metabolizing enzymes were measured
in infants (n = 18) and older children (noninfants) with ALL (n = 24). In
the present study, infant ALL cells were 3.3-fold more sensitive to Ara-C
(P =.007) and accumulated 2.3-fold more Ara-CTP (P =.011) upon exposure to
Ara-C, compared with older children with ALL. Real-time quantitative
reverse trancriptase-polymerase chain reaction (RT-PCR) (TaqMan) revealed
that infants express 2-fold less of the Ara-C phosphorylating enzyme
deoxycytidine kinase (dCK) mRNA (P =.026) but 2.5-fold more mRNA of the
equilibrative nucleoside transporter 1 (hENT1), responsible for Ara-C
membrane transport (P =.001). The mRNA expression of pyrimidine
nucleotidase I (PN-I), cytidine deaminase (CDA), and deoxycytidylate
deaminase (dCMPD) did not differ significantly between both groups. hENT1
mRNA expression inversely correlated with in vitro resistance to Ara-C
(r(s) = -0.58, P =.006). The same differences concerning dCK and hENT1
mRNA expression were observe
Neuroblastoma is composed of two super-enhancer-associated differentiation states
Genetics of disease, diagnosis and treatmen