Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia

Abstract

Abnormal replication timing has been observed in cancer but no study has comprehensively evaluated this misregulation. We generated genome-wide replication-timing profiles for pediatric leukemias from 17 patients and three cell lines, as well as normal B and T cells. Nonleukemic EBV-transformed lymphoblastoid cell lines displayed highly stable replicationtiming profiles that were more similar to normal T cells than to leukemias. Leukemias were more similar to each other than to B and T cells but were considerably more heterogeneous than nonleukemic controls. Some differences were patient specific, while others were found in all leukemic samples, potentially representing early epigenetic events. Differences encompassed large segments of chromosomes and included genes implicated in other types of cancer. Remarkably, differences that distinguished leukemias aligned in register to the boundaries of developmentally regulated replicationtiming domains that distinguish normal cell types. Most changes did not coincide with copy-number variation or translocations. However, many of the changes that were associated with translocations in some leukemias were also shared between all leukemic samples independent of the genetic lesion, suggesting that they precede and possibly predispose chromosomes to the translocation. Altogether, our results identify sites of abnormal developmental control of DNA replication in cancer that reveal the significance of replication-timing boundaries to chromosome structure and function and support the replication domain model of replication-timing regulation. They also open new avenues of investigation into the chromosomal basis of cancer and provide a potential novel source of epigenetic cancer biomarkers.

The LMO2 oncogene regulates DNA replication in hematopoietic cells

“…LMO2 binding to replication initiation zones reported here overlaps with early G1 replication segments described in lymphoid cells (39,42), a possibility that may be favored by its interaction with MLL2 (Fig. 1A).…”

“…2B). We aligned these 45 replication initiation zones with ERG1 segments identified in mammalian cells (39,42) and found that 68% of …”

Comment l’approche génomique aide à comprendre le processus d’initiation de la réplication

“…Après passage sur une colonne de fractionnement, les fragments d'Okazaki sont purifiés grâce à l'EdU, l'ARN hydrolysé à la soude, et les ADN simples brins obtenus sont analysés par séquençage haut-débit. D. Purification des sites d'incorporation de la bromodésoxyuridine (BrdU)/Edu (d'après [13]). Après un marquage à la BrdU/EdU, l'ADN est isolé des cellules puis dénaturé.…”

“…L'absence d'origines bien localisées serait ainsi une des causes de la fragilité de ces régions du génome [10][11][12]. Les délétions récurrentes et les régions où s'accumulent les mutations ponctuelles dans les cancers sont, pour la plupart, localisées dans des régions répliquées en fin de phase S [10,[13][14][15]. Inversement, les régions répliquées en début de phase S contiennent des régions fréquemment amplifiées [13][14][15].…”

“…Les délétions récurrentes et les régions où s'accumulent les mutations ponctuelles dans les cancers sont, pour la plupart, localisées dans des régions répliquées en fin de phase S [10,[13][14][15]. Inversement, les régions répliquées en début de phase S contiennent des régions fréquemment amplifiées [13][14][15]. Il existerait donc une relation, peutêtre causale, entre la densité en origines de réplication d'une région du génome et la nature des réarrangements chromosomiques que l'on observe dans les cancers.…”