Investigation of relapse prediction in infants with MLL-rearranged Acute Lymphoblastic Leukemia

In infants with ALL, accurate relapse prediction would enable treatment strategies that take relapse risk into account, with potential benefits for both low- and high-risk patients. Through analysis of bone marrow biopsies taken at initial diagnosis, we show that single-cell RNA sequencing can predict future relapse occurrence.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

2 Datasets 2 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001005461	This dataset contains two experiments. 1) Single cell RNA-seq of diagnostic samples from patients with MLL-rearranged infant ALL that underwent relapse or not (samples ending in R relapsed, samples ending in N did not). For some of the patients, multiple indipendent plates were produced (each plate is a sample). 2) in vitro prednisolone exposure experiment. diagnostic bone marrow samples from patient 4662R were cultured for three days with and without prednisolone. Single cell experiments were conducted according to Muraro et al (cell systems, 2016, doi:10.1016/j.cels.2016.09.002). Cell barcodes and UMI sequences are embedded in the header of each fastq entry. Cell barcodes irrelevant to this experiment were removed before submission.	NextSeq 500	11
EGAD00001007752	This dataset contains two experiments. 1) Single cell RNA-seq of peripheral blood diagnostic samples from patients with MLL-rearranged infant ALL that underwent relapse or not (samples ending in R relapsed, samples ending in N did not), sequenced with SORT-seq (see cell systems, 2016, doi:10.1016/j.cels.2016.09.002). For some of the patients, multiple indipendent plates were produced (each plate is a sample). Barcode-well correspondence can be found here: https://bitbucket.org/princessmaximacenter/sharq/src/master/data/celseq2_bc384-v4.csv . 2) Single cell RNA-seq of peripheral blood diagnostic samples from patients with MLL-rearranged infant ALL that underwent relapse or not (samples ending in R relapsed, samples ending in N did not), sequenced with10x Genomics Version 2.	NextSeq 500	26

Publications	Citations
Identification and characterization of relapse-initiating cells in MLL-rearranged infant ALL by single-cell transcriptomics. Candelli T, Schneider P, Garrido Castro P, Jones LA, Bodewes E, Rockx-Brouwer D, Pieters R, Holstege FCP, Margaritis T, Stam RW. Leukemia 36: 2022 58-67	10
Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells. Morris V, Wang D, Li Z, Marion W, Hughes T, Sousa P, Harada T, Sui SH, Naumenko S, Kalfon J, Sensharma P, Falchetti M, Vinicius da Silva R, Candelli T, Schneider P, Margaritis T, Holstege FCP, Pikman Y, Harris M, Stam RW, Orkin SH, Koehler AN, Shalek AK, North TE, Pimkin M, Daley GQ, Lummertz da Rocha E, Rowe RG. Cell Rep 39: 2022 110752	6

Publications

Citations

Identification and characterization of relapse-initiating cells in MLL-rearranged infant ALL by single-cell transcriptomics.
Candelli T, Schneider P, Garrido Castro P, Jones LA, Bodewes E, Rockx-Brouwer D, Pieters R, Holstege FCP, Margaritis T, Stam RW. Leukemia 36: 2022 58-67

Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells.
Morris V, Wang D, Li Z, Marion W, Hughes T, Sousa P, Harada T, Sui SH, Naumenko S, Kalfon J, Sensharma P, Falchetti M, Vinicius da Silva R, Candelli T, Schneider P, Margaritis T, Holstege FCP, Pikman Y, Harris M, Stam RW, Orkin SH, Koehler AN, Shalek AK, North TE, Pimkin M, Daley GQ, Lummertz da Rocha E, Rowe RG. Cell Rep 39: 2022 110752