Finding structural variation from the patient-derived xenografts of pediatric T-cell leukemia at the single-cell level

In this study, we aimed to identify somatic structural variation of T-cell acute lymphoblastic leukemias (T-ALLs_ from patient-derived xenografts (PDX) at the single-cell level. For this purpose, we performed strand-specific single-cell sequencing of PDX-derived T-ALL relapse samples from two juvenile patients (P1, P33). To validate structural variation detected via scTRIP, we profiled whole exome sequencing (WES) data from P33 (samples taken during initial disease, remission, relapse), and mate-pair sequencing data from P1 (relapse).

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

3 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
EGAD00001004499	In this study, we aimed to identify somatic structural variation of T-cell acute lymphoblastic leukemias (T-ALLs_ from patient-derived xenografts (PDX) at the single-cell level. For this purpose, we performed strand-specific single-cell sequencing of PDX-derived T-ALL relapse samples from two juvenile patients (P1, P33). To validate structural variation detected via scTRIP, we profiled whole exome sequencing (WES) data from P33 (samples taken during initial disease, remission, relapse), and mate-pair sequencing data from P1 (relapse).	Illumina HiSeq 2000 NextSeq 500	124
EGAD00001008325	In this study, we profiled single-cell transcriptome (10X genomics) of Patient-derived xenografts (PDX) T-ALL replase samples from P1 patient. Primary human T-ALL cells were recovered from cryopreserved bone marrow aspirates of patients enrolled in the ALL-BFM 2009 study. Patient-derived xenografts (PDX) were generated as previously described by intrafemoral injection of 1 Million viable primary ALL cells in NSG mice110 PDX-derived (P1)28 cells were frozen until processing. For scRNA-seq library preparation, cryopreserved cells were thawed rapidly at 37 ℃ and resuspended in 10 ml warm Roswell Park Memorial Institute (RPMI) medium with 100 μg/ml Dnase I. Cells were centrifuged for 5 mins at 300 g, and resuspended in ice-cold phosphate buffered saline (PBS) with 2% foetal bovine serum (FBS) and 5mM EDTA. Cells were stained on ice with anti-murine-CD45-PE (mCD45)(clone 30-F11; BioLegend; 1:20) in the dark for 30 mins. 1:100 DAPI was added and incubated in the dark for 5 mins before sorting. Triple negative cells (DAPI-mCD45-GFP-) were sorted (Fig. S27) using a BD FACSAria™ Fusion Cell Sorter into ice cold 0.03% bovine serum albumin (BSA) in PBS. All isolated cells were immediately used for scRNA-seq libraries, which were generated as per the standard 10x Genomics Chromium 3′ (v.3.1 Chemistry) protocol. Completed libraries were sequenced on a NextSeq5000 sequencer (HIGH-mode, 75 bp paired-end).	NextSeq 500	1
EGAD00001009172	PDX model of T-ALL under treatment of CB-103 and Vehicle was analyzed by single-cell transcriptomics using 10X Genomics technology.	NextSeq 500	4

Publications	Citations
Single-cell analysis of structural variations and complex rearrangements with tri-channel processing. Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Benes V, Schrappe M, Mardin BR, Kulozik AE, Bornhauser B, Bourquin JP, Marschall T, Korbel JO. Nat Biotechnol 38: 2020 343-354	35
Functional analysis of structural variants in single cells using Strand-seq. Jeong H, Grimes K, Rauwolf KK, Bruch PM, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann JC, Marschall T, Nowak D, Bourquin JP, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO. Nat Biotechnol 41: 2023 832-844	8

Publications

Citations

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.
Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Benes V, Schrappe M, Mardin BR, Kulozik AE, Bornhauser B, Bourquin JP, Marschall T, Korbel JO. Nat Biotechnol 38: 2020 343-354

Functional analysis of structural variants in single cells using Strand-seq.
Jeong H, Grimes K, Rauwolf KK, Bruch PM, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann JC, Marschall T, Nowak D, Bourquin JP, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO. Nat Biotechnol 41: 2023 832-844