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Series GSE198253 Query DataSets for GSE198253
Status Public on Dec 19, 2023
Title Unravelling the heterogeneous molecular landscape of pediatric post-transplant lymphoproliferative disorders
Platform organisms Homo sapiens; Mus musculus
Sample organism Homo sapiens
Experiment type SNP genotyping by SNP array
Genome variation profiling by SNP array
Summary It is unknown whether pediatric monomorphic post-transplant lymphoproliferative disorders (mPTLD) display similar genetic features than the immunocompetent counterpart and if they resemble adult mPTLD. We have investigated 39 pediatric mPTLD, 33 diffuse large B-cell lymphoma (DLBCL) and six Burkitt lymphoma (BL), by an integrated approach, including fluorescence in situ hybridization, cell of origin determination (COO), targeted gene sequencing and copy-number arrays. According to COO, 24/28 DLBCL (86%) were classified as activated B-cell (ABC) and all six BL were germinal center B cell (GCB)-type. Thirty-three out of 37 investigated mPTLD were positive for EBV infection. Overall, PTLD-BL carried mutations in MYC in addition to ID3 and DDX3X, ARID1A or CCND3 and a higher mutational burden than PTLD-DLBCL (12.3 vs 6.2, P = 0.01). CN profile of PTLD-BL was less complex than in IC-BL (1 vs 6.26; P < 0.005). PTLD-DLBCL showed a very heterogeneous genomic profile characterized by a lower number of mutations (2.4 vs 6.5, P=0.01) and less CNA (2.10 vs 4.36 ; P < 0.05) than in IC patients. Pathway enrichment analysis revealed that epigenetic modifiers and Notch pathway (4 cases each) were the most recurrently affected. In conclusion, these findings further unravel for the first time the molecular heterogeneity of pediatric mPTLD and provide new parameters for the design of more effective therapeutic strategies.
Overall design Thirty-nine monomorphic PTLD <19 years-old (mean 10y, gender 25 male/14 female) were recruited and analyzed for germinal center markers, IRF4 and EBER expression. Presence of MYC, PAX5, IRF4, BCL2, BCL6 and 11q alterations was investigated by FISH. Additional molecular studies included clonality, copy number (CN) arrays, cell of origin-COO (Nanostring) and mutational analyses (Custom 167 lymphoma related genes panel, SureSelectXT, Agilent).
Contributor(s) Salmeron Villalobos J, Castrejon de Anta N, Balagué O, Salaverria I
Citation(s) 37053555
Submission date Mar 09, 2022
Last update date Dec 20, 2023
Contact name Itziar Salaverria
Organization name Hospital Clínic
Street address Rossello 153
City Barcelona
ZIP/Postal code 08036
Country Spain
Platforms (2)
GPL18602 [OncoScan] Affymetrix OncoScan FFPE Assay
GPL18603 Illumina Hiseq 1000 (Mus musculus)
Samples (26)
GSM5942277 Postransplant lymphoproliferative disorder (PTLD) 2
GSM5942278 Postransplant lymphoproliferative disorder (PTLD) 7
GSM5942279 Postransplant lymphoproliferative disorder (PTLD) 10
BioProject PRJNA814282

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE198253_Processed_Oncoscan_PTLD_DATA.xlsx 17.5 Kb (ftp)(http) XLSX
GSE198253_RAW.tar 629.9 Mb (http)(custom) TAR (of CEL, OSCHP)
Processed data provided as supplementary file
Processed data are available on Series record

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