Integrated single cell analysis in transformed follicular lymphoma

Histological transformation of follicular lymphoma to aggressive form occurs 2-3% per year with poor outcome. Divergent evolution and an altered tumour-microenvironment (TME) have been implicated during transformation. However, phenotypic consequences of this evolution and its implication in TME remain unknown. To address this, we performed single cell whole genome and whole transcriptome sequencing of paired pre/post transformation patient samples. We further performed scWTS of additional samples from patients without transformation. Our analysis revealed evolutionary dynamics of transformation at unprecedented resolution. Integration of scWGS and scWTS identified pathways upregulated during evolution. scWTS analysis revealed a shifting TME landscape, with an exhausted signature emerging during transformation. Using multi-color immunofluorescence we transferred these findings to a TME-based transformation biomarker, subsequently validated in independent pretreatment cohorts. Taken together, our results provide a comprehensive view of the combined genomic and phenotypic evolution of malignant cells during transformation, and shifting cross-talk between malignant cells and TME.

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

45 Datasets

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Dataset ID	Description	Technology	Samples
EGAD00001010204	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0167_003 for Follicular lymphoma patient sample TFRI_Cont_2	Illumina HiSeq 2500	1
EGAD00001010205	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0168_003 for Follicular lymphoma patient sample TFRI_Cont_3	Illumina HiSeq 2500	1
EGAD00001010206	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0169_003 for Follicular lymphoma patient sample TFRI_Cont_4	Illumina HiSeq 2500	1
EGAD00001010207	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0170_003 for Follicular lymphoma patient sample TFRI_Cont_5	Illumina HiSeq 2500	1
EGAD00001010208	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0171_003A for Follicular lymphoma patient sample TFRI_Cont_6	Illumina HiSeq 2500	1
EGAD00001010209	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0178_003A for Follicular lymphoma patient sample TFRI_Cont_8	Illumina HiSeq 2500	1
EGAD00001010210	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0183_003A for Follicular lymphoma patient sample TFRI_Cont_9	Illumina HiSeq 2500	1
EGAD00001010211	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0187_003A for Follicular lymphoma patient sample TFRI_Cont_10	Illumina HiSeq 2500	1
EGAD00001010212	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0188_003A for Follicular lymphoma patient sample TFRI_Cont_11	Illumina HiSeq 2500	1
EGAD00001010213	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0197_003A for Follicular lymphoma patient sample TFRI_Cont_12	Illumina HiSeq 2500	1
EGAD00001010214	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_003A for Follicular lymphoma patient sample TFRI_Cont_13	Illumina HiSeq 2500	1
EGAD00001010215	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0167_001 for Follicular lymphoma patient sample TFRIPAIR2_FL	Illumina HiSeq 2500	1
EGAD00001010216	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0168_001 for Follicular lymphoma patient sample TFRIPAIR3_FL	Illumina HiSeq 2500	1
EGAD00001010217	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0169_001 for Follicular lymphoma patient sample TFRIPAIR4_FL	Illumina HiSeq 2500	1
EGAD00001010218	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0170_001A for Follicular lymphoma patient sample TFRIPAIR5_FL	Illumina HiSeq 2500	1
EGAD00001010219	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0171_001A for Follicular lymphoma patient sample TFRI_Pair_6_FL	Illumina HiSeq 2500	1
EGAD00001010220	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0178_001A for Follicular lymphoma patient sample TFRIPAIR8_FL	Illumina HiSeq 2500	1
EGAD00001010221	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0183_001A for Follicular lymphoma patient sample TFRIPAIR9_FL	Illumina HiSeq 2500	1
EGAD00001010222	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0187_001A for Follicular lymphoma patient sample TFRIPAIR10_FL	Illumina HiSeq 2500	1
EGAD00001010223	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0188_001A for Follicular lymphoma patient sample TFRIPAIR11_FL	Illumina HiSeq 2500	1
EGAD00001010224	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0197_001A for Follicular lymphoma patient sample TFRIPAIR12_FL	Illumina HiSeq 2500	1
EGAD00001010225	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_001A for Follicular lymphoma patient sample TFRI_Pair_13_FL	Illumina HiSeq 2500	1
EGAD00001010226	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0167_002 for Diffuse large B-cell lymphoma patient sample TFRIPAIR2_DLBCL	Illumina HiSeq 2500	1
EGAD00001010227	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0168_002 for Diffuse large B-cell lymphoma patient sample TFRIPAIR3_DLBCL	Illumina HiSeq 2500	1
EGAD00001010228	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0169_002 for Diffuse large B-cell lymphoma patient sample TFRIPAIR4_DLBCL	Illumina HiSeq 2500	1
EGAD00001010229	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0170_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR5_DLBCL	Illumina HiSeq 2500	1
EGAD00001010230	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0171_002A for Diffuse large B-cell lymphoma patient sample TFRI_Pair_6_DLBCL	Illumina HiSeq 2500	1
EGAD00001010231	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0178_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR8_DLBCL	Illumina HiSeq 2500	1
EGAD00001010232	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0183_002A for Diffuse large B-cell lymphoma patient sample TFRI_Pair_9_DLBCL	Illumina HiSeq 2500	1
EGAD00001010234	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0188_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR11_DLBCL	Illumina HiSeq 2500	1
EGAD00001010235	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0197_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR12_DLBCL_rel	Illumina HiSeq 2500	1
EGAD00001010236	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_002A for Diffuse large B-cell lymphoma patient sample TFRI_Pair_13_DLBCL	Illumina HiSeq 2500	1
EGAD00001010237	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_004A for Lymph node patient sample RLN_02_5Prime	Illumina HiSeq 2500	1
EGAD00001010238	10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_005A for Lymph node patient sample RLN_03_5Prime	Illumina HiSeq 2500	1
EGAD00001010239	DLP+ Single Cell Genomic Library 98211 for Diffuse large B-cell lymphoma patient sample TFRIPAIR11_DLBCL	HiSeq X Ten	1
EGAD00001010240	DLP+ Single Cell Genomic Library A98180 for Diffuse large B-cell lymphoma patient sample TFRI_Pair_13_DLBCL	HiSeq X Ten	1
EGAD00001010241	DLP+ Single Cell Genomic Library A98193 for Follicular lymphoma patient sample TFRI_Pair_6_FL	HiSeq X Ten	1
EGAD00001010242	DLP+ Single Cell Genomic Library A98203 for Diffuse large B-cell lymphoma patient sample TFRIPAIR8_DLBCL	HiSeq X Ten	1
EGAD00001010243	DLP+ Single Cell Genomic Library A98205 for Follicular lymphoma patient sample TFRIPAIR9_FL	HiSeq X Ten	1
EGAD00001010244	DLP+ Single Cell Genomic Library A98208 for Diffuse large B-cell lymphoma patient sample TFRIPAIR10_DLBCL	HiSeq X Ten	1
EGAD00001010245	DLP+ Single Cell Genomic Library A98221A for Follicular lymphoma patient sample TFRIPAIR5_FL	HiSeq X Ten	1
EGAD00001010246	DLP+ Single Cell Genomic Library A98225 for Diffuse large B-cell lymphoma patient sample TFRIPAIR12_DLBCL_rel	HiSeq X Ten	1
EGAD00001010247	DLP+ Single Cell Genomic Library A98288 for Follicular lymphoma patient sample TFRIPAIR2_FL	HiSeq X Ten	1
EGAD00001010248	DLP+ Single Cell Genomic Library A98297 for Follicular lymphoma patient sample TFRIPAIR3_FL	HiSeq X Ten	1
EGAD00001010249	DLP+ Single Cell Genomic Library A98167 for Diffuse large B-cell lymphoma patient sample TFRIPAIR4_DLBCL	HiSeq X Ten	1