Dissecting intratumor heterogeneity of nodal B cell lymphomas at transcriptional, genetic, and drug response levels (ICPSR doi:10.11588/data/VRJUNV)
(scRNA-seq in nodal B cell lymphoma)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
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Document Description

Citation

Title:

Dissecting intratumor heterogeneity of nodal B cell lymphomas at transcriptional, genetic, and drug response levels

Identification Number:

doi:10.11588/data/VRJUNV

Distributor:

heiDATA

Date of Distribution:

2020-04-06

Version:

1

Bibliographic Citation:

Tobias Roider; Julian Seufert; Alexey Uvarovskii; Felix Frauhammer; Marie Bordas; Nima Abedpour; Marta Stolarczyk; Jan-Philipp Mallm; Sophie A. Herbst; Peter-Martin Bruch; Hyatt Balke-Want; Michael Hundemer; Karsten Rippe; Benjamin Goeppert; Martina Seiffert; Benedikt Brors; Gunhild Mechtersheimer; Thorsten Zenz; Martin Peifer; Björn Chapuy; Matthias Schlesner; Carsten Müller-Tidow; Stefan Fröhling; Wolfgang Huber; Simon Anders; Sascha Dietrich, 2020, "Dissecting intratumor heterogeneity of nodal B cell lymphomas at transcriptional, genetic, and drug response levels", https://doi.org/10.11588/data/VRJUNV, heiDATA, V1, UNF:6:AlKw3YwYZ82Ty5CxnC4D5w== [fileUNF]

Study Description

Citation

Title:

Dissecting intratumor heterogeneity of nodal B cell lymphomas at transcriptional, genetic, and drug response levels

Alternative Title:

scRNA-seq in nodal B cell lymphoma

Identification Number:

doi:10.11588/data/VRJUNV

Authoring Entity:

Tobias Roider (Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany)

Julian Seufert (Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany)

Alexey Uvarovskii (Center for Molecular Biology of the University of Heidelberg, Heidelberg, Germany)

Felix Frauhammer (Center for Molecular Biology of the University of Heidelberg, Heidelberg, Germany)

Marie Bordas (Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany)

Nima Abedpour (University of Cologne, Department for Translational Genomics, Cologne, Germany)

Marta Stolarczyk (Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany)

Jan-Philipp Mallm (Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, Heidelberg, Germany)

Sophie A. Herbst (Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany)

Peter-Martin Bruch (Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany)

Hyatt Balke-Want (University of Cologne, Department for Translational Genomics, Cologne, Germany)

Michael Hundemer (Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany)

Karsten Rippe (Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, Heidelberg, Germany)

Benjamin Goeppert (Institute of Pathology, University of Heidelberg, Heidelberg, Germany)

Martina Seiffert (Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany)

Benedikt Brors (Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany)

Gunhild Mechtersheimer (Institute of Pathology, University of Heidelberg, Heidelberg, Germany)

Thorsten Zenz (Department of Medical Oncology and Hematology, University of Zürich, Zürich, Switzerland)

Martin Peifer (University of Cologne, Department for Translational Genomics, Cologne, Germany)

Björn Chapuy (Clinic for Hematology and Medical Oncology, University Medicine Göttingen, Göttingen, Germany)

Matthias Schlesner (Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany)

Carsten Müller-Tidow (Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany)

Stefan Fröhling (Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany)

Wolfgang Huber (European Molecular Biology Laboratory (EMBL), Heidelberg, Germany)

Simon Anders (Center for Molecular Biology of the University of Heidelberg, Heidelberg, Germany)

Sascha Dietrich (Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany)

Distributor:

heiDATA

Date of Distribution:

2020-04-06

Study Scope

Keywords:

Medicine, Health and Life Sciences

Abstract:

Tumour heterogeneity encompasses both the malignant cells and their microenvironment. While heterogeneity between individual patients is known to affect the efficacy of cancer therapy, most personalized treatment approaches do not account for intratumor heterogeneity. We addressed this issue by studying the heterogeneity of nodal B cell lymphoma by single cell RNA-sequencing and transcriptome-informed flow cytometry. We identified transcriptionally distinct malignant subpopulations and compared their drug response and genomic profiles. Malignant subpopulations of the same patient responded strikingly different to anti-cancer drugs ex vivo, which recapitulated subpopulation-specific drug sensitivity during in vivo treatment. Infiltrating T cells represented the majority of non-malignant cells, whose gene expression signatures were similar across all donors, whereas the frequencies of T cell subsets varied significantly between the donors. Our data provide insights into the heterogeneity of nodal B cell lymphoma and highlight the relevance of intratumor heterogeneity for personalized cancer therapy.

Notes:

10x data processed by CellRanger: sparse-matrix format with raw UMI counts. For detailed format description, see <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices">https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices</a>.

Methodology and Processing

File Description--f3382

File: AnnotationCells.tab

  • Number of cases: 26594

  • No. of variables per record: 1

  • Type of File: text/tab-separated-values

Notes:

UNF:6:5fjnKQ0MiCiccCbgx/Dyxw==

File Description--f3383

File: Annotation_Tcells.tab

  • Number of cases: 8862

  • No. of variables per record: 1

  • Type of File: text/tab-separated-values

Notes:

UNF:6:NUwQFL4G9cwzqMGh4Ab4jA==

File Description--f2843

File: sample_sheet.tab

  • Number of cases: 12

  • No. of variables per record: 8

  • Type of File: text/tab-separated-values

Notes:

UNF:6:dLH9pDgli3I+s+BIDRvtBQ==

Variable Description

List of Variables:

Variables

Sample;Barcode;Population

f3382 Location:

Variable Format: character

Notes: UNF:6:5fjnKQ0MiCiccCbgx/Dyxw==

Barcode;Sample;Population

f3383 Location:

Variable Format: character

Notes: UNF:6:NUwQFL4G9cwzqMGh4Ab4jA==

SampleName

f2843 Location:

Variable Format: character

Notes: UNF:6:BAo//803ZVWvc8cyDIX4kw==

Tissue

f2843 Location:

Variable Format: character

Notes: UNF:6:CT+eHHdhTxKjMQq6THXujA==

Sex

f2843 Location:

Variable Format: character

Notes: UNF:6:vesnBEh9wKLHVFmV2U2+5g==

Entity

f2843 Location:

Variable Format: character

Notes: UNF:6:evTXaE1XVPxSNunJZXZSfQ==

Diagnosis

f2843 Location:

Variable Format: character

Notes: UNF:6:ZqK3PZ5lnlaw/7IpQY6syA==

Subclassification

f2843 Location:

Variable Format: character

Notes: UNF:6:Y36uGgIEoK0/uCGe7RvY2g==

Batch

f2843 Location:

Summary Statistics: Min. 1.0; Mean 1.4166666666666665; Valid 12.0; StDev 0.5149286505444373; Max. 2.0

Variable Format: numeric

Notes: UNF:6:5OOy8v37V/5CazRviM2QaQ==

CellrangerVersion

f2843 Location:

Variable Format: character

Notes: UNF:6:I4hBoPc0EbFTGTe9TJ8K3A==

Other Study-Related Materials

Label:

DLBCL1.zip

Notes:

application/zip

Other Study-Related Materials

Label:

DLBCL2.zip

Notes:

application/zip

Other Study-Related Materials

Label:

DLBCL3.zip

Notes:

application/zip

Other Study-Related Materials

Label:

FL1.zip

Notes:

application/zip

Other Study-Related Materials

Label:

FL2.zip

Notes:

application/zip

Other Study-Related Materials

Label:

FL3.zip

Notes:

application/zip

Other Study-Related Materials

Label:

FL4.zip

Notes:

application/zip

Other Study-Related Materials

Label:

rLN1.zip

Notes:

application/zip

Other Study-Related Materials

Label:

rLN2.zip

Notes:

application/zip

Other Study-Related Materials

Label:

rLN3.zip

Notes:

application/zip

Other Study-Related Materials

Label:

tFL1.zip

Notes:

application/zip

Other Study-Related Materials

Label:

tFL2.zip

Notes:

application/zip