# Integrated spatial and multimodal single cell transcriptomics reveals the in situ topography of splenic marginal zone lymphoma.

Pauline Gravelle

► To cite this version:

Pauline Gravelle. Integrated spatial and multimodal single cell transcriptomics reveals the in situ topography of splenic marginal zone lymphoma.. 10X Genomics European Single Cell Discovery Symposium., 10X Genomics, 2022, Paris, France. inserm-04831426

HAL Id: inserm-04831426

https://inserm.hal.science/inserm-04831426v1

Submitted on 11 Dec 2024

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# Multimodal single cell technologies: Tools & Applications to decipher B cell lymphoma heterogeneity

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10×GENOMICS

European Single Cell Discovery Symposium 2022

The tale of a single cell

May 24-June 2 | Stockholm, Cambridge, Paris, Frankfurt

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P. GRAVELLE,

J.P. CERAPIO ARROYO, C. LAURENT & J.J. FOURNIE

CHU Purpan, Pathology Department
Cancer Research Center of Toulouse, IUC-T, Team NoLymits

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Hôpitaux de Toulouse

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Inserm

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Research area: Improving Therapeutic Strategies for Lymphoma

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Study of lymphoma cells and their microenvironment to predict
therapeutic response & discover new targets
Previous TEAM Achievements :

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Ysebaert, L., and Fournie, J.J. Leukemia & Lymphoma 2011.

Ysebaert, L., & al. Blood 2010.

Gravelle, P., & al. Am J Pathol 2014.

Péricart S. & al. Cancers 2018.
Previous TEAM Achievements :

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Ysebaert, L., and Fournie, J.J. Leukemia & Lymphoma 2011.

Ysebaert, L., & al. Blood 2010.

Gravelle, P., & al. Am J Pathol 2014.

Péricart S. & al. Cancers 2018.
<figure><img src="image_14.png" /><figcaption># Cellular Indexing of Transcriptomes & Epitopes (CITEseq) and Single cell immune profiling (sc-RNA-Seq 5'-VDJ): Pipelines</figcaption></figure>

- Clonotypes identification (ME + B cells)

- TILs GEP vs Lymphoma cells GEP

- Anti-tumoral immune response study
# Cellular Indexing of Transcriptomes & Epitopes (CITEseq) and Single cell immune profiling (sc-RNA-Seq 5'-VDJ): Pipelines

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- Clonotypes identification (ME + B cells)

- TILs GEP vs Lymphoma cells GEP

- Anti-tumoral immune response study
Signatures outperform single genes

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B lymphocytes

1 gene

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4 genes

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# Profiling transcriptomic signatures at single cell level

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Exploration of CITE-Seq datas through Phenotype mapping

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Active File : AC_d1_er_pbmc.tsv

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Exploration of CITE-Seq datas through Phenotype mapping

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ODT-Ab “paired” confrontation
- cell surface markers

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ODT-Ab vs gene / signature confrontation
- cell surface markers vs GEP
Differentiation trajectories in physiological & pathological context

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pseudotime

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age of cells (& more)

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Minimum Spanning Tree
# Differentiation trajectories in physiological & pathological context

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pseudotime

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age of cells (& more)

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Minimum Spanning Tree

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• Normal T cells

• TILs
Differentiation trajectories in tumor context

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Analytical process

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**Cohort:** 3 B-NHL patients, 2 HD

**Organs:** tumor / blood

**Technologies:** CITE-3', 5', Spatial transcriptomics
Application to lymphoma samples : "Integrated spatial and multimodal single cell transcriptomics reveals the in situ topography of B-NHLs"

Analytical process

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**Cohort:** 3 B-NHL patients, 2 HD

**Organs:** tumor / blood

**Technologies:** CITE-3', 5', Spatial transcriptomics

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CITE-3' & 5' datas: valid **Integration**
'Public' and 'private' areas
Application to lymphoma samples : "Integrated spatial and multimodal single cell transcriptomics reveals the in situ topography of B-NHLs"

Hierarchical clustering & Signature explorer

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Application to lymphoma samples : "Integrated spatial and multimodal single cell transcriptomics reveals the in situ topography of B-NHLs"

<figure><img src="image_43.png" /><figcaption>Tumor clones</figcaption></figure>
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6 steps differentiation trajectory
Trajectories – GC B cells [Holmes & al., 2020 ; Steward & al., 2021 ; ...]

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2 steps differentiation trajectory
(ANGLE)
Trajectories: “in-house” dataset injection

HD blood

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> Homogeneous repartition of
blood B lymphocytes among the
6 peripheral subsets

HD tissue

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> Light zone accumulation of
tissular B cells
Application to lymphoma samples : “Integrated spatial and multimodal single cell transcriptomics reveals the in situ topography of B-NHLs”

Trajectories: “in-house” dataset injection

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<figure><img src="image_50.png" /><figcaption>Single-Cell Spatial Explorer</figcaption></figure>
# Application to lymphoma samples : what's about in situ topography of B-NHLs ?
## Link with spatial transcriptomics.

### What is required ?

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Any image associated
with a CSV data table
with XY coordinates

or

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transcriptomic data pre-processing

or

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Single-Cell Signature Explorer
29 000 Human signatures and pathways

or

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Single-Cell Virtual Cytometer

selection of distinct cells populations

or

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complex pixel
selections

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Applications ?

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Confidential -
Unpublished
results -
do not post
B cell activated

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Applications ?

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B-NHL “in-house” dataset example

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# To conclude...

**In summary:**

- Open source softwares library : https://sites.google.com/site/fredsoftwares/products

- Signatures exploration > new targets identification

**Specific to B-NHLs:**

- Blood vs tumor: similar hyperexpanded clone

- Inter patients variability (tumor clones, tissue morphology,...)

- Clone detection in situ thanks to Spatial transcriptomics

**Limits:**

- Spatial transcriptomics > “mini bulk”

- Cell composition analysis blurred

**Needs:**

- Structured tissues

- Single cell resolution of the Spatial technic
# Acknowledgements to:

## Cancer Research Center of Toulouse

### Pole technologique

Juan Pablo CERAPIO

Frederic PONT

Marie TOSOLINI

Marion PERRIER

Emeline SAROT

Laetitia LIGAT

Frederic LOPEZ

### Genotoul

### Plateforme GeT

Frédéric MARTINS

https://sites.google.com/site/fredsoftwares/products

## Cancer Research Center of Toulouse

### CL team

Jean-Jacques FOURNIE

Camille LAURENT

Anne QUILLET-MARY

Loïc YSEBAERT

Sarah CADOT

Don Marc FRANCHINI

Nicolas CURDY

Olivia LANVIN

Mary POUPOT

Marcin DOMAGALA

Christine BEZOMBES

Carla FARIA

Fabien GAVA

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Pôle
TECHNOLOGIQUE
CRCT

TOUCAN
LABORATOIRE D'EXCELLENCE TOULOUSE CANCER

FONDATION ARC
POUR LA RECHERCHE
SUR LE CANCER

Reconnue d'utilité publique

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calmip

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Genotoul
GENOPOLE TOULOUSE

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UNIVERSITÉ
TOULOUSE III
PAUL SABATIER

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INSTITUT UNIVERSITaire
dU CANCER DE TOULOUSE

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