PLATFORM FOR MULTIOMIC ANALYSIS OF HEMATOPOIESIS OR THE IMMUNE SYSTEM IN PATIENTS WITH HEMATOLOGICAL MALIGNANCIES OR AFTER CSH ALLOGRAFT (ALL/AML/MPS/MDS)

Preclinical development

Cell therapy
Immunotherapy

Preclinical research (TRL 4-5)

Multiomic analysis of allograft patient samples to study new therapeutic targets aimed at limiting relapse (GvL) or preventing allogeneic reactions (GvHD).

Integrative approaches adapted to rare or limited patient samples. These approaches enable us to explore a wide range of biological dimensions in order to characterize circulating immune cells, their functional profile and their environment.

Description

Scope of research activities

Multiomic analysis of samples from allograft patients:

Ancillary studies for clinical trials
Retrospective studies
Biomarker research
Identification of therapeutic targets

Conduct of studies

Steps:

Identification of the scientific question to be addressed, and the available samples.
Definition of exploration modalities according to project needs (mass cytometry, metabolomics, single-cell transcriptomics, single-cell TCR/BCR sequence, microbiota exploration by 16S sequencing or shotgun metagenomics).
Identification of associated clinical data
Preparation of a data analysis plan, including raw data cleaning and normalization, dimensional reduction steps, cluster/signature/pathway identification, and statistical analyses (uni/multivariate, multinomial logistic regression, predictive model, etc.)
Preparation of regulatory applications adapted to the research methodology, preparation of a data management plan
Implementation of experiments following study planning, organization of interim meetings to monitor project progress and results
Final analysis and communication of results and conclusions

Research infrastructure

Experimental and analytical platforms:

Mass (CyPS) or spectral (Aurora) cytometry
Metabolomics (MetaboHUB)
Single-cell sequencing (10X genomics, Chromium controller): scRNAseq, scATAC-seq, scTCR-seq, CITE-seq
scDNA-seq (Tapestri)

Biological resources:

Biological collection in support of a trial (ancillary study)
Collection of blood mononuclear cells (PBMC), plasma or dry pellet (CRYOSTEM multicenter collection)
Retrospective stool collection (monocentric)

Quality assurance

Sharing of original biological data on public repositories and source code on GitHub in compliance with the FAIR (Findable, Accessible, Interoperable, Reusable) principle.

Specifications

The platform

Multiomic analysis of hematopoiesis or the immune system in patients with hematological malignancies or after HSC allogeneic transplantation.

The studies

Analysis of immune phenotype by mass cytometry:

Unsupervised identification of immune subpopulations (FlowSOM algorithm)
Characterization of functional profile (activated, depleted, cytotoxic)

Single-cell transcriptomic analysis:

Unsupervised identification of immune populations by surface phenotype (CITE-seq) or transcriptome (scRNAseq)
Analysis of cell cycle, differentially expressed genes (Seurat) or enriched biological pathways (GSEA)
Analysis of ligand-receptor interactions and target genes (NicheNET)
Pseudo-time trajectory analysis (Slingshot, Monocle3)

Metabolomics analysis:

Relative or absolute quantification of targeted or non-targeted metabolites
Analysis of enriched metabolic pathways
Identification of metabolic signatures by PCA, PLSDA

Examples of partnerships

Operational tolerance after hematopoietic stem cell transplantation – Characterization of the transcriptional, immunological, and metabolomic features of operational tolerance in two cohorts of individuals who received HSCT from an HLA-matched sibling donor.

Partner: Ghent University (Dr Yvan Saeys, Data mining and modeling for biomedicine, VIB)

Role of Donor Clonal Hematopoiesis in Allogeneic Hematopoietic Stem-Cell Transplantation - Clonal hematopoiesis of indeterminate potential (CHIP) occurs in the blood of approximately 20% of older persons. CHIP is linked to an increased risk of hematologic malignancies and of all-cause mortality; thus, the eligibility of stem-cell donors with CHIP is questionable. We comprehensively investigated how donor CHIP affects outcome of allogeneic hematopoietic stem-cell transplantation (HSCT).

Partner: Charité, University Medical Center, Berlin (Pr Frederic Damm)