Max Planck Institute for Molecular Genetics
About the Max Planck Institute for Molecular Genetics
The MPIMG is one of the key research institutes for molecular biology and is recognised internationally as a stronghold of genome and genetics research. The overall goal of the combined efforts of MPIMG departments is to gain insight into the development of diseases on a molecular level, thus contributing to the development of novel cause-related medical treatments. The MPIMG has a large next generation sequencing facility and has outstanding expertise in the field of NGS technology development, operating both Illumina and SOLiD platforms, and in bioinformatics analysis of large-scale genomic information and modelling of complex data. The facility has been used for several large sequencing projects including current participation in the 1000 Genomes project, in GEUVADIS, in two ICGC projects (International Cancer Genome Consortium), the Blueprint project and the OncoTrack project.
The group of Marie-Laure Yaspo is currently involved in the Marie-Curie ITN “VacTrain”, an initial training network for vaccinologists funded by the EU under the FP7 Marie Curie Action (Grant number: 316655). In this framework, B cell antibody repertoires for monitoring immune responses that are observed in disease and after vaccination are being sequenced (see http://www.vactrain.eu/). As part of VacTrain, a bioinformatics analysis pipeline for repertoire sequencing data has been established, which can be tailored for use in the proposed project.
In addition to experience in repertoire sequencing, the Max Planck Society, together with the spin-off company Alacris Theranostics GmbH, holds IP on a novel technique for single-cell high-throughput analysis of immune repertoires (Hans-Jörg Warnatz, Jörn Glökler and Hans Lehrach, European patent application EP12154726, filed on February 9, 2012, International application PCT/EP2013/052328, published on August 15, 2013).
The main task of MPIMG in TREGeneration is the monitoring of the fate of infused Tregs. Since it is not clear that the infused cells will remain in the circulation in sufficient numbers for a long time, the sensitivity of the monitoring technique is crucial. We will monitor regulatory T cell therapy using next generation sequencing of T cell receptor beta-chain (TCRB) transcripts, which provides sufficient sensitivity for detection of remaining circulating T cells in the patients’ peripheral blood, even if a large proportion of the cells are cleared from circulation.
For reliable T cell monitoring, it is vital to characterise in detail the TCRB gene repertoire of the infused T cell population as well as the patients’ TCRB repertoire before cell infusion using deep sequencing. These data constitute the basis to allow discrimination between endogenous and infused cells. After T cell infusion, T cells from the patient will be monitored by TCRB sequencing every week after infusion for the first month and then every month for up to 6 months.
The profiling of T cells includes sorting into 3-7 different subsets prior to sequencing analysis, to be able to track the fate of each clonotype among these subsets:
• CD4+ CD25+ regulatory T cells (naïve/memory),
• CD4+ CD25- non-regulatory T cells (naïve/memory), and
• CD8+ T cells (naïve/memory).
Sorted subsets will be analysed from all samples of each time point. RNA isolation and TCRB amplification will be done at the MPIMG. Sequencing library preparation will be done at Alacris Theranostics GbmH.
The TCR beta-chains of the infused cells and the patients’ cells before infusion will be sequenced with long paired-end reads, characterizing these T cell clones in detail, using the long-read kit (2x250 or 2x300 bases paired-end) on the Illumina MiSeq platform in the MPIMG. This read length will allow complete characterization of the V-D-J rearrangements and the complementarity determining regions (CDRs) of each cell’s TCR beta-chain, allowing for in-depth repertoire analysis of the infused T cell population.
The samples from the time points after infusion will be sequenced on the Illumina HiSeq platform (2x100 bases paired-end), since shorter reads are enough here to reliably track the fate of the clones from the well-characterized infused cell population. The sequencing on the HiSeq platform will be done at Alacris Theranostics GmbH.