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Working group "Infection & Immunity"

PD Dr. rer. nat Christof Geldmacher & Dr. rer. nat Kathrin Held


Infection and immunity group

Group Members:
Lisa Rogers (PhD, Bioinformatics)
Mohamed Ahmed (PhD)
Tabea Eser (MSc, cand. Dr. rer. nat)
Claudia Bräu-Heberger (Technical assistant)
Sabine Rappe (Technical assistant)
Danni Wang (MSc, cand. Dr. rer. nat)
Luming Lin (MSc, cand. Dr. rer. nat)
Olga Baranov (Dr. rer. nat, Bioinformatics)

International Group members
Dr. Mkunde Chachage (PhD, MSc, NIMR-Mbeya Medical Research Center, Tanzania)
Wilbert Mbuya (Msc, cand. Dr. rer. nat, NIMR-Mbeya Medical Research Center, Tanzania)

MD Doctoral, Master and Bachelor students

Yuka Nadai (cand. med. n.n.)
Augusta Horvath (cand. med. n.n.)
Nora Pieroth (cand. med. n.n.)
Isabel Brand (cand. med. n.n.)
Leonard Gilbert (cand. med. n.n.)

International PhD students
Nadia Sitoe (PhD candidate, Instituto Nacional da Mozambique, Maputo, Mozambique)
Caleb Muefong (cand. Dr. hum. biol., Medical Research Council, Banjul, The Gambia)

Main funding organizations: DZIF, DFG, EU Horizon 2020, EDCTP

Research Interests

The "Infection & Immunity" work group concentrates on dissecting the host response to infection and vaccination during human cohort studies with primary focus on SARS-CoV2 infection, the Human Immunodeficiency Virus (HIV), oncogenic Human Papilloma Viruses (HPV), Mycobacterium tuberculosis (MTB) and helminth infections (together with AG Inge Kroidl). This includes the molecular characterization of the infecting pathogen, identification of correlates of immune protection from infection and disease progression, biomarker discovery for TB diagnostics and treatment monitoring, characterization of HIV reservoirs, as well as mapping of B cell epitopes upon vaccination. Besides the analysis of systemic cellular and humoral immune responses, the group has proficiency in the analysis of effector cell subsets in human tissue samples using multiplex fluorescence immunohistochemistry combined with detection of viral nucleic acids using in situ hybridization to study the micro-environment of virus-infected cells. The capacity for bioinformatic analysis of large-scale RNA sequencing data and microscopy images is undergoing further development.

The working group is closely affiliated with the international Clinical Trials Unit from the German Center for Infection Research (DZIF) and contributes to human subject specimen processing and biobanking during large international clinical trials and observational studies.  The group collaborates closely with the NIMR-Mbeya Medical Research Center in Mbeya, Tanzania and the Instituto Nacional da Saude in Maputo, Mozambique as well as other African Research Centers to support improving the capacity for infectious disease research in endemic settings on the African continent.

Besides pure research activities, we also offer GCP conform laboratory services to partners from the biomedical industry during clinical phase 1 to phase 3 vaccine trials. This includes management of investigational medical products,  human sample processing, biobanking and international sample logistics.

Research Technology Platforms and Laboratory services

Platform: Polychromatic flow cytometry and flow cytometric cell sorting for in-depth characterization of human cells
The laboratory is equipped with a 13-colour Beckmann Coulter CytoFLEX Flow Cytometer and has vast experience in the flow cytometric analysis of human cells. This includes characterisation of pathogen-specific T cells after in vitro restimulation or by HLA tetramer staining as well as any other cell type in the blood. The laboratory uses the Flow Cytometry core unit CyTUM-MIH (weblink: for flow cytometric cell sorting at biosafety S2 and S3 level to allow for downstream analyses of DNA and RNA in sorted cells.

Representative dot plots for the phenotypic characterisation of pathogen-specific CD4 T cells. 
Expression of a specific T cell activation marker after in vitro restimulation on pathogen-specific CD4 T cells under various disease conditions. Pathogen-specific cells are boxed in red. Copyright: Ahmed et al, 2018

Platform: Peptide microarray analyses of pathogen-specific antibody responses
The laboratory serves as a core peptide array laboratory for the European HIV Vaccine Alliance ( We use a fully validated peptide microarray assay to map and analyse specific antigenic regions recognized by antibodies elicited by vaccination. The technology is established for both, clinical and preclinical specimen. The technology allows reactivity testing against up to 8000 different peptides in triplicates in multiple samples simultaneously. Custom design of the peptide microarray is performed in collaboration with Dr. Georgios Pollakis (University of Liverpool, weblink Bioinformatic downstream analysis of generated data is well established and can be adapted depending on the research question.

Antibody epitope mapping using peptide microarrays.
Peptide microarrays are used for epitope mapping of antibody responses against the HIV envelope protein. Thus enabling us to identify specific antigenic regions recognized by antibodies elicited by different vaccines.
The upper panel shows a representative peptide microarray scan and the lower panel depicts the analysis of recognised epitopes along the HIV envelope protein. Copyright: University of Munich

Platform: Histological characterisation of tissue-resident cells in their natural microenvironment
Histological techniques provide valuable information on cells within their natural environment, such as their relative positioning within the tissue and cell-cell interactions. To take advantage of this information, the laboratory thas established multiplex fluorescence immunohistochemistry for numerous cell markers in combination with the detection of nucleic acids using in situ hybridisation. Customisable semi-automated analysis tools are established for the most common staining panels. We have access to various microscopes via the Core Facility Bioimaging at the Biomedical Center (BMC) ( depending on the application in question.

An HIV infected T cell is attacked by a granzyme B expressing T cell.
Combined in situ hybridization for HIV RNA and immunohistochemical staininig for T-cell markers on human lymph node sections. The large image shows an overlay of all channels, with the smaller panels showing each channel separately. Combined visualisation of viral RNA and immune cells enables the study of immune cells in their natural micro-environment.
Scale Bar 50µm. Copyright: University of Munich

Platform: Transcriptome analysis by RNA sequencing

Transcriptome analysis is well established within the lab, with bioinformatic workflows developed in house.  A particular focus of our research includes the analysis of low abundant cell populations for the discovery of novel biomarkers. We have expertise in high-throughput analysis of whole blood collected in clinical trials and observational studies as well as in low-input RNA sequencing of sorted rare cell populations such as pathogen-specific T cells.

Differential expression of various genes in healthy and sick individuals.
The transcriptome of pathogen-specific T cells of patients and healthy controls was sequenced using RNA-seq. After differential gene expression analysis, genes that distinguish between healthy controls and patients were identified and visualised above. Copyright: University of Munich

Laboratory services, Consultancies and international clinical study logistics

The laboratory can provide laboratory services for human sample processing and analysis for clinical studies in Munich and elsewhere. This includes the processing of blood samples (Plasma, Serum, Isolation of Peripheral Blood Mononuclear Cells). The group also has tremendous experience in supporting large international clinical with a specific emphasis on Africa. We therefore provide support on sample and reagent logistics, capacity development and the analytic process in multiple national and international study set ups. Please contact us for more information.