Systems Immunology and Single Cell Biology
- Immunology, Infection and Cancer
- Junior Research Group
Dr. Felix Hartmann
Group Leader
We aim to establish spatial immunometabolism as a framework for understanding immune regulation in tissues. Immune cell function is shaped not only by intrinsic metabolic programs, but by spatially organized metabolic niches emerging from multicellular interactions. By integrating single-cell metabolic profiling, spatial imaging, and computational modeling, we uncover the organizing principles of tumor–immune ecosystems and translate them into strategies for precision immunotherapy.
Scientific Program
Our research program is structured around three interconnected pillars that together define a quantitative framework for Spatial Immunometabolism.
1. Quantifying Metabolic States in Human Tissues
We develop and apply high-dimensional single-cell and spatial technologies to measure metabolic regulation directly in intact human tissues.
Using antibody-based metabolic profiling, multiplexed imaging, and spatial mass spectrometry approaches, we quantify the metabolic states of immune, stromal, and malignant cells in situ. Rather than relying solely on transcriptional inference, we measure the regulatory protein networks that determine pathway activity and functional capacity.
A central focus is the analysis of human clinical samples, where we investigate how spatially resolved metabolic states relate to tumor progression, immune dysfunction, and clinical outcome.
2. Computational Modeling of Metabolic Programs
Spatial single-cell data are inherently multimodal and high-dimensional. We develop computational frameworks that integrate metabolic state, cellular composition, and spatial organization into interpretable multicellular programs.
Instead of analyzing individual markers in isolation, we identify coordinated metabolic and cellular patterns that define tumor–immune ecosystem states. Our goal is to transform complex spatial data into mechanistic and predictive models of tissue organization.
3. Mechanistic Dissection of Metabolic Niches
Quantitative mapping and modeling generate hypotheses about how metabolic interactions shape immune function. We test these hypotheses using patient-derived tumor organoids and ex vivo tissue systems.
By genetically perturbing metabolic enzymes using CRISPR-based approaches, we examine how specific tumor or stromal metabolic programs influence T cell and macrophage function within controlled microenvironments.
This allows us to move from correlation to causation and to define actionable metabolic interactions that may be therapeutically targeted.
Why Spatial Immunometabolism Matters
Immune cells operate in metabolically constrained environments.
Tumors exploit nutrient competition, hypoxia, and metabolite signaling to suppress immunity.
Current immunotherapies often fail because these metabolic barriers remain poorly understood and insufficiently targeted.
By quantifying metabolic regulation directly in tissues, we aim to:
- Reveal mechanisms of immune dysfunction
- Identify predictive biomarkers of therapeutic response
- Inform rational metabolic interventions in cancer
Selected Recognition & Funding
Our research is supported by competitive national and international funding, including:
- European Research Council (ERC Starting Grant 2023)
- Helmholtz Young Investigator Program
- DKTK (German Cancer Consortium)
- Foundation and industry-supported research initiatives
These awards support a long-term program to establish quantitative spatial immunometabolism as a central framework in cancer research.
Selected Publications
Hartmann, F. J.
Tanevski J., Vulliard L., Ibarra-Arellano M., Shapiro D., Hartmann F. J. & Saez-Rodriguez J.
Glauner T. A., Truxa S., Cetin M., Schlüter K., Calafato D., Hartmann, F. J.
Cosgrove, J., Marçais, A., Hartmann, F. J., Bergthaler, A., Zanoni, I., Corrado, M., Perié, L., Cabezas-Wallscheid, N., Bousso, P., Alexandrov, T., Kielian, T., Martínez-Martín, N., Opitz, C. A., & Lyssiotis, C. A.
Hartmann, F. J., Mrdjen, D., McCaffrey, E., Glass, D. R., Greenwald, N. F., Bharadwaj, A., Khair, Z., Verberk, S. G. S., Baranski, A., Baskar, R., Graf, W., Van Valen, D., Van den Bossche, J., Angelo, M., & Bendall, S. C.
Complete list of Publications
Maas SLN, Tang Y, Stutheit-Zhao E, Rahmanzade R, Blume C, Hielscher T, Zettl F, Benfatto S, Calafato D, Sill M, Benotmane JK, Yabo YA, Behling F, Suwala A, Kardo H, Ritter M, Peyre M, Sankowski R, Okonechnikov K, Sievers P, Patel A, Reuss D, Friedrich MJ, Stichel D, Schrimpf D, Van den Bosch TPP, Beck K, Wirsching HG, Jungwirth G, Hanemann CO, Lamszus K, Etminan N, Unterberg A, Mawrin C, Remke M, Ayrault O, Lichter P, Reifenberger G, Platten M, Kacprowski T, List M, Pauling JK, Baumbach J, Milde T, Grossmann R, Ram Z, Ratliff M, Mallm JP, Neidert MC, Bos EM, Prinz M, Weller M, Acker T, Hartmann FJ, Preusser M, Tabatabai G, Herold-Mende C, Krieg SM, Jones DTW, Pfister SM, Wick W, Kalamarides M, von Deimling A, Heiland DH, Hovestadt V, Gerstung M, Schlesner M ; German “Aggressive Meningiomas” Consortium (KAM) ; Sahm F.
Li X, Lebeaupin C, Kadianaki A, Druelle-Cedano C, Vesper N, Rennert C, Huguet-Pradell J, Gomez Ramos B, Fan C, Piecyk RS, Zizmare L, Ramadori P, Li L, Frick L, Qiu M, Zhang C, Martins Nascentes Melo L, Ranvir VP, Shen P, Hanselmann J, Kosla J, Fernández-Vaquero M, Vucur M, Baskaran P, Bao X, Coleman OI, Tang Y, Cetin M, Chen Z, Jang I, Del Prete S, Rahbari M, Zhang P, Pham TV, Hou Y, Sun A, Gu L, Kim LC, Rothermel U, Heide D, Ali A, Gallage S, Talvard-Balland N, Piqué-Gili M, Gris-Oliver A, Bevilacqua A, Schlicker L, Duffey A, Unger K, Szydlowska M, Hetzer J, Odom DT, Machauer T, Bucci D, Sant P, Lee JH, Rösler J, Meckelmann SW, Schreck J, Murray S, Simon MC, Nahnsen S, Schulze A, Ho PC, Jugold M, Breuhahn K, Mallm JP, Schirmacher P, Roth S, Rahbari N, Tschaharganeh DF, Roessler S, Goeppert B, Bengsch B, Andrieux G, Boerries M, Malek NP, Prinz M, Weber A, Zeiser R, Tamayo P, Bronsert P, Kurowski K, Thimme R, Yuan D, Carretero R, Luedde T, Pinyol R, Hartmann FJ, Karin M, Tasdogan A, Trautwein C, Mall M, Hofmann M, Llovet JM, Haller D, Kaufman RJ, Heikenwälder M.
Hartmann FJ.
Mrdjen D, Cannon BJ, Amouzgar M, Kim Y, Liu C, Vijayaragavan K, Camacho C, Spence A, McCaffrey EF, Bharadwaj A, Tebaykin D, Bukhari S, Bosse M, Hartmann FJ, Kagel A, Oliveria JP, Yakabi K, Serrano GE, Corrada MM, Kawas CH, Tibshirani R, Beach TG, Corces MR, Greenleaf W, Angelo RM, Montine T, Bendall SC.
Learning tissue representation by identification of persistent local patterns in spatial omics data.
Tanevski J, Vulliard L, Ibarra-Arellano MA, Schapiro D, Hartmann FJ, Saez-Rodriguez J.
Kumar R, Hartmann FJ, Favaro P, Ho D, Bruce T, Goldston M, Spence A, McCaffrey EF, Bendall SC, Angelo M.
Greenwald NF, Nederlof I, Sowers C, Ding DY, Park S, Kong A, Houlahan KE, Varra SR, de Graaf M, Geurts V, Liu CC, Ranek JS, Voorwerk L, de Maaker M, Kagel A, McCaffrey E, Khan A, Yeh CY, Fullaway CC, Khair Z, Bai Y, Piyadasa H, Risom T, Delmastro A, Hartmann FJ, Mangiante L, Sotomayor-Vivas C, Schumacher TN, Ma Z, Bosse M, van de Vijver MJ, Tibshirani R, Horlings HM, Curtis C, Kok M, Angelo M.
Cosgrove J, Marçais A, Hartmann FJ, Bergthaler A, Zanoni I, Corrado M, Perié L, Cabezas-Wallscheid N, Bousso P, Alexandrov T, Kielian T, Martínez-Martín N, Opitz CA, Lyssiotis CA, Argüello RJ, Van den Bossche J.
Adamik J, Munson PV, Maurer DM, Hartmann FJ, Bendall SC, Argüello RJ, Butterfield LH.
Mrdjen D, Amouzgar M, Cannon B, Liu C, Spence A, McCaffrey E, Bharadwaj A, Tebaykin D, Bukhari S, Hartmann FJ, Kagel A, Vijayaragavan K, Oliveria JP, Yakabi K, Serrano GE, Corrada MM, Kawas CH, Camacho C, Bosse M, Tibshirani R, Beach TG, Angelo M, Montine T, Bendall SC.
Robinson ML, Glass DR, Duran V, Agudelo Rojas OL, Sanz AM, Consuegra M, Sahoo MK, Hartmann FJ, Bosse M, Gelvez RM, Bueno N, Pinsky BA, Montoya JG, Maecker H, Estupiñan Cardenas MI, Villar Centeno LA, Garrido EMR, Rosso F, Bendall SC, Einav S.
Munson PV, Adamik J, Hartmann FJ, Favaro PMB, Ho D, Bendall SC, Combes AJ, Krummel MF, Zhang K, Kelley RK, Butterfield LH.
Adamik J, Munson PV, Hartmann FJ, Combes AJ, Pierre P, Krummel MF, Bendall SC, Argüello RJ, Butterfield LH.
Amouzgar M, Glass DR, Baskar R, Averbukh I, Kimmey SC, Tsai AG, Hartmann FJ, Bendall SC.
Ackerman SE, Pearson CI, Gregorio JD, Gonzalez JC, Kenkel JA, Hartmann FJ, Luo A, Ho PY, LeBlanc H, Blum LK, Kimmey SC, Luo A, Nguyen ML, Paik JC, Sheu LY, Ackerman B, Lee A, Li H, Melrose J, Laura RP, Ramani VC, Henning KA, Jackson DY, Safina BS, Yonehiro G, Devens BH, Carmi Y, Chapin SJ, Bendall SC, Kowanetz M, Dornan D, Engleman EG, Alonso MN.
Geeraerts X, Fernández-Garcia J, Hartmann FJ, de Goede KE, Martens L, Elkrim Y, Debraekeleer A, Stijlemans B, Vandekeere A, Rinaldi G, De Rycke R, Planque M, Broekaert D, Meinster E, Clappaert E, Bardet P, Murgaski A, Gysemans C, Nana FA, Saeys Y, Bendall SC, Laoui D, Van den Bossche J, Fendt SM, Van Ginderachter JA.
Alspach E, Chow RD, Demehri S, Guerriero JL, Gujar S, Hartmann FJ, Helmink BA, Hudson WH, Ho WJ, Ma L, Maier BB, Maltez VI, Miller BC, Moran AE, Parry EM, Pillai PS, Rafiq S, Reina-Campos M, Rosato PC, Rudqvist NP, Ruhland MK, Sagiv-Barfi I, Sahu AD, Samstein RM, Schürch CM, Sen DR, Thommen DS, Wolf Y, Zappasodi R.
Hartmann FJ, Mrdjen D, McCaffrey E, Glass DR, Greenwald NF, Bharadwaj A, Khair Z, Verberk SGS, Baranski A, Baskar R, Graf W, Van Valen D, Van den Bossche J, Angelo M, Bendall SC.
Glass DR, Tsai AG, Oliveria JP, Hartmann FJ, Kimmey SC, Calderon AA, Borges L, Glass MC, Wagar LE, Davis MM, Bendall SC.
Tsai AG, Glass DR, Juntilla M, Hartmann FJ, Oak JS, Fernandez-Pol S, Ohgami RS, Bendall SC.
Hartmann FJ, Bendall SC.
Galli E, Hartmann FJ, Schreiner B, Ingelfinger F, Arvaniti E, Diebold M, Mrdjen D, van der Meer F, Krieg C, Nimer FA, Sanderson N, Stadelmann C, Khademi M, Piehl F, Claassen M, Derfuss T, Olsson T, Becher B.
Hartmann FJ, Babdor J, Gherardini PF, Amir ED, Jones K, Sahaf B, Marquez DM, Krutzik P, O'Donnell E, Sigal N, Maecker HT, Meyer E, Spitzer MH, Bendall SC.
Hartmann FJ, Simonds EF, Vivanco N, Bruce T, Borges L, Nolan GP, Spitzer MH, Bendall SC.
Hartmann FJ, Simonds EF, Bendall SC.
Krieg C, Nowicka M, Guglietta S, Schindler S, Hartmann FJ, Weber LM, Dummer R, Robinson MD, Levesque MP, Becher B.
Mrdjen D, Pavlovic A, Hartmann FJ, Schreiner B, Utz SG, Leung BP, Lelios I, Heppner FL, Kipnis J, Merkler D, Greter M, Becher B.
Mrdjen D, Pavlovic A, Hartmann FJ, Schreiner B, Utz SG, Leung BP, Lelios I, Heppner FL, Kipnis J, Merkler D, Greter M, Becher B.
Krieg C, Nowicka M, Guglietta S, Schindler S, Hartmann FJ, Weber LM, Dummer R, Robinson MD, Levesque MP, Becher B.
Nowicka M, Krieg C, Crowell HL, Weber LM, Hartmann FJ, Guglietta S, Becher B, Levesque MP, Robinson MD.
Mrdjen D, Hartmann FJ, Becher B.
Hartmann FJ, Bernard-Valnet R, Quériault C, Mrdjen D, Weber LM, Galli E, Krieg C, Robinson MD, Nguyen XH, Dauvilliers Y, Liblau RS, Becher B.
Mair F, Hartmann FJ, Mrdjen D, Tosevski V, Krieg C, Becher B.
Croxford AL, Lanzinger M, Hartmann FJ, Schreiner B, Mair F, Pelczar P, Clausen BE, Jung S, Greter M, Becher B.
Hartmann FJ, Khademi M, Aram J, Ammann S, Kockum I, Constantinescu C, Gran B, Piehl F, Olsson T, Codarri L, Becher B.
Schmidt HH, Ge Y, Hartmann FJ, Conrad H, Klug F, Nittel S, Bernhard H, Domschke C, Schuetz F, Sohn C, Beckhove P.
Parmentier J, Hartmann FJ, Fricker G.
Join the Lab
We seek highly motivated researchers with backgrounds in:
- Immunology
- Computational biology
- Systems biology
- Spatial omics technologies
- Quantitative modeling
Successful candidates are intellectually independent, collaborative, and motivated to work at the interface of technology development and mechanistic biology.
Our trainees benefit from:
- Strong international collaborations
- Interdisciplinary mentoring
- Exposure to cutting-edge spatial and computational technologies
- Competitive national and international research networks
PhD and postdoctoral applicants are encouraged to contact us with a CV, brief research statement, and references.
Current Members
Our interdisciplinary team brings together expertise in immunology, proteomics, spatial biology, and computational modeling. Together, we investigate how metabolic programs are organized in tissues and how they shape immune function within the tumor microenvironment.
We foster an open, collaborative, and supportive research environment. Scientific independence, critical thinking, and methodological rigor are central to our training philosophy.
Our group includes researchers from diverse disciplinary backgrounds and career stages, united by the goal of advancing Spatial Immunometabolism.
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Dr. Felix Hartmann
Group Leader
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Dr. Loan Vulliard
Postdoctoral Researcher
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Dr. Yu-Le Wu
Postdoctoral Researcher
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Sven Truxa
Postdoctoral Researcher
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Miray Cetin
PhD Student
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Jennifer Zimmermann
PhD Student
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Kilian Merz
PhD Student
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Domenico Calafato
PhD Student
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Kathleen Schlüter
PhD Student
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Simon Frank
Master Student
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Leonie Ellen Sander
Bachelor Student
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Vincent Paul
Bachelor Student
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Philippe Aumont
Master Intern
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Lara Schneider
Lab Technician
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Paul Esslinger
Junior Research Staff
Training and Mentorship
We are committed to training the next generation of scientists at the interface of immunology, spatial biology, and computational modeling.
Our mentoring approach emphasizes scientific independence, quantitative thinking, and conceptual clarity. Trainees are encouraged to develop their own research ideas, present their work internationally, and build interdisciplinary collaborations.
In addition to project-specific supervision, we provide structured guidance in:
- Experimental design and quantitative data analysis
- Scientific writing and grant preparation
- Conference presentations and networking
- Career development inside and outside academia
Members of the lab are integrated into national and international research networks (DKTK) and graduate programs, and benefit from close interaction with clinical and computational collaborators.
Our alumni have successfully transitioned to doctoral and postdoctoral positions at leading research institutions (e.g. Universities in Paris, Stockholm, Bonn, Berlin).
Protocols and Software
Our experimental protocols can be found on our Protocols.io
Our code and data analysis packages are located on our GitHub
News and Highlights
Recent news, updates and celebrations are posted on our LinkedIn
Get in touch with us
Dr. Felix Hartmann
Group LeaderPostal address: