Dr Antoine-Emmanuel Saliba

Single-cell Analysis

The research group led by Emmanuel Saliba explores host-pathogen interactions in high resolution at the single-cell level. They develop and integrate single-cell genomics, imaging and computational approaches to decipher the microenvironments of individual pathogens and shed light on the heterogeneity of host responses and disease outcomes.

Our research and approach

Novel technological leaps are enabling scientists to chart a comprehensive map of the cells across the body, to define their states and to determine their responses to infectious agents in unprecedented detail. Yet how a host either contains the spread of a pathogen, or subsets of pathogens escape host immune surveillance still remains poorly understood.

Emmanuel Saliba’s group investigates RNA and RNA processing as a read-out to determine the cell state of both hosts and pathogens at the single-cell level. Their work, involving pathogens such as Salmonella and respiratory viruses with cell culture models, organoids, and clinical samples, analyses, categorizes and clusters cells to decipher cellular microenvironments and understand infectious disease progression.

They employ single-cell RNA seq, spatial transcriptomics, and RNA imaging to capture the RNA transcript census expressed within a host and pathogen. Further temporal single-cell analysis using RNA metabolic labelling provides insights into the history of a cell. These high-resolution analyses potentially enable the prediction of cell behavior and can unlock gene regulatory networks underlying infectious processes. This work is key in the development of precision diagnostics and therapeutics.

Team members

Fabian Imdahl

Fabian Imdahl

PhD Student

Oliver Dietrich

Oliver Dietrich

PhD Student

Tobias Krammer

Tobias Krammer

PhD Student

Nina DiFabion

Nina DiFabion

Technical Assistant

Research projects

Persistent bacterial infections are caused by a minor subpopulation of intracellular pathogens, called ‘persisters’, that reside in different cell types and tissue locations for years asymptomatically. These subpopulations establish a specific cellular organization, which enables them to evade immune surveillance and chemotherapeutic treatment. Histological studies have described complex tissue remodelling during the infection and emerging in vivo studies at the single-cell level have begun to reveal the heterogeneity of infection foci. 

However, the cellular architecture of the infection foci and the identification of favoured niches within this complex tissue landscape that impact disease outcome remain open questions. For example, Salmonella are believed to reside in a large variety of cells including macrophages, neutrophils, dendritic cells and epithelial cells. These large cell types exist as a myriad of different sub-classes, which were - until recently - not appreciated. Similarly, within an infected tissue such as the spleen many infected cells escape inflammatory lesions and disseminate into tissues. Therefore, single-cell studies in an in vivo context are necessary to understand the heterogeneity inherent in infected cells, their microenvironment and their function. The Single-cell Analysis group develops and combines in vitro and in vivo single-cell transcriptomics to decipher the cellular organization of infection foci and their functional consequences for infection outcome.

The recent emergence of single-cell genome-wide transcriptomics is proving to be a powerful approach to decipher both cellular identities and function making it possible to study heterogeneity. This is being facilitated by the development of automated platforms that enable the processing of hundreds and thousands of single-cells in parallel. In the context of infection we have pioneered the use of single-cell RNA-seq to investigate heterogeneity in the response of mouse bone marrow-derived macrophages to Salmonella focusing on bacteria with different growth status including non-growing ‘persisters’ that have been linked to recurrent infections. We have described how Salmonella impact the wide spectrum of host polarization and revealed the existence of a subset of macrophages that escape inflammatory and immune activation programs. While providing new insights into the host response, the study was limited to analyzing infected cells from in vitro cultures. The next step is now to decipher the response of single cells of infected tissues, which remains an unmet challenge.

Moreover, the Single-cell Analysis group is fully committed to developing the full potential of single-cell RNA-seq for addressing fundamental scientific questions of infection biology in general, at the HIRI as well as at other locations of the HZI.



Homozygous BCMA gene deletion in response to anti-BCMA CAR T cells in a patient with multiple myeloma

Da Vià MC, Dietrich O, Truger M, Arampatzi P, Duell J, Heidemeier A, Zhou X, Danhof S, Kraus S, Chatterjee M, …, Saliba A, Rasche L (2021)

Nature Medicine 27 (4): 616-619

Opposing Wnt signals regulate cervical squamocolumnar homeostasis and emergence of metaplasia

Chumduri C, Gurumurthy RK, Berger H, Dietrich O, Kumar N, Koster S, Brinkmann V, Hoffmann K, Drabkina M, Arampatzi P, …, Saliba A, Meyer TF (2021)

Nature Cell Biology 23 (2): 184

The healing myocardium mobilises a distinct B-cell subset through a CXCL13-CXCR5-dependent mechanism

Heinrichs M, Ashour D, Siegel J, Büchner L, Wedekind G, Heinze KG, Arampatzi P, Saliba A, Cochain C, Hofmann U, Frantz S, Ramos GC (2021)

Cardiovascular research (Online ahead of print)

Time-Resolved scRNA-Seq Tracks the Adaptation of a Sensitive MCL Cell Line to Ibrutinib Treatment

Fuhr V, Vafadarnejad E, Dietrich O, Arampatzi P, Riedel A, Saliba A, Rosenwald A, Rauert-Wunderlich H (2021)

International journal of molecular sciences 22 (5): 2276

Initial HCV infection of adult hepatocytes triggers a temporally structured transcriptional program containing diverse pro- and anti-viral elements

Tegtmeyer B, Vieyres G, Todt D, Lauber C, Ginkel C, Engelmann M, Herrmann M, Pfaller CK, Vondran FW, Broering R, …, Pietschmann T, Brown RJ (2021)

Journal of Virology (Online ahead of print)

A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity

Bernhardt L, Dittrich M, El-Merahbi R, Saliba A, Müller T, Sumara G, Vogel J, Nichols-Burns S, Mitchell M, Haaf T, El Hajj N (2021)

Scientific Reports 11: 1979


Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Bernardes JP, Mishra N, Tran F, Bahmer T, Best L, Blase JI, Bordoni D, Franzenburg J, Geisen U, Josephs-Spaulding J, …, Schultze JL, Rosenstiel P (2020)

Immunity 53 (6): 1296-1314

Dynamics of Cardiac Neutrophil Diversity in Murine Myocardial Infarction

Vafadarnejad E, Rizzo G, Krampert L, Arampatzi P, Arias-Loza A, Nazzal Y, Rizakou A, Knochenhauer T, Bandi SR, Nugroho VA, …, Saliba AE, Cochain C (2020)

Circulation Research 127 (9): 232-249

LifeTime and improving European healthcare through cell-based interceptive medicine

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, …, Vidal M, Voet T (2020)

Nature 587 (7834): 377-386

Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria

Imdahl F, Vafadarnejad E, Homberger C, Saliba AE, Vogel J (2020)

Nature Microbiology 5 (10): 1202

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, …, Saliba AE, Sander LE (2020)

Cell 182 (6): 1419-1440

Eleven grand challenges in single-cell data science

Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, …, Shah SP, Schönhuth A (2020)

Genome Biology 21: 31

Advances and challenges in single-cell RNA-seq of microbial communities

Imdahl F, Saliba A (2020)

Current Opinion in Microbiology 57: 102-110

Tracheal brush cells release acetylcholine in response to bitter tastants for paracrine and autocrine signaling

Hollenhorst MI, Jurastow I, Nandigama R, Appenzeller S, Li L, Vogel J, Wiederhold S, Althaus M, Empting M, Altmüller J, …, Saliba AE, Krasteva-Christ G (2020)

The FASEB Journal 34 (1): 316-332


scSLAM-seq reveals core features of transcription dynamics in single cells

Erhard F, Baptista MA, Krammer T, Hennig T, Lange M, Arampatzi P, Jürges CS, Theis FJ, Saliba AE, Dölken L (2019)

Nature 571 (7765): 419-423


Salmonella persisters undermine host immune defenses during antibiotic treatment

Stapels DA, Hill PW, Westermann AJ, Fisher RA, Thurston TL, Saliba AE, Blommestein I, Vogel J, Helaine S (2018)

Science 362 (6419): 1156-1160

Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes

Pezoldt J, Pasztoi M, Zou M, Wiechers C, Beckstette M, Thierry GR, Vafadarnejad E, Floess S, Arampatzi P, Buettner M, …, Saliba AE, Huehn J (2018)

Nature Communications 9: 3903

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis

Cochain C, Vafadarnejad E, Arampatzi P, Pelisek J, Winkels H, Ley K, Wolf D, Saliba AE, Zernecke A (2018)

Circulation Research 122 (12): 1661-1674

Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry

Winkels H, Ehinger E, Vassallo M, Buscher K, Dinh HQ, Kobiyama K, Hamers AA, Cochain C, Vafadarnejad E, Saliba AE, …, Ley K, Wolf D (2018)

Circulation Research 122 (12): 1675-1688

Genome organization and DNA accessibility control antigenic variation in trypanosomes

Müller LS, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, …, Sebra RP, Siegel TN (2018)

Nature 563 (7729): 121-125

Tolerogenic Transcriptional Signatures of Steady-State and Pathogen-Induced Dendritic Cells

Vendelova E, Ashour D, Blank P, Erhard F, Saliba A, Kalinke U, Lutz MB (2018)

Frontiers in Immunology 9: 333


Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess

Saliba AE, Westermann AJ, Vogel J (2017)

BIOspektrum 23 (5): 525-528

New RNA-seq approaches for the study of bacterial pathogens

Saliba AE, Santos SC, Vogel J (2017)

Current Opinion in Microbiology 35: 78-87


A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin A (2016)

Nature Protocols 11 (6): 1021-38

Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella

Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DA, Schulte LN, Helaine S, Vogel J (2016)

Nature Microbiology 2: 16206


The systematic analysis of protein-lipid interactions comes of age

Saliba AE, Vonkova I, Gavin A (2015)

Nature Reviews Molecular Cell Biology 16 (12): 753-61

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains

Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, …, Bork P, Gavin A (2015)

Cell Reports 12 (9): 1519-30


A quantitative liposome microarray to systematically characterize protein-lipid interactions

Saliba AE, Vonkova I, Ceschia S, Findlay GM, Maeda K, Tischer C, Deghou S, van Noort V, Bork P, Pawson T, Ellenberg J, Gavin A (2014)

Nature Methods 11 (1): 47-50

Single-cell RNA-seq: advances and future challenges

Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014)

Nucleic Acids Research 42 (14): 8845-60


Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays

Saliba AE, Saias L, Psychari E, Minc N, Simon D, Bidard F, Mathiot C, Pierga J, Fraisier V, Salamero J, …, Malaquin L, Viovy J (2010)

Proceedings of the National Academy of Sciences of the United States of America 107 (33): 14524-9


Cellules tumorales circulantes et cancer du sein : méthodes de détection et résultats cliniques

Bidard F, Saliba AE, Saias L, Degeorges A, Cremoux Pd, Viovy J, Vincent-Salomon A, Mathiot C, Pierga J, Gramont A (2009)

Bulletin du Cancer 96 (1): 73-86


Nanotechnology serving biochips – The Toulouse example

Vieu C, Malaquin L, Thibault C, Saliba AE, Daran E, Dildan M, Carcenac F, Leberre V, Trevisiol E, François JM (2004)

Biofutur (250): 41-45