Prof. Antoine-Emmanuel Saliba
Über
Antoine-Emmanuel Saliba studierte Bioverfahrenstechnik am Institut National des Sciences Appliqués (INSA) in Toulouse (Frankreich) und promovierte in der Forschungsgruppe von Jean-Louis Viovy am Institut Curie in Paris. Er setzte mikrofluidbasierte Systeme zur Sortierung und Analyse seltener Subpopulationen von Krebszellen ein. Anschließend arbeitete er als Stipendiat der interdisziplinären Postdoc Initiative (EIPOD) des Europäischen Laboratoriums für Molekularbiologie (EMBL) in Heidelberg. Dort war er an der Entwicklung innovativer systembiologischer Ansätze zur Analyse von Protein-Lipid-Wechselwirkungen beteiligt. Als Postdoc kam er anschließend ans Labor von Jörg Vogel in Würzburg und etablierte dort die Technologie der Einzelzell-RNA-Sequenzierung. Mit deren Hilfe verfolgte er beispielsweise das Schicksal einzelner Zellen während einer Infektion mit Salmonella enterica. Seit 2017 leitet er die Gruppe Einzelzellanalyse am HIRI. Er ist seit 2023 außerdem Professor (W2) an der Medizinischen Fakultät der Universität Würzburg.
2024
Human cytomegalovirus exploits STING signaling and counteracts IFN/ISG induction to facilitate infection of dendritic cells
Costa B, Becker J, Krammer T, Mulenge F, Durán V, Pavlou A, Gern OL, Chu X, Li Y, Cicin-Šain L, …, Erhard F, Kalinke U (2024)
Nature Communications 15 (1): 1745DOI: 10.1038/s41467-024-45614-3
2023
Sequential Antigen-loss and Branching Evolution in Lymphoma after CD19- and CD20-Targeted T-cell Redirecting Therapy
Duell J, Leipold AM, Appenzeller S, Fuhr V, Rauert-Wunderlich H, Da Vià MC, Dietrich O, Toussaint C, Imdahl F, Eisele F, …, Saliba AE, Rasche L (2023)
Blood 143 (8): 685-696DOI: 10.1182/blood.2023021672
Brain-to-gut trafficking of alpha-synuclein by CD11c+ cells in a mouse model of Parkinson's disease
McFleder RL, Makhotkina A, Groh J, Keber U, Imdahl F, Peña Mosca J, Peteranderl A, Wu J, Tabuchi S, Hoffmann J, …, Volkmann J, Ip CW (2023)
Nature Communications 14 (1): 7529DOI: 10.1038/s41467-023-43224-z
Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms
Reuter C, Hauf L, Imdahl F, Sen R, Vafadarnejad E, Fey P, Finger T, Jones NG, Walles H, Barquist L, …, Groeber-Becker F, Engstler M (2023)
Nature Communications 14 (1): 7660DOI: 10.1038/s41467-023-43437-2
Microglia-mediated demyelination protects against CD8+ T cell-driven axon degeneration in mice carrying PLP defects
Groh J, Abdelwahab T, Kattimani Y, Hörner M, Loserth S, Gudi V, Adalbert R, Imdahl F, Saliba AE, Coleman M, …, Simons M, Martini R (2023)
Nature Communications 14 (1): 6911DOI: 10.1038/s41467-023-42570-2
Genetic inhibition of CARD9 accelerates the development of atherosclerosis in mice through CD36 dependent-defective autophagy
Zhang Y, Vandestienne M, Lavillegrand JR, Joffre J, Santos-Zas I, Lavelle A, Zhong X, Le Goff W, Guérin M, Al-Rifai R, …, Sokol H, Ait-Oufella H (2023)
Nature Communications 14 (1): 4622DOI: 10.1038/s41467-023-40216-x
Short-range interactions between fibrocytes and CD8+ T cells in COPD bronchial inflammatory response
Eyraud E, Maurat E, Sac-Epée JM, Henrot P, Zysman M, Esteves P, Trian T, Dupuy JW, Leipold A, Saliba AE, …, Berger P, Dupin I (2023)
eLife 12: RP85875DOI: 10.7554/eLife.85875
Lymph node medulla regulates the spatiotemporal unfolding of resident dendritic cell networks
Ugur M, Labios RJ, Fenton C, Knöpper K, Jobin K, Imdahl F, Golda G, Hoh K, Grafen A, Kaisho T, …, Bajénoff M, Kastenmüller W (2023)
Immunity 58 (8): 1778-1793.e10DOI: 10.1016/j.immuni.2023.06.020
Cytotoxic CNS-associated T cells drive axon degeneration by targeting perturbed oligodendrocytes in PLP1 mutant mice
Abdelwahab T, Stadler D, Knöpper K, Arampatzi P, Saliba AE, Kastenmüller W, Martini R, Groh J (2023)
iScience 26 (5): 106698DOI: 10.1016/j.isci.2023.106698
An interferon gamma response signature links myocardial aging and immunosenescence
Ashour D, Rebs S, Arampatzi P, Saliba AE, Dudek J, Schulz R, Hofmann U, Frantz S, Cochain C, Streckfuß-Bömeke K, Ramos GC (2023)
Cardiovascular Research 119 (14): 2458-2468DOI: 10.1093/cvr/cvad068
Advancing massive transcriptional profiling of single bacteria
Saliba AE (2023)
Cell Reports Methods 3 (2): 100416DOI: 10.1016/j.crmeth.2023.100416
A primary cell-based in vitro model of the human small intestine reveals host olfactomedin 4 induction in response to Salmonella Typhimurium infection
Däullary T, Imdahl F, Dietrich O, Hepp L, Krammer T, Fey C, Neuhaus W, Metzger M, Vogel J, Westermann AJ, Saliba AE, Zdzieblo D (2023)
Gut Microbes 15 (1): 2186109DOI: 10.1080/19490976.2023.2186109
Th17.1 cell driven sarcoidosis-like inflammation after anti-BCMA CAR T cells in multiple myeloma
Leipold AM, Werner RA, Düll J, Jung P, John M, Stanojkovska E, Zhou X, Hornburger H, Ruckdeschel A, Dietrich O, …, Saliba AE, Rasche L (2023)
Leukemia 37 (3): 650-658DOI: 10.1038/s41375-023-01824-0
Myocardial Milieu Favors Local Differentiation of Regulatory T Cells
Delgobo M, Weiß E, ElDin Ashour D, Richter L, Popiolkowski L, Arampatzi P, Stangl V, Arias-Loza P, Mariotti-Ferrandiz E, Rainer PP, …, Frantz S, Campos Ramos G (2023)
Circulation Research 132 (5): 565-582DOI: 10.1161/CIRCRESAHA.122.322183
Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19
Zhang B, Zhang Z, Koeken VACM, Kumar S, Aillaud M, Tsay HC, Liu Z, Kraft ARM, Soon CF, Odak I, …, Schulte LN, Li Y (2023)
Cell Genomics 3 (2): 100232DOI: 10.1016/j.xgen.2022.100232
A MATQ-seq-Based Protocol for Single-Cell RNA-seq in Bacteria
Homberger C, Saliba AE, Vogel J (2023)
Methods in Molecular Biology 2584: 105-121DOI: 10.1007/978-1-0716-2756-3_4
Integrated single-cell analysis based classification of vascular mononuclear phagocytes in mouse and human atherosclerosis
Zernecke A, Erhard F, Weinberger T, Schulz C, Ley K, Saliba AE, Cochain C (2023)
Cardiovascular Research 119 (8): 1676-1689DOI: 10.1093/cvr/cvac161
Dynamics of monocyte-derived macrophage diversity in experimental myocardial infarction
Rizzo G, Gropper J, Piollet M, Vafadarnejad E, Rizakou A, Bandi SR, Arampatzi P, Krammer T, DiFabion N, Dietrich O, …, Saliba AE, Cochain C (2023)
Cardiovascular Research 119 (3): 772-785DOI: 10.1093/cvr/cvac113
Rapid neutrophil mobilisation by VCAM-1+ endothelial extracellular vesicles
Akbar N, Braithwaite AT, Corr EM, Koelwyn GJ, van Solingen C, Cochain C, Saliba AE, Corbin A, Pezzolla D, Møller Jørgensen M, …, Melling GE, Shanmuganathan M (2023)
Cardiovascular Research 119 (1): 236-251DOI: 10.1093/cvr/cvac012
2022
JAK2V617F mutation drives vascular resident macrophages toward a pathogenic phenotype and promotes dissecting aortic aneurysm
Al-Rifai R, Vandestienne M, Lavillegrand JR, Mirault T, Cornebise J, Poisson J, Laurans L, Esposito B, James C, Mansier O, …, Rautou PE, Ait-Oufella H (2022)
Nature Communications 13 (1): 6592DOI: 10.1038/s41467-022-34469-1
Postnatal expansion of mesenteric lymph node stromal cells towards reticular and CD34+ stromal cell subsets
Pezoldt J, Wiechers C, Zou M, Litovchenko M, Biocanin M, Beckstette M, Sitnik K, Palatella M, van Mierlo G, Chen W, …, Deplancke B, Huehn J (2022)
Nature Communications 13 (1): 7227DOI: 10.1038/s41467-022-34868-4
Time-resolved single-cell RNA-seq using metabolic RNA labelling
Erhard F, Saliba AE, Lusser A (2022)
Nature Reviews Methods Primers 2 (1): 331DOI: 10.1038/s43586-022-00157-z
Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis
Aguilar C, Pauzuolis M, Pompaiah M, Vafadarnejad E, Arampatzi P, Fischer M, Narres D, Neyazi M, Kayisoglu Ö, Sell T, …, Saliba AE, Bartfeld S (2022)
Nature Communications 13 (1): 5878DOI: 10.1038/s41467-022-33165-4
Eine Einzelzell-RNA-Sequenzierung identifiziert Metabolismus und CD52 als neue Angriffspunkte in Ibrutinib-persistenten Mantelzelllymphomzellen
Fuhr V, Vafadarnejad E, Dietrich O, Arampatzi P, Riedel A, Saliba AE, Rosenwald A, Rauert-Wunderlich H (2022)
Die Pathologie 43 (1): 31–35DOI: 10.1007/s00292-022-01136-7
Fibroblastic reticular cells mitigate acute graft-versus-host disease via MHCII-dependent maintenance of regulatory T cells
Shaikh H, Pezoldt J, Mokhtari Z, Gamboa Vargas J, Le DD, Peña Mosca J, Arellano-Viera E, Kern MA, Graf C, Beyersdorf N, …, Huehn J, Beilhack A (2022)
JCI Insight 7 (22): e154250DOI: 10.1172/jci.insight.154250
Landscape and age dynamics of immune cells in the Egyptian rousette bat
Friedrichs V, Toussaint C, Schäfer A, Rissmann M, Dietrich O, Mettenleiter TC, Pei G, Balkema-Buschmann A, Saliba AE, Dorhoi A (2022)
Cell Reports 40 (10): 111305DOI: 10.1016/j.celrep.2022.111305
Nonproductive exposure of PBMCs to SARS-CoV-2 induces cell-intrinsic innate immune responses
Kazmierski J, Friedmann K, Postmus D, Emanuel J, Fischer C, Jansen J, Richter A, Bosquillon de Jarcy L, Schüler C, Sohn M, …, Niemeyer D, Goffinet C (2022)
Molecular Systems Biology 18 (8): e10961DOI: 10.15252/msb.202210961
Lymphatic migration of unconventional T cells promotes site-specific immunity in distinct lymph nodes
Ataide MA, Knöpper K, Cruz de Casas P, Ugur M, Eickhoff S, Zou M, Shaikh H, Trivedi A, Grafen A, Yang T, …, Gasteiger G, Kastenmüller W (2022)
Immunity 55 (10): 1813–1828.e9DOI: 10.1016/j.immuni.2022.07.019
Complement activation induces excessive T cell cytotoxicity in severe COVID-19
Georg P, Astaburuaga-García R, Bonaguro L, Brumhard S, Michalick L, Lippert LJ, Kostevc T, Gäbel C, Schneider M, Streitz M, …, Sawitzki B, PA-COVID-19 Study Group (2022)
Cell 185 (3): 493-512.e25DOI: 10.1016/j.cell.2021.12.040
Type 1 conventional dendritic cells maintain and guide the differentiation of precursors of exhausted T cells in distinct cellular niches
Dähling S, Mansilla AM, Knöpper K, Grafen A, Utzschneider DT, Ugur M, Whitney PG, Bachem A, Arampatzi P, Imdahl F, …, Bedoui S, Kastenmüller W (2022)
Immunity 55 (4): 656-670.e8DOI: 10.1016/j.immuni.2022.03.006
Interleukin-23 receptor expressing γδ T cells locally promote early atherosclerotic lesion formation and plaque necrosis in mice
Gil-Pulido J, Amézaga N, Jorgacevic I, Manthey HD, Rösch M, Brand T, Cidlinsky P, Schäfer S, Beilhack A, Saliba AE, …, Cochain C, Zernecke A (2022)
Cardiovascular Research 118 (14): 2932-2945DOI: 10.1093/cvr/cvab359
2021
Effector differentiation downstream of lineage commitment in ILC1s is driven by Hobit across tissues
Friedrich C, Taggenbrock RLRE, Doucet-Ladevèze R, Golda G, Moenius R, Arampatzi P, Kragten NAM, Kreymborg K, Gomez de Agüero M, Kastenmüller W, …, van Gisbergen KPJM, Gasteiger G (2021)
Nature Immunology 22 (10): 1256-1267DOI: 10.1038/s41590-021-01013-0
Dysregulated Immunometabolism Is Associated with the Generation of Myeloid-Derived Suppressor Cells in Staphylococcus aureus Chronic Infection
Dietrich O, Heinz A, Goldmann O, Geffers R, Beineke A, Hiller K, Saliba AE, Medina E (2021)
Journal of Innate Immunity: 1-18DOI: 10.1159/000519306
SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis
Wendisch D, Dietrich O, Mari T, von Stillfried S, Ibarra IL, Mittermaier M, Mache C, Chua RL, Knoll R, Timm S, …, Saliba AE, Sander LE (2021)
Cell 184 (26): 6243-6261.e27DOI: 10.1016/j.cell.2021.11.033
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 AE, Cochain C, Hofmann U, Frantz S, Campos Ramos G (2021)
Cardiovascular Research 117 (13): 2664-2676DOI: 10.1093/cvr/cvab181
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 AE, Rosenwald A, Rauert-Wunderlich H (2021)
International Journal of Molecular Sciences 22 (5): 2276DOI: 10.3390/ijms22052276
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 AE, Rasche L (2021)
Nature Medicine 27 (4): 616-619DOI: 10.1038/s41591-021-01245-5
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 95 (10)DOI: 10.1128/JVI.00245-21
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 AE, Müller T, Sumara G, Vogel J, Nichols-Burns S, Mitchell M, Haaf T, El Hajj N (2021)
Scientific Reports 11: 1979DOI: 10.1038/s41598-021-81226-3
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 AE, Meyer TF (2021)
Nature Cell Biology 23 (2): 184–197DOI: 10.1038/s41556-020-00619-0
2020
Advances and challenges in single-cell RNA-seq of microbial communities
Imdahl F, Saliba A (2020)
Current Opinion in Microbiology 57: 102-110DOI: 10.1016/j.mib.2020.10.001
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): e232-249DOI: 10.1161/CIRCRESAHA.120.317200
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): 1202–1206DOI: 10.1038/s41564-020-0774-1
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): 1419-1440DOI: 10.1016/j.cell.2020.08.001
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): 316-332DOI: 10.1096/fj.201901314RR
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: 31DOI: 10.1186/s13059-020-1926-6
2019
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): 419-423DOI: 10.1038/s41586-019-1369-y
2018
Tolerogenic Transcriptional Signatures of Steady-State and Pathogen-Induced Dendritic Cells
Vendelova E, Ashour D, Blank P, Erhard F, Saliba AE, Kalinke U, Lutz MB (2018)
Frontiers in Immunology 9: 333DOI: 10.3389/fimmu.2018.00333
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: 3903DOI: 10.1038/s41467-018-06423-7
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): 1156-1160DOI: 10.1126/science.aat7148
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): 1661-1674DOI: 10.1161/CIRCRESAHA.117.312509
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): 1675-1688DOI: 10.1161/CIRCRESAHA.117.312513
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): 121-125DOI: 10.1038/s41586-018-0619-8
2017
Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess
Saliba AE, Westermann AJ, Vogel J (2017)
BIOspektrum 23 (5): 525-528DOI: 10.1007/s12268-017-0836-y
New RNA-seq approaches for the study of bacterial pathogens
Saliba AE, Santos SC, Vogel J (2017)
Current Opinion in Microbiology 35: 78-87DOI: 10.1016/j.mib.2017.01.001
2016
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): 1021-38DOI: 10.1038/nprot.2016.059
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: 16206DOI: 10.1038/nmicrobiol.2016.206
2015
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): 1519-30DOI: 10.1016/j.celrep.2015.07.054
The systematic analysis of protein-lipid interactions comes of age
Saliba AE, Vonkova I, Gavin A (2015)
Nature Reviews Molecular Cell Biology 16 (12): 753-61DOI: 10.1038/nrm4080
2014
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): 47-50DOI: 10.1038/nmeth.2734
Single-cell RNA-seq: advances and future challenges
Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014)
Nucleic Acids Research 42 (14): 8845-60DOI: 10.1093/nar/gku555
2010
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)
PNAS 107 (33): 14524-9DOI: 10.1073/pnas.1001515107
2009
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): 73-86DOI: 10.1684/bdc.2008.0797
2004
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