Turn single-cell data into immunological insights


A system-view of Bordetella pertussis booster vaccine responses in adults primed with whole-cell versus acellular vaccine in infancy

Ricardo da Silva Antunes, Ferran Soldevila, Mikhail Pomaznoy, Mariana Babor, Jason Bennett, Yuan Tian, Natalie Khalil, Yu Qian, Aishwarya Mandava, Richard H Scheuermann, Mario Cortese, Bali Pulendran, Christopher D Petro, Adrienne P Gilkes, Lisa A Purcell, Alessandro Sette, and Bjoern Peters

JCI Insight . 2021 Apr 8;6(7):141023.

The increased incidence of whooping cough worldwide suggests that current vaccination against Bordetella pertussis infection has limitations in quality and duration of protection. The resurgence of infection has been linked to the introduction of acellular vaccines (aP), which have an improved safety profile compared with the previously used whole-cell (wP) vaccines. To determine immunological differences between aP and wP priming in infancy, we performed a systems approach of the immune response to booster vaccination. Transcriptomic, proteomic, cytometric, and serologic profiling revealed multiple shared immune responses with different kinetics across cohorts, including an increase of blood monocyte frequencies and strong antigen-specific IgG responses. Additionally, we found a prominent subset of aP-primed individuals (30%) with a strong differential signature, including higher levels of expression for CCL3, NFKBIA, and ICAM1. Contrary to the wP individuals, this subset displayed increased PT-specific IgE responses after boost and higher antigen-specific IgG4 and IgG3 antibodies against FHA and FIM2/3 at baseline and after boost. Overall, the results show that, while broad immune response patterns to Tdap boost overlap between aP- and wP-primed individuals, a subset of aP-primed individuals present a divergent response. These findings provide candidate targets to study the causes and correlates of waning immunity after aP vaccination.

...Show more>>

Molecular Signatures of Dengue Virus-Specific IL-10/IFN-γ Co-producing CD4 T Cells and Their Association with Dengue Disease

Yuan Tian, Grégory Seumois, Luzia M De-Oliveira-Pinto, Jose Mateus, Sara Herrera-de la Mata, Cheryl Kim, Denise Hinz, ND Suraj Goonawardhana, Aruna D de Silva, Sunil Premawansa, Gayani Premawansa, Ananda Wijewickrama, Angel Balmaseda, Alba Grifoni, Pandurangan Vijayanand, Eva Harris, Bjoern Peters, Alessandro Sette, and Daniela Weiskopf

Cell Rep. 2019 Dec 24;29(13):4482-4495.e4.

Dengue virus (DENV) can cause diseases ranging from dengue fever (DF) to more severe dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). Whether antiviral T cells contribute to the protection against or pathogenesis of severe disease is not well defined. Here, we identified antigen-specific IL-10+IFN-γ+ double-positive (DP) CD4 T cells during acute DENV infection. While the transcriptomic signatures of DP cells partially overlapped with those of cytotoxic and type 1 regulatory CD4 T cells, the majority of them were non-cytotoxic/Tr1 and included IL21, IL22, CD109, and CCR1. Although we observed a higher frequency of DP cells in DHF, the transcriptomic profile of DP cells was similar in DF and DHF, suggesting that DHF is not associated with the altered phenotypic or functional attributes of DP cells. Overall, this study revealed a DENV-specific DP cell subset in patients with acute dengue disease and argues against altered DP cells as a determinant of DHF.

...Show more>>

Transcriptomic immune-profiles of human flavivirus specific T cell responses

Alba Grifoni, Yuan Tian, Alessandro Sette, and Daniela Weiskopf

Immunology. 2019 Nov 28.

The Flavivirus genus of viruses includes dengue (DENV), Zika (ZIKV), yellow fever (YFV), Japanese encephalitis (JEV), and West Nile (WNV) viruses. Infections with those species combined are prevalent in tropical and sub-tropical areas affecting millions of people ranging from asymptomatic to severe form of the disease and thus posing a serious threat to global public health. Several studies imply a role for T cells in the protection but also pathogenesis against the different flavivirus species. Identifying flavivirus specific T cell immune profiles and determine how pre-exposure of one species might affect the immune response against subsequent infections from other species is important to further define the role of T cells in the immune response against infection. Understanding the immune-profiles of flavivirus specific T cell response in natural infection is important to understand the T cell response in the context of vaccination. In this review, we summarize the current knowledge on human immune-profiles of flavivirus-specific T cell reactivity comparing natural infection with the acute form of the disease and vaccination comparing them in different flavivirus infection.

...Show more>>

Human T Cell Response to Dengue Virus Infection

Yuan Tian, Alba Grifoni, Alessandro Sette, and Daniela Weiskopf

Front. Immunol., 04 September 2019

DENV is a major public health problem worldwide, thus underlining the overall significance of the proposed Program. The four dengue virus (DENV) serotypes (1–4) cause the most common mosquito-borne viral disease of humans, with 3 billion people at risk for infection and up to 100 million cases each year, most often affecting children. The protective role of T cells during viral infection is well-established. Generally, CD8 T cells can control viral infection through several mechanisms, including direct cytotoxicity, and production of pro-inflammatory cytokines such as IFN-γ and TNF-α. Similarly, CD4 T cells are thought to control viral infection through multiple mechanisms, including enhancement of B and CD8 T cell responses, production of inflammatory and anti-viral cytokines, cytotoxicity, and promotion of memory responses. To probe the phenotype of virus-specific T cells, epitopes derived from viral sequences need to be known. Here we discuss the identification of CD4 and CD8 T cell epitopes derived from DENV and how these epitopes have been used by researchers to interrogate the phenotype and function of DENV-specific T cell populations.

...Show more>>

A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer

Brian H Lee, Geoffrey Kelly, Shermineh Bradford, Melanie Davila, Xinzheng V Guo, El-ad David Amir, Emily M Thrash, Michael Solga, Joanne Lannigan, Brian Sellers, Julian Candia, John Tsang, Ruth Montgomery, Stanley Tamaki, Tara Sigdel, Minnie Sarwal, Lewis Lanier, Yuan Tian, Cheryl Kim, Denise Hinz, Bjoern Peters, Alessandro Sette, and Adeeb Rahman

Cytometry A. 2019 Jul 30

Mass cytometry is a powerful tool for high dimensional single cell characterization. Since the introduction of the first commercial CyTOF mass cytometer by DVS Sciences in 2009, mass cytometry technology has matured and become more widely utilized, with sequential platform upgrades designed to address specific limitations and to expand the capabilities of the platform. The 3rd generation Fluidigm Helios mass cytometer introduced a number of upgrades over the previous CyTOF2. One of these new features is a modified narrow bore sample injector that generates smaller ion clouds, which is expected to improve sensitivity and throughput. However, following rigorous testing we find that the narrow-bore sample injector may have unintended negative consequences on data quality and result in lower median signal intensities and higher coefficients of variation in antibody expression. We describe an alternative Helios acquisition protocol using a wider bore injector, which largely mitigates these data quality issues. We directly compare these two protocols in a multi-site study of 10 Helios instruments across 7 institutions and show that the modified protocol improves data quality and reduces inter-instrument variability. These findings highlight and address an important source of technical variability in mass cytometry experiments that is of particular relevance in the setting of multi-center studies.

...Show more>>

Dengue-specific CD8+ T cell subsets display specialized transcriptomic and TCR profiles

Yuan Tian, Mariana Babor, Jerome Lane, Grégory Seumois, Shu Liang, ND Suraj Goonawardhana, Aruna D De Silva, Elizabeth J Phillips, Simon A Mallal, Ricardo da Silva Antunes, Alba Grifoni, Pandurangan Vijayanand, Daniela Weiskopf, Bjoern Peters, and Alessandro Sette

J Clin Invest. 2019 Mar 18;130. pii: 123726.

Accumulating evidence demonstrates that CD8+ T cells contribute to protection from severe dengue virus (DENV) disease and vaccine efficacy. Nevertheless, molecular programs associated with DENV-specific CD8+ T cell subsets have not been defined. Here, we studied the transcriptomic profiles of human DENV-specific CD8+ T cells isolated after stimulation with DENV epitopes from donors who had been infected with DENV multiple times and would therefore be expected to have significant levels of adaptive immunity. We found that DENV-specific CD8+ T cells mainly consisted of effector memory subsets, namely CD45RA−CCR7− effector memory (Tem) and CD45RA+CCR7− effector memory re-expressing CD45RA (Temra) cells, which enacted specific gene expression profiles upon stimulation with cognate antigens. DENV-specific CD8+ T cell subsets in general, and Temra cells in particular, were fully activated and polyfunctional, yet associated with relatively narrow transcriptional responses. Furthermore, we found that DENV-specific CD8+ Tem and Temra cells showed some unique T cell receptor features in terms of overlap and variable (V) gene usage. This study provides a transcriptomic definition of DENV-specific activated human CD8+ T cell subsets and defines a benchmark profile that vaccine-specific responses could aim to reproduce.

...Show more>>

A Review on T Cell Epitopes Identified Using Prediction and Cell-Mediated Immune Models for Mycobacterium tuberculosis and Bordetella pertussis

Yuan Tian, Ricardo Filipe Da Silva Antunes, John Sidney, Cecilia S Lindestam Arlehamn, Alba Grifoni, Sandeep Kumar Dhanda, Sinu Paul, Bjoern Peters, Daniela Weiskopf, and Alessandro Sette

Front Immunol. 2018 Nov 29;9:2778.

In the present review, we summarize work from our as well as other groups related to the characterization of bacterial T cell epitopes, with a specific focus on two important pathogens, namely, Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), and Bordetella pertussis (BP), the bacterium that causes whooping cough. Both bacteria and their associated diseases are of large societal significance. Although vaccines exist for both pathogens, their efficacy is incomplete. It is widely thought that defects and/or alteration in T cell compartments are associated with limited vaccine effectiveness. As discussed below, a full genome-wide map was performed in the case of Mtb. For BP, our focus has thus far been on the antigens contained in the acellular vaccine; a full genome-wide screen is in the planning stage. Nevertheless, the sum-total of the results in the two different bacterial systems allows us to exemplify approaches and techniques that we believe are generally applicable to the mapping and characterization of human immune responses to bacterial pathogens. Finally, we add, as a disclaimer, that this review by design is focused on the work produced by our laboratory as an illustration of approaches to the study of T cell responses to Mtb and BP, and is not meant to be comprehensive, nor to detract from the excellent work performed by many other groups.

...Show more>>

Immuno-proteomic interrogation of dengue infection reveals novel HLA haplotype-specific MHC-I antigens

Kavya Swaminathan, Niclas Olsson, Peder J Lund, Caleb D Marceau, Lisa E Wagar, Yuan Tian, John Sidney, Daniela Weiskopf, Karim Majzoub, Eva Harris, Mark M Davis, Alessandro Sette, Jan E Carette, and Joshua E Elias


Broadly effective vaccines against dengue virus (DENV) infection have remained elusive, despite rising infection rates in the developing world. Infection-specific peptide ligands presented on Major Histocompatibility Complexes (MHC) open new avenues for developing T-cell-based interventions. Past efforts towards mapping viral MHC epitopes were based on computational predictions that only partially reflected actual antigen presentation. To empirically identify DENV-specific MHC ligands, we developed an immuno-proteomics approach for interrogating DENV- and self-derived MHC ligands from infected B-lymphocytes. Here, we report four fundamental findings: First, over 700 infection-specific MHC-ligands reflected host cellular responses to DENV that were not apparent from the proteome. Second, we report 121 viral MHC-I ligands (108 novel) which clustered into discrete hotspots across the DENV polyprotein, some of which spanned DENV polyprotein components, described here as MHC ligands for the first time. Third, we found DENV ligands which were distinctly presented by MHC alleles previously associated with either high or low anti-DENV response. Fourth, we demonstrate that while our in vitro assay only overlapped with a small fraction of previously described DENV T-cell epitopes, several novel MHC ligands identified here were recognized by T-cells from DENV-infected patients despite having low binding affinities. Together, these discoveries suggest that virus and host-derived MHC ligands have under-exploited potential for describing the cell biology of DENV infection, and as candidates for designing effective DENV vaccines.

...Show more>>

Cutting Edge: Transcriptional Profiling Reveals Multifunctional and Cytotoxic Antiviral Responses of Zika Virus–Specific CD8+ T Cells

Alba Grifoni, Priscilla Costa-Ramos, John Pham, Yuan Tian, Sandy L Rosales, Grégory Seumois, John Sidney, Aruna D de Silva, Lakshmanane Premkumar, Matthew H Collins, Mars Stone, Phillip J Norris, Claudia ME Romero, Anna Durbin, Michael J Ricciardi, Julie E Ledgerwood, Aravinda M de Silva, Michael Busch, Bjoern Peters, Pandurangan Vijayanand, Eva Harris, Andrew K Falconar, Esper Kallas, Daniela Weiskopf, and Alessandro Sette

J Immunol. 2018 Nov 9. pii: ji1801090.

Zika virus (ZIKV) constitutes an increasing public health problem. Previous studies have shown that CD8+ T cells play an important role in ZIKV-specific protective immunity. We have previously defined antigenic targets of the ZIKV-specific CD8+ T cell response in humans. In this study, we characterized the quality and phenotypes of these responses by a combined use of flow cytometry and transcriptomic methods, using PBMCs from donors deriving from different geographical locations collected in the convalescent phase of infection. We show that ZIKV-specific CD8+ T cells are characterized by a polyfunctional IFN-γ signature with upregulation of TNF-α, TNF receptors, and related activation markers, such as CD69, as well as a cytotoxic signature characterized by strong upregulation of GZMB and CRTAM. The signature is stable and not influenced by previous dengue virus exposure, geographical location, or time of sample collection postinfection. To our knowledge, this work elucidates the first in-depth characterization of human CD8+ T cells responding to ZIKV infection.

...Show more>>

Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA

Yuan Tian, Mariana Babor, Jerome Lane, Veronique Schulten, Veena S Patil, Grégory Seumois, Sandy L Rosales, Zheng Fu, Gaelle Picarda, Julie Burel, Jose Zapardiel-Gonzalo, Rashika N Tennekoon, Aruna D Silva, Sunil Premawansa, Gayani Premawansa, Ananda Wijewickrama, Jason A Greenbaum, Pandurangan Vijayanand, Daniela Weiskopf, Alessandro Sette, and Bjoern Pete

Nat Commun. 2017 Nov 13;8(1):1473.

The expression of CD45RA is generally associated with naive T cells. However, a subset of effector memory T cells re-expresses CD45RA (termed TEMRA) after antigenic stimulation with unknown molecular characteristics and functions. CD4 TEMRA cells have been implicated in protective immunity against pathogens such as dengue virus (DENV). Here we show that not only the frequency but also the phenotype of CD4 TEMRA cells are heterogeneous between individuals. These cells can be subdivided into two major subsets based on the expression of the adhesion G protein-coupled receptor GPR56, and GPR56+ TEMRA cells display a transcriptional and proteomic program with cytotoxic features that is distinct from effector memory T cells. Moreover, GPR56+ TEMRA cells have higher levels of clonal expansion and contain the majority of virus-specific TEMRA cells. Overall, this study reveals the heterogeneity of CD4 TEMRA cells and provides insights into T-cell responses against DENV and other viral pathogens.

...Show more>>