Turn single-cell data into immunological insights


A Population of CD4+CD8+ Double-Positive T Cells Associated with Risk of Plasma Leakage in Dengue Viral Infection

Esther Dawen Yu, Hao Wang, Ricardo da Silva Antunes, Yuan Tian, Rashmi Tippalagama, Shakila U Alahakoon, Gayani Premawansa, Ananda Wijewickrama, Sunil Premawansa, Aruna Dharshan De Silva, April Frazier, Alba Grifoni, Alessandro Sette, and Daniela Weiskopf


According to the WHO 2009 classification, dengue with warning signs is at the risk of developing severe form of dengue disease. One of the most important warning signs is plasma leakage, which can be a serious complication associated with higher morbidity and mortality. We report that the frequency of CD4+CD8+ double-positive (DP) T cells is significantly increased in patients at risk of developing plasma leakage. Transcriptomic analysis demonstrated that CD4+CD8+ DP cells were distinct from CD4+ Single Positive (SP) T cells but co-clustered with CD8+ SP cells, indicating a largely similar transcriptional profile. Twenty significant differentially expressed (DE) genes were identified between CD4+CD8+ DP and CD8+ SP cells. These genes encode OX40 and CCR4 proteins as well as other molecules associated with cell signaling on the cell surface (NT5E, MXRA8, and PTPRK). While comparing the profile of gene expression in CD4+CD8+ DP cells from patients with and without warning signs of plasma leakage, similar expression profile was observed, implying a role of CD4+CD8+ DP cells in plasma leakage through a quantitative increase rather than functional alteration. This study provided novel insight into the host immune response during the acute febrile phase of DENV infection and the role of CD4+CD8+ DP T cells in the pathogenesis of plasma leakage.

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Single-cell immunology of SARS-CoV-2 infection

Yuan Tian, Lindsay N Carpp, Helen E R Miller, Michael Zager, Evan W Newell, and Raphael Gottardo

Nat Biotechnol.

Gaining a better understanding of the immune cell subsets and molecular factors associated with protective or pathological immunity against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 could aid the development of vaccines and therapeutics for coronavirus disease 2019 (COVID-19). Single-cell technologies, such as flow cytometry, mass cytometry, single-cell transcriptomics and single-cell multi-omic profiling, offer considerable promise in dissecting the heterogeneity of immune responses among individual cells and uncovering the molecular mechanisms of COVID-19 pathogenesis. Single-cell immune-profiling studies reported to date have identified innate and adaptive immune cell subsets that correlate with COVID-19 disease severity, as well as immunological factors and pathways of potential relevance to the development of vaccines and treatments for COVID-19. For facilitation of integrative studies and meta-analyses into the immunology of SARS-CoV-2 infection, we provide standardized, download-ready versions of 21 published single-cell sequencing datasets (over 3.2 million cells in total) as well as an interactive visualization portal for data exploration.

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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.

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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.

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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.

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