The Route of Vaccine Administration Determines Whether Blood Neutrophils Undergo Long-Term Phenotypic Modifications

Innate immunity modulates adaptive immunity and defines the magnitude, quality, and longevity of antigen-specific T- and B- cell immune memory. Various vaccine and administration factors influence the immune response to vaccination, including the route of vaccine delivery. We studied the dynamics of innate cell responses in blood using a preclinical model of non-human primates immunized with a live attenuated vaccinia virus, a recombinant Modified vaccinia virus Ankara (MVA) expressing a gag-pol-nef fusion of HIV-1, and mass cytometry. We previously showed that it induces a strong, early, and transient innate response, but also late phenotypic modifications of blood myeloid cells after two months when injected subcutaneously. Here, we show that the early innate effector cell responses and plasma inflammatory cytokine profiles differ between subcutaneous and intradermal vaccine injection. Additionally, we show that the intradermal administration fails to induce more highly activated/mature neutrophils long after immunization, in contrast to subcutaneous administration. Different batches of antibodies, staining protocols and generations of mass cytometers were used to generate the two datasets. Mass cytometry data were analyzed in parallel using the same analytical pipeline based on three successive clustering steps, including SPADE, and categorical heatmaps were compared using the Manhattan distance to measure the similarity between cell cluster phenotypes. Overall, we show that the vaccine per se is not sufficient for the late phenotypic modifications of innate myeloid cells, which are evocative of innate immune training. Its route of administration is also crucial, likely by influencing the early innate response, and systemic inflammation, and vaccine biodistribution.

Dynamic metabolic change of cancer cells induced by natural killer cells at single-cell level studied by label-free mass cytometry

Natural killer cell（NK cell）is an important immune cell which attracts increasing attention in cancer immunotherapy. Due to the heterogeneity of cells, individual cancer cell shows different resistance to NK cytotoxicity,...

Ancestry-based differences in the immune system are associated with lupus severity

Systemic lupus erythematosus (SLE) affects 1 in 537 of African American (AA) women, which is >2-fold more than European American (EA) women. AA patients also develop the disease at a younger age, have more severe symptoms, and a greater chance of early mortality. We used a multi-omics approach to uncover ancestry-specific immune alterations in SLE patients and healthy controls that may contribute to disease disparities. Cell composition, signaling, and epigenetics were evaluated by mass cytometry; droplet-based single cell transcriptomics and paired proteogenomics (scRNA-Seq/scCITE-Seq). Soluble mediator levels were measured in plasma and stimulated whole blood. Toll-like receptor (TLRs) pathways are activated by vaccination and microbial infection, and are also key drivers of autoimmune disease. We observed enhanced TLR3/4/7/8/9-related gene expression in immune cells from AA versus EA SLE patients. TLR7/8/9 and IFNα phospho-signaling responses were heightened even in immune cells from healthy AA versus EA controls. TLR stimulation of healthy AA and EA immune cells recapitulated the distinct ancestry-associated SLE immunophenotypes. Thus, healthy individuals show ancestry-based differences in innate immune pathways that could influence the course and severity of lupus and other diseases.

Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment

A holistic understanding of tissue and organ structure and function requires the detection of molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) enables simultaneous detection of up to 40 antigens and transcripts using metal-tagged antibodies but has so far been restricted to two-dimensional imaging. Here we report the development of 3D IMC for multiplexed 3D tissue analysis at single-cell resolution and demonstrate the utility of the technology by analysis of human breast cancer samples. The resulting 3D models reveal cellular and microenvironmental heterogeneity and cell-level tissue organization not detectable in two dimensions. 3D IMC will prove powerful in the study of phenomena occurring in 3D space such as tumor cell invasion and is expected to provide invaluable insights into cellular microenvironments and tissue architecture.

Using Imaging Mass Cytometry to Define Cell Identities and Interactions in Human Tissues

In the evolving landscape of highly multiplexed imaging techniques that can be applied to study complex cellular microenvironments, this review characterizes the use of imaging mass cytometry (IMC) to study the human kidney. We provide technical details for antibody validation, cell segmentation, and data analysis specifically tailored to human kidney samples, and elaborate on phenotyping of kidney cell types and novel insights that IMC can provide regarding pathophysiological processes in the injured or diseased kidney. This review will provide the reader with the necessary background to understand both the power and the limitations of IMC and thus support better perception of how IMC analysis can improve our understanding of human disease pathogenesis and can be integrated with other technologies such as single cell sequencing and proteomics to provide spatial context to cellular data.

MIAAIM: Multi-omics image integration and tissue state mapping using topological data analysis and cobordism learning

High-parameter tissue imaging enables detailed molecular analysis of single cells in their spatial environment. However, the comprehensive characterization and mapping of tissue states through multimodal imaging across different physiological and pathological conditions requires data integration across multiple imaging systems. Here, we introduce MIAAIM (Multi-omics Image Alignment and Analysis by Information Manifolds) a modular, reproducible computational framework for aligning data across bioimaging technologies, modeling continuities in tissue states, and translating multimodal measures across tissue types. We demonstrate MIAAIM's workflows across diverse imaging platforms, including histological stains, imaging mass cytometry, and mass spectrometry imaging, to link cellular phenotypic states with molecular microenvironments in clinical biopsies from multiple tissue types with high cellular complexity. MIAAIM provides a robust foundation for the development of computational methods to integrate multimodal, high-parameter tissue imaging data and enable downstream computational and statistical interrogation of tissue states.

Disrupted Peyer's patch microanatomy in COVID-19 including germinal centre atrophy independent of local virus

Confirmed SARS-coronavirus-2 infection with gastrointestinal symptoms and changes in microbiota associated with coronavirus disease 2019 (COVID-19) severity have been previously reported, but the disease impact on the architecture and cellularity of ileal Peyers patches (PP) remains unknown. Here we analysed post-mortem tissues from throughout the gastrointestinal (GI) tract of patients who died with COVID-19. When virus was detected by PCR in the GI tract, immunohistochemistry identified virus in epithelium and lamina propria macrophages, but not in lymphoid tissues. Immunohistochemistry and imaging mass cytometry (IMC) analysis of ileal PP revealed depletion of germinal centres (GC), disruption of B cell/T cell zonation and decreased potential B and T cell interaction and lower nuclear density in COVID-19 patients. This occurred independent of the local viral levels. The changes in PP demonstrate that the ability to mount an intestinal immune response is compromised in severe COVID-19, which could contribute to observed dysbiosis.