Session 5

Day 2 (December 13) of our ESSB conference starts with another hot topic: Spatial Immunology! Sanja Vickovic (vickovictechinnovation.com) will present a keynote lecture on spatial multi-omics strategies. Camilla Engblom will talk about her approach to analyze immune repertoires at the spatial level.
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Spatial Immunology

Chairs: Anja Hauser Sanja Vickovic

Friday, 13.12.2024, 08:30 am

Keynote Speaker: Sanja Vickovic

New York Genome Center, Department of Biomedical Engineering and the Irving Center for Cancer Dynamics at Columbia University, Scilifelab Fellow at Uppsala University

Developing spatial multi-omics sequencing strategies

Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. In recent years, we developed high-definition spatial transcriptomics and multi-omics technologies, which captures RNA, protein information or microbiota from histological tissue sections on spatially barcoded arrays. Using these approaches, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.

Biosketch

Sanja Vicković, PhD, is a Core Faculty Member and Director, Technology Innovation Lab, at the New York Genome Center. She holds joint appointments as an Assistant Professor at the Fu Foundation School of Engineering and Applied Science and the Herbert and Florence Irving Institute for Cancer Dynamics at Columbia University, and as a Wallenberg Academy Fellow of the Royal Swedish Academy of Sciences and the Royal Swedish Academy of Engineering Sciences at Uppsala University.Dr. Vicković is an experienced and accomplished engineer and an inventor of the spatial transcriptomic technology called “Visium” and now commercialized by 10x Genomics. In addition to being a skilled technologist, Dr. Vicković also has training and experience in mathematics and biological sciences. Prior to joining the NYGC in 2022, Dr. Vicković had already collaborated with the NYGC, playing a crucial role in the first demonstration of the application of spatial transcriptomics to a disease model in collaboration with researchers at the NYGC’s Center for Genomics of Neurodegenerative Disease. Dr. Vicković joined the NYGC from the Broad Institute of MIT and Harvard, where she was a Wallenberg Fellow in Aviv Regev’s lab. She obtained her PhD in Gene Technology from the KTH Royal Institute of Technology, Stockholm.

Camilla Engblom

SciLifeLab, Division of Immunology and Allergy, Department of Medicine Solna, Center of Molecular Medicine, Karolinska Institutet, Stockholm and Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden

Spatially resolving B cell clonal dynamics

B cells perform functions critical to human health, including antibody production and antigen presentation. B cells develop, differentiate, and expand in spatially distinct sites across the body. B cells express clonal heritable B cell receptors (BCR), either as membrane-bound or secreted antibodies, that confer exquisite molecular (i.e., antigen) specificity. B cell receptors can be defined by sequencing, but these methods require tissue dissociation, which loses the anatomical location, and the surrounding functionally relevant environmental cues. Linking specific BCR sequences to their molecular and cellular surroundings, i.e., ‘clonal niche’, could help us understand and harness B cell activity. A technological bottleneck has been to capture the location of BCR sequences, and by extension B cell clonal responses, directly within tissues. We recently developed a spatial transcriptomics-based approach (Spatial VDJ) and associated computational pipelines to reconstruct B cell clonality in human tissues. Here, we present adaptation of Spatial VDJ to murine tissue to enable preclinical studies and B cell receptor dynamics under inflammatory conditions, including cancer.

Biosketch

Dr. Camilla Engblom is a SciLifeLab Fellow and an Assistant Professor in the Division of Immunology and Allergy and the Department of Medicine, Solna at the Karolinska Institutet (KI). Dr. Engblom received her PhD in Immunology from Harvard University in 2017 focusing on long-range cancer-host interactions involving myeloid cells (Dr. Mikael Pittet’s lab at Massachusetts General Hospital/Harvard Medical School). As a MSCA postdoctoral fellow in Dr. Jonas Frisén’s lab (KI), Dr. Engblom developed a spatial transcriptomics-based tool (Spatial VDJ) to map B cell and T cell receptors within human tissues. Located at SciLifeLab and the Center for Molecular Medicine (KI), the Engblom lab’s main research focus is to spatially and functionally resolve B cell clonal dynamics during cancer.

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Session 5

Spatial Immunology