{"doi":"10.1101/2023.03.16.533003","title":"Universal recording of cell-cell contacts <i>in vivo</i> for interaction-based transcriptomics","abstract":"Abstract Cellular interactions are essential for tissue organization and functionality. In particular, immune cells rely on direct and usually transient interactions with other immune and non-immune populations to specify and regulate their function. To study these “kiss-and-run” interactions directly in vivo , we previously developed LIPSTIC (Labeling Immune Partnerships by SorTagging Intercellular Contacts), an approach that uses enzymatic transfer of a labeled substrate between the molecular partners CD40L and CD40 to label interacting cells. Reliance on this pathway limited the use of LIPSTIC to measuring interactions between CD4 + helper T cells and antigen presenting cells, however. Here, we report the development of a universal version of LIPSTIC (uLIPSTIC), which can record physical interactions both among immune cells and between immune and non-immune populations irrespective of the receptors and ligands involved. We show that uLIPSTIC can be used, among other things, to monitor the priming of CD8 + T cells by dendritic cells, reveal the cellular partners of regulatory T cells in steady state, and identify germinal center (GC)-resident T follicular helper (Tfh) cells based on their ability to interact cognately with GC B cells. By coupling uLIPSTIC with single-cell transcriptomics, we build a catalog of the immune populations that physically interact with intestinal epithelial cells (IECs) and find evidence of stepwise acquisition of the ability to interact with IECs as CD4 + T cells adapt to residence in the intestinal tissue. Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell–cell interactions across multiple biological systems.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":390128,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":13,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9502,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":854594,"name":"Maria Cecília Campos Canesso","orcid":"0000-0002-2562-662X","position":1,"is_corresponding":false},{"id":950016,"name":"Sarah Walker","orcid":"0009-0007-9310-2776","position":2,"is_corresponding":false},{"id":266891,"name":"Aleksey Chudnovskiy","orcid":"0000-0002-5806-1725","position":3,"is_corresponding":false},{"id":630610,"name":"Johanne T. Jacobsen","orcid":"0000-0001-9757-1923","position":4,"is_corresponding":false},{"id":855815,"name":"Jana Bilanovic","orcid":"0000-0002-0143-9694","position":5,"is_corresponding":false},{"id":850103,"name":"Sara Martina Parigi","orcid":"0000-0002-4788-3571","position":6,"is_corresponding":false},{"id":1161430,"name":"Karol Fiedorczuk","orcid":"0000-0001-7439-0222","position":7,"is_corresponding":false},{"id":104382,"name":"Elaine Fuchs","orcid":"0000-0002-0978-5137","position":8,"is_corresponding":false},{"id":295160,"name":"Angelina M. Bilate","orcid":"0000-0003-4575-786X","position":9,"is_corresponding":false},{"id":989455,"name":"Giulia Pasqual","orcid":"0000-0002-1476-2669","position":10,"is_corresponding":false},{"id":66190,"name":"Daniel Mucida","orcid":"0000-0002-0000-0452","position":11,"is_corresponding":false},{"id":349760,"name":"Yuri Pritykin","orcid":"0000-0001-6589-981X","position":12,"is_corresponding":false},{"id":266895,"name":"Gabriel D. Victora","orcid":"0000-0001-8807-348X","position":13,"is_corresponding":false},{"id":989454,"name":"Sandra Nakandakari-Higa","orcid":"0000-0001-8293-2992","position":0,"is_corresponding":true}],"reference_count":72,"raw_metadata":null,"created_at":"2026-07-19T01:18:32.854511Z","pmid":"36993443","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}