{"doi":"10.1101/2021.06.07.447395","title":"T helper 2 transcriptional profile predicts single-cell HIV envelope-specific polyfunctional CD4+ T cells correlated with reduced risk of infection in RV144 trial","abstract":"Abstract Despite the critical role antigen-specific T cells play in responding to viral infections, their aggregate frequencies in peripheral blood have not correlated with clinical protection during HIV infection. However, a subset of HIV-specific CD4+ T cells, termed polyfunctional T cells, can produce multiple effector cytokines simultaneously. In the RV144 HIV vaccine trial, polyfunctional T cells correlated with reduced risk of HIV infection. Little is known about what differentiates polyfunctional T cells from other vaccine-elicited T cells. Therefore, we developed a novel live-cell multiplexed cytokine capture assay, to identify and transcriptionally profile vaccine-specific polyfunctional CD4+ T cells. We applied these methods to samples from the HVTN 097 clinical trial of the same vaccine regimen as RV144. We discovered two surface receptors that were enriched among polyfunctional CD4+ T cells and a Th2-biased signature ( IL-4, IL-5 , and IL-13 ) that specifically predicted the envelope-specific polyfunctional CD4+ T cells that were correlated with reduced risk of HIV infection in RV144. By linking single-cell transcriptional and functional profiles, we may be able to further define the role of vaccine-elicited polyfunctional T cells in contributing to effective immunity. Key Points Novel ex vivo multiplexed cytokine capture assay to enumerate and single-cell sort polyfunctional T cells for downstream analyses Polyfunctional T cells were specifically detected among the HIV envelope-stimulated CD4+ T cells Single-cell RNA sequencing identified novel surface markers enriched among vaccine-specific polyfunctional CD4+ T cells Th2 transcriptional signature predicted polyfunctional CD4+ T cell profile that had correlated with reduced risk of HIV infection in the RV144 HIV efficacy trial","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":224622,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9634,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":630373,"name":"Yuan Tian","orcid":"0000-0001-7782-8613","position":1,"is_corresponding":false},{"id":826645,"name":"Casey Thayer","orcid":"0000-0002-3971-1323","position":2,"is_corresponding":false},{"id":378921,"name":"Aaron Seese","orcid":"0000-0002-5877-6229","position":3,"is_corresponding":false},{"id":232694,"name":"Robert A. Amezquita","orcid":"0000-0001-6868-7193","position":4,"is_corresponding":false},{"id":52019,"name":"M. Juliana McElrath","orcid":"0000-0003-2276-7117","position":5,"is_corresponding":false},{"id":331738,"name":"Stephen C. De Rosa","orcid":"0000-0003-3871-4618","position":6,"is_corresponding":false},{"id":18054,"name":"Raphaël Gottardo","orcid":"0000-0002-3867-0232","position":7,"is_corresponding":false},{"id":288617,"name":"Kristen W. Cohen","orcid":"0000-0002-8901-9941","position":0,"is_corresponding":true}],"reference_count":27,"raw_metadata":null,"created_at":"2026-07-18T23:54:18.470602Z","pmid":null,"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":[]}