{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T06:04:49Z","timestamp":1790661889093,"version":"4.1.0"},"reference-count":25,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2026,8,30]],"date-time":"2026-08-30T00:00:00Z","timestamp":1788048000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,30]],"date-time":"2026-08-30T00:00:00Z","timestamp":1788048000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["390874280"],"award-info":[{"award-number":["390874280"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Eur J Immunol"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Vaccine\u2010induced transcriptional responses have been extensively characterized at the gene level, but whether vaccination also alters transcript isoform usage remains largely unexplored. Here, we reanalyzed longitudinal whole\u2010blood RNA\u2010seq data from a discovery cohort of mRNA COVID\u201019 vaccine recipients using the IsoformSwitchAnalyzeR framework and validated the findings in an independent cohort. Key findings were validated by full\u2010length RNA long\u2010read sequencing and extended to four additional vaccine cohorts covering distinct platforms and pathogens. mRNA vaccination induced a rapid and transient wave of differential transcript usage, peaking at 24\u00a0h post\u2010vaccination with 131 isoforms significantly altered across 107 genes, before largely resolving by Day 14. Isoform switching events were reproducible across independent cohorts and confirmed by full\u2010length RNA long\u2010read sequencing. Structural annotation of switching transcripts, including\n                    <jats:italic>RMI2<\/jats:italic>\n                    ,\n                    <jats:italic>WARS1<\/jats:italic>\n                    , and\n                    <jats:italic>NT5C3A<\/jats:italic>\n                    , revealed changes affecting predicted protein domains and signal peptides. Notably, highly concordant isoform switching patterns were observed across MVA\u2010based SARS\u2010CoV\u20102, influenza, and Ebola vaccine cohorts and showed dose\u2010dependent modulation. Overall, differential transcript isoform usage is a rapid and transient feature of the early human immune response to vaccination that was observed across multiple vaccine platforms. These findings reveal an underappreciated layer of transcriptional regulation that complements conventional gene\u2010level analyses and warrants integration into future vaccine immunogenicity studies.\n                  <\/jats:p>","DOI":"10.1002\/eji.70277","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T05:42:13Z","timestamp":1788154933000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Isoform\u2010Level Analysis Reveals Reproducible Early Changes in Transcript Usage During Human Vaccine Responses"],"prefix":"10.1002","volume":"56","author":[{"given":"Lennart","family":"Riemann","sequence":"first","affiliation":[{"name":"Institute of Immunology, Hannover Medical School  Hannover Germany"},{"name":"Department of Pediatric Pneumology, Allergology, and Neonatology Hannover Medical School  Hannover Germany"},{"name":"Cluster of Excellence RESIST (EXC 2155) Hannover Medical School  Hannover Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed","family":"Hassan","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics Hannover Medical School  Hannover Germany"},{"name":"Genomics &amp; Single\u2010Cell Core Unit Hannover Medical School  Hannover Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Swantje","family":"Hammerschmidt","sequence":"additional","affiliation":[{"name":"Institute of Immunology, Hannover Medical School  Hannover Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja","family":"Schimrock","sequence":"additional","affiliation":[{"name":"Institute of Immunology, Hannover Medical School  Hannover Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunnar","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics Hannover Medical School  Hannover Germany"},{"name":"Genomics &amp; Single\u2010Cell Core Unit Hannover Medical School  Hannover Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nataliya Di","family":"Donato","sequence":"additional","affiliation":[{"name":"Cluster of Excellence RESIST (EXC 2155) Hannover Medical School  Hannover Germany"},{"name":"Institute of Human Genetics Hannover Medical School  Hannover Germany"},{"name":"Genomics &amp; Single\u2010Cell Core Unit Hannover Medical School  Hannover Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reinhold","family":"F\u00f6rster","sequence":"additional","affiliation":[{"name":"Institute of Immunology, Hannover Medical School  Hannover Germany"},{"name":"Cluster of Excellence RESIST (EXC 2155) Hannover Medical School  Hannover Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,8,30]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41590\u2010022\u201001328\u20106"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2023.104947"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010021\u201003791\u2010x"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2015.11.012"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41590\u2010022\u201001329\u20105"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11247"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqad084"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.1158\/1541\u20107786.MCR\u201016\u20100459"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/cam4.5533"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.111905"},{"key":"e_1_2_12_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s12276-018-0196-9"},{"key":"e_1_2_12_13_1","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.aal2434"},{"key":"e_1_2_12_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/ni.1688"},{"key":"e_1_2_12_15_1","doi-asserted-by":"publisher","DOI":"10.1002\/eji.202451236"},{"key":"e_1_2_12_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41541\u2010023\u201000801\u2010z"},{"key":"e_1_2_12_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010022\u201005670\u20105"},{"key":"e_1_2_12_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2017.08.023"},{"key":"e_1_2_12_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz247"},{"key":"e_1_2_12_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4197"},{"key":"e_1_2_12_21_1","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.7563.2"},{"key":"e_1_2_12_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx428"},{"key":"e_1_2_12_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr1065"},{"key":"e_1_2_12_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010021\u201001156\u20103"},{"key":"e_1_2_12_25_1","doi-asserted-by":"crossref","unstructured":"J.Hallgren K. 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