{"id":"https://openalex.org/W4414946457","doi":"https://doi.org/10.1101/2025.10.08.681095","title":"A Single-Cell Atlas of Transcriptional and Immunoglobulin Repertoire Evolution in Early B Cell Development","display_name":"A Single-Cell Atlas of Transcriptional and Immunoglobulin Repertoire Evolution in Early B Cell Development","publication_year":2025,"publication_date":"2025-10-08","ids":{"openalex":"https://openalex.org/W4414946457","doi":"https://doi.org/10.1101/2025.10.08.681095","pmid":"https://pubmed.ncbi.nlm.nih.gov/41278878","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/12632473"},"language":"en","primary_location":{"id":"doi:10.1101/2025.10.08.681095","doi":"https://doi.org/10.1101/2025.10.08.681095","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.10.08.681095","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/10/08/2025.10.08.681095.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2025/10/08/2025.10.08.681095.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093817760","display_name":"Charlotte N. DiBiase","orcid":"https://orcid.org/0009-0007-8473-9134","observed_orcids":["https://orcid.org/0009-0007-8473-9134"]},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charlotte DiBiase","raw_affiliation_strings":["Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA","The Scripps Research Institute"],"raw_orcid":"https://orcid.org/0009-0007-8473-9134","affiliations":[{"raw_affiliation_string":"Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA","institution_ids":["https://openalex.org/I123431417"]},{"raw_affiliation_string":"The Scripps Research Institute","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054535186","display_name":"Jonathan Hurtado","orcid":"https://orcid.org/0000-0003-4145-7042","observed_orcids":["https://orcid.org/0000-0003-4145-7042"]},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Hurtado","raw_affiliation_strings":["Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA","The Scripps Research Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA","institution_ids":["https://openalex.org/I123431417"]},{"raw_affiliation_string":"The Scripps Research Institute","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067720514","display_name":"Bryan S. Briney","orcid":"https://orcid.org/0000-0001-9535-2866","observed_orcids":["https://orcid.org/0000-0001-9535-2866"]},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bryan Briney","raw_affiliation_strings":["Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA 92037 USA","Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA","Multi-Omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA 92037 USA","San Diego Center for AIDS Research, The Scripps Research Institute, La Jolla, CA 92037 USA","Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA","The Scripps Research Institute"],"raw_orcid":"https://orcid.org/0000-0001-9535-2866","affiliations":[{"raw_affiliation_string":"Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA 92037 USA","institution_ids":["https://openalex.org/I123431417"]},{"raw_affiliation_string":"Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA","institution_ids":["https://openalex.org/I123431417"]},{"raw_affiliation_string":"Multi-Omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA 92037 USA","institution_ids":["https://openalex.org/I123431417"]},{"raw_affiliation_string":"San Diego Center for AIDS Research, The Scripps Research Institute, La Jolla, CA 92037 USA","institution_ids":["https://openalex.org/I123431417"]},{"raw_affiliation_string":"Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA","institution_ids":["https://openalex.org/I123431417"]},{"raw_affiliation_string":"The Scripps Research Institute","institution_ids":["https://openalex.org/I123431417"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5067720514"],"corresponding_institution_ids":["https://openalex.org/I123431417"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9380000233650208,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9380000233650208,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.04699999839067459,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.002400000113993883,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/b-cell-development","display_name":"B cell development","score":0.9760000109672546},{"id":"https://openalex.org/keywords/pro-b-cells","display_name":"pro-B cells","score":0.7139999866485596},{"id":"https://openalex.org/keywords/antibody-repertoire","display_name":"antibody repertoire","score":0.7120000123977661},{"id":"https://openalex.org/keywords/b-cell-receptor","display_name":"B cell receptor","score":0.7630000114440918},{"id":"https://openalex.org/keywords/lymphopoiesis","display_name":"lymphocyte development","score":0.7870000004768372},{"id":"https://openalex.org/keywords/autoreactivity","display_name":"autoreactivity","score":0.7059999704360962},{"id":"https://openalex.org/keywords/single-cell-transcriptomics","display_name":"single-cell transcriptomics","score":0.6460000276565552},{"id":"https://openalex.org/keywords/bone-marrow","display_name":"bone marrow","score":0.7070000171661377}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8016999959945679},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.7817999720573425},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5268999934196472},{"id":"https://openalex.org/C36394416","wikidata":"https://www.wikidata.org/wiki/Q949267","display_name":"Immunoglobulin light chain","level":3,"score":0.5005999803543091},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.46880000829696655},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4607999920845032},{"id":"https://openalex.org/C2910693471","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody Repertoire","level":3,"score":0.45910000801086426},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4235999882221222},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4207000136375427},{"id":"https://openalex.org/C2778453870","wikidata":"https://www.wikidata.org/wiki/Q188930","display_name":"B cell","level":3,"score":0.3707999885082245},{"id":"https://openalex.org/C43907098","wikidata":"https://www.wikidata.org/wiki/Q903924","display_name":"breakpoint cluster region","level":3,"score":0.3668000102043152},{"id":"https://openalex.org/C96007430","wikidata":"https://www.wikidata.org/wiki/Q3776943","display_name":"Immunoglobulin heavy chain","level":3,"score":0.3506999909877777},{"id":"https://openalex.org/C3020196193","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Immunoglobulin gene","level":3,"score":0.3497999906539917},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3490999937057495},{"id":"https://openalex.org/C113646796","wikidata":"https://www.wikidata.org/wiki/Q50263283","display_name":"Recombination-activating gene","level":4,"score":0.33500000834465027},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.3346000015735626},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3172000050544739},{"id":"https://openalex.org/C128526571","wikidata":"https://www.wikidata.org/wiki/Q619302","display_name":"Somatic hypermutation","level":4,"score":0.314300000667572},{"id":"https://openalex.org/C157695867","wikidata":"https://www.wikidata.org/wiki/Q1100474","display_name":"B-cell receptor","level":4,"score":0.3093000054359436},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.30469998717308044},{"id":"https://openalex.org/C113968399","wikidata":"https://www.wikidata.org/wiki/Q7559241","display_name":"Somatic evolution in cancer","level":3,"score":0.2906000018119812},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.28940001130104065},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.2888000011444092},{"id":"https://openalex.org/C2992511266","wikidata":"https://www.wikidata.org/wiki/Q1093098","display_name":"Gene rearrangement","level":3,"score":0.28040000796318054},{"id":"https://openalex.org/C137756551","wikidata":"https://www.wikidata.org/wiki/Q2386881","display_name":"Immunoglobulin class switching","level":4,"score":0.2728999853134155},{"id":"https://openalex.org/C2780254951","wikidata":"https://www.wikidata.org/wiki/Q1093098","display_name":"V(D)J recombination","level":4,"score":0.26109999418258667},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2533999979496002},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.2513999938964844}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1101/2025.10.08.681095","doi":"https://doi.org/10.1101/2025.10.08.681095","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.10.08.681095","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/10/08/2025.10.08.681095.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:41278878","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41278878","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:11440056","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12632473","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1101/2025.10.08.681095","doi":"https://doi.org/10.1101/2025.10.08.681095","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.10.08.681095","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/10/08/2025.10.08.681095.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.504800021648407,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G9000124410","display_name":null,"funder_award_id":"AI 036214","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000144868","display_name":null,"funder_award_id":"AI135995","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000857639","display_name":"Center for Viral Systems Biology (CViSB)","funder_award_id":"U19AI135995","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G9000866212","display_name":"San Diego Center for AIDS Research (SD CFAR)","funder_award_id":"P30AI036214","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G9000894303","display_name":"The Multi-omics Vaccine Evaluation (MOVE) Consortium","funder_award_id":"P01AI177683","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G9000900821","display_name":"Consortium for HIV/AIDS Vaccine Development","funder_award_id":"UM1AI144462","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G9000910214","display_name":"Genetic, structural and functional profiling of the human antibody response to arenavirus infection","funder_award_id":"R01AI171438","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414946457.pdf","grobid_xml":"https://content.openalex.org/works/W4414946457.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7216712716","https://openalex.org/W2559203725","https://openalex.org/W2735206790","https://openalex.org/W3039986691","https://openalex.org/W4410717487","https://openalex.org/W4391490243","https://openalex.org/W2027231041","https://openalex.org/W2765845267","https://openalex.org/W4200242693","https://openalex.org/W4416447022"],"abstract_inverted_index":{"The":[0],"development":[1,193],"of":[2,57,69,101,110,122,145,164,171,179,183],"human":[3],"B":[4,47,72,125,173],"cells":[5,48,73,126],"in":[6,61,106,151],"the":[7,55,58,66,83,107,165,180],"bone":[8],"marrow":[9],"can":[10],"be":[11,26],"separated":[12],"into":[13],"functionally":[14],"and":[15,29,31,34,76,113,149,154,167,187],"transcriptionally":[16],"distinct":[17],"subsets,":[18],"which":[19,80],"while":[20],"canonically":[21],"described":[22],"have":[23],"yet":[24],"to":[25,53,120],"profiled":[27],"deeply":[28],"individually":[30],"with":[32,127,134],"NGS":[33],"bioinformatic":[35],"techniques.":[36],"In":[37],"this":[38],"study,":[39],"single-cell":[40],"RNA":[41],"sequencing":[42],"was":[43],"performed":[44],"on":[45],"65,110":[46],"from":[49],"six":[50],"healthy":[51],"donors":[52],"observe":[54],"foundation":[56],"diversity":[59],"observed":[60],"mature":[62],"immune":[63],"repertoires.":[64],"Following":[65],"established":[67],"narrative":[68],"development,":[70],"committed":[71],"undergo":[74],"heavy":[75,146],"light":[77,114],"chain":[78,115,147],"recombination,":[79],"together":[81],"form":[82],"functional":[84],"BCR.":[85],"However,":[86],"a":[87,142,161,176],"granular":[88],"per-subset":[89],"phenotypic":[90],"analysis":[91],"reveals":[92],"proliferative":[93],"bursts":[94],"following":[95],"each":[96],"recombination":[97,103],"event,":[98],"an":[99],"aspect":[100],"BCR":[102],"previously":[104],"undescribed":[105],"pro-B":[108],"phase":[109],"development.":[111],"Heavy":[112],"pairing":[116],"becomes":[117],"more":[118],"similar":[119],"that":[121],"mature,":[123],"circulating":[124],"progress":[128],"through":[129],"lymphopoiesis,":[130],"deleting":[131],"features":[132],"associated":[133],"autoreactivity.":[135],"Prominent":[136],"among":[137],"these":[138],"repertoire":[139,168,192],"alterations":[140],"is":[141],"substantial":[143],"shortening":[144],"CDR3s,":[148],"changes":[150],"V,":[152],"D,":[153],"J":[155],"gene":[156],"usage.":[157],"This":[158],"study":[159],"provides":[160],"detailed":[162],"snapshot":[163],"transcriptomic":[166],"genetics":[169],"landscape":[170],"developing":[172],"cells,":[174],"providing":[175],"deeper":[177],"understanding":[178],"repertoire-shaping":[181],"influence":[182],"early":[184],"selection":[185],"processes,":[186],"introducing":[188],"new":[189],"avenues":[190],"for":[191],"research.":[194]},"counts_by_year":[],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2025-10-10T00:00:00"}
