{"id":"https://openalex.org/W7225428825","doi":"https://doi.org/10.64898/2026.11.05.764679","title":"Preferential Isoform Usage and Isoform Switching in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Profile","display_name":"Preferential Isoform Usage and Isoform Switching in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Profile","publication_year":2026,"publication_date":"2026-11-06","ids":{"openalex":"https://openalex.org/W7225428825","doi":"https://doi.org/10.64898/2026.11.05.764679"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.05.764679","doi":"https://doi.org/10.64898/2026.11.05.764679","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.05.764679","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.05.764679.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.05.764679.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5105672841","display_name":"Richa Rai","orcid":"https://orcid.org/0000-0002-9957-2708","observed_orcids":["https://orcid.org/0000-0002-9957-2708"]},"institutions":[{"id":"https://openalex.org/I91357014","display_name":"Banaras Hindu University","ror":"https://ror.org/04cdn2797","country_code":"IN","type":"education","lineage":["https://openalex.org/I91357014"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Richa Rai","raw_affiliation_strings":["Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India;","institution_ids":["https://openalex.org/I91357014"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161043025","display_name":"Arya Das","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Arya Das","raw_affiliation_strings":["Agrigenome Labs PVT LTD, Cochin, India;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Agrigenome Labs PVT LTD, Cochin, India;","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161026384","display_name":"Sudhir Kumar Chauhan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I91357014","display_name":"Banaras Hindu University","ror":"https://ror.org/04cdn2797","country_code":"IN","type":"education","lineage":["https://openalex.org/I91357014"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sudhir Kumar Chauhan","raw_affiliation_strings":["Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India;","institution_ids":["https://openalex.org/I91357014"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063642077","display_name":"Vikas Vikram Singh","orcid":"https://orcid.org/0000-0001-6304-9942","observed_orcids":["https://orcid.org/0000-0001-6304-9942"]},"institutions":[{"id":"https://openalex.org/I91357014","display_name":"Banaras Hindu University","ror":"https://ror.org/04cdn2797","country_code":"IN","type":"education","lineage":["https://openalex.org/I91357014"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Vikas Vikram Singh","raw_affiliation_strings":["Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India;","institution_ids":["https://openalex.org/I91357014"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108118128","display_name":"Madhukar Rai","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I51317819","display_name":"Institute of Medical Sciences","ror":"https://ror.org/04y75dx46","country_code":"IN","type":"education","lineage":["https://openalex.org/I51317819","https://openalex.org/I91357014"]},{"id":"https://openalex.org/I91357014","display_name":"Banaras Hindu University","ror":"https://ror.org/04cdn2797","country_code":"IN","type":"education","lineage":["https://openalex.org/I91357014"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Madhukar Rai","raw_affiliation_strings":["Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India","institution_ids":["https://openalex.org/I51317819","https://openalex.org/I91357014"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061706766","display_name":"Dinesh Velayutham","orcid":"https://orcid.org/0000-0002-9425-7266","observed_orcids":["https://orcid.org/0000-0002-9425-7266"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dinesh Velayutham","raw_affiliation_strings":["Agrigenome Labs PVT LTD, Cochin, India;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Agrigenome Labs PVT LTD, Cochin, India;","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062935442","display_name":"Geeta Rai","orcid":"https://orcid.org/0000-0001-8162-8964","observed_orcids":["https://orcid.org/0000-0001-8162-8964"]},"institutions":[{"id":"https://openalex.org/I91357014","display_name":"Banaras Hindu University","ror":"https://ror.org/04cdn2797","country_code":"IN","type":"education","lineage":["https://openalex.org/I91357014"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Geeta Rai","raw_affiliation_strings":["Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India;","institution_ids":["https://openalex.org/I91357014"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5062935442"],"corresponding_institution_ids":["https://openalex.org/I91357014"],"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/T10308","display_name":"Systemic Lupus Erythematosus Research","score":0.9545999765396118,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10308","display_name":"Systemic Lupus Erythematosus Research","score":0.9545999765396118,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.04500000178813934,"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/T11330","display_name":"Systemic Sclerosis and Related Diseases","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/systemic-lupus-erythematosus","display_name":"systemic lupus erythematosus","score":1.0},{"id":"https://openalex.org/keywords/isoform-switching","display_name":"isoform switching","score":0.7120000123977661},{"id":"https://openalex.org/keywords/differential-isoform-usage","display_name":"differential isoform usage","score":0.9670000076293945},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"alternative splicing","score":0.9470000267028809},{"id":"https://openalex.org/keywords/autoantibody-profile","display_name":"autoantibody profile","score":0.824999988079071},{"id":"https://openalex.org/keywords/anti-dsdna-antibodies","display_name":"anti-dsDNA antibodies","score":0.8989999890327454},{"id":"https://openalex.org/keywords/anti-ena-antibodies","display_name":"anti-ENA antibodies","score":0.7950000166893005},{"id":"https://openalex.org/keywords/intron-retention","display_name":"intron retention","score":0.5929999947547913},{"id":"https://openalex.org/keywords/ighm","display_name":"IGHM","score":0.7599999904632568},{"id":"https://openalex.org/keywords/naca","display_name":"NACA","score":0.8970000147819519},{"id":"https://openalex.org/keywords/tnfaip2","display_name":"TNFAIP2","score":0.9990000128746033},{"id":"https://openalex.org/keywords/upstream-open-reading-frames","display_name":"upstream open reading frames","score":0.8080000281333923},{"id":"https://openalex.org/keywords/rna-binding-proteins","display_name":"RNA-binding proteins","score":0.6970000267028809},{"id":"https://openalex.org/keywords/transcriptome-heterogeneity","display_name":"transcriptome heterogeneity","score":0.5950000286102295},{"id":"https://openalex.org/keywords/autoantigens","display_name":"autoantigens","score":0.8029999732971191}],"concepts":[{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.9355999827384949},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.777400016784668},{"id":"https://openalex.org/C163764329","wikidata":"https://www.wikidata.org/wiki/Q785022","display_name":"Autoantibody","level":3,"score":0.6664000153541565},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5687999725341797},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.499099999666214},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41839998960494995},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.41760000586509705},{"id":"https://openalex.org/C2780130043","wikidata":"https://www.wikidata.org/wiki/Q192360","display_name":"Autoimmunity","level":3,"score":0.4106999933719635},{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.3977000117301941},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3718999922275543},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.3504999876022339},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.3434000015258789},{"id":"https://openalex.org/C2779075594","wikidata":"https://www.wikidata.org/wiki/Q8084905","display_name":"Autoimmune disease","level":3,"score":0.33809998631477356},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3174000084400177},{"id":"https://openalex.org/C2776670291","wikidata":"https://www.wikidata.org/wiki/Q1779300","display_name":"Connective tissue disease","level":4,"score":0.3151000142097473},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31189998984336853},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.3086000084877014},{"id":"https://openalex.org/C2780942790","wikidata":"https://www.wikidata.org/wiki/Q372016","display_name":"Pathogenesis","level":2,"score":0.2980000078678131},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.2955000102519989},{"id":"https://openalex.org/C2778453870","wikidata":"https://www.wikidata.org/wiki/Q188930","display_name":"B cell","level":3,"score":0.28130000829696655},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.27950000762939453},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.27639999985694885},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.26919999718666077},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.26350000500679016},{"id":"https://openalex.org/C2775915377","wikidata":"https://www.wikidata.org/wiki/Q188297","display_name":"Lupus erythematosus","level":3,"score":0.25690001249313354},{"id":"https://openalex.org/C135979968","wikidata":"https://www.wikidata.org/wiki/Q609809","display_name":"Protein isoform","level":5,"score":0.2533000111579895}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.05.764679","doi":"https://doi.org/10.64898/2026.11.05.764679","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.05.764679","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.05.764679.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.05.764679","doi":"https://doi.org/10.64898/2026.11.05.764679","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.05.764679","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.05.764679.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[{"id":"https://openalex.org/study-designs/observational-study","display_name":"Observational Study"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225428825.pdf","grobid_xml":"https://content.openalex.org/works/W7225428825.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2556559016","https://openalex.org/W4313383198","https://openalex.org/W4313358831","https://openalex.org/W1968800676","https://openalex.org/W4416450972","https://openalex.org/W2164693982","https://openalex.org/W2086205843","https://openalex.org/W3194963328","https://openalex.org/W2542805980","https://openalex.org/W4415000544"],"abstract_inverted_index":{"RNA":[0],"sequencing":[1],"has":[2],"advanced":[3],"our":[4],"understanding":[5],"of":[6,51,112,169,186],"molecular":[7],"heterogeneity":[8],"in":[9,92,189],"systemic":[10],"lupus":[11],"erythematosus":[12],"(SLE),":[13],"yet":[14],"most":[15],"studies":[16],"have":[17],"focused":[18],"on":[19],"differential":[20,65],"gene":[21],"expression":[22],"(DGE),":[23],"which":[24],"overlooks":[25],"transcript-level":[26],"complexity.":[27],"Alternative":[28],"splicing":[29],"and":[30,39,69,83,87,94,144,182],"polyadenylation":[31],"generate":[32],"multiple":[33],"isoforms":[34,53],"from":[35,123],"a":[36,113,137,161,170,179],"single":[37],"gene,":[38,163],"their":[40],"dysregulation":[41,188],"may":[42],"contribute":[43],"to":[44,126,147],"autoimmune":[45],"pathogenesis,":[46],"including":[47],"through":[48],"the":[49,98,101,118,124,127,157],"production":[50],"non-canonical":[52],"with":[54,131,167],"potential":[55],"autoantigenic":[56],"properties.":[57],"To":[58],"explore":[59],"this":[60],"underexamined":[61],"dimension,":[62],"we":[63],"analysed":[64],"isoform":[66,71,107,142,165,176],"usage":[67],"(DIU)":[68],"major":[70],"switching":[72,108],"(MIS)":[73],"across":[74],"SLE":[75],"subgroups":[76],"stratified":[77],"by":[78,110],"autoantibody":[79],"profile:":[80],"anti-dsDNA+,":[81],"anti-ENA+":[82,119],"anti-dsDNA+ENA+.":[84],"Subgroup-specific":[85],"DIU":[86],"MIS":[88],"events":[89],"were":[90],"enriched":[91],"RNA-binding":[93],"transcription-related":[95],"functions.":[96],"In":[97,117,156],"anti-dsDNA+":[99],"subgroup,":[100,120,159],"T-cell":[102],"receptor":[103],"adaptor":[104],"GRAP2":[105],"showed":[106,141,164],"accompanied":[109],"expansion":[111],"non-coding":[114],"retained-intron":[115],"transcript.":[116,155,172],"IGHM":[121],"switched":[122,151],"membrane-bound":[125],"secretory":[128],"form,":[129],"consistent":[130],"an":[132],"antibody-secreting":[133],"cell":[134,149],"signature;":[135],"NACA,":[136],"reported":[138],"IgE":[139],"autoantigen,":[140],"switching;":[143],"BRI3,":[145],"linked":[146],"TNF-\u03b1-induced":[148,162],"death,":[150],"toward":[152],"its":[153],"protein-coding":[154],"anti-dsDNA+ENA+":[158],"TNFAIP2,":[160],"redistribution":[166],"loss":[168],"uORF-containing":[171],"These":[173],"findings":[174],"highlight":[175],"regulation":[177],"as":[178],"distinct,":[180],"subgroup-specific":[181],"functionally":[183],"relevant":[184],"layer":[185],"transcriptomic":[187],"SLE.":[190]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-07T00:00:00"}
