{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:11:19Z","timestamp":1785409879021,"version":"3.56.0"},"reference-count":28,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T00:00:00Z","timestamp":1781481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32371153"],"award-info":[{"award-number":["32371153"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32371153"],"award-info":[{"award-number":["32371153"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007129","name":"Shandong Province Natural Science Foundation","doi-asserted-by":"crossref","award":["ZR2020QC071"],"award-info":[{"award-number":["ZR2020QC071"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>Accurately quantifying the expression of individual transcript isoforms remains a formidable challenge, especially in contexts such as neurodegenerative diseases and cancers, which are characterized by high isoform diversity. The present study introduces a junction-based method, named differential splicing frequency analysis (DSFA), which enables more sensitive detection of differential splicing using RNA-seq data. Unlike the existing exon-, isoform-, and event-based methods, DSFA quantifies splice junction usage. We applied DSFA to Alzheimer\u2019s disease (AD)-associated genes through large-scale RNA-seq data mining. The present study is the first to establish that the APP770-, APP751-, APP695-, and APP752-encoding isoforms represent major isoforms of the APP gene. Three important findings are: (1) the APP752-encoding isoform exhibits immune cell specificity; (2) the relative proportion of the APP752-encoding isoform increases during the differentiation of induced pluripotent stem cells (iPSCs) into microglia, akin to the increase in relative proportion of the APP695-encoding isoform during iPSC differentiation into neurons; and (3) the APP751-encoding isoform predominates in both cancer and immune cells. Additionally, we identified APP\/58417N and App\/52804N as differentially expressed splice junctions in humans and mice, respectively. Through over-expression of U1 snRNA in human embryonic stem cell (hESC)-derived neurons, we found that U1 snRNA over-expression decreases the usage of APP\/58417N in neurons, similar to the effects observed in AD samples. Our research highlights that the major isoforms of a gene can differ markedly in their expression across tissue and cell types.<\/jats:p>","DOI":"10.3390\/cells15121086","type":"journal-article","created":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T15:00:48Z","timestamp":1781535648000},"page":"1086","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Investigating Alzheimer\u2019s Disease-Associated Genes Using Differential Splicing Frequency Analysis"],"prefix":"10.3390","volume":"15","author":[{"given":"Yang","family":"Yao","sequence":"first","affiliation":[{"name":"Department of Neurology, Tianjin First Central Hospital, Nankai University, Tianjin 300192, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sha","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Nankai University, Tianjin 300071, China"},{"name":"State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi","family":"Cheng","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Nankai University, Tianjin 300071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shunmei","family":"Chen","sequence":"additional","affiliation":[{"name":"Biomedical Engineering Research Institute, Kunming Medical University, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiyao","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Nankai University, Tianjin 300071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingsong","family":"Shi","sequence":"additional","affiliation":[{"name":"National Clinical Research Center for Kidney Diseases, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing 210016, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongsheng","family":"Wei","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Nankai University, Tianjin 300071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5743-4657","authenticated-orcid":false,"given":"Tao","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Nankai University, Tianjin 300071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangyou","family":"Duan","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Qilu Normal University, Jinan 250200, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8919-1338","authenticated-orcid":false,"given":"Shan","family":"Gao","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Nankai University, Tianjin 300071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/j.ajog.2006.07.001","article-title":"Analysis of microarray experiments of gene expression profiling","volume":"195","author":"Tarca","year":"2006","journal-title":"Am. 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