{"id":13285,"date":"2023-10-02T09:46:00","date_gmt":"2023-10-02T13:46:00","guid":{"rendered":"https:\/\/www.med.unc.edu\/genetics\/?p=13285"},"modified":"2023-10-02T09:46:00","modified_gmt":"2023-10-02T13:46:00","slug":"researchers-connect-alzheimers-associated-genetic-variants-with-brain-cell-function","status":"publish","type":"post","link":"https:\/\/www.med.unc.edu\/genetics\/researchers-connect-alzheimers-associated-genetic-variants-with-brain-cell-function\/","title":{"rendered":"Researchers Connect Alzheimer\u2019s-Associated Genetic Variants with Brain Cell Function"},"content":{"rendered":"<p class=\"post-excerpt\">Led by scientists at UNC-Chapel Hill and UC-San Francisco, research reveals new non-coding genetic variants associated with Alzheimer\u2019s disease functioning in microglia \u2013 brain cells already implicated in the progression of this often-fatal neurodegenerative condition. Yun Li, PhD, professor of genetics, is the lead UNC School of Medicine researcher.<\/p>\n<hr \/>\n<figure id=\"32336\" class=\"thumbnail wp-caption alignright featured-image\"><a href=\"https:\/\/news.unchealthcare.org\/wp-content\/uploads\/sites\/1159\/2023\/09\/Screenshot-2023-09-22-080854.png\" data-slb-active=\"1\" data-slb-asset=\"1071397006\" data-slb-internal=\"0\" data-slb-group=\"32334\"><img loading=\"lazy\" decoding=\"async\" class=\"attachment-medium size-medium wp-post-image\" src=\"https:\/\/news.unchealthcare.org\/wp-content\/uploads\/sites\/1159\/2023\/09\/Screenshot-2023-09-22-080854-300x298.png\" alt=\"\" width=\"300\" height=\"298\" \/><\/a><figcaption class=\"caption wp-caption-text\">Representative immunofluorescence staining of microglia-specific marker IBA-1. Credit: Yang et. al (2023).<\/figcaption><\/figure>\n<p><strong>CHAPEL HILL, N.C.<\/strong>\u00a0\u2013 Scientists studying Alzheimer\u2019s disease (AD) have identified thousands of genetic variants in the genome in the development of this progressive neurodegenerative disease.<\/p>\n<p>These variants are predominantly located in genomic regions that do not code for proteins, making it difficult to understand which variants confer individuals\u2019 risk of AD. Non-coding variants were once thought to be \u201cjunk DNA\u201d by scientists. In recent years, these variants have been appreciated for playing crucial roles in controlling gene expression across tissues and cell types. However, linking these non-coding variants to the genes they regulate and effects on AD-related functions is a daunting task.<\/p>\n<p>Now, researchers at the University of North Carolina at Chapel Hill and The University of California, San Francisco, have identified the connections of risk variants with functions in microglia and then how they may contribute to AD.<\/p>\n<p>\u201cMicroglia are brain\u2019s immune cells and are critically important for AD,\u201d said\u00a0<a href=\"https:\/\/yunliweb.its.unc.edu\/\">Yun Li<\/a>, PhD, professor of genetics and biostatistics in the<a href=\"https:\/\/www.med.unc.edu\/\">\u00a0UNC School of Medicine<\/a>\u00a0and\u00a0<a href=\"https:\/\/sph.unc.edu\/\">UNC Gillings School of Global Public Health<\/a>. \u201cOur study focuses squarely on the critical genomic regions that are important for regulating microglia cells. These variants and regions we\u2019ve uncovered will serve as a great starting point for conducting further experiments in microglia.\u201d<\/p>\n<p>Li and\u00a0<a href=\"https:\/\/shenlab.ucsf.edu\/\">Yin Shen, PhD<\/a>, associate professor at the Institute of Human Genetics and the Department of Neurology at UC-San Francisco, and their teams performed a detailed analysis in microglia of potential functional regions harboring genetic variants associated with AD. They discovered 181 new regions of interest containing 308 prioritized variants, which were previously not considered to play a role in Alzheimer\u2019s disease. Their results\u00a0<a href=\"https:\/\/urldefense.com\/v3\/__https:\/www.nature.com\/articles\/s41588-023-01506-8__;!!LQC6Cpwp!o9p9oljTMR4bz-Uih2gafPQb_AebWXsjGvCg9Mcz9tHx4KDpMpJwgCDfoBvcvNQm-LEWzNIcTXaXNSjYXg43$\">were published<\/a>\u00a0in\u00a0<em>Nature Genetics<\/em>.<\/p>\n<p><strong>Fine-Mapping<\/strong><strong>\u00a0and\u00a0<\/strong><strong>CRISPRi<\/strong><\/p>\n<figure id=\"attachment_30337\" class=\"thumbnail wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" class=\" wp-image-30337\" src=\"https:\/\/news.unchealthcare.org\/wp-content\/uploads\/sites\/1159\/2023\/03\/YunLiPhotoWeb-738x714-1-300x290.jpg\" alt=\"\" width=\"237\" height=\"229\" \/><figcaption class=\"caption wp-caption-text\">Yun Li, PhD<\/figcaption><\/figure>\n<p>Li and her colleagues started from 37 genetic loci associated with AD to prioritize risk variants and their residing potential functional regions \u2014 termed candidate cis-regulatory regions (cCRE) \u2014 in microglia, they performed a process called fine-mapping. One locus at a time, they studied the associated variants with a special consideration of epigenetic signatures and 3D genome interaction annotations indicating their likelihood of functioning in microglia.<\/p>\n<p>After prioritizing variants that are most likely to exert their effect on AD through gene regulatory function in microglia, they performed CRISPR interference (CRISPRi) screening experiments to nail down the exact regions that affect microglia gene expression using human pluripotent stem cell differentiated microglia.<\/p>\n<p>Using this epigenomic editing technology, the researchers can \u201cperturb\u201d candidate regions to see whether any tested genomic regions can impact downstream gene expression. They found that turning off one region can often impact a \u201cwhole neighborhood\u201d of genes, much like a blackout on a power grid.<\/p>\n<p>\u201cWe have been asking the wrong question,\u201d said Li. \u201cWe should be asking what the targeting gene or\u00a0<em>genes<\/em>\u00a0of these variants are affecting the microglia. Sometimes, one variant may affect the expression of multiple genes in the neighborhood.\u201d<\/p>\n<p><strong>Identifying One Among the Rest<\/strong><\/p>\n<p>Additionally, each region could contain several AD-associated genetic variants. Researchers then needed to pinpoint which variants are causal among the many that were identified through genetic analysis. Such precision is crucial for understanding the mechanisms by which non-coding variants contribute to the development of AD.<\/p>\n<p>The team employed a cutting-edge genome editing technique \u2013 prime editing, which allows them to introduce one single DNA base substitution at a time and to assess individual variant function at the\u00a0<em>TSPAN14<\/em>\u00a0AD risk locus. Through this method, they were able to identify one specific variant, differentiating it from another which is almost perfectly correlated and in the same cCRE region, to be responsible for\u00a0<em>TSPAN14<\/em>\u00a0expression.<\/p>\n<p><strong>Linking Non-Coding Variants to Functions Beyond Gene Expression<\/strong><\/p>\n<p>More importantly, the responsible variant further negatively affected a cascade of downstream cellular processes, including the maturation of ADAM10 protein and soluble TREM2 shredding in microglia. Since all three aforementioned genes are known to be risk genes for AD, the study successfully links an AD non-coding variant to functions in microglia beyond control of gene expression.<\/p>\n<p>Their research findings, Li said, will serve as a new foundation from which other researchers can discover more causal variants of AD, predict disease risks, and develop more effective therapies. \u00a0This work was also made possible in collaboration with\u00a0<a href=\"https:\/\/directory.weill.cornell.edu\/person\/profile\/lig2033\">Li Gan<\/a>\u2019s group from the Helen and Robert Appel Alzheimer\u2019s Disease Research Institute, Weill Cornell Medical College.<\/p>\n<p>Li, Shen, and Gan labs will continue to expand the analysis of AD risk variants using more complex model systems that mimic the human brain, such as human cerebral organoids.<\/p>\n<p>&nbsp;<\/p>\n<p>This article originally appeared in <a href=\"https:\/\/news.unchealthcare.org\/2023\/09\/researchers-connect-alzheimers-associated-genetic-variants-with-brain-cell-function?utm_source=Vital+Signs&amp;utm_campaign=Vital+Signs+9-28-23&amp;utm_medium=email\">the UNC Health Newsroom<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Led by scientists at UNC-Chapel Hill and UC-San Francisco, research reveals new non-coding genetic variants associated with Alzheimer\u2019s disease functioning in microglia \u2013 brain cells already implicated in the progression of this often-fatal neurodegenerative condition. Yun Li, PhD, professor of genetics, is the lead UNC School of Medicine researcher.<\/p>\n","protected":false},"author":28418,"featured_media":2975,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[2],"tags":[56],"class_list":["post-13285","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-news","tag-li","odd"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.8 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Researchers Connect Alzheimer\u2019s-Associated Genetic Variants with Brain Cell Function | Department of Genetics<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.med.unc.edu\/genetics\/researchers-connect-alzheimers-associated-genetic-variants-with-brain-cell-function\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Researchers Connect Alzheimer\u2019s-Associated Genetic Variants with Brain Cell Function | Department of Genetics\" \/>\n<meta property=\"og:description\" content=\"Led by scientists at UNC-Chapel Hill and UC-San Francisco, research reveals new non-coding genetic variants associated with Alzheimer\u2019s disease functioning in microglia \u2013 brain cells already implicated in the progression of this often-fatal neurodegenerative condition. 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