{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T04:45:13Z","timestamp":1775882713709,"version":"3.50.1"},"posted":{"date-parts":[[2025,1,8]]},"group-title":"Genetics","reference-count":76,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,1,8]],"date-time":"2025-01-08T00:00:00Z","timestamp":1736294400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>BACKGROUND<\/jats:title>\n                  <jats:p>\n                    Synonymous variant\n                    <jats:italic>NC_000007.14:g.100373690T&gt;C<\/jats:italic>\n                    (\n                    <jats:italic>rs2405442:T&gt;C<\/jats:italic>\n                    ) in the Paired Immunoglobulin-like Type 2 Receptor Alpha (\n                    <jats:italic>PILRA<\/jats:italic>\n                    ) gene was previously associated with decreased risk for Alzheimer\u2019s disease (AD) in genome-wide association studies, but its biological impact is largely unknown.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>OBJECTIVE<\/jats:title>\n                  <jats:p>\n                    We hypothesized that\n                    <jats:italic>rs2405442:T&gt;C<\/jats:italic>\n                    decreases mRNA and protein levels by destroying a ramp of slowly translated codons at the 5\u2019 end of\n                    <jats:italic>PILRA<\/jats:italic>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>METHODS<\/jats:title>\n                  <jats:p>\n                    We assessed\n                    <jats:italic>rs2405442:T&gt;C<\/jats:italic>\n                    predicted effects on\n                    <jats:italic>PILRA<\/jats:italic>\n                    through quantitative polymerase chain reactions (qPCR) and enzyme-linked immunosorbent assays (ELISA) using Chinese hamster ovary (CHO) cells.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>RESULTS<\/jats:title>\n                  <jats:p>\n                    Both mRNA (\n                    <jats:italic>P<\/jats:italic>\n                    =1.9184 \u00d7 10\n                    <jats:sup>\u221213<\/jats:sup>\n                    ) and protein (\n                    <jats:italic>P<\/jats:italic>\n                    =0.01296) levels significantly decreased in the mutant versus the wildtype in the direction that we predicted based on destroying a ramp sequence.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>CONCLUSIONS<\/jats:title>\n                  <jats:p>\n                    We show that\n                    <jats:italic>rs2405442:T&gt;C<\/jats:italic>\n                    alone directly impacts\n                    <jats:italic>PILRA<\/jats:italic>\n                    mRNA and protein expression, and ramp sequences may play a role in regulating AD-associated genes without modifying the protein product.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Research in Context<\/jats:title>\n                  <jats:list list-type=\"order\">\n                    <jats:list-item>\n                      <jats:p>\n                        <jats:bold>Systematic review:<\/jats:bold>\n                        Genetic variants identified through genome-wide association studies often lack biological support for their association with Alzheimer\u2019s disease. Although synonymous variant\n                        <jats:italic>rs2405442:T&gt;C<\/jats:italic>\n                        in\n                        <jats:italic>PILRA<\/jats:italic>\n                        was previously reported as protective against Alzheimer\u2019s disease, its effects have generally been attributed to linkage with missense variant,\n                        <jats:italic>rs1859788:A&gt;G<\/jats:italic>\n                        .\n                      <\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>\n                        <jats:bold>Interpretation:<\/jats:bold>\n                        We show that\n                        <jats:italic>rs2405442:T&gt;C<\/jats:italic>\n                        alone decreases mRNA and protein levels by destroying a ramp of slowly translated codons at the beginning of\n                        <jats:italic>PILRA<\/jats:italic>\n                        . We also show that a ramp sequence is present in\n                        <jats:italic>PILRA<\/jats:italic>\n                        and likely regulates mRNA and protein levels, thus offering a plausible biological mechanism explaining\n                        <jats:italic>rs2405442:T&gt;C<\/jats:italic>\n                        association with Alzheimer\u2019s disease independent of\n                        <jats:italic>rs1859788:A&gt;G<\/jats:italic>\n                        .\n                      <\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>\n                        <jats:bold>Future directions:<\/jats:bold>\n                        We provide the first protocol to evaluate how disease-associated variants impact ramp sequences, which could explain why some genetic variants are reported by genome-wide association studies. Future studies might examine if the ramp sequence could be therapeutically targeted to regulate\n                        <jats:italic>PILRA<\/jats:italic>\n                        expression without changing the protein product.\n                      <\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>","DOI":"10.1101\/2025.01.06.631528","type":"posted-content","created":{"date-parts":[[2025,1,8]],"date-time":"2025-01-08T13:45:26Z","timestamp":1736343926000},"source":"Crossref","is-referenced-by-count":0,"title":["Ramp sequence may explain synonymous variant association with Alzheimer\u2019s disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (\n                  <i>PILRA<\/i>\n                  )"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5309-1570","authenticated-orcid":false,"given":"Justin B.","family":"Miller","sequence":"first","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY 40506, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J. Anthony","family":"Brandon","sequence":"additional","affiliation":[{"name":"Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lauren M.","family":"McKinnon","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hady W.","family":"Sabra","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY 40506, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chloe C.","family":"Lucido","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY 40506, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Josue D.","family":"Gonzalez Murcia","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kayla A.","family":"Nations","sequence":"additional","affiliation":[{"name":"Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel H.","family":"Payne","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark T.W.","family":"Ebbert","sequence":"additional","affiliation":[{"name":"Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY 40506, USA"},{"name":"Department of Neuroscience, University of Kentucky, Lexington, KY 40506, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John S.K.","family":"Kauwe","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Perry G.","family":"Ridge","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT 84602"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2026041020530685000_2025.01.06.631528v1.1","doi-asserted-by":"publisher","DOI":"10.1001\/archpsyc.63.2.168"},{"key":"2026041020530685000_2025.01.06.631528v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-022-01024-z"},{"key":"2026041020530685000_2025.01.06.631528v1.3","doi-asserted-by":"publisher","DOI":"10.1007\/s11882-013-0417-1"},{"key":"2026041020530685000_2025.01.06.631528v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41398-018-0150-6"},{"key":"2026041020530685000_2025.01.06.631528v1.5","doi-asserted-by":"publisher","DOI":"10.1001\/archneurol.2010.201"},{"key":"2026041020530685000_2025.01.06.631528v1.6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0016616"},{"key":"2026041020530685000_2025.01.06.631528v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2802"},{"key":"2026041020530685000_2025.01.06.631528v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.neurobiolaging.2016.02.024"},{"key":"2026041020530685000_2025.01.06.631528v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2023.104511"},{"key":"2026041020530685000_2025.01.06.631528v1.10","doi-asserted-by":"publisher","DOI":"10.1093\/brain\/awv268"},{"key":"2026041020530685000_2025.01.06.631528v1.11","doi-asserted-by":"publisher","DOI":"10.1212\/nxg.0000000000000576"},{"key":"2026041020530685000_2025.01.06.631528v1.12","doi-asserted-by":"publisher","DOI":"10.18632\/aging.100801"},{"key":"2026041020530685000_2025.01.06.631528v1.13","doi-asserted-by":"publisher","DOI":"10.1038\/srep46263"},{"key":"2026041020530685000_2025.01.06.631528v1.14","doi-asserted-by":"publisher","DOI":"10.1017\/S135561771700039X"},{"key":"2026041020530685000_2025.01.06.631528v1.15","doi-asserted-by":"publisher","DOI":"10.1007\/s12035-015-9664-6"},{"key":"2026041020530685000_2025.01.06.631528v1.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.neulet.2015.10.007"},{"key":"2026041020530685000_2025.01.06.631528v1.17","doi-asserted-by":"publisher","DOI":"10.1136\/jnnp.55.10.956"},{"key":"2026041020530685000_2025.01.06.631528v1.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.neurobiolaging.2016.08.001"},{"key":"2026041020530685000_2025.01.06.631528v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/srep43270"},{"key":"2026041020530685000_2025.01.06.631528v1.20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0186595"},{"key":"2026041020530685000_2025.01.06.631528v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2016.02.041"},{"key":"2026041020530685000_2025.01.06.631528v1.22","doi-asserted-by":"publisher","DOI":"10.1038\/s41380-018-0298-8"},{"key":"2026041020530685000_2025.01.06.631528v1.23","doi-asserted-by":"publisher","DOI":"10.1038\/nrneurol.2012.135"},{"key":"2026041020530685000_2025.01.06.631528v1.24","doi-asserted-by":"publisher","DOI":"10.1212\/WNL.0000000000002923"},{"key":"2026041020530685000_2025.01.06.631528v1.25","doi-asserted-by":"publisher","DOI":"10.1001\/archpsyc.1987.01800170026005"},{"key":"2026041020530685000_2025.01.06.631528v1.26","doi-asserted-by":"publisher","DOI":"10.1016\/j.jalz.2017.04.011"},{"key":"2026041020530685000_2025.01.06.631528v1.27","doi-asserted-by":"publisher","DOI":"10.1016\/S0197-4580(00)00183-4"},{"key":"2026041020530685000_2025.01.06.631528v1.28","doi-asserted-by":"publisher","DOI":"10.1007\/s00415-005-0019-5"},{"key":"2026041020530685000_2025.01.06.631528v1.29","doi-asserted-by":"publisher","DOI":"10.1212\/WNL.36.9.1179"},{"key":"2026041020530685000_2025.01.06.631528v1.30","doi-asserted-by":"publisher","DOI":"10.1038\/nature08185"},{"key":"2026041020530685000_2025.01.06.631528v1.31","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-020-00742-5"},{"key":"2026041020530685000_2025.01.06.631528v1.32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0020221"},{"key":"2026041020530685000_2025.01.06.631528v1.33","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq009"},{"key":"2026041020530685000_2025.01.06.631528v1.34","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1313"},{"key":"2026041020530685000_2025.01.06.631528v1.35","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13810-1"},{"key":"2026041020530685000_2025.01.06.631528v1.36","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1193"},{"key":"2026041020530685000_2025.01.06.631528v1.37","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-11-r110"},{"key":"2026041020530685000_2025.01.06.631528v1.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2010.03.031"},{"key":"2026041020530685000_2025.01.06.631528v1.39","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku646"},{"key":"2026041020530685000_2025.01.06.631528v1.40","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000396"},{"key":"2026041020530685000_2025.01.06.631528v1.41","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-019-0118-2"},{"key":"2026041020530685000_2025.01.06.631528v1.42","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-78803-3"},{"key":"2026041020530685000_2025.01.06.631528v1.43","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa863"},{"key":"2026041020530685000_2025.01.06.631528v1.44","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqac039"},{"key":"2026041020530685000_2025.01.06.631528v1.45","doi-asserted-by":"publisher","DOI":"10.1038\/ni.2456"},{"key":"2026041020530685000_2025.01.06.631528v1.46","doi-asserted-by":"publisher","DOI":"10.1126\/science.1260419"},{"key":"2026041020530685000_2025.01.06.631528v1.47","doi-asserted-by":"publisher","DOI":"10.1002\/path.2440"},{"key":"2026041020530685000_2025.01.06.631528v1.48","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201545897"},{"key":"2026041020530685000_2025.01.06.631528v1.49","doi-asserted-by":"publisher","DOI":"10.15252\/emmm.201606210"},{"key":"2026041020530685000_2025.01.06.631528v1.50","doi-asserted-by":"publisher","DOI":"10.1038\/nn.4587"},{"key":"2026041020530685000_2025.01.06.631528v1.51","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-021-03986-5"},{"key":"2026041020530685000_2025.01.06.631528v1.52","doi-asserted-by":"publisher","DOI":"10.1111\/nan.12452"},{"key":"2026041020530685000_2025.01.06.631528v1.53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007427"},{"key":"2026041020530685000_2025.01.06.631528v1.54","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0311-9"},{"key":"2026041020530685000_2025.01.06.631528v1.55","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1049"},{"key":"2026041020530685000_2025.01.06.631528v1.56","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1016"},{"key":"2026041020530685000_2025.01.06.631528v1.57","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1001025"},{"key":"2026041020530685000_2025.01.06.631528v1.58","first-page":"1","article-title":"Annotating and prioritizing human non-coding variants with RegulomeDB","volume":"2","year":"2023","journal-title":"Nature Genetics"},{"key":"2026041020530685000_2025.01.06.631528v1.59","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaz1776"},{"key":"2026041020530685000_2025.01.06.631528v1.60","first-page":"1","article-title":"FANTOM5 CAGE profiles of human and mouse samples","volume":"4","year":"2017","journal-title":"Scientific data"},{"key":"2026041020530685000_2025.01.06.631528v1.61","doi-asserted-by":"publisher","DOI":"10.1126\/science.1168978"},{"key":"2026041020530685000_2025.01.06.631528v1.62","doi-asserted-by":"publisher","DOI":"10.1006\/meth.2001.1262"},{"key":"2026041020530685000_2025.01.06.631528v1.63","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1974"},{"key":"2026041020530685000_2025.01.06.631528v1.64","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2016.08.012"},{"key":"2026041020530685000_2025.01.06.631528v1.65","doi-asserted-by":"publisher","DOI":"10.1101\/2022.03.20.485034"},{"key":"2026041020530685000_2025.01.06.631528v1.66","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0232260"},{"key":"2026041020530685000_2025.01.06.631528v1.67","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2019.106697"},{"key":"2026041020530685000_2025.01.06.631528v1.68","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa863"},{"key":"2026041020530685000_2025.01.06.631528v1.69","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.6984"},{"key":"2026041020530685000_2025.01.06.631528v1.70","doi-asserted-by":"publisher","DOI":"10.1111\/cla.12183"},{"key":"2026041020530685000_2025.01.06.631528v1.71","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-32358-1"},{"key":"2026041020530685000_2025.01.06.631528v1.72","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0040180"},{"key":"2026041020530685000_2025.01.06.631528v1.73","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3336"},{"key":"2026041020530685000_2025.01.06.631528v1.74","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2010.02.036"},{"key":"2026041020530685000_2025.01.06.631528v1.75","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.3147"},{"key":"2026041020530685000_2025.01.06.631528v1.76","doi-asserted-by":"publisher","DOI":"10.1038\/s41419-021-03838-x"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.01.06.631528","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T03:53:15Z","timestamp":1775879595000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.01.06.631528"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,8]]},"references-count":76,"URL":"https:\/\/doi.org\/10.1101\/2025.01.06.631528","relation":{},"subject":[],"published":{"date-parts":[[2025,1,8]]},"subtype":"preprint"}}