The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force.
Qingbo S WangRyuya EdahiroHo NamkoongTakanori HasegawaYuya ShiraiKyuto SoneharaHiromu TanakaHo LeeRyunosuke SaikiTakayoshi HyugajiEigo ShimizuKotoe KatayamaMasahiro KanaiTatsuhiko NaitoNoah SasaKenichi YamamotoYasuhiro KatoTakayoshi MoritaKazuhisa TakahashiNorihiro HaradaToshio NaitoMakoto HikiYasushi MatsushitaHaruhi TakagiMasako IchikawaAi NakamuraSonoko HaradaYuuki SandhuHiroki KabataKatsunori MasakiHirofumi KamataShinnosuke IkemuraShotaro ChubachiSatoshi OkamoriHideki TeraiAtsuho MoritaTakanori AsakuraJunichi SasakiHiroshi MorisakiYoshifumi UwaminoKosaku NankiSho UchidaShunsuke UnoTomoyasu NishimuraTakashri IshiguroTaisuke IsonoShun ShibataYuma MatsuiChiaki HosodaKenji TakanoTakashi NishidaYoichi KobayashiYotaro TakakuNoboru TakayanagiSoichiro UedaAi TadaMasayoshi MiyawakiMasaomi YamamotoEriko YoshidaReina HayashiTomoki NagasakaSawako AraiYutaro KanekoKana SasakiEtsuko TagayaMasatoshi KawanaKen ArimuraKunihiko TakahashiTatsuhiko AnzaiSatoshi ItoAkifumi EndoYuji UchimuraYasunari MiyazakiTakayuki HondaTomoya TateishiShuji TohdaNaoya IchimuraKazunari SonobeChihiro Tani SassaJun NakajimaYasushi NakanoYukiko NakajimaRyusuke AnanRyosuke AraiYuko KuriharaYuko HaradaKazumi NishioTetsuya UedaMasanori AzumaRyuichi SaitoToshikatsu SadoYoshimune MiyazakiRyuichi SatoYuki HarutaTadao NagasakiYoshinori YasuiYoshinori HasegawaYoshikazu MutohTomoki KimuraTomonori SatoReoto TakeiSatoshi HagimotoYoichiro NoguchiYasuhiko YamanoHajime SasanoSho OtaYasushi NakamoriKazuhisa YoshiyaFukuki SaitoTomoyuki YoshiharaDaiki WadaHiromu IwamuraSyuji KanayamaShuhei MaruyamaTakashi YoshiyamaKen OhtaHiroyuki KokutoHideo OgataYoshiaki TanakaKenichi ArakawaMasafumi ShimodaTakeshi OsawaHiroki TatenoIsano HaseShuichi YoshidaShoji SuzukiMiki KawadaHirohisa HorinouchiFumitake SaitoKeiko MitamuraMasao HagiharaJunichi OchiTomoyuki UchidaRie BabaDaisuke AraiTakayuki OguraHidenori TakahashiShigehiro HagiwaraGenta NagaoShunichiro KonishiIchiro NakachiKoji MurakamiMitsuhiro YamadaHisatoshi SugiuraHirohito SanoShuichiro MatsumotoNozomu KimuraYoshinao OnoHiroaki BabaYusuke SuzukiSohei NakayamaKeita MasuzawaShinichi NambaTakayuki ShiroyamaYoshimi NodaTakayuki NiitsuYuichi AdachiTakatoshi EnomotoSaori AmiyaReina HaraYuta YamaguchiTeruaki MurakamiTomoki KugeKinnosuke MatsumotoYuji YamamotoMakoto YamamotoMidori YonedaKazunori TomonoKazuto KatoHaruhiko HirataYoshito TakedaHidefumi KohTadashi ManabeYohei FunatsuFumimaro ItoTakahiro FukuiKeisuke ShinozukaSumiko KohashiMasatoshi MiyazakiTomohisa ShokoMitsuaki KojimaTomohiro AdachiMotonao IshikawaKenichiro TakahashiTakashi InoueToshiyuki HiranoKeigo KobayashiHatsuyo TakaokaKazuyoshi WatanabeNaoki MiyazawaYasuhiro KimuraReiko SadoHideyasu SugimotoAkane KamiyaNaota KuwaharaAkiko FujiwaraTomohiro MatsunagaYoko SatoTakenori OkadaYoshihiro HiraiHidetoshi KawashimaAtsuya NaritaKazuki NiwaYoshiyuki SekikawaKoichi NishiMasaru NishitsujiMayuko TaniJunya SuzukiHiroki NakatsumiTakashi OguraHideya KitamuraEri HagiwaraKota MurohashiHiroko OkabayashiTakao MochimaruShigenari NukagaRyosuke SatomiYoshitaka OyamadaNobuaki MoriTomoya BabaYasutaka FukuiMitsuru OdateShuko MashimoYasushi MakinoKazuma YagiMizuha HashiguchiJunko KagyoTetsuya ShiomiSatoshi FukeHiroshi SaitoTomoya TsuchidaShigeki FujitaniMumon TakitaDaiki MorikawaToru YoshidaTakehiro IzumoMinoru InomataNaoyuki KuseNobuyasu AwanoMari ToneAkihiro ItoYoshihiko NakamuraKota HoshinoJunichi MaruyamaHiroyasu IshikuraTohru TakataToshio OdaniMasaru AmishimaTakeshi HattoriYasuo ShichinoheTakashi KagayaToshiyuki KitaKazuhide OhtaSatoru SakagamiKiyoshi KoshidaKentaro HayashiTetsuo ShimizuYutaka KozuHisato HiranumaYasuhiro GonNamiki IzumiKaoru NagataKen UedaReiko TakiSatoko HanadaKodai KawamuraKazuya IchikadoKenta NishiyamaHiroyuki MuranakaKazunori NakamuraNaozumi HashimotoKeiko WakaharaSakamoto KojiNorihito OmoteAkira AndoNobuhiro KodamaYasunari KaneyamaShunsuke MaedaTakashige KurakiTakemasa MatsumotoKoutaro YokoteTaka-Aki NakadaRyuzo AbeTaku OshimaTadanaga ShimadaMasahiro HaradaTakeshi TakahashiHiroshi OnoToshihiro SakuraiTakayuki ShibusawaYoshifumi KimizukaAkihiko KawanaTomoya SanoChie WatanabeRyohei SuematsuHisako SageshimaAyumi YoshifujiKazuto ItoSaeko TakahashiKota IshiokaMorio NakamuraMakoto MasudaAya WakabayashiHiroki WatanabeSuguru UedaMasanori NishikawaYusuke ChiharaMayumi TakeuchiKeisuke OnoiJun ShinozukaAtsushi SueyoshiYoji NagasakiMasaki OkamotoSayoko IshiharaMasatoshi ShimoYoshihisa TokunagaYu KusakaTakehiko OhbaSusumu IsogaiAki OgawaTakuya InoueSatoru FukuyamaYoshihiro EriguchiAkiko YonekawaKeiko Kan-OKoichiro MatsumotoKensuke KanaokaShoichi IharaKiyoshi KomutaYoshiaki InoueShigeru ChibaKunihiro YamagataYuji HiramatsuHirayasu KaiKoichiro AsanoTsuyoshi OgumaYoko ItoSatoru HashimotoMasaki YamasakiYu KasamatsuYuko KomaseNaoya HidaTakahiro TsuburaiBaku OyamaMinoru TakadaHidenori KandaYuichiro KitagawaTetsuya FukutaTakahito MiyakeShozo YoshidaShinji OguraShinji AbeYuta KonoYuki TogashiHiroyuki TakoiRyota KikuchiShinichi OgawaTomouki OgataShoichiro IshiharaArihiko KanehiroShinji OzakiYasuko FuchimotoSae WadaNobukazu FujimotoKei NishiyamaMariko TerashimaSatoru BeppuKosuke YoshidaOsamu NarumotoHideaki NagaiNobuharu OoshimaMitsuru MotegiAkira UmedaKazuya MiyagawaHisato ShimadaMayu EndoYoshiyuki OhiraMasafumi WatanabeSumito InoueAkira IgarashiMasamichi SatoHironori SagaraAkihiko TanakaShin OhtaTomoyuki KimuraYoko ShibataYoshinori TaninoTakefumi NikaidoHiroyuki MinemuraYuki SatoYuichiro YamadaTakuya HashinoMasato ShinokiHajime IwagoeHiroshi TakahashiKazuhiko FujiiHiroto KishiMasayuki KanaiTomonori ImamuraTatsuya YamashitaMasakiyo YatomiToshitaka MaenoShinichi HayashiMai TakahashiMizuki KuramochiIsamu KamimakiYoshiteru TominagaTomoo IshiiMitsuyoshi UtsugiAkihiro OnoToru TanakaTakeru KashiwadaKazue FujitaYoshinobu SaitoMasahiro SeikeHiroko WatanabeHiroto MatsuseNorio KodakaChihiro NakanoTakeshi OshioTakatomo HirouchiShohei MakinoMoritoki EgiYosuke OmaeYasuhito NannyaTakafumi UenoTomomi TakanoKazuhiko KatayamaMasumi AiAtsushi KumanogohToshiro SatoNaoki HasegawaKatsushi TokunagaMakoto IshiiRyuji KoikeYuko KitagawaAkinori KimuraSeiya ImotoSatoru MiyanoSeishi OgawaTakanori KanaiKoichi FukunagaYukinori OkadaPublished in: Nature communications (2022)
Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection.
Keyphrases
- coronavirus disease
- sars cov
- gene expression
- genome wide
- respiratory syndrome coronavirus
- rna seq
- dna methylation
- single cell
- early onset
- small molecule
- bone marrow
- high resolution
- copy number
- machine learning
- long non coding rna
- deep learning
- infectious diseases
- genome wide identification
- big data
- binding protein
- heat shock