Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus.
Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus.
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DOI：
10.1126/science.abf1970
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发表时间：
2022-04-08
期刊：
影响因子：
56.9
通讯作者：
Ye, Chun Jimmie
中科院分区：
文献类型：
--
作者：
Perez, Richard K.;Gordon, M. Grace;Subramaniam, Meena;Kim, Min Cheol;Hartoularos, George C.;Targ, Sasha;Sun, Yang;Ogorodnikov, Anton;Bueno, Raymund;Lu, Andrew;Thompson, Mike;Rappoport, Nadav;Dahl, Andrew;Lanata, Cristina M.;Matloubian, Mehrdad;Maliskova, Lenka;Kwek, Serena S.;Li, Tony;Slyper, Michal;Waldman, Julia;Dionne, Danielle;Rozenblatt-Rosen, Orit;Fong, Lawrence;Dall'Era, Maria;Balliu, Brunilda;Regev, Aviv;Yazdany, Jinoos;Criswell, Lindsey A.;Zaitlen, Noah;Ye, Chun Jimmie
系统性红斑狼疮（SLE）是一种异质性自身免疫性疾病。与SLE相关的循环免疫细胞类型和状态的知识仍然不完整。我们使用多重单细胞RNA测序（mux-seq）分析了超过120万外周血单个核细胞（162例，99例对照）。病例表现为单核细胞中1型干扰素刺激基因（ISGs）表达升高，与单核细胞ISG表达相关的naïve CD4+ T细胞减少，限制性细胞毒性GZMH+ CD8+ T细胞增加。细胞类型特异性表达特征预测病例对照状态，并将患者分为两种分子亚型。我们整合了密集的基因分型数据来绘制细胞特异性顺式表达的数量性状位点，并将sli相关变异与细胞特异性表达联系起来。这些结果表明，mux-seq是一种系统的方法，可以表征细胞组成，识别转录特征，并注释与SLE相关的遗传变异。系统性红斑狼疮（SLE）是一种异质性自身免疫性疾病，在亚洲、非洲和西班牙血统的女性和个体中患病率较高。大量转录组分析表明，1型干扰素信号传导增加、淋巴细胞激活失调和凋亡清除失败是疾病的标志。参与这些过程的许多基因都接近与SLE相关的约100个位点。尽管取得了这一进展，但对SLE循环免疫细胞的全面普查仍然不完整，并且注释介导遗传关联的细胞类型和背景仍然具有挑战性。过去，流式细胞术和大量转录组学分析被用于分析SLE中循环免疫细胞的组成和基因表达。然而，流式细胞术由于使用有限的已知标记物而存在偏差，而大量转录组分析没有足够的能力来检测细胞类型特异性表达差异。外周血单核细胞（PBMCs）的单细胞RNA测序（scRNA-seq）具有作为一种全面、公正的方法同时分析循环免疫细胞的组成和转录状态的潜力。然而，scRNA-seq在人群队列中的应用受到样本量、成本和对技术变异的易感性的限制。为了克服这些限制，我们先前开发了多路scRNA-seq (multi -seq)，以实现对人群队列进行系统和经济有效的scrna测序。我们使用多重序列分析了来自162例SLE病例和99例亚洲或欧洲血统的健康对照的120多万pbmc。SLE病例在pbmc的组成和状态上都存在差异。淋巴细胞组成分析显示naïve CD4+ T细胞减少，限制性GZMH+ CD8+ T细胞增加。对8种细胞类型的转录组学分析显示，经典单核细胞表达最高水平的泛细胞型和骨髓特异性1型干扰素刺激基因（ISGs）。单核细胞中ISGs的表达与naïve CD4+ T细胞丰度呈负相关。细胞类型特异性表达特征准确预测病例对照状态并将患者分层为分子亚型。通过整合基因分型数据并使用一种新的矩阵分解方法，我们在8种细胞类型中绘制了共享的和细胞类型特异性的顺式表达数量性状位点（cis- eqtl）。细胞类型特异性的cis- eqtl富集于相同或相关细胞类型特异性的开放染色质区域。顺式- eqtl和全基因组关联研究结果的联合分析能够鉴定与免疫介导疾病相关的细胞类型，精细绘制疾病相关位点，并发现新的SLE关联。相互作用分析确定了对基因表达的影响通过干扰素激活在患者中进一步改变的变异。SLE的诊断和治疗仍然具有挑战性。疾病表现和治疗反应的异质性突出了改进分子表征的必要性。在一个大型的多种族队列中，我们证明了mux-seq作为一种系统的方法来表征细胞组成，鉴定细胞类型特异性转录组特征，并注释与SLE相关的遗传变异。检测SLE的细胞和遗传相关因素。遗传多路复用能够对数百名SLE患者和非SLE患者进行单细胞分析。这些资料显示SLE患者表现出细胞组成和细胞类型特异性基因表达的变化，这些变化被用来模拟疾病状态和严重程度。此外，还制作了细胞类型特异性的顺式- eqtl图谱，并用于注释与SLE相关的遗传位点。
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (162 cases, 99 controls) with multiplexed single-cell RNA sequencing (mux-seq). Cases exhibited elevated expression of type 1 interferon–stimulated genes (ISGs) in monocytes, reduction of naïve CD4+ T cells that correlated with monocyte ISG expression, and expansion of repertoire-restricted cytotoxic GZMH+ CD8+ T cells. Cell type–specific expression features predicted case-control status and stratified patients into two molecular subtypes. We integrated dense genotyping data to map cell type–specific cis–expression quantitative trait loci and to link SLE-associated variants to cell type–specific expression. These results demonstrate mux-seq as a systematic approach to characterize cellular composition, identify transcriptional signatures, and annotate genetic variants associated with SLE. Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with elevated prevalence in women and individuals of Asian, African, and Hispanic ancestry. Bulk transcriptomic profiling has implicated increased type 1 interferon signaling, dysregulated lymphocyte activation, and failure of apoptotic clearance as hallmarks of disease. Many genes participating in these processes are proximal to the ~100 loci associated with SLE. Despite this progress, a comprehensive census of circulating immune cells in SLE remains incomplete, and annotating the cell types and contexts that mediate genetic associations remains challenging. Historically, flow cytometry and bulk transcriptomic analyses were used to profile the composition and gene expression of circulating immune cells in SLE. However, flow cytometry is biased by its use of a limited set of known markers, whereas bulk transcriptomic profiling does not have sufficient power to detect cell type–specific expression differences. Single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) holds potential as a comprehensive and unbiased approach to simultaneously profile the composition and transcriptional states of circulating immune cells. However, application of scRNA-seq to population cohorts has been limited by sample throughput, cost, and susceptibility to technical variability. To overcome these limitations, we previously developed multiplexed scRNA-seq (mux-seq) to enable systematic and cost-effective scRNA-seq of population cohorts. We used mux-seq to profile more than 1.2 million PBMCs from 162 SLE cases and 99 healthy controls of either Asian or European ancestry. SLE cases exhibited differences in both the composition and state of PBMCs. Analysis of lymphocyte composition revealed a reduction in naïve CD4+ T cells and an increase in repertoire-restricted GZMH+ CD8+ T cells. Analysis of transcriptomic profiles across eight cell types revealed that classical monocytes expressed the highest levels of both pan–cell type and myeloid-specific type 1 interferon-stimulated genes (ISGs). The expression of ISGs in monocytes was inversely correlated with naïve CD4+ T cell abundance. Cell type–specific expression features accurately predicted case-control status and stratified patients into molecular subtypes. By integrating genotyping data and using a novel matrix decomposition method, we mapped shared and cell type–specific cis–expression quantitative trait loci (cis-eQTLs) across eight cell types. Cell type–specific cis-eQTLs were enriched for regions of open chromatin specific to the same or related cell types. Joint analysis of cis-eQTLs and genome-wide association study results enabled identification of cell types relevant to immune-mediated diseases, fine-mapping of disease-associated loci, and discovery of novel SLE associations. Interaction analysis identified variants whose effects on gene expression are further modified by interferon activation across patients. SLE remains challenging to diagnose and treat. The heterogeneity of disease manifestations and treatment response highlight the need for improved molecular characterization. In a large multiethnic cohort, we demonstrate mux-seq as a systematic approach to characterize cellular composition, identify cell type–specific transcriptomic signatures, and annotate genetic variants associated with SLE. Detection of cellular and genetic correlates of SLE. Genetic multiplexing enabled single-cell profiling of hundreds of individuals with and without SLE. These profiles revealed that SLE patients exhibit changes in cell composition and cell type–specific gene expression, which were used to model disease status and severity. Additionally, cell type–specific cis-eQTL maps were produced and used to annotate and contextualize genetic loci associated with SLE.
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影响因子：
64.8
作者：
Bycroft C;Freeman C;Petkova D;Band G;Elliott LT;Sharp K;Motyer A;Vukcevic D;Delaneau O;O'Connell J;Cortes A;Welsh S;Young A;Effingham M;McVean G;Leslie S;Allen N;Donnelly P;Marchini J
通讯作者：
Marchini J
影响因子：
30.8
作者：
Barrett, Jeffrey C.;Clayton, David G.;Concannon, Patrick;Akolkar, Beena;Cooper, Jason D.;Erlich, Henry A.;Julier, Cecile;Morahan, Grant;Nerup, Jorn;Nierras, Concepcion;Plagnol, Vincent;Pociot, Flemming;Schuilenburg, Helen;Smyth, Deborah J.;Stevens, Helen;Todd, John A.;Walker, Neil M.;Rich, Stephen S.
通讯作者：
Rich, Stephen S.
影响因子：
30.8
作者：
Finucane HK;Reshef YA;Anttila V;Slowikowski K;Gusev A;Byrnes A;Gazal S;Loh PR;Lareau C;Shoresh N;Genovese G;Saunders A;Macosko E;Pollack S;Brainstorm Consortium;Perry JRB;Buenrostro JD;Bernstein BE;Raychaudhuri S;McCarroll S;Neale BM;Price AL
通讯作者：
Price AL
影响因子：
30.8
作者：
Calderon, Diego;Nguyen, Michelle L. T.;Pritchard, Jonathan K.
通讯作者：
Pritchard, Jonathan K.
系统性红斑狼疮
影响因子：
81.5
作者：
Kaul, Arvind;Gordon, Caroline;Hughes, Graham
通讯作者：
Hughes, Graham