摘要:目的 采用單細胞測序技術(shù)揭示非酒精性脂肪肝炎(NASH)小鼠肝組織T淋巴細胞單細胞水平的異質(zhì)性和轉(zhuǎn)錄組學特征,為研究T淋巴細胞在NASH中的作用機制提供新的依據(jù)。方法 6只C57BL/6雄性小鼠隨機分為普通飼料喂養(yǎng)的對照組和膽堿蛋氨酸缺乏飼料喂養(yǎng)的NASH組,每組各3只。造模6周后取小鼠肝組織進行單細胞RNA測序。分析T淋巴細胞單細胞亞群的特異性差異表達基因,分別行降維聚類、細胞類型注釋、t分布隨機鄰域嵌入(t-SNE)、小提琴圖、基因本體(GO)功能富集分析和京都基因與基因組百科全書(KEGG)通路富集分析。利用免疫熒光染色觀察兩組小鼠肝臟中Tcrα(T淋巴細胞分子標志)、Tcf7、Cxcr6(特征標志基因)的表達情況。計量資料兩組間比較采用成組t檢驗。結(jié)果 小鼠肝臟中共鑒定出2個T淋巴細胞亞群:(1)第6簇T淋巴細胞占比從對照組的58.5%降低到NASH組的48.7%。前4位特異性基因包括Nsg2、Cd8b1、Cd8a和Tcf7。該簇65%的細胞表達Tcf7(第6簇特征標志基因),定義為Tcf7 + T淋巴細胞亞群。GO和KEGG富集分析顯示,它們參與調(diào)控T淋巴細胞活化、白細胞黏附、結(jié)合泛素樣蛋白連接酶,以及輔助性T淋巴細胞(Th)17、Th1、Th2細胞分化等信號通路。(2)第7簇T淋巴細胞占比從對照組的41.5%增高到NASH組的51.3%。前4位特異性基因包括Cd40lg、Tcrg-C1、Il2rα和Cxcr6。該簇90%的細胞表達Cxcr6,定義為Cxcr6 + T淋巴細胞亞群。GO和KEGG富集分析提示,該亞群參與調(diào)控T淋巴細胞活化、細胞因子產(chǎn)生,以及T淋巴細胞受體信號通路、Th17細胞分化與MAPK信號通路。
免疫熒光結(jié)果顯示,與對照組相比,NASH組小鼠肝臟中Tcf7蛋白和Tcrα蛋白共染陽性區(qū)域減少(1.80%±0.67% vs 0.33%±0.13%,Plt;0.05),而Cxcr6蛋白和Tcrα蛋白共染陽性區(qū)域增加(0.50%±0.09% vs 2.66%±0.33%,Plt;0.001)。結(jié)論 NASH小鼠肝臟中 Tcf7 + T淋巴細胞的占比降低,而 Cxcr6 + T淋巴細胞的占比增高,揭示了 NASH小鼠肝組織 T淋巴細胞的特征和差異。
關(guān)鍵詞:非酒精性脂肪性肝炎;T淋巴細胞;單細胞測序;小鼠,近交C57BL
基金項目:上海市浦東新區(qū)衛(wèi)生健康委員會醫(yī)學學科建設(shè)項目(PWYgf2021-02)
Characteristics of T cells in the liver tissues of mice with nonalcoholic steatohepatitis
MAO Ting 1 ,XU Mingyi 1 ,WANG Jiayi 2
1. Department of Gastroenterology,Shanghai East Hospital,Tongji University,Shanghai 200120,China;2. Department of Gastroenterology,Shanghai General Hospital,Shanghai Jiao Tong University,Shanghai 200080,China
Corresponding author:WANG Jiayi,18017028830@163.com (ORCID:0009-0004-8097-5288)
Abstract:Objective To investigate the heterogeneity and transcriptomic characteristics of T-cell subsets in the liver of mice with nonalcoholic steatohepatitis (NASH) at the single-cell level using single-cell RNA sequencing (scRNA-seq),and to provide a reference for studying the mechanism of action of T cells in NASH. Methods Six male C57BL/6 mice were randomly divided into control group fed with regular diet and NASH group fed with methionine-choline-deficient (MCD) diet,with three mice in each group,and liver tissue was collected for scRNA-seq after 6 weeks of modeling. Specific differentially expressed genes were analyzed between T-cell subsets,and related analyses were performed,including dimension clustering,cell type annotation,t-distributed stochastic neighbor embedding (t-SNE),violin plot,gene ontology (GO) functional enrichment analysis,and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Immunofluorescent staining was used to observe the expression of the T cell marker Tcrα and the specific marker genes Tcf7 and Cxcr6 in the liver of mice in the two groups. The independent-samples t test was used for comparison of continuous data between two groups. Results Two T cell subsets were identified in the liver of mice,and the percentage of cluster 6 decreased from 58.5% in the control group to 48.7% in the NASH group. The top four specific genes were Nsg2,Cd8b1,Cd8a,and Tcf7. Tcf7,a characteristic marker gene for cluster 6,was expressed in 65% of cells in cluster 6,and therefore,cluster 6 was defined as Tcf7 + T cells. The GO and KEGG enrichment analyses showed that the differentially expressed genes of cluster 6 were involved in T cell activation,leukocyte adhesion,binding ubiquitin-like protein ligase,and the signaling pathways for Th17,Th1,and Th2 cell differentiation. The percentage of cluster 7 increased from 41.5% in the control group to 51.3% in the NASH group. The top four specific genes of cluster 7 were Cd40lg,Tcrg-C1,Il2rα,and Cxcr6. Cxcr6 was expressed in 90% of cells in cluster 7,and therefore,cluster 7 was defined as Cxcr6 + T cells. The GO and KEGG enrichment analyses showed that cluster 7 was involved in T cell activation,cytokine production,the T cell receptor signaling pathway,and the Th17 cell differentiation and MAPK signaling pathway. Immunofluorescence assay showed that compared with the control group,the NASH group showed a significant reduction in the area with positive co-expression of Tcf7 protein and Tcrα protein (1.80%±0.67% vs 0.33%±0.13%,Plt;0.05) and a significant increase in the area with positive co-expression of Cxcr6 protein and Tcrα protein (0.50%±0.09% vs 2.66%±0.33%,Plt;0.001). Conclusion There is a reduction in the percentage of Tcf7 + T cells and an increase in the percentage of Cxcr6 +T cells in NASH mice,revealing the characteristics and differences of T cells in the liver of NASH mice.
Key words:Non-Alcoholic Steatohepatitis;T-Lymphocytes;Single-cell RNA Sequencing;Mice,Inbred C57BL
Research funding:Medical Discipline Construction Project of Pudong Health Committee of Shanghai (PWYgf2021-02)
非酒精性脂肪性肝炎(NASH)是非酒精性脂肪性肝?。∟AFLD)進一步進展為肝硬化和肝細胞癌的關(guān)鍵環(huán)節(jié)。隨著肥胖和代謝綜合征的流行,NASH和NAFLD已成為全球慢性肝病的最主要病因,嚴重危害人民生命健康[1]。單細胞 RNA 測序(single-cell RNA sequencing,scRNA-seq)是一種在單細胞水平上對轉(zhuǎn)錄組進行擴增和測序的新技術(shù)[2]。相比于傳統(tǒng)的轉(zhuǎn)錄組測序,單細胞RNA測序?qū)α私飧闻K非實質(zhì)細胞,如炎癥細胞尤為有效[3]。Su等 [4]通過 scRNA-seq分析發(fā)現(xiàn)了健康和 NAFLD 小鼠肝臟中非實質(zhì)細胞的基因表達譜改變。T淋巴細胞是細胞免疫反應(yīng)的效應(yīng)細胞。近年來,人們逐漸認識到T淋巴細胞在 NAFLD 發(fā)病過程中的重要作用。Koda 等[5]發(fā)現(xiàn),CD69 + CD103 ? CD8 + T 淋巴細胞在高脂高膽固醇誘導的NASH小鼠肝臟中顯著富集。有研究發(fā)現(xiàn),NAFLD患者的外周血中炎癥因子IL-10、IL-17、IL-23及TGF-β1的水平和輔助性T淋巴細胞(Th)17的水平呈正相關(guān)[6],且Th17細胞和IL-17的水平與NASH患者的病情嚴重程度呈正相關(guān)[7]。但在單細胞水平上研究T淋巴細胞在NASH中的特征改變?nèi)允怯斜匾?。因此,本研究采用scRNA-seq技術(shù)對健康小鼠和NASH小鼠的肝組織內(nèi)T淋巴細胞進行分群,旨在揭示NASH小鼠肝組織中不同T淋巴細胞亞群的轉(zhuǎn)錄組學特征。
1 資料與方法
1.1 實驗動物 選取8周齡C57BL/6雄性小鼠6只,隨機分為對照組和NASH組,每組各3只。對照組喂養(yǎng)普通飼料,NASH 組喂養(yǎng)膽堿蛋氨酸缺乏(methionine-choline-deficient,MCD)飼料,造模6周后處死小鼠,取肝組織進行scRNA-seq以獲得基因表達譜數(shù)據(jù)(上海鯨舟基因科技有限公司)[8]。
1.2 研究方法
1.2.1 scRNA-seq 使用 Seurat 3.0 軟件包讀取 scRNA-seq數(shù)據(jù),并為每個數(shù)據(jù)創(chuàng)建一個Seurat對象。排除獨特分子標志lt;200或gt;10 000的細胞及線粒體基因含量高于25%的細胞,并根據(jù)獨特分子標志細胞總計數(shù)進行對數(shù)標準化后,對前2 000個高可變基因使用主成分分析的降維算法進行降維,隨后基于主成分分析降維結(jié)果以0.6的分辨率進行聚類。
1.2.2 細胞注釋和分簇 使用Seurat 3.0中的FindAllMarkers函數(shù)篩選出所有細胞類群中的標志基因,并使用 R 包Single R 1.4.1內(nèi)置的小鼠RNA測序數(shù)據(jù)庫作為參考數(shù)據(jù)集對細胞亞群進行細胞類型注釋。通過白細胞分化抗原3α(the cluster of the differentiation 3α,Cd3α)、白細胞分化抗原8α(Cd8α)、白細胞分化抗原4(Cd4)和T淋巴細胞受體α(T cell receptor alpha,Tcrα)來鑒定T淋巴細胞。
1.2.3 特異性差異表達基因(以下簡稱“特異性基因”)分析 使用 Seurat3.0 中的 FindMarkers 函數(shù)用于篩選scRNA-seq數(shù)據(jù)中的差異表達基因,設(shè)置log 2 (FC)gt;0.25為閾值,并對基因的顯著性P值進行檢驗矯正。隨后使用 t 分布隨機鄰域嵌入(t-distributed stochastic neighbor embedding,t-SNE)對數(shù)據(jù)進行可視化,再通過小提琴圖來可視化每個聚類中表達的特異性基因。
1.2.4 功能富集分析 采用Cluster Profiler R軟件包對特異性基因集進行基因本體(gene ontology,GO)功能富集分析和京都基因與基因組百科全書(Kyoto encyclopedia of genes and genomes,KEGG)通路富集分析。GO數(shù)據(jù)庫是從生物學過程、細胞組分、分子功能3個方面對基因和基因產(chǎn)物進行分類注釋。
1.2.5 免疫熒光染色 分別將對照組小鼠和 NASH 組小鼠肝臟切片進行烤片、脫蠟、水化、抗原修復和血清封閉后,加入以下一抗:Tcrα(Abcam公司,貨號:ab288432)、Tcf7(Abcam公司,貨號:ab315392)和Cxcr6(Boster公司,貨號:BA3082),并置于 4 ℃冰箱中孵育過夜。次日滴加Alexa 488(Yeasen公司,貨號:34106ES60)、Alexa 594(Yeasen 公司,貨號:33112ES60)標記的熒光二抗和DAPI染液后封片??贵w稀釋倍數(shù)均為1∶200。使用熒光顯微鏡拍照觀察,并用Image J1.8.0軟件進行熒光面積占比測定。
1.3 統(tǒng)計學方法 使用SPSS 19.0、Graphpad prism 10和Image J軟件對熒光免疫結(jié)果進行統(tǒng)計分析和可視化處理。計量資料采用 x ˉ ±s表示,兩組間比較采用成組 t檢驗。特異性基因分析中的P值用Seurat 3.0軟件包中的Wilcoxon秩和檢驗和Bonferroni校正來檢驗,富集分析通過 ClusterProfiler 函數(shù)實現(xiàn),并使用 Fisher 精確檢驗和FDR矯正。Plt;0.05為差異有統(tǒng)計學意義。
2 結(jié)果
2.1 NASH小鼠肝組織T淋巴細胞亞群的分群和各亞群的變化 從 NASH組小鼠和對照組小鼠的肝臟中分離出單細胞,得到來自對照組的4 336個細胞和來自NASH組的3 893個細胞[8]。通過分析所有細胞中表達不同的基因,共鑒定出21個細胞簇。其中,第6、7簇被鑒定為T淋巴細胞(圖1a)。比較兩組T淋巴細胞亞群的占比情況發(fā)現(xiàn),第6簇T淋巴細胞的比例從對照組的58.5%降低到NASH組的48.7%,而第7簇T淋巴細胞則從對照組的41.5%增高到NASH組的51.3%(圖1b)。熱圖顯示了第6、7簇T淋巴細胞前10位特異性基因(圖1c)。
2.2 第6簇T淋巴細胞的轉(zhuǎn)錄組學特征 為進一步研究第6簇T淋巴細胞的轉(zhuǎn)錄組學特征,通過t-SNE分析顯示,第6簇T淋巴細胞的前10位特異性基因,包括神經(jīng)元特異性基因2(neuron-specific gene 2,Nsg2)、白細胞分化抗原8b1(the cluster of the differentiation 8 subunit beta 1,Cd8b1)、Cd8a、轉(zhuǎn)錄因子 7(transcription factor 7,Tcf7)(圖2a)和其他6個特異性基因(表1)。通過小提琴圖顯示第6簇前4位特異性基因(圖2b)。表1顯示,65%的第6簇T淋巴細胞表達Tcf7(pct_FC排名第4,但pct_FC前三的基因在第 6 簇 T 淋巴細胞中的表達率均低于50%)。因此Tcf7作為第6簇T淋巴細胞的特征標志基因,定義為Tcf7 + T淋巴細胞亞群。KEGG途徑富集分析顯示,第6簇T淋巴細胞參與T淋巴細胞受體、Th17細胞分化和Th1、Th2細胞分化等多個炎癥相關(guān)信號通路的調(diào)控(圖2c)。GO富集分析結(jié)果顯示,第6簇T淋巴細胞特異表達基因主要參與活化T淋巴細胞、白細胞細胞間黏附、磷酸化的負調(diào)控的生物學過程,核糖體、肌動蛋白細胞骨架、細胞質(zhì)的細胞組分,以及結(jié)合mRNA、結(jié)合泛素樣蛋白連接酶、結(jié)合鳥苷酸的分子功能(圖2d)。
2.3 第7簇T淋巴細胞的轉(zhuǎn)錄組學特征 t-SNE分析發(fā)現(xiàn),第7簇T淋巴細胞特異性表達白細胞分化抗原40配體基因(Cd40lg)、γ鏈T細胞受體抗原1(T-cell receptors gamma-chain 1,Tcrg-C1)、白細胞介素2受體α(interleukin-2receptor α,Il2rα)、CXC 趨化因子受體 6(C-X-C motif chemokine receptor 6,Cxcr6)(圖3a)和其他6個基因(表2)。通過小提琴圖顯示出第7簇前4位特異性基因(圖3b)。表 2 顯示,在第 7 簇中,90% 的 T 淋巴細胞表達 Cxcr6(pct_FC排名第4,且pct_FC排名前3位的基因在第7簇T淋巴細胞中表達率均低于50%)。因此Cxcr6是第7簇T淋巴細胞的特征標志基因,定義為Cxcr6 + T淋巴細胞亞群。KEGG途徑富集分析顯示,第7簇顯著富集的通路包括T淋巴細胞受體信號通路、Th17細胞分化和MAPK信號通路(圖3c)。GO富集分析顯示,第7簇的特異性基因主要參與T淋巴細胞活化、免疫效應(yīng)過程的調(diào)控、細胞因子產(chǎn)生的生物學過程,細胞質(zhì)、核糖體、神經(jīng)元間突觸的細胞組分,以及結(jié)合嘌呤核糖核苷、結(jié)合GTP、泛素樣蛋白連接酶的分子功能(圖3d)。
2.4 免疫熒光驗證NASH小鼠肝組織中兩種T淋巴細胞的變化 免疫熒光染色結(jié)果顯示,與對照組相比,NASH組小鼠肝組織Tcf7蛋白和Tcrα蛋白共染陽性區(qū)域顯著減少(1.80%±0.67% vs 0.33%±0.13%,Plt;0.05)(圖4a、b);而Cxcr6蛋白和Tcrα蛋白共染陽性區(qū)域顯著增加(0.50%±0.09% vs 2.66%±0.33%,Plt;0.001)(圖 4c、d)。以上免疫熒光結(jié)果均與單細胞測序的分析趨勢一致。
3 討論
NASH是NAFLD病情進展的關(guān)鍵階段,以5%以上的肝細胞脂肪變、小葉內(nèi)炎癥、肝細胞氣球樣變?yōu)樘卣鳎?],是一種影響了全球約1/4人口的慢性肝臟疾病,可發(fā)展為肝硬化和肝癌[10-11],是當前研究熱點之一。但NASH發(fā)病機制尚不完全清楚[12]。
T淋巴細胞作為適應(yīng)型免疫的重要組成成分,占肝臟內(nèi)淋巴細胞的50%以上。根據(jù)識別抗原提呈細胞上不同類型的主要組織相容性復合物,T淋巴細胞可以被劃分為CD4 + T淋巴細胞和CD8 + T淋巴細胞[13]。Wolf等 [14]發(fā)現(xiàn),在MCD飲食喂養(yǎng)的小鼠肝臟中,CD8 + T淋巴細胞數(shù)量增高且活性增強,并引發(fā)由該種飲食所誘導的肝損傷,但不會影響肝內(nèi)脂質(zhì)代謝。Her等[15]發(fā)現(xiàn)CD4 + T淋巴細胞可能通過釋放促炎因子IL-17A和干擾素γ促進NAFLD有關(guān)的炎癥和脂肪變性向纖維化轉(zhuǎn)變過程。
相比于傳統(tǒng)細胞測序方法,單細胞測序不僅使獲得的遺傳信息更加精確,還能檢測微量的基因表達水平[16]。近年來,單細胞測序技術(shù)的應(yīng)用促進了人們對慢性肝臟疾病中 T淋巴細胞亞群復雜異質(zhì)性的了解。Li等[17]發(fā)現(xiàn),與健康人群的肝臟相比,NAFLD患者肝臟內(nèi)的CD4 + T淋巴細胞數(shù)目增多,并發(fā)現(xiàn)了CD4 + T淋巴細胞內(nèi)4個差異表達基因(MIGI3、RCAN3、DOCK10和SAMD12)與NAFLD有關(guān)。Huang等[18]發(fā)現(xiàn),在NAFLD斑馬魚肝臟內(nèi),CD8 + T淋巴細胞可分為6個亞群(CD8-gzmk、CD8-rorc、CD8-ccl38.6、CD8-lta、CD8-mki67和CD8-mcm4),而CD4 + T淋巴細胞可分為4個亞群(CD4-foxp3a、CD4-cd28、CD4-cebpb和CD4-mki67)。
本研究通過對健康小鼠和MCD誘導的NASH小鼠的肝臟進行單細胞測序,重點研究篩選出的2個T淋巴細胞亞群:(1)第6簇T淋巴細胞在NASH小鼠肝臟中的占比從對照組的58.5%降低到NASH組的48.7%。65%的該簇T淋巴細胞表達Tcf7,因而作為該簇的標志基因。功能富集分析發(fā)現(xiàn),該T淋巴細胞亞群主要發(fā)揮活化T淋巴細胞、白細胞細胞間黏附、結(jié)合泛素樣蛋白連接酶等作用,并參與調(diào)控Th17、Th1、Th2細胞分化等多個炎癥相關(guān)信號通路。免疫熒光染色結(jié)果證實,NASH組小鼠肝組織中Tcf7 + T淋巴細胞較對照組減少。Tcf7基因編碼產(chǎn)生T淋巴細胞因子1(T cell factor-1,TCF1),并參與Wnt/β連環(huán)蛋白信號通路,在分化T淋巴細胞方面發(fā)揮重要作用。Yu等[19]發(fā)現(xiàn),在Wnt/β連環(huán)蛋白信號通路的調(diào)節(jié)下,TCF1通過誘導Gata結(jié)合蛋白3的產(chǎn)生促進Th2的分化。Th2細胞主要分泌細胞因子IL-4/5/6/10等,主要發(fā)揮抗炎作用[20]。過度表達的TCF1可以促進腫瘤細胞的增殖、侵襲和轉(zhuǎn)移,并抑制凋亡[21]。Gui等 [22]發(fā)現(xiàn),與原發(fā)性肝癌和正常肝組織相比,Tcf7 + CD8 + 記憶T淋巴細胞特異性富集于轉(zhuǎn)移性肝癌中。(2)此外,還發(fā)現(xiàn)第7簇T淋巴細胞的比例從對照組的41.5%增高到NASH組的51.3%。90%的該簇T淋巴細胞表達Cxcr6基因(作為標志基因)。GO富集分析提示,第7簇的特異性基因主要發(fā)揮T淋巴細胞活化和產(chǎn)生細胞因子的功能。KEGG通路富集分析發(fā)現(xiàn),第7簇T淋巴細胞顯著富集的通路包括T淋巴細胞受體信號通路、Th17細胞分化和MAPK信號通路。同時,免疫熒光結(jié)果顯示,與對照組相比,NASH組小鼠肝組織中Cxcr6 + T淋巴細胞增加。Cxcr6最初被發(fā)現(xiàn)表達于人類記憶T淋巴細胞[23],表達Cxcr6基因的CD8 + T淋巴細胞可依賴IL-15促進肝細胞凋亡[24],激活Cxcr6通路可促進肝內(nèi)自然殺傷T淋巴細胞聚集,進而加重肝內(nèi)炎癥反應(yīng)并促進肝纖維化[25]。但Tcf7 + T淋巴細胞和Cxcr6 + T淋巴細胞在NASH中的具體機制尚未有研究報道,有待進一步地深入研究。
綜上所述,通過 NASH小鼠肝臟的單細胞測序,在NASH中篩選出2個肝組織T淋巴細胞亞群:Tcf7 + T淋巴細胞的占比降低,推測其可能通過促進Th2細胞的分化發(fā)揮抗炎作用;而Cxcr6 + T淋巴細胞的占比增高,推測其可能通過MAPK信號通路發(fā)揮促炎作用。
倫理學聲明:本研究方案于2022年3月1日經(jīng)由上海市東方醫(yī)院(同濟大學附屬東方醫(yī)院)醫(yī)學倫理委員會審批,批號:[2022]研預審第(054)號,符合實驗室動物管理與使用準則。
利益沖突聲明:本文不存在任何利益沖突。
作者貢獻聲明:冒婷負責實驗和數(shù)據(jù)整理分析,撰寫論文;徐銘益負責數(shù)據(jù)分析和撰寫論文;王佳軼負責論文修改,對研究的思路和設(shè)計有關(guān)鍵貢獻。
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收稿日期:2024-07-24;錄用日期:2024-09-23
本文編輯:林姣
引證本文:MAO T, XU MY, WANG JY. Characteristics of T cells in the liver tissues of mice with nonalcoholic steatohepatitis[J].J Clin Hepatol, 2025, 41(3): 461-468.
冒婷, 徐銘益, 王佳軼 . 非酒精性脂肪性肝炎小鼠模型肝組織 T淋巴細胞的特征分析[J]. 臨床肝膽病雜志, 2025, 41(3):461-468.