摘要""目的:基于單細(xì)胞測序和機器學(xué)習(xí)算法構(gòu)建心力衰竭(HF)的診斷模型,并探索HF病人中細(xì)胞間通訊。方法:使用Seurat包對單細(xì)胞轉(zhuǎn)錄組測序(scRNA-seq)數(shù)據(jù)質(zhì)控、降維、聚類和注釋。通過AUCell評估各細(xì)胞亞群的免疫活性,選擇免疫活性最高的細(xì)胞亞群進行后續(xù)分析?;谂哭D(zhuǎn)錄組測序(Bulk RNA-seq)數(shù)據(jù),使用limma包篩選差異表達基因并進行基因集富集分析(GSEA)。進一步將疾病分類被作為反應(yīng)變量,差異基因作為解釋變量,通過4種機器學(xué)習(xí)模型來篩選具有診斷價值的巨噬細(xì)胞相關(guān)特征基因,并通過受試者工作特征(ROC)曲線評估關(guān)鍵基因的診斷能力。構(gòu)建列線圖預(yù)測HF發(fā)生的總風(fēng)險分?jǐn)?shù)。最后使用CellChat來探索細(xì)胞亞群之間的細(xì)胞間相互作用。結(jié)果:與正常樣本相比,HF病人中巨噬細(xì)胞的比例高于正常樣本,且巨噬細(xì)胞免疫活性評分最高。巨噬細(xì)胞亞群差異基因富集分析表明,白細(xì)胞介導(dǎo)的免疫過程和抗原的處理和呈遞顯著富集。多種機器學(xué)習(xí)算法相交結(jié)果發(fā)現(xiàn)SERPINA3、GPAT3、ANPEP和FCGBP可作為特征基因并與巨噬細(xì)胞密切相關(guān)。ROC曲線表明,診斷模型具有很好的預(yù)測能力。細(xì)胞通訊發(fā)現(xiàn),由巨噬細(xì)胞移動抑制因子(MIF)介導(dǎo)的成纖維細(xì)胞-巨噬細(xì)胞以及ANNEXIN介導(dǎo)的巨噬細(xì)胞-中性粒細(xì)胞之間的信號通路表現(xiàn)出復(fù)雜的傳出和傳入動力學(xué)。結(jié)論:4個關(guān)鍵基因作為生物標(biāo)志物具有良好的診斷價值。巨噬細(xì)胞介導(dǎo)的免疫過程以及細(xì)胞間通訊在HF的免疫微環(huán)境中起著關(guān)鍵作用。
關(guān)鍵詞""心力衰竭;單細(xì)胞測序;機器學(xué)習(xí);診斷模型;細(xì)胞通訊
doi:10.12102/j.issn.1672-1349.2025.04.006
Single-cell Sequencing Combined with Machine Learning Algorithms Reveals Cell-cell Communication and Key Regulatory Genes in Patients with Heart Failure
WANG Xuefu RAO Jin ZHANG Li LIU Xuwen ZHANG Yufeng
1.School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai "200093, China;
2. Shanghai Changzheng Hospital, Shanghai "200003, China; 3. School of Medicine, Guangxi University
Corresponding Author "ZHANG Yufeng, E-mail: zyflwj@smmu.edu.cn
Abstract Objective:To construct a diagnostic model for heart failure(HF) based on single-cell sequencing and machine learning algorithms,and explore cell-cell communication in HF patients.Methods:The Seurat package was used for quality control,dimensionality reduction, clustering,and annotation of single-cell transcriptome(scRNA-seq) data.The immune activity of each cell subset was evaluated using AUCell,and the cell subset with the highest immune activity was selected for further analysis.Differential expression genes were screened using the limma package based on bulk transcriptome(Bulk RNA-seq) data,and gene set enrichment analysis(GSEA) was performed.Furthermore,disease classification was used as the response variable and differential genes as the explanatory variables to select macrophage-related feature genes with diagnostic value through four machine learning models.The diagnostic ability of key genes was evaluated using receiver operating characteristic(ROC) curves.Bar plots were also constructed to predict the overall risk score of HF occurrence. Finally,CellChat was used to explore cell-cell interactions between cell subtypes.Results:Compared to normal samples, the proportion of macrophages in HF patients was higher,and macrophages had the highest immune activity score.Gene enrichment analysis of macrophage subtypes showed significant enrichment of leukocyte-mediated immune processes and antigen processing and presentation.The intersection of multiple machine learning algorithms revealed that SERPINA3,GPAT3,ANPEP,and FCGBP could serve as feature genes and were closely related to macrophages.Receiver operator characteristic(ROC) curves demonstrated that our diagnostic model had good predictive ability.Cell communication analysis revealed complex outgoing and incoming dynamics in the signaling pathways between fibroblast-macrophage mediated-neutrophil mediated by MIF and macrophages--neutrophils mediated by ANNEXIN.Conclusion:The four key genes serve as biomarkers and have good diagnostic value. Macrophage-mediated immune processes and cell-cell communication play a crucial role in the immune microenvironment of HF.
Keywords""heart failure; single cell sequencing; machine learning; diagnostic models; cell communication
心力衰竭(HF)是一種復(fù)雜的臨床綜合征,是心血管疾病的終末期表現(xiàn)[1-2]。新出現(xiàn)的證據(jù)表明,炎癥激活和免疫浸潤與心力衰竭的發(fā)病、進展和預(yù)后密切相關(guān)[3-4]。浸潤免疫細(xì)胞釋放轉(zhuǎn)化生長因子-β1(TGF-β1)和腫瘤壞死因子α(TNF-α)等細(xì)胞因子,促進心臟重塑[5]。因此,研究心力衰竭發(fā)展中的免疫微環(huán)境改變和關(guān)鍵調(diào)節(jié)因子,對心力衰竭的早期診斷以及預(yù)后具有重要意義。巨噬細(xì)胞是先天性和適應(yīng)性免疫應(yīng)答的重要組成部分,在心血管系統(tǒng)的正常運作中發(fā)揮作用[6]。有研究表明,巨噬細(xì)胞來源的白細(xì)胞介素10(IL-10)在高血壓或心力衰竭的發(fā)展過程中過量分泌,促進心臟的促纖維化機制[7]。此外,在高血壓心力衰竭病人中,Trem2缺陷的巨噬細(xì)胞使促血管生成基因程序的表達受損,促炎性細(xì)胞因子的表達增加[8]。雖然對于巨噬細(xì)胞研究取得了一定成果,但其在心力衰竭中的詳細(xì)機制仍未完全了解。批量轉(zhuǎn)錄組測序(Bulk RNA-seq)已經(jīng)對導(dǎo)致心力衰竭發(fā)病機制提供了重要的見解,但缺少細(xì)胞特異性信息。因此,本研究通過Bulk RNA-seq聯(lián)合單細(xì)胞轉(zhuǎn)錄組測序(scRNA-seq)進一步揭示心力衰竭病人中細(xì)胞間通訊以及關(guān)鍵調(diào)控基因。
1 資料與方法
1.1 數(shù)據(jù)收集
本研究所使用的數(shù)據(jù)集均下載于基因表達綜合數(shù)據(jù)庫(GEO)。GSE222144為scRNA-seq,包括一個正常樣本和一個心力衰竭樣本的測序數(shù)據(jù)[9]。GSE57338為Bulk RNA-seq,共有313例有/無心力衰竭的個體[10]。GSE26887作為外部驗證集,進一步評估模型的準(zhǔn)確性[11]。
1.2 scRNA-seq數(shù)據(jù)處理
scRNA-seq數(shù)據(jù)分析是通過使用Seurat包進行的[12]。對于最初的質(zhì)量控制過濾,排除了低質(zhì)量的細(xì)胞(基因表達少于300或線粒體基因表達超過25%)。然后,使用harmony包來整合不同處理的數(shù)據(jù)集,并消除批次效應(yīng)[13]。使用主成分分析(principal component analysis,PCA)進行降維,以探索異質(zhì)性并通過FindAllMarkers函數(shù)找到特定聚類的標(biāo)記基因,使用CellMarker 2.0將細(xì)胞亞群注釋為已知細(xì)胞類型[14]。
1.3 免疫相關(guān)基因集評分
基于AUCell R包計算免疫相關(guān)基因集的曲線下面積(AUC),生成每個細(xì)胞的基因表達排名,以估計每個細(xì)胞中的高表達基因集比例[15]。使用AUCell_exploreThresholds函數(shù)來確定識別基因組活躍細(xì)胞的閾值。得到基因集分?jǐn)?shù)后,使用Seurat內(nèi)置的函數(shù)將每個細(xì)胞的AUC得分映射到細(xì)胞亞群,以評估各細(xì)胞亞群的免疫活性。
1.4 Bulk RNA-seq差異基因的篩選
通過GEOquery包從GEO數(shù)據(jù)庫下載GSE57338的原始數(shù)據(jù)并進行歸一化。使用limma包篩選差異表達基因。調(diào)整后的Plt;0.05,|logFC|>0.5被認(rèn)為是差異表達的基因。
1.5 差異基因富集分析
通過FindMarkers函數(shù)獲取巨噬細(xì)胞亞群中差異基因,通過clusterProfiler R包進行京都基因與基因組百科全書(KEGG)通路富集分析和基因本體(GO)功能富集分析,從而對差異基因進行功能定位。對Bulk RNA-seq差異分析獲取的基因進行基因集富集分析(GSEA)以揭示差異基因關(guān)鍵功能。
1.6 巨噬細(xì)胞關(guān)鍵調(diào)控基因的篩選及驗證
穩(wěn)定和顯著的特征對于預(yù)測心力衰竭發(fā)病和進展風(fēng)險至關(guān)重要。疾病分類被認(rèn)為是反應(yīng)變量,差異基因作為解釋變量建立4種機器學(xué)習(xí)模型(包括LightGBM、XGBoost、RF、SVM)來篩選具有診斷價值的巨噬細(xì)胞相關(guān)特征基因。
1.7 特征基因與免疫細(xì)胞相關(guān)性分析
通過單樣本基因集富集分析(ssGSEA)算法評估特征基因與28種免疫細(xì)胞的相關(guān)性。
1.8 細(xì)胞間通訊分析
使用CellChat推斷細(xì)胞亞群之間的細(xì)胞間相互作用關(guān)系[16]。根據(jù)受體和配體的表達預(yù)測潛在的相互作用強度,推斷細(xì)胞狀態(tài)特異性通信并篩選所有細(xì)胞組中差異表達的信號通路及相關(guān)基因。
2 結(jié)果
2.1 心力衰竭組織中的單細(xì)胞景觀
正常(Con)和心力衰竭的單細(xì)胞樣本經(jīng)過質(zhì)控,共獲得18 104個細(xì)胞和24 781個基因。樣本合并分析發(fā)現(xiàn)不同樣本之間存在潛在的批次效應(yīng),因此,本研究用harmony算法校正批次效應(yīng)(見圖1)。選擇0.3作為細(xì)胞亞群區(qū)分的最佳分辨率,共獲得14個細(xì)胞亞群。根據(jù)亞群標(biāo)記基因,亞群被注釋為9個不同的細(xì)胞系,包括成纖維細(xì)胞(fibroblast)、內(nèi)皮細(xì)胞(endothelial cell)、B細(xì)胞(B cell)、中性粒細(xì)胞(neutrophils cell)、自然殺傷細(xì)胞(NK cell)、巨噬細(xì)胞(macrophages)、平滑肌細(xì)胞(smooth muscle cell)、神經(jīng)元細(xì)胞(neuronal cell)和心肌細(xì)胞(cardiomyocytes),見圖2、圖3。此外,本研究發(fā)現(xiàn)心力衰竭病人中巨噬細(xì)胞的比例高于正常樣本(見圖4)。因此,后續(xù)分析主要聚焦于巨噬細(xì)胞。圖5顯示了每種細(xì)胞類型的代表性標(biāo)記基因的表達水平。
2.2 免疫相關(guān)基因集評分
為了研究心力衰竭中的免疫特征,AUCell R軟件包被用來確定每個細(xì)胞系的免疫活性(見圖6)。巨噬細(xì)胞和中性粒細(xì)胞AUC值最高,表現(xiàn)出更高的免疫活性。詳見圖7。此外,基于GSE57338數(shù)據(jù)集的免疫浸潤分析進一步證實了巨噬細(xì)胞高浸潤的特征。詳見圖8。由于巨噬細(xì)胞亞群心力衰竭組明顯增加,進一步對巨噬細(xì)胞簇中的差異基因進行GO和KEGG分析。GO術(shù)語主要與白細(xì)胞的細(xì)胞-細(xì)胞黏連、白細(xì)胞遷移和白細(xì)胞介導(dǎo)的免疫過程有關(guān),而KEGG分析表明,吞噬體、抗原的處理和呈遞以及核因子-κB(NF-κB)信號通路顯著富集。詳見圖9、圖10。
2.3 Bulk RNA-seq差異基因的篩選
為了研究心力衰竭病人基因的表達特征,本研究分析了GSE57338中的313個樣本,其中包括177例心力衰竭病人樣本和136名正常樣本。通過Limma包篩選出428個差異表達的基因(見圖11)。GSEA富集分析結(jié)果與巨噬細(xì)胞亞群的表達特征具有相似性,吞噬作用與免疫和炎癥反應(yīng)顯著富集(見圖12)。以上結(jié)果表明巨噬細(xì)胞是心力衰竭病人中免疫過程的主要參與者。
2.4 巨噬細(xì)胞關(guān)鍵調(diào)控基因的篩選
Bulk RNA-seq差異基因與巨噬細(xì)胞亞群中的差異基因相交,共獲得27個差異表達的巨噬細(xì)胞相關(guān)基因(見圖13)。機器學(xué)習(xí)在預(yù)測心力衰竭發(fā)病方面具有更高的準(zhǔn)確性,因此,應(yīng)用多種機器學(xué)習(xí)算法篩選特征變量。基于LASSO算法,獲得6個特征變量(見圖14)。圖15顯示RF算法對變量的重要性排名順序。此外,基于XGBoost和LightGBM模型的SHAP依賴分析描述了預(yù)測模型的單個特征變量的重要性(見圖16、圖17)。特征變量的SHAP值越高,心力衰竭的可能性就越大。值得注意的是,所有的算法中最重要的變量是SERPINA3。最后,多種機器學(xué)習(xí)算法結(jié)果相交,發(fā)現(xiàn)SERPINA3、GPAT3、ANPEP和FCGBP可調(diào)控心力衰竭的進展,并與巨噬細(xì)胞密切相關(guān)(見圖18)。
進一步行ssGSEA分析也表明,SERPINA3、ANPEP和FCGBP與巨噬細(xì)胞的浸潤呈顯著正相關(guān),而GPAT3與巨噬細(xì)胞的活性呈顯著負(fù)相關(guān)(見圖19)。
2.5 特征基因的驗證
構(gòu)建邏輯回歸模型來探索特征基因和心力衰竭之間的關(guān)聯(lián)。森林圖(見圖20)所示的多變量邏輯回歸分析顯示,4個標(biāo)記物的表達與心力衰竭獨立相關(guān)。列線圖給每個特征變量值分配一個分值,通過將所有特征變量的分值相加得到患心力衰竭的總風(fēng)險分?jǐn)?shù),見圖21。此外,4個基因的表達水平在兩個數(shù)據(jù)集中都有明顯差異,見圖22、圖23。隨后,在訓(xùn)練隊列和外部隊列中進行ROC分析,結(jié)果表明,4個診斷基因具有較高的預(yù)測價值,尤其是SERPINA3。詳見圖24、圖25。
2.6 scRNA-seq數(shù)據(jù)中細(xì)胞間通訊分析
為了破譯不同細(xì)胞間的配體-受體相互作用關(guān)系,本研究使用CellChat分析了9個細(xì)胞簇之間的通信。CellChat結(jié)果表明,成纖維細(xì)胞是信號的主要發(fā)出者,而巨噬細(xì)胞是主要的接受者(見圖26、圖27)。細(xì)胞之間通過31條途徑相互作用,而由巨噬細(xì)胞移動抑制因子(MIF)介導(dǎo)的成纖維細(xì)胞-巨噬細(xì)胞以及ANNEXIN介導(dǎo)的巨噬細(xì)胞-中性粒細(xì)胞之間的信號通路表現(xiàn)出復(fù)雜的傳出和傳入動力學(xué)(見圖28)。成纖維細(xì)胞是MIF信號的主要來源,而巨噬細(xì)胞是主要受體(見圖29)。巨噬細(xì)胞是ANNEXIN信號的主要生產(chǎn)者,而中性粒細(xì)胞充當(dāng)巨噬細(xì)胞釋放ANNEXIN信號的靶細(xì)胞(見圖30)。進一步鑒定了信號通路中的配體-受體對,其中MIF信號傳導(dǎo)由MIF-(CD74+CXCR4)和MIF-(CD74+CD44)配體-受體介導(dǎo),而ANNEXIN信號傳導(dǎo)主要由ANXA1-FPR1和ANXA1-FPR2配體-受體介導(dǎo)(見圖31)。上述通路中配體和受體的表達水平見圖32。
3 討論
心力衰竭是一種并發(fā)癥發(fā)生率高、預(yù)后差的心血管臨床綜合征[17]。心力衰竭病人心臟重塑的發(fā)展伴隨著更高的炎癥狀態(tài),伴有纖維化、心肌細(xì)胞凋亡以及心功能的改變[18]。隨著單細(xì)胞技術(shù)發(fā)展,這為剖析存在于健康和患病組織中的細(xì)胞類型提供了新工具。最近,這些方法被用來更深入地破譯心臟的細(xì)胞和轉(zhuǎn)錄景觀如何受到疾病的影響[19]。在本研究中,通過scRNA-seq聯(lián)合BulkRNA-seq測序數(shù)據(jù)揭示了心力衰竭病人基因表達水平與免疫細(xì)胞浸潤和免疫相關(guān)功能有關(guān)。首先,通過AUCell包對每個細(xì)胞中免疫基因集進行評分,發(fā)現(xiàn)巨噬細(xì)胞得分最高,說明巨噬細(xì)胞是心力衰竭病人中與免疫功能最相關(guān)的細(xì)胞類型。其次,使用4種機器學(xué)習(xí)算法,建立了一個對心力衰竭具有出色的診斷性能的診斷模型,ROC曲線證明了模型的診斷性能。最后,細(xì)胞間通訊揭示了成纖維細(xì)胞、巨噬細(xì)胞和中性粒細(xì)胞在心肌重塑中的串?dāng)_作用。
研究表明,炎癥反應(yīng)是心力衰竭發(fā)展的重要因素[20]。細(xì)胞通過分泌一些趨化因子和細(xì)胞因子調(diào)節(jié)心力衰竭中的免疫細(xì)胞趨化性,這在心肌重塑中起著至關(guān)重要的作用。心臟巨噬細(xì)胞是具有高可塑性和適應(yīng)性的異質(zhì)性群體,在組織纖維化反應(yīng)中也起著關(guān)鍵作用[21]。已知常駐巨噬細(xì)胞通過調(diào)節(jié)細(xì)胞因子和生長因子的合成來響應(yīng)免疫微環(huán)境,并產(chǎn)生大量促纖維化生長因子調(diào)節(jié)纖維化的過程[22]。本研究中,單細(xì)胞譜系中巨噬細(xì)胞的百分比在心力衰竭的進展中顯著增加。因此,巨噬細(xì)胞相關(guān)標(biāo)志物可能是心力衰竭診療更有效的手段。基于上述結(jié)論,本研究進一步利用機器學(xué)習(xí)算法來確定心力衰竭的巨噬細(xì)胞相關(guān)基因診斷特征。特征選擇是一種機器學(xué)習(xí)算法,該算法最大的優(yōu)點是可以去除冗余和不相關(guān)的特征,從而降低輸入維度,提高模型的準(zhǔn)確性,并降低模型的復(fù)雜性[23]。同樣,在本研究中,結(jié)合了4種機器學(xué)習(xí)算法,包括LightGBM、XGBoost、RF、SVM。4種算法的特征交叉顯示,SERPINA3、GPAT3、ANPEP和FCGBP是潛在的心力衰竭診斷標(biāo)記物。此外,多變量邏輯回歸分析顯示,4個基因的診斷特征在預(yù)測心力衰竭方面表現(xiàn)出高度的鑒別力。外部數(shù)據(jù)集ROC曲線的AUC值也證實了結(jié)果的可靠性。
現(xiàn)有研究表明,SERPINA3與免疫反應(yīng)密切相關(guān)[24]。SERPINA3通過抑制IκB激酶(IKK)復(fù)合物的形成和NF-κB活化來抑制巨噬細(xì)胞中的細(xì)胞因子活性[25]。SERPINA3的高表達會對心臟功能產(chǎn)生不利影響,并增加死亡率或心臟事故[26]。SERPINA3可以作為具有巨大潛力的心力衰竭預(yù)測生物標(biāo)志物。GPAT3是與脂質(zhì)代謝相關(guān)的基因,越來越多的報道表明,活化的巨噬細(xì)胞改變脂質(zhì)組成,脂肪酸合成的靶向調(diào)節(jié)可能會影響巨噬細(xì)胞的炎癥反應(yīng)[27-28]。因此,GPAT3水平升高可能影響巨噬細(xì)胞脂質(zhì)代謝紊亂驅(qū)動心力衰竭中巨噬細(xì)胞的炎癥反應(yīng)。ANPEP是一種廣泛表達的外酶,在各種炎癥性疾病中起重要作用[29]。作為一種酶,ANPEP通過切割其N端來調(diào)節(jié)細(xì)胞因子的活性,并通過減少與MHCⅡ結(jié)合的參與抗原加工的多肽,從而調(diào)節(jié)免疫細(xì)胞的發(fā)育和活性[30]。本研究中,抗原的加工與呈遞的過程顯著富集。FCGBP是黏膜免疫防御的重要組成部分,參與保護性免疫[31]。此外,F(xiàn)CGBP也可作為一種抗原發(fā)揮作用,其被巨噬細(xì)胞識別并呈現(xiàn)給T細(xì)胞,激活了主要的防御機制[32]。除了在黏膜上皮的先天免疫防御中的作用外,F(xiàn)CGBP也可能起結(jié)構(gòu)性作用。據(jù)報道,F(xiàn)CGBP在主動脈中表達,其是腹主動脈瘤破裂病人中下調(diào)最嚴(yán)重的基因[33]。對于FCGBP的研究主要聚焦于黏膜和腫瘤等疾病,在心力衰竭中的作用鮮有報道。因此,F(xiàn)CGBP轉(zhuǎn)錄的調(diào)節(jié)可能成為潛在的治療靶點。為了破譯不同細(xì)胞間的配體-受體相互作用,本研究使用CellChat分析了9個細(xì)胞簇之間的通信。成纖維細(xì)胞-巨噬細(xì)胞以及巨噬細(xì)胞-中性粒細(xì)胞在心力衰竭中表現(xiàn)出更強的相互作用,這表明細(xì)胞相互作用本質(zhì)上影響心力衰竭的進展。有趣的是,本課題組發(fā)現(xiàn)成纖維細(xì)胞出現(xiàn)高水平的巨噬細(xì)胞遷移抑制因子的表達。MIF相關(guān)的配體-受體相互作用在心力衰竭中被高度激活。MIF對脂肪變性具有保護作用,導(dǎo)致巨噬細(xì)胞數(shù)量減少[34]。此外,CXCR4、CD74和MIF的共表達可以增強細(xì)胞的存活和遷移能力。無論是單獨還是組合,都會促進細(xì)胞死亡,并導(dǎo)致MIF驅(qū)動的遷移反應(yīng)消除[35]。ANNEXIN信號傳導(dǎo)主要由ANXA1-FPR1和ANXA1-FPR2配體-受體介導(dǎo)。研究表明,配體ANXA1和受體FPRs可以促進中性粒細(xì)胞和巨噬細(xì)胞的成熟,并將它們遷移到受損的肺部組織中[36]。心肌缺血再灌注過程中,ANXA1的下調(diào)加劇了炎癥反應(yīng),同時心臟收縮功能減弱[37]??傊?,推測這些配體、受體的結(jié)合傳遞促炎或抗炎信號,從而介導(dǎo)心力衰竭過程免疫反應(yīng)。
綜上所述,本研究選定的4個關(guān)鍵基因作為生物標(biāo)志物具有良好的診斷價值,為心力衰竭的診療提供了一定的參考。同時,我們也破譯了不同細(xì)胞間的配體-受體相互作用在心力衰竭的免疫微環(huán)境中的關(guān)鍵作用。然而,本研究也存在不足之處,單細(xì)胞測序數(shù)據(jù)納入樣本較少,且結(jié)果未進行后續(xù)實驗驗證。此外,理論結(jié)果到臨床實踐中的轉(zhuǎn)化仍有很長的路要走。
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(收稿日期:2023-06-21)
(本文編輯"王麗)