[摘要]目的探討卵巢癌細(xì)胞在常氧與低氧環(huán)境培養(yǎng)下mRNA表達(dá)譜的差異。方法將卵巢癌細(xì)胞株SKOV3置于低氧(2%)與常氧(21%)環(huán)境下培養(yǎng),應(yīng)用氧探針進(jìn)行細(xì)胞乏氧狀態(tài)檢測(cè),應(yīng)用高通量測(cè)序?qū)?xì)胞內(nèi)整體的mRNA進(jìn)行測(cè)序,應(yīng)用生物信息學(xué)分析工具對(duì)測(cè)序結(jié)果進(jìn)行基因表達(dá)差異分析與功能富集分析,應(yīng)用逆轉(zhuǎn)錄實(shí)時(shí)熒光定量PCR進(jìn)行相關(guān)差異基因表達(dá)的進(jìn)一步驗(yàn)證。結(jié)果與常氧培養(yǎng)的細(xì)胞相比,在低氧環(huán)境下培養(yǎng)的細(xì)胞共有999個(gè)基因表達(dá)顯著上調(diào),646個(gè)基因表達(dá)顯著下調(diào)。這些表達(dá)差異基因參與細(xì)胞外基質(zhì)形成、細(xì)胞黏附、糖酵解、纖毛組裝等生物學(xué)過程以及癌癥信號(hào)、PI3K-AKT信號(hào)、RNA轉(zhuǎn)運(yùn)以及腫瘤膽堿代謝等信號(hào)通路。逆轉(zhuǎn)錄實(shí)時(shí)熒光定量PCR結(jié)果驗(yàn)證了低氧組的HILPDA、MT1B、CA9、MT1X與LOX-L2基因表達(dá)明顯高于常氧組,而低氧組的WARS1、CHAC1、PSAT1、UPP1與DDX5基因表達(dá)明顯低于常氧組。結(jié)論本研究揭示了在不同濃度氧環(huán)境下卵巢癌細(xì)胞mRNA轉(zhuǎn)錄水平差異表達(dá)的相關(guān)基因及分子通路,為進(jìn)一步探討低氧環(huán)境對(duì)卵巢癌細(xì)胞生長(zhǎng)影響的潛在分子機(jī)制提供實(shí)驗(yàn)基礎(chǔ)。
[關(guān)鍵詞]低氧;轉(zhuǎn)錄組;卵巢癌;SKOV3細(xì)胞
doi:10.3969/j.issn.1674-7593.2024.03.016
Transcriptome Analysis of Ovarian Cancer Cell Line SKOV3Grown in a Hypoxic Environment
Wang Xin1,Du Zhenwu2,Li Jing1,Zhu He1**
1Department of obstetrics and gynecology,the Second Norman Bethune Hospital of Jilin University,ChangChun130041;2Department oforthopedics research institute,the Second Norman Bethune Hospital of Jilin University,ChangChun130041
**Corresponding author:Zhu He,email:zhuhe@jlu.edu.cn
[Abstract]ObjectiveTo explore the differences in mRNA expression profiles of ovarian cancer cells cultured in normoxic and hypoxic environments.MethodsThe ovarian cancer SKOV3 cells were cultured separately in low oxygen(2% oxygen) and normal oxygen(21% oxygen) environments.Oxygen probes were used to detect cellular hypoxia status.The whole mRNAs expressed within cells were detected using high-through RNA sequencing,and bioinformatics analysis tools were used to analyze gene expression differences and functional enrichment of the genes,and reverse transcription quantitative real-time PCR was used to further verify the related differential gene expression.ResultsCompared with cells cultured under normal oxygen,cells cultured under low oxygen environment showed a total of 999 significantly upregulated gene expressions and 646 significantly downregulated gene expressions.These differentially expressed genes were involved in biological processes such as extracellular matrix formation,cell adhesion,glycolysis,ciliary assembly,as well as signaling pathways such as cancer signaling,PI3K-AKT signaling,RNA transport,and tumor choline metabolism.The reverse transcription quantitative real-time PCR results confirmed that the expression of HILPDA,MT1B,CA9,MT1X and LOX-L2 genes in the hypoxic group were significantly higher than those in the normoxic group,while the expression of WARS1,CHAC1,PSAT1,UPP1 and DDX5 genes in the hypoxic group were significantly lower than those in the normoxic group.ConclusionThis study revealed the differentially expressed genes and molecular pathways of mRNA transcription levels in ovarian cancer cells under different oxygen concentrations environments,providing an experimental basis for further exploring the potential molecular mechanisms of the impact of low oxygen environments on the growth of ovarian cancer.
[Key words]Hypoxic;Transcriptome;Ovarian cancer;SKOV3 cell
卵巢癌占女性生殖系統(tǒng)癌癥相關(guān)死亡率的首位[1-2]。卵巢癌患者中多數(shù)為老年女性,這部分患者由于身體狀態(tài)差,常伴有其他疾病,所以對(duì)治療響應(yīng)差,成為卵巢癌治療值得關(guān)注的人群[3-4]。當(dāng)前針對(duì)卵巢癌患者的化療方案為鉑類藥物聯(lián)合紫杉醇,部分患者在治療初期時(shí)得到緩解,但仍有許多患者復(fù)發(fā)并出現(xiàn)化療耐藥性[5-6]。腫瘤細(xì)胞在體內(nèi)生長(zhǎng)的內(nèi)環(huán)境即腫瘤的微環(huán)境,對(duì)腫瘤細(xì)胞生長(zhǎng)發(fā)育及藥物治療的反應(yīng)均可產(chǎn)生調(diào)控作用,其中腫瘤組織的低氧狀態(tài)是其內(nèi)環(huán)境的重要特征[7-8]。在低氧環(huán)境下可誘發(fā)腫瘤組織新生血管,提高腫瘤細(xì)胞抗凋亡、抗藥物治療及轉(zhuǎn)移能力[9-11]。但低氧誘導(dǎo)腫瘤細(xì)胞分子信號(hào)的轉(zhuǎn)變及對(duì)化療藥物產(chǎn)生抗性的分子機(jī)制尚未完全闡明[12]。在過去的幾十年里,轉(zhuǎn)錄組分析已成為在分子水平上研究人類疾病最常用的方法之一,通過該方法在多種疾病中發(fā)現(xiàn)了許多分子生物標(biāo)志物和治療靶點(diǎn)[13]。通過轉(zhuǎn)錄組學(xué)方法進(jìn)行細(xì)胞內(nèi)全體mRNA轉(zhuǎn)錄情況的觀察將有助發(fā)現(xiàn)低氧狀態(tài)下細(xì)胞轉(zhuǎn)變的關(guān)鍵基因與分子通路[14-15]。本研究將通過高通量RNA測(cè)序檢測(cè)在常氧與低氧狀態(tài)下的SKOV3卵巢癌細(xì)胞的全局mRNA表達(dá)譜,旨在揭示常氧與低氧環(huán)境下卵巢癌細(xì)胞的表達(dá)差異基因與相關(guān)調(diào)控的重要分子途徑,為明確卵巢癌細(xì)胞在低氧環(huán)境下產(chǎn)生化療藥物抗性的分子機(jī)制提供實(shí)驗(yàn)依據(jù),為低氧環(huán)境為目標(biāo)的藥物開發(fā)提供分子靶點(diǎn)。
1材料與方法
1.1SKOV3卵巢癌細(xì)胞的低氧培養(yǎng)與低氧狀態(tài)驗(yàn)證
SKOV3細(xì)胞以1×104 個(gè)/孔接種于24孔細(xì)胞培養(yǎng)板,置于MIC-101缺氧培養(yǎng)小室,小室內(nèi)含有2% O2、5% CO2及93% N2。將小室與同步接種SKOV3細(xì)胞的24孔板置于37℃、5% CO2培養(yǎng)箱內(nèi)培養(yǎng)(含有21% O2,常氧組)。培養(yǎng)24 h后,應(yīng)用ROS-ID○R "Hypoxia/Oxidative Stress Detection Kit(購自美國Enzo Life Sciences公司)進(jìn)行細(xì)胞低氧狀態(tài)檢測(cè)。
1.2細(xì)胞內(nèi)mRNA表達(dá)譜高通量測(cè)序
將SKOV3細(xì)胞以1×105個(gè)/mL細(xì)胞數(shù)接種于25 cm2培養(yǎng)瓶,分別在常氧與低氧環(huán)境培養(yǎng)72 h(每組3瓶),然后吸去培養(yǎng)基,加入1 mL Trizol溶液(購自美國Thermo Fisher Scientific公司),用吸頭吹打,充分裂解細(xì)胞,將細(xì)胞裂解液置于凍存管內(nèi)置于液氮內(nèi)迅速冷凍。檢測(cè)樣本置于干冰保存運(yùn)輸至武漢華大基因測(cè)序公司,委托進(jìn)行細(xì)胞全轉(zhuǎn)錄組的RNA測(cè)序。
1.3RNA測(cè)序結(jié)果分析
測(cè)序獲得原始數(shù)據(jù),根據(jù)數(shù)據(jù)質(zhì)控進(jìn)行初步過濾,高質(zhì)量序列數(shù)據(jù)針對(duì)參考序列進(jìn)行比對(duì),完成測(cè)序數(shù)據(jù)在參考序列上的分布情況,根據(jù)判斷比對(duì)結(jié)果完成基因表達(dá)數(shù)據(jù)獲取。所得基因的表達(dá)值表示為每千個(gè)堿基的轉(zhuǎn)錄每百萬映射的Transcript(TPM)值,該值通過歸一化映射讀數(shù)的量化數(shù)量來計(jì)數(shù)。兩個(gè)不同組之間RNA-seq數(shù)據(jù)的差異表達(dá)分析通過Dr.tom-web進(jìn)行(https://biosys.bgi.com/#/report/project/projectList)。低氧組與常氧組之間的差異表達(dá)基因判定標(biāo)準(zhǔn)為Q值(P值的校正值)<0.05、|Log2(TPM低氧組/TPM常氧組)|≥2。
1.4基因功能富集分析
表達(dá)差異基因應(yīng)用DAVID數(shù)據(jù)庫(https://david.ncifcrf.gov/)進(jìn)行基因本體論(Gene ontology,GO)分析及京都基因百科全書(Kyoto Encyclopedia of Gene and Genome,KEGG)分析。
1.5差異基因PCR檢測(cè)驗(yàn)證
應(yīng)用TRIzol試劑(購自美國Thermo Fisher Scientific公司)分別從低氧與常氧培養(yǎng)72 h的SKOV3細(xì)胞分離總RNA。使用TranScript Uni All-in-One SuperMix cDNA合成試劑盒(購自北京全式金生物技術(shù)股份有限公司)將總細(xì)胞RNA逆轉(zhuǎn)錄為cDNA,以獲得cDNA為模板應(yīng)用RansStart○R "Green qPCR SuperMix(購自北京全式金生物技術(shù)股份有限公司)試劑進(jìn)行逆轉(zhuǎn)錄實(shí)時(shí)熒光定量PCR(RT-qPCR)反應(yīng)檢測(cè)細(xì)胞內(nèi)每個(gè)基因的mRNA表達(dá)水平。檢測(cè)引物序列參考Huang等[16]文獻(xiàn),引物委托上海生工合成,WARS1正向引物5′-GCAGGAAGGGAAACTGAAAGA-3′,反向引物5′-GACGAGTCAAGACCAGGTTG-3′;DDX5正向引物5′-AGAGAGGCGATGGGCCTATTT-3′,反向引物5′-CTTCAAGCGACATGCTCTACAA-3′;UPP1正向引物5′-AACAGAGCAGGCAGTGGATA-3′,反向引物5′-ATACGCCTGCTTGTCCTTCT-3′;PSAT1 正向引物5′-GTCCAGTGGAGCCCCAAAA-3′,反向引物5′-TGCCTCCCACAGACCTATGC-3′;CHAC1正向引物5′-GTGTGGTGACGCTCCTTGAA-3′,反向引物5′-TGGTATCGTAGCCACCAAGC-3′;MT1B正向引物5′-GATCCCAACTGCTCCTGCACCACA-3′,反向引物5′-AAGAATGTAGCAAACCGGTCAGGGTAGTT-3′;CA9正向引物5′-TAAGCAGCTCCACACCCTCT-3′,反向引物5′-TCTCATCTGCACAAGGAACG-3′;MT1X正向引物5′-GACCCCAACTGCTCCTGCTCG-3′,反向引物5′-GATGTAGCAAACGGGTCAGGGTTGTAC-3′;HILPDA正向引物5′-CCGACTTTCCTCCGGACT-3′,反向引物5′-CCTTCTGAAAGGCCTCTGG-3′;LOXL2正向引物5′-CATCTGGATGTACAACTGCCACATA-3′,反向引物5′-AGCCCGCTGAAGTGCTCAA-3′。PCR反應(yīng)體系為20 μL,反應(yīng)條件為94 ℃、5 min,94 ℃、15 s,55 ℃、15 s,72 ℃、30 s,共計(jì)40個(gè)循環(huán),循環(huán)后設(shè)置熔解曲線反應(yīng)。RT-qPCR反應(yīng)通過ABI 7500 FAST實(shí)時(shí)定量PCR儀完成,檢測(cè)結(jié)果應(yīng)用2-ΔΔCT方法進(jìn)行定量分析。
1.6統(tǒng)計(jì)學(xué)方法
應(yīng)用SPSS21.0統(tǒng)計(jì)學(xué)軟件進(jìn)行數(shù)據(jù)分析,兩組間采用t檢驗(yàn),以P<0.05為差異有統(tǒng)計(jì)學(xué)意義。
2結(jié)果
2.1SKOV3細(xì)胞低氧狀態(tài)檢測(cè)結(jié)果
SKOV3細(xì)胞置于低氧裝置(含2% O2)及常氧(含21% O2)培養(yǎng)24 h后,通過低氧探針檢測(cè)細(xì)胞缺氧狀態(tài),結(jié)果顯示低氧培養(yǎng)的細(xì)胞的細(xì)胞質(zhì)中紅色熒光顯著強(qiáng)于常氧組,見圖1。說明通過該缺氧裝置可誘導(dǎo)細(xì)胞處于低氧狀態(tài),后續(xù)實(shí)驗(yàn)O2采取2%濃度模擬低氧環(huán)境。
2.2低氧組相對(duì)常氧組細(xì)胞mRNA差異表達(dá)基因分析結(jié)果
以每個(gè)基因mRNA表達(dá)的定量TPM值為計(jì)算目標(biāo),相對(duì)于常氧組,低氧組共有999個(gè)基因表達(dá)顯著上調(diào),646個(gè)基因表達(dá)顯著下調(diào),基因表達(dá)差異的火山圖見圖2,表達(dá)上調(diào)的前5個(gè)基因是MT1B(Metallothionein 1B,基因號(hào)4490),CA9(Carbonic anhydrase 9,基因號(hào)768),MT1X(Metallothionein 1X,基因號(hào)4501),HILPDA(Hypoxia inducible lipid droplet associate,基因號(hào)29923),LOXL2(Lysyl oxidase like 2,基因號(hào)4017);表達(dá)下調(diào)的前5個(gè)基因是WARS1(Tryptophanyl-tRNA synthetase 1,基因號(hào)7453),DDX5(DEAD-box helicase 5,基因號(hào)54606),UPP1(Uridine phosphorylase 1,基因號(hào)7378),PSAT1(Phosphoserine aminotransferase 1,基因號(hào)29968),CHAC1(ChaC glutathione specific gamma-glutamylcyclotransferase 1,基因號(hào)79094)。
2.3基因表達(dá)譜分析差異表達(dá)基因的RT-qPCR驗(yàn)證
為進(jìn)一步證實(shí)基因測(cè)序mRNA表達(dá)譜的正確性,對(duì)5個(gè)上調(diào)基因與5個(gè)下調(diào)基因應(yīng)用RT-qPCR進(jìn)行檢測(cè),結(jié)果顯示低氧組的HILPDA、MT1B、CA9、MT1X與LOX-L2基因表達(dá)明顯高于常氧組,而低氧組的WARS1、CHAC1、PSAT1、UPP1與DDX5基因表達(dá)明顯低于常氧組,該結(jié)果趨勢(shì)與RNA測(cè)序結(jié)果相一致,見圖3。
2.4低氧組相對(duì)常氧組細(xì)胞mRNA差異表達(dá)基因的GO分析
應(yīng)用DAVID數(shù)據(jù)庫對(duì)999個(gè)上調(diào)基因與646個(gè)下調(diào)基因進(jìn)行GO分析,包括基因的生物學(xué)過程、基因表達(dá)蛋白的細(xì)胞定位與基因的分子功能。結(jié)果顯示上調(diào)基因涉及的生物學(xué)過程包括細(xì)胞外基質(zhì)形成、細(xì)胞黏附、經(jīng)典糖酵解、血小板脫顆粒、炎癥反應(yīng)等;分子功能涉及蛋白酶結(jié)合、絲氨酸內(nèi)肽酶抑制因子活性、膠原蛋白結(jié)合、鈣離子結(jié)合、糖胺聚糖結(jié)合等;基因表達(dá)產(chǎn)物的位置包括細(xì)胞外區(qū)域、細(xì)胞外間隙、細(xì)胞外泌體、細(xì)胞外基質(zhì)、細(xì)胞質(zhì)膜組成部分,見圖4。
下調(diào)基因涉及的生物學(xué)過程包括纖毛組裝、以DNA為模板的轉(zhuǎn)錄、負(fù)向調(diào)節(jié)蛋白磷酸化、以DNA為模板的轉(zhuǎn)錄調(diào)節(jié)、纖毛形成等;分子功能顯著富集于金屬離子結(jié)合、核酸結(jié)合、ATP結(jié)合、DNA結(jié)合、核苷酸結(jié)合等;基因表達(dá)產(chǎn)物的位置包括細(xì)胞質(zhì)、核質(zhì)、中心體、細(xì)胞核、纖毛基體,見圖5。
2.5低氧組相對(duì)常氧組細(xì)胞mRNA差異表達(dá)基因的KEGG通路分析結(jié)果
DAVID在線軟件結(jié)果顯示:上調(diào)組基因富集于PI3K-AKT信號(hào)通路、細(xì)胞因子及細(xì)胞因子受體相互作用、癌癥信號(hào)通路、HTLV1感染、黏著斑等,見圖6A;下調(diào)組基因富集于脂肪細(xì)胞因子信號(hào)通路、腫瘤膽堿代謝、RNA轉(zhuǎn)運(yùn)、ErbB信號(hào)通路、氨基酸生物合成等,見圖6B。
3討論
在本研究中,通過RNA測(cè)序方法檢測(cè)了上皮性卵巢癌癥SKOV3細(xì)胞在常氧與低氧環(huán)境中的基因mRNA表達(dá)譜。鑒定了SKOV3細(xì)胞在低氧培養(yǎng)環(huán)境相對(duì)于常氧培養(yǎng)共計(jì)999個(gè)基因表達(dá)顯著上調(diào),646個(gè)基因表達(dá)顯著下調(diào),其中10個(gè)基因表達(dá)差異通過RT-qPCR得到驗(yàn)證。應(yīng)用GO和通路富集分析明確差異基因所在的信號(hào)通路與所產(chǎn)生的物學(xué)功能。
當(dāng)前大多數(shù)在體外針對(duì)腫瘤開展的實(shí)驗(yàn)研究是在約大氣中氧含量(21%)條件下進(jìn)行的,而體內(nèi)不同器官的生理氧含量通常在3%~10%,特別是大多數(shù)腫瘤在體內(nèi)處于缺氧或1%~2%的氧環(huán)境中[17]。這種體內(nèi)外不同氧含量環(huán)境造成腫瘤細(xì)胞內(nèi)基因表達(dá)與信號(hào)網(wǎng)絡(luò)激活表現(xiàn)出明顯的差異,從而造成體外研究的腫瘤細(xì)胞生物學(xué)功能及對(duì)藥物治療敏感性均與體內(nèi)不同。因此,在低氧環(huán)境下進(jìn)行對(duì)腫瘤的實(shí)驗(yàn)研究將更接近腫瘤在體內(nèi)微環(huán)境中的生理病理狀態(tài)[18-19]。本實(shí)驗(yàn)通過將卵巢癌細(xì)胞株置于含有2% O2(生理性缺氧狀態(tài))的小室內(nèi),通過低氧探針檢測(cè)到細(xì)胞處于一種缺氧狀態(tài),從而成功建立細(xì)胞的低氧模型,為進(jìn)一步探討低氧環(huán)境下細(xì)胞內(nèi)的基因變化提供實(shí)驗(yàn)基礎(chǔ)。
SKOV3細(xì)胞為人卵巢癌腺癌細(xì)胞系,是從一位白人女性卵巢腺癌患者的腹腔積液中分離得到,屬于上皮漿液性腫瘤來源,該細(xì)胞對(duì)幾種化療藥物都耐藥,包括順鉑和阿霉素等[20]。由于上皮高級(jí)別漿液癌占整個(gè)卵巢腫瘤的60%以上,因此在研究人卵巢癌的病理生理及藥物治療的模型時(shí)多采用該腫瘤細(xì)胞株為體外研究模型。Olbryt等[21]應(yīng)用基因芯片檢測(cè)方法探討了卵巢癌細(xì)胞SKOV3在不同低氧環(huán)境下(間隔低氧與持續(xù)慢性低氧)與大氣氧環(huán)境生長(zhǎng)的轉(zhuǎn)錄組mRNA表達(dá)的差異,發(fā)現(xiàn)間隔缺氧改變的基因表達(dá)數(shù)少于慢性缺氧,并且具有較低的倍數(shù)變化。然而在間隔缺氧表達(dá)的基因?qū)τ诩?xì)胞的影響明顯大于在長(zhǎng)期缺氧環(huán)境表達(dá)的基因,包括白細(xì)胞介素-8、纖溶酶原激活劑和表皮生長(zhǎng)因子通路相關(guān)基因。Zhang等[22]對(duì)Olbryt等[21]上傳在GEO數(shù)據(jù)庫的數(shù)據(jù)(GSE53012)重新進(jìn)行分析,篩選出9個(gè)hub基因,包括ESR1、MMP2、ErbB2、MYC、VIM、CYBB、EDN1、SERPINE1和PDK,這些基因主要參與增殖對(duì)卵巢癌細(xì)胞的作用,包括調(diào)節(jié)細(xì)胞增殖、細(xì)胞黏附、細(xì)胞遷移的正向調(diào)節(jié)、局灶性黏附和細(xì)胞外基質(zhì)結(jié)合。本研究通過RNA測(cè)序發(fā)現(xiàn)了在低氧環(huán)境下高表達(dá)的5個(gè)基因(HILPDA、MT1B、CA9、MT1X與LOX-L2)與低表達(dá)的5個(gè)基因(WARS1、CHAC1、PSAT1、UPP1與DDX5),通過RT-qPCR證實(shí)這10個(gè)基因在低氧環(huán)境下與常氧環(huán)境下表達(dá)差異,這些基因生物學(xué)功能與細(xì)胞增殖功能相關(guān),包括細(xì)胞外基質(zhì)形成、細(xì)胞黏附、經(jīng)典糖酵解、血小板脫顆粒、炎癥反應(yīng)等,為進(jìn)一步探索低氧環(huán)境下卵巢癌生長(zhǎng)與發(fā)展提供分子靶點(diǎn)。
本研究通路分析顯示上調(diào)基因主要富集于癌癥通路、PI3K-AKT信號(hào)通路、ECM-受體相互作用、HIF-1信號(hào)通路等信號(hào)通路,而下調(diào)基因則主要富集于腫瘤膽堿代謝、氨基酸生物合成等信號(hào)通路,說明在低氧環(huán)境下增殖能力增強(qiáng),而分化能力下降。PI3K-AKT信號(hào)通路是腫瘤細(xì)胞增殖的經(jīng)典通路,促進(jìn)卵巢癌細(xì)胞增殖、轉(zhuǎn)移[23]。在一項(xiàng)對(duì)比鉑耐藥及鉑敏感患者的轉(zhuǎn)錄組測(cè)序的研究中,鉑耐藥患者表達(dá)改變的基因同樣也富集于PI3K-AKT信號(hào)通路[24]。另一項(xiàng)研究中鉑耐藥細(xì)胞的表達(dá)改變基因則顯著富集于ECM-受體相互作用信號(hào)通路[25]。這些研究結(jié)果說明低氧環(huán)境下細(xì)胞轉(zhuǎn)錄組轉(zhuǎn)變成抑制藥物治療的基因表達(dá)模式。
綜上所述,通過轉(zhuǎn)錄組測(cè)序分析,進(jìn)一步明確了卵巢癌細(xì)胞在低氧環(huán)境下的整個(gè)基因表達(dá)改變以及涉及的信號(hào)通路,該研究結(jié)果為進(jìn)一步研究老年卵巢癌治療提供新的思路和突破點(diǎn)。
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(2024-02-28收稿)