摘要:目的" 利用糖酵解相關(guān)LncRNA構(gòu)建肺腺癌患者的預后模型,幫助臨床預測個體化藥物療效和疾病復發(fā)情況。方法" 綜合TCGA和GSEA數(shù)據(jù)庫,篩選與肺腺癌中糖酵解相關(guān)lncRNA表達數(shù)據(jù),利用LASSO和Cox回歸分析構(gòu)建預后模型,繪制受試者工作特征曲線(ROC)并加以校準,將臨床病理特征和風險評分進行整合構(gòu)建列線圖,分析免疫細胞分布、免疫相關(guān)分子和藥物敏感性的差異與風險評分的關(guān)系。結(jié)果" 在GSEA數(shù)據(jù)庫中共選取出4個有效糖酵解基因集(BioCarta、Hallmark、KEGG、REACTOME和WP),與TCGA數(shù)據(jù)中的lncRNA表達數(shù)據(jù)結(jié)合獲得1025個與糖酵解相關(guān)的lncRNA。差異分析獲得186個在腫瘤組織和正常組織間差異表達的糖酵解相關(guān)lncRNA;單因素Cox、LASSO回歸分析獲得19個與預后相關(guān)的lncRNA。多因素Cox比例風險回歸分析獲得了由12個lncRNA 組成的預測模型。模型ACU提示預測性能較好,1、3、5年生存時間的AUC分別為0.711、0.713和0.699,并且可將肺腺癌區(qū)分為高、低風險組,高、低風險組的總生存期(OS)比較,差異有統(tǒng)計學意義(P<0.05)。單因素和多因素Cox分析顯示,風險評分可作為預測肺腺癌生存狀態(tài)的獨立預后指標,并且風險評分的預測性能優(yōu)于其它臨床病理特征。此外,不同的性別、T、N、M和Stage分期的風險評分比較,差異有統(tǒng)計學意義(P<0.05)。風險評分與臨床病理特征構(gòu)建的列線圖對1、3、5年預后的預測能力均有提升(1、3、5年生存時間的AUC分別為0.741、0.750和0.715)。高、低風險組間免疫微環(huán)境比較,差異有統(tǒng)計學意義(P<0.05),表現(xiàn)為多數(shù)免疫細胞與低風險評分呈正相關(guān)。藥物敏感性分析提示絲裂霉素C、紫杉醇、雷帕霉素、多西他賽和厄洛替尼的藥物敏感性在高、低風險組間也存在區(qū)別。結(jié)論" 糖酵解相關(guān)lncRNA構(gòu)建的肺腺癌預后模型可以高效準確的預測肺腺癌患者的預后,具有一定的臨床意義。
關(guān)鍵詞:肺腺癌;糖酵解;lncRNA;預后;列線圖;藥物敏感性
中圖分類號:R734.2" " " " " " " " " " " " " " " " "文獻標識碼:A" " " " " " " " " " " " " " " " "DOI:10.3969/j.issn.1006-1959.2024.05.001
文章編號:1006-1959(2024)05-0001-12
Construct a Prognostic Model for Patients with Lung Adenocarcinoma
by Using Glycolysis-related LncRNA
DING Dan,ZHAO Rong-chang,DING Yan,ZHANG Dan-dan,CAI Jian
(Department of Oncology,Taixing People’s Hospital,Taixing 225400,Jiangsu,China)
Abstract:Objective" To construct a prognostic model of lung adenocarcinoma patients by using glycolysis-related LncRNA, and to help predict the efficacy of individualized drugs and disease recurrence.Methods" The TCGA and GSEA databases were used to screen the expression data of lncRNA related to glycolysis in lung adenocarcinoma. The prognostic model was constructed by LASSO and Cox regression analysis. The receiver operating characteristic curve (ROC) was drawn and calibrated. The clinicopathological features and risk scores were integrated to construct a nomogram. The relationship between immune cell distribution, immune-related molecules and drug sensitivity and risk score was analyzed.Results" Four effective glycolysis gene sets (BioCarta, Hallmark, KEGG, REACTOME and WP) were selected from the GSEA database, and 1025 glycolystic-related lncRNAs were obtained by combining with the expression data of lncRNAs in the TCGA data. A total of 186 glycolytic-related lncRNAs were differentially expressed between tumor and normal tissues by differential analysis, and 19 prognostic related lncRNAs were obtained by univariate COX and LASSO regression analysis. A prediction model consisting of 12 lncRNAs was obtained by Cox proportional hazard regression analysis. The ACU value of the model suggested that the prediction performance was good, and the AUC of 1, 3 and 5 years survival time were 0.711, 0.713 and 0.699, respectively. The patients with lung adenocarcinoma could be divided into high and low risk groups, and the difference of overall survival (OS) between the two groups was statistically significant (Plt;0.05). Univariate and multivariate Cox analysis showed that risk score could be used as an independent prognostic indicator for the survival of lung adenocarcinoma, and the risk score predicted better than other clinicopathologic features. In addition, there were statistically significant differences in risk scores between genders, T, N, M, and Stage (Plt;0.05). Risk scores and histograms constructed with clinicopathological features improved prognostic ability at 1,3, and 5 years (AUC at 1, 3, and 5 years survival time was 0.741, 0.750, and 0.715, respectively). There were statistically significant differences in immune microenvironment between the high and low risk groups, showing that most immune cells were positively correlated with the low risk score. Drug sensitivity analysis suggested that there were significant differences in drug sensitivity of mitomycin C, paclitaxel, rapamycin, docetaxel and erotinib between the two groups.Conclusion" The prognosis model of lung adenocarcinoma constructed by glycolysis-related lncRNA can effectively and accurately predict the prognosis of patients with lung adenocarcinoma, which has certain clinical significance.
Key words:Lung adenocarcinoma;Glycolysis;lncRNA;Prognostic;Nomogram;Drug sensitivity
肺癌(lung cancer)在全球癌癥相關(guān)人類死亡中占據(jù)很大比例[1,2]。肺腺癌(lung adenocarcinoma)作為肺癌最常見的病理類型,其個體化治療越來越受到臨床醫(yī)生的關(guān)注[3]。腫瘤的發(fā)生和發(fā)展根本在于基因的改變,這就會造成即使在家庭和經(jīng)濟因素被去除后,同樣的性別、體能狀態(tài)評分、年齡和 TNM 分期的患者對治療的反應和總生存時間并不一定會相同。因此,迫切的需要探索出有效的微觀分子生物標志物來預測肺腺癌患者的治療效果和預后。
充分了解腫瘤細胞與正常細胞在代謝和增殖方面的差異對于預測癌癥患者的預后和臨床治療反應至關(guān)重要。細胞主要通過糖代謝獲取能量來完成其生物活動,肺腺癌細胞也不例外。以往研究表明[4,5],癌細胞最顯著的代謝變化是Warburg效應的發(fā)生,表現(xiàn)為腫瘤細胞有氧糖酵解增加,依賴糖酵解途徑產(chǎn)生三磷酸腺苷(ATP)。鑒于腫瘤細胞中這種獨特的代謝改變,很多研究已經(jīng)嘗試并改進了靶向治療模式[6-8],并且越來越多的研究也證實使用糖酵解相關(guān)基因來建立腫瘤預后評估模型的可行性[9-12]。此外,在對長鏈非編碼 RNA (lncRNA)的深入研究中,發(fā)現(xiàn)它在多種生物過程中均發(fā)揮重要作用,例如基因表達的調(diào)節(jié)、細胞增殖、分化和凋亡[13-16]。近年來,已經(jīng)對lncRNA 作為預后分子標志物進行了廣泛的研究,發(fā)現(xiàn)lncRNA 具有很強的組織特異性[17-19],可有效用于腫瘤預測模型的構(gòu)建。
肺腺癌作為嚴重威脅人類生命健康的一種疾病,亟需精準治療的實施來減少它對患癌患者帶來危害。在目前日益發(fā)展的科學技術(shù)中,已不缺乏靶向治療和免疫治療這些精準治療的手段,但受益的人群需要進一步篩選。那么通過腫瘤預測模型的構(gòu)建來滿足可制定精準治療方案和預測患者的生存時間的這些要求,對于肺腺癌患者具有重大意義。既往已有大量文獻提示利用LncRNA構(gòu)建的預測模型可以使得治療更加精準化,然而lncRNA涉及的功能種類繁多,未詳細劃分種類的lncRNA對于腫瘤研究貢獻降低,例如糖酵解的相關(guān)的LncRNA在肺腺癌中的作用就未能闡明。為此,本研究通過綜合分析將糖酵解相關(guān)LncRNA以預后模型的研究方式來評估其在肺腺患者中表達水平、免疫浸潤狀態(tài)和預后生存的的關(guān)系。
1材料與方法
1.1臨床信息和lncRNA表達數(shù)據(jù)獲取" 在TCGA數(shù)據(jù)庫(https://cancergenome.nih.gov/)的數(shù)據(jù)存儲模塊中選擇肺腺癌患者的基因(包括mRNA和lncRNA)表達數(shù)據(jù)以及臨床信息數(shù)據(jù)進行下載,共獲得522例患者的可靠數(shù)據(jù)。通過Perl(版本5.32.1.1)語言的運行將基因的表達數(shù)據(jù)和類別信息進行整理,同時將所有患者的性別、年齡、T分期、N分期、M分期、Stage分期及生存情況進行了提取整合(表1)。隨后再次利用Perl語言對配套的基因組注釋文件與mRNA和lncRNA對應的類別信息編碼進行比對,將lncRNA的表達數(shù)據(jù)單獨分離出。
1.2篩選差異表達的糖酵解相關(guān)lncRNA并構(gòu)建模型" 在GSEA(gene Set Enrichment Analysis)數(shù)據(jù)庫(http://www.broadinstitute.org/gsea/index.jsp)中搜索糖酵解基因集,共獲得326個基因。利用R軟件(version 4.0.5)進行Pearson相關(guān)性分析,獲得與糖酵解基因相關(guān)的lncRNA(設置的參數(shù)為P<0.001,|Correlation Coefficient|>0.4)。對腫瘤組織與正常組織間糖酵解相關(guān)lncRNA進行差異表達分析[設置參數(shù)為Cut-off標準為|log2fold change(logFC)|>1.5,P<0.05;FDR(1 discovery rate)<0.05]。對差異表達的lncRNA進行單因素Cox回歸分析,過濾條件為P<0.05。然后通過LASSO回歸和二次Cox回歸分析構(gòu)建模型。風險公式為:βlncRNA1×lncRNA1的表達量+βlncRNA2×lncRNA2的表達量+βlncRNA3×lncRNA3的表達量 +…+ βlncRNAn×lncRNAn的表達量,其中β是Cox分析中coef值。
1.3模型性能評估和列線圖的構(gòu)建" 通過生存ROC軟件包,繪制ROC曲線來評估預后模型的準確性。利用性能表現(xiàn)最好的曲線下面積(AUC)的Cut-off值將肺腺癌患者重新劃分為低風險組和高風險組,并評估低風險組和高風險組之間的生存時間差異,繪制Kaplan-Meier曲線。?字2檢驗分析臨床病理特征在高、低風險組間的差異,并在帶狀圖中顯示結(jié)果,其中P<0.001=***,<0.01=**,<0.05=*。用Wilcoxon signed-rank 檢驗分析不同性別、年齡、T分期、N分期、M分期和Stage分期中風險評分的差異。最后將性別、年齡、Stage分期和風險評分進行整合構(gòu)建列線圖。
1.4免疫微環(huán)境和藥物療效差異性分析" 為了闡明免疫微環(huán)境與風險評分的關(guān)系,在R軟件中利用Wilcoxon signed rank檢驗和Spearman相關(guān)性分析,通過XCELL、TIMER、QUANTISEQ、MCPcounter、EPIC、CIBERSORT和CIBERSORT- ABS方法獲取肺腺癌患者免疫細胞分布的差異(設置標準:P<0.05)。并比較低風險組和高風險組間免疫檢查點抑制相關(guān)基因表達水平差異。最后利用pRRophetic程序包,計算了常用藥物的IC50(半數(shù)抑制濃度)來評估lncRNA預后模型分組的肺腺癌患者的臨床治療反應差異。
2結(jié)果
2.1差異表達的lncRNA" 通過GSEA分析軟件的運行后,發(fā)現(xiàn)在BioCarta、Hallmark、KEGG、REACTOME和WP 4個基因集中腫瘤組織樣本與正常組織樣本之間糖酵解相關(guān)基因表達存在差異(P<0.05)。依據(jù)分析結(jié)果發(fā)現(xiàn)在腫瘤樣本中糖酵解富集最差的是BioCarta基因集(圖1A),最明顯的是Hallmark基因集(圖1B),其次是REACTOME基因集(圖1C),然后是WP基因集(圖1D)。這些基因集內(nèi)的基因均可作為明確的糖酵解相關(guān)基因進行后續(xù)分析。
2.2差異表達的糖酵解相關(guān)lncRNA及模型構(gòu)建" 從TCGA數(shù)據(jù)庫中522例肺腺癌患者的轉(zhuǎn)錄譜數(shù)據(jù)中共提取出了13 162個lncRNA,其中1025個是與糖酵解相關(guān)的。通過腫瘤組織與正常組織的比較后獲得了186個差異表達的lncRNA(圖2A、圖2B)。單變量Cox回歸分析共獲得37個lncRNA(圖2C)。LASSO回歸算法進一步分析這些lncRNA,篩選出19個lncRNA(圖3A、圖3B),再次進行單變量Cox分析,得到12個預后相關(guān)的lncRNA(圖3C),最后采用多因素Cox比例風險回歸分析獲得構(gòu)建預后模型的所需的系數(shù)和lncRNA(表2)。預后模型公式的具體計算為:0.073×LINC00941表達量+0.031×FAM83A-AS1表達量+0.075×LINC01116的表達量+0.021×AL365181.3表達量-0.137×AC103591.3表達量-0.203×TDRKH-AS1表達量+0.110×AC007773.1表達量+0.135×MIR193BHG表達量+0.080×MYO16-AS1表達量+0.014×AC003092.1表達量+0.108×LINC01843表達量+0.181×AL031667.3表達量)。
2.3糖酵解相關(guān)lncRNA模型的評估與驗證" 12個lncRNA構(gòu)成的預后模型的1、3、5年生存時間的AUC分別為0.711、0.713和0.699(圖4A)。采用Akaike信息準則(AIC)從3年生存ROC曲線最大值點確定Cut-off值(圖4B)。然后,利用這個值將TCGA數(shù)據(jù)庫中的肺腺癌患者重新劃分為低風險組和高風險組,兩組患者的生存時間存在差異(P=6.373e-13)(圖4C)。所有患者的風險評分和生存狀態(tài)都繪制在圖5A、圖5B中。單因素Cox分析提示,年齡(P=0.351,HR=1.007,95%CI:0.992~1.023)、性別(P=0.571,HR=1.089,95%CI:0.810~1.464),Stage分期(P<0.001,HR=1.625,95%CI:1.414~1.869),風險評分(P<0.001,HR=1.120,95%CI:1.093~1.147)是預后因子(圖5A)。多因素Cox分析提示,Stage分期(P<0.001,HR=1.601,95%CI:1.386~1.850)和風險評分(P<0.001,HR=1.113,95%CI:1.085~1.141)可作為獨立預后因子(圖5B)。此外,本研究還發(fā)現(xiàn)風險評分的AUC值高于Stage分期(圖5C)。患者的生存狀態(tài)與風險評分的關(guān)系見圖6A、圖6B。
2.4肺腺癌患者的臨床病理特征與風險評分之間的關(guān)系" 患者臨床病理特征與風險評分的關(guān)系見圖7A、圖7B。Wilcoxon signed-rank檢驗發(fā)現(xiàn)性別(圖7C)、T分期(圖7D)、N分期(圖7E)、M分期(圖7F)和Stage分期(圖7G)與風險評分顯著相關(guān)。隨后構(gòu)建的列線圖(圖8A)的校準結(jié)果提示,列線圖對1、3和5年生存時間的預測是符合實際的生存結(jié)果(圖8B、圖8C和圖8D),其中1、3、5年的AUC分別為0.741、0.750和0.715(圖8E、圖8F和圖8G)。
2.5免疫細胞浸潤分析" 結(jié)果顯示,淋巴祖細胞、CD4+ Th2細胞、CD4+(非調(diào)節(jié)性)細胞、單核細胞和NK細胞的出現(xiàn)主要與低風險呈正相關(guān)(圖9A)。同時也發(fā)現(xiàn)低風險評分與CD28(圖9B)、CD40(圖9C)、CTLA4(圖9D)、ICOS(圖9E)、TIGIT(圖9F)和TNFRSF4(圖9G)的高表達呈正相關(guān)(P<0.05),而與LAG3(圖9H)和PDCD1(圖9I)無關(guān)(P>0.05)。還發(fā)現(xiàn)順鉑(圖10A)、吉非替尼(圖10B)和吉西他濱(圖10C)的IC50在高、低風險組間無顯著差異。而絲裂霉素C(圖10D)、紫杉醇(圖10E)、雷帕霉素(圖10F)、厄洛替尼(圖10G)和多西他賽(圖10H)低風險組中有更高的IC50。
3討論
隨著手術(shù)、化療、靶向治療和放療等多種積極治療手段的發(fā)展,肺腺癌患者的生存率和生活質(zhì)量得到了提高。但是,只有充分評估與基因變化相關(guān)的風險,才能制定出真正個體化的治療方案。根據(jù)多種基因的表達狀態(tài)可將肺腺癌進一步分為不同的治療亞型和預后亞型。例如,具有EGFR突變和ALK融合突變的肺腺癌患者比沒有這些突變的患者有更好的治療選擇和更高的生存率[20,21]。此外,隨著免疫療法的發(fā)展,研究人員發(fā)現(xiàn)只有一部分的肺腺癌患者可以從這些治療中受益[22]。因此,不同患者對治療反應的問題仍有待解決。到目前為止,許多研究已表明可用多個分子標記物進行組合評分,可以有效的預測患者預后和評估藥物對患者的潛在療效。其中,乳腺癌21基因表達分析是最成熟的方法之一,它可以預測患者的預后、疾病復發(fā)和腫瘤轉(zhuǎn)移,并可用于指導治療計劃,協(xié)助制定患者的個體化治療策略[23]。關(guān)于肺腺癌分子標記物的研究已經(jīng)有很多,然而這些研究的研究方向各不相同(如開發(fā)免疫預后模型[24]、自噬相關(guān)基因預后模型[25]、鐵死亡相關(guān)基因預后模型[26])。但目前尚不清楚哪一種模型最為準確。因此,只有不斷的創(chuàng)新模型的構(gòu)建方法才能尋找出最為適用的模型
本研究中使用了由糖酵解相關(guān)基因構(gòu)建的預后模型作為參考,以此來獲得更可靠的肺腺癌預后模型。首先,獲得LUAD中糖酵解相關(guān)基因,結(jié)合lncRNA固有優(yōu)勢,選擇差異表達相關(guān)lncRNA作為構(gòu)建預后模型的基石。然后,在進行改進的LASSO回歸(包括交叉驗證、多次重復和隨機刺激)和COX回歸分析后,發(fā)現(xiàn)由12個與糖酵解相關(guān)的lncRNA組成的預后模型具有更好的獨立預后預測性能。結(jié)合該模型的臨床特點所構(gòu)建的列線圖具有更好的性能和更實際的臨床應用價值。由于按模型分組的患者的生存時間存在差異,在尋找原因時發(fā)現(xiàn)這種差異的原因在于按模型分組后的患者在腫瘤病理特征和免疫應答上存在差異,對治療藥物的敏感性也存在差異。因此,更加能確信通過本方法獲得的lncRNA模型能夠為肺腺癌患者的臨床治療帶來很好的輔助作用。
最近,已經(jīng)有大量的研究使用lncRNA來構(gòu)建肺腺癌的預后模型。有研究使用了免疫相關(guān)的lncRNA,但在數(shù)據(jù)處理過程中,由于沒有使用LASSO回歸進行有效的篩選,可能會導致模型預測結(jié)果與實際結(jié)果有偏差,并且列線圖中沒有將模型與臨床病理特征相結(jié)合,因此無法評估年齡、性別和Stage分期對模型的影響[27]。Wang Y等[28]通過探索lncRNA相關(guān)的ceRNA網(wǎng)絡獲得了預后生物標志物,但他們沒有計算模型的AUC值。Geng W等[29]發(fā)現(xiàn)與基因組不穩(wěn)定性相關(guān)的體細胞突變相關(guān)的lncRNA可能是肺腺癌的預后信號,獲得的模型雖然具有良好的預測性能,但基于該模型的群體之間的免疫微環(huán)境差異尚未進一步探討。Jiang A等[30]驗證了使用自噬相關(guān)的lncRNA可作為肺腺癌患者預后生物標志物,但該風險模型沒有計算出1、3和5年生存時間的AUC,因此無法判斷其準確性。而本文的基于腫瘤代謝特征的預后模型具有以下特點:①理論基礎(chǔ)充分:糖酵解作為一種常見的腫瘤變化的代謝特征,已被許多研究者證實具有相關(guān)性;②數(shù)據(jù)篩選合理:采用改進的LASSO回歸和Cox回歸分析處理的數(shù)據(jù)更加可靠;③列線圖和藥物敏感性的預測提供了更好的臨床適用性。
雖然構(gòu)建的模型具有上述優(yōu)點,但也存在一些不足。對于12個lncRNA,無法通過其它數(shù)據(jù)庫進行驗證,主要是因為部分lncRNA是最近才被發(fā)現(xiàn)。LINC00941、FAM83A-AS1、TDRKH-AS1、LINC01843與肺腺癌的發(fā)生發(fā)展有關(guān)[31,32],而AL365181.3、AC103591.3、AC003092.1、AL031667.3為新轉(zhuǎn)錄本。AC007773.1、MIR193BHG和MYO16-AS1則被發(fā)現(xiàn)與其他癌癥的侵襲進展相關(guān)[33]。LINC01116在非小細胞肺癌對吉非替尼的耐藥性中發(fā)揮重要作用。因此,當未來有更好的實驗研究資源時,希望這些lncRNA的預測能力可以在更多的肺腺癌患者中得到驗證。
總之,本次鑒定出的模型在患者的生存時間和藥物治療效果上均有較好的預測能力。同時,lncRNA與免疫應答的結(jié)合,不僅可以提高模型的準確性,也為免疫治療的研究開辟了新的方向。
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收稿日期:2023-02-28;修回日期:2023-05-02
編輯/成森