CN108570501B - Multiple myeloma molecular typing and application - Google Patents
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Abstract
本发明公开了多发性骨髓瘤分子分型及应用。本发明提供了产品,包括获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质;上述产品还包括运行多发性骨髓瘤贝叶斯分类器的设备;本发明鉴定出了一个与MCL1基因共表达的基因模块(简称为MCL1‑M),并应用它将多发性骨髓瘤分成为两个主要亚型,即MCL‑M‑High亚型和MCL‑M‑Low亚型。这两个亚型具有显著不同的预后与遗传学特征。The invention discloses molecular typing and application of multiple myeloma. The invention provides products, including substances for obtaining or detecting the expression of 97 genes in patients with multiple myeloma tumors to be tested; the above products also include equipment for running a Bayesian classifier of multiple myeloma; the invention identifies a The MCL1 gene co-expressed gene module (referred to as MCL1‑M for short) was used to divide multiple myeloma into two main subtypes, MCL‑M‑High and MCL‑M‑Low. The two subtypes have significantly different prognostic and genetic features.
Description
技术领域technical field
本发明属于生物技术领域,尤其涉及一种多发性骨髓瘤分子分型及应用。The invention belongs to the field of biotechnology, and in particular relates to molecular typing and application of multiple myeloma.
背景技术Background technique
多发性骨髓瘤(Multiple Myeloma,MM)是一种由浆细胞恶性增殖所导致的肿瘤,是第二常见的血液肿瘤,在中国的发病率为1~2/十万人。多发性骨髓瘤是好发于年龄大于60岁的老年人群中,随着我国老龄化程度的加重,其发病率逐年提升,已成为严重威胁老年人健康的一种疾病。多发性骨髓瘤的典型特征为骨髓中存在大量异常增生的浆细胞,这种浆细胞会分泌一种异常的免疫球蛋白或免疫球蛋白片段,即M蛋白。Multiple Myeloma (MM) is a tumor caused by the malignant proliferation of plasma cells, and is the second most common blood tumor, with an incidence of 1-2/100,000 people in China. Multiple myeloma is a common disease in the elderly over 60 years old. With the aggravation of aging in my country, the incidence rate is increasing year by year, and it has become a disease that seriously threatens the health of the elderly. Multiple myeloma is typically characterized by the presence of large numbers of abnormally proliferating plasma cells in the bone marrow that secrete an abnormal immunoglobulin or immunoglobulin fragment, the M protein.
随着蛋白酶体抑制剂如硼替佐米和免疫调节药物如来那度胺的应用,多发性骨髓瘤的生存情况有了明显的改善。但是,多发性骨髓瘤目前仍然无法被完全治愈。多发性骨髓瘤在生物学上和临床上具有高度的异质性,因此,其对多药物联合治疗的反应及治疗后生存情况在不同的病人中具有巨大的差异。造成这种差异的生物学机制目前尚未被充分理解,在一定程度上阻碍了个性化精准治疗的进行。因此,为了加深对多发性骨髓瘤生物学本质的理解,辅助临床治疗决策,开发简单可靠的分子分型系统迫在眉睫。目前,国际上已经有几个多发性骨髓瘤分子分型系统被提出来。例如,Bergsagel等人鉴定了8种具有不同的细胞周期蛋白D(Cyclin D)表达和染色体易位的多发性骨髓瘤亚型。使用无偏无假设的转录组分析,Zhan和Broyl等人提出多发性骨髓瘤具有7-10个分子亚型,根据病人生存期的长短,这些亚型可以被进一步简化为高风险组和低风险组。此外,与预后相关的基因表达特征如UAMS-70和UAMS-17,UAMS-80,IFM-15,Millennium-100,EMC-92,基因扩增指数如GPI-5,MRC-IX-6以及中心体扩增指数也被提出。但以上分子分型和表达特征并不能预测药物治疗反应,也不能与浆细胞的发育过程相关联,而且用于分子分型的基因与多发性骨髓瘤病因之间的关联也未被阐明。Survival in multiple myeloma has improved markedly with the introduction of proteasome inhibitors such as bortezomib and immunomodulatory drugs such as lenalidomide. However, multiple myeloma is still not completely cured. Multiple myeloma is biologically and clinically highly heterogeneous, and therefore, its response to multidrug combination therapy and post-treatment survival vary widely among different patients. The biological mechanisms responsible for this difference are currently not fully understood, which to a certain extent hinders the development of personalized precision therapy. Therefore, in order to deepen the understanding of the biological nature of multiple myeloma and assist clinical treatment decisions, it is urgent to develop a simple and reliable molecular typing system. At present, several molecular typing systems for multiple myeloma have been proposed internationally. For example, Bergsagel et al. identified 8 multiple myeloma subtypes with distinct Cyclin D (Cyclin D) expression and chromosomal translocations. Using unbiased and hypothetical transcriptome analysis, Zhan and Broyl et al. proposed that multiple myeloma has 7-10 molecular subtypes, which can be further simplified into high-risk and low-risk groups, depending on how long the patient survives. Group. In addition, prognostic-related gene expression signatures such as UAMS-70 and UAMS-17, UAMS-80, IFM-15, Millennium-100, EMC-92, gene amplification indices such as GPI-5, MRC-IX-6, and central A body expansion index was also proposed. However, these molecular typing and expression signatures do not predict drug treatment response, nor do they correlate with the development of plasma cells, and the association between the genes used for molecular typing and the etiology of multiple myeloma has not been elucidated.
发明内容SUMMARY OF THE INVENTION
本发明一个目的是提供获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质的用途。An object of the present invention is to provide the use of obtaining or detecting substances expressed in 97 genes in a patient with multiple myeloma tumors to be tested.
本发明提供了获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质在制备预测待测多发性骨髓瘤肿瘤患者预后生存率的产品中的应用。The invention provides the application of obtaining or detecting the substances expressed in 97 genes of the multiple myeloma tumor patients to be tested in preparing a product for predicting the prognosis and survival rate of the multiple myeloma tumor patients to be tested.
本发明还提供了获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质在制备预测多发性骨髓瘤肿瘤患者预后生存期产品中的应用。The invention also provides the application of obtaining or detecting the substances expressed by 97 genes in the multiple myeloma tumor patients to be tested in preparing a product for predicting the prognosis and survival period of the multiple myeloma tumor patients.
本发明还提供了获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质在制备预测多发性骨髓瘤肿瘤患者预后存活风险产品中的应用。The invention also provides the application of obtaining or detecting the substances expressed in 97 genes in the multiple myeloma tumor patients to be tested in preparing a product for predicting the prognosis and survival risk of the multiple myeloma tumor patients.
本发明另一个目的是提供获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和运行多发性骨髓瘤贝叶斯分类器的设备的用途。Another object of the present invention is to provide the use of a device for obtaining or detecting the expression of 97 genes in a patient with multiple myeloma tumors to be tested and for running a Bayesian classifier for multiple myeloma.
本发明提供了获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和运行多发性骨髓瘤贝叶斯分类器的设备在制备预测待测多发性骨髓瘤肿瘤患者预后生存率的产品中的应用。The invention provides equipment for obtaining or detecting 97 gene expression substances in patients with multiple myeloma tumors to be tested and equipment for running a Bayesian classifier of multiple myeloma. application in the product.
本发明还提供了获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和运行多发性骨髓瘤贝叶斯分类器的设备在制备预测多发性骨髓瘤肿瘤患者预后生存期产品中的应用。The invention also provides equipment for obtaining or detecting 97 gene expression substances in the multiple myeloma tumor patients to be tested and running the multiple myeloma Bayesian classifier in the preparation of a product for predicting the prognosis and survival period of the multiple myeloma tumor patients Applications.
本发明还提供了获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和运行多发性骨髓瘤贝叶斯分类器的设备在制备预测多发性骨髓瘤肿瘤患者预后存活风险产品中的应用。The invention also provides equipment for obtaining or detecting 97 gene expression substances in the multiple myeloma tumor patients to be tested and running the multiple myeloma Bayesian classifier in the preparation of a product for predicting the prognosis and survival risk of multiple myeloma tumor patients Applications.
上述97个基因为如下:The above 97 genes are as follows:
ACBD3、ADAR、ADSS、ALDH2、ANP32E、ANXA2、ATF3、ATP8B2、CACYBP、CAPN2、CCND1、CCT3、CDC42SE1、CERS2、CHSY3、CLIC1、CLMN、COPA、CSNK1G3、DAP3、DENND1B、ENSA、EPRS、EPSTI1、EVL、FAM13A、FAM49A、FLAD1、FRZB、GLRX2、HAX1、HDGF、HLA-A、HLA-B、HLA-C、HLA-F、HLA-G、IL6R、ISG20L2、JTB、KLF2、LAMTOR2、LDHA、MCL1、MOXD1、MRPL24、MRPL9、MVP、MYL6、NDUFS2、NOP58、NOTCH2NL、NTAN1、PAK1、PI4KB、PIEZO1、PIK3AP1、PIM2、PIP5K1B、PMVK、POGZ、PPIA、PRCC、PRKCA、PRRC2C、PSMB4、PSMD4、RAB29、RCBTB2、SCAMP3、SCAPER、SDHC、SEL1L3、SELPLG、SHC1、SIDT1、SSR2、STAP1、TAP1、TIMM17A、TLR10、TMCO1、TOR1AIP2、TOR3A、TP53INP1、TPM3、TRANK1、TROVE2、UAP1、UBE2Q1、UBQLN4、UHMK1、VPS45、YY1AP1、ZC3H11A、ZFP36和ZNF593。ACBD3, ADAR, ADSS, ALDH2, ANP32E, ANXA2, ATF3, ATP8B2, CACYBP, CAPN2, CCND1, CCT3, CDC42SE1, CERS2, CHSY3, CLIC1, CLMN, COPA, CSNK1G3, DAP3, DENND1B, ENSA, EPRS, EPSTI1, EVL, FAM13A, FAM49A, FLAD1, FRZB, GLRX2, HAX1, HDGF, HLA-A, HLA-B, HLA-C, HLA-F, HLA-G, IL6R, ISG20L2, JTB, KLF2, LAMTOR2, LDHA, MCL1, MOXD1, MRPL24, MRPL9, MVP, MYL6, NDUFS2, NOP58, NOTCH2NL, NTAN1, PAK1, PI4KB, PIEZO1, PIK3AP1, PIM2, PIP5K1B, PMVK, POGZ, PPIA, PRCC, PRKCA, PRRC2C, PSMB4, PSMD4, RAB29, RCBTB2, SCAMP3, SCAPER, SDHC, SEL1L3, SELPLG, SHC1, SIDT1, SSR2, STAP1, TAP1, TIMM17A, TLR10, TMCO1, TOR1AIP2, TOR3A, TP53INP1, TPM3, TRANK1, TROVE2, UAP1, UBE2Q1, UBQLN4, UHMK1, VPS45, YY1AP1, ZC3H11A, ZFP36 and ZNF593.
上述多发性骨髓瘤贝叶斯分类器按照包括如下步骤的方法获得:The above Bayesian classifier for multiple myeloma is obtained according to a method comprising the following steps:
1)获得n个多发性骨髓瘤样本的97个基因的表达量数据;1) Obtain the expression data of 97 genes of n multiple myeloma samples;
2)将所述n个多发性骨髓瘤样本的97个基因的表达量数据用ConsensusClustering聚类算法分为MCL1-M-High和MCL1-M-Low两个亚型;2) dividing the expression data of the 97 genes of the n multiple myeloma samples into two subtypes, MCL1-M-High and MCL1-M-Low, using the ConsensusClustering clustering algorithm;
3)基于步骤2的两个亚型、步骤1)的n个多发性骨髓瘤样本的97个基因的表达量数据、n个多发性骨髓瘤样本的预后生存期数据,用朴素贝叶斯方法构建得到素贝叶斯分类器。3) Based on the two subtypes in
上述步骤3)为先将所述n个多发性骨髓瘤样本按照样本数量比大于1:1的比例随机划分训练集和验证集;再使用训练中的所述97个基因的表达量数据,并结合所述用Consensus Clustering聚类算法获得的各样本MCL1-M-High和MCL1-M-Low亚型标签,使用R语言机器学习包klaR包中的朴素贝叶斯算法建立预测单个患者MCL1-M-High亚型和MCL1-M-Low亚型的多发性骨髓瘤贝叶斯分类器;The above step 3) is to first randomly divide the n multiple myeloma samples into a training set and a verification set according to a ratio of the number of samples greater than 1:1; then use the expression data of the 97 genes in the training, and Combined with the MCL1-M-High and MCL1-M-Low subtype labels of each sample obtained by the Consensus Clustering clustering algorithm, the naive Bayes algorithm in the R language machine learning package klaR package was used to establish a prediction of single patient MCL1-M - Bayesian classifier of multiple myeloma of High subtype and MCL1-M-Low subtype;
上述所述获得各个多发性骨髓瘤样本的97个基因的表达量数据的方式为检测或者从数据库中获得。The method for obtaining the expression data of the 97 genes of each multiple myeloma sample described above is detection or obtaining from a database.
本发明第3个目的是提供一种产品。The third object of the present invention is to provide a product.
本发明提供的产品,包括获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和运行多发性骨髓瘤贝叶斯分类器的设备。The products provided by the present invention include obtaining or detecting substances expressed in 97 genes in the multiple myeloma tumor patients to be tested and equipment for running the multiple myeloma Bayesian classifier.
上述产品中,所述产品具有如下至少一种功能:Among the above-mentioned products, the product has at least one of the following functions:
1)预测待测多发性骨髓瘤肿瘤患者预后生存率;1) Predict the prognosis and survival rate of patients with multiple myeloma tumors to be tested;
2)预测多发性骨髓瘤肿瘤患者预后生存期;2) Predict the prognosis and survival time of patients with multiple myeloma tumors;
3)预测多发性骨髓瘤肿瘤患者预后存活风险。3) Predict the prognosis and survival risk of patients with multiple myeloma tumors.
上述产品还包括记载检测方法的载体;The above product also includes a carrier for recording the detection method;
所述检测方法包括如下步骤:所述检测方法包括如下步骤:用所述获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质得到所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用所述多发性骨髓瘤贝叶斯分类器进行分类,属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者预测预后生存期显著低于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者。The detection method includes the following steps: the detection method includes the following steps: obtaining 97 samples of the multiple myeloma tumor patient to be detected by using the obtained or detected substance expressed by 97 genes in the multiple myeloma tumor patient to be detected. Gene expression data; then the expression data of the 97 genes of the multiple myeloma tumor patients to be tested are classified by the multiple myeloma Bayesian classifier, which belong to the MCL1-M-High subtype. The predicted prognosis survival of patients with multiple myeloma tumors was significantly lower than that of patients with multiple myeloma tumors belonging to the MCL1-M-Low subtype.
上述产品中,所述待测多发性骨髓瘤肿瘤患者为单个患者或多个患者。In the above product, the multiple myeloma tumor patient to be tested is a single patient or multiple patients.
本发明第4个目的是提供构建对多发性骨髓瘤肿瘤患者进行分型的模型的方法。The fourth object of the present invention is to provide a method for constructing a model for the typing of multiple myeloma tumor patients.
本发明提供的方法包括如下步骤:The method provided by the present invention comprises the following steps:
1)获得n个多发性骨髓瘤样本的97个基因的表达量数据;1) Obtain the expression data of 97 genes of n multiple myeloma samples;
2)将所述n个多发性骨髓瘤样本的97个基因的表达量数据用ConsensusClustering聚类算法分为MCL1-M-High和MCL1-M-Low两个亚型;2) dividing the expression data of the 97 genes of the n multiple myeloma samples into two subtypes, MCL1-M-High and MCL1-M-Low, using the ConsensusClustering clustering algorithm;
3)基于步骤2)的两个亚型、步骤1)的n个多发性骨髓瘤样本的97个基因的表达量数据、n个多发性骨髓瘤样本的预后生存期数据,用朴素贝叶斯方法构建得到素贝叶斯分类器,即为目的模型。3) Based on the two subtypes in step 2), the expression data of 97 genes of n multiple myeloma samples in step 1), and the prognosis and survival data of n multiple myeloma samples, use Naive Bayesian The method constructs the prime Bayes classifier, which is the target model.
上述产品还包括运行多发性骨髓瘤贝叶斯分类器的设备(该设备可以是光盘或者电脑等。);The above products also include equipment for running the Bayesian classifier of multiple myeloma (the equipment can be a CD-ROM or a computer, etc.);
上述产品还包括记载检测方法的载体;The above product also includes a carrier for recording the detection method;
所述检测方法包括如下步骤:用所述获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质得到所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用所述多发性骨髓瘤贝叶斯分类器进行分类,属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者预测预后生存期显著低于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者。The detection method comprises the following steps: obtaining or detecting the expression data of the 97 genes in the multiple myeloma tumor patient to be detected by using the substance obtained or detecting the expression of the 97 genes in the multiple myeloma tumor patient to be detected; The expression data of the 97 genes of the multiple myeloma tumor patients to be tested are classified by the multiple myeloma Bayesian classifier, and the multiple myeloma tumor patients belonging to the MCL1-M-High subtype are predicted to be tested. Prognostic survival was significantly lower than patients with multiple myeloma tumors under test belonging to the MCL1-M-Low subtype.
上述产品中,所述待测多发性骨髓瘤肿瘤患者为单个患者或多个患者。In the above product, the multiple myeloma tumor patient to be tested is a single patient or multiple patients.
上述产品中,所述n个多发性骨髓瘤样本为551例样本。Among the above products, the n multiple myeloma samples are 551 samples.
或所述大于1:1的比例为按照2:1的比例随机划分训练集和验证集。Or the ratio greater than 1:1 is to randomly divide the training set and the validation set according to the ratio of 2:1.
上述产品具有如下至少一种功能:The above products have at least one of the following functions:
1)预测待测多发性骨髓瘤肿瘤患者预后生存率;1) Predict the prognosis and survival rate of patients with multiple myeloma tumors to be tested;
2)预测多发性骨髓瘤肿瘤患者预后生存期;2) Predict the prognosis and survival time of patients with multiple myeloma tumors;
3)预测多发性骨髓瘤肿瘤患者预后存活风险。3) Predict the prognosis and survival risk of patients with multiple myeloma tumors.
本发明的另一个目的是提供构建对多发性骨髓瘤肿瘤患者进行分型的模型的方法。Another object of the present invention is to provide a method of constructing a model for the typing of patients with multiple myeloma tumors.
本发明提供的方法,包括如下步骤:The method provided by the present invention comprises the following steps:
1)获得n个多发性骨髓瘤样本的97个基因的表达量数据;1) Obtain the expression data of 97 genes of n multiple myeloma samples;
2)将所述n个多发性骨髓瘤样本的97个基因的表达量数据用ConsensusClustering聚类算法分为MCL1-M-High和MCL1-M-Low两个亚型;2) dividing the expression data of the 97 genes of the n multiple myeloma samples into two subtypes, MCL1-M-High and MCL1-M-Low, using the ConsensusClustering clustering algorithm;
3)基于步骤2)的两个亚型、步骤1)的n个多发性骨髓瘤样本的97个基因的表达量数据、n个多发性骨髓瘤样本的预后生存期数据,用朴素贝叶斯方法构建得到素贝叶斯分类器,即为目的模型。3) Based on the two subtypes in step 2), the expression data of 97 genes of n multiple myeloma samples in step 1), and the prognosis and survival data of n multiple myeloma samples, use Naive Bayesian The method constructs the prime Bayes classifier, which is the target model.
上述获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和/或所述运行多发性骨髓瘤贝叶斯分类器的设备或上述方法得到的模型在制备预测待测多发性骨髓瘤肿瘤患者预后生存率的产品中的应用也是本发明保护的范围。The above-mentioned substances for obtaining or detecting the expression of 97 genes in patients with multiple myeloma tumors to be tested and/or the equipment for running the Bayesian classifier of multiple myeloma or the models obtained by the above-mentioned methods are used to predict the multiple myeloma tumors to be tested. The application in the product of the prognosis and survival rate of tumor patients is also the scope of protection of the present invention.
上述获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和/或所述运行多发性骨髓瘤贝叶斯分类器的设备或上述方法得到的模型在制备预测多发性骨髓瘤肿瘤患者预后生存期产品中的应用也是本发明保护的范围。The above-mentioned substances for obtaining or detecting the expression of 97 genes in patients with multiple myeloma tumors to be tested and/or the equipment for running the Bayesian classifier of multiple myeloma or the models obtained by the above-mentioned methods are used to prepare and predict multiple myeloma tumors. The application in the product of patient prognosis and survival is also the scope of protection of the present invention.
上述获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和/或所述运行多发性骨髓瘤贝叶斯分类器的设备或上述方法得到的模型在制备预测多发性骨髓瘤肿瘤患者预后存活风险产品中的应用也是本发明保护的范围。The above-mentioned substances for obtaining or detecting the expression of 97 genes in patients with multiple myeloma tumors to be tested and/or the equipment for running the Bayesian classifier of multiple myeloma or the models obtained by the above-mentioned methods are used to prepare and predict multiple myeloma tumors. The application in the product of patient prognosis survival risk is also the scope of the protection of the present invention.
本发明还提供了一种对待测多发性骨髓瘤肿瘤患者分型的方法,包括如下步骤:The present invention also provides a method for classifying patients with multiple myeloma tumors to be tested, comprising the following steps:
检测或获得所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用上述多发性骨髓瘤贝叶斯分类器进行分型,得到待测多发性骨髓瘤肿瘤患者是属于MCL1-M-High亚型还是MCL1-M-Low亚型。Detect or obtain the expression data of the 97 genes of the multiple myeloma tumor patient to be tested; and then use the above-mentioned multiple myeloma Bayesian classification for the expression data of the 97 genes of the multiple myeloma tumor patient to be tested. According to the classification of the multiple myeloma tumor patients to be tested, whether they belong to the MCL1-M-High subtype or the MCL1-M-Low subtype.
本发明还提供了一种预测多发性骨髓瘤肿瘤患者预后存活风险的方法,包括如下步骤:检测或获得所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用上述多发性骨髓瘤贝叶斯分类器进行分型,属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者预测预后存活率低于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者。The present invention also provides a method for predicting the prognosis and survival risk of multiple myeloma tumor patients, comprising the steps of: detecting or obtaining the expression data of 97 genes of the multiple myeloma tumor patients to be detected; The expression data of 97 genes in patients with multiple myeloma tumors were classified by the above-mentioned Bayesian classifier for multiple myeloma, and the patients with multiple myeloma tumors belonging to the MCL1-M-High subtype were predicted to predict the prognosis and survival rate. lower than in patients with multiple myeloma tumors to be tested belonging to the MCL1-M-Low subtype.
本发明还提供了一种预测多发性骨髓瘤肿瘤患者预后存活风险的方法,包括如下步骤:检测或获得所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用上述多发性骨髓瘤贝叶斯分类器进行分型,属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者预后存活率低的风险大;属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者的预后存活率低的风险小。The present invention also provides a method for predicting the prognosis and survival risk of multiple myeloma tumor patients, comprising the steps of: detecting or obtaining the expression data of 97 genes of the multiple myeloma tumor patients to be detected; The expression data of 97 genes were measured in patients with multiple myeloma tumors. The above Bayesian classifier for multiple myeloma was used for classification. The patients with multiple myeloma tumors belonging to the MCL1-M-High subtype had a poor prognosis and survival rate. The risk of poor prognosis in patients with multiple myeloma tumors belonging to the MCL1-M-Low subtype is small.
上述基因的表达量均为肿瘤细胞中的基因表达量。The expression levels of the above genes are all gene expression levels in tumor cells.
为了克服以上缺陷,发明人探索了围绕生发中心(GC)浆细胞发育过程中保守的关键信号通路的基因共表达网络是否能够辅助阐明MM发病机制并应用于MM的分子分型。发明人重点寻找了多发性骨髓瘤中控制B细胞向浆细胞分化过程中失调的基因网络,因为它可能在多发性骨髓瘤的形成中起到关键作用。经过上述分析,鉴定出了一个与MCL1基因共表达的基因模块(简称为MCL1-M),并应用它将多发性骨髓瘤分成为两个主要亚型,即MCL-M-High亚型和MCL-M-Low亚型。这两个亚型具有显著不同的预后与遗传学特征,更重要的是,该分类系统还能预测病人对硼替佐米的治疗的反应并且与浆细胞的发育阶段相关。这些发现能为今后个体化精准治疗的实施铺平了道路,也能提高对多发性骨髓瘤病因的理解。To overcome the above drawbacks, the inventors explored whether gene co-expression networks surrounding key signaling pathways conserved during germinal center (GC) plasma cell development could aid in the elucidation of MM pathogenesis and its application in molecular typing of MM. The inventors focused on finding a gene network in multiple myeloma that controls the dysregulation of B cell differentiation into plasma cells, as it may play a key role in the development of multiple myeloma. After the above analysis, a gene module co-expressed with the MCL1 gene (referred to as MCL1-M) was identified and applied to divide multiple myeloma into two main subtypes, namely MCL-M-High subtype and MCL -M-Low subtype. The two subtypes have significantly different prognostic and genetic features, and more importantly, the classification system predicts patient response to bortezomib treatment and correlates with the developmental stage of plasma cells. These findings could pave the way for future implementation of individualized precision therapy and improve understanding of the etiology of multiple myeloma.
附图说明Description of drawings
图1为GSE2658验证集中贝叶斯分类器分型结果ROC图。Figure 1 shows the ROC diagram of the Bayesian classifier typing results in the GSE2658 validation set.
图2为MMRF数据集中贝叶斯分类器分型结果ROC图。Figure 2 shows the ROC diagram of the Bayesian classifier typing results in the MMRF dataset.
图3为GSE19784数据集中贝叶斯分类器分型结果ROC图。Figure 3 is the ROC diagram of the Bayesian classifier typing results in the GSE19784 dataset.
图4为GSE2658中多发性骨髓瘤MCL1-M-High和MCL1-M-Low分子亚型的总体生存曲线。Figure 4 is an overall survival curve of multiple myeloma MCL1-M-High and MCL1-M-Low molecular subtypes in GSE2658.
图5为GSE2658中多发性骨髓瘤MCL1-M-High和MCL1-M-Low分子亚型的总体生存曲线。Figure 5 is an overall survival curve of multiple myeloma MCL1-M-High and MCL1-M-Low molecular subtypes in GSE2658.
图6为GSE19784中多发性骨髓瘤MCL1-M-High和MCL1-M-Low分子亚型的总体生存曲线(上图)和无进展生存曲线(下图)。Figure 6 is an overall survival curve (upper panel) and progression-free survival curve (lower panel) of multiple myeloma MCL1-M-High and MCL1-M-Low molecular subtypes in GSE19784.
图7为GS19784中MCL1-M-High和MCL1-M-Low亚型病人对硼替佐米治疗具有不同的反应。Figure 7 shows that patients with MCL1-M-High and MCL1-M-Low subtypes in GS19784 have different responses to bortezomib treatment.
具体实施方式Detailed ways
下述实施例中所使用的实验方法如无特殊说明,均为常规方法。The experimental methods used in the following examples are conventional methods unless otherwise specified.
下述实施例中所用的材料、试剂等,如无特殊说明,均可从商业途径得到。The materials, reagents, etc. used in the following examples can be obtained from commercial sources unless otherwise specified.
实施例1、多发性骨髓瘤的分子诊断标志物的筛选及分子分型的实施Example 1. Screening of molecular diagnostic markers for multiple myeloma and implementation of molecular typing
利用NCBI GEO公共数据库提供的多发性骨髓瘤表达量数据集GSE2658,通过皮尔森相关性分析,获得了87个与MCL1共表达的基因,并以此为基础,鉴定出了46个在低表达MCL1-M基因的多发性骨髓瘤样本中富集的基因。为了更稳定的进行分子分型,这133个基因中36个分类效力不高的被进一步筛除,最终97个稳定差异表达且丰度相对较高的分类基因被保留了下来。Using the multiple myeloma expression data set GSE2658 provided by the NCBI GEO public database, through Pearson correlation analysis, 87 genes co-expressed with MCL1 were obtained. -M gene enriched in multiple myeloma samples. For more stable molecular typing, 36 of the 133 genes with low classification efficiency were further screened, and finally 97 classified genes with stable differential expression and relatively high abundance were retained.
97个基因的名称如下:The names of the 97 genes are as follows:
ACBD3、ADAR、ADSS、ALDH2、ANP32E、ANXA2、ATF3、ATP8B2、CACYBP、CAPN2、CCND1、CCT3、CDC42SE1、CERS2、CHSY3、CLIC1、CLMN、COPA、CSNK1G3、DAP3、DENND1B、ENSA、EPRS、EPSTI1、EVL、FAM13A、FAM49A、FLAD1、FRZB、GLRX2、HAX1、HDGF、HLA-A、HLA-B、HLA-C、HLA-F、HLA-G、IL6R、ISG20L2、JTB、KLF2、LAMTOR2、LDHA、MCL1、MOXD1、MRPL24、MRPL9、MVP、MYL6、NDUFS2、NOP58、NOTCH2NL、NTAN1、PAK1、PI4KB、PIEZO1、PIK3AP1、PIM2、PIP5K1B、PMVK、POGZ、PPIA、PRCC、PRKCA、PRRC2C、PSMB4、PSMD4、RAB29、RCBTB2、SCAMP3、SCAPER、SDHC、SEL1L3、SELPLG、SHC1、SIDT1、SSR2、STAP1、TAP1、TIMM17A、TLR10、TMCO1、TOR1AIP2、TOR3A、TP53INP1、TPM3、TRANK1、TROVE2、UAP1、UBE2Q1、UBQLN4、UHMK1、VPS45、YY1AP1、ZC3H11A、ZFP36和ZNF593。ACBD3, ADAR, ADSS, ALDH2, ANP32E, ANXA2, ATF3, ATP8B2, CACYBP, CAPN2, CCND1, CCT3, CDC42SE1, CERS2, CHSY3, CLIC1, CLMN, COPA, CSNK1G3, DAP3, DENND1B, ENSA, EPRS, EPSTI1, EVL, FAM13A, FAM49A, FLAD1, FRZB, GLRX2, HAX1, HDGF, HLA-A, HLA-B, HLA-C, HLA-F, HLA-G, IL6R, ISG20L2, JTB, KLF2, LAMTOR2, LDHA, MCL1, MOXD1, MRPL24, MRPL9, MVP, MYL6, NDUFS2, NOP58, NOTCH2NL, NTAN1, PAK1, PI4KB, PIEZO1, PIK3AP1, PIM2, PIP5K1B, PMVK, POGZ, PPIA, PRCC, PRKCA, PRRC2C, PSMB4, PSMD4, RAB29, RCBTB2, SCAMP3, SCAPER, SDHC, SEL1L3, SELPLG, SHC1, SIDT1, SSR2, STAP1, TAP1, TIMM17A, TLR10, TMCO1, TOR1AIP2, TOR3A, TP53INP1, TPM3, TRANK1, TROVE2, UAP1, UBE2Q1, UBQLN4, UHMK1, VPS45, YY1AP1, ZC3H11A, ZFP36 and ZNF593.
这97个基因随后将作为用于分型的分类因子。利用GSE2658数据集的551例多发性骨髓瘤样本中这97个基因的表达量数据,首先使用Consensus Clustering聚类算法以无监督的聚类方式把这551例多发性骨髓瘤分为了MCL1-M-High和MCL1-M-Low两个亚型。但基于聚类的分类方法不能针对单独样本进行分子分型。为了实施个体化诊断,这551例样本按照2:1的比例被随机划分训练集(369例)和验证集(182例),用于建立和评估个体化的分类器。取样采取了分层取样的方式,以保证训练集和测试集中MCL1-M-High和MCL1-M-Low两个亚型的比例与原来维持一致。These 97 genes will then serve as classification factors for typing. Using the expression data of these 97 genes in 551 multiple myeloma samples from the GSE2658 dataset, we first used the Consensus Clustering clustering algorithm to classify the 551 multiple myeloma cases into MCL1-M- There are two subtypes, High and MCL1-M-Low. However, cluster-based classification methods cannot perform molecular typing of individual samples. In order to implement individualized diagnosis, the 551 samples were randomly divided into training set (369 cases) and validation set (182 cases) according to the ratio of 2:1, which were used to build and evaluate individualized classifiers. Sampling adopts a stratified sampling method to ensure that the ratio of the two subtypes of MCL1-M-High and MCL1-M-Low in the training set and the test set is consistent with the original.
根据训练集中369例样本的97个分类基因的表达量数据和Consensus Clustering聚类算法分成的MCL1-M-High和MCL1-M-Low两个亚型标签,使用R语言中机器学习包klaR包提供的朴素贝叶斯算法建立了可预测单个患者MCL1-M-High亚型和MCL1-M-Low亚型的多发性骨髓瘤贝叶斯分类器。According to the expression data of 97 classified genes of 369 samples in the training set and the two subtype labels of MCL1-M-High and MCL1-M-Low divided by the Consensus Clustering clustering algorithm, the machine learning package klaR package in R language is used to provide The Naive Bayes algorithm built a multiple myeloma Bayesian classifier that predicted the MCL1-M-High and MCL1-M-Low subtypes in individual patients.
并利用验证集中182例样本评估了其分类的准确度。The classification accuracy was evaluated using 182 samples in the validation set.
根据返回的准确度,不断迭代优化模型,最终使分类的准确度超过了95%,该分类器的准确度数据见表1,受试者工作曲线(ROC)见图1。According to the returned accuracy, the model is iteratively optimized, and finally the classification accuracy exceeds 95%. The accuracy data of the classifier is shown in Table 1, and the receiver operating curve (ROC) is shown in Figure 1.
表1.利用GSE2658数据集建立的分类器在验证集中的准确度Table 1. The accuracy of the classifier built with the GSE2658 dataset in the validation set
为了确定利用GSE2658数据集建立的分类器能够被推广应用。发明人随后利用该分类器预测了NCI发布的多发性骨髓瘤大型数据集MMRF及GEO多发性骨髓瘤表达量数据集GSE19784中样本的分子亚型。In order to confirm that the classifier built using the GSE2658 dataset can be generalized and applied. The inventors then used this classifier to predict the molecular subtypes of the samples in the multiple myeloma large dataset MMRF and the GEO multiple myeloma expression dataset GSE19784 published by NCI.
MMRF数据集不同于GSE2658,其基因的表达量通过RNA-seq获得,而非芯片。其预测的结果如表2,ROC图见图2。The MMRF dataset is different from GSE2658 in that the expression levels of its genes were obtained by RNA-seq instead of microarray. The predicted results are shown in Table 2, and the ROC diagram is shown in Figure 2.
表2.利用GSE2658数据集建立的分类器的在MMRF数据集中的准确度Table 2. Accuracy of classifiers built with GSE2658 dataset in MMRF dataset
结果显示,即使跨平台,该分类器也能保持很高的准确度,这说明它具有较高的推广应用价值。The results show that the classifier can maintain a high accuracy even across platforms, which shows that it has high promotion and application value.
GSE19784也是一个多发性骨髓瘤的表达量数据集,与GSE2618一样,采用的是U1332.0Plus芯片测量基因表达量。但是,两者来由不同的实验在不同的时间进行检测,实验条件可能具有差别,这导致两者的数据在分布和噪音水平上显著不同。该数据库亚型预测结果见表3,ROC曲线见图3。GSE19784 is also a multiple myeloma expression dataset. Like GSE2618, the U1332.0Plus chip is used to measure gene expression. However, the two origins are detected at different times in different experiments, and the experimental conditions may be different, which results in significantly different data distributions and noise levels between the two. The subtype prediction results of the database are shown in Table 3, and the ROC curve is shown in Figure 3.
表3.利用GSE2658数据集建立的分类器的在GSE19784数据集中的准确度Table 3. Accuracy of classifiers built with GSE2658 dataset on GSE19784 dataset
结果显示,该分类器能较好的克服上述问题,依然保持较高的准确度。The results show that the classifier can better overcome the above problems and still maintain a high accuracy.
实施例2、多发性骨髓瘤的贝叶斯分类器在预测患者预后存活率中的应用Example 2. Application of Bayesian classifier of multiple myeloma in predicting patient prognosis and survival rate
一、数据库GSE26581. Database GSE2658
根据GSE2658数据库551例多发性骨髓瘤患者样本(治疗前检测)的97个分类基因的表达量数据,采用实施例1获得的多发性骨髓瘤贝叶斯分类器将该551例样本分类,得到249例MCL1-M-High亚型多发性骨髓瘤和302例MCL1-M-Low亚型多发性骨髓瘤。According to the expression data of 97 classified genes in 551 multiple myeloma patient samples (detected before treatment) in the GSE2658 database, the 551 samples were classified by the Bayesian classifier of multiple myeloma obtained in Example 1, and 249 Cases of MCL1-M-High subtype multiple myeloma and 302 MCL1-M-Low subtype multiple myeloma.
跟踪随访551例样本患者治疗后72个月,根据随访结果,进行生存分析(K-M分析及cox回归分析),结果如图4所示,可以看到,MCL1-M-High和MCL1-M-Low两个多发性骨髓瘤亚型具有显著不同的预后,MCL1-M-High亚型的总体生存率比MCL1-M-Low亚型要低(log-rank检验,p=0.0201,似然比检验,风险比1.588,p=0.0212)。551 sample patients were followed up for 72 months after treatment. According to the follow-up results, survival analysis (K-M analysis and cox regression analysis) was performed. The results are shown in Figure 4. It can be seen that MCL1-M-High and MCL1-M-Low The two multiple myeloma subtypes had significantly different prognosis, with the MCL1-M-High subtype having a lower overall survival rate than the MCL1-M-Low subtype (log-rank test, p=0.0201, likelihood ratio test, Hazard ratio 1.588, p=0.0212).
因此,采用贝叶斯分类器利用MCL1基因群97个基因进行分型,可以用来预测待测患者的预后。Therefore, the use of Bayesian classifier to use the 97 genes of the MCL1 gene group for typing can be used to predict the prognosis of the patient to be tested.
二、数据库MMRF2. Database MMRF
根据MMRF数据集中534例多发性骨髓瘤患者样本(治疗前检测)MCL1基因群97个分类基因的表达量数据,分别采用实施例1获得的多发性骨髓瘤贝叶斯分类器将该534例样本分为MCL1-M-High(231例)和MCL1-M-Low两个亚型(303例)。According to the expression data of 97 classified genes of MCL1 gene group in 534 samples of multiple myeloma patients in the MMRF dataset (detected before treatment), the Bayesian classifier of multiple myeloma obtained in Example 1 was used to separate the 534 samples. Divided into two subtypes, MCL1-M-High (231 cases) and MCL1-M-Low (303 cases).
跟踪随访534例样本患者治疗后48个月,根据随访结果,进行生存分析(K-M分析及cox回归分析),结果如图5所示,可以看到,在MMRF数据集中,MCL1-M-High和MCL1-M-Low两个亚型同样具有显著不同的预后,MCL1-M-High亚型的总体生存率比MCL1-M-Low亚型要低(log-rank检验,p=0.006663,似然比检验,风险比1.838,p=0.00706)。534 sample patients were followed up for 48 months after treatment. According to the follow-up results, survival analysis (K-M analysis and cox regression analysis) was performed. The results are shown in Figure 5. It can be seen that in the MMRF data set, MCL1-M-High and The two subtypes of MCL1-M-Low also have significantly different prognosis, and the overall survival rate of the MCL1-M-High subtype is lower than that of the MCL1-M-Low subtype (log-rank test, p=0.006663, likelihood ratio test, hazard ratio 1.838, p=0.00706).
该结果表明,不管基因表达量数据来自于哪个平台,采用贝叶斯分类器利用MCL1基因群97个基因进行分型,可以用来预测待测患者的预后。The results indicate that no matter which platform the gene expression data comes from, the use of Bayesian classifier to classify 97 genes of the MCL1 gene group can be used to predict the prognosis of the patients to be tested.
三、数据库GSE197843. Database GSE19784
根据数据库GSE19784中验证集304例多发性骨髓瘤患者样本(治疗前检测)的MCL1基因群97个分类基因的表达量数据,分别采用实施例1获得的多发性骨髓瘤贝叶斯分类器将该304例样本分为MCL1-M-High(107例)和MCL1-M-Low两个亚型(196例)。According to the expression data of 97 classified genes of the MCL1 gene group in the validation set of 304 multiple myeloma patient samples (pre-treatment detection) in the database GSE19784, the multiple myeloma Bayesian classifier obtained in Example 1 was used to separate the The 304 samples were divided into two subtypes, MCL1-M-High (107 cases) and MCL1-M-Low (196 cases).
跟踪随访304例样本患者治疗后96个月,根据随访结果,进行生存分析(K-M分析及cox回归分析),结果如图6所示(A为总体生存率,B为无进展生存率),可以看到,在GSE19784数据集中,MCL1-M-High和MCL1-M-Low两个亚型同样具有显著不同的预后,MCL1-M-High亚型的总体生存率比MCL1-M-Low亚型要低(log-rank检验,p<0.0001,似然比检验,风险比1.91,p=0.0002)。GSE19784数据集也包括疾病的进展信息,因此我们也分析了无进展生存率的差别,类似的,MCL1-M-High亚型的无进展生存率也比MCL1-M-Low亚型要低log-rank检验,p=0.0282,似然比检验,风险比1.36,p=0.031)该结果再次表明,采用贝叶斯分类器利用MCL1基因群97个基因进行分型,可以用来预测待测患者的预后。The 304 sample patients were followed up for 96 months after treatment. According to the follow-up results, survival analysis (K-M analysis and cox regression analysis) was performed. The results are shown in Figure 6 (A is the overall survival rate, B is the progression-free survival rate). See, in the GSE19784 dataset, the two subtypes MCL1-M-High and MCL1-M-Low also have significantly different prognosis, the overall survival rate of the MCL1-M-High subtype is better than that of the MCL1-M-Low subtype Low (log-rank test, p<0.0001, likelihood ratio test, hazard ratio 1.91, p=0.0002). The GSE19784 dataset also includes disease progression information, so we also analyzed the difference in progression-free survival. Similarly, the MCL1-M-High subtype has a log-lower PFS rate than the MCL1-M-Low subtype. rank test, p=0.0282, likelihood ratio test, hazard ratio 1.36, p=0.031) This result once again shows that the use of Bayesian classifiers for typing with 97 genes of the MCL1 gene group can be used to predict the patient's disease. Prognosis.
实施例3、多发性骨髓瘤的分子诊断标志物及分型在预测待测患者是否能够用硼替佐米治疗Example 3. Molecular diagnostic markers and typing of multiple myeloma in predicting whether the patient to be tested can be treated with bortezomib
GSE19784多发性骨髓瘤的表达量数据集来自于一项III期药物的临床试验(HOVON-65/GMMG-HD4),附有病人的药物治疗方案。该试验把病人随机分到了两组分别接受VAD(155例)和PAD(148例)两种药物组合,两者的差别在于PAD方案多了硼替佐米(商品名:万珂)这种药物。入组病人的基因表达量数据都采集于治疗前。The GSE19784 multiple myeloma expression dataset was obtained from a clinical trial of a phase III drug (HOVON-65/GMMG-HD4), with the patient's drug regimen. The trial randomly divided patients into two groups to receive VAD (155 cases) and PAD (148 cases) two drug combinations, the difference between the two is that the PAD regimen has more bortezomib (trade name: Velcade). The gene expression data of the enrolled patients were collected before treatment.
按上述MCL1-M分子分型对病人进行了分层,然后分别在MCL1-M-High(PAD 51例,VAD 56例)和MCL1-M-Low(PAD 104例,VAD 92例)两个亚型中按药物治疗方案进分组进行了生存分析(K-M分析及cox回归分析)。The patients were stratified according to the above-mentioned MCL1-M molecular classification, and then were divided into two subgroups, MCL1-M-High (51 PAD, VAD 56) and MCL1-M-Low (PAD 104, VAD 92). The patients were divided into groups according to the drug treatment plan and the survival analysis (K-M analysis and cox regression analysis) was carried out.
结果如图7所示,A为MCL1-M-High组的总体生存率,B为MCL1-M-Low组的总体生存率,C为MCL1-M-High组的无进展生存率,D为MCL1-M-Low组的无进展生存率;可以观察到,使用硼替佐米的PAD药物仅能延长MCL1-M-High组中患者的生存期,尤其是无进展生存期(图7左侧,MCL-M-High组,右侧MCL-M-Low组;上方,总体生存曲线,下方,无进展生存曲线),这揭示了硼替佐米在临床上能够延缓MCL-M-High组病人的复发恶化,但在MCL-M-Low组病人中却没有任何效果。综上所述,实施本发明的分子分型可以指导临床用药,可以避免在MCL1-M-Low组病人中使用硼替佐米,一方面可以减轻患者的经济负担,一方面也能使患者少承担药物治疗带来的副作用。The results are shown in Figure 7, A is the overall survival rate of the MCL1-M-High group, B is the overall survival rate of the MCL1-M-Low group, C is the progression-free survival rate of the MCL1-M-High group, and D is the MCL1 - Progression-free survival in the M-Low group; it can be observed that the PAD drug with bortezomib only prolongs the survival of patients in the MCL1-M-High group, especially the progression-free survival (Fig. 7 left, MCL -M-High group, right MCL-M-Low group; top, overall survival curve, bottom, progression-free survival curve), which revealed that bortezomib can clinically delay the recurrence and deterioration of patients in the MCL-M-High group , but there was no effect in the MCL-M-Low group of patients. To sum up, the implementation of the molecular typing of the present invention can guide clinical medication and avoid the use of bortezomib in patients in the MCL1-M-Low group. Side effects from drug treatment.
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