结直肠癌原发与配对转移肿瘤遗传异质性研究进展

结直肠癌(colorectal cancer, CRC)是我国常见的致死性肿瘤类型之一。根据体细胞突变谱预测抗EGFR单抗治疗疗效已成为转移性结直肠癌(metastatic colorectal cancer, mCRC)治疗的标准步骤。由于临床上转移样本难以获得,只能采用原发肿瘤替代进行检测。原发和配对转移肿瘤间的遗传异质性会导致原发灶取样无法代表转移灶突变谱。目前CRC原发和配对转移肿瘤间遗传异质性程度仍存在争议。本文就CRC原发和配对转移基因组谱的对比研究进行了综述,并讨论了原发与配对转移肿瘤遗传异质性形成的原因及应对策略。     

肿瘤异质性：精准医学需破解的难题

肿瘤异质性是恶性肿瘤的重要特征,表现为同一种恶性肿瘤不同患者个体之间或者同一患者体内不同部位肿瘤细胞间从基因型到表型上存在的差异.这种差异可表现为不同的遗传背景、不同的病理类型、不同的分化状态、不同的基因突变谱和转录组、蛋白质组表达谱等,体现了恶性肿瘤在演进过程中的高度复杂性和多样性.肿瘤异质性给肿瘤的治疗带来极大的困难,一直是肿瘤发生发展机制研究领域重要的科学问题.本文综述了肿瘤异质性的生物学特征及其可能的形成机制,并对"精准医学"时代如何针对肿瘤异质性设计更为有效的个性化治疗方案进行了思考.     

元阳3个长期连续栽培水稻地方品种内部遗传异质性分析

水稻地方品种是稻种资源的重要组成部分,遗传多样性十分丰富,具有推广改良品种所缺少或没有的优质种质,是水稻育种和稻种起源、进化研究不可缺少的过渡材料。目前,对水稻地方品种间遗传多样性研究较多,而对其内部异质性研究甚微。本研究用24对微卫星(SSR)引物对云南元阳梯田3个栽种历史悠久的水稻地方品种的内部遗传异质性进行了分析。共检测出117个等位基因,香农指数为红脚老粳居群(0.5911)>白脚老粳A居群(0.4875)>月亮谷居群(0.3070)。结果显示:3个地方品种的内部遗传异质性丰富,且遗传异质性主要得益于个体间,而非居群间。     

单细胞测序技术在肝癌研究中的应用

传统的细胞遗传信息研究方法是对大量混合细胞进行高通量测序,得到一群细胞基因表达的平均值,忽视了细胞间存在的异质性。肝癌作为一种人类常见的恶性致命肿瘤,其内部肿瘤细胞存在高度异质性,群体水平分析无法精确揭示其恶性细胞克隆结构和免疫微环境的细胞种类、状态和亚群分布,因此迫切需要进行单细胞水平的分析,这将有助于深入了解肝癌发病机制,进行精准肝癌分型指导临床治疗。同时发现,新型治疗靶点及有效生物标记物,为肝癌患者今后进行精准诊疗提供参考。本文综述了单细胞基因组和转录物组测序技术在肝癌免疫微环境、肝癌细胞异质性、肝癌细胞演化与诊疗和肝癌转移机制及生物标志物研究中的应用。本文还总结了在肝癌研究中,单细胞多组学测序技术在发现新肿瘤亚群、精确识别肿瘤细胞间的异质性和了解肿瘤微环境构成等方面的优势。     

循环肿瘤细胞单细胞测序——液体活检的新视角

循环肿瘤细胞是实体肿瘤原发灶或转移灶侵袭、脱落进入外周血的,具有高活力、高转移潜能的肿瘤细胞。由于肿瘤存在异质性,导致肿瘤组织高通量测序分析难以发现低丰度肿瘤干细胞的基因组特征。循环肿瘤细胞单细胞测序,通过比较患者外周血循环肿瘤细胞、肿瘤原发灶和转移灶及转移淋巴结中单细胞基因组、转录组和表观遗传组的差异,避免肿瘤异质性的干扰,为认识肿瘤的生物学进程提供了全新视角。现综述了运用单细胞测序技术分析实体肿瘤外周血循环肿瘤细胞基因组变异的主要技术和研究进展。     

医学遗传学中遗传异质性含义的解析

遗传异质性是医学遗传学中的重要概念。介绍了遗传异质性的产生原因,基本类型及研究意义。通过实例,解析了等位基因异质性和基因座异质性两大类型,阐述了遗传异质性在医学教学和临床实践中的作用。     

Nature:药物治疗可造成肿瘤适应性进化

<正>近日,来自美国的科学家在著名国际期刊nature发表了一项最新研究成果,他们通过对进行了PI(3)Kα抑制剂BYL719治疗的肿瘤转移病人进行基因测序,发现PTEN在基因组中的变化会导致肿瘤细胞出现对BYL719的抵抗作用。这项研究为临床应用PI(3)Kα抑制剂治疗肿瘤提供了重要参考价值。大范围深度的肿瘤基因组测序已经发现肿瘤异质性特点,并为不同肿瘤细胞克隆的转移进化特性提供了重要见解。但在另一个层面上,肿瘤进化可能受到治疗方法的选择压力,类似于在感染性疾病方面发生的情况。研究人员对一名携带PIK3CA基因突变并发生肿瘤转移的乳腺癌病     

肺癌恶性胸腔积液中稀有肿瘤细胞的鉴定与单细胞测序分析

肿瘤细胞的异质性是指肿瘤细胞在基因组或表型水平上具有不同特征。在外界环境压力或人为杀伤因素刺激下,肿瘤细胞具有不同的响应方式,从而导致它们在细胞增殖、侵袭转移及耐药能力等方面产生差别,尤其是一部分具有转移能力的肿瘤细胞能脱离原位组织并在远处器官形成转移灶。因此,肿瘤细胞的异质性为其发生转移和耐药提供了可能。传统的肿瘤异质性研究主要基于不同位置原位组织样本中的群体细胞,缺乏单细胞层面的解析,尤其是对具有转移能力的肿瘤细胞的异质性研究。本研究建立了基于肺癌恶性胸腔积液中转移性肿瘤细胞的单细胞研究路线,首先利用代谢标志物鉴定恶性胸腔积液中高代谢活性的肿瘤细胞,其次通过单细胞Sanger测序揭示这些肿瘤细胞具有一致的驱动基因突变特征,然后利用高通量测序技术对肿瘤细胞染色体拷贝数变异进行分析,从而揭示同一患者具有转移能力的肿瘤细胞即使具有相同的驱动基因突变特征,但在基因组层面上仍具有异质性,可进一步细分为若干子群。本研究结果对于更深入地理解肿瘤转移机制具有重要意义。     

上皮间质转化在肿瘤转移中的研究进展

转移侵袭是恶性肿瘤的基本特征和重要标志,也是导致患者死亡的最主要原因。研究表明,超过80%的恶性肿瘤患者最终死于肿瘤转移。本文综述了DNA甲基化、DNA羟甲基化、组蛋白修饰等表观遗传机制在上皮间质转化中的作用机制,以及肿瘤转移相关信号通路在上皮间质转化中的研究进展。其机制的阐明有可能为肿瘤治疗提供新的方向。     

肿瘤干细胞及其模型的研究现状及临床治疗最新进展

癌症发生最有名的模型之一肿瘤CSCcancer stem cell(CSC)模型已经被确立为一种细胞机制,有助于体现不同类型的肿瘤表型和功能的异质性。然而,最新研究突出显示了肿瘤CSC模型的复杂性和挑战性:CSC表型在不同的病人间有本质上的不同,肿瘤可能含有多种表型或遗传上不同的CSC,转移的肿瘤CSC可能由原始肿瘤CSC进展而来,肿瘤细胞可进行可逆的表型的改变。虽然在特定情况下,肿瘤CSC的概念具有临床相关性,但越来越多的证据表明,定位、鉴定出肿瘤灶中所有亚型的肿瘤CSC将对临床上预防肿瘤复发具有特殊意义。有以下几个因素可以促使异质性的发生:基因突变,后生的变化,与微环境间的相互作用以及存在或缺失细胞分级等。肿瘤异质性可以用不同的细胞机制来解释。虽然CSC具有CSC自我更新和分化的特性,但是它们不一定是正常组织CSC转化而形成的。这种CSC模型引起了科研工作者广泛的关注,我们结合新近的相关文献综述如下。     

Intra-tumor Genetic Heterogeneity and Mortality in Head and Neck Cancer: Analysis of Data from The Cancer Genome Atlas

Background

Although the involvement of intra-tumor genetic heterogeneity in tumor progression, treatment resistance, and metastasis is established, genetic heterogeneity is seldom examined in clinical trials or practice. Many studies of heterogeneity have had prespecified markers for tumor subpopulations, limiting their generalizability, or have involved massive efforts such as separate analysis of hundreds of individual cells, limiting their clinical use. We recently developed a general measure of intra-tumor genetic heterogeneity based on whole-exome sequencing (WES) of bulk tumor DNA, called mutant-allele tumor heterogeneity (MATH). Here, we examine data collected as part of a large, multi-institutional study to validate this measure and determine whether intra-tumor heterogeneity is itself related to mortality.

Methods and Findings

Clinical and WES data were obtained from The Cancer Genome Atlas in October 2013 for 305 patients with head and neck squamous cell carcinoma (HNSCC), from 14 institutions. Initial pathologic diagnoses were between 1992 and 2011 (median, 2008). Median time to death for 131 deceased patients was 14 mo; median follow-up of living patients was 22 mo. Tumor MATH values were calculated from WES results. Despite the multiple head and neck tumor subsites and the variety of treatments, we found in this retrospective analysis a substantial relation of high MATH values to decreased overall survival (Cox proportional hazards analysis: hazard ratio for high/low heterogeneity, 2.2; 95% CI 1.4 to 3.3). This relation of intra-tumor heterogeneity to survival was not due to intra-tumor heterogeneity’s associations with other clinical or molecular characteristics, including age, human papillomavirus status, tumor grade and TP53 mutation, and N classification. MATH improved prognostication over that provided by traditional clinical and molecular characteristics, maintained a significant relation to survival in multivariate analyses, and distinguished outcomes among patients having oral-cavity or laryngeal cancers even when standard disease staging was taken into account. Prospective studies, however, will be required before MATH can be used prognostically in clinical trials or practice. Such studies will need to examine homogeneously treated HNSCC at specific head and neck subsites, and determine the influence of cancer therapy on MATH values. Analysis of MATH and outcome in human-papillomavirus-positive oropharyngeal squamous cell carcinoma is particularly needed.

Conclusions

To our knowledge this study is the first to combine data from hundreds of patients, treated at multiple institutions, to document a relation between intra-tumor heterogeneity and overall survival in any type of cancer. We suggest applying the simply calculated MATH metric of heterogeneity to prospective studies of HNSCC and other tumor types.     

Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing

A single tumor may contain cells with different somatic mutations. By characterizing this genetic heterogeneity within tumors, advances have been made in the prognosis, treatment and understanding of tumorigenesis. In contrast, the extent of epigenetic intra-tumor heterogeneity and how it influences tumor biology is under-explored. We have characterized epigenetic heterogeneity within individual tumors using next-generation sequencing. We used deep single molecule bisulfite sequencing and sample-specific DNA barcodes to determine the spectrum of MLH1 promoter methylation across an average of 1000 molecules in each of 33 individual samples in parallel, including endometrial cancer, matched blood and normal endometrium. This first glimpse, deep into each tumor, revealed unexpectedly heterogeneous patterns of methylation at the MLH1 promoter within a subset of endometrial tumors. This high-resolution analysis allowed us to measure the clonality of methylation in individual tumors and gain insight into the accumulation of aberrant promoter methylation on both alleles during tumorigenesis.     

Tumor heterogeneity: Causes and consequences

With rare exceptions, spontaneous tumors originate from a single cell. Yet, at the time of clinical diagnosis, the majority of human tumors display startling heterogeneity in many morphological and physiological features, such as expression of cell surface receptors, proliferative and angiogenic potential. To a substantial extent, this heterogeneity might be attributed to morphological and epigenetic plasticity, but there is also strong evidence for the co-existence of genetically divergent tumor cell clones within tumors. In this perspective, we summarize the sources of intra-tumor phenotypic heterogeneity with emphasis on genetic heterogeneity. We review experimental evidence for the existence of both intra-tumor clonal heterogeneity as well as frequent evolutionary divergence between primary tumors and metastatic outgrowths. Furthermore, we discuss potential biological and clinical implications of intra-tumor clonal heterogeneity.     

Applying unmixing to gene expression data for tumor phylogeny inference

Background  

While in principle a seemingly infinite variety of combinations of mutations could result in tumor development, in practice it appears that most human cancers fall into a relatively small number of "sub-types," each characterized a roughly equivalent sequence of mutations by which it progresses in different patients. There is currently great interest in identifying the common sub-types and applying them to the development of diagnostics or therapeutics. Phylogenetic methods have shown great promise for inferring common patterns of tumor progression, but suffer from limits of the technologies available for assaying differences between and within tumors. One approach to tumor phylogenetics uses differences between single cells within tumors, gaining valuable information about intra-tumor heterogeneity but allowing only a few markers per cell. An alternative approach uses tissue-wide measures of whole tumors to provide a detailed picture of averaged tumor state but at the cost of losing information about intra-tumor heterogeneity.     

PDTX模型的研究进展

细胞源性异种移植(cell line-derived xenografts,CDX)与原发肿瘤相比失去了肿瘤的异质性和基因的多样性,在临床前的实验中不能有效评估肿瘤药物的疗效和安全性,致使临床药物高消耗而没有达到治疗疾病的目的,严重阻碍了临床药物的发展;人源性肿瘤组织异种移植(patient-derived tumor xenografts,PDTX)保持了原发肿瘤的分子学、基因学和病理学特征,而且经过在小鼠体内传代它仍保持了原发肿瘤的这些特性,为肿瘤的个体化治疗提供了更好的模型。PDTX模型的这些特性与CDX模型相比在肿瘤的个体化治疗方面更具有指导意义。本文将就PDTX模型的特征及其在肿瘤研究领域中的应用作系统阐述。     

Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution

Background

Genomic analysis of multi-focal renal cell carcinomas from an individual with a germline VHL mutation offers a unique opportunity to study tumor evolution.

Results

We perform whole exome sequencing on four clear cell renal cell carcinomas removed from both kidneys of a patient with a germline VHL mutation. We report that tumors arising in this context are clonally independent and harbour distinct secondary events exemplified by loss of chromosome 3p, despite an identical genetic background and tissue microenvironment. We propose that divergent mutational and copy number anomalies are contingent upon the nature of 3p loss of heterozygosity occurring early in tumorigenesis. However, despite distinct 3p events, genomic, proteomic and immunohistochemical analyses reveal evidence for convergence upon the PI3K-AKT-mTOR signaling pathway. Four germline tumors in this young patient, and in a second, older patient with VHL syndrome demonstrate minimal intra-tumor heterogeneity and mutational burden, and evaluable tumors appear to follow a linear evolutionary route, compared to tumors from patients with sporadic clear cell renal cell carcinoma.

Conclusions

In tumors developing from a germline VHL mutation, the evolutionary principles of contingency and convergence in tumor development are complementary. In this small set of patients with early stage VHL-associated tumors, there is reduced mutation burden and limited evidence of intra-tumor heterogeneity.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0433-z) contains supplementary material, which is available to authorized users.     

CAR T targets and microenvironmental barriers of osteosarcoma

Osteosarcoma (OS) is one of the most common malignancies in children and adolescents. Multimodal chemotherapy and aggressive surgical resection have improved the prognosis of patients with osteosarcoma. However, the prognosis of OS patients with unresectable advanced tumors, distant metastasis or chemotherapy is still poor. Chimeric antigen receptor (CAR) T cells have achieved remarkable success in the treatment of hematologic malignancies, injecting new vitality into the field of adoptive cell therapy. However, the efficacy in solid tumors has been largely limited. The reason for the poor curative effect of solid tumors is mainly the heterogeneity of solid tumor antigen, immune escape, tumor microenvironment barrier, resistance of immunosuppressive cells and inhibitory factors, which lead to the obstruction of CAR T cell infiltration and the aggravation of failure. Potential antigenic targets for osteosarcoma CAR T cell therapy are under continuous exploration. Some of the antigenic targets, such as anti-HER2-CAR T cells, have achieved good results in preclinical studies, and some of them have entered clinical studies and achieved certain clinical effects. In this review, we discuss the research progress of potential antigen targets and osteosarcoma microenvironment of CAR T cells in the treatment of osteosarcoma.     

Inflammatory infiltrates of experimental mammary cancers

The purpose of this review was to summarize observations on the type and function of inflammatory infiltrates of mouse mammary tumors and to speculate on the underlying mechanisms and the significance of infiltrates to mammary tumor biology. Although the major conclusion is that much more work is needed, certain themes seem to be emerging. The number of infiltrating cells can be very high but is unrelated to biological behavior of the tumors. What seems to be important is the relative contributions of inflammatory cell subsets. In the case of T-cell subsets and NK cells, the infiltrates from tumors of long-term cell lines so far seem uninformative. The general characteristics are similar to those of infiltrates from rapidly proliferating, normal mammary tissues. These characteristics do not correlate with diverse biological behavior or malignant potential. A more informative model appears to be one in which the development of tumors from preneoplastic tissue can be observed. Here our attention is currently focused on NK cells. By contrast, the correlation between activated TAM and metastatic behavior suggests that our transplantable MMT lines may be biologically relevant in the study of infiltrating macrophages. We are especially interested in the role of TAM in the generation of tumor cell variability. Overall, our data indicate that the host infiltrate is another manifestation of both inter- and intra-tumor heterogeneity and, as such, is not simply a response to, but, rather, a part of the tumor ecosystem. Unraveling the cellular and molecular mechanisms that govern the inflammatory cell component of tumors should provide insight into the types of cellular interactions that result in tumor development and progression.     

The inhibition of TNF-alpha anti-tumoral properties by blocking antibodies promotes tumor growth in a rat model

Tumor necrosis factor (TNF) antagonists represent a milestone in the therapy of autoimmune conditions. Anti-TNF antibodies have been approved for clinical use and during the last eight years thousands of patients have been treated. However, the long-term sequelae of anti-TNF agents in promoting carcinogenesis remain unclear. This study sought to define the role of intra-tumor TNF-alpha production on cancer cell progression and to determine whether TNF-alpha antibodies can suppress anti-tumoral immunity. Using an experimental animal tumor model we demonstrate that anti-TNF-alpha antibodies hinder anti-tumor immune responses and promote growth of immunogenic rat colon tumors (REG) that are always rejected by immunocompetent untreated rats. The major role of TNF-alpha in the anti-tumoral immune response was confirmed by transfecting progressive and tolerogenic rat colon tumor cells (PRO) with the TNF-alpha gene. PRO tumor cells secreting TNF-alpha induce tumor-infiltrating dendritic cell (DC) activation. This triggers a potent immune response leading to tumor rejection and long-lasting immunity. Therefore, the prominent role of TNF-alpha in anti-tumoral immune responses underscores the need for caution and close surveillance following the administration of TNF inhibitors.