Intra-Tumor Heterogeneity of Cancer Cells and Its Implications for Cancer Treatment

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Intra-Tumor Heterogeneity of Cancer Cells and Its Implications for Cancer Treatment npg Acta Pharmacologica Sinica (2015) 36: 1219–1227 www.nature.com/aps Review Intra-tumor heterogeneity of cancer cells and its implications for cancer treatment Xiao-xiao SUN, Qiang YU* Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China Recent studies have revealed extensive genetic and non-genetic variation across different geographical regions of a tumor or through- out different stages of tumor progression, which is referred to as intra-tumor heterogeneity. Several causes contribute to this phe- nomenon, including genomic instability, epigenetic alteration, plastic gene expression, signal transduction, and microenvironmental differences. These variables may affect key signaling pathways that regulate cancer cell growth, drive phenotypic diversity, and pose challenges to cancer treatment. Understanding the mechanisms underlying this heterogeneity will support the development of effec- tive therapeutic strategies. Key words cancer cells; intra-tumor heterogeneity; genetic heterogeneity; signal transduction; cancer therapy Acta Pharmacologica Sinica (2015) 36: 1219–1227; doi: 10.1038/aps.2015.92; published online 21 Sep 2015 Introduction improve the understanding and management of this heteroge- Solid tumors are heterogeneous neoplasms composed of dif- neity in cancer treatment. ferent types of cells, including cancer cells as well as mesen- chymal cells, endovascular cells, and immune cells[1]. In addi- Heterogeneity in genetic mutation tion to the complex tissue architecture of a tumor, cancer cells Genomic aberrations in cancers have been recognized for a within a single tumor are also heterogeneous in their molecu- long time; these include base-pair substitutions, focal dele- lar signatures; this is referred to as intra-tumor heterogene- tions/amplifications, tandem duplications, chromosomal rear- ity[2-4]. These cell-to-cell variations in genetic signature, gene rangements and whole-genome duplications[7]. Recent studies expression, and post-translational modifications are recog- further revealed extensive variations in genomic aberrations nized in almost every type of cancer (Table 1). However, cur- within tumors. For example, in glioblastomas (GBMs), the rent therapies treat cancer as a homogenous disease. Targeted copy number variation of two commonly amplified receptor drugs have been developed against single or multiple aber- tyrosine kinases (RTKs), EGFR and PDGFRA, was identified rant molecular signatures based on the diagnosis of the mixed among cells from the same tumor specimen using multicolor populations of cancer cells, in most cases based on a single fluorescent in situ hybridization (FISH) mapping[8, 9]. More- biopsy[5, 6]. Thus, it is not surprising that drug resistance, both over, the majority of the cells had a mutual exclusive amplifi- intrinsic and adaptive, occur extensively in all types of cancer. cation of these two genes, whereas co-amplification was only Understanding the specific driving forces behind different observed in a minority of the cancer cells. There also seemed subtypes of intra-tumor heterogeneity will facilitate a better to be a spatial distribution of the differential gene amplifica- understanding of the nature of cancer, and will provide insight tions, with one or the other type of gene predominating in cer- into the development of more effective cancer therapies. tain areas of the same specimen. In particular, the PDGFRA- In this review, we summarize the evidence for both genetic amplified cells tended to be present close to the endothelial and non-genetic heterogeneity within a tumor, and focus cells. Similar intra-tumor heterogeneous genetic alterations on the possible origins and their impact on drug resistance. were also observed in other types of cancers. Gerlinger et al Finally, we discuss the strategies that could be adopted to performed whole-exome sequencing on DNA extracted from multiple regions of tumor samples obtained from one clear- cell renal cell carcinoma (ccRCC) patient[10]. Nine primary- * To whom correspondence should be addressed. E-mail [email protected] tumor regions of the nephrectomy specimen and two regions Received 2015-08-12 Accepted 2015-09-06 of the excised chest-wall metastasis were analyzed. Among all npg www.nature.com/aps Sun XX et al 1220 Table 1. Intra-tumor heterogeneity in different cancer types. Cancer type Types of heterogeneity Reference(s) Brain Mutations, amplifications and expressions of genes related to oncogenic signaling, proliferation, [8, 9, 18, 31, 33, 40] immune response and hypoxia, CD133 expression Renal Mutations, chromosome aberrations, DNA ploidy [10] Breast Cell surface marker expressions, genotypic alterations [11-13, 16, 41, 42] Leukemia Expressions of multiple cell surface markers, Ki-67, Bcl-2, cyclin D, cyclin E and RAS, [14, 23-28, 30, 35-37] phosphorylations of signaling proteins Colorectal CD133 and receptor tyrosine kinase expressions, phosphorylations of signaling proteins [19, 20, 34, 43] Melanoma Expressions of multiple cell surface markers and cytoplasmic proteins [21, 22, 44, 45] Lung DNA ploidy, EGFR and BRAF V600E mutations, p53, c-Myc and Ki-67 expressions, phosphorylations of [29, 31, 38, 46] signaling proteins Sarcoma O-glycosylation of MT1-MMP [39] Head and neck Genotypic alterations [47] of the nonsynonymous point mutations, insertions, and dele- profiles of approximately 6000 genes in 430 cells were quan- tions that changed the protein amino acid sequences, approxi- titatively analyzed. Although the gene expression profiles mately 31% of the mutations were ubiquitous across every of individual cells from the same tumor were more similar tumor region, 46% were shared by several but not all regions, to each other than those from different tumors, variable gene and 22% were present only in a single region. In breast can- expression between individual cells from the same tumor was cers, spatial and temporal intra-tumor heterogeneity have also common. According to this study, cell-to-cell variability been observed using comparative genomic hybridization and was evident in genes related to multiple cellular functions, FISH mapping[11, 12]. A recent genome-wide sequencing study including oncogenic signaling, proliferation, and the immune of 21 breast cancers has shown that although every tumor has and hypoxia responses. In particular, RTKs such as EGFR, a dominant subclonal lineage of tumor cells, subclonal diversi- PDGFRA, FGFR1 and their ligands, which are important fication was prominent in every tumor, and most of the muta- therapeutic targets, were expressed in a mosaic fashion. More- tions were found in just a fraction of the cells[13]. over, the splicing patterns of the mRNAs of these genes were Integrative analysis of all these genetic changes in a single also variable. For example, in one GBM sample, 7% of cells cancer and in-depth evaluation of the topographical infor- expressed wild-type EGFR, 19% expressed EGFRvIII, which mation, especially the function of this variation will greatly is an oncogenic mutant form with a deletion of exon 2–7, and enhance our understanding on cancer heterogeneity and 25% expressed EGFR del4, which is another oncogenic variant inform its use in cancer treatment. with a deletion of exon 4. In addition, 1% to 2% of cells co- expressed both wild-type EGFR and the EGFRvIII variant. Heterogeneity in gene expression In addition to genetic alterations, intra-tumor heterogeneity is Heterogeneity in protein modification also common in gene expression. The clusters of differentia- Differential posttranslational modifications of proteins have tion (CD) antigens were among the first and are the most fre- also been found in different cancer cells from the same tumor. quently identified proteins that are heterogeneously expressed A pioneer study of three well-characterized subpopulations within a tumor. For example, differential expression of CD34/ of colorectal carcinoma (CRC) cells that were isolated from CD38 in acute myeloid leukemia (AML) cells[14, 15], CD24/CD44 a single primary colon cancer has revealed a great degree of in breast cancer cells[16, 17], CD133 in colon cancers and brain heterogeneity in phosphorylation modifications of cytosolic tumors[18-20], and CD271 in melanoma cells[21, 22] have been fre- and membrane proteins, and a mechanism beyond differential quently found in patient samples. The so-called cancer hall- gene expression has been demonstrated[34]. Since then, het- mark genes, such as c-KIT[23], cyclins[24, 25], Ki67[25], Bcl-2[26-28], erogeneous modifications of multiple signaling proteins have c-Myc[29], RAS[30] and EGFR[31, 32] have also been frequently been identified, including STAT, ERK, p38, GSK3β, β-catenin, found to be differentially expressed within a single tumor. NF-κB, AKT, PTEN, S6 and Src family kinases[28, 35-38]. In addi- With the advances in deep-sequencing technology, the tion, intra-tumor heterogeneity in O-glycosylation has also examination of single-cell gene expression profiles has become been reported[39]. popular. In a large-scale study, full-length transcriptomes of 672 cells from five freshly resected human GBMs were gener- The origins of intra-tumor heterogeneity ated using SMART-seq (switching mechanism at the 5′ end of Intrinsic factors the RNA template sequencing) technology (96–192 cells per The various types of intra-tumor heterogeneity are generated tumor)[33]. After depleting the infiltrating immune cells as well by different mechanisms, which can be categorized as cell- as genes
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