Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer

Li, Yingrui; Xu, Xun; Song, Liying; Hou, Yong; Li, Zesong; Tsang, Shirley; Li, Fuqiang; Im, Kate M.; Wu, Kui; Wu, Huawei; Ye, Xiaofei; Li, Guibo; Wang, Linlin; Zhang, Bo; Liang, Jie; Xie, Wei; Wu, Renhua; Jiang, Hui; Liu, Xiao; Yu, Chang; Zheng, Hancheng; Jian, Min; Nie, Lei; Wan, Lei; Shi, Min; Sun, Xiaojuan; Tang, Aifa; Guo, Guangwu; Gui, Yaoting; Cai, Zhiming; Li, Jingxiang; Wang, Wen; Zhang, Lu; Zhang, Xiuqing; Bolund, Lars; Kristiansen, Karsten; Wang, Jian; Yang, Huanming; Dean, Michael; Wang, Jun

doi:10.1186/2047-217x-1-12

Cited by 104 publications

(102 citation statements)

References 36 publications

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“…The six somatic mutations that were discovered in the present study were single base changes, and none of them had previously been identified in the TCC genome. The novel nonsynonymous mutation genes that were detected did not include the well-known bladder cancer genes (FGFR3, RAS, TP53 and RB1) and contrasted with the findings of previous studies (14)(15)(16). This discrepancy may be due to differing experimental conditions, and algorithm and filter use.…”

Section: Discussioncontrasting

confidence: 56%

Novel somatic mutations identified by whole-exome sequencing in muscle-invasive transitional cell carcinoma of the bladder

Pan

et al. 2016

Oncology Letters

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Abstract. Transitional cell carcinoma (TCC) is the one of the most commonly observed types of cancer globally. The identification of novel disease-associated genes in TCC has had a significant effect on the diagnosis and treatment of bladder cancer; however, there may be a large number of novel genes that have not been identified. In the present study, the exomes of two individuals who were diagnosed with muscle-invasive TCC (MI-TCC) were sequenced to investigate potential variants. Subsequently, following algorithm and filter analysis, Sanger sequencing was used to validate the results of deep sequencing. Immunohistochemistry (IHC) was employed to observe the differences in HECT, C2 and WW domain-containing E3 ubiquitin protein ligase 1 (HECW1) protein expression between tumor tissues and para-carcinoma tissues. A total of 6 nonsynonymous mutation genes were identified in MI-TCC, identified as copine VII, RNA binding motif protein, X-linked-like 3, acyl-CoA synthetase medium-chain family member 2A, HECW1, zinc finger protein 273 and trichohyalin. Furthermore, 5 cases were identified to possess a HECW1 gene mutation in 61 MI-TCC specimens, and all of these were point mutations located at exon 11 on chromosome 7.The mutation categories of HECW1 had 4 missense mutations and 1 nonsense mutation. IHC revealed that HECW1 protein was expressed at significantly increased levels in MI-TCC compared with normal bladder urothelium (P<0.001). The present study provided a novel approach for investigating genetic changes in the MI-TCC exome, and identified the novel mutant gene HECW1, which may possess a significant role in the pathogenesis of TCC.

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Section: Discussioncontrasting

confidence: 56%

Novel somatic mutations identified by whole-exome sequencing in muscle-invasive transitional cell carcinoma of the bladder

Pan

et al. 2016

Oncology Letters

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“…In recent years, a large number of studies have been reported using single cell analysis to analyze individual tumor cells isolated from breast cancer (Navin et al, 2011; Deng et al, 2014; Wang et al, 2014; Eirew et al, 2015), colon cancer (Zong et al, 2012; Yu et al, 2014), pancreatic adenocarcinomas (Ruiz et al, 2011), muscle-invasive bladder cancer (Li et al, 2012b), intestinal cancer (Grün et al, 2015), lung adenocarcinoma cancer (Kim et al, 2015), renal cell carcinoma (Gerlinger et al, 2012; Li et al, 2012b), and acute myeloid leukemia (Ding et al, 2012; Hughes et al, 2014; Paguirigan et al, 2015). For example, Navin and colleagues investigated copy number variation in single tumor cells using DOP WGA followed by DNA sequencing to determine cell population structure and tumor evolution patterns in a single breast tumor (Navin et al, 2011).…”

Section: Application Of Single Cell Analysismentioning

confidence: 99%

Single Cell Isolation and Analysis

Zhang

Xin

et al. 2016

Front. Cell Dev. Biol.

280

234

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Individual cell heterogeneity within a population can be critical to its peculiar function and fate. Subpopulations studies with mixed mutants and wild types may not be as informative regarding which cell responds to which drugs or clinical treatments. Cell to cell differences in RNA transcripts and protein expression can be key to answering questions in cancer, neurobiology, stem cell biology, immunology, and developmental biology. Conventional cell-based assays mainly analyze the average responses from a population of cells, without regarding individual cell phenotypes. To better understand the variations from cell to cell, scientists need to use single cell analyses to provide more detailed information for therapeutic decision making in precision medicine. In this review, we focus on the recent developments in single cell isolation and analysis, which include technologies, analyses and main applications. Here, we summarize the historical background, limitations, applications, and potential of single cell isolation technologies.

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“…Analyses of the somatic mutant allele frequency spectrum and clonal structure revealed that the tumor cells were derived from a single ancestral cell, but that subsequent evolution occurred, leading to two distinct tumor cell subpopulations which provide evidence for the monoclonal origin of TCC [26]. …”

Section: Generation Model Of Tumor Heterogeneitymentioning

confidence: 99%

Bladder Tumor Heterogeneity: The Impact on Clinical Treatment

Chen¹,

Qi²,

Cao³

et al. 2015

Urol Int

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Bladder cancer relapse and treatment failure in most patients have often been attributed to chemoresistance in tumor cells and metastasis. Emerging evidence indicates that tumor heterogeneity may play an equally important role and extends to virtually all measurable properties of cancer cells. Although the idea of tumor heterogeneity is not new, little attention has been paid to applying it to understand and control bladder cancer progression. With the development of biotechnology, such as Gene sequencing, recent advances in understanding its generation model, original basis, consequent problems, and derived therapies provide great potential for tumor heterogeneity to be considered a new insight in the treatment of bladder cancers.

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Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer

Cited by 104 publications

References 36 publications

Novel somatic mutations identified by whole-exome sequencing in muscle-invasive transitional cell carcinoma of the bladder

Novel somatic mutations identified by whole-exome sequencing in muscle-invasive transitional cell carcinoma of the bladder

Single Cell Isolation and Analysis

Bladder Tumor Heterogeneity: The Impact on Clinical Treatment

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