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Volumn 173, Issue 4, 2018, Pages 879-893.e13

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

Author keywords

breast cancer genomics; cancer aneuploidy; chemotherapy; copy number evolution; intratumor heterogeneity; single cell sequencing; therapy resistance; triple negative breast cancer; tumor evolution

Indexed keywords

DNA; RNA; ANTINEOPLASTIC AGENT; TRANSCRIPTOME;

EID: 85045475727     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2018.03.041     Document Type: Article
Times cited : (744)

References (93)
  • 5
    • 84896689570 scopus 로고    scopus 로고
    • Molecular profiling of the residual disease of triple-negative breast cancers after neoadjuvant chemotherapy identifies actionable therapeutic targets
    • Balko, J.M., Giltnane, J.M., Wang, K., Schwarz, L.J., Young, C.D., Cook, R.S., Owens, P., Sanders, M.E., Kuba, M.G., Sánchez, V., et al. Molecular profiling of the residual disease of triple-negative breast cancers after neoadjuvant chemotherapy identifies actionable therapeutic targets. Cancer Discov. 4 (2014), 232–245.
    • (2014) Cancer Discov. , vol.4 , pp. 232-245
    • Balko, J.M.1    Giltnane, J.M.2    Wang, K.3    Schwarz, L.J.4    Young, C.D.5    Cook, R.S.6    Owens, P.7    Sanders, M.E.8    Kuba, M.G.9    Sánchez, V.10
  • 8
    • 85046579774 scopus 로고    scopus 로고
    • Manual On Setting Up, Using, And Understanding Random Forests V3.1.
    • Breiman, L. (2002). Manual On Setting Up, Using, And Understanding Random Forests V3.1.
    • (2002)
    • Breiman, L.1
  • 9
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Cancer Genome Atlas, N., Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490 (2012), 61–70.
    • (2012) Nature , vol.490 , pp. 61-70
  • 11
    • 55249109006 scopus 로고    scopus 로고
    • Tumour hypoxia affects the responsiveness of cancer cells to chemotherapy and promotes cancer progression
    • Cosse, J.P., Michiels, C., Tumour hypoxia affects the responsiveness of cancer cells to chemotherapy and promotes cancer progression. Anticancer. Agents Med. Chem. 8 (2008), 790–797.
    • (2008) Anticancer. Agents Med. Chem. , vol.8 , pp. 790-797
    • Cosse, J.P.1    Michiels, C.2
  • 12
    • 34447519947 scopus 로고    scopus 로고
    • A gene transcription signature of the Akt/mTOR pathway in clinical breast tumors
    • Creighton, C.J., A gene transcription signature of the Akt/mTOR pathway in clinical breast tumors. Oncogene 26 (2007), 4648–4655.
    • (2007) Oncogene , vol.26 , pp. 4648-4655
    • Creighton, C.J.1
  • 17
    • 85015372802 scopus 로고    scopus 로고
    • T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
    • Donaldson, J., T-Distributed Stochastic Neighbor Embedding for R (t-SNE). R package version 0, 2016, 1–3.
    • (2016) R package version 0 , pp. 1-3
    • Donaldson, J.1
  • 18
    • 84951574149 scopus 로고    scopus 로고
    • MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
    • Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A.K., Slichter, C.K., Miller, H.W., McElrath, M.J., Prlic, M., et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol., 16, 2015, 278.
    • (2015) Genome Biol. , vol.16 , pp. 278
    • Finak, G.1    McDavid, A.2    Yajima, M.3    Deng, J.4    Gersuk, V.5    Shalek, A.K.6    Slichter, C.K.7    Miller, H.W.8    McElrath, M.J.9    Prlic, M.10
  • 27
    • 84872202078 scopus 로고    scopus 로고
    • GSVA: gene set variation analysis for microarray and RNA-seq data
    • Hänzelmann, S., Castelo, R., Guinney, J., GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics, 14, 2013, 7.
    • (2013) BMC Bioinformatics , vol.14 , pp. 7
    • Hänzelmann, S.1    Castelo, R.2    Guinney, J.3
  • 28
    • 0036359548 scopus 로고    scopus 로고
    • Hypoxia–a key regulatory factor in tumour growth
    • Harris, A.L., Hypoxia–a key regulatory factor in tumour growth. Nat. Rev. Cancer 2 (2002), 38–47.
    • (2002) Nat. Rev. Cancer , vol.2 , pp. 38-47
    • Harris, A.L.1
  • 29
    • 84862010661 scopus 로고    scopus 로고
    • fpc: Flexible Procedures for Clustering
    • 21–10
    • Hennig, C., fpc: Flexible Procedures for Clustering. R package version, 2015 21–10.
    • (2015) R package version
    • Hennig, C.1
  • 30
    • 84872799328 scopus 로고    scopus 로고
    • Recent agents targeting HIF-1α for cancer therapy
    • Hu, Y., Liu, J., Huang, H., Recent agents targeting HIF-1α for cancer therapy. J. Cell. Biochem. 114 (2013), 498–509.
    • (2013) J. Cell. Biochem. , vol.114 , pp. 498-509
    • Hu, Y.1    Liu, J.2    Huang, H.3
  • 33
    • 85037359221 scopus 로고    scopus 로고
    • Comparison of methods to detect differentially expressed genes between single-cell populations
    • Jaakkola, M.K., Seyednasrollah, F., Mehmood, A., Elo, L.L., Comparison of methods to detect differentially expressed genes between single-cell populations. Brief. Bioinform. 18 (2017), 735–743.
    • (2017) Brief. Bioinform. , vol.18 , pp. 735-743
    • Jaakkola, M.K.1    Seyednasrollah, F.2    Mehmood, A.3    Elo, L.L.4
  • 35
    • 34247880280 scopus 로고    scopus 로고
    • Akt involvement in paclitaxel chemoresistance of human ovarian cancer cells
    • Kim, S.H., Juhnn, Y.S., Song, Y.S., Akt involvement in paclitaxel chemoresistance of human ovarian cancer cells. Ann. N Y Acad. Sci. 1095 (2007), 82–89.
    • (2007) Ann. N Y Acad. Sci. , vol.1095 , pp. 82-89
    • Kim, S.H.1    Juhnn, Y.S.2    Song, Y.S.3
  • 36
    • 84923911546 scopus 로고    scopus 로고
    • Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
    • Kim, H., Zheng, S., Amini, S.S., Virk, S.M., Mikkelsen, T., Brat, D.J., Grimsby, J., Sougnez, C., Muller, F., Hu, J., et al. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution. Genome Res. 25 (2015), 316–327.
    • (2015) Genome Res. , vol.25 , pp. 316-327
    • Kim, H.1    Zheng, S.2    Amini, S.S.3    Virk, S.M.4    Mikkelsen, T.5    Brat, D.J.6    Grimsby, J.7    Sougnez, C.8    Muller, F.9    Hu, J.10
  • 40
    • 84988579306 scopus 로고    scopus 로고
    • Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks
    • Langdon, W.B., Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks. BioData Min., 8, 2015, 1.
    • (2015) BioData Min. , vol.8 , pp. 1
    • Langdon, W.B.1
  • 41
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., Salzberg, S.L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 (2012), 357–359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 42
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li, B., Dewey, C.N., RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 2011, 323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 46
    • 68249093818 scopus 로고    scopus 로고
    • Targeting the phosphoinositide 3-kinase pathway in cancer
    • Liu, P., Cheng, H., Roberts, T.M., Zhao, J.J., Targeting the phosphoinositide 3-kinase pathway in cancer. Nat. Rev. Drug Discov. 8 (2009), 627–644.
    • (2009) Nat. Rev. Drug Discov. , vol.8 , pp. 627-644
    • Liu, P.1    Cheng, H.2    Roberts, T.M.3    Zhao, J.J.4
  • 48
    • 84859949610 scopus 로고    scopus 로고
    • The extracellular matrix: a dynamic niche in cancer progression
    • Lu, P., Weaver, V.M., Werb, Z., The extracellular matrix: a dynamic niche in cancer progression. J. Cell Biol. 196 (2012), 395–406.
    • (2012) J. Cell Biol. , vol.196 , pp. 395-406
    • Lu, P.1    Weaver, V.M.2    Werb, Z.3
  • 49
    • 0001641514 scopus 로고
    • Mutations of Bacteria from Virus Sensitivity to Virus Resistance
    • Luria, S.E., Delbrück, M., Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics 28 (1943), 491–511.
    • (1943) Genetics , vol.28 , pp. 491-511
    • Luria, S.E.1    Delbrück, M.2
  • 50
    • 84931025210 scopus 로고    scopus 로고
    • Clonality inference in multiple tumor samples using phylogeny
    • Malikic, S., McPherson, A.W., Donmez, N., Sahinalp, C.S., Clonality inference in multiple tumor samples using phylogeny. Bioinformatics 31 (2015), 1349–1356.
    • (2015) Bioinformatics , vol.31 , pp. 1349-1356
    • Malikic, S.1    McPherson, A.W.2    Donmez, N.3    Sahinalp, C.S.4
  • 51
    • 84955619540 scopus 로고    scopus 로고
    • Epithelial-mesenchymal transition: a new target in anticancer drug discovery
    • Marcucci, F., Stassi, G., De Maria, R., Epithelial-mesenchymal transition: a new target in anticancer drug discovery. Nat. Rev. Drug Discov. 15 (2016), 311–325.
    • (2016) Nat. Rev. Drug Discov. , vol.15 , pp. 311-325
    • Marcucci, F.1    Stassi, G.2    De Maria, R.3
  • 56
    • 84919917563 scopus 로고    scopus 로고
    • Ward's Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward's Criterion?
    • Murtagh, F., Legendre, P., Ward's Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward's Criterion?. J. Classif. 31 (2014), 274–295.
    • (2014) J. Classif. , vol.31 , pp. 274-295
    • Murtagh, F.1    Legendre, P.2
  • 57
    • 84893860363 scopus 로고    scopus 로고
    • Tumor evolution in response to chemotherapy: phenotype versus genotype
    • Navin, N.E., Tumor evolution in response to chemotherapy: phenotype versus genotype. Cell Rep. 6 (2014), 417–419.
    • (2014) Cell Rep. , vol.6 , pp. 417-419
    • Navin, N.E.1
  • 59
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: Predicting amino acid changes that affect protein function
    • Ng, P.C., Henikoff, S., SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 31 (2003), 3812–3814.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 60
    • 85046580554 scopus 로고    scopus 로고
    • copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression
    • Nilsen, G., Liestol, K., Lingjaerde, O.C., copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression. R package version, 2013, 1120.
    • (2013) R package version , pp. 1120
    • Nilsen, G.1    Liestol, K.2    Lingjaerde, O.C.3
  • 61
    • 84880934918 scopus 로고    scopus 로고
    • THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data
    • Oesper, L., Mahmoody, A., Raphael, B.J., THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Genome Biol., 14, 2013, R80.
    • (2013) Genome Biol. , vol.14 , pp. R80
    • Oesper, L.1    Mahmoody, A.2    Raphael, B.J.3
  • 62
    • 84922732814 scopus 로고    scopus 로고
    • Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data
    • Oesper, L., Satas, G., Raphael, B.J., Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. Bioinformatics 30 (2014), 3532–3540.
    • (2014) Bioinformatics , vol.30 , pp. 3532-3540
    • Oesper, L.1    Satas, G.2    Raphael, B.J.3
  • 63
    • 3543105225 scopus 로고    scopus 로고
    • Circular binary segmentation for the analysis of array-based DNA copy number data
    • Olshen, A.B., Venkatraman, E.S., Lucito, R., Wigler, M., Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5 (2004), 557–572.
    • (2004) Biostatistics , vol.5 , pp. 557-572
    • Olshen, A.B.1    Venkatraman, E.S.2    Lucito, R.3    Wigler, M.4
  • 64
    • 44449111555 scopus 로고    scopus 로고
    • Loss of E-cadherin promotes metastasis via multiple downstream transcriptional pathways
    • Onder, T.T., Gupta, P.B., Mani, S.A., Yang, J., Lander, E.S., Weinberg, R.A., Loss of E-cadherin promotes metastasis via multiple downstream transcriptional pathways. Cancer Res. 68 (2008), 3645–3654.
    • (2008) Cancer Res. , vol.68 , pp. 3645-3654
    • Onder, T.T.1    Gupta, P.B.2    Mani, S.A.3    Yang, J.4    Lander, E.S.5    Weinberg, R.A.6
  • 65
    • 84884709908 scopus 로고    scopus 로고
    • Extracellular matrix components in breast cancer progression and metastasis
    • Oskarsson, T., Extracellular matrix components in breast cancer progression and metastasis. Breast 22:Suppl 2 (2013), S66–S72.
    • (2013) Breast , vol.22 , pp. S66-S72
    • Oskarsson, T.1
  • 66
    • 84945990416 scopus 로고    scopus 로고
    • Targeting the PI3K/AKT/mTOR pathway: biomarkers of success and tribulation
    • Owonikoko, T.K., Khuri, F.R., Targeting the PI3K/AKT/mTOR pathway: biomarkers of success and tribulation. Am. Soc. Clin. Oncol. Educ. Book, 2013.
    • (2013) Am. Soc. Clin. Oncol. Educ. Book
    • Owonikoko, T.K.1    Khuri, F.R.2
  • 70
    • 84995663924 scopus 로고    scopus 로고
    • Hypoxia promotes chemoresistance in acute lymphoblastic leukemia cell lines by modulating death signaling pathways
    • Petit, C., Gouel, F., Dubus, I., Heuclin, C., Roget, K., Vannier, J.P., Hypoxia promotes chemoresistance in acute lymphoblastic leukemia cell lines by modulating death signaling pathways. BMC Cancer, 16, 2016, 746.
    • (2016) BMC Cancer , vol.16 , pp. 746
    • Petit, C.1    Gouel, F.2    Dubus, I.3    Heuclin, C.4    Roget, K.5    Vannier, J.P.6
  • 71
    • 84926507971 scopus 로고    scopus 로고
    • limma powers differential expression analyses for RNA-sequencing and microarray studies
    • Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., Smyth, G.K., limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, 2015, e47.
    • (2015) Nucleic Acids Res. , vol.43 , pp. e47
    • Ritchie, M.E.1    Phipson, B.2    Wu, D.3    Hu, Y.4    Law, C.W.5    Shi, W.6    Smyth, G.K.7
  • 74
    • 79951548848 scopus 로고    scopus 로고
    • phangorn: phylogenetic analysis in R
    • Schliep, K.P., phangorn: phylogenetic analysis in R. Bioinformatics 27 (2011), 592–593.
    • (2011) Bioinformatics , vol.27 , pp. 592-593
    • Schliep, K.P.1
  • 75
    • 0142166332 scopus 로고    scopus 로고
    • Targeting HIF-1 for cancer therapy
    • Semenza, G.L., Targeting HIF-1 for cancer therapy. Nat. Rev. Cancer 3 (2003), 721–732.
    • (2003) Nat. Rev. Cancer , vol.3 , pp. 721-732
    • Semenza, G.L.1
  • 76
  • 79
    • 85046594488 scopus 로고    scopus 로고
    • timescape: Patient Clonal Timescapes
    • Smith, M., timescape: Patient Clonal Timescapes. R package version 1.1.0, 2017.
    • (2017) R package version 1.1.0
    • Smith, M.1
  • 81
  • 85
    • 84929661801 scopus 로고    scopus 로고
    • Advances and applications of single-cell sequencing technologies
    • Wang, Y., Navin, N.E., Advances and applications of single-cell sequencing technologies. Mol. Cell 58 (2015), 598–609.
    • (2015) Mol. Cell , vol.58 , pp. 598-609
    • Wang, Y.1    Navin, N.E.2
  • 86
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    • Wang, K., Li, M., Hakonarson, H., ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res., 38, 2010, e164.
    • (2010) Nucleic Acids Res. , vol.38 , pp. e164
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 88
    • 27944455289 scopus 로고    scopus 로고
    • A comparison study: applying segmentation to array CGH data for downstream analyses
    • Willenbrock, H., Fridlyand, J., A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics 21 (2005), 4084–4091.
    • (2005) Bioinformatics , vol.21 , pp. 4084-4091
    • Willenbrock, H.1    Fridlyand, J.2
  • 89
    • 84942518519 scopus 로고    scopus 로고
    • Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR
    • Yang, H., Wang, K., Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat. Protoc., 2015, 1556–1566.
    • (2015) Nat. Protoc. , pp. 1556-1566
    • Yang, H.1    Wang, K.2
  • 91
    • 84988884535 scopus 로고    scopus 로고
    • An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
    • Yuan, J., Sims, P.A., An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq. Sci. Rep., 6, 2016, 33883.
    • (2016) Sci. Rep. , vol.6 , pp. 33883
    • Yuan, J.1    Sims, P.A.2
  • 93
    • 84948407218 scopus 로고    scopus 로고
    • Epithelial-to-mesenchymal transition is dispensable for metastasis but induces chemoresistance in pancreatic cancer
    • Zheng, X., Carstens, J.L., Kim, J., Scheible, M., Kaye, J., Sugimoto, H., Wu, C.C., LeBleu, V.S., Kalluri, R., Epithelial-to-mesenchymal transition is dispensable for metastasis but induces chemoresistance in pancreatic cancer. Nature 527 (2015), 525–530.
    • (2015) Nature , vol.527 , pp. 525-530
    • Zheng, X.1    Carstens, J.L.2    Kim, J.3    Scheible, M.4    Kaye, J.5    Sugimoto, H.6    Wu, C.C.7    LeBleu, V.S.8    Kalluri, R.9


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