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Single-Cell Multiomics: Dissecting Cancer

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Part of the book series: Algorithms for Intelligent Systems ((AIS))

Abstract

Rapid progress in next generation sequencing technologies provided deeper insights into the mechanism underlying disease pathology. It has broadened our horizon to understand the cellular processes at individual cell level. Single-cell analysis allowed uncovering new dimensions that could track the trajectories of distant cell lineage in tumor development. In recent years, the popularity of single-cell omics gained utmost momentum. Our review focuses on the use of single-cell omics in cellular model of cancer and its clinical application. It also highlights the potential of using multiomics approach to understand the cellular heterogeneity at multiple layers. The data generated using single-cell multiomics revealed the key biological processes, mechanism of cellular heterogeneity, and resistance mechanism. The knowledge captured from the single-cell analysis facilitated a wider understanding of disease and in developing efficient treatment strategies.

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References

  1. Ren X, Kang B, Zhang Z (2018) Understanding tumor ecosystems by single-cell sequencing: promises and limitations. Genome Biol 19(1):211

    Article  Google Scholar 

  2. Chen F et al (2015) New horizons in tumor microenvironment biology: challenges and opportunities. BMC Med 13:45

    Article  Google Scholar 

  3. Yuan Y et al (2016) Role of the tumor microenvironment in tumor progression and the clinical applications (Review). Oncol Rep 35(5):2499–2515

    Article  Google Scholar 

  4. Guan J, Chen J (2013) Mesenchymal stem cells in the tumor microenvironment. Biomed Rep 1(4):517–521

    Article  Google Scholar 

  5. Kamdje AHN et al (2017) Mesenchymal stromal cells’ role in tumor microenvironment: involvement of signaling pathways. Cancer Biol Med 14(2):129–141

    Article  Google Scholar 

  6. Arena S et al (2018) Characterization of tumor-derived mesenchymal stem cells potentially differentiating into cancer-associated fibroblasts in lung cancer. Clin Transl Oncol 20(12):1582–1591

    Article  Google Scholar 

  7. Ishihara S, Ponik SM, Haga H (2017) Mesenchymal stem cells in breast cancer: response to chemical and mechanical stimuli. Oncoscience 4(11–12):158–159

    Google Scholar 

  8. Fouad YA, Aanei C (2017) Revisiting the hallmarks of cancer. Am J Cancer Res 7(5):1016–1036

    Google Scholar 

  9. Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144(5):646–674

    Article  Google Scholar 

  10. Wang M et al (2017) Role of tumor microenvironment in tumorigenesis. J Cancer 8(5):761–773

    Article  Google Scholar 

  11. Thunnissen E, van der Oord K, den Bakker M (2014) Prognostic and predictive biomarkers in lung cancer. A review. Virchows Arch 464(3):347–358

    Article  Google Scholar 

  12. McNamara MG, Sahebjam S (2013) Mason WP (2013) Emerging biomarkers in glioblastoma. Cancers (Basel) 5(3):1103–11019

    Article  Google Scholar 

  13. Henry NL, Hayes DF (2012) Cancer biomarkers. Mol Oncol 6(2):140–146

    Article  Google Scholar 

  14. Roma-Rodrigues C et al (2019) Targeting tumor microenvironment for cancer therapy. Int J Mol Sci 20(4):840

    Article  Google Scholar 

  15. Kim J, Bae JS (2016) Tumor-associated macrophages and neutrophils in tumor microenvironment. Mediat Inflamm 2016:6058147

    Google Scholar 

  16. Quail DF, Joyce JA (2013) Microenvironmental regulation of tumor progression and metastasis. Nat Med 19(11):1423–1437

    Article  Google Scholar 

  17. Hida K et al (2018) Contribution of tumor endothelial cells in cancer progression. Int J Mol Sci 19(5):1272

    Article  Google Scholar 

  18. Maishi N, Hida K (2017) Tumor endothelial cells accelerate tumor metastasis. Cancer Sci 108(10):1921–1926

    Article  Google Scholar 

  19. Onimaru M, Yonemitsu Y (2011) Angiogenic and lymphangiogenic cascades in the tumor microenvironment. Front Biosci (Schol Ed) 3:216–225

    Article  Google Scholar 

  20. Hui L, Chen Y (2015) Tumor microenvironment: sanctuary of the devil. Cancer Lett 368(1):7–13

    Article  MathSciNet  Google Scholar 

  21. Wu T, Dai Y (2017) Tumor microenvironment and therapeutic response. Cancer Lett 387:61–68

    Article  Google Scholar 

  22. Walker C, Mojares E, Del Rio Hernandez A (2018) Role of extracellular matrix in development and cancer progression. Int J Mol Sci 19(10):3028

    Article  Google Scholar 

  23. Sokolenko AP, Imyanitov EN (2018) Molecular diagnostics in clinical oncology. Front Mol Biosci 5:76

    Article  Google Scholar 

  24. Ryu D et al (2016) Deciphering intratumor heterogeneity using cancer genome analysis. Hum Genet 135(6):635–642

    Article  Google Scholar 

  25. Wei Q et al (2017) Multiregion whole-exome sequencing of matched primary and metastatic tumors revealed genomic heterogeneity and suggested polyclonal seeding in colorectal cancer metastasis. Ann Oncol 28(9):2135–2141

    Article  Google Scholar 

  26. Varon-Gonzalez C, Navarro N (2019) Epistasis regulates the developmental stability of the mouse craniofacial shape. Heredity (Edinb) 122(5):501–512

    Article  Google Scholar 

  27. Racle J et al (2017) Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. Elife 6:e26476

    Article  Google Scholar 

  28. Lo PK, Zhou Q (2018) Emerging techniques in single-cell epigenomics and their applications to cancer research. J Clin Genom 1(1)

    Google Scholar 

  29. Bartoschek M et al (2018) Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing. Nat Commun 9(1):5150

    Article  Google Scholar 

  30. Li H et al (2018) Author correction: reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat Genet 50(12):1754

    Article  Google Scholar 

  31. Muller S et al (2017) Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment. Genome Biol 18(1):234

    Article  Google Scholar 

  32. Valdes-Mora F et al (2018) Single-cell transcriptomics in cancer immunobiology: the future of precision oncology. Front Immunol 9:2582

    Article  Google Scholar 

  33. Navin N et al (2011) Tumour evolution inferred by single-cell sequencing. Nature 472(7341):90–94

    Article  Google Scholar 

  34. Wang Y et al (2014) Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512(7513):155–160

    Article  Google Scholar 

  35. Francis JM et al (2014) EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing. Cancer Discov 4(8):956–971

    Article  Google Scholar 

  36. Xu X et al (2012) Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell 148(5):886–895

    Article  Google Scholar 

  37. Yu C et al (2014) Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing. Cell Res 24(6):701–712

    Article  Google Scholar 

  38. Wu H et al (2017) Evolution and heterogeneity of non-hereditary colorectal cancer revealed by single-cell exome sequencing. Oncogene 36(20):2857–2867

    Article  Google Scholar 

  39. Li Y et al (2012) Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer. Gigascience 1(1):12

    Article  MathSciNet  Google Scholar 

  40. Gawad C, Koh W, Quake SR (2014) Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics. Proc Natl Acad Sci USA 111(50):17947–17952

    Article  Google Scholar 

  41. Li C et al (2017) Single-cell exome sequencing identifies mutations in KCP, LOC440040, and LOC440563 as drivers in renal cell carcinoma stem cells. Cell Res 27(4):590–593

    Article  MathSciNet  Google Scholar 

  42. Yang Z et al (2017) Single-cell sequencing reveals variants in ARID1A, GPRC5A and MLL2 driving self-renewal of human bladder cancer stem cells. Eur Urol 71(1):8–12

    Article  MathSciNet  Google Scholar 

  43. Caswell DR, Swanton C (2017) The role of tumour heterogeneity and clonal cooperativity in metastasis, immune evasion and clinical outcome. BMC Med 15(1):133

    Article  Google Scholar 

  44. Leung ML et al (2017) Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer. Genome Res 27(8):1287–1299

    Article  Google Scholar 

  45. Eirew P et al (2015) Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature 518(7539):422–426

    Article  Google Scholar 

  46. Baxter E et al (2014) Epigenetic regulation in cancer progression. Cell Biosci 4:45

    Article  Google Scholar 

  47. Chatterjee A, Rodger EJ, Eccles MR (2018) Epigenetic drivers of tumourigenesis and cancer metastasis. Semin Cancer Biol 51:149–159

    Article  Google Scholar 

  48. Xi Y et al (2018) Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. BMC Genom 19(1):150

    Article  Google Scholar 

  49. Li LC, Carroll PR, Dahiya R (2005) Epigenetic changes in prostate cancer: implication for diagnosis and treatment. J Natl Cancer Inst 97(2):103–115

    Article  Google Scholar 

  50. Kanwal R, Gupta S (2010) Epigenetics and cancer. J Appl Physiol 109(2):598–605

    Article  Google Scholar 

  51. Litzenburger UM et al (2017) Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biol 18(1):15

    Article  Google Scholar 

  52. Guo H et al (2013) Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res 23(12):2126–2135

    Article  Google Scholar 

  53. Gaiti F et al (2019) Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia. Nature 569(7757):576–580

    Article  Google Scholar 

  54. Farlik M et al (2015) Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep 10(8):1386–1397

    Article  Google Scholar 

  55. Buenrostro JD et al (2015) Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523(7561):486–490

    Article  Google Scholar 

  56. Patel AP et al (2014) Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 344(6190):1396–1401

    Article  Google Scholar 

  57. Tirosh I et al (2016) Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352(6282):189–196

    Article  Google Scholar 

  58. Giustacchini A et al (2017) Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia. Nat Med 23(6):692–702

    Article  Google Scholar 

  59. Lawson DA et al (2015) Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells. Nature 526(7571):131–135

    Article  Google Scholar 

  60. Liu Y, Cao X (2016) Immunosuppressive cells in tumor immune escape and metastasis. J Mol Med (Berl) 94(5):509–522

    Article  Google Scholar 

  61. Zheng C et al (2017) Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing. Cell 169(7):1342–1356

    Article  Google Scholar 

  62. Chung W et al (2017) Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer. Nat Commun 8:15081

    Article  Google Scholar 

  63. Roth A et al (2014) PyClone: statistical inference of clonal population structure in cancer. Nat Methods 11(4):396–398

    Article  Google Scholar 

  64. Miller CA et al (2014) SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput Biol 10(8):e1003665

    Article  Google Scholar 

  65. Zou M, Jin R, Au KF (2018) Revealing tumor heterogeneity of breast cancer by utilizing the linkage between somatic and germline mutations. Brief Bioinform

    Google Scholar 

  66. Zhang J et al (2014) Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science 346(6206):256–259

    Article  Google Scholar 

  67. Zhang LL et al (2017) Multiregion sequencing reveals the intratumor heterogeneity of driver mutations in TP53-driven non-small cell lung cancer. Int J Cancer 140(1):103–108

    Article  Google Scholar 

  68. Ledgerwood LG et al (2016) The degree of intratumor mutational heterogeneity varies by primary tumor sub-site. Oncotarget 7(19):27185–27198

    Article  Google Scholar 

  69. Yan T et al (2019) Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma. Nat Commun 10(1):1670

    Article  Google Scholar 

  70. Hao JJ et al (2016) Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma. Nat Genet 48(12):1500–1507

    Article  Google Scholar 

  71. Kim TM et al (2015) Subclonal genomic architectures of primary and metastatic colorectal cancer based on intratumoral genetic heterogeneity. Clin Cancer Res 21(19):4461–4472

    Article  Google Scholar 

  72. Ahmed M, Li LC (2013) Adaptation and clonal selection models of castration-resistant prostate cancer: current perspective. Int J Urol 20(4):362–371

    Article  Google Scholar 

  73. Horning AM et al (2018) Single-cell RNA-seq reveals a subpopulation of prostate cancer cells with enhanced cell-cycle-related transcription and attenuated androgen response. Cancer Res 78(4):853–864

    Article  Google Scholar 

  74. Casasent AK, Edgerton M, Navin NE (2017) Genome evolution in ductal carcinoma in situ: invasion of the clones. J Pathol 241(2):208–218

    Article  Google Scholar 

  75. Casasent AK et al (2018) Multiclonal invasion in breast tumors identified by topographic single cell sequencing. Cell 172(1–2):205–217

    Article  Google Scholar 

  76. Sottoriva A et al (2015) A big bang model of human colorectal tumor growth. Nat Genet 47(3):209–216

    Article  Google Scholar 

  77. Sarkar S et al (2013) Cancer development, progression, and therapy: an epigenetic overview. Int J Mol Sci 14(10):21087–21113

    Article  Google Scholar 

  78. Byler S et al (2014) Genetic and epigenetic aspects of breast cancer progression and therapy. Anticancer Res 34(3):1071–1077

    Google Scholar 

  79. Byler S, Sarkar S (2014) Do epigenetic drug treatments hold the key to killing cancer progenitor cells? Epigenomics 6(2):161–165

    Article  Google Scholar 

  80. Campbell PJ et al (2010) The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467(7319):1109–1113

    Article  Google Scholar 

  81. Sosa Iglesias V et al (2018) Drug resistance in non-small cell lung cancer: a potential for NOTCH targeting? Front Oncol 8:267

    Article  Google Scholar 

  82. Lopez-Verdin S et al (2018) Molecular markers of anticancer drug resistance in head and neck squamous cell carcinoma: a literature review. Cancers (Basel) 10(10):376

    Article  Google Scholar 

  83. Ansell A et al (2016) Epidermal growth factor is a potential biomarker for poor cetuximab response in tongue cancer cells. J Oral Pathol Med 45(1):9–16

    Article  Google Scholar 

  84. Sauna ZE, Ambudkar SV (2001) Characterization of the catalytic cycle of ATP hydrolysis by human P-glycoprotein. The two ATP hydrolysis events in a single catalytic cycle are kinetically similar but affect different functional outcomes. J Biol Chem 276(15):11653–11661

    Article  Google Scholar 

  85. Hilgendorf C et al (2007) Expression of thirty-six drug transporter genes in human intestine, liver, kidney, and organotypic cell lines. Drug Metab Dispos 35(8):1333–1340

    Article  Google Scholar 

  86. Haber M et al (2006) Association of high-level MRP1 expression with poor clinical outcome in a large prospective study of primary neuroblastoma. J Clin Oncol 24(10):1546–1553

    Article  Google Scholar 

  87. Friedrich RE, Punke C, Reymann A (2004) Expression of multi-drug resistance genes (mdr1, mrp1, bcrp) in primary oral squamous cell carcinoma. Vivo 18(2):133–147

    Google Scholar 

  88. Rivlin N et al (2011) Mutations in the p53 Tumor Suppressor Gene: Important Milestones at the Various Steps of Tumorigenesis. Genes Cancer 2(4):466–474

    Article  Google Scholar 

  89. Holohan C et al (2013) Cancer drug resistance: an evolving paradigm. Nat Rev Cancer 13(10):714–726

    Article  Google Scholar 

  90. Kobayashi S et al (2005) EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. N Engl J Med 352(8):786–792

    Article  Google Scholar 

  91. Razis E et al (2011) Evaluation of the association of PIK3CA mutations and PTEN loss with efficacy of trastuzumab therapy in metastatic breast cancer. Breast Cancer Res Treat 128(2):447–456

    Article  Google Scholar 

  92. Cook KL et al (2014) Hydroxychloroquine inhibits autophagy to potentiate antiestrogen responsiveness in ER+breast cancer. Clin Cancer Res 20(12):3222–3232

    Article  Google Scholar 

  93. Curtin NJ (2012) DNA repair dysregulation from cancer driver to therapeutic target. Nat Rev Cancer 12(12):801–817

    Article  Google Scholar 

  94. Nogueira GAS et al (2018) Polymorphisms in DNA mismatch repair pathway genes predict toxicity and response to cisplatin chemoradiation in head and neck squamous cell carcinoma patients. Oncotarget 9(51):29538–29547

    Article  Google Scholar 

  95. Chae YK et al (2018) Epithelial-mesenchymal transition (EMT) signature is inversely associated with T-cell infiltration in non-small cell lung cancer (NSCLC). Sci Rep 8(1):2918

    Article  Google Scholar 

  96. Bearzatto A et al (2000) Epigenetic regulation of the MGMT and hMSH6 DNA repair genes in cells resistant to methylating agents. Cancer Res 60(12):3262–3270

    Google Scholar 

  97. Navin N et al (2010) Inferring tumor progression from genomic heterogeneity. Genome Res 20(1):68–80

    Article  Google Scholar 

  98. McGranahan N, Swanton C (2017) Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future. Cell 168(4):613–628

    Article  Google Scholar 

  99. Van Allen EM et al (2015) Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science 350(6257):207–211

    Article  Google Scholar 

  100. Rizvi NA et al (2015) Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348(6230):124–128

    Article  Google Scholar 

  101. Fares CM et al (2019) Mechanisms of resistance to immune checkpoint blockade: why does checkpoint inhibitor immunotherapy not work for all patients? Am Soc Clin Oncol Educ Book 39:147–164

    Article  Google Scholar 

  102. Tang F et al (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6(5):377–382

    Article  Google Scholar 

  103. Zheng GX et al (2016) Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nat Biotechnol 34(3):303–311

    Article  Google Scholar 

  104. Gierahn TM et al (2017) Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat Methods 14(4):395–398

    Article  Google Scholar 

  105. Wang Y, Navin NE (2015) Advances and applications of single-cell sequencing technologies. Mol Cell 58(4):598–609

    Article  Google Scholar 

  106. Hou Y et al (2016) Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res 26(3):304–319

    Article  Google Scholar 

  107. Lambrechts D et al (2018) Phenotype molding of stromal cells in the lung tumor microenvironment. Nat Med 24(8):1277–1289

    Article  Google Scholar 

  108. Ma KY et al (2019) Single-cell RNA sequencing of lung adenocarcinoma reveals heterogeneity of immune response-related genes. JCI Insight 4(4):e121387

    Article  Google Scholar 

  109. Pantel K, Speicher MR (2016) The biology of circulating tumor cells. Oncogene 35(10):1216–1224

    Article  Google Scholar 

  110. Zhu Z et al (2018) Progress and challenges of sequencing and analyzing circulating tumor cells. Cell Biol Toxicol 34(5):405–415

    Article  Google Scholar 

  111. Yadavalli S et al (2017) Data-driven discovery of extravasation pathway in circulating tumor cells. Sci Rep 7:43710

    Article  Google Scholar 

  112. Krebs MG et al (2014) Molecular analysis of circulating tumour cells-biology and biomarkers. Nat Rev Clin Oncol 11(3):129–144

    Article  Google Scholar 

  113. Arya SK, Lim B, Rahman AR (2013) Enrichment, detection and clinical significance of circulating tumor cells. Lab Chip 13(11):1995–2027

    Article  Google Scholar 

  114. Khoo BL et al (2015) Short-term expansion of breast circulating cancer cells predicts response to anti-cancer therapy. Oncotarget 6(17):15578–15593

    Article  Google Scholar 

  115. Cristofanilli M et al (2004) Circulating tumor cells, disease progression, and survival in metastatic breast cancer. N Engl J Med 351(8):781–791

    Article  Google Scholar 

  116. Balakrishnan A et al (2019) Circulating Tumor Cell cluster phenotype allows monitoring response to treatment and predicts survival. Sci Rep 9(1):7933

    Article  Google Scholar 

  117. Lianidou ES, Markou A, Strati A (2015) The role of CTCs as tumor biomarkers. Adv Exp Med Biol 867:341–367

    Article  Google Scholar 

  118. Shaw JA et al (2017) Mutation analysis of cell-free DNA and single circulating tumor cells in metastatic breast cancer patients with high circulating tumor cell counts. Clin Cancer Res 23(1):88–96

    Article  Google Scholar 

  119. De Luca F et al (2016) Mutational analysis of single circulating tumor cells by next generation sequencing in metastatic breast cancer. Oncotarget 7(18):26107–26119

    Google Scholar 

  120. Gao Y et al (2017) Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells. Genome Res 27(8):1312–1322

    Article  Google Scholar 

  121. Ni X et al (2013) Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. Proc Natl Acad Sci USA 110(52):21083–21088

    Article  Google Scholar 

  122. Carter L et al (2017) Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer. Nat Med 23(1):114–119

    Article  Google Scholar 

  123. Yu M et al (2013) Circulating breast tumor cells exhibit dynamic changes in epithelial and mesenchymal composition. Science 339(6119):580–584

    Article  Google Scholar 

  124. Ting DT et al (2014) Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells. Cell Rep 8(6):1905–1918

    Article  Google Scholar 

  125. Miyamoto DT et al (2015) RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance. Science 349(6254):1351–1356

    Article  Google Scholar 

  126. Grillet F et al (2017) Circulating tumour cells from patients with colorectal cancer have cancer stem cell hallmarks in ex vivo culture. Gut 66(10):1802–1810

    Article  Google Scholar 

  127. Baslan T et al (2012) Genome-wide copy number analysis of single cells. Nat Protoc 7(6):1024–1041

    Article  Google Scholar 

  128. Leung ML et al (2015) SNES: single nucleus exome sequencing. Genome Biol 16:55

    Article  Google Scholar 

  129. Gao R et al (2017) Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer. Nat Commun 8(1):228

    Article  Google Scholar 

  130. Macosko EZ et al (2015) Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161(5):1202–1214

    Article  Google Scholar 

  131. Grindberg RV et al (2013) RNA-sequencing from single nuclei. Proc Natl Acad Sci USA 110(49):19802–19807

    Article  Google Scholar 

  132. Shapiro E, Biezuner T, Linnarsson S (2013) Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet 14(9):618–630

    Article  Google Scholar 

  133. Bernard V et al (2019) Single-cell transcriptomics of pancreatic cancer precursors demonstrates epithelial and microenvironmental heterogeneity as an early event in neoplastic progression. Clin Cancer Res 25(7):2194–2205

    Article  Google Scholar 

  134. Kim C et al (2018) Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell 173(4):879–893

    Article  Google Scholar 

  135. Azizi E et al (2018) Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Cell 174(5):1293–1308

    Article  Google Scholar 

  136. Liu M et al (2017) Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer. BMC Cancer 17(1):787

    Article  Google Scholar 

  137. Lavin Y et al (2017) Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses. Cell 169(4):750–765

    Article  Google Scholar 

  138. Dey SS et al (2015) Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol 33(3):285–289

    Article  Google Scholar 

  139. Wu L et al (2015) Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells. Gigascience 4:51

    Article  Google Scholar 

  140. Dago AE et al (2014) Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells. PLoS ONE 9(8):e101777

    Article  Google Scholar 

  141. Zhao L et al (2013) High-purity prostate circulating tumor cell isolation by a polymer nanofiber-embedded microchip for whole exome sequencing. Adv Mater 25(21):2897–2902

    Article  Google Scholar 

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Sambath, J., Patel, K., Limaye, S., Kumar, P. (2020). Single-Cell Multiomics: Dissecting Cancer. In: Srinivasa, K., Siddesh, G., Manisekhar, S. (eds) Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Algorithms for Intelligent Systems. Springer, Singapore. https://doi.org/10.1007/978-981-15-2445-5_14

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