Single-cell multiomics reveals heterogeneous cell states linked to metastatic potential in liver cancer cell lines

[1]  Bertrand Z. Yeung,et al.  Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells , 2021, Nature Biotechnology.

[2]  Howard Y. Chang,et al.  ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis , 2021, Nature Genetics.

[3]  Huanming Yang,et al.  Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma , 2020, Cell.

[4]  M. E. Paul,et al.  Animal model of intrahepatic metastasis of hepatocellular carcinoma: establishment and characteristic , 2020, Scientific Reports.

[5]  Fei Gao,et al.  CNGBdb: China National GeneBank DataBase. , 2020, Yi chuan = Hereditas.

[6]  Martin J. Aryee,et al.  Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling , 2020, Nature Biotechnology.

[7]  Yan Lu,et al.  Analysis of single‐cell RNAseq identifies transitional states of T cells associated with hepatocellular carcinoma , 2020, Clinical and translational medicine.

[8]  D. Lambrechts,et al.  A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling , 2020, Cell Research.

[9]  Shuofeng Hu,et al.  Dissecting transcriptional heterogeneity in primary gastric adenocarcinoma by single cell RNA sequencing , 2020, Gut.

[10]  K. Tarte,et al.  Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer. , 2020, Cancer discovery.

[11]  P. Lampertico,et al.  Epidemiology and surveillance for hepatocellular carcinoma: New trends. , 2020, Journal of hepatology.

[12]  Fei Gao,et al.  CNSA: a data repository for archiving omics data , 2020, bioRxiv.

[13]  Zhifeng Wang,et al.  A portable and cost-effective microfluidic system for massively parallel single-cell transcriptome profiling , 2019, bioRxiv.

[14]  Jianrong Lu.  The Warburg metabolism fuels tumor metastasis , 2019, Cancer and Metastasis Reviews.

[15]  S. Imbeaud,et al.  Analysis of Liver Cancer Cell Lines Identifies Agents With Likely Efficacy Against Hepatocellular Carcinoma and Markers of Response. , 2019, Gastroenterology.

[16]  E. Ruppin,et al.  Functional Genomic Complexity Defines Intratumor Heterogeneity and Tumor Aggressiveness in Liver Cancer , 2019, Scientific Reports.

[17]  G. Mills,et al.  Characterization of hypoxia-associated molecular features to aid hypoxia-targeted therapy , 2019, Nature Metabolism.

[18]  C. Blanpain,et al.  EMT Transition States during Tumor Progression and Metastasis. , 2019, Trends in cell biology.

[19]  D. Merico,et al.  Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases. , 2019, Cancer cell.

[20]  Keji Zhao,et al.  Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity , 2019, Cell.

[21]  Christoph Hafemeister,et al.  Comprehensive integration of single cell data , 2018, bioRxiv.

[22]  J. Condeelis,et al.  The Different Routes to Metastasis via Hypoxia-Regulated Programs. , 2018, Trends in cell biology.

[23]  Angela M. Jarrett,et al.  Mathematical models of tumor cell proliferation: A review of the literature , 2018, Expert review of anticancer therapy.

[24]  Patrick J. Paddison,et al.  Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma , 2021, Molecular systems biology.

[25]  Hien Dang,et al.  Single‐cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma , 2018, Hepatology.

[26]  E. Furth,et al.  EMT Subtype Influences Epithelial Plasticity and Mode of Cell Migration. , 2018, Developmental cell.

[27]  T. Voet,et al.  Identification of the tumour transition states occurring during EMT , 2018, Nature.

[28]  Ruibin Xi,et al.  Diverse modes of clonal evolution in HBV-related hepatocellular carcinoma revealed by single-cell genome sequencing , 2018, Cell Research.

[29]  P. Kaufman,et al.  Ki-67: more than a proliferation marker , 2018, Chromosoma.

[30]  Hien Dang,et al.  The significance of intertumor and intratumor heterogeneity in liver cancer , 2018, Experimental & Molecular Medicine.

[31]  K. Hunter.  Faculty Opinions recommendation of Phenotypic heterogeneity of disseminated tumour cells is preset by primary tumour hypoxic microenvironments. , 2017 .

[32]  H. Swerdlow,et al.  Large-scale simultaneous measurement of epitopes and transcriptomes in single cells , 2017, Nature Methods.

[33]  Boxi Kang,et al.  Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing , 2017, Cell.

[34]  J. Colinge,et al.  Cell-Cycle Regulation Accounts for Variability in Ki-67 Expression Levels. , 2017, Cancer research.

[35]  M. Gönen,et al.  Actual 10-Year Survivors After Resection of Hepatocellular Carcinoma , 2017, Annals of Surgical Oncology.

[36]  Michael R. Padgen,et al.  Phenotypic heterogeneity of disseminated tumour cells is preset by primary tumour hypoxic microenvironments , 2017, Nature Cell Biology.

[37]  S. Påhlman,et al.  Therapeutic targeting of hypoxia and hypoxia-inducible factors in cancer. , 2016, Pharmacology & therapeutics.

[38]  R. Aebersold,et al.  On the Dependency of Cellular Protein Levels on mRNA Abundance , 2016, Cell.

[39]  Lu Wen,et al.  Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas , 2016, Cell Research.

[40]  A. Azab,et al.  The role of hypoxia in cancer progression, angiogenesis, metastasis, and resistance to therapy. , 2015 .

[41]  Mark A Feitelson,et al.  Sustained proliferation in cancer: Mechanisms and novel therapeutic targets. , 2015, Seminars in cancer biology.

[42]  R. Weinberg,et al.  Epithelial-Mesenchymal Plasticity: A Central Regulator of Cancer Progression. , 2015, Trends in cell biology.

[43]  K. Chok,et al.  Strategies to increase the resectability of hepatocellular carcinoma. , 2015, World journal of hepatology.

[44]  J. Yun,et al.  A novel vascular pattern promotes metastasis of hepatocellular carcinoma in an epithelial–mesenchymal transition–independent manner , 2015, Hepatology.

[45]  Howard Y. Chang,et al.  Single-cell chromatin accessibility reveals principles of regulatory variation , 2015, Nature.

[46]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[47]  Xudong Dai,et al.  Molecular portraits of epithelial, mesenchymal, and hybrid States in lung adenocarcinoma and their relevance to survival. , 2015, Cancer research.

[48]  M. Zern,et al.  Hepatoma SK Hep-1 Cells Exhibit Characteristics of Oncogenic Mesenchymal Stem Cells with Highly Metastatic Capacity , 2014, PloS one.

[49]  S. Thorgeirsson,et al.  SnapShot: Hepatocellular carcinoma. , 2014, Cancer cell.

[50]  M Choolani,et al.  An EMT spectrum defines an anoikis-resistant and spheroidogenic intermediate mesenchymal state that is sensitive to e-cadherin restoration by a src-kinase inhibitor, saracatinib (AZD0530) , 2013, Cell Death and Disease.

[51]  Jing-jing Hu,et al.  Expression of intercellular adhesion molecule 1 by hepatocellular carcinoma stem cells and circulating tumor cells. , 2013, Gastroenterology.

[52]  Yong Zhang,et al.  Identifying ChIP-seq enrichment using MACS , 2012, Nature Protocols.

[53]  Sven Diederichs,et al.  The hallmarks of cancer , 2012, RNA biology.

[54]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[55]  I. Ng,et al.  CD24(+) liver tumor-initiating cells drive self-renewal and tumor initiation through STAT3-mediated NANOG regulation. , 2011, Cell stem cell.

[56]  Jianren Gu,et al.  Cancer stem/progenitor cells are highly enriched in CD133+CD44+ population in hepatocellular carcinoma , 2009, International journal of cancer.

[57]  A. Paradiso,et al.  EGFR and VEGFR as potential target for biological therapies in HCC cells. , 2008, Cancer letters.

[58]  S. Fan,et al.  Significance of CD90+ cancer stem cells in human liver cancer. , 2008, Cancer cell.

[59]  Xin Wei Wang,et al.  Activation of hepatic stem cell marker EpCAM by Wnt-beta-catenin signaling in hepatocellular carcinoma. , 2007, Cancer research.

[60]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[61]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[62]  C. Ball,et al.  Identification of genes periodically expressed in the human cell cycle and their expression in tumors. , 2002, Molecular biology of the cell.

[63]  S. Ye,et al.  Establishment of cell clones with different metastatic potential from the metastatic hepatocellular carcinoma cell line MHCC97. , 2001, World journal of gastroenterology.

[64]  J. Kearney,et al.  AC133, a novel marker for human hematopoietic stem and progenitor cells. , 1997, Blood.

[65]  M. Hendrix,et al.  Experimental co-expression of vimentin and keratin intermediate filaments in human breast cancer cells results in phenotypic interconversion and increased invasive behavior. , 1997, The American journal of pathology.

[66]  H. Dvorak,et al.  Tumor cells secrete a vascular permeability factor that promotes accumulation of ascites fluid. , 1983, Science.

[67]  T. Yamane,et al.  Growth of human hepatoma cells lines with differentiated functions in chemically defined medium. , 1982, Cancer research.

[68]  Ivan Damjanov,et al.  Controlled synthesis of HBsAg in a differentiated human liver carcinoma-derived cell line , 1979, Nature.

[69]  P. Person.  Otto warburg: “on the origin of cancer cells” , 1957 .

[70]  S. Finch,et al.  Phenotypic Heterogeneity , 2020, Statistics for Biology and Health.

[71]  P. Vaupel,et al.  Hypoxia Compromises Anti-Cancer Immune Responses. , 2020, Advances in experimental medicine and biology.

[72]  J. Mesirov,et al.  The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.

[73]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[74]  E. Negelein,et al.  THE METABOLISM OF CARCINOMA CELLS , 2011 .

[75]  D. Woodfield.  Hepatocellular carcinoma. , 1986, The New Zealand medical journal.

[76]  Claire Cardie,et al.  Proceedings of the Eighteenth International Conference on Machine Learning, 2001, p. 577–584. Constrained K-means Clustering with Background Knowledge , 2022 .