The Repertoire of Serous Ovarian Cancer Non-genetic Heterogeneity Revealed by Single-Cell Sequencing of Normal Fallopian Tube Epithelial Cells

Ahmed, 2010, Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary, J. Pathol., 221, 49, 10.1002/path.2696 Anastassiou, 2011, Human cancer cells express Slug-based epithelial-mesenchymal transition gene expression signature obtained in vivo, BMC Cancer, 11, 529, 10.1186/1471-2407-11-529 Anglesio, 2013, Type-specific cell line models for type-specific ovarian cancer research, PLoS One, 8, e72162, 10.1371/journal.pone.0072162 Ansieau, 2008, Induction of EMT by twist proteins as a collateral effect of tumor-promoting inactivation of premature senescence, Cancer Cell, 14, 79, 10.1016/j.ccr.2008.06.005 Ardighieri, 2014, Characterization of the immune cell repertoire in the normal fallopian tube, Int. J. Gynecol. Pathol., 33, 581, 10.1097/PGP.0000000000000095 Baron, 2016, A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure, Cell Syst., 3, 346, 10.1016/j.cels.2016.08.011 Bell, 2011, Integrated genomic analyses of ovarian carcinoma, Nature, 474, 609, 10.1038/nature10166 Bentink, 2012, Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer, PLoS One, 7, e30269, 10.1371/journal.pone.0030269 Bertucci, 2012, Basal breast cancer: a complex and deadly molecular subtype, Curr. Mol. Med., 12, 96, 10.2174/156652412798376134 Biton, 2018, T helper cell cytokines modulate intestinal stem cell renewal and differentiation, Cell, 175, 1307, 10.1016/j.cell.2018.10.008 Bonome, 2008, A gene signature predicting for survival in suboptimally debulked patients with ovarian cancer, Cancer Res., 68, 5478, 10.1158/0008-5472.CAN-07-6595 Brock, 2009, Non-genetic heterogeneity––a mutation-independent driving force for the somatic evolution of tumours, Nat. Rev. Genet., 10, 336, 10.1038/nrg2556 Butler, 2018, Integrating single-cell transcriptomic data across different conditions, technologies, and species, Nat. Biotechnol., 36, 411, 10.1038/nbt.4096 Campbell, 2018, Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data, Nat. Commun., 9, 2442, 10.1038/s41467-018-04696-6 Cerny, 2016, Estrogen receptor alpha (ESR1)-dependent regulation of the mouse oviductal transcriptome, PLoS One, 11, e0147685, 10.1371/journal.pone.0147685 Chandrasekaran, 2016, MicroRNA-214 suppresses growth, migration and invasion through a novel target, high mobility group AT-hook 1, in human cervical and colorectal cancer cells, Br. J. Cancer, 115, 741, 10.1038/bjc.2016.234 Chen, 2018, Consensus on molecular subtypes of high-grade serous ovarian carcinoma, Clin. Cancer Res., 24, 5037, 10.1158/1078-0432.CCR-18-0784 Clyman, 1966, Electron microscopy of the human fallopian tube, Fertil. Steril., 17, 281, 10.1016/S0015-0282(16)35940-4 Comer, 1998, Induction of a differentiated ciliated cell phenotype in primary cultures of fallopian tube epithelium, Hum. Reprod., 13, 3114, 10.1093/humrep/13.11.3114 Crijns, 2009, Survival-related profile, pathways, and transcription factors in ovarian cancer, PLoS Med., 6, e24, 10.1371/journal.pmed.1000024 Crow, 1994, Morphology and ultrastructure of fallopian-tube epithelium at different stages of the menstrual-cycle and menopause, Hum. Reprod., 9, 2224, 10.1093/oxfordjournals.humrep.a138428 Dai, 2015, Breast cancer intrinsic subtype classification, clinical use and future trends, Am. J. Cancer Res., 5, 2929 Davis, 2014, Targeting EMT in cancer: opportunities for pharmacological intervention, Trends Pharmacol. Sci., 35, 479, 10.1016/j.tips.2014.06.006 Dobin, 2012, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 Domcke, 2013, Evaluating cell lines as tumour models by comparison of genomic profiles, Nat. Commun., 4, 2126, 10.1038/ncomms3126 Ducie, 2017, Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma, Nat. Commun., 8, 990, 10.1038/s41467-017-01217-9 Eckert, 2019, Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts, Nature, 474, 609 Eden, 2007, Discovering motifs in ranked lists of DNA sequences, PLoS Comput. Biol., 3, 508, 10.1371/journal.pcbi.0030039 Eden, 2009, GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists, BMC Bioinformatics, 10, 48, 10.1186/1471-2105-10-48 Etemadmoghadam, 2009, Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas, Clin. Cancer Res., 15, 1417, 10.1158/1078-0432.CCR-08-1564 Fan, 2018, Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data, Genome Res., 28, 1217, 10.1101/gr.228080.117 Fessler, 2016, Colorectal cancer subtypes: developmental origin and microenvironmental regulation, Trends Cancer, 2, 505, 10.1016/j.trecan.2016.07.008 Ford, 2013, The Wnt gatekeeper SFRP4 modulates EMT, cell migration and downstream Wnt signalling in serous ovarian cancer cells, PLoS One, 8, e54362, 10.1371/journal.pone.0054362 Fresno Vara, 2004, PI3K/Akt signalling pathway and cancer, Cancer Treat. Rev., 30, 193, 10.1016/j.ctrv.2003.07.007 Ganzfried, 2013, curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome, Database (Oxford), 2013, bat013, 10.1093/database/bat013 Ghosh, 2017, In vivo genetic cell lineage tracing reveals that oviductal secretory cells self-renew and give rise to ciliated cells, Development, 144, 3031 Gilbertson, 2011, Mapping cancer origins, Cell, 145, 25, 10.1016/j.cell.2011.03.019 Ginestet, 2011, ggplot2: elegant graphics for data analysis, J. R. Stat. Soc. Ser. A Stat. Soc., 174, 245, 10.1111/j.1467-985X.2010.00676_9.x Ginestier, 2007, ALDH1 is a marker of normal and malignant human mammary stem cells and a predictor of poor clinical outcome, Cell Stem Cell, 1, 555, 10.1016/j.stem.2007.08.014 Goldman, 2018, The UCSC Xena Platform for cancer genomics data visualization and interpretation, bioRxiv, 326470 Greaves, 2012, Clonal evolution in cancer, Nature, 481, 306, 10.1038/nature10762 Gregory, 2008, The mir-200 family and mir-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1, Nat. Cell Biol., 10, 593, 10.1038/ncb1722 Grün, 2015, Single-cell messenger RNA sequencing reveals rare intestinal cell types, Nature, 525, 251, 10.1038/nature14966 Gupta, 2011, Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells, Cell, 146, 633, 10.1016/j.cell.2011.07.026 Hanahan, 2011, Hallmarks of cancer: the next generation, Cell, 144, 646, 10.1016/j.cell.2011.02.013 Hechenbichler, 2004 Hellner, 2016, Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: discovery and validation studies, Ebiom, 10, 137, 10.1016/j.ebiom.2016.06.048 Honkaniemi, 1992, Fos and jun in rat central amygdaloid nucleus and paraventricular nucleus after stress, Neuroreport, 3, 849, 10.1097/00001756-199210000-00007 Huang, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 4, 44, 10.1038/nprot.2008.211 Huang, 2009, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Res., 37, 1, 10.1093/nar/gkn923 Ince, 2007, Transformation of different human breast epithelial cell types leads to distinct tumor phenotypes, Cancer Cell, 12, 160, 10.1016/j.ccr.2007.06.013 Ince, 2015, Characterization of twenty-five ovarian tumour cell lines that phenocopy primary tumours, Nat. Commun., 6, 7419, 10.1038/ncomms8419 Ishay-Ronen, 2019, Gain fat-lose metastasis: converting invasive breast cancer cells into adipocytes inhibits cancer metastasis, Cancer Cell, 35, 17, 10.1016/j.ccell.2018.12.002 Jiang, 2006, Expression of chemokine CXCL12 and its receptor CXCR4 in human epithelial ovarian cancer: an independent prognostic factor for tumor progression, Gynecol. Oncol., 103, 226, 10.1016/j.ygyno.2006.02.036 Kalluri, 2016, The biology and function of fibroblasts in cancer, Nat. Rev. Cancer, 16, 582, 10.1038/nrc.2016.73 Kang, 2004, Epithelial-mesenchymal transitions: twist in development and metastasis, Cell, 118, 277, 10.1016/j.cell.2004.07.011 Karatzoglou, 2004, kernlab- an S4Package for kernel methods in R, J. Stat. Softw., 11, 1 Karlan, 2014, POSTN/TGFBI-associated stromal signature predicts poor prognosis in serous epithelial ovarian cancer, Gynecol. Oncol., 132, 334, 10.1016/j.ygyno.2013.12.021 Kessler, 2015, The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids, Nat. Commun., 6, 8989, 10.1038/ncomms9989 Kim, 2012, High-grade serous ovarian cancer arises from fallopian tube in a mouse model, Proc. Natl. Acad. Sci. U S A, 109, 3921, 10.1073/pnas.1117135109 Klein, 2015, Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells, Cell, 161, 1187, 10.1016/j.cell.2015.04.044 Klos Dehring, 2013, Deuterosome-mediated centriole biogenesis, Dev. Cell, 27, 103, 10.1016/j.devcel.2013.08.021 Koboldt, 2013, Using VarScan 2 for germline variant calling and somatic mutation detection, Curr. Protoc. Bioinformatics, 44, 15.4.1, 10.1002/0471250953.bi1504s44 Konecny, 2014, Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer, J. Natl. Cancer Inst., 106, 11, 10.1093/jnci/dju249 Koshiyama, 2017, Subtypes of ovarian cancer and ovarian cancer screening, Diagnostics (Basel), 7, 12, 10.3390/diagnostics7010012 Kuhn, 2012, Ki-67 labeling index as an adjunct in the diagnosis of serous tubal intraepithelial carcinoma, Int. J. Gynecol. Pathol., 31, 416, 10.1097/PGP.0b013e31824cbeb4 Labidi-Galy, 2017, High grade serous ovarian carcinomas originate in the fallopian tube, Nat. Commun., 8, 1093, 10.1038/s41467-017-00962-1 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Law, 2014, voom: precision weights unlock linear model analysis tools for RNA-seq read counts, Genome Biol., 15, R29, 10.1186/gb-2014-15-2-r29 Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 Li, 2016, Myosins as fundamental components during tumorigenesis: diverse and indispensable, Oncotarget, 7, 46785, 10.18632/oncotarget.8800 Liao, 2014, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, 30, 923, 10.1093/bioinformatics/btt656 Liu, 2013, The IGF2 intronic miR-483 selectively enhances transcription from IGF2 fetal promoters and enhances tumorigenesis, Genes Dev., 27, 2543, 10.1101/gad.224170.113 Macintyre, 2018, Copy number signatures and mutational processes in ovarian carcinoma, Nat. Genet., 45, 1127 Macosko, 2015, Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets, Cell, 161, 1202, 10.1016/j.cell.2015.05.002 Mahalingaiah, 2015, Chronic oxidative stress leads to malignant transformation along with acquisition of stem cell characteristics, and epithelial to mesenchymal transition in human renal epithelial cells, J. Cell. Physiol., 230, 1916, 10.1002/jcp.24922 Marusyk, 2012, Intra-tumour heterogeneity: a looking glass for cancer?, Nat. Rev. Cancer, 12, 323, 10.1038/nrc3261 Mateescu, 2011, miR-141 and miR-200a act on ovarian tumorigenesis by controlling oxidative stress response, Nat. Med., 17, 1627, 10.1038/nm.2512 McCarthy, 2017, Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R, Bioinformatics, 33, 1179, 10.1093/bioinformatics/btw777 McGinnis, 2019, DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors, Cell Syst., 8, 329, 10.1016/j.cels.2019.03.003 McGranahan, 2017, Clonal heterogeneity and tumor evolution: past, present, and the future, Cell, 168, 613, 10.1016/j.cell.2017.01.018 McLean, 2005, The role of focal-adhesion kinase in cancer––a new therapeutic opportunity, Nat. Rev. Cancer, 5, 505, 10.1038/nrc1647 Meacham, 2013, Tumour heterogeneity and cancer cell plasticity, Nature, 501, 328, 10.1038/nature12624 Mora-Castilla, 2016, Miniaturization technologies for efficient single-cell library preparation for next-generation sequencing, J. Lab. Autom., 21, 557, 10.1177/2211068216630741 Nalepa, 2018, Fanconi anaemia and cancer: an intricate relationship, Nat. Rev. Cancer, 18, 168, 10.1038/nrc.2017.116 Newman, 2015, Robust enumeration of cell subsets from tissue expression profiles, Nat. Methods, 12, 453, 10.1038/nmeth.3337 Ng, A., Jordan, M., and Weiss, Y. (2002). On Spectral clustering: analysis and an algorithm. NIPS'01 Proceedings of the 14th International Conference on Neural Information Processing Systems: Natural and Synthetic, pp. 849–856. Nieto, 2016, EMT: 2016, Cell, 166, 21, 10.1016/j.cell.2016.06.028 Nowell, 1976, The clonal evolution of tumor cell populations, Science, 194, 23, 10.1126/science.959840 Obenchain, 2014, VariantAnnotation: a bioconductor package for exploration and annotation of genetic variants, Bioinformatics, 30, 2076, 10.1093/bioinformatics/btu168 Paik, 2012, Stem-like epithelial cells are concentrated in the distal end of the fallopian tube: a site for injury and serous cancer initiation, Stem Cells, 30, 2487, 10.1002/stem.1207 Patel, 2014, Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma, Science, 344, 1396, 10.1126/science.1254257 Perets, 2013, Transformation of the fallopian tube secretory epithelium leads to high-grade serous ovarian cancer in Brca;Tp53;Pten models, Cancer Cell, 24, 751, 10.1016/j.ccr.2013.10.013 Peters, 1986, Nature of "basal" and “reserve” cells in oviductal and cervical epithelium in man, J. Clin. Pathol., 39, 306, 10.1136/jcp.39.3.306 Phipson, 2016, Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression, Ann. Appl. Stat., 10, 946, 10.1214/16-AOAS920 Picelli, 2014, Full-length RNA-seq from single cells using Smart-seq2, Nat. Protoc., 9, 171, 10.1038/nprot.2014.006 Pils, 2012, Validating the impact of a molecular subtype in ovarian cancer on outcomes: a study of the OVCAD Consortium, Cancer Sci., 103, 1334, 10.1111/j.1349-7006.2012.02306.x Pisco, 2013, Non-Darwinian dynamics in therapy-induced cancer drug resistance, Nat. Commun., 4, 2467, 10.1038/ncomms3467 Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033 Rimmer, 2014, Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications, Nat. Genet., 46, 912, 10.1038/ng.3036 Ritchie, 2015, limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res., 43, e47, 10.1093/nar/gkv007 Satija, 2015, Spatial reconstruction of single-cell gene expression data, Nat. Biotechnol., 33, 495, 10.1038/nbt.3192 Schmidt, 2015, Stem-cell-like properties and epithelial plasticity arise as stable traits after transient Twist1 activation, Cell Rep., 10, 131, 10.1016/j.celrep.2014.12.032 Schwede, 2018, The impact of stroma on the discovery of molecular subtypes and prognostic gene signatures in serous ovarian cancer, bioRxiv, 14 Seirup, 2019, Tradeoff between more cells and higher read depth for single-cell RNA-seq spatial ordering analysis of the liver lobule, bioRxiv Singh, 2010, EMT, cancer stem cells and drug resistance: an emerging axis of evil in the war on cancer, Oncogene, 29, 4741, 10.1038/onc.2010.215 Soneson, 2018, Bias, robustness and scalability in single-cell differential expression analysis, Nat. Methods, 18, 255, 10.1038/nmeth.4612 Stuart, 2019, Comprehensive integration of single-cell data, Cell, 177, 1888, 10.1016/j.cell.2019.05.031 Svensson, 2019, Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq, bioRxiv Svensson, 2018, Exponential scaling of single-cell RNA-seq in the past decade, Nat. Protoc., 13, 599, 10.1038/nprot.2017.149 Tan, 2013, Functional genomics identifies five distinct molecular subtypes with clinical relevance and pathways for growth control in epithelial ovarian cancer, EMBO Mol. Med., 5, 1051, 10.1002/emmm.201201823 Tan, 1999, Metallothionein expression and nuclear size in benign, borderline, and malignant serous ovarian tumours, J. Pathol., 189, 60, 10.1002/(SICI)1096-9896(199909)189:1<60::AID-PATH387>3.0.CO;2-J Thomas, 2003, PANTHER: a library of protein families and subfamilies indexed by function, Genome Res., 13, 2129, 10.1101/gr.772403 Topham, 2018, Tissue-resident memory CD8+ T cells: from phenotype to function, Front Immunol., 9, 515, 10.3389/fimmu.2018.00515 Torre, 2018, Ovarian cancer statistics, 2018, CA Cancer J. Clin., 68, 284, 10.3322/caac.21456 Tothill, 2008, Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome, Clin. Cancer Res., 14, 5198, 10.1158/1078-0432.CCR-08-0196 van Deursen, 2014, The role of senescent cells in ageing, Nature, 509, 439, 10.1038/nature13193 Visvader, 2011, Cells of origin in cancer, Nature, 469, 314, 10.1038/nature09781 Wang, 2002, Cloning, characterization, and expression of calcyphosine 2, a novel human gene encoding an EF-hand Ca(2+)-binding protein, Biochem. Biophys. Res. Commun., 291, 414, 10.1006/bbrc.2002.6461 Wang, 2013, Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity, Nat. Cell Biol., 15, 274, 10.1038/ncb2697 Wu, 2016, Impact of oviductal versus ovarian epithelial cell of origin on ovarian endometrioid carcinoma phenotype in the mouse, J. Pathol., 240, 341, 10.1002/path.4783 Yang, 2004, Twist, a master regulator of morphogenesis, plays an essential role in tumor metastasis, Cell, 117, 927, 10.1016/j.cell.2004.06.006 Yin, 2016, EFEMP1 promotes ovarian cancer cell growth, invasion and metastasis via activated the AKT pathway, Oncotarget, 7, 47938, 10.18632/oncotarget.10296 Yoshihara, 2010, Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets, PLoS One, 5, e9615, 10.1371/journal.pone.0009615 Yoshihara, 2012, High-risk ovarian cancer based on 126-gene expression signature is uniquely characterized by downregulation of antigen presentation pathway, Clin. Cancer Res., 18, 1374, 10.1158/1078-0432.CCR-11-2725 Zafar, 2016, Monovar: single-nucleotide variant detection in single cells, Nat. Methods, 13, 505, 10.1038/nmeth.3835 Zhang, 2019, Cancer-associated stroma significantly contributes to the mesenchymal subtype signature of serous ovarian cancer, Gynecol. Oncol., 152, 368, 10.1016/j.ygyno.2018.11.014 Zhang, 2019, Both fallopian tube and ovarian surface epithelium are cells-of-origin for high-grade serous ovarian carcinoma, Nat. Commun., 10, 5367, 10.1038/s41467-019-13116-2 Ziegenhain, 2017, Comparative analysis of single-cell RNA sequencing methods, Mol. Cell, 65, 631, 10.1016/j.molcel.2017.01.023