Connecting past and present: single-cell lineage tracing

Adair JE, Enstrom MR (2021) A key toolbox for cellular barcoding analysis. Nat Comput Sci 1:251–252

Article  Google Scholar 

Alemany A, Florescu M, Baron CS, Peterson-Maduro J, van Oudenaarden A (2018) Whole-organism clone tracing using single-cell sequencing. Nature 556:108–112

CAS  Article  Google Scholar 

Andrews TS, Kiselev VY, McCarthy D, Hemberg M (2021) Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nat Protoc 16:1–9

CAS  Article  Google Scholar 

Baron CS, van Oudenaarden A (2019) Unravelling cellular relationships during development and regeneration using genetic lineage tracing. Nat Rev Mol Cell Biol 20:753–765

CAS  Article  Google Scholar 

Bergen V, Lange M, Peidli S, Wolf FA, Theis FJ (2020) Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotechnol 38:1408–1414

CAS  Article  Google Scholar 

Biddy BA, Kong W, Kamimoto K, Guo C, Waye SE, Sun T, Morris SA (2018) Single-cell mapping of lineage and identity in direct reprogramming. Nature 564:219–224

CAS  Article  Google Scholar 

Bizzotto S, Dou Y, Ganz J, Doan RN, Kwon M, Bohrson CL, Kim SN, Bae T, Abyzov A, Network NBSM (2021) Landmarks of human embryonic development inscribed in somatic mutations. Science 371:1249–1253

CAS  Article  Google Scholar 

Blanpain C, Simons BD (2013) Unravelling stem cell dynamics by lineage tracing. Nat Rev Mol Cell Biol 14:489–502

CAS  Article  Google Scholar 

Bock C, Boutros M, Camp JG, Clarke L, Clevers H, Knoblich JA, Liberali P, Regev A, Rios AC, Stegle O et al (2021) The organoid cell atlas. Nat Biotechnol 39:13–17

CAS  Article  Google Scholar 

Bowling S, Sritharan D, Osorio FG, Nguyen M, Cheung P, Rodriguez-Fraticelli A, Patel S, Yuan WC, Fujiwara Y, Li BE, et al (2020) An engineered CRISPR-Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells. Cell 181(6):1410–1422

Bramlett C, Jiang D, Nogalska A, Eerdeng J, Contreras J, Lu R (2020) Clonal tracking using embedded viral barcoding and high-throughput sequencing. Nat Protoc 15:1436–1458

CAS  Article  Google Scholar 

Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM (2018) The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science 360:eaar5780

Buckingham ME, Meilhac SM (2011) Tracing cells for tracking cell lineage and clonal behavior. Dev Cell 21:394–409

CAS  Article  Google Scholar 

Bystrykh LV, Belderbos ME (2016) Clonal analysis of cells with cellular barcoding: when numbers and sizes matter. Methods Mol Biol 1516:57–89

CAS  Article  Google Scholar 

Bystrykh LV, de Haan G, Verovskaya E (2014) Barcoded vector libraries and retroviral or lentiviral barcoding of hematopoietic stem cells. Methods Mol Biol 1185:345–360

Article  Google Scholar 

Camp JG, Treutlein B (2017) Human organomics: a fresh approach to understanding human development using single-cell transcriptomics. Development 144:1584–1587

CAS  Article  Google Scholar 

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ et al (2019) The single-cell transcriptional landscape of mammalian organogenesis. Nature 566:496–502

CAS  Article  Google Scholar 

Chan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG et al (2019) Molecular recording of mammalian embryogenesis. Nature 570:77–82

CAS  Article  Google Scholar 

Chow KK, Budde MW, Granados AA, Cabrera M, Yoon S, Cho S, Huang TH, Koulena N, Frieda K L, Cai L et al (2021) Imaging cell lineage with a synthetic digital recording system. Science 372:eabb3099

Clarke R, Terry AR, Pennington H, Hasty C, MacDougall MS, Regan M, Merrill BJ (2020) Sequential activation of guide RNAs to enable successive CRISPR-Cas9 activities. Mol Cell 81(2):226–238

Cotterell J, Vila-Cejudo M, Batlle-Morera L, Sharpe J (2020) Endogenous CRISPR/Cas9 arrays for scalable whole-organism lineage tracing. Development 147(9):dev184481

Denoth-Lippuner A, Jaeger BN, Liang T, Royall LN, Chie SE, Buthey K, Machado D, Korobeynyk VI, Kruse M, Munz CM et al (2021) Visualization of individual cell division history in complex tissues using iCOUNT. Cell Stem Cell 28(11):2020–2034

Drakhlis L, Biswanath S, Farr CM, Lupanow V, Teske J, Ritzenhoff K, Franke A, Manstein F, Bolesani E, Kempf H et al (2021) Human heart-forming organoids recapitulate early heart and foregut development. Nat Biotechnol 39:737–746

CAS  Article  Google Scholar 

Egli D, Zuccaro MV, Kosicki M, Church GM, Bradley A, Jasin M (2018) Inter-homologue repair in fertilized human eggs? Nature 560:E5–E7

CAS  Article  Google Scholar 

Eid A, Alshareef S, Mahfouz MM (2018) CRISPR base editors: genome editing without double-stranded breaks. Biochem J 475:1955–1964

CAS  Article  Google Scholar 

Espinosa-Medina, I, Garcia-Marques, J, Cepko, C, and Lee, T (2019) High-throughput dense reconstruction of cell lineages. Open Biol 9: 190229.

Espinoza DA, Mortlock RD, Koelle SJ, Wu C, Dunbar CE (2021) Interrogation of clonal tracking data using barcodetrackR. Nat Comput Sci 1:280–289

Article  Google Scholar 

Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF (2018) Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 360:eaar3131.

Feng J, DeWitt WS III, McKenna A, Simon N, Willis AD, Matsen FA IV (2021) Estimation of cell lineage trees by maximum-likelihood phylogenetics. Ann Appl Stat 15(343–362):320

Google Scholar 

Figueres-Onate M, Sanchez-Gonzalez R, Lopez-Mascaraque L (2020) Deciphering neural heterogeneity through cell lineage tracing. Cell Mol Life Sci 78(5):1971–1982

Forrow A, Schiebinger G (2021) LineageOT is a unified framework for lineage tracing and trajectory inference. Nat Commun 12:4940

CAS  Article  Google Scholar 

Frieda KL, Linton JM, Hormoz S, Choi J, Chow KK, Singer ZS, Budde MW, Elowitz MB, Cai L (2017) Synthetic recording and in situ readout of lineage information in single cells. Nature 541:107–111

CAS  Article  Google Scholar 

Garcia-Marques J, Yang CP, Espinosa-Medina I, Mok K, Koyama M, Lee T (2019) Unlimited genetic switches for cell-type-specific manipulation. Neuron 104: 227-238 e227.

Garcia-Marques J, Espinosa-Medina I, Ku KY, Yang CP, Koyama M, Yu HH, Lee T (2020) A programmable sequence of reporters for lineage analysis. Nat Neurosci 23(12):1618–1628

Garrison BS, Yant SR, Mikkelsen JG, Kay MA (2007) Postintegrative gene silencing within the Sleeping Beauty transposition system. Mol Cell Biol 27:8824–8833

CAS  Article  Google Scholar 

Gerrits A, Dykstra B, Kalmykowa OJ, Klauke K, Verovskaya E, Broekhuis MJ, de Haan G, Bystrykh LV (2010) Cellular barcoding tool for clonal analysis in the hematopoietic system. Blood 115:2610–2618

CAS  Article  Google Scholar 

Girskis K, Woodworth M (2016) Genetic Techniques for cell lineage tracing in the nervous system. Short Course 31.

Gong W, Granados AA, Hu J, Jones MG, Raz O, Salvador-Martinez I, Zhang H, Chow KK, Kwak IY, Retkute R et al (2021) Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees. Cell Syst 12(8):810–826

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J (2018) CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response. Nat Med 24:927–930

CAS  Article  Google Scholar 

Han X, Chen H, Huang D, Chen H, Fei L, Cheng C, Huang H, Yuan GC, Guo G (2018) Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. Genome Biol 19:47

CAS  Article  Google Scholar 

He J, Zhang G, Almeida AD, Cayouette M, Simons BD, Harris WA (2012) How variable clones build an invariant retina. Neuron 75:786–798

CAS  Article  Google Scholar 

He Z, Maynard A, Jain A, Gerber T, Petri R, Lin HC, Santel M, Ly K, Dupre JS, Sidow L et al (2022) Lineage recording in human cerebral organoids. Nat Methods 19:90–99

CAS  Article  Google Scholar 

Hofbauer P, Jahnel SM, Mendjan S (2021a) In vitro models of the human heart. Development 148(16):dev199672

Hofbauer P, Jahnel SM, Papai N, Giesshammer M, Deyett A, Schmidt C, Penc M, Tavernini K, Grdseloff N, Meledeth C, et al (2021b) Cardioids reveal self-organizing principles of human cardiogenesis. Cell 184:3299-3317 e3222.

Hsu YC (2015) Theory and practice of lineage tracing. Stem Cells 33:3197–3204

Article  Google Scholar 

Huang Q, Garrett A, Bose S, Blocker S, Rios AC, Clevers H, Shen X (2021) The frontier of live tissue imaging across space and time. Cell Stem Cell 28:603–622

CAS  Article  Google Scholar 

Hwang B, Lee JH, Bang D (2018) Single-cell RNA sequencing technologies and bioinformatics pipelines. Exp Mol Med 50:96

Article  Google Scholar 

Hwang B, Lee W, Yum SY, Jeon Y, Cho N, Jang G, Bang D (2019) Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements. Nat Commun 10:1234

Article  Google Scholar 

Ihry RJ, Worringer KA, Salick MR, Frias E, Ho D, Theriault K, Kommineni S, Chen J, Sondey M, Ye C et al (2018) p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat Med 24:939–946

CAS  Article  Google Scholar 

Jones MG, Khodaverdian A, Quinn JJ, Chan MM, Hussmann JA, Wang R, Xu C, Weissman JS, Yosef N (2020) Inference of single-cell phylogenies from lineage tracing data using Cassiopeia. Genome Biol 21:92

Article  Google Scholar 

Kalhor K, Church GM (2019) Single-cell CRISPR-based lineage tracing in mice. Biochemistry 58:4775–4776

CAS  Article  Google Scholar 

Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM (2018) Developmental barcoding of whole mouse via homing CRISPR. Science 361.

Kebschull JM, Zador AM (2018) Cellular barcoding: lineage tracing, screening and beyond. Nat Methods 15:871–879

CAS  Article  Google Scholar 

Kester L, van Oudenaarden A (2018) Single-cell transcriptomics meets lineage tracing. Cell Stem Cell 23:166–179

CAS  Article  Google Scholar 

Kim IS, Wu J, Rahme GJ, Battaglia S, Dixit A, Gaskell E, Chen H, Pinello L, Bernstein BE (2020) Parallel single-cell RNA-Seq and genetic recording reveals lineage decisions in developing embryoid bodies. Cell Rep 33:108222.

Klein AM, Simons BD (2011) Universal patterns of stem cell fate in cycling adult tissues. Development 138:3103–3111

CAS  Article  Google Scholar 

Klein AM, Nakagawa T, Ichikawa R, Yoshida S, Simons BD (2010) Mouse germ line stem cells undergo rapid and stochastic turnover. Cell Stem Cell 7:214–224

CAS  Article  Google Scholar 

Kong W, Biddy BA, Kamimoto K, Amrute JM, Butka EG, Morris SA (2020) Cell tagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution. Nat Protoc 15:750–772

CAS  Article  Google Scholar 

Kwon GS, Viotti M, Hadjantonakis AK (2008) The endoderm of the mouse embryo arises by dynamic widespread intercalation of embryonic and extraembryonic lineages. Dev Cell 15:509–520

CAS  Article  Google Scholar 

La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, Lidschreiber K, Kastriti ME, Lonnerberg P, Furlan A et al (2018) RNA velocity of single cells. Nature 560:494–498

Article  Google Scholar 

Lafzi A, Moutinho C, Picelli S, Heyn H (2018) Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies. Nat Protoc 13:2742–2757

CAS  Article  Google Scholar 

Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP, Knoblich JA (2013) Cerebral organoids model human brain development and microcephaly. Nature 501:373–379

CAS  Article  Google Scholar 

Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E et al (2021) Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat Biotechnol 39:451–461

CAS  Article  Google Scholar 

Lederer AR, La Manno G (2020) The emergence and promise of single-cell temporal-omics approaches. Curr Opin Biotechnol 63:70–78

CAS  Article 

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