Single-cell technologies and analyses in hematopoiesis and hematological malignancies

Stubbington, 2017, Single-cell transcriptomics to explore the immune system in health and disease, Science, 358, 58, 10.1126/science.aan6828 Svensson, 2018, Exponential scaling of single-cell RNA-seq in the past decade, Nat Protoc, 13, 599, 10.1038/nprot.2017.149 Lodato, 2018, Aging and neurodegeneration are associated with increased mutations in single human neurons, Science, 359, 555, 10.1126/science.aao4426 Ludwig, 2019, Lineage tracing in humans enabled by mitochondrial mutations and single-cell genomics, Cell, 176, 1325, 10.1016/j.cell.2019.01.022 Paul, 2015, Transcriptional heterogeneity and lineage commitment in myeloid progenitors, Cell, 163, 1663, 10.1016/j.cell.2015.11.013 Velten, 2017, Human haematopoietic stem cell lineage commitment is a continuous process, Nat Cell Biol, 19, 271, 10.1038/ncb3493 Genovese, 2014, Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence, N Engl J Med, 371, 2477, 10.1056/NEJMoa1409405 Jan, 2012, Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia, Sci Transl Med, 4, 10.1126/scitranslmed.3004315 Miles, 2020, Single-cell mutation analysis of clonal evolution in myeloid malignancies, Nature, 587, 477, 10.1038/s41586-020-2864-x Jerby-Arnon, 2018, A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade, Cell, 175, 10.1016/j.cell.2018.09.006 Tang, 2009, mRNA-Seq whole-transcriptome analysis of a single cell, Nat Methods, 6, 377, 10.1038/nmeth.1315 Jaitin, 2014, Massively parallel single-cell RNA-Seq for marker-free decomposition of tissues into cell types, Science, 343, 776, 10.1126/science.1247651 Picelli, 2017, Single-cell RNA-sequencing: the future of genome biology is now, RNA Biol, 14637 Macosko, 2015, Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets, Cell, 161, 1202, 10.1016/j.cell.2015.05.002 Zheng, 2017, Massively parallel digital transcriptional profiling of single cells, Nat Commun, 8, 14049, 10.1038/ncomms14049 Islam, 2014, Quantitative single-cell RNA-seq with unique molecular identifiers, Nat Methods, 11, 163, 10.1038/nmeth.2772 Ramsköld, 2012, Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells, Nat Biotechnol, 30, 777, 10.1038/nbt.2282 Picelli, 2014, Full-length RNA-seq from single cells using Smart-seq2, Nat Protoc, 9, 171, 10.1038/nprot.2014.006 Hashimshony, 2012, CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification, Cell Rep, 2, 666, 10.1016/j.celrep.2012.08.003 Hashimshony, 2016, CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq, Genome Biol, 17, 77, 10.1186/s13059-016-0938-8 Erhard, 2019, scSLAM-seq reveals core features of transcription dynamics in single cells, Nature, 571, 419, 10.1038/s41586-019-1369-y Hendriks, 2019, NASC-seq monitors RNA synthesis in single cells, Nat Commun, 10, 3138, 10.1038/s41467-019-11028-9 Qiu, 2020, Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq, Nat Methods, 17, 991, 10.1038/s41592-020-0935-4 Sheng, 2017, Effective detection of variation in single-cell transcriptomes using MATQ-seq, Nat Methods, 14, 267, 10.1038/nmeth.4145 Fan, 2015, Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos, Genome Biol, 16, 148, 10.1186/s13059-015-0706-1 Hayashi, 2018, Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, Nat Commun, 9, 619, 10.1038/s41467-018-02866-0 Verboom, 2019, SMARTer single cell total RNA sequencing, Nucleic Acids Res, 47, e93, 10.1093/nar/gkz535 Hu, 2020, Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation, Nat Commun, 11, 5148, 10.1038/s41467-020-18976-7 Lebrigand, 2020, High throughput error corrected Nanopore single cell transcriptome sequencing, Nat Commun, 11, 4025, 10.1038/s41467-020-17800-6 Hagemann-Jensen, 2020, Single-cell RNA counting at allele and isoform resolution using Smart-seq3, Nat Biotechnol, 38, 708, 10.1038/s41587-020-0497-0 Keren-Shaul, 2019, MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing, Nat Protoc, 14, 1841, 10.1038/s41596-019-0164-4 Schraivogel, 2020, Targeted Perturb-seq enables genome-scale genetic screens in single cells, Nat Methods, 17, 629, 10.1038/s41592-020-0837-5 Srivatsan, 2020, Massively multiplex chemical transcriptomics at single-cell resolution, Science, 367, 45, 10.1126/science.aax6234 Cusanovich, 2015, Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing, Science, 348, 910, 10.1126/science.aab1601 Buenrostro, 2015, Single-cell chromatin accessibility reveals principles of regulatory variation, Nature, 523, 486, 10.1038/nature14590 Mezger, 2018, High-throughput chromatin accessibility profiling at single-cell resolution, Nat Commun, 9, 3647, 10.1038/s41467-018-05887-x Satpathy, 2018, Transcript-indexed ATAC-seq for precision immune profiling, Nat Med, 24, 580, 10.1038/s41591-018-0008-8 Rubin, 2019, Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks, Cell, 176, 10.1016/j.cell.2018.11.022 Chen, 2018, A rapid and robust method for single cell chromatin accessibility profiling, Nat Commun, 9, 5345, 10.1038/s41467-018-07771-0 Satpathy, 2019, Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion, Nat Biotechnol, 37, 925, 10.1038/s41587-019-0206-z Lareau, 2021, Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling, Nat Biotechnol, 451, 10.1038/s41587-020-0645-6 Lareau, 2019, Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility, Nat Biotechnol, 37, 916, 10.1038/s41587-019-0147-6 Gao, 2020, Genome-wide profiling of nucleosome position and chromatin accessibility in single cells using scMNase-seq, Nat Protoc, 15, 68, 10.1038/s41596-019-0243-6 Skene, 2017, An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites, Elife, 6, e21856, 10.7554/eLife.21856 Ku, 2019, Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification, Nat Methods, 16, 323, 10.1038/s41592-019-0361-7 Chen, 2018, Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity, Nat Commun, 9, 4590, 10.1038/s41467-018-07115-y Reyes, 2019, Simultaneous profiling of gene expression and chromatin accessibility in single cells, Adv Biosyst, 3, 10.1002/adbi.201900065 Vitak, 2017, Sequencing thousands of single-cell genomes with combinatorial indexing, Nat Methods, 14, 302, 10.1038/nmeth.4154 Zahn, 2017, Scalable whole-genome single-cell library preparation without preamplification, Nat Methods, 14, 167, 10.1038/nmeth.4140 Laks, 2019, Clonal decomposition and DNA replication states defined by scaled single-cell genome sequencing, Cell, 179, 10.1016/j.cell.2019.10.026 Pellegrino, 2018, High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics, Genome Res, 28, 1345, 10.1101/gr.232272.117 Han, 2018, SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells, Genome Res, 28, 75, 10.1101/gr.223263.117 Hou, 2016, Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas, Cell Res, 26, 304, 10.1038/cr.2016.23 Dey, 2015, Integrated genome and transcriptome sequencing of the same cell, Nat Biotechnol, 33, 285, 10.1038/nbt.3129 Rodriguez-Meira, 2019, Unravelling intratumoral heterogeneity through high-sensitivity single-cell mutational analysis and parallel RNA sequencing, Mol Cell, 73, 10.1016/j.molcel.2019.01.009 Nam, 2019, Somatic mutations and cell identity linked by genotyping of transcriptomes, Nature, 571, 355, 10.1038/s41586-019-1367-0 Kang, 2016, Single cell-resolution Western blotting, Nat Protoc, 11, 1508, 10.1038/nprot.2016.089 Agasti, 2012, Photocleavable DNA barcode–antibody conjugates allow sensitive and multiplexed protein analysis in single cells, J Am Chem Soc, 134, 18499, 10.1021/ja307689w Wang, 2019, Highly multiplexed profiling of cell surface proteins on single circulating tumor cells based on antibody and cellular barcoding, Anal Bioanal Chem, 411, 5373, 10.1007/s00216-019-01666-9 Yang, 2016, Single-cell, multiplexed protein detection of rare tumor cells based on a beads-on-barcode antibody microarray, Anal Chem, 88, 5373, 10.1021/acs.analchem.6b03086 Shahi, 2017, Abseq: ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding, Sci Rep, 7, 44447, 10.1038/srep44447 Bendall, 2011, Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum, Science, 332, 687, 10.1126/science.1198704 Budnik, 2018, SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation, Genome Biol, 19, 161, 10.1186/s13059-018-1547-5 Dou, 2019, High-throughput single cell proteomics enabled by multiplex isobaric labeling in a nanodroplet sample preparation platform, Anal Chem, 91, 13119, 10.1021/acs.analchem.9b03349 Specht, 2021, Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2, Genome Biol, 22, 50, 10.1186/s13059-021-02267-5 Shekaramiz, 2018, Protein fishing from single live cells, J Nanobiotechnol, 16, 67, 10.1186/s12951-018-0395-5 Pham, 2021, Single-cell proteomic analysis, WIREs Mech Dis, 13, e1503, 10.1002/wsbm.1503 Kharchenko, 2014, Bayesian approach to single-cell differential expression analysis, Nat Methods, 11, 740, 10.1038/nmeth.2967 Zappia, 2018, Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database, PLOS Comput Biol, 14, 10.1371/journal.pcbi.1006245 Luecken, 2019, Current best practices in single-cell RNA-seq analysis: a tutorial, Mol Syst Biol, 15, e8746, 10.15252/msb.20188746 Vieth, 2019, A systematic evaluation of single cell RNA-seq analysis pipelines, Nat Commun, 10, 4667, 10.1038/s41467-019-12266-7 Parekh, 2018, zUMIs—a fast and flexible pipeline to process RNA sequencing data with UMIs, Gigascience., 7, giy059, 10.1093/gigascience/giy059 Petukhov, 2018, dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments, Genome Biol, 19, 78, 10.1186/s13059-018-1449-6 Iacono, 2018, bigSCale: an analytical framework for big-scale single-cell data, Genome Res, 28, 878, 10.1101/gr.230771.117 Vallejos, 2015, Bayesian analysis of single-cell sequencing data, PLOS Comput Biol, 11, 10.1371/journal.pcbi.1004333 Bacher, 2017, SCnorm: robust normalization of single-cell RNA-seq data, Nat Methods, 14, 584, 10.1038/nmeth.4263 Risso, 2018, A general and flexible method for signal extraction from single-cell RNA-seq data, Nat Commun, 9, 284, 10.1038/s41467-017-02554-5 Anders, 2010, Differential expression analysis for sequence count data, Genome Biol, 11, R106, 10.1186/gb-2010-11-10-r106 Lun, 2016, Pooling across cells to normalize single-cell RNA sequencing data with many zero counts, Genome Biol, 17, 75, 10.1186/s13059-016-0947-7 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, 15, 550, 10.1186/s13059-014-0550-8 Hafemeister, 2019, Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression, Genome Biol, 20, 296, 10.1186/s13059-019-1874-1 Butler, 2018, Integrating single-cell transcriptomic data across different conditions, technologies, and species, Nat Biotechnol, 36, 411, 10.1038/nbt.4096 Stuart, 2019, Integrative single-cell analysis, Nat Rev Genet, 20, 257, 10.1038/s41576-019-0093-7 Korsunsky, 2019, Fast, sensitive and accurate integration of single-cell data with Harmony, Nat Methods, 16, 1289, 10.1038/s41592-019-0619-0 Li, 2017, Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors, Nat Genet, 49, 708, 10.1038/ng.3818 Žurauskienė, 2016, pcaReduce: hierarchical clustering of single cell transcriptional profiles, BMC Bioinformatics, 17, 140, 10.1186/s12859-016-0984-y Wolf, 2018, SCANPY: large-scale single-cell gene expression data analysis, Genome Biol, 19, 15, 10.1186/s13059-017-1382-0 Trapnell, 2014, The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells, Nat Biotechnol, 32, 381, 10.1038/nbt.2859 Wolf, 2019, PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells, Genome Biol, 20, 59, 10.1186/s13059-019-1663-x La Manno, 2018, RNA velocity of single cells, Nature, 560, 494, 10.1038/s41586-018-0414-6 Bergen, 2020, Generalizing RNA velocity to transient cell states through dynamical modeling, Nat Biotechnol, 38, 1408, 10.1038/s41587-020-0591-3 Álvarez-Errico, 2015, Epigenetic control of myeloid cell differentiation, identity and function, Nat Rev Immunol, 15, 7, 10.1038/nri3777 Watcham, 2019, New insights into hematopoietic differentiation landscapes from single-cell RNA sequencing, Blood, 133, 1415, 10.1182/blood-2018-08-835355 Akashi, 2000, A clonogenic common myeloid progenitor that gives rise to all myeloid lineages, Nature, 404, 193, 10.1038/35004599 Orkin, 2008, Hematopoiesis: an evolving paradigm for stem cell biology, Cell, 132, 631, 10.1016/j.cell.2008.01.025 Liggett, 2020, Unraveling hematopoiesis through the lens of genomics, Cell, 182, 1384, 10.1016/j.cell.2020.08.030 Regev, 2017, The human cell atlas, Elife, 6, e27041, 10.7554/eLife.27041 Hay, 2018, The Human Cell Atlas bone marrow single-cell interactive web portal, Exp Hematol, 68, 51, 10.1016/j.exphem.2018.09.004 Zheng, 2018, Molecular transitions in early progenitors during human cord blood hematopoiesis, Mol Syst Biol, 14, e8041, 10.15252/msb.20178041 Karamitros, 2018, Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells, Nat Immunol, 19, 85, 10.1038/s41590-017-0001-2 Pellin, 2019, A comprehensive single cell transcriptional landscape of human hematopoietic progenitors, Nat Commun, 10, 2395, 10.1038/s41467-019-10291-0 Schep, 2017, chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data, Nat Methods, 14, 975, 10.1038/nmeth.4401 Buenrostro, 2018, Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation, Cell, 173, 10.1016/j.cell.2018.03.074 Bendall, 2014, Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development, Cell, 157, 714, 10.1016/j.cell.2014.04.005 Glass, 2020, An integrated multi-omic single-cell atlas of human B cell identity, Immunity, 53, 10.1016/j.immuni.2020.06.013 King, 2021, Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics, Sci Immunol, 6, eabe6291, 10.1126/sciimmunol.abe6291 Park, 2020, A cell atlas of human thymic development defines T cell repertoire formation, Science, 367, eaay3224, 10.1126/science.aay3224 Le, 2020, Single-cell RNA-Seq mapping of human thymopoiesis reveals lineage specification trajectories and a commitment spectrum in T cell development, Immunity, 52, 10.1016/j.immuni.2020.05.010 Villani, 2017, Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors, Science, 356, eaah4573, 10.1126/science.aah4573 van Galen, 2019, Single-cell RNA-Seq reveals AML hierarchies relevant to disease progression and immunity, Cell, 176, 10.1016/j.cell.2019.01.031 Morita, 2020, Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics, Nat Commun, 11, 5327, 10.1038/s41467-020-19119-8 Giustacchini, 2017, Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia, Nat Med, 23, 692, 10.1038/nm.4336 Wiseman, 2020, Chronic myelomonocytic leukaemia stem cell transcriptomes anticipate disease morphology and outcome, EBioMedicine, 58, 10.1016/j.ebiom.2020.102904 Acha, 2021, Analysis of intratumoral heterogeneity in myelodysplastic syndromes with isolated del(5q) using a single cell approach, Cancers (Basel), 13, 841, 10.3390/cancers13040841 Gawad, 2014, Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics, Proc Natl Acad Sci USA, 111, 17947, 10.1073/pnas.1420822111 Good, 2018, Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse, Nat Med, 24, 474, 10.1038/nm.4505 Anderson, 2020, The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution, Sci Rep, 10, 19173, 10.1038/s41598-020-76157-4 Rabilloud, 2021, Single-cell profiling identifies pre-existing CD19-negative subclones in a B-ALL patient with CD19-negative relapse after CAR-T therapy, Nat Commun, 12, 865, 10.1038/s41467-021-21168-6 Milpied, 2018, Human germinal center transcriptional programs are de-synchronized in B cell lymphoma, Nat Immunol, 19, 1013, 10.1038/s41590-018-0181-4 Roider, 2020, Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels, Nat Cell Biol, 22, 896, 10.1038/s41556-020-0532-x Albertí-Servera, 2021, Single-cell DNA amplicon sequencing reveals clonal heterogeneity and evolution in T-cell acute lymphoblastic leukemia, Blood, 137, 801, 10.1182/blood.2020006996 Borcherding, 2019, Single-cell profiling of cutaneous T-cell lymphoma reveals underlying heterogeneity associated with disease progression, Clin Cancer Res, 25, 2996, 10.1158/1078-0432.CCR-18-3309 Kriangkum, 2015, Single-cell analysis and next-generation immuno-sequencing show that multiple clones persist in patients with chronic lymphocytic leukemia, PLoS One, 10, 10.1371/journal.pone.0137232 Wang, 2017, Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia, Genome Res, 27, 1300, 10.1101/gr.217331.116 Myhrvold, 2018, Single cell profiling of phospho-protein levels in chronic lymphocytic leukemia, Oncotarget, 9, 9273, 10.18632/oncotarget.23949 Gaiti, 2019, Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia, Nature, 569, 576, 10.1038/s41586-019-1198-z Ledergor, 2018, Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma, Nat Med, 24, 1867, 10.1038/s41591-018-0269-2 Jang, 2019, Molecular signatures of multiple myeloma progression through single cell RNA-Seq, Blood Cancer J, 9, 2, 10.1038/s41408-018-0160-x Maia, 2020, Biological and clinical significance of dysplastic hematopoiesis in patients with newly diagnosed multiple myeloma, Blood, 135, 2375, 10.1182/blood.2019003382 Sarkar, 2017, Dynamic analysis of human natural killer cell response at single-cell resolution in B-Cell non-Hodgkin lymphoma, Front Immunol, 8, 1736, 10.3389/fimmu.2017.01736 Mangano, 2019, Precise detection of genomic imbalances at single-cell resolution reveals intra-patient heterogeneity in Hodgkin's lymphoma, Blood Cancer J, 9, 92, 10.1038/s41408-019-0256-y Aoki, 2019, Single-cell transcriptome analysis reveals disease-defining T-cell subsets in the tumor microenvironment of classic Hodgkin lymphoma, Cancer Discov, 10, 406, 10.1158/2159-8290.CD-19-0680 Fisher, 2020, Unraveling the architecture of classic Hodgkin lymphoma one cell at a time, Cancer Discov, 10, 342, 10.1158/2159-8290.CD-19-1538 Luo, 2017, Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex, Science, 357, 600, 10.1126/science.aan3351 Mulqueen, 2018, Highly scalable generation of DNA methylation profiles in single cells, Nat Biotechnol, 36, 428, 10.1038/nbt.4112 Clark, 2017, Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq), Nat Protoc, 12, 534, 10.1038/nprot.2016.187 Luo, 2018, Robust single-cell DNA methylome profiling with snmC-seq2, Nat Commun, 9, 3824, 10.1038/s41467-018-06355-2