A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.
Journal
Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904
Informations de publication
Date de publication:
01 2023
01 2023
Historique:
received:
26
07
2022
accepted:
25
10
2022
pubmed:
22
12
2022
medline:
18
1
2023
entrez:
21
12
2022
Statut:
ppublish
Résumé
Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new 'gland-associated immune niche' has implications for respiratory health.
Identifiants
pubmed: 36543915
doi: 10.1038/s41588-022-01243-4
pii: 10.1038/s41588-022-01243-4
pmc: PMC9839452
doi:
Substances chimiques
Immunoglobulin A
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
66-77Subventions
Organisme : Wellcome Trust
ID : WT211276/Z/18/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 206194
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/5005579/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/W00111X/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S005579/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 211276
Pays : United Kingdom
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2022. The Author(s).
Références
Angelidis, I. et al. An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nat. Commun. 10, 963 (2019).
doi: 10.1038/s41467-019-08831-9
Kato, A., Hulse, K. E., Tan, B. K. & Schleimer, R. P. B-lymphocyte lineage cells and the respiratory system. J. Allergy Clin. Immunol. 131, 933–957 (2013).
doi: 10.1016/j.jaci.2013.02.023
Schiller, H. B. et al. The human lung cell atlas: a high-resolution reference map of the human lung in health and disease. Am. J. Respir. Cell Mol. Biol. 61, 31–41 (2019).
doi: 10.1165/rcmb.2018-0416TR
Ardini-Poleske, M. E. et al. LungMAP: the molecular atlas of lung development program. Am. J. Physiol. Lung Cell. Mol. Physiol. 313, L733–L740 (2017).
doi: 10.1152/ajplung.00139.2017
Wilbrey-Clark, A., Roberts, K. & Teichmann, S. A. Cell atlas technologies and insights into tissue architecture. Biochem. J. 477, 1427–1442 (2020).
doi: 10.1042/BCJ20190341
Plasschaert, L. W. et al. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377–381 (2018).
doi: 10.1038/s41586-018-0394-6
Vieira Braga, F. A. et al. A cellular census of human lungs identifies novel cell states in health and in asthma. Nat. Med. 25, 1153–1163 (2019).
doi: 10.1038/s41591-019-0468-5
Adams, T. S. et al. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Sci. Adv. 6, eaba1983 (2020).
doi: 10.1126/sciadv.aba1983
Goldfarbmuren, K. C. et al. Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium. Nat. Commun. 11, 2485 (2020).
doi: 10.1038/s41467-020-16239-z
Sikkema, L. et al. An integrated cell atlas of the human lung in health and disease. Preprint at bioRxiv https://doi.org/10.1101/2022.03.10.483747 (2022).
Travaglini, K. J. et al. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature 587, 619–625 (2020).
doi: 10.1038/s41586-020-2922-4
Sun, X. et al. A census of the lung: CellCards from LungMAP. Dev. Cell 57, 112–145 (2022).
doi: 10.1016/j.devcel.2021.11.007
Kleshchevnikov et al. Cell2location maps fine-grained cell types in spatial transcriptomics. Nat Biotechnol 40, 661–671 https://doi.org/10.1038/s41587-021-01139-4 (2022).
Kapoor, V. N. et al. Gremlin 1
doi: 10.1038/s41590-021-00920-6
Wang, X. et al. Follicular dendritic cells help establish follicle identity and promote B cell retention in germinal centers. J. Exp. Med. 208, 2497–2510 (2011).
doi: 10.1084/jem.20111449
Marshall, A. J. et al. FDC-SP, a novel secreted protein expressed by follicular dendritic cells. J. Immunol. 169, 2381–2389 (2002).
doi: 10.4049/jimmunol.169.5.2381
Elliot, J. G. et al. Aggregations of lymphoid cells in the airways of nonsmokers, smokers, and subjects with asthma. Am. J. Respir. Crit. Care Med. 169, 712–718 (2004).
doi: 10.1164/rccm.200308-1167OC
Elmentaite, R., Kumasaka, N., Roberts, K. et al. Cells of the human intestinal tract mapped across space and time. Nature 597, 250–255 (2021). https://doi.org/10.1038/s41586-021-03852-1
Baarsma, H. A. et al. Noncanonical WNT-5A signaling impairs endogenous lung repair in COPD. J. Exp. Med. 214, 143–163 (2017).
doi: 10.1084/jem.20160675
Castaldi, P. J. et al. Genome-wide association identifies regulatory loci associated with distinct local histogram emphysema patterns. Am. J. Respir. Crit. Care Med. 190, 399–409 (2014).
doi: 10.1164/rccm.201403-0569OC
Spira, A. et al. Gene expression profiling of human lung tissue from smokers with severe emphysema. Am. J. Respir. Cell Mol. Biol. 31, 601–610 (2004).
doi: 10.1165/rcmb.2004-0273OC
Doherty, L. & Sanjay, A. LGRs in skeletal tissues: an emerging role for Wnt-associated adult stem cell markers in bone. JBMR 4, e10380 (2020).
Bochukova, E. G. et al. Rare mutations of FGFR2 causing Apert syndrome: identification of the first partial gene deletion, and an Alu element insertion from a new subfamily. Hum. Mutat. 30, 204–211 (2009).
doi: 10.1002/humu.20825
Adam, M. P. et al. (eds.) Gene Reviews (University of Washington, 2008).
Chen, B., Banton, M. C., Singh, L., Parkinson, D. B. & Dun, X.-P. Single cell transcriptome data analysis defines the heterogeneity of peripheral nerve cells in homeostasis and regeneration. Front. Cell. Neurosci. 15, 624826 (2021).
doi: 10.3389/fncel.2021.624826
Gerber, D. et al. Transcriptional profiling of mouse peripheral nerves to the single-cell level to build a sciatic nerve ATlas (SNAT). eLife 10, e58591 (2021).
doi: 10.7554/eLife.58591
Renthal, W. et al. Transcriptional reprogramming of distinct peripheral sensory neuron subtypes after axonal injury. Neuron 108, 128–144 (2020).
doi: 10.1016/j.neuron.2020.07.026
Wolbert, J. et al. Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity. Proc. Natl Acad. Sci. USA 117, 9466–9476 (2020).
doi: 10.1073/pnas.1912139117
Adameyko, I. & Ernfors, P. Nerves do it again: donation of mesenchymal cells for tissue regeneration. Cell Stem Cell 24, 195–197 (2019).
doi: 10.1016/j.stem.2019.01.006
Murfee, W. L., Skalak, T. C. & Peirce, S. M. Differential arterial/venous expression of NG2 proteoglycan in perivascular cells along microvessels: identifying a venule-specific phenotype. Microcirculation 12, 151–160 (2005).
doi: 10.1080/10739680590904955
Proebstl, D. et al. Pericytes support neutrophil subendothelial cell crawling and breaching of venular walls in vivo. J. Exp. Med. 209, 1219–1234 (2012).
doi: 10.1084/jem.20111622
Madissoon, E. et al. scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation. Genome Biol. 21, 1 (2019).
doi: 10.1186/s13059-019-1906-x
Nowicki-Osuch, K. et al. Molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition. Science 373, 760–767 (2021).
doi: 10.1126/science.abd1449
Widdicombe, J. H. & Wine, J. J. Airway gland structure and function. Physiol. Rev. 95, 1241–1319 (2015).
doi: 10.1152/physrev.00039.2014
Meyrick, B., Sturgess, J. M. & Reid, L. A reconstruction of the duct system and secretory tubules of the human bronchial submucosal gland. Thorax 24, 729–736 (1969).
doi: 10.1136/thx.24.6.729
Hegab, A. E. et al. Isolation and in vitro characterization of basal and submucosal gland duct stem/progenitor cells from human proximal airways. Stem Cells Transl. Med. 1, 719–724 (2012).
doi: 10.5966/sctm.2012-0056
Tata, A. et al. Myoepithelial cells of submucosal glands can function as reserve stem cells to regenerate airways after injury. Cell Stem Cell 22, 668–683 (2018).
doi: 10.1016/j.stem.2018.03.018
Hegab, A. E. et al. Novel stem/progenitor cell population from murine tracheal submucosal gland ducts with multipotent regenerative potential. Stem Cells 29, 1283–1293 (2011).
doi: 10.1002/stem.680
Young, A. M. H. et al. A map of transcriptional heterogeneity and regulatory variation in human microglia. Nat. Genet. 53, 861–868 (2021).
doi: 10.1038/s41588-021-00875-2
Borchers, M. T. et al. The role of T cells in the regulation of acrolein-induced pulmonary inflammation and epithelial-cell pathology. Res. Rep. Health Eff. Inst.(146), 5–29 (2009).
Motz, G. T. et al. Chronic cigarette smoke exposure primes NK cell activation in a mouse model of chronic obstructive pulmonary disease. J. Immunol. 184, 4460–4469 (2010).
doi: 10.4049/jimmunol.0903654
Wortham, B. W., Eppert, B. L., Flury, J. L., Morgado Garcia, S. & Borchers, M. T. TLR and NKG2D signaling pathways mediate CS-induced pulmonary pathologies. PLoS ONE 8, e78735 (2013).
doi: 10.1371/journal.pone.0078735
Deprez, M. et al. A single-cell atlas of the human healthy airways. Am. J. Respir. Crit. Care Med. 202, 1636–1645 (2020).
doi: 10.1164/rccm.201911-2199OC
Chakarov, S. et al. Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches. Science 363, eaau0964 (2019).
doi: 10.1126/science.aau0964
Evren, E. et al. Distinct developmental pathways from blood monocytes generate human lung macrophage diversity. Immunity 54, 259–275 (2021).
doi: 10.1016/j.immuni.2020.12.003
Pirzgalska, R. M. et al. Sympathetic neuron-associated macrophages contribute to obesity by importing and metabolizing norepinephrine. Nat. Med. 23, 1309–1318 (2017).
doi: 10.1038/nm.4422
Wolf, Y. et al. Brown-adipose-tissue macrophages control tissue innervation and homeostatic energy expenditure. Nat. Immunol. 18, 665–674 (2017).
doi: 10.1038/ni.3746
Hulsmans, M. et al. Macrophages facilitate electrical conduction in the heart. Cell 169, 510–522 (2017).
doi: 10.1016/j.cell.2017.03.050
Chang, D., Sharma, L. & Dela Cruz, C. S. Chitotriosidase: a marker and modulator of lung disease. Eur. Respir. Rev. 29, 190143 (2020).
doi: 10.1183/16000617.0143-2019
Artur Krężel, W. M. The functions of metamorphic metallothioneins in zinc and copper metabolism. Int. J. Mol. Sci. 18, 1237 (2017).
doi: 10.3390/ijms18061237
Subramanian Vignesh, K. & Deepe, G. S. Jr. Metallothioneins: emerging modulators in immunity and infection. Int. J. Mol. Sci. 18, 2197 (2017).
doi: 10.3390/ijms18102197
Takano, H. et al. Protective role of metallothionein in acute lung injury induced by bacterial endotoxin. Thorax 59, 1057–1062 (2004).
doi: 10.1136/thx.2004.024232
Mukaida, N. Pathophysiological roles of interleukin-8/CXCL8 in pulmonary diseases. Am. J. Physiol. Lung Cell. Mol. Physiol. 284, L566–L577 (2003).
doi: 10.1152/ajplung.00233.2002
Reynolds, G. et al. Developmental cell programs are co-opted in inflammatory skin disease. Science 371, eaba6500 (2021).
doi: 10.1126/science.aba6500
Hadley, G. A., Bartlett, S. T., Via, C. S., Rostapshova, E. A. & Moainie, S. The epithelial cell-specific integrin, CD103 (alpha E integrin), defines a novel subset of alloreactive CD8
doi: 10.4049/jimmunol.159.8.3748
Dominguez-Conde et al. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science (2022)Vol 376, Issue 6594. https://doi.org/10.1126/science.abl5197
Piet, B. et al. CD8 T cells with an intraepithelial phenotype upregulate cytotoxic function upon influenza infection in human lung. J. Clin. Invest. 121, 2254–2263 (2011).
doi: 10.1172/JCI44675
Wu, T. et al. Lung-resident memory CD8 T cells (TRM) are indispensable for optimal cross-protection against pulmonary virus infection. J. Leukoc. Biol. 95, 215–224 (2014).
doi: 10.1189/jlb.0313180
Ghilas et al. Natural killer cells and dendritic epidermal γδ T cells orchestrate type 1 conventional DC spatiotemporal repositioning toward CD8+ T cellsiScience. 2021 Sep 24; 24(9): 103059. https://doi.org/10.1016/j.isci.2021.103059
Böttcher, J. P. et al. NK cells stimulate recruitment of cDC1 into the tumor microenvironment promoting cancer immune control. Cell 172, 1022–1037 (2018).
doi: 10.1016/j.cell.2018.01.004
Ma, M. et al. NKG2CNKG2A natural killer cells are associated with a lower viral set point and may predict disease progression in individuals with primary HIV infection. Front. Immunol. 8, 1176 (2017).
doi: 10.3389/fimmu.2017.01176
Fang, M. et al. CD94 is essential for NK cell-mediated resistance to a lethal viral disease. Immunity 34, 579–589 (2011).
doi: 10.1016/j.immuni.2011.02.015
Triebel, F. et al. LAG-3, a novel lymphocyte activation gene closely related to CD4. J. Exp. Med. 171, 1393–1405 (1990).
doi: 10.1084/jem.171.5.1393
Siegers, G. M., Barreira, C. R., Postovit, L.-M. & Dekaban, G. A. CD11d β2 integrin expression on human NK, B, and γδ T cells. J. Leukoc. Biol. 101, 1029–1035 (2017).
doi: 10.1189/jlb.3AB0716-326RR
Treiner, E. et al. Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1. Nature 422, 164–169 (2003).
doi: 10.1038/nature01433
Corthésy, B. Multi-faceted functions of secretory IgA at mucosal surfaces. Front. Immunol. 4, 185 (2013).
doi: 10.3389/fimmu.2013.00185
Kunkel, E. J. & Butcher, E. C. Plasma-cell homing. Nat. Rev. Immunol. 3, 822–829 (2003).
doi: 10.1038/nri1203
Morteau, O. et al. An indispensable role for the chemokine receptor CCR10 in IgA antibody-secreting cell accumulation. J. Immunol. 181, 6309–6315 (2008).
doi: 10.4049/jimmunol.181.9.6309
O’Connor, B. P. et al. BCMA is essential for the survival of long-lived bone marrow plasma cells. J. Exp. Med. 199, 91–98 (2004).
doi: 10.1084/jem.20031330
Soutar, C. A. Distribution of plasma cells and other cells containing immunoglobulin in the respiratory tract of normal man and class of immunoglobulin contained therein. Thorax 31, 158–166 (1976).
doi: 10.1136/thx.31.2.158
Yoshida et al. Local and systemic responses to SARS-CoV-2 infection in children and adults. Nature 602, 321–327 (2022). https://doi.org/10.1038/s41586-021-04345-x
Collin, A. M. et al. Lung immunoglobulin A immunity dysregulation in cystic fibrosis. EBioMedicine 60, 102974 (2020).
doi: 10.1016/j.ebiom.2020.102974
Zhu, J. et al. Plasma cells and IL-4 in chronic bronchitis and chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 175, 1125–1133 (2007).
doi: 10.1164/rccm.200602-161OC
Rowley, A. H. et al. IgA plasma cell infiltration of proximal respiratory tract, pancreas, kidney, and coronary artery in acute Kawasaki disease. J. Infect. Dis. 182, 1183–1191 (2000).
doi: 10.1086/315832
Matsuo, K. et al. CCL28-deficient mice have reduced IgA antibody-secreting cells and an altered microbiota in the colon. J. Immunol. 200, 800–809 (2018).
doi: 10.4049/jimmunol.1700037
Wilson, E. & Butcher, E. C. CCL28 controls immunoglobulin (Ig)A plasma cell accumulation in the lactating mammary gland and IgA antibody transfer to the neonate. J. Exp. Med. 200, 805–809 (2004).
doi: 10.1084/jem.20041069
Jin, S. et al. Inference and analysis of cell-cell communication using CellChat. Nat. Commun. 12, 1–20 (2021).
doi: 10.1038/s41467-021-21246-9
Lee, A. Y. S. et al. Expression of membrane-bound CC chemokine ligand 20 on follicular T helper cells in T–B-cell conjugates. Front. Immunol. 8, 1871 (2017).
doi: 10.3389/fimmu.2017.01871
Elgueta, R. et al. CCR6-dependent positioning of memory B cells is essential for their ability to mount a recall response to antigen. J. Immunol. 194, 505–513 (2015).
doi: 10.4049/jimmunol.1401553
Bowman, E. P. et al. Developmental switches in chemokine response profiles during B cell differentiation and maturation. J. Exp. Med. 191, 1303–1318 (2000).
doi: 10.1084/jem.191.8.1303
He, B. et al. Intestinal bacteria trigger T cell-independent immunoglobulin A(2) class switching by inducing epithelial-cell secretion of the cytokine APRIL. Immunity 26, 812–826 (2007).
doi: 10.1016/j.immuni.2007.04.014
Beagley, K. W. et al. Interleukins and IgA synthesis. Human and murine interleukin 6 induce high rate IgA secretion in IgA-committed B cells. J. Exp. Med. 169, 2133–2148 (1989).
doi: 10.1084/jem.169.6.2133
Hirano, T. et al. Complementary DNA for a novel human interleukin (BSF-2) that induces B lymphocytes to produce immunoglobulin. Nature 324, 73–76 (1986).
doi: 10.1038/324073a0
Ladjemi, M. Z. et al. Increased IgA production by B-cells in COPD via lung epithelial interleukin-6 and TACI pathways. Eur. Respir. J. 45, 980–993 (2015).
doi: 10.1183/09031936.00063914
Nish, S. A. et al. T cell-intrinsic role of IL-6 signaling in primary and memory responses. eLife 3, e01949 (2014).
doi: 10.7554/eLife.01949
Gong, Y.-Z. et al. Differentiation of follicular helper T cells by salivary gland epithelial cells in primary Sjögren’s syndrome. J. Autoimmun. 51, 57–66 (2014).
doi: 10.1016/j.jaut.2013.11.003
Mercedes Rincon, C. G. I. Role of IL-6 in asthma and other inflammatory pulmonary diseases. Int. J. Biol. Sci. 8, 1281 (2012).
doi: 10.7150/ijbs.4874
Savelikhina, I., Ostrovskyy, M., Ostrovska, K., Kulynych-Miskiv, M. & Varunkiv, O. Proinflammatory cytokine IL-6 detetion in severe COPD patients: focus on roflumilast. Eur. Respir. J. 52, OA3267 (2018).
Tillie-Leblond, I. et al. Balance between proinflammatory cytokines and their inhibitors in bronchial lavage from patients with status asthmaticus. Am. J. Respir. Crit. Care Med. 159, 487–494 (1999).
doi: 10.1164/ajrccm.159.2.9805115
Rossi, G. A. et al. Human ciliated bronchial epithelial cells: expression of the HLA-DR antigens and of the HLA-DR alpha gene, modulation of the HLA-DR antigens by gamma-interferon and antigen-presenting function in the mixed leukocyte reaction. Am. J. Respir. Cell Mol. Biol. 3, 431–439 (1990).
doi: 10.1165/ajrcmb/3.5.431
Kalb, T. H., Chuang, M. T., Marom, Z. & Mayer, L. Evidence for accessory cell function by class II MHC antigen-expressing airway epithelial cells. Am. J. Respir. Cell Mol. Biol. 4, 320–329 (1991).
doi: 10.1165/ajrcmb/4.4.320
Cagnoni, F. et al. CD40 on adult human airway epithelial cells: expression and proinflammatory effects. J. Immunol. 172, 3205–3214 (2004).
doi: 10.4049/jimmunol.172.5.3205
Gormand, F. et al. CD40 expression by human bronchial epithelial cells. Scand. J. Immunol. 49, 355–361 (1999).
doi: 10.1046/j.1365-3083.1999.00510.x
Tanaka, H. et al. CD40 and IFN-gamma dependent T cell activation by human bronchial epithelial cells. J. Med. Invest. 48, 109–117 (2001).
Shenoy, A. T. et al. Antigen presentation by lung epithelial cells directs CD4
doi: 10.1038/s41467-021-26045-w
Ladjemi, M. Z. et al. Bronchial epithelial IgA secretion is impaired in asthma. Role of IL-4/IL-13. Am. J. Respir. Crit. Care Med. 197, 1396–1409 (2018).
doi: 10.1164/rccm.201703-0561OC
Planté-Bordeneuve, T. et al. The pIgR-IgA system as a new player in lung fibrosis. Eur. Respir. J. 58, PA867 (2021).
Sterlin, D. et al. IgA dominates the early neutralizing antibody response to SARS-CoV-2. Sci. Transl. Med. 13, eabd2223 (2021).
doi: 10.1126/scitranslmed.abd2223
Bleier, B. S., Ramanathan, M. & Lane, A. P. COVID-19 vaccines may not prevent nasal SARS-CoV-2 infection and asymptomatic transmission. Otolaryngol. Head. Neck Surg. 164, 305–307 (2021).
doi: 10.1177/0194599820982633
Tiboni, M., Casettari, L. & Illum, L. Nasal vaccination against SARS-CoV-2: synergistic or alternative to intramuscular vaccines? Int. J. Pharm. 603, 120686 (2021).
doi: 10.1016/j.ijpharm.2021.120686
Krishnaswami, S. R. et al. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat. Protoc. 11, 499–524 (2016).
doi: 10.1038/nprot.2016.015
Radtke, A. J. et al. IBEX: a versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues. Proc. Natl Acad. Sci. USA 117, 33455–33465 (2020).
doi: 10.1073/pnas.2018488117
Young, M. D. & Behjati, S. SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. Gigascience 9, giaa151 (2020).
doi: 10.1093/gigascience/giaa151
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
doi: 10.1186/s13059-017-1382-0
Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
doi: 10.1038/s41592-019-0619-0
Polański, K. et al. BBKNN: fast batch alignment of single cell transcriptomes. Bioinformatics 36, 964–965 (2020).
Lopez, R., Regier, J., Cole, M. B., Jordan, M. I. & Yosef, N. Deep generative modeling for single-cell transcriptomics. Nat. Methods 15, 1053–1058 (2018).
doi: 10.1038/s41592-018-0229-2
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
doi: 10.1073/pnas.0506580102
Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).
doi: 10.1038/s41586-019-0969-x
Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408–1414 (2020).
doi: 10.1038/s41587-020-0591-3
Sturm, G. et al. Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. Bioinformatics 36, 4817–4818 (2020).
doi: 10.1093/bioinformatics/btaa611
Stephenson, E. et al. Single-cell multi-omics analysis of the immune response in COVID-19. Nat. Med. 27, 904–916 (2021).
doi: 10.1038/s41591-021-01329-2
Elmentaite, R. et al. Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn’s disease. Dev. Cell 55, 771–783 (2020).
doi: 10.1016/j.devcel.2020.11.010
Shrine, N. et al. New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat. Genet. 51, 1067 (2019).
doi: 10.1038/s41588-019-0438-3
Dann, E., Henderson, N. C., Teichmann, S. A., Morgan, M. D. & Marioni, J. C. Differential abundance testing on single-cell data using k-nearest neighbor graphs. Nat. Biotechnol. 40, 245–253 (2022).
doi: 10.1038/s41587-021-01033-z