Duncker, H. R. Vertebrate lungs: structure, topography and mechanics. A comparative perspective of the progressive integration of respiratory system, locomotor apparatus and ontogenetic development. Respir. Physiol. Neurobiol. 144, 111–124 (2004).
Longo, S., Riccio, M. & McCune, A. R. Homology of lungs and gas bladders: insights from arterial vasculature. J. Morphol. 274, 687–703 (2013).
Zheng, W. et al. Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung. PLoS ONE 6, e24019 (2011).
Wang, K. et al. African lungfish genome sheds light on the vertebrate water-to-land transition. Cell 184, 1362–1376.e18 (2021).
Bi, X. et al. Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes. Cell 184, 1377–1391.e14 (2021).
Thompson, A. W. et al. The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nat. Genet. 53, 1373–1384 (2021).
Pelster, B. Using the swimbladder as a respiratory organ and/or a buoyancy structure—Benefits and consequences. J. Exp. Zool. Part A: Ecol. Integr. Physiol. 335, 831–842 (2021).
Uhlén, M. et al. Tissue-based map of the human proteome. Science 347, 1260419 (2015).
Jorgensen, J. M. & Joss, J. The Biology Of Lungfishes (CRC Press, 2011).
Cui, X., Friedman, M., Qiao, T., Yu, Y. & Zhu, M. The rapid evolution of lungfish durophagy. Nat. Commun. 13, 2390 (2022).
Hsia, C. C., Schmitz, A., Lambertz, M., Perry, S. F. & Maina, J. N. Evolution of air breathing: oxygen homeostasis and the transitions from water to land and sky. Compr. Physiol. 3, 849–915 (2013).
Otero, O. Current knowledge and new assumptions on the evolutionary history of the African lungfish, Protopterus, based on a review of its fossil record. Fish. Fish. 12, 235–255 (2011).
Garofalo, F. et al. Signal molecule changes in the gills and lungs of the African lungfish Protopterus annectens, during the maintenance and arousal phases of aestivation. Nitric Oxide 44, 71–80 (2015).
Lajus, D. L. & Alekseev, V. R. in Dormancy in Aquatic Organisms. Theory, Human Use and Modeling (eds Alekseev, V. R. & Pinel-Alloul, B.) 53–69 (Springer, 2019).
Perry, S. et al. Control of breathing in African lungfish (Protopterus dolloi): a comparison of aquatic and cocooned (terrestrialized) animals. Respir. Physiol. Neurobiol. 160, 8–17 (2008).
Heimroth, R. D. et al. The lungfish cocoon is a living tissue with antimicrobial functions. Sci. Adv. 7, eabj0829 (2021).
Sturla, M., Paola, P., Carlo, G., Angela, M. M. & Maria, U. B. Effects of induced aestivation in Protopterus annectens: a histomorphological study. J. Exp. Zool. 292, 26–31 (2002).
Heimroth, R. D., Casadei, E. & Salinas, I. Effects of experimental terrestrialization on the skin mucus proteome of African Lungfish (Protopterus dolloi). Front. Immunol. 9, 1259 (2018).
Amelio, D. & Garofalo, F. The NOS/NO system in an example of extreme adaptation: the African lungfish. J. Therm. Biol. 90, 102594 (2020).
Chng, Y. R. et al. Aestivation induces changes in the mRNA expression levels and protein abundance of two isoforms of urea transporters in the gills of the African Lungfish, Protopterus annectens. Front. Physiol. 8, 71 (2017).
Chng, Y. R. et al. Molecular characterization of aquaporin 1 and aquaporin 3 from the gills of the African lungfish, Protopterus annectens, and changes in their branchial mRNA expression levels and protein abundance during three phases of aestivation. Front. Physiol. 7, 532 (2016).
Weber, R. E., Johansen, K., Lykkeboe, G. & Maloiy, G. O. Oxygen-binding properties of hemoglobins from estivating and active African lungfish. J. Exp. Zool. 199, 85–96 (1977).
Biscotti, M. A. et al. The lungfish transcriptome: a glimpse into molecular evolution events at the transition from water to land. Sci. Rep. 6, 1–12 (2016).
Zhao, L., Wang, S., Lou, F., Gao, T. & Han, Z. Phylogenomics based on transcriptome data provides evidence for the internal phylogenetic relationships and potential terrestrial evolutionary genes of lungfish. Front. Mar. Sci. 8 (2021).
Freedman, A. H., Clamp, M. & Sackton, T. B. Error, noise and bias in de novo transcriptome assemblies. Mol. Ecol. Resour. 21, 18–29 (2021).
Tosches, M. A. et al. Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles. Science 360, 881–888 (2018).
Levy, S. et al. A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. Cell 184, 2973–2987.e18 (2021).
Chen, D. et al. Single cell atlas for 11 non-model mammals, reptiles and birds. Nat. Commun. 12, 7083 (2021).
Wang, J. et al. Tracing cell-type evolution by cross-species comparison of cell atlases. Cell Rep. 34, 108803 (2021).
Meyer, A. et al. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 590, 284–289 (2021).
Meng, J. & Wang, W.-X. Highly sensitive and specific responses of oyster hemocytes to copper exposure: single-cell transcriptomic analysis of different cell populations. Environ. Sci. Technol. 56, 2497–2510 (2022).
Siebert, S. et al. Stem cell differentiation trajectories in Hydra resolved at single-cell resolution. Science 365 (2019).
Koiwai, K. et al. Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process. eLife 10, e66954 (2021).
Sun, X. et al. Cell type diversity in scallop adductor muscles revealed by single-cell RNA-Seq. Genomics 113, 3582–3598 (2021).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
McInnes, L., Healy, J. & Melville, J. UMAP: Uniform manifold approximation and projection for dimension reduction. Preprint at arxiv.org/abs/1802.03426v3 (2020).
Maina, J. N. The morphology of the lung of the African lungfish, Protopterus aethiopicus: a scanning electron-microscopic study. Cell Tissue Res 250, 191–196 (1987).
Wang, Y. et al. The effects and mechanisms of SLC34A2 in tumorigenesis and progression of human non-small cell lung cancer. J. Biomed. Sci. 22, 52 (2015).
Corut, A. et al. Mutations in SLC34A2 cause pulmonary alveolar microlithiasis and are possibly associated with testicular microlithiasis. Am. J. Hum. Genet 79, 650–656 (2006).
Zhang, L. et al. A high-resolution cell atlas of the domestic pig lung and an online platform for exploring lung single-cell data. J. Genet. Genomics 48, 411–425 (2021).
Crapo, J. D., Barry, B. E., Gehr, P., Bachofen, M. & Weibel, E. R. Cell number and cell characteristics of the normal human lung. Am. Rev. Respir. Dis. 126, 332–337 (1982).
Treutlein, B. et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371–375 (2014).
Kadur Lakshminarasimha Murthy, P. et al. Human distal lung maps and lineage hierarchies reveal a bipotent progenitor. Nature 604, 111–119 (2022).
Liao, Y. et al. Cell landscape of larval and adult Xenopus laevis at single-cell resolution. Nat. Commun. 13, 4306 (2022).
Cao, J. et al. A human cell atlas of fetal gene expression. Science 370, eaba7721 (2020).
Brigida, I. et al. T-cell defects in patients with ARPC1B germline mutations account for combined immunodeficiency. Blood 132, 2362–2374 (2018).
Prager, I. & Watzl, C. Mechanisms of natural killer cell-mediated cellular cytotoxicity. J. Leukoc. Biol. 105, 1319–1329 (2019).
Krzewski, K. & Coligan, J. E. Human NK cell lytic granules and regulation of their exocytosis. Front. Immunol. 3, 335 (2012).
Fridman, S. Ontogeny of the osmoregulatory capacity of teleosts and the role of ionocytes. Front. Mar. Sci. 7, 709 (2020).
Sturla, M., Masini, M. A., Prato, P., Grattarola, C. & Uva, B. Mitochondria-rich cells in gills and skin of an African lungfish, Protopterus annectens. Cell Tissue Res. 303, 351–358 (2001).
Ip, Y. K. et al. Evidence for the involvement of branchial Vacuolar-type H(+)-ATPase in the acidification of the external medium by the West African lungfish, Protopterus annectens, exposed to ammonia-loading conditions. Comp. Biochem Physiol. A: Mol. Integr. Physiol. 273, 111297 (2022).
Gil, J. & Weibel, E. R. Improvements in demonstration of lining layer of lung alveoli by electron microscopy. Respir. Physiol. 8, 13–36 (1969).
Cohen, M. et al. Lung single-cell signaling interaction map reveals basophil role in macrophage imprinting. Cell 175, 1031–1044.e18 (2018).
Perry, S. F. The chloride cell: structure and function in the gills of freshwater fishes. Annu. Rev. Physiol. 59, 325–347 (1997).
Morgan, M. & Tovell, P. W. A. The structure of the gill of the trout, Salmo gairdneri (Richardson). Z. f.ür. Zellforsch. Mikroskopische Anat. 142, 147–162 (1973).
Mootha, V. K. et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–273 (2003).
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).
Enderle, J. D. in Introduction to Biomedical Engineering 3rd edn (eds. Enderle, J. D. & Bronzino, J. D.) 447–508 (Academic Press, 2012).
Roszell, B. R., Tao, J. Q., Yu, K. J., Huang, S. & Bates, S. R. Characterization of the Niemann-Pick C pathway in alveolar type II cells and lamellar bodies of the lung. Am. J. Physiol. Lung Cell Mol. Physiol. 302, L919–L932 (2012).
Page, M. M. et al. Upregulation of intracellular antioxidant enzymes in brain and heart during estivation in the African lungfish Protopterus dolloi. J. Comp. Physiol. B 180, 361–369 (2010).
Kockx, M. et al. Secretion of Apolipoprotein E From Macrophages Occurs via a Protein Kinase A- and calcium-dependent pathway along the microtubule network. Circulation Res. 101, 607–616 (2007).
Kraal, G., van der Laan, L. J., Elomaa, O. & Tryggvason, K. The macrophage receptor MARCO. Microbes Infect. 2, 313–316 (2000).
Turton, H. A. et al. Soluble P-selectin and von willebrand factor rise in healthy volunteers following non-exertional ascent to high altitude. Front. Physiol. 13, 825819 (2022).
Hiong, K. C. et al. Aestivation induces changes in transcription and translation of coagulation factor II and fibrinogen gamma chain in the liver of the African lungfish Protopterus annectens. J. Exp. Biol. 218, 3717–3728 (2015).
Efremova, M., Vento-Tormo, M., Teichmann, S. A. & Vento-Tormo, R. CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes. Nat. Protoc. 15, 1484–1506 (2020).
Herzog, B., Pellet-Many, C., Britton, G., Hartzoulakis, B. & Zachary, I. C. VEGF binding to NRP1 is essential for VEGF stimulation of endothelial cell migration, complex formation between NRP1 and VEGFR2, and signaling via FAK Tyr407 phosphorylation. Mol. Biol. Cell 22, 2766–2776 (2011).
Abhinand, C. S., Raju, R., Soumya, S. J., Arya, P. S. & Sudhakaran, P. R. VEGF-A/VEGFR2 signaling network in endothelial cells relevant to angiogenesis. J. Cell Commun. Signal 10, 347–354 (2016).
Lu, D., Shang, G., He, X., Bai, X.-C. & Zhang, X. Architecture of the Sema3A/PlexinA4/Neuropilin tripartite complex. Nat. Commun. 12, 3172 (2021).
Jiao, B. et al. Class-3 semaphorins: potent multifunctional modulators for angiogenesis-associated diseases. Biomed. Pharmacother. 137, 111329 (2021).
Hu, C. & Jiang, X. Role of NRP-1 in VEGF-VEGFR2-independent tumorigenesis. Target Oncol. 11, 501–505 (2016).
Yang, W. J. et al. Semaphorin-3C signals through Neuropilin-1 and PlexinD1 receptors to inhibit pathological angiogenesis. EMBO Mol. Med. 7, 1267–1284 (2015).
Weber, R. & Jensen, F. Respiratory Adaptations in Lungfish Blood and Hemoglobin (eds Jørgrnsen, J. J. and Joss, J.) 283–303 (Science Publishers, 2011).
Loong, A. M. et al. Increased urea synthesis and/or suppressed ammonia production in the African lungfish, Protopterus annectens, during aestivation in air or mud. J. Comp. Physiol. B 178, 351–363 (2008).
Mlewa, C., Green, J. & Dunbrack, R. The General Natural History of the African Lungfishes (eds Jorgensen, J. M. & Joss, J.) (CRC Press, 2010).
Evans, D. H., Piermarini, P. M. & Choe, K. P. The multifunctional fish gill: dominant site of gas exchange, osmoregulation, acid-base regulation, and excretion of nitrogenous waste. Physiol. Rev. 85, 97–177 (2005).
Inokuchi, M., Hiroi, J. & Kaneko, T. Why can Mozambique Tilapia acclimate to both freshwater and seawater? insights from the plasticity of ionocyte functions in the Euryhaline Teleost. Front. Physiol. 13, 914277 (2022).
Wilson, J. M. & Laurent, P. Fish gill morphology: inside out. J. Exp. Zool. 293, 192–213 (2002).
Tseng, Y. C. & Hwang, P. P. Some insights into energy metabolism for osmoregulation in fish. Comp. Biochem Physiol. C: Toxicol. Pharm. 148, 419–429 (2008).
Feher, J. in Quantitative Human Physiology 2nd edn (ed. Feher, J.) 507–515 (Academic Press, 2012).
Shalhoub, J., Falck-Hansen, M. A., Davies, A. H. & Monaco, C. Innate immunity and monocyte-macrophage activation in atherosclerosis. J. Inflamm. 8, 9 (2011).
Parihar, A., Eubank, T. D. & Doseff, A. I. Monocytes and macrophages regulate immunity through dynamic networks of survival and cell death. J. Innate Immun. 2, 204–215 (2010).
Ma, W. T., Gao, F., Gu, K. & Chen, D. K. The role of monocytes and macrophages in autoimmune diseases: a comprehensive review. Front Immunol. 10, 1140 (2019).
Gaspari, A. A. Innate and adaptive immunity and the pathophysiology of psoriasis. J. Am. Acad. Dermatol 54, S67–S80 (2006).
Alberts, B. et al. in Molecular Biology of the Cell. 4th edn (Dries, D. J.) (Garland Science, 2002).
Sender, R. & Milo, R. The distribution of cellular turnover in the human body. Nat. Med. 27, 45–48 (2021).
Rudd, P. M., Elliott, T., Cresswell, P., Wilson, I. A. & Dwek, R. A. Glycosylation and the immune system. Science 291, 2370–2376 (2001).
Laurent, P. et al. The vasculature of the gills in the aquatic and aestivating lungfish (Protopterus aethiopicus). J. Morphol. 156, 173–208 (1978).
Zardoya, R. & Meyer, A. The complete nucleotide sequence of the mitochondrial genome of the lungfish (Protopterus dolloi) supports its phylogenetic position as a close relative of land vertebrates. Genetics 142, 1249–1263 (1996).
Joss, J. M. Lungfish evolution and development. Gen. Comp. Endocrinol. 148, 285–289 (2006).
Raredon, M. S. B. et al. Single-cell connectomic analysis of adult mammalian lungs. Sci. Adv. 5, eaaw3851 (2019).
Jiang, M. et al. Characterization of the zebrafish cell landscape at single-cell resolution. Front. Cell Dev. Biol. 9 (2021).
West, A. C. et al. Immunologic profiling of the Atlantic Salmon Gill by single nuclei transcriptomics. Front. Immunol. 12, 669889 (2021).
Sprague, J. et al. The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res. 31, 241–243 (2003).
Frohnhöfer, H. G. et al. Spermidine, but not spermine, is essential for pigment pattern formation in zebrafish. Biol. Open 5, 736–744 (2016).
Yi, X. et al. The effector of Hippo signaling, Taz, is required for formation of the micropyle and fertilization in zebrafish. PLoS Genet. 15, e1007408 (2019).
Noël, E. S. et al. Organ-specific requirements for Hdac1 in liver and pancreas formation. Dev. Biol. 322, 237–250 (2008).
Ashworth, S. et al. Cofilin-1 inactivation leads to proteinuria-studies in zebrafish, mice and humans. PLoS ONE 5, e12626 (2010).
Jeong, Y. M. et al. Induction of clusterin expression by neuronal cell death in Zebrafish. J. Genet. Genomics 41, 583–589 (2014).
Izumi, H. et al. A novel SLC34A2 mutation in a patient with pulmonary alveolar microlithiasis. Hum. Genome Var. 4, 16047 (2017).
Segawa, H., Shiozaki, Y., Kaneko, I. & Miyamoto, K. The role of sodium-dependent phosphate transporter in phosphate homeostasis. J. Nutr. Sci. Vitaminol. (Tokyo) 61, S119–S121 (2015).
Wang, D., Haviland, D. L., Burns, A. R., Zsigmond, E. & Wetsel, R. A. A pure population of lung alveolar epithelial type II cells derived from human embryonic stem cells. Proc. Natl Acad. Sci. USA 104, 4449–4454 (2007).
Bridges, J. P. et al. LPCAT1 regulates surfactant phospholipid synthesis and is required for transitioning to air breathing in mice. J. Clin. Invest. 120, 1736–1748 (2010).
Takahashi, H., Sano, H., Chiba, H. & Kuroki, Y. Pulmonary surfactant proteins A and D: innate immune functions and biomarkers for lung diseases. Curr. Pharm. Des. 12, 589–598 (2006).
Hiroshima, Y. et al. S100A8/A9 and S100A9 reduce acute lung injury. Immunol. Cell Biol. 95, 461–472 (2017).
Cui, H. et al. Monocyte-derived alveolar macrophage apolipoprotein E participates in pulmonary fibrosis resolution. JCI Insight 5 (2020).
McClelland, M., Zhao, L., Carskadon, S. & Arenberg, D. Expression of CD74, the receptor for macrophage migration inhibitory factor, in non-small cell lung cancer. Am. J. Pathol. 174, 638–646 (2009).
Chan, T. W. et al. RNA editing in cancer impacts mRNA abundance in immune response pathways. Genome Biol. 21, 268 (2020).
Yu, Z. et al. Lys29-linkage of ASK1 by Skp1−Cullin 1−Fbxo21 ubiquitin ligase complex is required for antiviral innate response. eLife 5, e14087 (2016).
Wegner, N. in Encyclopedia of Fish Physiology: From Genome to Environment Vol. 2 (eds Farrell, A. P., Stevens, E. D., Cech, J.J. & Richards, J.G.) 803–811 (Academic Press, 2011).
Laurent, P. & Dunel, S. Morphology of gill epithelia in fish. Am. J. Physiol. 238, R147–R159 (1980).
Wright, D. E. Morphology of the gill epithelium of the Lungfish, Lepidosiren paradoxa. Cell Tissue Res. 153, 365–381 (1974).
Adriaensen, D., Scheuermann, D. W., Timmermans, J. P. & De Groodt-Lasseel, M. H. Neuroepithelial endocrine cells in the lung of the lungfish Protopterus aethiopicus. An electron- and fluorescence-microscopical investigation. Acta Anat. (Basel) 139, 70–77 (1990).
Icardo, J. M. Lungs and gas bladders: morphological insights. Acta Histochem 120, 605–612 (2018).
Deprez, M. et al. A single-cell atlas of the human healthy airways. Am. J. Respir. Crit. Care Med 202, 1636–1645 (2020).
Kim, E. et al. Maternal gut bacteria drive intestinal inflammation in offspring with neurodevelopmental disorders by altering the chromatin landscape of CD4+ T cells. Immunity 55, 145–158.e7 (2022).
Kim, E., Tran, M., Sun, Y. & Huh, J. R. Isolation and analyses of lamina propria lymphocytes from mouse intestines. STAR Protoc. 3, 101366 (2022).
Liu, C. et al. A portable and cost-effective microfluidic system for massively parallel single-cell transcriptome profiling. bioRxiv doi.org/10.1101/818450 (2019).
Wang, F. et al. Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level. Nat. Commun. 13, 3620 (2022).
Young, M. D. & Behjati, S. SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. Gigascience 9 (2020).
McGinnis, C. S., Murrow, L. M. & Gartner, Z. J. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 8, 329–337.e4 (2019).
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics 16, 284–287 (2012).
Liberzon, A. et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 1, 417–425 (2015).
Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform. 14, 128 (2013).
Kuleshov, M. V. et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44, W90–W97 (2016).
Xie, Z. et al. Gene set knowledge discovery with Enrichr. Curr. Protoc. 1, e90 (2021).