Recessive missense LAMP3 variant associated with defect in lamellar body biogenesis and fatal neonatal interstitial lung disease in dogs
Autoři:
Kati J. Dillard aff001; Matthias Ochs aff005; Julia E. Niskanen aff001; Meharji Arumilli aff001; Jonas Donner aff008; Kaisa Kyöstilä aff001; Marjo K. Hytönen aff001; Marjukka Anttila aff004; Hannes Lohi aff001
Působiště autorů:
Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
aff001; Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
aff002; Folkhälsan Research Center, Helsinki, Finland
aff003; Veterinary Bacteriology and Pathology Research Unit, Finnish Food Authority, Helsinki, Finland
aff004; Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany
aff005; Institute of Functional Anatomy, Charité - Universitaetsmedizin Berlin, Berlin, Germany
aff006; German Center for Lung Research (DZL), Berlin, Germany
aff007; Genoscoper Laboratories Ltd (Wisdom Health), Helsinki, Finland
aff008
Vyšlo v časopise:
Recessive missense LAMP3 variant associated with defect in lamellar body biogenesis and fatal neonatal interstitial lung disease in dogs. PLoS Genet 16(3): e32767. doi:10.1371/journal.pgen.1008651
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008651
Souhrn
Neonatal interstitial lung diseases due to abnormal surfactant biogenesis are rare in humans and have never been reported as a spontaneous disorder in animals. We describe here a novel lung disorder in Airedale Terrier (AT) dogs with clinical symptoms and pathology similar to the most severe neonatal forms of human surfactant deficiency. Lethal hypoxic respiratory distress and failure occurred within the first days or weeks of life in the affected puppies. Transmission electron microscopy of the affected lungs revealed maturation arrest in the formation of lamellar bodies (LBs) in the alveolar epithelial type II (AECII) cells. The secretory organelles were small and contained fewer lamellae, often in combination with small vesicles surrounded by an occasionally disrupted common limiting membrane. A combined approach of genome-wide association study and whole exome sequencing identified a recessive variant, c.1159G>A, p.(E387K), in LAMP3, a limiting membrane protein of the cytoplasmic surfactant organelles in AECII cells. The substitution resides in the LAMP domain adjacent to a conserved disulfide bond. In summary, this study describes a novel interstitial lung disease in dogs, identifies a new candidate gene for human surfactant dysfunction and brings important insights into the essential role of LAMP3 in the process of the LB formation.
Klíčová slova:
Cellular structures and organelles – Dogs – Genome-wide association studies – Interstitial lung diseases – Lungs – Mammalian genomics – Pets and companion animals – Surfactants
Zdroje
1. Fehrenbach H. Alveolar epithelial type II cell: Defender of the alveolus revisited. Respir. Res. 2001;2: 33–46. doi: 10.1186/rr36 11686863
2. Ochs M. The closer we look the more we see? Quantitative microscopic analysis of the pulmonary surfactant system. Cell Physiol Biochem. 2010;25: 27–40. doi: 10.1159/000272061 20054142
3. Dietl P, Haller T, Mair N, Frick M. Mechanisms of Surfactant Exocytosis in Alveolar Type II Cells In Vitro and In Vivo. Physiology. 2001;16: 239.
4. Dell'Angelica EC, Mullins C, Caplan S, Bonifacino JS. Lysosome-related organelles. FASEB J. 2000;14: 1265–1278. doi: 10.1096/fj.14.10.1265 10877819
5. Weaver TE, Na C, Stahlman M. Biogenesis of lamellar bodies, lysosome-related organelles involved in storage and secretion of pulmonary surfactant. Semin. Cell Dev. Biol. 2002;13: 263–270. doi: 10.1016/s1084952102000551 12243725
6. Nogee LM. Interstitial lung disease in newborns. Semin Fetal Neonatal Med. 2017;22: 227–233. doi: 10.1016/j.siny.2017.03.003 28363760
7. Shulenin S, Nogee LM, Annilo T, Wert SE, Whitsett JA, Dean M. ABCA3 Gene Mutations in Newborns with Fatal Surfactant Deficiency. N. Engl. J. Med. 2004;350: 1296–1303. doi: 10.1056/NEJMoa032178 15044640
8. Nogee LM, de Mello DE, Dehner LP, Colten HR. Brief report: Genome Sequence protein B in congenital alveolar proteinosis. N. Engl. J. Med. 1993;328: 406–410. doi: 10.1056/NEJM199302113280606 8421459
9. Nogee LM, Dunbar AE, Wert SE, Askin F, Hamvas A, Whitsett JA. A Mutation in the Surfactant Protein C Gene Associated with Familial Interstitial Lung Disease. N Engl J Med. 2001;344: 573–579. doi: 10.1056/NEJM200102223440805 11207353
10. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005;438: 803–819. doi: 10.1038/nature04338 16341006
11. Hytönen MK, Lohi H. Canine models of human rare disorders. Rare Diseases. 2016;4: e1241362. doi: 10.1080/21675511.2016.1241362 27803843
12. Wielaender F, Sarviaho R, James F, Hytonen MK, Cortez MA, Kluger G, et al. Generalized myoclonic epilepsy with photosensitivity in juvenile dogs caused by a defective DIRAS family GTPase 1. Proc Natl Acad Sci U S A. 2017;114: 2669–2674. doi: 10.1073/pnas.1614478114 28223533
13. Kaukonen M, Woods S, Ahonen S, Lemberg S, Hellman M, Hytönen MK, et al. Maternal Inheritance of a Recessive RBP4 Defect in Canine Congenital Eye Disease. Cell Reports. 2018;23: 2643–2652. doi: 10.1016/j.celrep.2018.04.118 29847795
14. Holopainen S, Hytönen MK, Syrjä P, Arumilli M, Järvinen A, Rajamäki M, et al. ANLN truncation causes a familial fatal acute respiratory distress syndrome in Dalmatian dogs. PLoS genetics. 2017;13: e1006625. doi: 10.1371/journal.pgen.1006625 28222102
15. Hug P, Anderegg L, Kehl A, Jagannathan V, Leeb T. AKNA Frameshift Variant in Three Dogs with Recurrent Inflammatory Pulmonary Disease. Genes. 2019;10: 567. doi: 10.3390/genes10080567 31357536
16. Anderegg L, Im Hof Gut M, Hetzel U, Howerth EW, Leuthard F, Kyöstilä K, et al. NME5 frameshift variant in Alaskan Malamutes with primary ciliary dyskinesia. PLoS genetics. 2019;15: e1008378. doi: 10.1371/journal.pgen.1008378 31479451
17. Saint-Vis B, Vincent J, Vandenabeele S, Vanbervliet B, Pin J-, Aït-Yahia S, et al. A Novel Lysosome-Associated Membrane Glycoprotein, DC-LAMP, Induced upon DC Maturation, Is Transiently Expressed in MHC Class II Compartment. Immunity. 1998;9: 325–336. doi: 10.1016/s1074-7613(00)80615-9 9768752
18. Akasaki K, Nakamura N, Tsukui N, Yokota S, Murata S, Katoh R, et al. Human dendritic cell lysosome-associated membrane protein expressed in lung type II pneumocytes. Arch. Biochem. Biophys. 2004;425: 147–157. doi: 10.1016/j.abb.2004.02.042 15111122
19. Salaun B, de Saint-Vis B, Pacheco Y, Pacheco N, Riesler A, Isaac S, et al. CD208/Dendritic Cell-Lysosomal Associated Membrane Protein Is a Marker of Normal and Transformed Type II Pneumocytes. Am. J. Pathol. 2004;164: 861–871. doi: 10.1016/S0002-9440(10)63174-4 14982840
20. Lewin G, Hurtt ME. Pre- and Postnatal Lung Development: An Updated Species Comparison. Birth Defects Res. 2017;109: 1519–1539. doi: 10.1002/bdr2.1089 28876535
21. Bertocci B, Lecoeuche D, Sterlin D, Kuhn J, Gaillard B, De Smet A, et al. Klhl6 Deficiency Impairs Transitional B Cell Survival and Differentiation. J. Immunol. 2017;199: 2408–2420. doi: 10.4049/jimmunol.1700708 28807996
22. Jansen RS, Mahakena S, de Haas M, Borst P, van de Wetering K. ATP-binding cassette subfamily C member 5 (ABCC5) functions as an efflux transporter of glutamate conjugates and analogs. J. Biol. Chem. 2015;290: 30429–30440. doi: 10.1074/jbc.M115.692103 26515061
23. Wolf De, Cornelia J. F, Yamaguchi H, Van Der Heijden I, Wielinga PR, Hundscheid SL, Ono N, et al. cGMP transport by vesicles from human and mouse erythrocytes. FEBS Journal. 2007;274: 439–450. doi: 10.1111/j.1742-4658.2006.05591.x 17229149
24. Yamano G, Funahashi H, Kawanami O, Zhao L, Ban N, Uchida Y, et al. ABCA3 is a lamellar body membrane protein in human lung alveolar type II cells. FEBS Lett. 2001;508: 221–225. doi: 10.1016/s0014-5793(01)03056-3 11718719
25. Choi Y, Chan AP. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics. 2015;31: 2745–2747. doi: 10.1093/bioinformatics/btv195 25851949
26. Bendl J, Stourac J, Salanda O, Pavelka A, Wieben ED, Zendulka J, et al. PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations. PLoS Comput. Biol. 2014;10: e1003440. doi: 10.1371/journal.pcbi.1003440 24453961
27. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011;7: 539–n/a. doi: 10.1038/msb.2011.75 21988835
28. Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, et al. Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nature biotechnology. 2016;34: 531–538. doi: 10.1038/nbt.3514 27065010
29. Vieira NM, Elvers I, Alexander MS, Moreira YB, Eran A, Gomes JP, et al. Jagged 1 Rescues the Duchenne Muscular Dystrophy Phenotype. Cell. 2015;163: 1204–1213. doi: 10.1016/j.cell.2015.10.049 26582133
30. Szafranski P, Liu Q, Karolak J, Song X, de Leeuw N, Faas B, et al. Association of rare non-coding SNVs in the lung-specific FOXF1 enhancer with a mitigation of the lethal ACDMPV phenotype. Hum Genet. 2019;138: 1301–1311. doi: 10.1007/s00439-019-02073-x 31686214
31. Arboleda-Velasquez JF, Lopera F, O’Hare M, Delgado-Tirado S, Marino C, Chmielewska N, et al. Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report. Nature Medicine. 2019;25: 1680–1683. doi: 10.1038/s41591-019-0611-3 31686034
32. Witschi H. Proliferation of type II alveolar cells: A review of common responses in toxic lung injury. Toxicology. 1976;5: 267–277. doi: 10.1016/0300-483x(76)90046-9 817421
33. Barkauskas CE, Cronce MJ, Rackley CR, Bowie EJ, Keene DR, Stripp BR, et al. Type 2 alveolar cells are stem cells in adult lung. J. Clin. Invest. 2013;123: 3025. doi: 10.1172/JCI68782 23921127
34. Ochs M, Nenadic I, Fehrenbach A, Albes JM, Wahlers T, Richter J, et al. Ultrastructural alterations in intraalveolar surfactant subtypes after experimental ischemia and reperfusion. Am. J. Respir. Crit. Care Med. 1999;160: 718–724. doi: 10.1164/ajrccm.160.2.9809060 10430751
35. Ochs M, Fehrenbach H, Richter J. Ultrastructure of canine type II pneumocytes during hypothermic ischemia of the lung: A study by means of conventional and energy filtering transmission electron microscopy and stereology. Anat. Rec. 2001;263: 118–126. doi: 10.1002/ar.1084 11360229
36. Edwards V, Cutz E, Viero S, Moore AM, Nogee L. Ultrastructure of Lamellar Bodies in Congenital Surfactant Deficiency. Ultrastruct. Pathol. 2005;29: 503–509. doi: 10.1080/01913120500323480 16316951
37. Stahlman MT, Phillips Gray M, Falconieri MW, Whitsett JA, Weaver TE. Lamellar Body Formation in Normal and Surfactant Protein B-Deficient Fetal Mice. Lab. Investig. 2000;80: 395–403. doi: 10.1038/labinvest.3780044 10744075
38. Citti A, Peca D, Petrini S, Cutrera R, Biban P, Haass C, et al. Ultrastructural Characterization of Genetic Diffuse Lung Diseases in Infants and Children: A Cohort Study and Review. Ultrastruct. Pathol. 2013;37: 356–365. doi: 10.3109/01913123.2013.811454 24047351
39. Glasser ST, Burhans MS, Korfhagen TR, Na C, Sly PD, Ross GF, et al. Altered Stability of Pulmonary Surfactant in SP-C-Deficient Mice. Proc. Natl. Acad. Sci. U.S.A. 2001;98: 6366–6371. doi: 10.1073/pnas.101500298 11344267
40. Liao X, Song L, Zhang L, Wang H, Tong Q, Xu J, et al. LAMP3 regulates hepatic lipid metabolism through activating PI3K/Akt pathway. Molecular and Cellular Endocrinology. 2018;470: 160–167. doi: 10.1016/j.mce.2017.10.010 29056532
41. Kanao H, Enomoto T, Kimura T, Fujita M, Nakashima R, Ueda Y, et al. Overexpression of LAMP3/TSC403/DC-LAMP Promotes Metastasis in Uterine Cervical Cancer. Cancer Research. 2005;65: 8640. doi: 10.1158/0008-5472.CAN-04-4112 16204031
42. Wilke S, Krausze J, Büssow K. Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx. BMC Biol. 2012;10: 62. doi: 10.1186/1741-7007-10-62 22809326
43. Terasawa K, Tomabechi Y, Ikeda M, Ehara H, Kukimoto-Niino M, Wakiyama M, et al. Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes. Biochem. Biophys. Res. Commun. 2016;479: 489–495. doi: 10.1016/j.bbrc.2016.09.093 27663661
44. Engelbrecht S, Kaltenborn E, Griese M, Kern S. The surfactant lipid transporter ABCA3 is N-terminally cleaved inside LAMP3-positive vesicles. FEBS Lett. 2010;584: 4306–4312. doi: 10.1016/j.febslet.2010.09.026 20863830
45. Brasch F, Ochs M, Kahne T, Guttentag S, Schauer-Vukasinovic V, Derrick M, et al. Involvement of Napsin A in the C- and N-terminal Processing of Surfactant Protein B in Type-II Pneumocytes of the Human Lung. J. Biol. Chem. 2003;278: 49006–49014. doi: 10.1074/jbc.M306844200 13129928
46. Johnson AL, Braidotti P, Pietra GG, Russo SJ, Kabore A, Wang W, et al. Post-Translational Processing of Surfactant Protein-C Proprotein. Targeting Motifs in the NH2-Terminal Flanking Domain Are Cleaved in Late Compartments. Am. J. Respir. Cell Mol. Biol. 2001;24: 253–263. doi: 10.1165/ajrcmb.24.3.4312 11245624
47. Cheong N, Muniswamy Madesh, Linda W. Gonzales, Ming Zhao, Kevin Yu, Philip L. Ballard, et al. Functional and Trafficking Defects in ATP Binding Cassette A3 Mutants Associated with Respiratory Distress Syndrome. J. Biol. Chem. 2006;281: 9791–9800. doi: 10.1074/jbc.M507515200 16415354
48. Ban N, Yoshihiro M, Hiromichi S, Yasukazu T, Mayumi S, Hiroyuki A, et al. ABCA3 as a Lipid Transporter in Pulmonary Surfactant Biogenesis. J. Biol. Chem. 2007;282: 9628–9634. doi: 10.1074/jbc.M611767200 17267394
49. Wittmann T, Schindlbeck U, Höppner S, Kinting S, Frixel S, Kröner C, et al. Tools to explore ABCA3 mutations causing interstitial lung disease. Pediatr. Pulmonol. 2016;51: 1284–1294. doi: 10.1002/ppul.23471 27177387
50. Mandrile G, Dubois A, Hoffman JD, Uliana V, Di Maria E, Malacarne M, et al. 3q26.33–3q27.2 microdeletion: A new microdeletion syndrome? Eur J Med Genet. 2013;56: 216–221. doi: 10.1016/j.ejmg.2013.01.005 23357683
51. Dasouki M, Roberts J, Santiago A, Saadi I, Hovanes K. Confirmation and further delineation of the 3q26.33–3q27.2 microdeletion syndrome. Eur J Med Genet. 2014;57: 76–80. doi: 10.1016/j.ejmg.2013.12.007 24462885
52. Somaschi M, Nogee LM, Sassi I, Danhaive O, Presi S, Boldrini R, et al. Unexplained Neonatal Respiratory Distress Due to Congenital Surfactant Deficiency. J. Pediatr. 2007;150: 649–653.e1. doi: 10.1016/j.jpeds.2007.03.008 17517255
53. Kennelliitto Suomen [Internet]. Koiranet Jalostustietojärjestelmä [cited 2018 Nov 8]. 2018. Available from: https://jalostus.kennelliitto.fi/.
54. Karnovsky MJ. Use of ferrocyanide-reduced osmium tetroxide in electron microscopy. Proc. 11th Ann.Meeting. Am Soc Cell Biol. 1971: 146a.
55. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81: 559–575. S0002-9297(07)61352-4 [pii]. doi: 10.1086/519795 17701901
56. Broeckx BJ, Hitte C, Coopman F, Verhoeven GE, De Keulenaer S, De Meester E, et al. Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. Sci Rep. 2015;5: 12810. doi: 10.1038/srep12810 26235384
57. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25: 1754–1760. doi: 10.1093/bioinformatics/btp324 19451168
58. Broad Institute Github repository [Internet]. Picard Toolkit [cited 2018 Nov 20]. 2018. Available from: http://broadinstitute.github.io/picard/.
59. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20: 1297–1303. doi: 10.1101/gr.107524.110 20644199
60. Layer RM, Kindlon N, Karczewski KJ, Exome Aggregation Consortium, Quinlan AR. Efficient genotype compression and analysis of large genetic-variation data sets. Nat Methods. 2016;13: 63–65. doi: 10.1038/nmeth.3654 26550772
61. Arumilli M, Layer R, Hytönen M, Lohi H. webGQT: A Graphical User Interface for Genotype Query Tools, Front Genet, Forthcoming 2020.
62. Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics (Oxford, England). 2012;28: i333–i339. doi: 10.1093/bioinformatics/bts378 22962449
63. Bao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mobile DNA. 2015;6: 11. doi: 10.1186/s13100-015-0041-9 26045719
64. Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, et al. The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. Genome research. 2017;27: 1916–1929. doi: 10.1101/gr.218032.116 28855259
65. Thongtharb A, Uchida K, Chambers JK, Kagawa Y, Nakayama H. Histological and immunohistochemical studies on primary intracranial canine histiocytic sarcomas. J. Vet. Med. Sci. 2016;78: 593–599. doi: 10.1292/jvms.15-0627 26668164
66. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 2012;40: e115. doi: 10.1093/nar/gks596 22730293
67. Donner J, Kaukonen M, Anderson H, Möller F, Kyöstilä K, Sankari S, et al. Genetic Panel Screening of Nearly 100 Mutations Reveals New Insights into the Breed Distribution of Risk Variants for Canine Hereditary Disorders. PloS one. 2016;11: e0161005. doi: 10.1371/journal.pone.0161005 27525650
68. Donner J, Anderson H, Davison S, Hughes AM, Bouirmane J, Lindqvist J, et al. Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs. PLoS genetics. 2018;14: e1007361. doi: 10.1371/journal.pgen.1007361 29708978
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