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): e1008651. doi:10.1371/journal.pgen.1008651
Kategorie: Research Article
doi: 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

Štítky
Genetika Reprodukční medicína

Článek vyšel v časopise

PLOS Genetics


2020 Číslo 3

Nejčtenější v tomto čísle

Tomuto tématu se dále věnují…


Kurzy

Zvyšte si kvalifikaci online z pohodlí domova

Kurz originály vs. generika
nový kurz
Autoři:

Klinická farmakokinetika betablokátorů
Autoři:

Současné možnosti terapie osteoartrózy
Autoři: MUDr. Jakub Holešovský

Preferovaná úlevová léčba Asthma Bronchiale
Autoři: PharmDr. Petr Sedlák

Inhibitory karboanhydrázy v léčbě glaukomu
Autoři: MUDr. Petr Výborný, CSc., FEBO

Všechny kurzy
Přihlášení
Zapomenuté heslo

Nemáte účet?  Registrujte se

Zapomenuté heslo

Zadejte e-mailovou adresu se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se