Production of An Incomplete Protein and Diamond Blockfan Anemia Disease Due to a New Nonsense Mutation in RPS19 Gene

Subject Areas : Journal of Animal Biology

Javad Roodgar Saffari ¹ , Mohamad Mahdi Forghanifard ² , Vajihe Zarrinpour ³

1 - Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
2 - Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
3 - Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran

Received: 2022-09-14 Accepted : 2023-01-08 Published : 2023-08-23

Keywords: RPS19, Whole Exome Sequencing, Diamond-Blackfan Anemia,

Abstract :

Congenital hypoplastic anemia or Diamond-Blackfan anemia (DBA) usually occurs in the first year of life, and most patients with DBA survive until the age of six. For every one million live births, five to seven babies are affected by this disease. In 80-85% of cases, this disorder is caused by mutation of the ribosomal protein gene, and in about 25% of these cases, the RPS19 gene is the cause of this condition. The defect of this gene can disrupt the balance of blood cells, which appears as normocytic anemia, severe anemia, and macrocytic changes, along with a decrease in reticulocytes in the bone marrow. Patients need long-term corticosteroids. Whole exome sequencing of the blood sample of a patient with DBA was performed. The pathogenic mutation was investigated in the patient, his family and 30 people. The three-dimensional structure of the protein was evaluated using homology modeling and the interaction of the mutated protein with other proteins in the 40S ribosomal subunit. Peripheral blood test revealed a mutation on exon 3 of PRS19 gene (H42fs c.126-127 ins TA NM-00102) and chromosomal region 19q13.2. This mutation was autosomal dominant, during which amino acid number 42 of histidine was converted into a stop codon and a shortened protein was produced. The behavior of this protein with the PRS18 gene in healthy and mutated states shows that when the mutation occurs in PRS19, the amino acids Leu45, Ala46, Pro47, Tyr48, Asp49, Glu50 and Trp52, which are important residues connected are converted to RPS18, they are no longer present in this protein. Therefore, the binding of truncated RPS19 to RPS18 is significantly reduced. Although it seems that the presence of these residues may not prevent the interaction of RPS19 with RPS16 in the mutant state, it is possible that the mutant protein disrupts the spatial arrangement of other proteins and affects the interactions. affect them.

References:

1. Assenov Y., Ramírez F., Schelhorn S.E., Lengauer T., Albrecht M. 2008. Computing topological parameters of biological networks. Bioinformatics, 24(2):282-284.


2. Boria I., Garelli E., Gazda H.T., Aspesi A., Quarello P., Pavesi E., Ferrante D., Meerpohl J.J., Kartal M., Da Costa L., Proust A., Leblanc T., Simansour M., Dahl N., Fröjmark A.S., Pospisilova D., Cmejla R., Beggs A.H., Sheen M.R., Landowski M., Buros C.M., Clinton C.M., Dobson L.J., Vlachos A., Atsidaftos E., Lipton J.M., Ellis S.R., Ramenghi U., Dianzani I. 2010. The ribosomal basis of Diamond‐Blackfan Anemia: mutation and database update. Human Mutation, 31(12): 1269-1279.


3. Del Orbe Barreto R., rrizabalaga B., De la Hoz A.B., García-Orad Á., Tejada M.I., Garcia-Ruiz J.C., Fidalgo T., Bento C., Manco L., Ribeiro M.L. 2016. Detection of new pathogenic mutations in patients with congenital haemolytic anaemia using next‐generation sequencing. Internatonal Journal of Laboratory Hematology, 38(6): 629-638.


4. DeLano W.L. 2002. The PyMOL molecular graphics system. Delano Scientific, San Carlos.


5. Gazda H., Lipton J.M., Willig T.N., Ball S., Niemeyer C.M., Tchernia G., Mohandas N., Daly M.J., Ploszynska A., Orfali K.A., Vlachos A., Glader B.E., Rokicka-Milewska R., Ohara A., Baker D., Pospisilova D., Webber A., Viskochil D.H., Nathan D.G., Beggs A.H., Sieff C.A. 2001. Evidence for linkage of familial Diamond-Blackfan anemia to chromosome 8p23. 3-p22 and for non-19q non-8p disease. Blood, 97(7): 2145-2150.


6. Gazda H.T., Sieff CA. 2006. Recent insights into the pathogenesis of diamond–Blackfan anaemia. British Journal of Haematology, 135(2): 149-157.


7. Gerrard G., Valgañón M., Foong H.E., Kasperaviciute D., Iskander D., Game L., Müller M., Aitman T.J., Roberts I., de la Fuente J., Foroni L., Karadimitris A. 2013.Target enrichment and high‐throughput sequencing of 80 ribosomal protein genes to identify mutations associated with Diamond‐Blackfan anaemia. British Journal of Haematology, 162(4): 530-536.


8. Hahn C.N., Chong C.E., Carmichael C.L., Wilkins E.J., Brautigan P.J., Li X.C., Babic M., Lin M., Carmagnac A., Lee Y.K., Kok C.H., Gagliardi L., Friend K.L., Ekert P.G., Butcher C.M., Brown A.L., Lewis I.D., To L.B., Timms A.E., Storek J., Moore S., Altree M., Escher R., Bardy P.G., Suthers G.K., D'Andrea R.J., Horwitz M.S., Scott H.S. 2011. Heritable GATA2 mutations associated with familial myelodysplastic syndrome and acute myeloid leukemia. Nature Genetics, 43(10): 1012.


9. Heo L., Park H., Seok C. 2013., GalaxyRefine: Protein structure refinement driven by side-chain repacking. Nucleic Acids Research, 41(W1): 384-388.


10. Khurana M.., Edwards D., Rescorla F., Miller C., He Y., Sierra Potchanant E., Nalepa G. 2018. Whole-exome sequencing enables correct diagnosis and surgical management of rare inherited childhood anemia. Cold Spring Harbor Molecular Case Studies, 4(5): a003152.


11. Laskowski R.A., MacArthur W., Moss D.S., Thornton J.M. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. International Journal of Applied Crystallography, 26(2): 283-291.


12. Laskowski R.A., Swindells M.B. 2011. LigPlot+: multiple ligand–protein interaction diagrams for drug discovery. ACS Publications.


13. Lipton J.M., Ellis S.R. 2009. Diamond-Blackfan anemia: diagnosis, treatment, and molecular pathogenesis. Hematology/Oncology Clinics of North America, 23(2): 261-282.


14. Li H., Lodish H.F., Sieff C.A. 2018. Critical issues in Diamond-Blackfan anemia and prospects for novel treatment. Hematology/Oncology Clinics of North America, 32(4): 701-712.


15. Liu X., Jian X., Boerwinkle E.J. 2013. dbNSFP v2.0: a database of human non‐synonymous SNVs and their functional predictions and annotations. Human Mutation, 34(9): E2393-E2402.


16. Miller S.A., Dykes D.D., Polesky H.F. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research, 16(3):1215.


17. Orrù, S., Aspesi A., Armiraglio M., Caterino M., Loreni F., Ruoppolo M., Santoro C., Dianzani I. 2007. Analysis of the ribosomal protein S19 interactome. Molecular and cellular Proteomics, 6(3): 382-393.


18. Proust A., Da Costa L., Rince P., Landois A., Tamary H., Zaizov R., Tchernia G., Delaunay J., 2003. Ten novel Diamond-Blackfan anemia mutations and three polymorphisms within the rps19 gene. The Hematology Journal, 4(2): 132-136.


19. Quarello P., Garelli E., Carando A., Brusco A., Calabrese R., Dufour C., Longoni D., Misuraca A., Vinti L., Aspesi A., Biondini L., Loreni F., Dianzani I., Ramenghi U. 2010. Diamond-Blackfan anemia: genotype-phenotype correlations in Italian patients with RPL5 and RPL11 mutations. Haematologica, 95(2): 206.


20. Rogers B.B., Bloom S.L., Buchanan G.R. 1997. Autosomal dominantly inherited Diamond-Blackfan anemia resulting in nonimmune hydrops. Obstetrics and Gynecology, 89(5): 805-807.


21. Roy V., Pérez W.S., Eapen M., Marsh J.C., Pasquini M., Pasquini R., Mustafa M.M., Bredeson C.N. 2005. Bone marrow transplantation for diamond-blackfan anemia. Biology of Blood Marrow and Transplantation, 11(8): 600-608.


22. Saladi S., Chattopadhyay T., Adiotomre P.J. 2004. Nomimmune hydrops fetalis due to Diamond-Blackfan anemia. Indian Pediatrics, 41(2): 187-188.


23. Sankaran V.G., Ghazvinian R., Do R., Thiru P., Vergilio J.A., Beggs A.H., Sieff C.A., Orkin S.H., Nathan D.G., Lander E.S., Gazda H.T. 2012. Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia. The Journal of Clinical Investigation, 122(7): 2439-2443.


24. Soranzo N., Spector T.D., Mangino M., Kühnel B., Rendon A., Teumer A., Willenborg C., Wright B., Chen L., Li M., Salo P., Voight B.F., Burns P., Laskowski R.A., Xue Y., Menzel S., Altshuler D., Bradley J.R., Bumpstead S., Burnett M.S., Devaney J., Döring A., Elosua R., Epstein S.E., Erber W., Falchi M., Garner S.F., Ghori M.J., Goodall A.H., Gwilliam R., Hakonarson H.H., Hall A.S., Hammond N., Hengstenberg C., Illig T., König I.R., Knouff C.W., McPherson R.., Melander O., Mooser V., Nauck M., Nieminen M.S., O'Donnell C.J., Peltonen L., Potter S.C., Prokisch H., Rader D.J., Rice C.M., Roberts R., Salomaa V., Sambrook J., Schreiber S., Schunkert H., Schwartz S.M., Serbanovic-Canic J., Sinisalo J., Siscovick D.S., Stark K., Surakka I, Stephens J, Thompson JR, Völker U., Völzke H, Watkins NA, Wells GA, Wichmann H.E., Van Heel D.A., Tyler-Smith C., Thein S.L., Kathiresan S., Perola M., Reilly M.P., Stewart A.F., Erdmann J., Samani N.J., Meisinger C., Greinacher A., Deloukas P., Ouwehand W.H., Gieger C.l., 2009. A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nature Genetics, 41(11): 1182-1190.


25. Szklarczyk D., Gable A.L., Lyon D., Junge A., Wyder S., Huerta-Cepas J., Simonovic M., Doncheva N.T., Morris J.H., Bork P., Jensen L.J. 2019. Mering CV.STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47(D1): D607-D613.


26. van Dooijeweert B., van Ommen C.H., Smiers F.J., Tamminga R.Y.J., Te Loo M.W., Donker A.E., Peters M., Granzen B., Gille H.J.J.P., Bierings M.B., MacInnes A.W., Bartels M. 2018. Pediatric Diamond‐Blackfan anemia in the Netherlands: An overview of clinical characteristics and underlying molecular defects. European Journa of Haematology, 100(2): 163-170.


27. Vilboux T., Lev A., Malicdan M.C., Simon A.J., Järvinen P., Racek T., Puchalka J., Sood R., Carrington B., Bishop K., Mullikin J., Huizing M., Garty B.Z., Eyal E., Wolach B., Gavrieli R., Toren A., Soudack M., Atawneh O.M., Babushkin T., Schiby G., Cullinane A., Avivi C., Polak-Charcon S., Barshack I., Amariglio N., Rechavi G., van der Werff ten Bosch J., Anikster Y., Klein C., Gahl W.A., Somech R. 2013. A congenital neutrophil defect syndrome associated with mutations in VPS45. The New England Journal of Medicine, 369(1):54-65.


28. Vlachos A., Rosenberg P.S., Atsidaftos E., Alter B.P., Lipton J.M. 2012. Incidence of neoplasia in Diamond Blackfan anemia: a report from the Diamond Blackfan Anemia Registry. Blood, 119(16): 3815-3819.


29. Walne A.J., Dokal A, Plagnol V, Beswick R., Kirwan M., de la Fuente J., Vulliamy T., Dokal I., Dokal A., Plagnol V., Beswick R., Kirwan M., de la Fuente J., Vulliamy T., Dokal I. 2012. Exome sequencing identifies MPL as a causative gene in familial aplastic anemia. Haematologica, 97(4): 524-528.