Variations in Hotspot Region of β-amyloid Precursor Protein (APP) Gene in Various Neurological Disorders from Hyderabad, a Cosmopolitan City of South India

Winnie Thomas¹, Sireesha Divyakolu¹, Vemula Ramana Sreekanth², Vallomkonda Ramesh Om Sai³, Vallomkonda Nagaratna³, Qurratulain Hasan^{1, 4} and Yog Raj Ahuja^1,

¹Department of Genetics and Molecular Medicine, Vasavi Medical and Research Centre, Lakdi-ka-pool, Hyderabad, Andhra Pradesh, India

²Department of Neurology, Apollo Hospital, Jubilee Hills, Hyderabad, Andhra Pradesh, India

³Department of Medical Sciences, National Institute of Mentally Handicapped (NIMH), Bowenpally, Hyderabad, India

⁴Department of Genetics and Molecular Medicine, Kamineni Hospital, LB Nagar, Hyderabad, Andhra Pradesh, India
Hyderabad science society, Mehdipatnam, Hyderabad, Telangana

Cite this paper:
Winnie Thomas, Sireesha Divyakolu, Vemula Ramana Sreekanth, Vallomkonda Ramesh Om Sai, Vallomkonda Nagaratna, Qurratulain Hasan and Yog Raj Ahuja. Variations in Hotspot Region of β-amyloid Precursor Protein (APP) Gene in Various Neurological Disorders from Hyderabad, a Cosmopolitan City of South India. International Journal of Clinical and Experimental Neurology. 2015; 3(1):4-10. doi: 10.12691/ijcen-3-1-2

Abstract

Non-synonymous mutations/ polymorphism in amyloid precursor protein (APP) gene cause overproduction of Aβ proteins or affect its split into Aβ40 and Aβ42 peptides. Aβ42 has been considered to be a toxic peptide playing a major role in the pathogenesis of Alzheimers (AD). Similar APP plaques were observed in the brains of Down syndrome (DS) patients and high level of plasma APP was observed in patients with severe Autism spectrum Disorder (ASD). The aim of this study was to evaluate exon 16 and 17, the hotspot regions of APP gene in patients with neurobehavioral disorders like AD, DS and ASD. A total of 75 cases were recruited in the study which included AD (n=25), DS (n=25), and ASD (n=25). Polymerase chain reaction (PCR) analysis and sequencing was carried out using exon-intron encompassing primers for the selected APP gene regions. In-silico analysis was also carried out to identify the impact of sequence variants on the protein structure. Three exonic variants, two in exon 16: V683V, H684Y and one in exon 17, H733Q were identified in sporadic AD cases. Apart from these, two intronic variants were also observed. In-silico analysis showed that H733Q mutation may affect the structure and function of APP, whereas H684Y mutation is neutral. In an ASD case, our analysis showed an intronic variation ie. An A insertion at c.1964-13_1964-12insA. In-silico analysis predicted that this variation affects the elongation feature of the protein. None of the DS cases had any variation in this hotspot region. Our data indicate that variations in the selected hotspot region of APP may play an important role in the aetiology of neurobehavioral disorders.

Keywords:
Alzheimer Disease exon 16 and 17 of APP gene Amyloid precursor protein (APP) Polymorphism mutations

This work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

References:

[1]	Alzheimer’s disease facts and figures. 2010. http://www.alz.org/documents custom/report alzfactsfigures 2010. Date of accession: 4 February 2013.
[2]	Newell KL, Hyman BT, Growdon JH, Hedley-Whyte ET. “Application of the National Institute on Aging (NIA)-Reagan Institute criteria for the neuropathological diagnosis of Alzheimer disease.” Journal of Neuropathology and Experimental Neurology, 58(11):1147-1155, November 1999.
[3]	Ge YW, Lahiri DK “Regulation of promoter activity of the APP gene by cytokines and growth factors: Implications in Alzheimer’s disease,” Annals of the New York Academy of Sciences, 973:463-467, November 2002.
[4]	Hassold T., Abruzzo M., Adkins K., Griffin D., Merrill M., Millie E., Saker D., Shen J., Zaragoza M. “Human aneuploidy: Incidence, origin and etiology,” Environmental and Molecular Mutagenesis, 28: 167-175, October 1996.
[5]	Epstein C.J., Korenberg J.R., Anneren G., Antonarakis S.E., Ayme S., Courchesne E., Epstein L.B., Fowler A., Groner Y., Huret J.L., “Protocols to establish genotype-phenotype correlations in Down syndrome,” American Journal of Human Genetics, 49:207-235, July 1991.
[6]	Capone GT. “Down syndrome: advances in molecular biology and the neurosciences,” Journal of Developmental & Behavioral Pediatrics, 22: 40-59, February 2001.
[7]	Ousley O1, Cermak T2. “Autism Spectrum Disorder: Defining Dimensions and Subgroups,” Current Developmental Disorders Reports, 1(1): 20-28, March 2014.
[8]	Ray B1, Long JM, Sokol DK, Lahiri DK. “Increased secreted amyloid precursor protein-α (sAPPα) in severe autism: proposal of a specific, anabolic pathway and putative biomarker,” PLoS One, 6(6):e20405, June 2011.
[9]	Daigle I & Li C. “APL-1, a Caenorhabditis elegans gene encoding a protein related to the human beta-amyloid protein precursor,” Proceedings of the National Academy of Sciences of the United States of America, 90:12045-12049, December 1993.
[10]	Luo LQ, Martin-Morris LE & White K: “Identification, secretion, and neural expression of APPL, a Drosophila protein similar to human amyloid protein precursor,” Journal of Neuroscience, 10: 3849-3861, December 1990.
[11]	Tanzi RE, Gusella JF, Watkins PC, Bruns GA, St George-Hyslop P, Van Keuren ML, Patterson D, Pagan S, Kurnit DM, Neve RL. “Amyloid beta protein gene: cDNA, mRNA distribution, and genetic linkage near the Alzheimer locus,” Science, 235: 880-884, February 1987.
[12]	Wasco W, Bupp K, Magendantz M, Gusella JF, Tanzi RE, Solomon F, “Identification of a mouse brain cDNA that encodes a protein related to the Alzheimer disease-associated amyloid beta protein precursor,” Proceedings of the National Academy of Sciences of the United States of America, 89: 10758-10762, November 1992.
[13]	Wasco W, Gurubhagavatula S, Paradis MD, Romano DM, Sisodia SS, Hyman BT, Neve RL, Tanzi RE, “Isolation and characterization of APLP2 encoding a homologue of the Alzheimer's associated amyloid beta protein precursor,” Nature Genetics, 5: 95-100, September 1993.
[14]	St George-Hyslop PH, Tanzi RE, Polinsky RJ, Haines JL, Nee L, Watkins PC, Myers RH, Feldman RG, Pollen D, Drachman D, et al. “The genetic defect causing familial Alzheimer’s disease maps on chromosome 21,” Science, 4791: 885-890, February 1987.
[15]	Levy E, Carman MD, Fernandez-Madrid IJ, Power MD, Lieberburg I, van Duinen SG, Bots GT, Luyendijk W, Frangione B. “Mutation of the Alzheimer’s disease amyloid gene in hereditary cerebral hemorrhage, Dutch type,” Science, 248(4959): 1124-1126, June 1990.
[16]	Hardy, J. C. & Crook, R. APP mutations table. http://www.alzforum.org/res/com/mut/app/table1.asp (2010).
[17]	McKhann G, Drachman D, Folstein M, Katzman R, Price D, Stadlan EM, “Clinical diagnosis of Alzheimer’s disease: report of the NINCDS-ADRDA work group under the auspices of Department of Health and Human Services Task Force on Alzheimer’s disease,” Neurology, 34: 939-944, July 1984.
[18]	Latha M, Vaidya S, Movva S, Chava S, Govindan S, Govatati S, Banoori M, Hasan Q, Kodati VL, “Molecular pathogenesis of endometriosis: Toll like receptor- 4 A896G (D299G) polymorphism: a novel explanation,” Genetic Testing and Molecular Biomarkers, 15:181-184, March 2011.
[19]	Crawford F, Hardy J, Mullan M, Goate A, Hughes D, Fidani L, Roques P, Rossor M, Chartier-Harlin MC, “Sequencing of exons 16 and 17 of the beta-amyloid precursor protein gene in 14 families with early onset Alzheimer's disease fails to reveal mutations in the beta-amyloid sequence,” Neuroscience Letters 133(1): 1-2, November 1991.
[20]	Murrell JR, Hake AM, Quaid KA, Farlow MR, Ghetti B, “Early-Onset Alzheimer Disease Caused by a New Mutation (V717L) in the Amyloid Precursor Protein Gene,” Archives of Neurology, 57: 885-887, June 2000.
[21]	Vaidya S, Shaik NA, Latha M, Chava S, Mohiuddin K, Yalla A, Rao KP, Kodati VL, Hasan Q, “No evidence for the role of somatic mutations and promoter hypermethylation of FH gene in the tumorigenesis of nonsyndromic uterine leiomyomas,” Tumour Biology, 33(5): 1411-1418, October 2012.
[22]	Ng PC & Henikoff S, “Predicting deleterious amino acid substitutions,” Genome Research, 11: 863-874, May 2001.
[23]	Ramensky V, Bork P, Sunyaev S, “Human non-synonymous SNPs: server and survey,” Nucleic Acids Research, 30: 3894-3900, September 2002.
[24]	Yue P& Moult J, “Identification and analysis of deleterious human SNPs,” Journal of Molecular Biology, 356: 1263-1274, March 2006.
[25]	Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P, “Automated inference of molecular mechanisms of disease from amino acid substitutions,” Bioinformatics, 25(21): 2744-2750, Novemeber 2009.
[26]	McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F, “Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor,” Bioinformatics, 26(16): 2069-70, August 2010.
[27]	Li H, Wetten S, Li L, St Jean PL, Upmanyu R, Surh L, Hosford D, Barnes MR, Briley JD, Borrie M, Coletta N, Delisle R, Dhalla D, Ehm MG, Feldman HH, Fornazzari L, Gauthier S, Goodgame N, Guzman D, Hammond S, Hollingworth P, Hsiung GY, Johnson J, Kelly DD, Keren R, Kertesz A, King KS, Lovestone S, Loy-English I, Matthews PM, Owen MJ, Plumpton M, Pryse-Phillips W, Prinjha RK, Richardson JC, Saunders A, Slater AJ, St George-Hyslop PH, Stinnett SW, Swartz JE, Taylor RL, Wherrett J, Williams J, Yarnall DP, Gibson RA, Irizarry MC, Middleton LT, Roses AD, “Candidate single nucleotide polymorphism from a genomewide association study of Alzheimer disease,” Archives of Neurology, 65: 45-53, January 2008.
[28]	Abraham R, Moskvina V, Sims R, Hollingworth P, Morgan A, Georgieva L, Dowzell K, Cichon S, Hillmer AM, O'Donovan MC, Williams J, Owen MJ, Kirov G, “A genome-wide association study for late-onset Alzheimer's disease using DNA pooling,” BMC Medical Genomics, 29; 1:44, September 2008.
[29]	Beecham GW, Martin ER, Li YJ, Slifer MA, Gilbert JR, Haines JL, Pericak-Vance MA, “Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease,” American Journal of Human Genetics, 84(1):35-43, January 2009.
[30]	Ertekin-Taner N, “Genetics of Alzheimer disease in the pre- and post-GWAS era,” Alzheimers Research and Therapy, 5; 2(1):3, March 2010.
[31]	Ma LL, Ou JR, Zhang W, Sun FR, Yu JT, Tan L, “ Single nucleotide polymorphism rs7294919 on chromosome 12q24.22 is associated with late-onset Alzheimer’s disease in Han Chinese,” Neuroscience Letters, 560:67-70, February 2014.
[32]	Johnston J, O'Neill C, Lannfelt L, Winblad B, Cowburn RF, “The significance of the Swedish APP670/671 mutation for the development of Alzheimer's disease amyloidosis. Neurochemistry International, 25(1): 73-80, July 1994.
[33]	Cruts M, Theuns J, Van Broeckhoven C, “Locus Specific mutation databases for neurodegenerative brain diseases,” Human Mutation, 33: 1340-1344, September 2012.
[34]	Iwatsubo T, Mann DM, Odaka A, Suzuki N, Ihara Y, “Amyloid beta protein (Aβ) deposition: A beta 42 precedes A beta 40 in Down syndrome,”Annals of Neurology, 37(3): 294-9, March 1995.
[35]	Tandon A, Rogaeva E, Mullan M, St George-Hyslop PH, “Molecular genetics of Alzheimer's disease: the role of beta-amyloid and the presenilins,” Current Opinion in Neurobiology, 13(4): 377-84, August 2000.
[36]	Holland A.J., Hon J., Huppert F.A., Stevens F, “Incidence and course of dementia in people with Down's syndrome: findings from a population-based study,” Journal of Intellectual Disability Research, 44: 138-146, April 2000.
[37]	Schupf N, Sergievsky GH, “Genetic and host factors for dementia in Down's syndrome,” British Journal of Psychiatry, 80: 405-10, May 2002.
[38]	Wegiel J, Frackowiak J, Mazur-Kolecka B, Schanen NC, Cook EH Jr, Sigman M, Brown WT, Kuchna I, Wegiel J, Nowicki K, Imaki H, Ma SY, Chauhan A, Chauhan V, Miller DL, Mehta PD, Flory M, Cohen IL, London E, Reisberg B, de Leon MJ, Wisniewski T, “Abnormal intracellular accumulation and extracellular Aβ deposition in idiopathic and Dup15q11.2-q13 autism spectrum disorders,” PLoS One, 7(5): e35414, May 2012.
[39]	Wakutani Y, Watanabe K, Adachi Y, Wada-Isoe K, Urakami K, Ninomiya H, Saido TC, Hashimoto T, Iwatsubo T, Nakashima K, “Novel amyloid precursor protein gene missense mutation (D678N) in probable familial Alzheimer's disease,” Journal of Neurology Neurosurgery and Psychiatry, 75(7): 1039-1042, July 2004.
[40]	Urakami K, Wakutani Y, Wada-Isoe K, Yamagata K, Adachi Y, Nakashima K, “ Analysis of causative genes and genetic risk factor in Alzheimer's disease,” Nihon Ronen Igakkai Zasshi, 38(6): 769-771, November 2001.
[41]	Rovelet-Lecrux A, Haunequin D, Raux G, Le Meur N, Laquerriere A, Vital A, Dumanchin C, Feuillette S, Brice A, Vercelletto M, Dubas F, Frebourg T Campion D, “APP locus duplication causes autosomal dominant early onset Alzheimer disease with cerebral amyloid angiopathy” Nature Genetics, 38: 24-26, January 2006.
[42]	Guerreiro RJ, Baquero M, Blesa R, Boada M, Brás JM, Bullido MJ, Calado A, Crook R, Ferreira C, Frank A, Gómez-Isla T, Hernández I, Lleó A, Machado A, Martínez-Lage P, Masdeu J, Molina-Porcel L, Molinuevo JL, Pastor P, Pérez-Tur J, Relvas R, Oliveira CR, Ribeiro MH, Rogaeva E, Sa A, Samaranch L, Sánchez-Valle R, Santana I, Tàrraga L, Valdivieso F, Singleton A, Hardy J, Clarimón J, “Genetic screening of Alzheimer's disease genes in Iberian and African samples yields novel mutations in presenilins and APP,” Neurobiol Aging. 2010; 31(5): 725-731, May 2010.
[43]	Liu ST, Howlett G, Barrow CJ, “Histidine-13 Is a Crucial Residue in the Zinc Ion-Induced Aggregation of the Aβ Peptide of Alzheimer's Disease.,” Biochemistry, 38 (29): 9373-9378, July 1999.
[44]	Jonsson T, Atwal JK, Steinberg S, Snaedal J, Jonsson PV, Bjornsson S, Stefansson H, Sulem P, Gudbjartsson D, Maloney J, Hoyte K, Gustafson A, Liu Y, Lu Y, Bhangale T, Graham RR, Huttenlocher J, Bjornsdottir G, Andreassen OA, Jönsson EG, Palotie A, Behrens TW, Magnusson OT, Kong A, Thorsteinsdottir U, Watts RJ, Stefansson K, “A mutation in APP protects against Alzheimer's disease and age-related cognitive decline,” Nature, 488(7409): 96-9, August 2012.
[45]	Tanzi RE, Vaula G, Romano DM, Mortilla M, Huang TL, Tupler RG, Wasco W, Hyman BT, Haines JL, Jenkins BJ, Kalaitsidaki M, Warren AC, McInnis MC, Antonarakis SE, Karlinsky H, Percy ME, Connor L, Growdon J, McIachlan DRC, Gusella JF, and St George-Hyslop P, “Assessment of amyloid beta-protein precursor gene mutations in a large set of familial and sporadic Alzheimer disease cases,” American Journal of Human Genetics, 51(2): 273-282, August 1992.