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BACE1gene variants do not influence BACE1 activity, levels of APP or Aβ isoforms in CSF in Alzheimer's disease

  • 1Email author,
  • 1,
  • 1,
  • 2, 3 and
  • 1
Molecular Neurodegeneration20105:37

  • Received: 16 June 2010
  • Accepted: 17 September 2010
  • Published:


The BACE1 gene encodes the beta-site APP-cleaving enzyme 1 and has been associated with Alzheimer's disease (AD). BACE1 is the most important β-secretase responsible for the generation of Alzheimer-associated amyloid β-proteins (Aβ) and may play a role in the amyloidogenic process in AD. We hypothesized that BACE1 gene variants might influence BACE1 activity or other markers for APP metabolism in the cerebrospinal fluid (CSF) and thereby contribute to the development of AD. We genotyped a Swedish sample of 269 AD patients for the rs638405 single nucleotide polymorphism (SNP) in the BACE1 gene and correlated genotype data to a broad range of amyloid-related biomarkers in CSF, including BACE1 activity, levels of Aβ40, Aβ42, α- and β-cleaved soluble APP (α-sAPP and β-sAPP), as well as markers for Alzheimer-type axonal degeneration, i.e., total-tau and phospho-tau181. Gene variants of BACE1 were neither associated with amyloid-related biomarkers, nor with markers for axonal degeneration in AD.


  • Amyloid Precursor Protein
  • Axonal Degeneration
  • BACE1 Activity
  • Amyloid Precursor Protein Metabolism
  • BACE1 Gene


Cleavage of the amyloid precursor protein (APP) by β- and γ-secretase gives rise to the amyloid β-protein (Aβ) found in senile plaques (SP) in Alzheimer's disease (AD). The BACE1 gene encodes the beta-site APP-cleaving enzyme 1 (OMIM 604252), which is involved in β-secretase activity [14]. The BACE1 gene is associated with AD [5, 6] and the BACE1 activity is elevated both in brain tissue and in CSF in AD [7, 8]. We hypothesized that BACE1 gene variants might influence the BACE1 activity or other amyloid-related biomarkers related to amyloid in the cerebrospinal fluid (CSF) and thereby contribute to developing AD. We tested a single nucleotide polymorphism (SNP) in the BACE1 gene to evaluate the genetic influence on BACE1 activity, levels of Aβ40, Aβ42, α- and β-cleaved soluble APP (α-sAPP and β-sAPP) in CSF from AD patients. Further we assessed the BACE1 genetic influence on markers for Alzheimer-type axonal degeneration (total-tau and phospho-tau181). The rs638405 SNP have a high allele frequency with a global frequency of the least common variant of 0.32. To our knowledge this is the first study investigates BACE1 genotype data in relation to BACE1 activity and other amyloid-related biomarkers in CSF from AD patients.

We studied a Swedish Caucasian sample of 269 AD patients (90 men and 179 women, mean age 74.7 ± 6.3 years) where CSF levels of total-tau, phospho-tau181 and Aβ42 were known. We measured the BACE1 activity, levels of α-sAPP, β-sAPP and Aβ40 in CSF samples from 84 of the patients. All participants were recruited at the Memory Clinic at the Malmö University Hospital. The patients gave informed consent to participate in the study, which was conducted according to the provisions of the Helsinki Declaration and approved by the local ethic committee. The diagnosis of "probable AD" was made according to the NINCDS-ADRDA criteria [9]. No AD patient had any of the known familial forms of autosomal dominant AD.

CSF samples were taken by lumbar puncture. BACE1 activity was determined with a sensitive and specific solution-based assay previously described [10]. Levels of total-tau, phospho-tau181 and Aβ42 were measured using established ELISA methods [11, 12] while α-sAPP, β-sAPP and Aβ40 were quantified using MSD immunoassays (Cat#: K11120E and K111FTE), (Meso Scale Discovery, Gaithersburg, MD, USA).

Genomic DNA was extracted from whole blood using standard methods. BACE1 alleles were determined using the Dynamic Allele Specific Hybridization (DASH) technique as described earlier [13]. Optimal assay conditions: 1.5 mM MgCl2, 200 μM dNTPs, 0.05 U/μl Taq polymerase, 0.15 pmol/μl forward biotinylated primer (5'-Biotin-ATCCGGCGGGAGTGGTATTATG-3'), 0.75 pmol/μl reverse primer (5'-GTCCATTGATCTCCACCCGCAC-3') (Invitrogen, Life Technologies) and 5-20 ng DNA, 1xPCR buffer in a final volume of 25 μl. The cycling profile was: 5 min 95°C, 40 cycles: 30 sec 95°C, 45 sec 60°C, 1 min 72°C and a final step of 10 min 72°C. To identify BACE1 alleles the probes 5'-CACAATGATCACCTCATAA-3' and 5'-CACAATGATGACCTCATAA-3' were used.

APOE genotyping was performed using minisequencing as described before [14]. Gene designations follow the recommendations of HUGO Gene Nomenclature Committee [15].

The genotype and allele frequencies of the BACE1 rs638405 and APOE ε4 are shown in table 1. The analysis of variance (ANOVA) was used to analyze the effects of BACE1 genetic variants on MMSE, BACE1 activity and CSF protein levels. To test the effects of known risk factors, e.g., age, sex and APOE ε4 we identified significantly relevant covariates for each outcome variable (MMSE and levels of AD CSF biomarkers) using forward stepwise linear regression. Hardy-Weinberg equilibrium was assessed by χ2 statistics. The criterion for significance was set at p < 0.05 for all statistical tests. Statistical analyses were performed with the SYSTAT11 (SYSTAT Software GmbH, Erkrath, Germany) software.
Table 1

BACE1 and APOE genotype and allele frequencies in AD patients



Genotype frequencies




AD (269)

50 (0.19)

117 (0.43)

102 (0.38)

Allele frequencies




AD (538)

217 (0.40)

321 (0.60)



Genotype frequencies

No ε4

One ε4

Two ε4

AD (269)

74 (0.28)

135 (0.50)

60 (0.22)

Allele frequencies




AD (538)

283 (0.53)

255 (0.47)


Abbreviations: Alzheimer's disease (AD). Number of total genotypes and alleles are given (N). Percentage of total is shown for the genotypes and alleles respectively.

We studied BACE1 gene variants in relation to BACE1 activity and levels of amyloid-related biomarkers in CSF from AD patients. In the linear regression analysis we found APOE ε4 to significantly interact with phospho-tau18, Aβ42 and MMSE. Subsequently, APOE ε4 was included as covariate in the statistic model. We found no effect of BACE1 gene variants on BACE1 activity or levels of Aβ40, Aβ42, α-sAPP and β-sAPP (Table 2). We compared CSF levels of markers for axonal degeneration (total-tau and phospho-tau181) between BACE1 gene variants and found no significant differences in protein levels (Table 2). The BACE1 SNP showed no association with MMSE (data not shown).
Table 2

BACE1 activity and biochemical markers in CSF and BACE1 genotypes in AD patients

BACE1genetic variants

CSF protein





Total-tau (pg/ml)

628.8 ± 38.7

612.7 ± 29.3

610.0 ± 33.4


Phospho-tau181 (pg/ml)

79.7 ± 3.9

73.8 ± 2.8

77.7 ± 3.4


42 (pg/ml)

408.7 ± 11.8

419.4 ± 9.2

408.3 ± 9.9


40 (pg/ml)

4869.9 ± 196.4

4894.8 ± 238.6

5030.7 ± 219.6


BACE1 (pM)

29.2 ± 2.5

31.8 ± 2.0

33.6 ± 3.3


α-sAPP (ng/ml)

645.8 ± 77.0

660.5 ± 40.6

620.5 ± 41.8


β-sAPP (ng/ml)

393.3 ± 37.8

408.0 ± 24.9

399.6 ± 22.6


Abbreviations: Alzheimer's disease (AD). Mean values (± SEM) are shown. Adjusted p-values are shown for respective comparison.

The APOE allele distribution followed the expected frequencies seen in AD populations (Table 1). Genotype frequencies conformed to Hardy-Weinberg equilibrium in AD patients.

We hypothesized that BACE1 gene variants might influence BACE1 activity or levels of amyloid-related biomarkers in the cerebrospinal fluid (CSF) and thereby contribute to the development of AD. A genome-wide screen of AD families has shown linkage to marker close to BACE1 [16] and the rs638405 SNP has been tested in a number of studies [5, 17]. Other studies have found association between the BACE1 gene and AD [5, 18]. Even though this SNP does not change the protein sequence it still can have functional effects based on earlier findings where BACE1 influenced levels of Aβ in CSF [6]. We tested if the rs2069456 SNP was associated with BACE1 activity or with levels of Aβ40, Aβ42, α-sAPP and β-sAPP in CSF from AD patients. Further we assessed the influence on total-tau and phospho-tau181. Gene variants of BACE1 were neither associated with amyloid-related biomarkers nor with markers for axonal degeneration. Our results do not support that variants of the BACE1 gene affects BACE1 activity or CSF levels of APP or Aβ isoforms in AD.



This work was supported by grants from Demensfonden.

Authors’ Affiliations

Institute of Neuroscience and Physiology, Department of Neurochemistry and Psychiatry, Sahlgrenska University Hospital, University of Gothenburg, Sweden
Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Sweden
Neuropsychiatric Clinic, Malmö University Hospital, Sweden


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