| Literature DB >> 19102732 |
Kathrin Scheckenbach1, Vera Balz, Martin Wagenmann, Thomas K Hoffmann.
Abstract
BACKGROUND: A combined aplasia, hypoplasia or atresia of lacrimal points and salivary glands is rarely diagnosed. Those patients suffer from epiphora, xerostomia and severe dental caries. This phenotype represents the autosomal-dominant aplasia of lacrimal and salivary glands syndrome (ALSG). Recently, aberrations of the Fibroblast Growth Factor 10 (FGF10) gene have been identified to be causative for this disorder.Entities:
Mesh:
Substances:
Year: 2008 PMID: 19102732 PMCID: PMC2626586 DOI: 10.1186/1471-2350-9-114
Source DB: PubMed Journal: BMC Med Genet ISSN: 1471-2350 Impact factor: 2.103
Oligonucleotide primers for amplification and sequence analysis of FGF10 in transcript and genomic DNA, and quality controls.
| 5'-UTR | 5-UTR-1 | 5'-CTC TCT CCT TGC CTT GCA TC-3' |
| Amplicon size: 456 bp | 1–2 | 5'-CTG GGG GTG GAT AAT TGG A-3' |
| Exon 1 | 1-1 | 5'-CAA TTT CCA GTG CCG AGA GT-3' |
| Amplicon size: 400 bp | 1–2 | 5'-CTG GGG GTG GAT AAT TGG A-3' |
| Exon 2 | 2-1 | 5'-GGA AAT ACT TGC CGG GTT TT-3' |
| Amplicon size: 439 bp | 2-2 | 5'-GCC CTT GAA ACA GTG GTG AC-3' |
| Exon 3 | 3-1 | 5'-GGA GTT CTC TGG ATG GCT TG-3' |
| Amplicon size: 392 bp | 3-2 | 5'-AAG CAG ACA TCT GCA ACG TG-3' |
| 3'-UTR | UTRS | 5'-GGA GTT CTC TGG ATG GCT TG-3' |
| Amplicon size: 1008 bp | PD3 | 5'-ATG CAT GTG GTG TGC TGA AT-3' |
| Amplification conditions: | ||
| 1 × 3 min at 94°C//35 × 30 sec at 94°C, 30 sec at 60°C, 1 min at 72°C//1 × 15 min at 72°C | ||
| 5'-UTR | 5-UTR-1 | 5'-CTC TCT CCT TGC CTT GCA TC-3' |
| Amplicon size: 330 bp | PD1 | 5'-TAG CTT TCT CCA GCG GAC AT-3' |
| Translated region | ||
| (exons 1–3) | 1-1 | 5'-CAA TTT CCA GTG CCG AGA GT-3' |
| Amplicon size: 770 bp | 3-2 | 5'-AAG CAG ACA TCT GCA ACG TG-3' |
| Amplification conditions: | ||
| 1 × 3 min at 94°C//35 × 20 sec at 94°C, 20 sec at 60°C, 1 min at 72°C//1 × 7 min at 72°C | ||
| 3'-UTR | PU2 | 5'-TCG GAG TTG TTG CCG TCA AAG-3' |
| Amplicon size: 1005 bp | PD3 | 5'-ATG CAT GTG GTG TGC TGA AT-3' |
| Amplification conditions: | ||
| 1 × 3 min at 94°C//35 × 20 sec at 94°C, 20 sec at 63°C, 1 min at 72°C//1 × 7 min at 72°C | ||
| Long range PCR | ||
| (Exons 2–3) | PU2 | 5'-TCG GAG TTG TTG CCG TCA AAG-3' |
| Amplicon size: | PD3 | 5'-ATG CAT GTG GTG TGC TGA AT-3' |
| gDNA = 6239 bp | ||
| cDNA wild type = 1005 bp | ||
| Amplification conditions: | ||
| 1 × 2 min at 93°C//10 × 15 sec at 93°C, 15 sec at 65°C, 8 min at 68°C//23 × 15 sec at 93°C, 15 sec at 63°C, 8 min + 20 sec elongation per cycle at 68°C | ||
| RT-PCR for polyacrylamid gels (semi-quantitative RT-PCR) | ||
| FGF10 Exons 1–3: | E1 | 5'-CGG GAA GGT CAG CGG GAC CA-3' |
| Amplicon size: 227 bp | E3as | 5'-TGC TGC CAG TTA AAT GAT GC-3' |
| FGF10 Exons 2–3: | PU2 | 5'-TCG GAG TTG TTG CCG TCA AAG-3' |
| Amplicon size: 416 bp | E3, 3'-UTR | 5'-CCT TCA AAG GCT GGC TTT CT-3' |
| beta-2-microglobulin | B2Ms | 5'-TTC ATC CAT CCG ACA TTG AA-3' |
| Amplicon size: 465 bp | B2Mas | 5'-TCT CTG CTC CCC ACC TCT AA-3' |
| Amplification conditions: | ||
| 1 × 15 min at 95°C//40 × 30 sec at 93°C, 90 sec at 60°C, 1 min at 72°C//15 min at 72°C | ||
| (aberrant transcript detection) | ||
| 1 × 15 min at 95°C//32 × 30 sec at 93°C, 90 sec at 60°C, 1 min at 72°C//15 min at 72°C | ||
| Exon 1/2 | P1 | 5'-CTC CTT CTC CTC TCC TT-3' |
| Amplicon size: 179 bp | P2 | 5'-GAT GTT ATC TCC AGG ATG CTG TA-3' |
| Probe E1/2 | 5'-GCT ATT CTC TTT CAC C-3' | |
| Exon 2/3 | P3 | 5'-GGG AAA CTC TAT GGC TCA AAA-3' |
| Amplicon size: 110 bp | P4 | 5'-CCT CCC ATT ATG CTG CCA GTT A-3' |
| Probe E2/3 | 5'-GGA AAA TGG ATA CAA TAC-3' | |
| Amplification conditions: | ||
| 1 × 15 min at 95°C//35 × 15 sec at 94°C, 30 sec at 56°C, 30 sec at 76°C | ||
| GAPDH (cDNA) | GA1 | 5'-ACC ACA GTC CAT GCC ATC AC-3' |
| Amplicon size: 451 bp | GA2 | 5'-TCC ACC ACC CTG TTG CTG TA-3' |
| Amplification conditions: | ||
| 1 × 3 min at 94°C//25 × 20 sec at 94°C, 20 sec at 66°C, 30 sec at 72°C//1 × 7 min at 72°C | ||
| beta-actin (gDNA) | BA1 | 5'-AGG CCA ACC GCG AGA AGA TGA-3' |
| Amplicon size: 732 bp | BA2 | 5'-GAA GTC CAG GGC GAC GTA GCA-3' |
| Amplification conditions: | ||
| 1 × 3 min at 94°C//30 × 20 sec at 94°C, 20 sec at 60°C, 30 sec at 72°C//1 × 7 min at 72°C | ||
Figure 1Computer tomography scans demonstrating the pathological findings of an ALSG patient. The pathological areas are marked. 1a: The patient shows an aplasia of both lacrimal punctae associated with a mucocele of the lacrimal sac imposing as a benign soft tissue tumor in the region of the medial canthus. 1b: Prosthetically (gold cap) treated teeth after caries-related destruction, especially in the molar region. 1c-d: Axial (c) and coronal (d) computer tomography scan demonstrating mucoceles originating from the lacrimal sac. The os lacrimale is partly destroyed, on the right side more pronounced than on the left side. 1e: Axial computer tomography scan showing a total aplasia of both parotid glands.
Figure 2a: A heterozygous sequence variation in the terminal nucleotide of intron 2 of the . The upper panel shows a representative electropherogram of a healthy individual. The middle and the lower panel demonstrate the sequence variation in genomic DNA derived from the patient and his brother. The changed nucleotide is marked by an arrow. 2b: Chart showing the exon/intron structure of the FGF10 gene. The characteristic polypyrimidine stretch and the consensus acceptor site are shown. The changed nucleotide is marked by an arrow.
Splice site prediction with NNSplice 0.9 and NetGene2 v. 2.4. AY604046.1
| 80131 | 80150 | tatgtttt | Exon 2 acceptor | |
| 85469 | 85488 | tcctttgc | Exon 2 acceptor | |
| 81353 | 81372 | tccctccc | Intron 2 | insertion of 4116 bp |
| 81899 | 81918 | ctaatatc | Intron 2 | insertion of 3570 bp |
| 82609 | 82628 | ctcccaat | Intron 2 | insertion of 2860 bp |
| 84430 | 84449 | ctattttt | Intron 2 | insertion of 1039 bp |
| 85062 | 85081 | tttccttc | Intron 2 | insertion of 407 bp |
| 86294 | 86313 | tctttcta | Exon 3, 3'-UTR | deletion of 825 bp |
| 86384 | 86403 | ttttattc | Exon 3, 3'-UTR | deletion of 915 bp |
| 80140 | TATGTTTTA | Exon 2 acceptor | ||
| 85478 | TCCTTTGCA | Exon 2 acceptor | ||
| 82618 | CTCCCAATA | Intron 2 | insertion of 2860 bp | |
| 86393 | TTTTATTCA | Exon 3, 3'-UTR | deletion of 915 bp | |
AY604046.1 Both algorithms anticipate the loss of the regular splice acceptor site of FGF10 exon 3 caused by the c.430-1, G > A aberration. Several alternative acceptor splice sites are proposed. Localization according to GenBank Accession No. AY604046.1.
Figure 3Analysis of FGF10 transcript applying long range RT-PCR. In order to analyze for transcripts that may include the entire intron 2, a long range RT-PCR protocol was established that works to amplify the 6.2 kb-fragment spanning from exon 2 to exon 3 using gDNA as template. Applying the optimized conditions to amplify the FGF10 transcript, no accordant PCR product was present. 1, 3: patient; 2, 4: control; MW: molecular weight marker.
Figure 4Detection and analysis of an aberrant transcript. 4a: Separation of FGF10 RT-PCR amplificates using sensitive silver-stained polyacrylamid gels reveals additional fragments for the patient's samples but not for control samples. Upper panel, Amplification of the FGF10 transcript using oligonucleotides designed to amplify exon 1 to exon 3 sequences; Lower panel, Amplification of the FGF10 transcript using oligonucleotides designed to amplify exon 2 to exon 3 sequences. C: control; P: patient. 4b: Sequence analysis of the excised and re-amplified additional exon 1/exon 3 fragment. The c.430-1, G > A aberration results in the use of an alternative splice acceptor site 127 bp upstream of exon 3. 4c: Putative effect of the 127 bp insertion on protein translation.