Tissue-specific reduction in splicing efficiency of IKBKAP due to the major mutation associated with familial dysautonomia

Abstract

We recently identified a mutation in the I-kappa B kinase associated protein (IKBKAP) gene as the major cause of familial dysautonomia (FD), a recessive sensory and autonomic neuropathy. This alteration, located at base pair 6 of the intron 20 donor splice site, is present on >99.5% of FD chromosomes and results in tissue-specific skipping of exon 20. A second FD mutation, a missense change in exon 19 (R696P), was seen in only four patients heterozygous for the major mutation. Here, we have further characterized the consequences of the major mutation by examining the ratio of wild-type to mutant (WT:MU) IKBKAP transcript in EBV-transformed lymphoblast lines, primary fibroblasts, freshly collected blood samples, and postmortem tissues from patients with FD. We consistently found that WT IKBKAP transcripts were present, albeit to varying extents, in all cell lines, blood, and postmortem FD tissues. Further, a corresponding decrease in the level of WT protein is seen in FD cell lines and tissues. The WT:MU ratio in cultured lymphoblasts varied with growth phase but not with serum concentration or inclusion of antibiotics. Using both densitometry and real-time quantitative polymerase chain reaction, we found that relative WT:MU IKBKAP RNA levels were highest in cultured patient lymphoblasts and lowest in postmortem central and peripheral nervous tissues. These observations suggest that the relative inefficiency of WT IKBKAP mRNA production from the mutant alleles in the nervous system underlies the selective degeneration of sensory and autonomic neurons in FD.Therefore, exploration of methods to increase the WT:MU IKBKAP transcript ratio in the nervous system offers a promising approach for developing an effective therapy for patients with FD.

Figure 1

IKBKAP amplicon sizes and their corresponding PCR products. A schematic representation of the primer sets and Taqman probes used to amplify either the WT or MU IKBKAP transcripts. PCR primers 19F–23R amplify both WT and MU bands. The real-time QPCR primers designated “WT-F/R” (forward/reverse) or “MU-F/R,” with their matching dual-labeled Taqman probes, amplify WT and MU transcripts, respectively. The position of WT-R primer in exon 20 was designed to specifically amplify only the WT message, whereas the MU-F primer located at the junction of exons 19 and 21 will amplify only the MU message. The dual-labeled Taqman probes have a melting temperature (Tm) of 7°C–10°C above the primer Tm for each amplicon. Primer and probe sequences were as follows: 19F: CCT GAG CAG CAA TCA TGT G; 23R: TAC ATG GTC TTC GTG ACA TC; WT-F: GCA GCA ATC ATG TGT CCC A; WT-R: ACC AGG GCT CGA TGA TGA A; WT Taqman probe: FAM-GTT CAC GGA TTG TCA CTG TTG TGC C-BHQ; MU-F: CAC AAA GCT TGT ATT ACA GAC T; MU-R: GAA GGT TTC CAC ATT TCC AAG; and MU Taqman probe: FAM-CTC AAT CTG ATT TAT GAT CAT AAC CCT AAG GTG-BHQ. The housekeeping gene 18S rRNA was used for normalization: 18S-F: GGC CCT GTA ATT GGA ATG AG; 18S-R: GCT ATT GGA GCT GGA ATT AC; and 18S Taqman probe: FAM-TGC TGG CAC CAG ACT TGC CCT C-BHQ.

Figure 2

A, Expression of WT and MU IKBKAP mRNA in various lymphoblast cell lines of patients with FD. A total of 81 FD lymphoblast cell lines were assayed, using a densitometric assay. Representative samples are shown, including the GM5106 (Coriell) sample used by Anderson et al. (2001). All FD lines consistently expressed both WT IKBKAP (upper band, lane 1–lane 10) and MU (lower band, lane 1–lane 10). Note that MU IKBKAP transcript is never detected in RNA from normal cells or tissues (lane 11–lane 12). L=100-bp ladder; 1=FD (MIN9741, new line); 2=FD (MIN9744, new line); 3=FD (MIN9741, new line); 4=Carrier (GM5105, Coriell); 5=FD (GM5107, Coriell); 6=FD (GM5106, Coriell); 7=FD (GM5106, established line); 8=FD (GM5041, established line); 9=FD (GUS13131, established line); 10=FD (GUS14939, established line); 11=non-FD control (GM5043, Coriell); and 12=non-FD control (GM5110, Coriell). WT amplicon size=363 bp; MU amplicon size=289 bp. B, Expression of WT and MU IKBKAP mRNA in postmortem FD tissue samples and cell lines. All samples were assayed and analyzed as described in our methodology. The relative WT:MU transcript ratio was consistently observed to be highest in FD lymphoblast lines, lowest in FD nervous system tissues, and intermediate in other tissues. The distinctive reduction of relative WT message in most of the CNS and PNS tissues corresponds to the tissue-specific pathology observed among patients with FD.

Figure 3

Graphical representation of relative WT and MU IKBKAP expression levels in various FD postmortem tissues and cultured cell lines, measured by use of real-time QPCR. The QPCR values were normalized using 18S rRNA, and the spleen tissue was used as the calibrator for relative comparisons between patient samples. A, Relative WT IKBKAP levels. The FD lymphoblast cell lines followed by the tonsil tissue showed relatively higher levels of WT message than any other patient tissues examined. B, Relative mutant IKBKAP levels. Several areas of the neocortex, as well as the brain stem medulla, striatum (caudate nucleus), spinal cord, and intercostal nerve tissue samples, showed relatively higher levels of the MU IKBKAP transcript compared with other patient tissues and cell lines investigated. Among the nonnervous tissues tested, only the tonsil, esophagus, and one of the lung samples (case B) showed relatively high MU IKBKAP levels, whereas the others had intermediate levels.

Figure 4

Western blot showing relative IKAP expression levels in FD postmortem tissues and cultured cell lines. Protein was extracted from several cell lines and postmortem tissues, as shown, and was run on 6% denaturing polyacrylamide gel. The samples were transferred to a PVDF membrane and stained with Ponceau-S to confirm equal protein loading. IKAP was detected using a C-terminal polyclonal antibody. Here, we show that IKAP levels are reduced in the FD lymphoblast and fibroblast samples compared with controls, and IKAP is either absent or below the level of antibody detection in FD brain tissues.