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Overview	Journal Articles	Popular Press	Conclusion

Journal Articles

 

"ABCA3 Gene Mutations in Newborns with Fatal Surfactant Deficiency" - NEJM

Shulenin et al. in their publication in 2004 presented an investigation on gene mutations resulting in fatal surfactant deficiency in newborns. As part of a study funded by the National Institutes of Health and the Eudowood Foundation, this group of collaborators examined the ABCA3 gene in order to determine its involvement in surfactant phospholipid metabolism and whether or not it could account for unexplained surfactant deficiency in full-term infants. They chose ABCA3 as a possible candidate gene because of:

1) its possible role in lipid transport

2) its location within alveolar type II cells

3) the association of other ABC genes with human diseases (Shulenin, 2004).

To begin the paper, the authors provide several paragraphs with background information defining key terms like “pulmonary surfactant”, “lamellar bodies”, as well as general information about ABC genes. They specifically describe the ABCA3 gene and its connection to surfactant and lamellar bodies, suggesting that ABCA3 could act as a candidate gene for surfactant deficiency in full-term infants. Most notably they express their aforementioned three reasons for focusing on ABCA3.

Methodology:

In order to accurately obtain samples for testing, the authors collected blood samples from 337 different infants suffering from severe respiratory disease between July 1995 and April 2003. To optimize the genetic pool as much as possible, various races were incorporated. All infants sampled were born after a minimum 36 weeks of gestation and exhibited persistent hypoxemic respiratory failure merely hours after birth—serving as a control so that variations could be accounted for without extraneous variables arising due to development of the patient.

In 15 infants, a cause of the lung disease was subsequently discovered. Forty-seven, were determined to have hereditary deficiency of SP-B as identified by loss-of-function mutations on both alleles of the gene, while 275 were screened for SP-B deficiencies and came back negative. Of these screened for SP-B mutations, 121 were analyzed for mutations in the gene for SP-C; 6 of which were found to harbor mutations. Finally, 21 of the remaining 115 infants were selected for analysis of the ABCA3 gene based off of family history or who had fatal disease in association with low surfactant protein levels in tracheal-aspirate fluid (Shulenin et al., 2004).

Table 1 (left) and Figure 2 (right) from Shulenin et al. Table 1 shows the 21 patients analyzed for ABCA3 mutations. 16 of 21 were identified with mutations. Figure 2: Location of ABCA3 Mutations. Exons encoding the ATP-binding dmains are shown in green. Degree of conservation of residues involved in missense mutations in the ABCA3 protein is shown below. Sequences of puffer fish and zebra fish are incomplete, showing gaps in the sequences. Finally, the first three noncoding exons are not shown.

 

DNA prepared from whole blood from the infants was sequenced using the ABI 3730 sequencer (Applied Biosystems) and analyzed using both SeqMan software (DNAStar) and Mutation Explorer software (SoftGenetics). Variants were determined through comparison with the reference ABCA3 sequence. Additionally, ABAC3 amino acid sequences were analyzed to determine conserved regions between organisms through BLAST via NCBI. The Mega2 program was then used to create a dendrogram, indicating evolutionary related sequences between organisms. Finally, a bootstrap test with 1000 replicates was preformed to test for accuracy. A bootstrap test with 95% or high shows strong evidence of an evolutionary realtion between the dendrogram branch and original set of sequences.

Results & Discussion:

Mutations were found in 16 of the 21 infants analyzed for variations in the ABCA3 gene. Of these observed, homozygous nonsense, homozygous frameshift, heterozygous insertion and splice-site mutations all were determined as can be seen in Figure 2 from Shulenin et al. Additionally, seven missense mutations located in conserved regions of the amino acid sequence were identified while none were found in control subjects. Here the authors express reservation with the identified missense mutations because they were unable to find similar variants in the public polymorphism database. The distribution of these mutations did not favor any particular race or ethnicity suggesting that such mutations are not restricted to a single group. Also, because varying mutations were discovered in different families, no common alleles can be associated with pulmonary disorders involving surfactant dysfunction. However, the authors note that the ABCA3 gene is hormonally regulated such that genetic variants in other genes could indirectly affect ABCA3 regulation. In addition, they suggest that ABCA3 fulfills its proposed role as a candidate gene and could be involved in other pulmonary disorder involving surfactant dysfunction such as asthma and interstitial lung disease occurring later on in life.

 

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References

Shulenin, Sergey, Lawrence M. Nogee, Tarmo Annilo, Susan E. Wert, Jeffrey A. Whitsett, and Michael Dean. "ABCA3 Gene Mutations in Newborns with Fatal Surfactant Deficiency." New England Journal of Medicine 350.13 (2004): 1296-303. Paper Link.