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Disease-Causing Mobile Element Identified with SMRT Sequencing, Validated with CRISPR

Monday, April 2, 2018

Structural variation in Mendelian disease endemic to Panay

The coast of Panay Island in the Philippines. U.S. Navy photo by Jennifer S. Kimball

In an exciting new Cell paper, scientists report identification of an intronic structural variant that causes a neurodegenerative Mendelian disorder that primarily affects people on the island of Panay in the Philippines. The team used a number of approaches, including SMRT Sequencing and the Iso-Seq method, to solve the medical mystery.

Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly” comes from lead authors Tatsiana Aneichyk, William Hendriks, Rachita Yadav, David Shin, and Dadi Gao; senior authors Cristopher Bragg and Michael Talkowski; and many collaborators at Massachusetts General Hospital, the Broad Institute, and other organizations.

The team targeted X-linked dystonia-parkinsonism (XDP), “an adult-onset neurodegenerative disease that has challenged conventional gene discovery for several decades.” Endemic to the island of Panay, the progressive disease was previously associated with several genetic variants, but none were deemed definitively causative. Scientists attribute that in part to a lack of solid annotation for this genomic region.

“We investigated XDP as an exemplar of an unsolved Mendelian disorder arising from a founder haplotype in an isolate population,” the team writes. “We hypothesized that the genetic diversity of XDP has not been captured by previous approaches and that unbiased assembly of the genome and transcriptome spanning the XDP haplotype could reveal additional sequences or aberrant transcripts unique to probands.” While most Mendelian analyses to date have used exomes or whole genome sequencing on short read platforms, the disease causing variation in the case of XDP is difficult to detect by these methods.   To that end, they applied a bevy of sequencing and analysis tools — including SMRT Sequencing, hybridization capture sequencing and scaffolding technologies — to study a large cohort of about 800 individuals, most of them affected males or carriers.

“Our results identified previously unknown genomic variants and assembled transcripts that were shared among XDP probands, but not observed in controls, including aberrant splicing and partial retention of intronic sequence proximal to the disease-specific SVA [SINE-VNTR-Alu retrotransposon] insertion in TAF1,” the scientists report. SMRT Sequencing of BAC clones from a proband generated a 200 kb region spanning TAF1, assembling the full SVA sequence.

TAF1 is a general transcription factor encoded on the human X chromosome and is expressed is all tissue types, but in the case of XDP, a portion of the mRNA transcript is spliced in a non-functional manner within the intron containing the SVA.  The team followed up on this observation with CRISPR/Cas9 editing to remove the SVA sequence in cell models derived from patient samples. Removal of the SVA by gene editing “rescued this XDP-specific transcriptional signature and normalized TAF1 expression,” proving that this mobile element really is the causal agent, the authors write.

“These data suggest that XDP may join a growing list of human diseases involving defective RNA splicing, [intron retention], and transcriptional alterations driven by transposable elements,” the team concludes. “These studies also illustrate the potential for layered genomic analyses to provide a roadmap for unsolved Mendelian disorders that is capable of simultaneously capturing coding and noncoding regulatory variation and interpreting their functional consequences in human disease.”

Scientists interested in exploring this type of work in their own labs can check out our SV and Iso-Seq application pages to learn more.

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