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Long-Read Sequencing Study Finds Genetic Culprit for Rare Neurological Condition

NEW YORK – With the help of long-read sequencing, an international team led by investigators at the University of Utah and the University of Tübingen has narrowed in on a repeat expansion linked to a serious, rare late-onset neurological condition called spinocerebellar ataxia 4 (SCA4).

The team published its findings in Nature Genetics on Monday.

"The only step to really improve the life of patients with inherited disease is to find out what the primary cause is," senior and corresponding author Stefan Pulst, chair of neurology at the University of Utah's Spencer Fox Eccles School of Medicine, said in a statement.

In their search for the genetic culprit, researchers from the University of Utah, the University of Tübingen, and other centers used targeted long-read sequencing and bioinformatics on an extended pedigree spanning more than 15 nuclear families from Utah to assess a chromosome 16 region implicated in SCA4 through linkage analyses in the mid-1990s.

"We were able to trace 15 nuclear families back to a likely common ancestor born in southern Sweden around the start of the 19th century using patient-provided information from census and ancestry records of the Church of Jesus Christ of Latter-day Saints," the authors explained.

Along with available records from Utah, the team's Pacific Biosciences HiFi and Oxford Nanopore Technologies-based sequencing analyses led to an SCA4-associated GGC repeat expansion in the transcription factor-coding polyglycine (polyG) gene ZFHX3. In contrast to the 21 repeats present in unaffected individuals, SCA4 patients had more than 40 copies of the repeat.

When they screened nearly 6,500 genome sequence datasets, the researchers identified seven additional affected individuals from families in Lübeck, Munich, and Tübingen, Germany, who carried the same repeat expansion.

With more detailed haplotype and rare variant analyses, meanwhile, the team determined that the repeat expansion represents a founder mutation shared between the SCA4 cases in Utah and Germany, though the Tübingen cases were missing one of the six ultrarare variants found in the other families.

Together, the authors explained, the results suggested that "the repeat expansion haplotypes can be traced to a single, very distant founder with a single de novo [single nucleotide variant] occurring after the repeat expansion event, resulting in two distinguishable alleles."

In fibroblast cell models of SCA4 and induced pluripotent stem cells from individuals with SCA4 — which both contained the ZFHX3 repeat expansion — the researchers saw a significant uptick in ZFHX3 protein levels and polyG aggregates relative to control cells, along with a decline in autophagic processes typically used to recycle proteins.

Those findings were backed up by antibody staining analyses showing neuronal intranuclear inclusions involving aggregates of ZFHX3, p62, and ubiquitin proteins in SCA4 brain sections, the team explained, noting that MRI data highlighted further ties between the ZFHX3 expansion length and SCA4 age of onset.

"This mutation is a toxic expanded repeat, and we think that it actually jams up how a cell deals with unfolded or misfolded proteins," Pulst explained, adding that "[w]e now can attack the effects of this mutation potentially at multiple levels."

Because the apparent disease mechanism resembled protein recycling problems previously described in a type of ataxia dubbed SCA2, for example, the authors pointed to the potential benefits of pursuing treatment options similar to those being tested in clinical trials for that condition.

The new findings also raise the possibility of offering genetic testing to individuals from affected families to understand their own risk of SCA4 and for making family planning decisions.

"Our study underscores the importance of identifying genetic variation, including novel repeat expansions, in extremely G+C-rich genomic regions, which may account for some of the missing heritability in neurodegenerative disorders," the authors wrote, adding that the results "add to the list of neurodegenerative diseases caused by polyG expansions."