AUTO-IMMUNE DISEASES ARE
common at the UDN, but by far the
majority of work at the Duke site – 85
per cent – is focused on diseases that
are suspected to have a genetic cause.
Following Ethan White’s cardiac event,
he and his brother were accepted into
the UDN in September 2017. In their
week of tests, the brothers saw experts
in genetics, cardiology, ophthalmology
and neuropsychology. Because he
suffers from type one diabetes, Ethan
was also seen by an endocrinologist,
although no link was found. To ensure
a comprehensive analysis, the UDN
even reached out to the Teem family
for a sample of Hogan’s DNA, which the
coroner was able to provide.
The team then sequenced the
brothers’ exome – the part of the
genome that makes up just 1-2 per
cent of our genetic data but is the part
most rich in mutations that have an
effect on disease. Exome sequencing
is not unique to the UDN; in fact, 75
per cent of UDN patients at the Duke
site have previously had their exome
analysed, but their doctors have been
unable to find any clues in the results.
As current estimates suggest 80 per
cent of disease mutations can be found
within the exome, however, the UDN
decided to start its investigation there.
“Our site has a very agnostic
approach to the genome,” says Shashi.
“We not only look at the genes which we
think might be causing the problem, but
all the other genes as well, picking out
variants that we think are compelling.
This approach has led us to pick out
candidate genes that otherwise might
be missed in a clinical laboratory.”
ARVC is caused by changes in one
of a number of genes that produce
proteins necessary for proper function
of the heart. These genetic changes
lead to an abnormal or missing protein,
causing a breakdown of the muscletissue and a build-up of fatty deposits.
This, in turn, significantly inhibits the
heart’s ability to function normally.
Changes within 13 genes are currently
known to cause ARVC – yet around 50
per cent of patients will come up with a
negative result when tested for them,
indicating the existence of additional
genes associated with ARVC – genes
that are as yet undiscovered.
In analysing the brothers’ exome,
the UDN uncovered something unique:
variants in a novel gene that they were
unable to locate in medical databases
compiling genetic data from more than
200,000 people who do not have rare
diseases. “Typically when a genetic
variant is very rare, we think there’s a
chance it could be disease-causing,”
says Heidi Cope, the lead genetic
counsellor on the case. “If we saw the
variant in 3,000 people, most likely it’s
benign, as you wouldn’t see it that often
in that many healthy people.”
With this gene a likely candidate, the
next step was to study it in different
models in order to monitor how the
gene is expressed and run tests without
having to study Ethan and Austin’s
hearts directly. Dr Andrew Landstrom,
a paediatric cardiologist working out of
a complex of labyrinthine laboratories
at Duke University, agreed to lend his
expertise to the case.
The main tool in Landstrom’s
arsenal is formed by induced pluri-
potent stem cells. In this process,
blood cells are taken from an affected
patient and, using molecular genetics,are encouraged to release all of their
differentiation, so reverting back to the
stem cell state. Essentially, this forms a
blank slate containing all of a patient’s
genetic information. By exposing these
stem cells to certain chemical signals,
researchers are able to steer them
towards becoming whichever type of
cell is most pertinent to their research,
from liver cells to lung cells.
In this case, Landstrom’s team
re-programmed stem cells from the
brothers to become heart cells, from
which they were able to grow heart
tissue. “These stem cells carry all the
same genetic markers as the patient
so we can use it as a tool, like having
their hearts right in front of us without
ever going near them,” Landstrom says.
He produces a tray of heart cells from
an incubator and places them under a
microscope. Swirls of heart tissue pulse
on the screen, something like a living
version of Van Gogh’s The Starry Night.
Researchers first look for evidence
that the gene they have identified
causes the cell to function as has
been hypothesised. Because defective
genes produce abnormal proteins, a cell
made up of these genes will function
abnormally. In this case, Austin, Ethan
and Hogan’s hearts displayed a high
build-up of fatty tissue. If the in-vitro
cells also develop this build-up, it will
be seen as a strong indication that the
gene identified by Cope and her team
is the culprit. In addition, the team
will monitor the in-vitro cells to see if
they develop the same arrhythmias
displayed by the brothers.
Frequently, as in this case, the UDN
also works with its Model Organism
Screening Center laboratories to model
genes in zebrafish models. Professor
Monte Westerfield, at the University of
Oregon, runs this programme. His team
use CRISPR Cas9 gene-editing tools to
generate a zebrafish embryo with the‘ANALYSING
THE
BROTHERS’
GENES
PRODUCED
SOMETHING
UNIQUE’11-19-FTUndiagnosedDiseases.indd 140 28/08/2019 04:00