Protein droplets may cause many types of genetic disease

Date:
February 8, 2023
Source:
Max-Planck-Gesellschaft
Summary:
Malfunction of cellular condensates is a disease mechanism relevant
for congenital malformations, common diseases, and cancer, new
research suggests.


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FULL STORY ==========================================================================
Most proteins localize to distinct protein-rich droplets in cells, also
known as "cellular condensates." Such proteins contain sequence features
that function as address labels, telling the protein which condensate
to move into.

When the labels get screwed up, proteins may end up in the wrong
condensate.

According to an international team of researchers from clinical
medicine and basic biology, this could be the cause of many unresolved diseases. The findings appeared in the journal Nature.


========================================================================== Patients with BPTA syndrome have characteristically malformed limbs
featuring short fingers and additional toes, missing tibia bones
in their legs and reduced brain size. As the researchers found out,
BPTAS is caused by a special genetic change that causes an essential
protein to migrate to the nucleolus, a large proteinaceous droplet in
the cell nucleus. As a result, the function of the nucleolar condensate
is inhibited and developmental disease develops.

"What we discovered in this one disease might apply to many more
disorders. It is likely not a rare unicorn that exists only once. We just
could not see the phenomenon until now because we did not know how to
look for it," says Denise Horn, a clinical geneticist at the Institute
of Medical and Human Genetics at Charite' -- Universita"tsmedizin Berlin.

In collaboration with scientists at the Max Planck Institute for Molecular Genetics (MPIMG) in Berlin, the University Hospital Schleswig-Holstein
(UKSH), and contributors from all around the world, the team is pushing
open a door to new diagnoses that could lead to the elucidation of
numerous other diseases as well as possible future therapies.

"We discovered a new mechanism that could be at play in a wide range of diseases, including hereditary diseases and cancer," says Denes Hnisz,
Research Group Leader at the MPIMG. "In fact, we have discovered over
600 similar mutations, 101 of which are known to be associated with
different disorders." "The actual work is just starting now," adds human geneticist Malte Spielmann of UKSH in Lu"beck and Kiel. "We will find
many more genes with such disease- causing mutations and can now test
their mode of action." An unusual mutation Affected individuals have
complex and striking malformations of the limbs, face, and nervous and
bone systems, only partially described by the already- long disease name "brachyphalangy-polydactyly-tibial aplasia/hypoplasia syndrome" (BPTAS).

"With fewer than ten documented cases worldwide, the disease is not
only rare, but ultra-rare," says Martin Mensah, clinical geneticist at
the Institute of Medical and Human Genetics at Charite'. To track down
the cause, he and his colleagues decoded the genome of five affected individuals and found that the gene for the protein HMGB1 was altered
in all patients.

This protein has the task of organizing the genetic material in the cell nucleus and facilitates the interaction of other molecules with the DNA,
for example to read genes.

In mice, a complete loss of the gene on both chromosomes is catastrophic
and leads to death of the embryo. In some patients with only one copy
mutated, however, the cells are using the intact copy on the other
chromosome, resulting only in mild neurodevelopmental delay. But the
newly discovered cases did not fit this scheme.

"All five unrelated individuals featured the same ultra-rare disorder
and had virtually the same mutation," says Mensah, who is a fellow
of the Clinician Scientist Program operated by the Berlin Institute
of Health at Charite' (BIH) and Charite'. "This is why we are sure
that the HMGB1 mutation is the cause of the disease. However, at that
point, we had no clue how the gene product functionally caused disease, especially given that loss-of-function mutations were reported to result
in other phenotypes." Charged protein extensions A closer look revealed
that different mutations of HMGB1 have different consequences. The
sequencing data showed that in the affected individuals with the severe malformations, the reading frame for the final third of the HMGB1 gene
is shifted.

After translation to protein, the corresponding region is now no longer equipped with negative but with positively charged amino acid building
blocks.

This can happen if a number of genetic letters not divisible by three
is missing in the sequence, because exactly three consecutive letters
always code for one building block of the protein.

However, the tail part of the protein does not have a defined structure.

Instead, this section hangs out of the molecule like a loose rubber
band. The purposes of such protein tails (also called "intrinsically
disordered regions") are difficult to study because they often become
effective only in conjunction with other molecules. So how might their
mutation lead to the observed disease? Protein droplets in the cell To
answer this question, the medical researchers approached biochemists Denes Hnisz and Henri Niskanen at the MPIMG, who work with cellular condensates
that control important genes. These droplet-like structures behave
much like the oil and vinegar droplets in a salad dressing. Composed
of a large number of different molecules, they are separated from their surroundings and can undergo dynamic changes.

"We think condensates are formed in the cell for practical reasons,"
Niskanen explains. Molecules for a specific task are grouped together
in this way, say to read a gene. For this task alone, he says, several
hundred proteins need to somehow make their way to the right place.

"Intrinsically disordered regions, which tend not to have an obvious biochemical role, are thought to be responsible for forming condensates," Niskanen says, giving an example to describe how important the physical properties of the protein extensions are in this regard. "I can easily
make a ball from many loose rubber bands that holds together relatively
tightly and that can be taken apart with little effort. A ball of
smooth fishing line or sticky tape, on the other hand, would behave
quite differently." Solidifying droplets The nucleolus within the cell
nucleus is also a condensate, which appears as a diffuse dark speck under
the microscope. This is where many proteins with positively charged tails
like to linger. Many of these provide the machinery required for protein synthesis, making this condensate essential for cellular functions.

The mutant protein HMGB1 with its positively charged molecular tail is attracted to the nucleolus as well, as the team observed from experiments
with isolated protein and with cell cultures.

But since the mutated protein region has also gained an oily, sticky
part, it tends to clump. The nucleolus loses its fluid-like properties
and increasingly solidifies, which Niskanen was able to observe under
the microscope. This impaired the vital functions of the cells -- with
the mutated protein, more cells in a culture died compared to a culture
of cells without the mutation.

Combing through databases The research team then searched databases
of genomic data from thousands of individuals looking for similar
incidents. In fact, the scientists were able to identify more than six
hundred similar mutations in 66 proteins, in which the reading frame
had been shifted by a mutation in the protein tail, making it both more positively charged and more "greasy." Of the mutations, 101 had previously
been linked to several different disorders.

For a cell culture assay, the team selected 13 mutant genes. In 12
out of 13 cases, the mutant proteins had a preference to localize into
the nucleolus.

About half of the tested proteins impaired the function of the nucleolus, resembling the disease mechanism of BPTA syndrome.

New explanations for existing diseases "For clinical research, our study
could have an eye-opening effect," says Malte Spielmann, who led the
research together with Denes Hnisz and Denise Horn. "In the future, we
can certainly elucidate the causes of some genetic diseases and hopefully
one day treat them." However, "congenital genetic diseases such as
BPTAS are almost impossible to cure even with our new knowledge," says
Horn. "Because the malformations already develop in the womb, they would
have to be treated with drugs before they develop. This would be very
difficult to do." But tumor diseases are also predominantly genetically determined, adds Hnisz: "Cellular condensates and the associated phase separation are a fundamental mechanism of the cell that also plays a
role in cancer. The chances of developing targeted therapies for this
are much better."
* RELATED_TOPICS
o Health_&_Medicine
# Genes # Human_Biology # Diseases_and_Conditions #
Gene_Therapy # Personalized_Medicine # Nervous_System #
Sickle_Cell_Anemia # Lymphoma
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o Breast_cancer o COPD o Arthritis o HPV_vaccine o
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========================================================================== Story Source: Materials provided by Max-Planck-Gesellschaft. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Martin A. Mensah, Henri Niskanen, Alexandre P. Magalhaes,
Shaon Basu,
Martin Kircher, Henrike L. Sczakiel, Alisa M. V. Reiter, Jonas
Elsner, Peter Meinecke, Saskia Biskup, Brian H. Y. Chung, Gregor
Dombrowsky, Christel Eckmann-Scholz, Marc Phillip Hitz, Alexander
Hoischen, Paul- Martin Holterhus, Wiebke Hu"lsemann, Kimia Kahrizi,
Vera M. Kalscheuer, Anita Kan, Mandy Krumbiegel, Ingo Kurth, Jonas
Leubner, Ann Carolin Longardt, Jo"rg D. Moritz, Hossein Najmabadi,
Karolina Skipalova, Lot Snijders Blok, Andreas Tzschach, Eberhard
Wiedersberg, Martin Zenker, Carla Garcia-Cabau, Rene' Buschow,
Xavier Salvatella, Matthew L.

Kraushar, Stefan Mundlos, Almuth Caliebe, Malte Spielmann,
Denise Horn, Denes Hnisz. Aberrant phase separation and
nucleolar dysfunction in rare genetic diseases. Nature, 2023;
DOI: 10.1038/s41586-022-05682-1 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2023/02/230208155720.htm

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