Journal News

MCP: Proteogenomics researchers find causes of immune disease

Laurel Oldach
April 01, 2019

Routine clinical sequencing has given doctors unprecedented insight into genetic disorders. However, genomics fails to diagnose up to half of patients who are tested. That’s the problem that scientists at universities in Munich and Berlin tackled in a recent study in the journal Molecular & Cellular Proteomics. With samples from patients in four countries and a novel database on the neutrophil proteome, Christoph Klein and colleagues diagnosed two children with severe congenital neutropenia using mass spectrometry-based proteomics when typical sequencing had failed.

NeutrophilsNeutrophils, like the one in the center of this photo, are loaded with granules full of proteases that make them difficult to study. Guy Waterval /Wikimedia Commons

“There are very few examples of people who use multiple omics to investigate rare diseases … (but) I think this is the future of personalized medicine,” said Klein, a physician and director of the Children’s Hospital of the University of Munich.

The patients’ disease affects their neutrophils, white blood cells packed with toxic proteins to deploy against bacteria. When neutrophil development is disrupted, which Klein estimates happens to 1 in 200,000 newborns, every bacterial or fungal infection can become a life-threatening medical emergency.

Klein’s lab has studied rare genetic causes of neutropenia for years, but proteomics was a new field for the group. Postdoctoral researcher Sebastian Hesse met proteogenomics expert Juri Rappsilber at a conference, sparking a collaboration to study the proteome and transcriptome of neutrophil granulocytes.

Neutrophils are post-mitotic and very fragile, which makes studying them a challenge.

“You can think of them as suicide bombers,” Klein said, explaining that the cells are full of granules loaded with proteases that make retrieving other proteins a challenge. Hesse painstakingly developed a protocol to collect intact proteins and mRNA from healthy neutrophils.

Using mass spectrometry, scientists led by co-first author Piotr Grabowski in the Rappsilber lab at the Technical University of Berlin analyzed the cells’ proteome. When they added transcriptomic data, they found strikingly little correlation with the proteome, so they chose to focus on protein in patient samples.

Next, Hesse collected neutrophils from 16 patients with congenital neutropenia. Some were in Germany; to find others, he had to travel.

“These patients are from various parts of the world — that’s another unique challenge of working with rare diseases,” Klein said. “Sebastian flew to Iran and Turkey, in a collaborative effort with the pediatric hospitals there.”

Back at home, after processing and freezing the samples, Hesse handed them off to Grabowski; the proteomics scientists repeated the analyses to see what proteins had changed in the patients’ blood.

The team used abnormal protein profiles to guide the diagnosis of two patients with inconclusive exome sequencing results.

In one child’s case, a pseudogene made it difficult to identify mutations in the protein-coding gene; in the second, incomplete coverage by exome sequencing had missed a key point mutation. Data on protein abundance in each patient led the researchers to run more specific genetic tests that proved conclusive.

“This highlights (that) even if you have highly controlled pipelines for genetic studies, there’s always a risk that you are not 100 percent correct,” Klein said.

The researchers did not set out to make diagnoses from patient proteomes, but the study highlights the value proteomics data can add.

“Cellular proteome studies are not in routine clinical use at this point,” Klein said. “But … I think there will be huge potential for proteome analysis at a very low cost down the road.”

The team plans to expand its studies to other patients with immune deficiencies, looking for new genetic mechanisms of disease.

Laurel Oldach

Laurel Oldach is a science writer for the ASBMB.

Join the ASBMB Today mailing list

Sign up to get updates on articles, interviews and events.

Latest in Science

Science highlights or most popular articles

In the future, lab mice will live in computer chips, not cages
Life in the Lab

In the future, lab mice will live in computer chips, not cages

July 11, 2020

As COVID-19 shuttered laboratories across the U.S., many researchers were forced to euthanize the animals they study. Lindsay Gray, a rodent surgeon in an animal research lab that faced this dilemma, argues here there is a safer, more effective way.

Proteomics reveals hallmarks of aging in brain stem cells
Journal News

Proteomics reveals hallmarks of aging in brain stem cells

July 09, 2020

Early in adulthood, the brain regenerates lost myelin effectively, but remyelination falters with age. Researchers seek to understand why — and what the change may mean for people with multiple sclerosis.

Ocean virus hijacks carbon-storing bacteria
Journal News

Ocean virus hijacks carbon-storing bacteria

July 07, 2020

A Journal of Biological Chemistry paper reports that these minuscule interactions could have ripple effects on global carbon dioxide levels.

CRISPR nanoparticles are the next big hope in Alzheimer’s disease treatments
News

CRISPR nanoparticles are the next big hope in Alzheimer’s disease treatments

July 04, 2020

Nearly 6 million Americans live with Alzheimer’s disease without solid treatment options.

Summer food science
Stroopwafels

Summer food science

July 02, 2020

For those of you bound for a summertime holiday weekend, we dug into recent research on the yummy foods you might serve at a socially distant picnic.

How lipid droplets stay in shape
Journal News

How lipid droplets stay in shape

June 30, 2020

Andrew Greenberg and colleagues discovered that the protein perilipin is involved in storage and hydrolysis of neutral lipids within these key structures in cells.