Study reveals why some patients with the hereditary disease remain healthy microbiologystudy

Alpha-1-antitrypsin is a so-called protease inhibitor, a type of enzyme inhibitor. It is produced in the liver but exerts its effects in the lungs, where it regulates immune cell activity. This regulation is crucial, and an overactive immune response can cause serious lung diseases.

However, some individuals carry a genetic mutation that causes the alpha-1 protein to fold incorrectly. As a result, too little functional alpha-1 is produced, and insufficient amounts reach the lungs.

The mutation is inherited from one or both parents. About 1 in 20 people in Europe carry the heterozygous form of the mutation—inherited from only one parent—and often experience no symptoms or only mild ones. In contrast, the rarer homozygous form, inherited from both parents, affects approximately 1 in 2,000 individuals and is much more severe.

These patients are at a higher risk of developing not only lung disease, such as chronic obstructive pulmonary disease (COPD), but also liver complications including severe fibrosis or even tumors.

One mutation, divergent paths

An international research team led by Matthias Mann at the Max Planck Institute of Biochemistry in Martinsried, near Munich, has now uncovered important new insights into the homozygous form of the condition. The findings are published in the journal Nature.

First author Florian Rosenberger, from the Department of Proteomics and Signal Transduction, explains, “In the homozygous form, something striking stands out. It is a monogenetic disease, meaning all patients carry the same mutation—so in theory, disease progression should be uniform. But that’s not what we see.

“One-third of patients develop severe liver fibrosis, where connective tissue accumulates and impairs liver function. Two-thirds, however, remain healthy. We wanted to understand why that is. What molecular mechanisms protect some patients while others develop disease?”

The team used a technique called Deep Visual Proteomics, developed collaboratively in Martinsried and Copenhagen by the proteomics research groups of Matthias Mann. This method applies advanced proteome analysis to identify disease mechanisms. For the Alpha-1 study, liver tissue samples from patients in Germany and Denmark were analyzed.

“We examined tissue across the full spectrum of disease stages,” Rosenberger continues. “Even in early stages—when clinical signs had not yet appeared—we could observe how the body in some cases successfully halted disease progression.”

For their analysis, the researchers employed a convolutional neural network (CNN)—a form of artificial intelligence originally trained to recognize faces and everyday objects in images.

Subtle differences with big impacts

The CNN also performed impressively on images of human liver tissue. It was able to differentiate between subtle structural variations in the disease, particularly the way alpha-1 protein aggregates in liver cells (hepatocytes). These aggregates are a hallmark of disease onset. “Our CNN could detect extremely fine differences in aggregate morphology,” says Rosenberger.

Two distinct forms stood out: crumb-like aggregates with a rough, irregular structure, and ball-like aggregates with a more defined appearance. This raised a key question: what determines which type appears—and are they random or biologically meaningful?

This is where the team made a breakthrough. They successfully reconstructed the sequence of molecular events—the formation of crumbs, balls, and the transitions between them—and identified their temporal order.

The crumb-like aggregates appeared first, as an early response of stressed cells. This was associated with activity in special cell compartments called peroxisomes. The ball-like aggregates emerged later, during more advanced stages of fibrosis.

Interestingly, however, the type of aggregate did not always correlate with disease severity. Even patients with only mild fibrosis could show the advanced ball-like morphology. “The shift from crumbs to balls was a key finding,” Rosenberger explains. “It reveals the sequence of compensatory responses liver cells mount in an effort to combat aggregate formation—and with it, liver fibrosis.”

Toward clinical applications

The improved AI-based image analysis played a pivotal role in uncovering these mechanisms. “Recent technological advances in mass spectrometry were crucial,” says Professor Mann. “We can now perform single-cell measurements, allowing us to extract detailed molecular information from just a small amount of tissue—even from individual diseased liver cells.”

The study’s findings may soon have clinical relevance. The development of fibrosis in individuals with the homozygous mutation could potentially be prevented.

“By reviewing patient histories, we saw that those with severe fibrosis lacked the early peroxisomal response,” says Rosenberger. “We now know this response is protective. Our goal is to develop an early warning system for liver fibrosis—a way to identify patients at risk before symptoms arise.”

Aleksander Krag, professor at the University of Southern Denmark and head of Odense Liver Research Center, emphasizes, “By capturing alpha-1 antitrypsin accumulation at the single-cell level, we have uncovered early molecular triggers of how alpha-1 antitrypsin deficiency progresses. This points toward actionable targets that could lead to improved therapies for patients.”

Pavel Strnad, a hepatologist at University Hospital Aachen and long-standing collaborator on the project, adds, “Erroneous protein folding is central to many human diseases, including Parkinson’s and Alzheimer’s. Studying a monogenic condition like Alpha-1 antitrypsin deficiency provides a unique opportunity to better understand disease progression.

“This work deepens our insight into protein folding disorders and their consequences, and will be important even beyond Alpha-1 antitrypsin deficiency.”