Researchers at Penn Medicine are advancing the understanding of disease mechanisms by using cryogenic electron microscopy (cryoEM) and cryo-electron tomography (cryoET). These imaging techniques allow scientists to visualize cellular structures and processes involved in diseases such as malaria, Alzheimer’s, and various lysosomal storage disorders.
Yi-Wei Chang, PhD, assistant professor of Biochemistry and Biophysics and associate director of the Institute of Structural Biology at the Perelman School of Medicine, shifted his focus from X-ray crystallography to cryoET after attending a pivotal lecture. “That talk set my life goal,” he said. “I said, ‘This is the way I want to do structural biology. I want to see structures in the cell while they are doing their function.’”
Chang’s research group investigates how pathogens like viruses, bacteria, and parasites invade human cells. In one study, they examined how the malaria parasite Plasmodium falciparum infects red blood cells. Malaria affects about 200 million people worldwide each year and causes approximately 600,000 deaths annually, according to the World Health Organization.
The team used cryoET to observe that P. falciparum utilizes organelles called rhoptries during infection. They identified two rhoptries and a structure known as the “rhoptry secretory apparatus,” which guides these organelles toward the parasite’s surface for delivery into host cells. The images demonstrated that this apparatus supports a membrane vesicle beneath the parasite’s surface to help breach host defenses—a process described as “parasite kissing and spitting.” Their findings were published in Nature Microbiology in July 2022.
Chang noted that visualizing these steps may reveal new targets for preventing infections caused by malaria and related parasites such as Toxoplasma and Cryptosporidium.
Penn Medicine researchers are also using cryoEM techniques to study other diseases. A team led by Moiseenkova-Bell focused on lysosomes—the cell's recycling centers—and what happens when they malfunction. When lysosomes fail to operate properly, it can result in lysosomal storage diseases or contribute to neurodegenerative conditions like Parkinson’s or Alzheimer’s disease.
Pharmacology graduate student Bridget McVeigh used cryoET to freeze individual lysosomes for detailed imaging. The resulting images revealed diverse structures: some lysosomes had multiple concentric layers; others contained protein fragments or appeared nearly empty. Their surfaces displayed three membrane-associated proteins: V-ATPase, flotillin, and clathrin. This work was published in Nature Communications in October 2025.
McVeigh highlighted unexpected complexity within lysosome structures compared with textbook descriptions: “It’s so different in textbooks, where lysosomes are just empty and circular, versus what we're actually seeing, where they're very heterogeneous in size and content.”
Efforts are also underway at Penn Medicine to apply these imaging methods directly to human tissues. Researchers adapted a physical sciences technique involving a focused beam of ions—acting like a miniature bread slicer—to thin samples for electron microscopy.
Benjamin Creekmore, PhD—a Penn MD/PhD student—processed brain tissue donated by Alzheimer’s patients using this method before imaging with cryoET. With assistance from Kathryn Kixmoeller, PhD (also an MD/PhD student), Creekmore prepared ultra-thin sections from deep within brain samples for high-resolution visualization.
Creekmore explained his motivation: “What kept me going was knowing that we were learning new things that people hadn't seen before about diseases that are really devastating for people—Alzheimer’s disease is, for a lot of people, one of the most dreaded diseases that they could get,” he said. “Working on something like that, it felt like it was making a difference.”
Their results showed evidence of tau protein tangles—a hallmark of Alzheimer’s—in their native environment using cryoET technology. They also observed myelin damage relevant to multiple sclerosis patients. This research was published in Nature Communications in March 2024.
The project included guidance from co-advisors Chang and Edward Lee, MD, PhD (professor of Pathology and Laboratory Medicine; co-director of Penn’s Institute on Aging), along with Ben Black, PhD (professor of Biochemistry and Biophysics).
Edward Lee commented on the significance: “It is amazing that we can see individual molecules and how they interact with each other,” Lee said. “When you finally see something in 3D, it makes sense. It all comes together.”
