Unraveling How E. histolytica Kills Cells and Evades the Immune System

The single-celled parasite Entamoeba histolytica infects approximately 50 million people each year, causing nearly 70,000 deaths. In most cases, this shape-shifting amoeba causes only mild symptoms, such as diarrhea. However, in some instances, it can lead to severe or even fatal disease by forming ulcers in the colon, destroying liver tissue, and invading the brain and lungs.

“It can kill anything you throw at it, any kind of human cell,” said Katherine Ralston, an Associate Professor in the Department of Microbiology and Molecular Genetics. E. histolytica can even evade the immune system and kill the very white blood cells that are meant to fight it.

Scientists have long struggled to understand how it does this. However, in a recent study published in Trends in Parasitology, Ralston and her lab outlined a strategy to tackle this mystery, using genetic tools to dissect the parasite’s proteins and genes.

“All parasites are understudied, but E. histolytica is especially enigmatic,” said Ralston. Developing the tools required to study it has taken years. Yet in the process, she has made unexpected discoveries that could lead to improved treatments.

Finding the Murder Weapon of a Microscopic Killer

E. histolytica enters the colon when a person consumes contaminated food or water, typically in developing nations with poor water sanitation. In the United States, it is most often seen in individuals who have recently traveled abroad or immigrated from other countries.

Its species name, histolytica, means “tissue-dissolving,” referring to its ability to create festering pockets of liquefied tissue—known as abscesses—in the organs it infects. As it damages organs, the parasite does not neatly consume the cells it destroys. Instead, it leaves the damaged cells to release their contents as it continues moving on to attack others.

Ralston began studying this formidable organism in 2011 during a postdoctoral fellowship at the University of Virginia. At the time, it was believed the parasite killed cells by injecting them with a toxin. But under the microscope, she observed something entirely different.

E. histolytica was taking bites out of human cells. Looking through the microscope, “You could see little parts of the human cell being broken off,” she said. The ingested cell fragments—visible as fluorescent green under her microscope—accumulated within the amoeba.

Her discovery that the parasite kills cells through this process, known as “trogocytosis,” was published in Nature in 2014.

This was important. To devise new therapies or vaccines, you really need to know how E. histolytica damages tissue.

Katherine Ralston, Associate Professor, University of California, Davis

In 2022, Ralston discovered that after the amoeba consumes parts of human cells, it becomes resistant to a key component of the human immune system: a class of molecules known as complement proteins, which help identify and eliminate invading cells.

In a new study posted to bioRxiv in October 2024, Ralston, along with graduate students Maura Ruyechan and Wesley Huang, found that the amoeba gains this resistance by ingesting proteins from the outer membranes of human cells and incorporating them onto its own surface. Two of these human proteins, CD46 and CD55, prevent complement proteins from binding to the amoeba’s membrane.

In effect, the amoebae kill human cells and then wear their protein “uniforms” as a disguise, allowing them to slip past the immune system undetected.

Building Tools for Scientific Discovery

With other pathogens, such as HIV and Salmonella, researchers have made rapid progress by identifying numerous genes and conducting high-throughput experiments to knock them out one by one, determining which are essential for causing disease. However, this approach has been far more challenging with E. histolytica.

Its genome, sequenced in 2005, is five times larger than that of Salmonella and 2,500 times larger than HIV’s. Analyzing it required years of advancement in bioinformatics. Still, a 2013 study revealed a promising clue: E. histolytica uses a cellular process known as RNA interference (RNAi) as a kind of “volume control” to regulate gene expression.

“We thought we could turn this into a tool for understanding its genome,” Ralston remarked. In 2021, she, Ruyechan, Huang, and six colleagues from UC Davis published a paper introducing one such tool: an “RNAi library” that allows them to selectively inhibit the expression of each of the parasite’s 8,734 known genes.

In their latest study, featured as the cover story this month in Trends in Parasitology, Ralston, Huang, and Ruyechan outline a strategy for using the RNAi system to quickly identify genes that are essential for key parasite functions, such as biting human cells or stealing their proteins.

They propose combining this method with the gene-editing tool CRISPR. This would allow them to tag proteins with fluorescent markers to track their interactions under a microscope, or to delete specific segments of genes and proteins in order to pinpoint the elements that could be targeted with new drugs.

“We now see a light at the end of the tunnel, and we think this could be achievable,” said Huang, who is advocating for the research community to develop CRISPR for application in the amoeba.

From Basic Research to Medical Breakthroughs

The story of E. histolytica underscores the value of basic research and how foundational discoveries can lead to medical breakthroughs years down the line.

It took researchers years to learn how to cultivate the parasite in the lab, and even longer for Ralston to uncover how it bites human cells and hijacks their proteins to evade the immune system.

Even after its genome was sequenced, scientists like Ralston needed additional time to develop the experimental tools necessary to study it in depth. This kind of groundwork is critical for identifying genes or proteins that could serve as targets for future vaccines or therapeutic drugs.

Science is a process of building. You have to build one tool upon another, until you are finally ready to discover new treatments.

Katherine Ralston, Associate Professor, University of California, Davis