Human Artificial Chromosomes Could Ferry Tons More DNA Cargo Into Cells

The human genetic blueprint is deceptively simple. Our genes are tightly wound into 46 X-shaped structures called chromosomes. Crafted by evolution, they carry DNA and replicate when cells divide, ensuring the stability of our genome over generations.

In 1997, a study torpedoed evolution’s playbook. For the first time, a team created an artificial human chromosome using genetic engineering. When delivered into a human cell in a petri dish, the artificial chromosome behaved much like its natural counterparts. It replicated as cells divided, leading to human cells with 47 chromosomes.

Rest assured, the goal wasn’t to artificially evolve our species. Rather, artificial chromosomes can be used to carry large chunks of human genetic material or gene editing tools into cells. Compared to current delivery systems—virus carriers or nanoparticles—artificial chromosomes can incorporate far more synthetic DNA.

In theory, they could be designed to ferry therapeutic genes into people with genetic disorders or add protective ones against cancer.

Yet despite over two decades of research, the technology has yet to enter the mainstream. One challenge is that the short DNA segments linking up to form the chromosomes stick together once inside cells, making it difficult to predict how the genes will behave.

This month, a new study from the University of Pennsylvania changed the 25-year-old recipe and built a new generation of artificial chromosomes. Compared to their predecessors, the new chromosomes are easier to engineer and use longer DNA segments that don’t clump once inside cells. They’re also a large carrier, which in theory could shuttle genetic material roughly the size of the largest yeast chromosome into human cells.

“Essentially, we did a complete overhaul of the old approach to HAC [human artificial chromosome] design and delivery,” study author Dr. Ben Black said in a press release.

“The work is likely to reinvigorate efforts to engineer artificial chromosomes in both animals and plants,” wrote the University of Georgia’s Dr. R. Kelly Dawe, who was not involved in the study.

Shape of You

Since 1997, artificial genomes have become an established  biotechnology. They’ve been used to rewrite DNA in bacteria, yeast, and plants, resulting in cells that can synthesize life-saving medications or eat plastic. They could also help scientists better understand the functions of the mysterious DNA sequences littered throughout our genome.

The technology also brought about the first synthetic organisms. In late 2023, scientists revealed yeast cells with half their genes replaced by artificial DNA—the team hopes to eventually customize every single chromosome. Earlier this year, another study reworked parts of a plant’s chromosome, further pushing the boundaries of synthetic organisms.

And by tinkering with the structures of chromosomes—for example, chopping off suspected useless regions—we can better understand how they normally function, potentially leading to treatments for diseases.

The goal of building human artificial chromosomes isn’t to engineer synthetic human cells. Rather, the work is meant to advance gene therapy. Current methods for carrying therapeutic genes or gene editing tools into cells rely on viruses or nanoparticles. But these carriers have limited cargo capacity.

If current delivery vehicles are like sailboats, artificial human chromosomes are like cargo ships, with the capacity to carry a far larger and wider range of genes.

The problem? They’re hard to build. Unlike bacteria or yeast chromosomes, which are circular in shape, our chromosomes are like an “X.” At the center of each is a protein hub called the centromere that allows the chromosome to separate and replicate when a cell divides.

In a way, the centromere is like a button that keeps fraying pieces of fabric—the arms of the chromosome—intact. Earlier efforts to build human artificial chromosomes focused on these structures, extracting DNA letters that could express proteins inside human cells to anchor the chromosomes. However, these DNA sequences rapidly grabbed onto themselves like double-sided tape, ending in balls that made it difficult for cells to access the added genes.

One reason could be that the synthetic DNA sequences were too short, making the mini-chromosome components unreliable. The new study tested the idea by engineering a far larger human chromosome assembly than before.

Eight Is the Lucky Number

Rather than an X-shaped chromosome, the team designed their human artificial chromosome as a circle, which is compatible with replication in yeast. The circle packed a hefty 760,000 DNA letter pairs—roughly 1/200 the size of an entire human chromosome.

Inside the circle were genetic instructions to make a sturdier centromere—the “button” that keeps the chromosome structure intact and can make it replicate. Once expressed inside a yeast cell, the button recruited the yeast’s molecular machinery to build a healthy human artificial chromosome.

In its initial circular form in yeast cells, the synthetic human chromosome could then be directly passed into human cells through a process called cell fusion. Scientists removed the “wrappers” around yeast cells with chemical treatments, allowing the cells’ components—including the artificial chromosome—to merge directly into human cells inside petri dishes.

Like benevolent extraterrestrials, the added synthetic chromosomes happily integrated into their human host cells. Rather than clumping into noxious debris, the circles doubled into a figure-eight shape, with the centromere holding the circles together. The artificial chromosomes happily co-existed with native X-shaped ones, without changing their normal functions.

For gene therapy, it’s essential that any added genes remain inside the body even as cells divide. This perk is especially important for fast-dividing cells like cancer, which can rapidly adapt to therapies. If a synthetic chromosome is packed with known cancer-suppressing genes, it could keep cancers and other diseases in check throughout generations of cells.

The artificial human chromosomes passed the test. They recruited proteins from the human host cells to help them spread as the cells divided, thus conserving the artificial genes over generations.

A Revival

Much has changed since the first human artificial chromosomes.

Gene editing tools, such as CRISPR, have made it easier to rewrite our genetic blueprint. Delivery mechanisms that target specific organs or tissues are on the rise. But synthetic chromosomes may be regaining some of the spotlight.

Unlike viral carriers, the most often used delivery vehicle for gene therapies or gene editors, artificial chromosomes can’t tunnel into our genome and disrupt normal gene expression—making them potentially far safer.

The technology has vulnerabilities though. The engineered chromosomes are still often lost when cells divide. Synthetic genes placed near the centromere—the “button” of the chromosome—may also disrupt the artificial chromosome’s ability to replicate and separate when cells divide.

But to Dawe, the study has larger implications than human cells alone. The principles of re-engineering centromeres shown in this study could be used for yeast and potentially be “applicable across kingdoms” of living organisms.

The method could help scientists better model human diseases or produce drugs and vaccines. More broadly, “It may soon be possible to include artificial chromosomes as a part of an expanding toolkit to address global challenges related to health care, livestock, and the production of food and fiber,” he wrote.

Image Credit: Warren Umoh / Unsplash

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