First mice engineered to survive COVID-19 like young, healthy humans

Researchers have genetically engineered the first mice that get a human-like form of COVID-19, according to a study published online November 1in Nature.

Led by researchers from NYU Grossman School of Medicine, the new work created lab mice with human genetic material for ACE2 -- a protein snagged by the pandemic virus so it can attach to human cells as part of the infection. The mice with this genetic change developed symptoms similar to young humans infected with the virus causing COVID-19, instead of dying upon infection as had occurred with prior mouse models.

"That these mice survive creates the first animal model that mimics the form of COVID-19 seen in most people -- down to the immune system cells activated and comparable symptoms," said senior study author Jef Boeke, the Sol and Judith Bergstein Director of the Institute for Systems Genetics at NYU Langone Health. "This has been a major missing piece in efforts to develop new drugs against this virus."

"Given that mice have been the lead genetic model for decades," added Boeke, "there are thousands of existing mouse lines that can now be crossbred with our humanized ACE2 mice to study how the body reacts differently to the virus in patients with diabetes or obesity, or as people age."

Problem of Large DNA

The new study revolves around a new method to edit DNA, the 3 billion "letters" of the genetic code that serve as instructions for building our cells and bodies.

While famous techniques like CRISPR enable the editing of DNA editing just one or a few letters at a time, some challenges require changes throughout genes that can be up to 2 million letters long. In such cases, it may be more efficient to build DNA from scratch, with far-flung changes made in large swaths of code pre-assembled and then swapped into a cell in place of its natural counterpart. Because human genes are so complex, Boeke's lab first developed its "genome writing" approach in yeast, one-celled fungi that share many features with human cells but that are simpler and easier to study.

More recently, Boeke's team adapted their yeast techniques to the mammalian genetic code, which is made up of not just of genes that encode proteins, but also of many switches that turn on different genes at different levels in different cell types. By studying this poorly understood "dark matter" that regulates genes, the research team was able to design living mice with cells that had more human-like levels of ACE gene activity for the first time. The study authors used yeast cells to assemble DNA sequences of up to 200,000 letters in a single step, and then delivered these "naked" DNAs into mouse embryonic stem cells using their new delivery method, mSwAP-In.

Overcoming the size limits of past methods, mSwAP-In delivered a humanized mouse model of COVID-19 pathology by "overwriting" 72 kilobases (kb) of mouse Ace2 code with 180 kb of the human ACE2 gene and its regulatory DNA.

To accomplish this cross-species swap, the study method cut into a key spot in the DNA code around the natural gene, swapped in a synthetic counterpart in steps, and with each addition, added a quality control mechanism so that only cells with the synthetic gene survived. The research team then worked with Sang Yong Kim at NYU's Rodent Genome Engineering Lab using a stem cell technique called "tetraploid complementation" to create a living mouse whose cells included the overwritten genes.

In addition, the researchers had previously designed a synthetic version of the gene Trp53, the mouse version of the human gene TP53, and swapped it into mouse cells. The protein encoded by this gene coordinates the cell's response to damaged DNA, and can even instruct cells containing it to die to prevent the build-up of cancerous cells. When this "guardian of the genome" itself becomes faulty, it is a major contributor to human cancers.

Whereas the ACE2 experiments had swapped in an unchanged version of a human gene, the synthetic, swapped-in Trp53 gene had been designed to no longer include a combination of molecular code letters -- cytosine (C) next to guanine (G) -- known to be vulnerable to random, cancer-causing changes. The researchers overwrote key CG "hotspots" with code containing a different DNA letter in adenine (A).

"The AG switch left the gene's function intact, but lessened its vulnerability to mutation, with the swap predicted to lead to a 10-to-50 fold lower mutation rate," said first author Weimin Zhang, PhD, a post-doctoral scholar in Boeke's lab. "Our goal is to demonstrate in a living test animal that this swap leads to fewer mutations and fewer resulting tumors, and those experiments are being planned."

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Pig kidney xenotransplantation performing optimally after 32 days in human body

Surgeons at NYU Langone Health have transplanted a genetically engineered pig kidney that continues to function well after 32 days in a man declared dead by neurologic criteria and maintained with a beating heart on ventilator support. This represents the longest period that a gene-edited pig kidney has functioned in a human, and the latest step toward the advent of an alternate, sustainable supply of organs for transplant.

The procedure, performed on July 14, 2023, and led by Robert Montgomery, MD, DPhil, the H. Leon Pachter, MD Professor of Surgery, chair of the Department of Surgery, and director of the NYU Langone Transplant Institute, was the fifth xenotransplant performed at NYU Langone. Observation is ongoing and the study will continue through mid-September 2023.

"This work demonstrates a pig kidney -- with only one genetic modification and without experimental medications or devices -- can replace the function of a human kidney for at least 32 days without being rejected," said Dr. Montgomery, who had previously performed the world's first genetically modified pig kidney transplant into a human decedent on September 25, 2021, followed by a second similar procedure on November 22, 2021. Surgeons with the Transplant Institute performed two genetically engineered pig heart transplants in summer 2022.

Removing Troublesome Gene Again Shows Promise

The first hurdle to overcome in xenotransplants is preventing so-called hyperacute rejection, which typically occurs just minutes after an animal organ is connected to the human circulatory system. By "knocking out" the gene that encodes the biomolecule known as alpha-gal -- which has been identified as responsible for a rapid antibody-mediated rejection of pig organs by humans -- immediate rejection has been avoided in all five xenotransplants at NYU Langone. Additionally, the pig's thymus gland, which is responsible for educating the immune system, was embedded underneath the outer layer of the kidney to stave off novel, delayed immune responses. The combination of modifications has been shown to prevent rejection of the organ while preserving kidney function.

To ensure the body's kidney function was sustained solely by the pig kidney, both of the transplant recipient's native kidneys were surgically removed. One pig kidney was then transplanted and started producing urine immediately without any signs of hyperacute rejection. During the observation phase, intensive care clinical staff maintained the decedent on support while the pig kidney's performance was monitored and sampled with weekly biopsies. Levels of creatinine, a bodily waste product found in the blood and an indicator of kidney function, were in the optimal range during the length of the study, and there was no evidence on biopsy of rejection.

The surgery was the latest in a larger study approved by a specific research ethics oversight board at NYU Langone and was performed after consultation with the New York State Department of Health. This important research, which study leaders say could save many lives in the future, was made possible by the family of a 57-year-old male who elected to donate his body after a brain death declaration and a circumstance in which his organs or tissues were not suitable for transplant.

LiveOnNY, the nonprofit organization that facilitates organ and tissue donation in the greater New York City area, was a critical partner in the effort to inform, support, and collaborate throughout the authorization process with the donor family.

A Big Leap Toward a New Organ Source

In the United States, there are more than 103,000 people on the waiting list for transplant, with nearly 88,000 of those waiting for a kidney, according to recent federal Organ Procurement and Transplantation Network (OPTN) data. In 2022, about 26,000 people received a kidney transplant. Meanwhile, nearly 808,000 people in the U.S. have end-stage renal disease.

"There are simply not enough organs available for everyone who needs one," said Dr. Montgomery, who received a hepatitis C-positive heart transplant himself in 2018. "Too many people are dying because of the lack of available organs, and I strongly believe xenotransplantation is a viable way to change that."

The kidney and thymus gland used in this procedure were procured from a GalSafeTM pig, an animal engineered by Revivicor, Inc., a subsidiary of United Therapeutics Corporation. In December 2020, the U.S. Food and Drug Administration (FDA) approved the GalSafe pig as a potential source for human therapeutics as well as a food source for people with alpha-gal syndrome, a meat allergy caused by a tick bite.

Less May Be More in Kidney Xenotransplants

While previous genetically engineered pig organ transplants have incorporated up to 10 genetic modifications, this latest study shows that a single-gene knockout pig kidney can still perform optimally for at least 32 days without rejection.

"We've now gathered more evidence to show that, at least in kidneys, just eliminating the gene that triggers a hyperacute rejection may be enough along with clinically approved immunosuppressive drugs to successfully manage the transplant in a human for optimal performance -- potentially in the long-term," said Dr. Montgomery.

The NYU Langone team used standard transplant immunosuppression medications combined with enhanced screening of porcine cytomegalovirus (pCMV) in the donor pig to ensure safety. Recent studies have shown pCMV may affect organ performance and potentially trigger organ failure. No pCMV was detected after 32 days, and close surveillance of porcine endogenous retrovirus (PERV), along with six other viruses of interest, was performed.

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