Bat biotech takes flight

Paratus is not alone in taking this comparative biology approach to drug discovery. There is a long history of pharmaceutical companies deriving therapeutic agents from the natural world, especially in the antibacterial and anticancer arena. And over the past decade, a handful of firms have tried to leverage comparative biology for therapeutic gain.

“It’s becoming a bit of a renaissance approach,” says Ashley Zehnder, cofounder and CEO of Fauna Bio, a company aimed at harnessing insights from hibernating squirrels, tenrecs and other mammals with unique physiological features. “There is real meat on the bones” of this strategy.

But Paratus is the most lavishly funded, with a who’s who of scientific founders, advisors and investors. Plus, the company has two key enabling technologies to power its bat-focused pursuits.

First, it has access to dozens of bat genomes, part of a unique partnership forged with an academic consortium called Bat1K that aims to sequence the DNA of all living bat species to chromosome-level assembly. In 2020, Bat1K researchers reported on the project’s first six genomes, which revealed bat-specific mutations in several immunity genes and regulatory RNAs that could serve as molecular targets for drug development. A preprint detailing another ten genomes went online earlier this year.

“You can learn a lot of things from by comparing genomes,” says Michael Hiller, a member of the Bat1K executive committee from the LOEWE Center for Translational Biodiversity Genomics in Frankfurt, Germany. But genomics alone “clearly has limitations.” It can provide drug hunters with valuable insights and potential therapeutic leads, Hiller notes, but experimental systems are then needed to validate the biological effects of observed genetic changes in a bat-relevant context.

Bats themselves are difficult to maintain and breed, let alone genetically engineer for research purposes. But researchers affiliated with Paratus have developed the next best thing: bat stem cells.

As reported in February 2023, a team led by company co-founder Thomas Zwaka, a stem cell biologist at the Icahn School of Medicine at Mount Sinai, devised a protocol for coaxing bat fibroblasts into forming induced pluripotent stem (iPS) cells (Fig. 1). Lead study author Marion Déjosez, who is married to Zwaka, is now directing efforts at Paratus to make different types of bat tissues from these cells to unlock the secrets of bat biology. “That opens a whole new horizon for experiments,” says Hiller, a co-author of the stem cell report.

Courtesy Phil Ferro, Paratus Sciences

Induced pluripotent cells from the greater horseshoe bat (Rhinolophus ferrumequinum) stained with Mitotracker and Bodipy, showing the mitochondria in red and lipids in green.

Add in the potential to manipulate the bat cells with gene-editing technologies and “these toolboxes can make the findings from comparative genomics a lot more translatable,” says Liliana Dávalos, an evolutionary biologist and Bat1K executive committee member from Stony Brook University in New York State.

With new drug targets should come new drug candidates that can be tested in more conventional pharmacological assays, including human cells and mouse disease models. Clinical trials could then follow. Yet, once Paratus gets to that point, it will be just another clinical-stage company. Its secret sauce lies in its preclinical discovery platform, says Lucio Iannone, a Paratus board member and financial backer from Leaps by Bayer, an investment arm of the German pharmaceutical giant.

“Everyone is looking for new targets in the pharmaceutical world,” he says. Informed by bat biology, Iannone argues, Paratus’s approach to target identification and validation could come to rule the roost.

The idea of using bats as a window into human health dates back more than a century to the work of Nobel Prize-winning immunologist Élie Metchnikoff, who turned to Indian fruit bats (Pteropus medius) to study the role of gut microbes in digestion in the early 1900s.

But it would take another 100 years or so — and the efforts of two pioneering scientists: Linfa Wang, director of the Emerging Infectious Diseases Program at the Duke–NUS Medical School in Singapore, and Emma Teeling, director of the Centre for Irish Bat Research at University College Dublin — for the concept to gain much traction.

A cave nectar bat (Eonycteris spelaea) fed watermelon juice after a routine health check.
Credit: Courtesy Randy Foo, bat colony manager, Duke-NUS Medical School

Trained as a biochemist, Wang got pulled into the world of bat biology in 1994, after the outbreak of a mysterious respiratory disease among horses and their trainers on the outskirts of Brisbane, Australia. The incident involved a new virus — later named Hendra, after the suburb where it was first described — and that virus, as it turned out, had originated in bats.

Wang, who was working at the Commonwealth Scientific and Industrial Research Organisation near Melbourne at the time, helped sequence the Hendra virus and started working on related bat-borne paramyxoviruses, including Nipah.

Then came severe acute respiratory syndrome (SARS). Global health official tasked Wang with pinpointing the origins of the 2003 epidemic. Within a couple years, he and his colleagues had traced the SARS coronavirus back to cave-dwelling horseshoe bats living in southern China.

Those virus-hunting projects got Wang thinking: “Is this a coincidence, or is there something about bats?” Wang quickly shifted his lab’s focus from the viruses to their bat hosts. Starting in the mid-2000s, he spearheaded efforts to sequence the genomes of two distantly related species, David’s myotis (Myotis davidii) and the black flying fox (Pteropus alecto), a project that ultimately revealed many genes implicated in DNA damage repair and immune response pathways. Wang and his colleagues also created immortalized cell lines from the brains, lungs, intestines and other organs of wild-caught Australian bats and then used these cells to systematically characterize the antiviral mechanisms of bats.

“My ‘batman’ career started from there,” Wang says.

Interrogations of the bats’ genomes, along with deeper dives into their interferon signaling and inflammasome sensor pathways, led Wang to formulate a theory about how the unique immune adaptations of bats came about. Perhaps, he thought, the reason why bats coexist with so many viruses can be explained by the evolution of flight. Muscle-powered wing flapping puts a lot of strain on the body, leading to the accumulation of DNA repair defects and toxic byproducts harmful to cells. To mitigate these challenges, bats presumably evolved strategies to minimize the negative consequences of their energetically demanding lifestyles.

One such strategy involves curbing inflammatory responses to free-floating DNA in the cytoplasm, thus allowing bat cells to maintain their cellular integrity in the face of genomic damage and metabolic stress. However, this protective mechanism comes at a price: increased susceptibility to viral infections. So, to combat this vulnerability, bats have developed a range of counter-defenses, with adaptations found, for example, in numerous interferon-related genes.

The opposing evolution pressures on bats eventually led to a delicate equilibrium in antiviral immunity. Bats boast a robust first-line shield against infection while also possessing the ability to regulate inflammation when viruses take hold within their cells. As an added outcome, the animals acquired a natural resilience against cancer and autoimmune diseases.

Bat biologists have generally embraced Wang’s hypothesis tying the animals’ superimmunity to their winged ways (Fig. 2). “It would be hard to explain bats unique viral tolerance without invoking flight,” says Cara Brook, a disease ecologist at the University of Chicago who studies fruit bats and their viruses on the island nation of Madagascar. “These are the downstream consequences of it.”

As a result, viral cytosolic DNA is tolerated and bats coexist with many viruses. (Adapted with permission from J. Xie et al. Cell Host Microbe 23, 297–301, 2018, Elsevier; image from LabXchange © The President and Fellows of Harvard College).

And the task for drug companies hoping to develop the next blockbuster treatment for inflammatory disease — a market generally seen as more lucrative than the anti-infective space — is now to “mimic some of these anti-inflammatory pathways through the existing human molecular architecture,” she says. (Brook is not affiliated with Paratus or any other drugmaker.)

A downstream consequence of bats’ adaptation to flight is dampened activity of inflammasomes, multiprotein complexes that form in response to danger signals and trigger a cascade of pro-inflammatory cytokines for fighting off infections and promoting wound healing. However, inflammasome activation also contributes to chronic inflammation, tissue damage and cell death. Achieving the optimal regulation of inflammasome function is vital for maintaining a healthy immune system — and, in bats, this regulation leans downward.

Over the past eight years, Wang and his colleagues have detailed six levels of regulation that contribute to this suppressed inflammasome response in bats. These include diminished activation of one sensor protein (NLRP3) and the complete loss of another (AIM2); negative regulation of an adaptor protein (ASC); plus the diminished activity of a key effector enzyme (caspase-1) and impaired cleavage of the interleukin-1β precursor, a critical step facilitating cytokine secretion.

“Every level is druggable,” notes Wang, and indeed many pharmaceutical companies are already pursuing these targets. At least six different NLRP3 inhibitors are in clinical trials, and an interleukin-1β–targeting antibody — Novartis’s Ilaris (canakinumab) — has been on the market for over a decade for treating several inflammatory disorders. Caspase-1 inhibitors have been tested, albeit unsuccessfully, and a small biotech company called ZyVersa Therapeutics expects to launch trials of an ASC-directed antibody candidate some time next year.

But Wang’s latest findings around how bats go about disrupting ASC function could lend themselves to new therapeutic strategies. As reported in May 2023, bats have a closely related protein called ASC2 that binds to ASC and prevents the adaptor protein from self-associating into the types of aggregates necessary for relaying inflammasome signals. In humans, ASC2 is poorly expressed and the protein is less able to interact with ASC. But by mutating just four amino acids in the human protein, Wang and his colleagues showed they could bestow on it bat-like functionality.

In experiments with activated macrophages, these four modifications in human ASC2 suppressed inflammation. Studies are ongoing to test whether this ‘batified’ form of the human protein — termed hupa4 ASC2 — can produce comparable immune-stifling effects in mouse models of infection and inflammatory disease. If successful, Wang envisions developing a recombinant form of the hupa4 protein for treating inflammatory disease. (Paratus has licensed some of the relevant intellectual property.)

As Wang’s lab delves deeper into the translational possibilities around ASC2, others are pursuing further investigations into some of his previous discoveries related to another facet of the innate immune system. In 2018, Wang’s group, in collaboration with researchers from the Wuhan Institute of Virology in China, showed that bats have a dampened interferon response to free-floating DNA in the cytoplasm — a common sign of viral infection or cellular damage — owing to a single amino acid change in a DNA-sensing protein called STING. All other mammals have a serine residue at the location in question (Ser358), but bats have a range of substitutions in their STING proteins that weaken interferon pathway induction.

Anna Bruchez, a virologist at Case Western Reserve University, is picking up where that study left off. She is characterizing how various STING sequences found among bats regulate immune responses in different ways. To do that, she has created libraries of human–bat hybrid STINGs with sequences from different bat species and is now looking for protein alterations that give rise to unique regulatory functions.

“It is a few steps removed from any therapeutic stuff,” says Bruchez. But, she adds: “You never know what you’re going to find.”

A similar credo has run through Paratus’s early research operations. After incorporating in April 2021, the company spent two years building out infrastructure, establishing relationships with thought leaders, and getting permits in place to work with bat tissue collected from all over the world. The company has two labs up and running — in New York City and Singapore — and has enlisted Wang and Teeling to serve as founding advisors. “Now,” says Ferro, “we’re really putting our heads down, taking what we’ve amassed and built, and using it to identify targets and validate our platforms’ value.”

The company was not always so singularly focused.

Paratus’s origins can be traced back to the earliest days of the COVID-19 pandemic, when Zwaka was looking for ways to contribute to the global research response. He used his expertise in stem cell biology to derive human lung cells for studying SARS-CoV-2 infections and for screening potential antiviral drugs. But a February 2020 report that linked the novel coronavirus to a probable bat origin also got Zwaka thinking: could he make similar kinds of lung cells from bats to gain insights into why these hosts do not exhibit the same level of sickness as humans?

“The first thing I thought was, ‘Let’s get iPS cells’,” he says.

Several research groups across the world had already established breeding colonies of different bat species — Wang, for example, has one in Singapore that houses a population of cave nectar bats (Eonycteris spelaea). But none of these colonies are home to horseshoe bats (genus Rhinolophus), the large-eared insect-eaters known to harbor SARS-like coronaviruses. And since Zwaka wanted to make iPS cells from a species that would be susceptible to SARS-CoV-2 infection, he realized that would need to turn to wild-caught specimens.

“We made a lot of phone calls,” Zwaka says. Eventually, he connected with Javier Juste, an evolutionary ecologist at the Spanish National Research Council’s Doñana Biological Station in Seville, who agreed to collect and send tissues from the greater horseshoe bat (R. ferrumequinum) to Zwaka’s lab in New York City.

After two months of preparation, Juste and a colleague went out one night in May 2020 and hand-netted two bats from a roost located inside an abandoned tunnel near the southwestern port city of Cádiz. The researchers then drove the animals some 650 kilometers to the airport in Madrid, euthanized them, prepared the tissues in a parking lot and, in the nick of time, managed to ship everything off on one of the few FedEx flights in operation at the time.

When Zwaka received the samples, he was in for a fortuitous surprise. Of the two bat specimens that Juste had sent him, one turned out to be a pregnant female. The fibroblasts of its embryo proved most amenable to cellular reprogramming.

He and his colleagues used the standard four ‘Yamanaka’ reprogramming factors but tweaked the ratios and added a few other molecules to get bat iPS cells to take hold. There was a lot of trial and error, notes Zwaka, and “I don’t think we would have figured out the protocol with adult fibroblasts as quickly,” he says.

In studying his iPS cells, Zwaka noticed a curious phenomenon. He knew that the bat genome, like those of most animals, was chock-full of viral sequences — remnants of infections at distant points in the evolutionary past. But an unusually large number of these endogenous viral sequences seemed to be reawakened in the pluripotent state, with evidence of viral proteins and active virus-like assemblies throughout the cells.

Expression profiling also suggested that the cells were responding to this viral revival. “It looked really like the cells were infected with something,” says Zwaka, “even when they were not.”

A fateful chain of Zoom calls then led to the inception of Paratus.

Zwaka told his friend and occasional collaborator, Rick Young of the Whitehead Institute, about the preliminary bat data. Young then relayed the findings to Amir Nashat, an executive partner at Polaris Partners with whom he had previously created a few other companies. “I was just telling him because I was excited about the biology,” Young recalls. “Amir jumped onto this immediately.”

Talk of forming a startup ensued, and they roped in mechanobiologist Paul Matsudaira, a former Whitehead colleague (and hiking buddy) of Young’s who had recently moved back to the United States after spending more than a decade at the National University of Singapore, to co-found the company. Riffing on the bat theme, they initially considered names such as Gotham Therapeutics (already taken) and Wayne Industries. Eventually, they settled on Paratus, Latin for “prepared.”

The name reflects some of the founders’ early concepts around using bat iPS cells as a pandemic preparedness tool. Perhaps, by cataloguing all the viral relics found in bat genomes and checking which viruses come alive in the stem cells, they could better predict future spillover events. Or maybe they could develop broad-spectrum antiviral drugs that worked against potential zoonotic threats.

Recognizing a gap in their knowledge of bat biology, the founders knew they would need to bring in others with more expertise. Zwaka, in his stem cell analyses, had relied heavily on genome assemblies from the Bat1K consortium. He proposed reaching out to the project’s co-director, Emma Teeling.

In the discussions that followed, Teeling suggested that Zwaka try making iPS cells from another bat species, and doing so from non-lethal biopsy samples — a method that would prove more acceptable to the conservation-conscious bat research community and the government agencies that oversee their expeditions. So, on her next trip to northern France, where she had been studying a colony of greater mouse-eared bats (Myotis myotis) since 2010, Teeling took tail and wing clippings from 18 animals and sent them off to Zwaka’s lab for cellular reprogramming.

“It worked right away,” Zwaka recalls. With the protocols honed on the embryonic cells, rewinding the developmental clock back on the adult cells was seamless. Zwaka and his colleagues have since generated bat iPS cells from around a half-dozen more species. They have also begun developing methods for turning the iPS cells into brain tissue, immune cells and other specialized cell types, a necessary step toward unraveling the distinctive molecular features that set bats apart.

In consultation with Teeling and later Wang, both of whom were brought on as scientific founders, the Paratus team soon began to think bigger than their initial focus on pandemic readiness and infectious disease. Teeling’s research on bat longevity, specifically her exploration of genes governing telomere preservation and microRNAs involved in regulating aging-related pathways, pointed to opportunities in the realms of oncology and other age-related diseases. Meanwhile, Wang’s endeavors highlighted the prospect of finding novel drug targets implicated in inflammation and autoimmunity.

Paratus’s mandate could transcend its original scope and encompass a broad range of biomedical research and therapeutic opportunities, the founders realized. “It’s more than the viruses,” says Matsudaira, who served as interim CSO in the company’s early days. “The real gold is in understanding the biology of bats.”

“It’s more than the viruses. The real gold is in understanding the biology of bats.” —Paul Matsudaira.

While Paratus remains the main biotech company pushing bat translational research forward, numerous academic scientists, independent of commercial affiliations, are also driving the field in new directions.

Despite pioneering work of Wang and others, “bat immunology is still relatively in its infancy,” says Hannah Frank, an evolutionary immunologist at Tulane University. And while most researchers have focused on innate immunity, less attention has been paid to the adaptive arm of the immune system and the humoral immune responses that contribute to antiviral defenses. With funding from the US National Institute of Allergy and Infectious Diseases, Frank and her colleagues are now delving into the role of B cells and antibodies.

Thinking beyond viruses, some researchers are looking into bat responses against bacterial infections. Several research teams have injected bats with bacterial endotoxins and shown that acute stress responses typical of other mammals do not kick in for bats. But unpublished experiments on blood samples — performed by Judith Mandl, an immunologist at McGill University in Montreal, and her colleagues — have taken this finding one step further.

According to Mandl, bat blood cells are much slower than human ones to mount an inflammatory response to the bacterial toxin. Then, when they do, “it’s much more muted,” she says. Moreover, the types of inflammation-associated genes that get switched on show little overlap between bats and humans. “So, it tells us that, both in terms of the magnitude of the response and also in terms of the response quality, there are fundamental differences,” Mandl says — differences that could now be mined for therapeutic targets.

However, that ability to tamp down inflammation is not entirely hardwired in the animals’ own physiology. Bats have intestinal microbes to thank for their immune superpowers as well. That became evident after a team led by behavioral ecologist Tinglei Jiang, from Northeast Normal University, and conservation biologist Jiang Feng, from Jilin Agricultural University — both based in Changchun, China — transferred bacteria from the feces of great roundleaf bats (Hipposideros armiger) into antibiotic-treated mice. Mice that received the bat poop showed stronger immune functions than mice that received bacteria taken from the guts of their own species. Recipients of the guano transplants also showed a greater tolerance to viral infection, with lower levels of inflammation and increased survival rates after exposure to influenza.

One limiting factor in all these experiments remains bat-specific research tools and reagents. Zwaka’s bat iPS cells fill one void, but a range of laboratory resources is needed, says Michael Letko, a molecular virologist at Washington State University. These include immortalized cell lines, recombinant cytokines, cross-reactive antibodies and more. “There’s a big dearth of those things in the community right now,” Letko says. “The basic stuff that we take for granted in the human molecular and cell biology world is just missing for bats — or, if it exists, it’s not always the easiest to get a hold of.”

Letko and his collaborator Arinjay Banerjee, a virologist at the University of Saskatchewan in Saskatoon, Canada, are determined to expand the toolbox. For the past year, they have been working toward establishing immortalized cell lines for all bat species currently held in research colonies. Simultaneously, they have been isolating species-matched cytokines and other reagents crucial for molecular investigations.

This effort is labor-intensive but crucial, Banerjee says. “There’s nothing low-hanging about our field.” Still, the work is necessary to accelerate discoveries that will pave the way for drug development, he contends.

For now, the main engine of target discovery in the bat research community remains squarely in their genomes. The Bat1K team, for example, recently surveyed ten bat genomes, looking for signatures of adaptive evolution in immune genes with relevance to human disease.

One gene in particular stood out. Known as ISG15, this interferon-stimulated gene encodes a protein involved in antiviral activity. The ISG15 protein normally forms dimers, leading to its secretion and the release of pro-inflammatory cytokines. But not so in two coronavirus-carrying bat lineages.

In horseshoe bats and leaf-nosed bats, the deletion of a particular amino acid prevents the formation of stable ISG15 dimers. Consequently, ISG15 sticks around inside the cell, where it gloms onto other newly synthesized proteins, a process known as ISGylation, which is critical to antiviral defenses. Drugs that modulate the dimerization of ISG15 in humans could therefore help to boost antiviral immunity without triggering excessive inflammation.

The researchers also found lineage-specific adaptations in genes linked to pathogen detection, complement activation, inflammatory signaling and B cell survival — all of which could be potential drug targets and require experimental follow-up. “These are things that are going to keep us busy for the next decade — at least,” Dávalos says.

Outside of immunity, some researchers have also begun interrogating genes underpinning the different feeding habits of bats. Most bats dine on beetles and other night-flying insects. Some — most famously, vampire bats — rely on the blood or flesh of other animals. And then there are the nectar- and fruit-eating bats that sustain themselves on a diet that, if adopted by humans, would invariably lead to diabetes and other metabolic problems.

Consider the Jamaican fruit bat (Artibeus jamaicensis). This Caribbean creature eats more than twice its body weight in figs and other sugar-laden fruits — every day. That’s about a Coke-can-worth of sugar, in an animal that is smaller than the can itself. A person with a comparable habit would have an elevated risk of diabetes, hypertension and obesity. Yet, as Nadav Ahituv, a geneticist at the University of California, San Francisco, points out: “Bats have something that allows them to control for all of this.”

Seeking to uncover that special something, Ahituv and his colleagues analyzed gene expression and chromatin accessibility patterns in the bats, comparing them to those from another North American species, the big brown bat (Eptesicus fuscus), known for its insect-eating behavior. Single-cell sequencing of the animals’ kidneys and pancreases revealed several molecular adaptations in the fruit eaters, including in genes and regulatory elements linked to electrolyte balance and insulin production.

Mutations in some of these same genes have been linked to diabetes in people. Yet in fruit bats, “these genes are regulated much more tightly,” says Ahituv (who is not affiliated with Bat1K or Paratus) — and therapeutics that replicate the regulatory effects observed in bats could help to treat metabolic disorders in humans.

Paratus has a stated interest in metabolism as well. But its initial focus remains on chronic inflammation. “We have to be very clever in which targets we chase,” says Teeling

Furthermore, as Zehnder cautions: “You have to really nail the human translatability part, particularly when you’re looking to convince people on the pharma side that either the assets you are developing or the platform you’ve created has relevance to humans.” Prospective partners and investors typically want to see corroborating evidence from human cell culture experiments and in human genetic databases. And if the research remains too exploratory, without tangible results that could pave the way for potential therapeutic products, they may withdraw funding — as Calico Life Sciences did after a 6.5-year effort to better understand the exceptional longevity of naked mole rats.

“We weren’t developing drugs fast enough,” says Rochelle Buffenstein, a former Calico scientist now at the University of Illinois Chicago. It’s a “cautionary tale,” she says, for other companies now seeking therapeutic inspiration from mammals with extreme adaptations.

Teeling acknowledges the challenges ahead, but maintains a steadfast belief that the ongoing research on bats will yield different outcomes. “This is how we change the world,” she says.

The industry will be closely watching to see whether bat-guided drug discovery, like the animals that inspired the approach, can soar to new heights.