Scientists Are Retooling Bacteria to Cure Disease

In a study carried out over the summer, a group of volunteers drank a white, peppermint-ish concoction laced with billions of bacteria. The microbes had been engineered to break down a naturally occurring toxin in the blood.

The vast majority of us can do this without any help. But for those who cannot, these microbes may someday become a living medicine.

The trial marks an important milestone in a promising scientific field known as synthetic biology. Two decades ago, researchers started to tinker with living things the way engineers tinker with electronics.

They took advantage of the fact that genes typically don’t work in isolation. Instead, many genes work together, activating and deactivating one another. Synthetic biologists manipulated these communications, creating cells that respond to new signals or respond in new ways.

Until now, the biggest impact has been industrial. Companies are using engineered bacteria as miniature factories, assembling complex molecules like antibiotics or compounds used to make clothing.

In recent years, though, a number of research teams have turned their attention inward. They want to use synthetic biology to fashion microbes that enter our bodies and treat us from the inside.

The bacterial concoction that volunteers drank this summer — tested by the company Synlogic — may become the first synthetic biology-based medical treatment to gain approval by the Food and Drug Administration.

The bacteria are designed to treat a rare inherited disease called phenylketonuria, or PKU. People with the condition must avoid dietary protein in foods such as meat and cheese, because their bodies cannot break down a byproduct, an amino acid called phenylalanine.

As phenylalanine builds up in the blood, it can damage neurons in the brain, leading to delayed development, intellectual disability and psychiatric disorders. The traditional treatment for PKU is a strict low-protein diet, accompanied by shakes loaded with nutritional supplements.

But in experiments on mice and monkeys, Synlogic’s bacteria showed promise as an alternative treatment. On Tuesday, company investigators announced positive results in a clinical trial with healthy volunteers.

The researchers are now going forward with a trial on people with PKU and expect to report initial results next year.

Tal Danino, a synthetic biologist at Columbia University, said that a number of other researchers are working on similar projects, but no one has moved forward as fast as Synlogic. “They’re leading the charge,” he said.

One of Synlogic’s co-founders, James J. Collins, a synthetic biologist at M.I.T., published one of synthetic biology’s first proofs of principle in 2000.

He and his colleagues endowed E. coli bacteria with a way to turn a gene on and off when they were exposed to certain chemicals — “like a light switch for genes,” Dr. Collins said in an interview.


Tal Danino


At first, the scientists envisioned using rewired bacteria as environmental sensors — perhaps detecting airborne biological weapons and producing a chemical signal in response.

But then came the microbiome.

In the mid-2000s, microbiologists began charting our inner menagerie of microbes, the vast diversity of organisms that live inside healthy people. The microbiome is continually carrying out complex biochemistry, some of which helps shield us from diseases, scientists found.

Synthetic biologists soon began wondering whether they could add engineered bacteria to the mix — perhaps as internal sensors for signs of disease, or even as gut-based factories that make drugs the body needs.

“You can’t overestimate the impact of the microbiome work,” said Jeff Hasty, a former student of Dr. Collins who now runs his own lab at the University of California, San Diego. “That, in a nutshell, changed everything.”

Dr. Collins and Timothy K. Lu, another synthetic biologist at M.I.T., co-founded Synlogic in 2013, and the company began looking for diseases to take on. One of their picks was PKU, which affects 16,500 people in the United States.

Drugs have recently become available that can drive down levels of phenylalanine. But they only work in a fraction of patients, and they come with side effects of their own.

“The current tools that we have available are not good enough,” said Christine S. Brown, the executive director of the National PKU Alliance.

For years, researchers have explored treating PKU with gene therapy, hoping to insert working versions of the defective gene, called PAH, into a patient’s own cells. But so far the approach has not moved beyond studies in mice.

Image
A transmission electron microscopy image of Synlogic’s newly engineered bacteria.CreditW.M.Keck Biological Imaging Facility, The Whitehead Institute

To Synlogic, PKU looked like a ripe opportunity to use synthetic biology to create a treatment that might gain government approval.

Company researchers selected a harmless strain of E. coli that’s been studied for more than a century. “Most people have healthy, good E. coli in their intestinal tracts,” said Paul Miller, the chief scientific officer of Synlogic.

The researchers inserted genes into the bacteria’s DNA so that once they arrived in the gut, they could break down phenylalanine like our own cells do.

One of the new genes encodes a pump that the bacteria use to suck up phenylalanine around them. A second gene encodes an enzyme that breaks down the phenylalanine into fragments. The bacteria then release the fragments, which get washed out in urine.

The Synlogic team wanted the microbes to break down phenylalanine only in the right place and at the right time in the human body. So they engineered the bacteria to keep their phenylalanine genes shut down if they sensed high levels of oxygen around them.

Only when they arrived in a place with little oxygen — the gut — did they turn on their engineered genes.

To test the bacteria, the researchers created mice with the mutation that causes PKU. When the mice received a dose of the bacteria, the phenylalanine in their blood dropped by 38 percent, compared with mice without the microbes.

The researchers also tried out the bacteria on healthy monkeys. When monkeys without the microbes ate a high-protein diet, they experienced a spike of phenylalanine in their blood. The monkeys with engineered bacteria in their guts experienced only a gentle bump.

For their human trial, Synlogic recruited healthy people to swallow the bacteria. Some took a single dose, while others drank increasingly large ones over the course of a week. After ingesting the bacteria, the volunteers drank a shake or ate solid food high in protein.

On Tuesday, Synlogic announced that the trial had demonstrated people could safely tolerate the bacteria. In addition, the more bacteria they ingested, the more bits of phenylalanine wound up in their urine — a sign the bacteria were doing their job.

The next step will be to see if the microbes can lower phenylalanine levels in people with PKU.

“I’m amazed at how fast we got to where we are,” said Dr. Collins, who was not involved in Synlogic’s PKU research.

In July, Dr. Danino and his colleagues published a review in the journal Cell Systems, cataloging a number of other disorders that researchers are designing synthetic microbes to treat, including inflammation and infections.

Dr. Danino and Dr. Hasty are currently collaborating on another project: how to use synthetic biology against cancer.

One huge challenge in developing drugs for cancer is that they often fail to penetrate tumors. But microbiome researchers have discovered that natural bacteria regularly infiltrate tumors and grow inside them.

Now scientists are engineering bacteria that can also make their way into tumors. Once there, they will unload molecules that attract immune cells, which the researchers hope will kill the cancer.

“I think anywhere there are bacteria in the body is an opportunity to engineer them to do something else,” said Dr. Danino.

 

This article was originally published in The New York Times.  Read the original article.

The Fertility Clinic That Cut IVF Prices in Half

The women in the waiting area come from as far as North Carolina and Michigan. Employees usher them into rooms decorated in earth tones. Elevator music plays and the beds are warmed.

The stirrups are the only sign that this isn’t a spa.

CNY Fertility Center is one of the busiest fertility clinics in the country, with four locations in Upstate New York and another soon to open in Atlanta. It’s also among the most affordable.

Embryologist Maureen Woodward places frozen embryos into storage tanks at the CNY Fertility Center in Syracuse. Instruments for moving embryos in culture dishes sit on desks throughout the embryology lab. Embryo samples are taken from a culture dish so that they can be frozen.PHOTOS: HEATHER AINSWORTH FOR THE WALL STREET JOURNAL

CNY is part of a small number of fertility clinics that charge a fraction of what other clinics do for in vitro fertilization (IVF). Doctors at these clinics argue that a high-volume, low-cost fertility program can make money, help start new families and open the market to people who otherwise couldn’t afford IVF. Insurance usually doesn’t fully cover these types of procedures.

Cost is a huge issue when it comes to who can access fertility treatments. “Fertility patients want options,” says Jake Anderson, a former venture capital partner who co-founded FertilityIQ, a San Francisco-based website that lets patients evaluate IVF clinics. “For years we thought there had to be trade-offs between price, volume and quality, but maybe we’ve been wrong all along.”

Robert Kiltz, the 62-year-old owner and director of the fertility clinic, says CNY charges $3,900 for one cycle of IVF. That’s about a third of the national average cost.

CNY patients must also pay for medications, monitoring and sometimes a frozen embryo transfer, bringing the total average cost to about $8,000 a cycle. That compares with a U.S. average of $20,700, as calculated by FertilityIQ, which has verified patient reviews of more than 400 fertility clinics. Its data come from more than 10,000 patients who have had IVF performed over the past 18 months.

The more than 190 IVF patients at CNY report a household income of $85,000 a year, compared with $182,000 nationally, according to FertilityIQ. Nearly 20% earn less than $50,000 a year, compared with just 4% nationally.

CNY’s birthrates, as reported to the Society for Assisted Reproductive Technology, a national organization of fertility specialists, are in line with national average by most accounts. In some age groups they are below average.

Dr. Kiltz says CNY has been profitable every year since its 1997 opening. Business has grown roughly 20% to 30% a year in recent years. “I believe we are opening up the market and making it more accessible and affordable to more people who don’t have access where they’re at,” Dr. Kiltz says.

Many outside experts say the clinic’s outcomes are respectable.

“He’s got very effective pregnancy rates for basically half the cost,” says David Adamson, a past president of the American Society for Reproductive Medicine and CEO of ARC Fertility, a national network of fertility clinics.

Dr. Kiltz says patients have few barriers at his clinics. Some clinics restrict fertility treatments if women are obese or too old or have a lot of previous failed cycles. He will take most anyone.

“Who deserves to have a baby? I don’t have any restrictions,” he says.

Not everyone agrees with that philosophy.

“Most fertility centers draw lines around people that they think intervention is futile based on age or hormone measures or other tests that make them say you don’t have the biology to become pregnant,” says Arthur Caplan, head of medical ethics at NYU School of Medicine.

Though there are no age cutoff guidelines for fertility clinics, Dr. Caplan has advocated a limit of 60 for single parents. “You want to protect the child’s best interest,” Dr. Caplan says.

Ms. Woodward prepares embryo culture dishes.
Ms. Woodward prepares embryo culture dishes. PHOTO: HEATHER AINSWORTH FOR THE WALL STREET JOURNAL

CNY has had one medical malpractice judgment against it in its 20-year history. A couple sued the clinic, Dr. Kiltz and another doctor there for breach of contract, medical malpractice and negligence.

Donald W. Boyajian, the attorney representing the couple, says the suit revolved around the clinic’s failure to screen an egg donor for genetic diseases. The couple had a daughter born with cystic fibrosis six years ago after using an egg donor for IVF at CNY. A jury issued a verdict in 2016 awarding the couple $8.2 million in damages and interest. CNY’s spokesman declined to discuss the case because the verdict is under appeal.

While CNY is among the longest-established low-cost, high-volume clinics, at least two others have similar models. In Colorado, High Quality Affordable fertility centers charges $5,800 for an IVF cycle, or about $9,000 to $10,000 all-included.

In Arizona, Mark Amols says he started an affordable fertility clinic after experiencing firsthand how unaffordable treatments are. He and his wife spent close to $20,000 on fertility treatments 11 years ago. Dr. Paul Magarelli, medical director and CEO of High Quality Affordable centers, helped Dr. Amols when he started New Direction Fertility Centers in Gilbert, Ariz., three years ago.

When he opened in 2015 he decided to charge patients $4,800 for a cycle of IVF, plus the cost of medications. High-volume clinics have more purchasing power and can negotiate better prices for materials and equipment, he says.

CNY patients gave the clinic a 2.5 out of 5 for how frequently they see a doctor, which is a low score, Mr. Anderson says. Dr. Kiltz acknowledges that he may have fewer reproductive endocrinologists on staff than other clinics. Nurse practitioners consult with and monitor women trying to get pregnant. “Some people might not like that model,” he says.

Norbert Gleicher, medical director and chief scientist at the Center for Human Reproduction in Manhattan, says of Dr. Kiltz, “He’s running a very tight ship. He’s doing a ton of cycles with a few physicians. So he’s delegating a lot of stuff to non-physician staff.” (Dr. Gleicher and Dr. Kiltz have no business relationship.)

At Dr. Gleicher’s clinic, three reproductive endocrinologists oversee about 800 IVF cycles a year. Last year CNY had five REs and oversaw roughly 2,500 cycles.

CNY’s flagship Syracuse clinic takes up 20,000 square feet. Most of the clinics also have a spa, called CNY Healing Arts. The spas offer acupuncture, massage and yoga for fertility patients and the general public.

About three years ago the clinic started offering payment plans and in-house financing. More than half of CNY’s patients end up with a one-to-two-year payment plan, for which they are charged a monthly $40 administrative fee.

Melissa and Paul Randazzo, seen here with 5-year-old Liliana and twins Violet, left, and Izabel, right. The Randazzos had their twins with the help of CNY.
Melissa and Paul Randazzo, seen here with 5-year-old Liliana and twins Violet, left, and Izabel, right. The Randazzos had their twins with the help of CNY.

Dr. Kiltz’s patients give CNY high ratings. It has an average ranking of 9.3 out of 10 with 193 reviews, placing it in the top 5% of clinics nationally, according to FertilityIQ. The average clinic on the site has a 7.4 rating.

Melissa Randazzo, a 32-year-old Michigan resident, paid nearly $25,000 to a local fertility clinic seven years ago to have her now-5-year-old daughter. She knew her family couldn’t afford that again. Through some research she found CNY. After two transfers, she had twin girls, Violet and Izabel, now 8 months old. The Randazzos used a two-year payment plan to pay for the IVF, spending a total of about $7,500, plus $1,000 in travel costs.

Ms. Randazzo, who runs a jewelry business from home, says of Dr. Kiltz, “I know he’s busy and I know he has a million patients, but when he came in the room, it was like we were the only people he was seeing that day.”

 

This article was originally published in The Wall Street Journal. Read the original article.

Why Your DNA Is Still Uncharted Territory

You have a gene called PNMA6F. All people do, but no one knows the purpose of that gene or the protein it makes. And as it turns out, PNMA6F has a lot of company in that regard.

In a study published Tuesday in PLOS Biology, researchers at Northwestern University reported that of our 20,000 protein-coding genes, about 5,400 have never been the subject of a single dedicated paper.

Most of our other genes have been almost as badly neglected, the subjects of minor investigation at best. A tiny fraction — 2,000 of them — have hogged most of the attention, the focus of 90 percent of the scientific studies published in recent years.

A number of factors are largely responsible for this wild imbalance, and they say a lot about how scientists approach science.

Researchers tend to focus on genes that have been studied for decades, for example. To take on an enigma like PNMA6F can put a scientist’s career at risk.

“This is very worrisome,” said Luís A. Nunes Amaral, a data scientist at Northwestern University and a co-author of the new study. “If the field keeps exploring the unknown this slowly, it will take us forever to understand these other genes.”

A gene may come to light because scientists encounter the protein it encodes. At other times, the first clue comes when scientists recognize that a stretch of DNA has some distinctive sequences that are shared by all genes.

But giving a gene a name doesn’t mean you know what it does.

Consider a gene called C1orf106. Scientists found it in 2002 but had no idea of its function. In 2011, researchers found that variants of this gene put people at risk of inflammatory bowel disease. Yet they still had no idea why.

In March, a team of researchers based at the Broad Institute in Cambridge, Mass., solved the mystery. They bred mice that couldn’t make proteins from C1orf106, and found that the animals developed leaky guts.

That protein, the scientists discovered, keeps intestinal cells properly glued together. Now investigators have a new way to look for treatments for inflammatory bowel disease.

Researchers noticed that something was wrong with the study of human genes as early as 2003. Just a small group of them attracted most of the scientific attention.

Genetics has changed dramatically since then. Scientists now have a detailed map of the human genome, showing the location of just about every gene on the human genome, and the technology for sequencing DNA has become staggeringly powerful.

Recently, Dr. Amaral and his colleagues checked to see if researchers had broadened their focus by analyzing millions of scientific papers published up to 2015. Our knowledge about human genes, the team found, remained wildly lopsided.

Not only did Dr. Amaral and his colleagues document the ongoing imbalance, they tested 430 possible explanations for why it exists, ranging from the size of the protein encoded by a gene to the date of its discovery.

It was possible, for example, that scientists were rationally focusing attention only on the genes that matter most. Perhaps they only studied the genes involved in cancer and other diseases.

That was not the case, it turned out. “There are lots of genes that are important for cancer, but only a small subset of them are being studied,” said Dr. Amaral.

[Like the Science Times page on Facebook. | Sign up for the Science Times newsletter.]

Just 15 explanations mostly accounted for how many papers have been published on a particular gene. The reasons have more to do with the working lives of scientists than the genes themselves.

For example, it’s easier to gather proteins that are secreted than ones that stay trapped inside cells. Dr. Amaral and his colleagues found that if a gene creates a secreted protein, that gene is much more likely to be well studied.

It’s also easier to study a human gene by looking at a related version in a mouse or some other lab animal. Scientists have succeeded in creating animal models for some genes but not others.

Genes that are studied in animal models tend to be studied a lot in humans, too, Dr. Amaral and his colleagues found.

A long history helps, too. The genes that are intensively studied now tend to be the ones that were discovered long ago.

Some 16 percent of all human genes were identified by 1991. Those genes were the subjects of about half of all genetic research published in 2015.

One reason is that the longer scientists study a gene, the easier it gets, noted Thomas Stoeger, a post-doctoral researcher at Northwestern and a co-author of the new report.

“People who study these genes have a head start over scientists who have to make tools to study other genes,” he said.

That head start may make all the difference in the scramble to publish research and land a job. Graduate students who investigated the least studied genes were much less likely to become a principal investigators later in their careers, the new study found.

“All the rewards are set up for you to study what has been well-studied,” Dr. Amaral said.

“With the Human Genome Project, we thought everything was going to change,” he added. “And what our analysis shows is pretty much nothing changed.”

If these trends continue as they have for decades, the human genome will remain a terra incognito for a long time. At this rate, it would take a century or longer for scientists to publish at least one paper on every one of our 20,000 genes.

That slow pace of discovery may well stymie advances in medicine, Dr. Amaral said. “We keep looking at the same genes as targets for our drugs. We are ignoring the vast majority of the genome,” he said.

Scientists won’t change their ways without a major shift in how science gets done, he added. “I can’t believe the system can move in that direction by itself,” he said.

Dr. Stoeger argued that the scientific community should recognize that a researcher who studies the least known genes may need extra time to get results.

“People who do something new need some protection,” he said.

Dr. Amaral proposed dedicating some research grants to the truly unknown, rather than safe bets.

“Some of the things we would be funding are going to fail,” he said. “But when they succeed, they’re going to open lots of opportunities.”

 

 

This article was originally published in The New York Times.  Read the original article.

WITH EMBRYO BASE EDITING, CHINA GETS ANOTHER CRISPR FIRST

SCIENTISTS IN THE US may be out in front developing the next generation of Crispr-based genetic tools, but it’s China that’s pushing those techniques toward human therapies the fastest. Chinese researchers were the first to Crispr monkeys, and non-viable embryos, and to stick Crispr’d cells into a real live human. And now, a team of scientists in China have used a cutting-edge Crispr technique, known as base editing, to repair a disease-causing mutation in viable human embryos.

Published last week in the journal Molecular Therapy, and reported first by Stat, the study represents significant progress over previous attempts to remodel the DNA of human embryos. That’s in part because the editing worked so well, and in part because that editing took place in embryos created by a standard in-vitro fertilization technique.

So-called “germline editing,” the contentious technologythat can permanently change the code in every cell in the human body, has been gaining acceptance in the last few years as research has pushed forward, illuminating the possibilities of Crispr. Immediately following those first reports of embryonic gene-editing in China in 2015, an international summit convened by the US National Academy of Sciences concluded that actually trying to produce a human pregnancy from such modified germlines was “irresponsible,” given ongoing safety concerns and lack of societal consensus. Two years later, a report from the NAS and the National Academy of Medicine stated that clinical trials for editing out heritable diseases could be permitted in the future, but only for serious conditions under stringent oversight.

Attitudes may be slowly changing: Last month, the United Kingdom’s Nuffield Council on Bioethics went so far as to say that heritable genome editing could be “ethically acceptable in some circumstances.” A Pew Research Council study released at the end of July found that 72 percent of Americans think changing an unborn baby’s DNA to treat a serious disease would be an appropriate use of gene-editing technology.

In the study published in Molecular Therapy, the Chinese scientists corrected a mutation that causes Marfan syndrome, an incurable connective tissue disorder that affects about 1 in 5,000 people. A single letter mistake in the gene for FBN1, which codes for the fibrillin protein, can cause a ripple effect of problems—from loose joints to weak vision to life-threatening tears in the heart’s walls. Starting with healthy eggs and sperm donated by a Marfan syndrome patient, the team of researchers from Shanghai Tech University and Guangzhou Medical University used an IVF technique to make viable human embryos. Then they injected the embryos with a Crispr construct known as a base editor, which swaps out a single DNA nucleotide for another—in this case, removing a “C” and replacing it with a “T”.1 They kept the embryos alive for another two days in the lab, long enough to run tests to see how well the editing worked.

Sequencing revealed that all 18 embryos had been edited, with 16 of the embryos bearing only the corrected version of the FBN1 gene. In two of the embryos, additional unwanted edits had also taken place. Previously, the most successful demonstration of gene editing in the human germline was the correction of a mutation that causes a hereditary heart condition in 42 out of 58 embryos. That study, which was published last year, used standard Crispr cut-and-paste technology.

“It’s a nice demonstration of the use of base editors to correct a well-known point mutation that causes a human genetic disease in a setting that may become therapeutically relevant,” says David Liu, whose lab at Harvard developed the base editor used to correct the Marfan mutation, though he was not involved in the study.

Rather than breaking the double-stranded DNA molecule and allowing the cell to repair itself with a healthy gene template, these newer versions of Crispr change just a single letter. If Crispr is a pair of molecular scissors, Liu’s base editors are more like a pencil with a squeaky new eraser. While the hope is that such precise gene-writing implements won’t cause the kind of sloppy chaos that Crispr 1.0 is capable of, Liu says it’s too early to make any general statements about their relative risks as a therapeutic. “Despite more than 50 publications using base editors from laboratories around the world, the entire field of base editing is only about two years old, and additional studies are needed to assess as many possible consequences of base editing as can be reasonably detected.”

Some of those studies are being conducted at Beam Therapeutics, the startup that Liu co-founded earlier this year with fellow Crispr pioneer Feng Zhang. Beam’s first license agreement with Harvard covers Liu’s C base editor, which makes programmable G-to-A or C-to-T edits, like the one used to correct the Marfan mutation. The second is the A base editor, which can do T-to-C as well as A-to-G edits. But don’t expect Beam to be erasing genetic diseases from the germline any time soon. The company is focused on using base editing to treat serious diseases in children and adults only, not on embryo editing, says CEO John Evans. “More consideration would be needed before society is ready to consider embryo editing, and we look forward to participating in the discussion.”

In the meantime, Beam will be just one of many US companies looking at an increasingly streamlined path for genetic medicines. In July, FDA Commissioner Scott Gottlieb announced a new regulatory framework for gene therapies to treat rare diseases. The agency issued a suite of six guidance documents updating the approval process. And on August 17, the FDA along with the National Institutes of Health proposed changes in the way the agencies together assess the safety of gene-therapy human trials.

Specifically, the proposals will eliminate review by the NIH’s Recombinant DNA Advisory Committee, which was established in 1974 to advise on emerging genetic technologies. In New England Journal of Medicineeditorial describing the changes, Gottlieb and NIH Director Francis Collins wrote it was their view that “there is no longer sufficient evidence to claim that the risks of gene therapy are entirely unique and unpredictable—or that the field still requires special oversight that falls outside our existing framework for ensuring safety.” A more streamlined approval process may help the US move faster in the long-run, though probably not enough to catch China’s head start. But when it comes to gene editing’s most controversial applications, there’s nothing wrong with being slow.

 

 

This article was originally published in Wired. Read the original article.