Scientists are studying cancer genomes to more precisely diagnose their patients' diseases - offering hope for targeted drug treatments.
Next, he recalls, he felt ushered into “the jaws of the medical system very quickly.” He spent a couple of days meeting with a team of doctors at Beth Israel Deaconess Medical Center in nearby Boston. One of them was from a medical field he hadn’t even known existed, a pulmonary interventionist, who would perform a biopsy on the mass in his lung.
“Knowing there was a medicine for my particular type of cancer was like a weight lifted off my shoulders."
A week later he and his wife Allison returned to meet with the oncologist, radiologist, pulmonary interventionist – his medical team. They confirmed his initial diagnosis: Stage 4 metastatic lung cancer that had spread to several parts of his body. “We just sat there, stunned,” he says. “I felt like I was getting hit by a wrecking ball over and over.”
An onslaught of medical terminology about what they had identified flowed over the shocked couple, but then the medical team switched gears, he recalls. They offered hope. “They told me, ‘Hey, you’re not a smoker, so that’s good,’” Reiner says. “‘There’s a good chance that what’s driving this disease for you is actually a genetic mutation, and we have ways to understand more about what that could be through some simple testing.’”
They told him about Foundation Medicine, a company launched in neighboring Cambridge, MA, in 2009 that develops, manufactures, and sells genomic profiling assays. These are tests that, according to the company’s website, “can analyze a broad panel of genes to detect the four main classes of genomic alterations known to drive cancer growth.” With these insights, certain patients can be matched with therapies targeted specifically for the genetic driver(s) of their cancer. The company maintains one of the largest cancer genomic databases in the world, with more than 500,000 patient samples profiled, and they have more than 65 biopharma partners.
According to Foundation Medicine, they are the only company that has FDA-approved tests for both tissue- and blood-based comprehensive genomic profiling tests. One other company has an FDA-approved biopsy test, and several other companies offer tissue-based genomic profiling. Additionally, several major cancer centers like Memorial Sloan Kettering in New York and Anderson Cancer Center in Texas have their own such testing platforms.
Currently, genomic profiling is more accessible for patients with advanced cancer, due to broader insurance coverage in later stages of disease.
“Right now, the vast majority of patients either have cancers for which we don’t have treatments or they have genetic alterations that are not known,” says Jorge Garcia, MD, Division Chief, Solid Tumor Oncology, UH Cleveland Medical Center, which has its own CGP testing platform. “However, a significant proportion of patients with advanced cancer have alterations that we can tap for therapeutic purposes.”
Foundation Medicine estimates that in 2017, just over 5 percent of advanced solid cancer patients in the U.S. received CGP testing. In 2021, they estimate that number is between 25 to 30 percent of advanced solid cancer patients in the U.S., which doesn’t include patients who are tested with small (less than 50 genes) panels. Their panel tests for more than 300 cancer-related genes.
“The good news is the platforms we are developing are better and more comprehensive, and they’re going to continue to be larger data sets,” Dr. Garcia adds.
In Reiner’s case, his team ordered comprehensive genetic profiling on both his tissue and blood, from Foundation Medicine.
At this point, Reiner still wasn’t sure what genetic mutations were or how they factored into cancer or what comprehensive genomic profiling entailed. That day, though, his team ushered the Reiners into the world of precision oncology that placed him on much more sure footing to learn about and fight the specific lung cancer that had been troubling him for more than a year.
What genetic alterations were driving his cancer? Foundation Medicine’s tests were about to find out.
At the core of these tests is next generation sequencing, a DNA sequencing technology. Since 2009, this has revolutionized genomic research, according to the National Center for Biotechnology Information, because it allows an entire human genome to be sequenced within one day. Cancer genomics posits that cancer is caused by mutations and is a disease of the genome. Now, cancer genomes can be systemically studied in their entirety. For cancer patients such as Reiner, NGS can provide a more precise diagnosis and classification of the disease, more accurate prognosis, and potentially the identification of targeted drug treatments. Ultimately, the technology can provide the basis of personalized cancer management.
The detailed reports supply patients and their oncologists with extensive information about the patient’s genomic profile and potential treatment options that they can discuss together. Reiner trusted his doctors that this approach was worth the two- or three-week wait to receive the Foundation Medicine report and the specifically targeted treatment, rather than immediately jump into a round of chemotherapy. He is especially grateful now, he says, because the report delivered a great deal of relief from his previously exhausting and growing anxiety about having cancer.
Reiner and his team learned his lung cancer contained the epidermal growth factor receptor (EGFR) mutation. That biomarker enabled his oncologist to prescribe Tagrisso (osimertinib), a medication developed to directly target that genetic mutation.
“Knowing there was a medicine for my particular type of cancer was like a weight lifted off my shoulders,” he says. “It only took a week or two before my cough finally started subsiding. This pill goes right after the particular piece of genetic material in the tumor that’s causing its growth.”
Dr. Jerry Mitchell, director field medical oncology, Foundation Medicine, in Columbus, Ohio, explains that genomic profiling is generating substantial impacts today. “This is a technology that is the standard of care across many advanced malignancies that takes patients from chemotherapy-only options to very targeted options or immunotherapy options,” he says. “You can also look at complex biomarkers, and these are not specific genetic changes but different genes across the tumor to get a biomarker.”
According to Dr. Mitchell, Foundation Medicine’s technology can test more than 324 different cancer-related genes in a single test. Thus, a growing number of patients are benefitting from comprehensive genetic profiling, due to the rapidly growing number of targeted therapies. While not all of the cancers are treatable yet, the company uses that information to partner with researchers to find new potential therapies for patient groups that may have rare mutations.
Since his tumor’s diagnosis, Reiner has undergone chemotherapy and a couple surgeries to treat the metastatic cancer in other parts of his body, but the drug Tagrisso has significantly reduced his lung tumor. Now, having learned so much during the past couple of years, he is grateful for precision oncology. He still reflects on the probability that, had the Tagrisso pill not been available in May 2019, he might have only survived for another six months or a year.
“Comprehensive Genomic Profiling is not some future state, but in both the U.S. and Europe, it is a very standard, accepted, and recommended first step to knowing how to treat your cancer,” says Dr. Mitchell, adding that he feels fortunate to be an oncologist in this era. “However, we know there are still people not getting this recommended testing, so we still have opportunities to find many more patients and impact them by knowing the molecular profile of their cancer.”
Phages, which are harmless viruses that destroy specific bacteria, are becoming useful tools to protect our food supply.
Food producers and packagers fight bacteria by potent chemicals, with chlorine being the go-to disinfectant. Cattle carcasses, for example, are typically washed by chlorine solutions as the animals' intestines are removed. Leafy greens are bathed in water with added chlorine solutions. However, because the same "bath" can be used for multiple veggie batches and chlorine evaporates over time, the later rounds may not kill all of the bacteria, sparing some. The natural and organic producers avoid chlorine, substituting it with lactic acid, a more holistic sanitizer, but even with all these efforts, some pathogens survive, sickening consumers and causing food recalls. As we farm more animals and grow more produce, while also striving to use fewer chemicals and more organic growing methods, it will be harder to control bacteria's spread.
"It took us a long time to convince the FDA phages were safe and efficient alternatives. But we had worked with them to gather all the data they needed, and the FDA was very supportive in the end."
Luckily, bacteria have their own killers. Called bacteriophages, or phages for short, they are viruses that prey on bacteria only. Under the electron microscope, they look like fantasy spaceships, with oblong bodies, spider-like legs and long tails. Much smaller than a bacterium, phages pierce the microbes' cells with their tails, sneak in and begin multiplying inside, eventually bursting the microbes open—and then proceed to infect more of them.
The best part is that these phages are harmless to humans. Moreover, recent research finds that millions of phages dwell on us and in us—in our nose, throat, skin and gut, protecting us from bacterial infections as part of our healthy microbiome. A recent study suggested that we absorb about 30 billion phages into our bodies on a daily basis. Now, ingeniously, they are starting to be deployed as anti-microbial agents in the food industry.
A Maryland-based phage research company called Intralytix is doing just that. Founded by Alexander Sulakvelidze, a microbiologist and epidemiologist who came to the United States from Tbilisi, the capital of Georgia, Intralytix makes and sells five different FDA-approved phage cocktails that work against some of the most notorious food pathogens: ListShield for Listeria, SalmoFresh for Salmonella, ShigaShield for Shigella, another foodborne bug, and EcoShield for E.coli, including the infamous strain that caused the Jack in the Box outbreak in 1993 that killed four children and sickened 732 people across four states. Last year, the FDA granted its approval to yet another Intralytix phage for managing Campylobacter contamination, named CampyShield. "We call it safety by nature," Sulakvelidze says.
Intralytix grows phages inside massive 1500-liter fermenters, feeding them bacterial "fodder."
Photo credit: Living Radiant Photography
Phage preparations are relatively straightforward to make. In nature, phages thrive in any body of water where bacteria live too, including rivers, lakes and bays. "I can dip a bucket into the Chesapeake Bay, and it will be full of all kinds of phages," Sulakvelidze says. "Sewage is another great place to look for specific phages of interest, because it's teeming with all sorts of bacteria—and therefore the viruses that prey on them."
In lab settings, Intralytix grows phages inside massive 1500-liter fermenters, feeding them bacterial "fodder." Once phages multiply enough, they are harvested, dispensed into containers and shipped to food producers who have adopted this disinfecting practice into their preparation process. Typically, it's done by computer-controlled sprayer systems that disperse mist-like phage preparations onto the food.
Unlike chemicals like chlorine or antibiotics, which kill a wide spectrum of bacteria, phages are more specialized, each feeding on specific microbial species. A phage that targets salmonella will not prey on listeria and vice versa. So food producers may sometimes use a combo of different phage preparations. Intralytix is continuously researching and testing new phages. With a contract from the National Institutes of Health, Intralytix is expanding its automated high-throughput robot that tests which phages work best against which bacteria, speeding up the development of the new phage cocktails.
Phages have other "talents." In her recent study, Jaroni found that phages have the ability to destroy bacterial biofilms—colonies of microorganisms that tend to grow on surfaces of the food processing equipment, surrounding themselves with protective coating that even very harsh chemicals can't crack.
"Phages are very clever," Jaroni says. "They produce enzymes that target the biofilms, and once they break through, they can reach the bacteria."
Convincing the FDA that phages were safe to use on food products was no easy feat, Sulakvelidze says. In his home country of Georgia, phages have been used as antimicrobial remedies for over a century, but the FDA was leery of using viruses as food safety agents. "It took us a long time to convince the FDA phages were safe and efficient alternatives," Sulakvelidze says. "But we had worked with them to gather all the data they needed, and the FDA was very supportive in the end."
The agency had granted Intralytix its first approval in 2006, and over the past 10 years, the company's sales increased by over 15-fold. "We currently sell to about 40 companies and are in discussions with several other large food producers," Sulakvelidze says. One indicator that the industry now understands and appreciates the science of phages was that his company was ranked as Top Food Safety Provider in 2021 by Food and Beverage Technology Review, he adds. Notably, phage sprays are kosher, halal and organic-certified.
Intralytix's phage cocktails to safeguard food from bacteria are approved for consumers in addition to food producers, but currently the company sells to food producers only. Selling retail requires different packaging like easy-to-use spray bottles and different marketing that would inform people about phages' antimicrobial qualities. But ultimately, giving people the ability to remove pathogens from their food with probiotic phage sprays is the goal, Sulakvelidze says.
It's not the company's only goal. Now Intralytix is going a step further, investigating phages' probiotic and therapeutic abilities. Because phages are highly specialized in the bacteria they target, they can be used to treat infections caused by specific pathogens while leaving the beneficial species of our microbiome intact. In an ongoing clinical trial with Mount Sinai, Intralytix is now investigating a potential phage treatment against a certain type of E. coli for patients with Crohn's disease, and is about to start another clinical trial for treating bacterial dysentery.
"Now that we have proved that phages are safe and effective against foodborne bacteria," Sulakvelidze says, "we are going to demonstrate their potential in therapeutic applications."
This article was first published by Leaps.org on October 27, 2021.