The discoveries that led the world to understand that cancer is a genetic disease unfolded one by one in the laboratory of Bert Vogelstein and Kenneth Kinzler.

Vogelstein

More than 40 years ago, when they first cracked open the Pandora’s box that is cancer, revealing first one and then a series of genetic mistakes responsible for colon cancer, it was a foreign concept. Today, their discoveries have led this lab, and others around the world, to develop genetic tests, screening diagnostics and targeted therapies for colon and other cancers.

Ushering in the age of molecular biology, Vogelstein, Kinzler and their co-collaborators were among the first to apply it to the study of a human disease, developing the knowledge and tools to look inside the submicroscopic molecules of the cell to reveal those rare, uncorrected errors in our DNA that put the cancer process in motion.

Kinzler

“When it comes to cancer genetics, Bert’s and Ken’s work is on the cutting edge of the cutting edge. They led the world to understand that cancer is a disease of genetic defects, and then led the first laboratory in the world to reveal what those defects are,” says Johns Hopkins Kimmel Cancer Center Director William Nelson.

The complexity of their genetic discoveries has been likened to finding one two-letter transposition within 20 volumes of Encyclopedia Brittanica and then figuring out how it got there. Some scientists consider them to be of the magnitude of finding a cause for polio. As transforming as these discoveries have been in the cancer world, they started simply and quietly in 1983 in a converted supermarket on the Johns Hopkins East Baltimore Medical Campus.

The Early Discoveries

At the time, very little was known about colon cancer. “The man who is really responsible for advancing the understanding of colon cancer is Benjamin Baker,” says Vogelstein.

Baker

Baker, a Johns Hopkins internist who followed Vogelstein’s work, was intrigued by the concept that cancer was caused by genes gone awry. While others were optimistically in search of the magic bullet that would bring down cancer in one fell swoop, Vogelstein’s studies were revealing a much more complicated disease process.

A genetic infrastructure unlike anything that had ever been described in human disease was being described. It centered on a delicate balance between cell growth accelerators, called oncogenes, and cell growth brakes, called tumor suppressor genes.

Alterations to these genes, either inherited or acquired throughout life, disrupted the delicate balance, giving an advantage to cell growth. Fundamentally, cancer is a normal cell that does not die. As the immortal cell divides, it eventually reveals itself in the form of a tumor.

While many researchers focused on the cancer, Vogelstein realized very early on that it was what precipitated the cancer that also mattered. He compared it to an iceberg — the cancer was the tip of the iceberg that could be seen, and the benign tumors were the layers beneath the water. He set out to identify the basis of the invisible layers beneath the surface that began forming decades before.

There was much skepticism about his approach.

“Cancers in animals were considered better to study because they were easier to manipulate,” says Vogelstein. “That was true in some ways, but our view was this was a human disease, and we wanted to study the real thing.”

The first grants Vogelstein submitted were rejected, but he persevered, and the findings that followed uncovered a genetic infrastructure that is now widely accepted to underlie the basis of all human tumor processes.

Using technologies they invented to see inside the cancer cell, they began to unravel the mystery of cancer.

Searching for the Errant Genes

Hamilton

As Vogelstein began his quest to uncover the hidden layers of the iceberg, Baker, who liked Vogelstein’s visionary approach, convinced his wife’s family to donate money from their Clayton Fund to the Vogelstein lab. This seed money, which brought together the Bowel Tumor Working Group, was a turning point in Vogelstein’s research.

This collaboration of seasoned clinicians and investigators and young up-and-comers began to shed the first light on the origin of colon cancer and, at the same time, triggered other investigators around the country and the world to look for similar patterns in other cancers.

At first, the discoveries came almost more quickly than they could be sorted out. In 1989, Vogelstein’s identification of p53 mutations in colon cancer started a media frenzy as investigators around the country, following the Vogelstein lab’s lead, found the same mutation in breast, lung and other cancers. “The p53 gene is the most common gene mutation among all cancers,” the reports read. 

A public eager for a quick fix pinned their hopes on this discovery as the holy grail of cancer. Vogelstein, his own toughest critic, was the first to dash these hopes. While he felt the discovery was important for advancing the science and technology of gene discovery, he was not looking for an answer in one gene. In fact, his lab’s work showed that the p53 alteration was a mutation that occurred late in the cancer process, which led them to the next question. What genetic alterations came before p53?

Inherent Clues

Vogelstein hypothesized that colon cancer resulted from a series of genetic alterations that evolved over decades, starting with small clusters of abnormal cells in the lining of the colon, advancing to benign tumors known as polyps, then to a cancerous tumor in the colon, and finally, to where p53 most likely came in, pushing the tumor to its most lethal form, as it spreads outside of the colon to other parts of the body. What Vogelstein wanted to do was identify the whole series of mutations and the order in which they occurred.

He decided to look among the rarest types of colon cancers for the answers — inherited colon cancer syndromes. Although they represented a small percentage of colon cancers, Vogelstein believed the same genetic underpinnings that led certain families to be plagued by an alarmingly high incidence of colon cancer, and typically at a much younger age, would shed light on colon cancers among the general population.

Each of us inherits two copies of every gene from our parents, one from our father and one from our mother. In inherited colon cancer syndromes, family members are born with only one good copy of a gene. Subsequent random mutations and assaults from diet and other behaviors knock out the one good copy. The cascade of cellular errors that ultimately results in cancer is put in motion.

Kinzler, Vogelstein’s research partner and co-director of their lab, pathologist Stanley Hamilton and other members of the Bowel Tumor Working Group looked for inherited in these hereditary cancers.

The Kinzler-Vogelstein team identified a mutation of the APC gene in familial adenomatous polyposis, a rare, inherited syndrome in which affected people get hundreds of benign tumors known as adenomas, or polyps, in the colon. Further studies showed the same mutation to be the one that jump-starts the cancer process in the nearly 140,000 people within the general population who are diagnosed with colon cancer each year.

Other researchers in the Vogelstein/Kinzler lab were uncovering the genetic culprits of two other inherited colon cancers. In particular, they discovered the genetic and biochemical basis of hereditary non-polyposis colon cancer, which accounts for more than 50% of inherited colon cancer syndromes.

In 1998, the team reported a genetic alteration affecting as many as 400,000 people nationwide — 6% of European descendant Jews (Ashkenazi). Gene testing for cancer was catapulted into mainstream medicine because, along with the discovery of the genes that caused these diseases, Vogelstein, Kinzler and colleagues developed tests that detected the mutations. These tests are now part of the routine management for patients with strong family histories of the disease, and dramatically changed how these patients are diagnosed and treated.

For the first time, clinicians could know which family members had inherited colorectal cancer-causing mutations so that those at risk could be monitored closely for cancer. As important, the tests also revealed family members who did not have the gene mutations, so they could be spared unnecessary screening measures. It was the first example of individualized, or precision, medicine for patients with typical forms of cancers.

A Test for Everyone

Sidransky

These finding were key to understanding how cancer originated, and were transforming for families with these hereditary forms, but they represented a small fraction of the cancers. Vogelstein and Kinzler also wanted to develop ways to intercept and prevent the 95% of cancers that occur sporadically among the general population.

They wondered if they could find cancer DNA among colon cells shed and passed in stool. If they could find APC mutations — the mutations that cause normal colon cells to form the benign polyps that occur before cancer — in cells found in stool, they could potentially prevent the cancer from ever occurring.

These studies, first undertaken in 1991 by David Sidransky, who later started his own lab using this method to detect cancer-specific DNA in urine, sputum and other body fluids, were moved forward by Giovanni Traverso and Frank Diehl.

The research led to the first noninvasive genetic screening test for cancer, distributed by Exact Sciences and marketed as Cologuard. The test, which had its origins in the Vogelstein/Kinzler lab, has by now been used by millions of people.

Vogelstein and Kinzler developed the test to address the underuse of screening colonoscopy among the general public.

“The stool test is noninvasive and essentially risk-free, and it uncovers the very first genetic event in the colon cancer process,” says Kinzler. This mutation could occur years before an actual cancer develops, giving clinicians ample time to cure or even prevent the cancer from occurring, he adds.

Cracking the Cancer Code

Building upon their colorectal cancer discoveries, researchers in the Vogelstein/Kinzler lab applied their methods to other cancers and cracked the genetic codes of more forms of the disease than any other research team in the world. Their work is considered the classic model, the paradigm for much of modern cancer research.

A foundational gift from the Ludwig Foundation allowed them to bring automated gene sequencing equipment to their laboratory, making it possible to simultaneously sequence millions of gene fragments. Research that once took years could now be done in days for a fraction of the cost of earlier studies. This meant an unprecedented, all-encompassing view of precisely what was happening inside the cancer cell was at last possible.

Despite the complexity, in 2006, they began accomplishing something that would have been impossible just a decade earlier. Using advanced technology, the team analyzed more than 30 million base pairs of DNA in a patient’s cancer and provided the first ever comprehensive blueprint of cancer — what goes wrong in the cellular instructional manual to cause cancer.

This task of monumental scope took the cancer world by storm, opened new areas of research and, for the first time, presented a full genetic understanding of one of humankind’s greatest threats.

With new, faster computing tools to sequence cancer DNA, the team in the Vogelstein/Kinzler lab completed 88 of the first 100 blueprints of human cancers, and inspired similar research in labs around the world.

The detailed maps of cancer they created provide guides by which scientists can pinpoint characteristics of each person’s cancer and tailor therapies and diagnostics to guide treatment — what we call precision medicine.

“Knowing the road map of cancer is key to attacking it. Now that we have identified the key gene mutations, we can focus on determining at what point in the cancer process they occur, whether they guide prognosis, and if they might be good targets for prevention or treatment,” said Vogelstein.

Genetic Tests for Cancer

These discoveries provided a detailed schematic for how tumors start and how they become progressively more dangerous as a result of heredity, random alterations or outside cell-damaging exposures that change DNA over the course of up to 30 years.

The last stage of metastasis, when the cancer spreads, and the stage that actually kills people occurs only in the last few years of this 30-year process, according to Vogelstein. Unfortunately, this is when many cancers are diagnosed. By this time, they have acquired so many gene alterations they are often resistant to treatment, he says.

He believed that if the cancers were detected before cancer cells spread to other parts of the body, most patients could be cured with surgery and drug treatment or potentially even surgery alone.

This led researchers in the Vogelstein/Kinzler lab to focus on ways to use their genetic discoveries to detect cancers earlier.

As tumor cells divide, they develop their own blood supply to get the nutrients they need to nourish and grow, and as a result, pieces of the cancer’s DNA get carried in the bloodstream, leaving telltale evidence of their existence. The DNA contains the alterations specific to the cancer — the accumulation of errors that occur as normal tissue transforms to evasive, deadly cancer. It’s been there all along, floating among a sea of normal cells; scientists had to develop the technology to see it and pull it out.

Next-generation sequencing technologies allowed millions of DNA molecules to be simultaneously and individually analyzed, providing the first opportunity to identify mutations in the bloodstream. However, the technology was fraught with inefficiencies and high error rates that limited their clinical application.

To correct for these sequencing errors, researchers in the Vogelstein/Kinzler lab developed a new technology called SafeSeqS (Safe Sequencing System) in 2011, and then built a better version in 2021 called SaferSeqS (Safer Sequencing System). The technology makes it possible to detect rare mutations in blood efficiently and accurately.

Detecting mutations in blood samples, now known as liquid biopsy, rather than via surgical biopsy provided the potential to detect cancer at its earliest stage.

It ushered in a series of screening tests developed in the Vogelstein/Kinzler lab, including PapSEEK, UroSEEK, CompCyst and CancerSEEK.

PapSEEK could be used on cervical fluid obtained during Pap tests (screening tests for cervical cancer) to detect mutations in 18 genes commonly mutated in endometrial and ovarian cancers. UroSEEK scours urine samples for 11 mutations associated with bladder and other urological cancers. CompCyst finds molecular markers in the fluid of pancreatic cysts to distinguish harmless cysts from those likely to develop into pancreatic cancers.

CancerSEEK is a first-of-its-kind test that screens for eight common cancer types in a single blood test. The cancers the test detects — ovarian, liver, stomach, pancreatic, esophageal, colorectal, lung and breast cancers — account for 60% of cancer deaths, and five of these cancers currently have no screening test. The hope is that the test will detect cancers early when they can be cured.

The test has been licensed by Exact Sciences to continue development as a multicancer screening test for the general population. Quest Diagnostics has licensed the technology to monitor people with cancer for signs of cancer recurrence or progression.

Looking to the Future

Papadopoulos

The complexity of cancer stems from the fact that it originates from our own cells. The genetic mutations that mark the genes of cancer cells are the only thing that distinguishes normal cells from cancer cells. However, it is this subtle difference and research spanning three decades that led to one of the most significant advances in cancer treatment.

It started in 1993, when researchers in the Vogelstein/Kinzler lab identified a genetic cause of Lynch syndrome, a hereditary form of colon cancer. Mutations to mismatch repair genes, which correct copying errors when DNA replicates and cells divide, cause high rates of additional mutations and an increased risk of developing colon cancer.

Vogelstein, Kinzler and lab member Nickolas Papadopoulos developed a test to screen for mismatch repair deficiency to allow families with a history of Lynch syndrome to be monitored for development of colon cancer.

Fast forward 20 years. Armed with an understanding of the genetic alterations that are responsible for cancer, the Kinzler-Vogelstein group cooperated with cancer immunology researchers to make an unprecedented suggestion. They suspected that cancers from patients with Lynch Syndrome would be extraordinarily sensitive to a new class of drugs, called immune checkpoint inhibitors, being developed by the cancer immunology group.

The discovery was key to a historic 2017 FDA approval of the immunotherapy drug pembrolizumab across all cancer types for any cancer that contains the mismatch repair genetic defect. It marked the first cancer drug approval based on a specific genetic profile and with no regard to where in the body the cancer started. The research community at large had doubts, leading the researchers to perform the clinical study themselves without the benefit of industry sponsorship.

Le

The clinical trial, led by Dung Le and Luis Diaz, demonstrated astonishing responses in patients with cancers that had mismatch repair deficiency/microsatellite instability. The historic discovery soon led to the FDA approval of the immunotherapy drug prembrolizumab across all cancer types for any cancer that contains the mismatch repair/microsatellite instability defect. It marked the first cancer drug approval based on a specific genetic profile with no regard to where in the body the cancer started.

“This illustrates the science of discovery, and how long it can take to fit the pieces together,” says Vogelstein. “It is a reflection of the strength and support of research at Johns Hopkins. No other institution had ever done something like this before, discovered the basis for a disease and designed a treatment that obtained FDA approval. This is virtually unique in the history of medicine.”

Researchers in the Vogelstein/Kinzler lab continue to contribute to immunotherapy discoveries, focusing on new ways to target specific gene mutations with immunotherapy.

“The history of medicine shows that when a disease is understood, it eventually becomes manageable,” says Vogelstein. “This understanding truly has been revolutionary in many other diseases. The next revolution is to take this knowledge we and others have gathered and help patients in ways that could only be imagined before this understanding came about.”