Profile of Rene Bernards

After finishing high school in the Netherlands, Rene Bernards initially considered studying medicine, but his brother convinced him to study biology. It turned out to be a fulfilling choice, and Bernards went on to have a fruitful career as a cancer biologist. Now a professor of molecular carcinogenesis at the Netherlands Cancer Institute in Amsterdam, Bernards was elected to the National Academy of Sciences in 2020 as an international member. Bernards has used functional genomic approaches to identify new drug combinations against cancers. His work has helped elucidate some of the pathways that lead to tumor formation and drug-resistance and led to the development of effective anticancer therapies. In his Inaugural Article, Bernards describes an experimental cancer drug combination with clinical potential (1).

Rene Bernards. Image credit: Andre Jagt (photographer).

From Medical Biology to Oncology

Bernards’ interest in biology and medicine drove him to study medical biology at the University of Amsterdam. “While I liked the medical lectures, I was not very fond of many of the biology lectures about the taxonomy of plants… and I was left in limbo for a while as to whether biology was really for me,” he says. That changed when he joined the lab of immunologist Richard Flavell. “Richard was an inspirational supervisor, so that was a very fortunate coincidence,” he says.

Bernards completed an internship with Flavell, who was studying the molecular basis of thalassemias. “Recombinant DNA was the hottest thing on the planet, and I was given an opportunity to work with recombinant DNA and with patient material,” says Bernards. “I suddenly realized this was what I wanted to spend my life on,” he says.

For his PhD, Bernards decided to join the laboratory of Alex van der Eb, who had recently developed a technique to introduce foreign DNA into human or mammalian cells. “That was the beginning of the era of functional genomics, where you try to introduce a gene into a cell and ask what it does, so his technology really opened up a tremendous opportunity in research,” says Bernards.

Bernards used the technology to study the adenovirus transforming genes E1A and E1B. Adenoviruses can transform cells; in some cases the transformed cells can form tumors in immunocompetent animals, and in other cases they can form tumors only in immunocompromised animals, explains Bernards. He decided to create chimeric plasmids containing different parts of oncogenic and nononcogenic adenoviruses to map the oncogenic activity. In 1983, Bernards discovered that unlike nononcogenic adenoviruses, oncogenic adenoviruses can suppress the expression of the HLA class 1 antigens, which made the transformed cells effectively invisible to T cells (2).

In 1985, Bernards began a postdoctoral stint in cancer biologist Robert Weinberg’s lab at the Whitehead Institute. Weinberg had recently shown that two human oncogenes—MYC and RAS—could collaborate to transform cells, and Bernards noticed parallels with the two adenovirus genes—E1A and E1B—that needed to collaborate to transform cells. “I said to Bob Weinberg I wanted to study whether MYC shares with E1A the ability to suppress HLA class 1 antigens because that would suggest that immune evasion is also relevant in human cells,” recalls Bernards. “Within nine months, I had a paper showing that in neuroblastoma, amplification of the MYCN oncogene caused downregulation of class 1 HLA antigens,” he says (3).

Soon after this report, Bernards set up his own lab at Massachusetts General Hospital in 1988. In 1992, he decided to return to the Netherlands to join the Netherlands Cancer Institute, where he has been ever since. “It was not because I didn't like it in the United States, but I had married a Dutch girl, who really wanted to go back to the Netherlands,” he says. “I thought at the time that this would be scientific suicide,” says Bernards.

The move turned out to be a blessing in disguise, allowing him to pursue an independent research trajectory. His new position also brought him in close contact with clinicians. “That also turned out to be a very good development because that really helped in the rapid translation of our findings,” he says.

Large-Scale Functional Gene Analysis

In his new lab in Amsterdam, Bernards decided to focus on large-scale functional gene analysis. “Rather than testing one gene, we wanted to start testing thousands of genes at the same time,” he says. Bernards developed cDNA expression libraries—putting collections of cDNAs into cells so that every cell expressed one new gene—and then searched for specific phenotypes. This powerful technique enabled Bernards to make many discoveries in the 1990s, but he was still looking to overcome a major hurdle—an inability to study loss-of-function mutations at a large scale in mammalian cells. “Making a mouse knockout for one gene would cost you two years, and that times 20,000 genes was not doable,” says Bernards.

The discovery of RNA interference in 2000 offered a solution. “RNA interference provided the opportunity to silence genes… If we could now do genome-scale loss-of-function screens, then we could really study cancer genomics at a completely new level,” says Bernards. In 2002, he published the first vector that could silence mammalian genes long-term, which would enable the creation of a genome-scale library to silence genes in the human genome (4).

However, creating such a library was a challenge. “I calculated that to make a genome-scale library, I had to have at least a million dollars, which for my lab at that time was an insurmountable amount of money,” says Bernards. “And even if I had that money, I didn't have access to the computational tools to design short hairpin RNAs for 20,000 genes in the human genome,” he says.

So Bernards called up his friend and former colleague Stephen Friend, with whom he had worked in the Weinberg lab and who was now head of oncology at Merck. “I told him, ‘Imagine if you and I could silence every gene in the human genome, how many new cancer targets could we discover?’” recalls Bernards. Friend agreed to collaborate and helped design 20,000 short hairpin RNAs and fund Bernards’ work on building the library. “That became a goldmine for the next decade,” says Bernards (5).

Exploring New Drug Combinations

Bernards’ first genome-scale screen was for resistance to the breast cancer drug Herceptin. He found that the loss of the PTEN tumor suppressor gene conferred resistance to Herceptin in cell culture. “We know from studying hundreds and thousands of patient samples that the PI3kinase-AKT-PTEN pathway is a major determinant of response to Herceptin in breast cancer,” says Bernards. He also developed a gene expression test for early breast cancer prognosis, called MammaPrint. “That is now used clinically and has helped women worldwide in optimizing their treatment decision,” he says.

Bernards’ next breakthrough was inspired by a lunchtime chat with a clinician. “This was in 2011, when we already had several targeted cancer therapeutics,” he says. Two drugs that had proved particularly useful were EGFR inhibitors, which were effective for EGFR-mutant lung cancers, and BRAF inhibitors, which were effective for BRAF-mutant melanomas. The clinician told him about a surprising result he had learned at a conference: A subgroup of colorectal cancer patients was found to have the same BRAF mutation seen in melanomas, but these patients failed to respond to the BRAF inhibitor Vemurafenib, which worked for BRAF-mutant melanomas.

Bernards was intrigued and happened to possess the technology needed to probe this question: Synthetic lethality screens with short hairpin RNA libraries. “We asked a simple question: Is there any gene whose silencing is lethal in the presence of Vemurafenib but is not lethal in the absence of Vemurafenib,” says Bernards.

Bernards found that EGFR-depletion was synthetic-lethal with BRAF inhibition. “When we added EGFR inhibitors in cell culture, we saw…that drugs that had no activity on their own, in combination became highly toxic,” says Bernards. The drug combination also turned out to work in animal models and led to a 2012 publication (6). “I ran back to the same clinician that I had talked to at lunch and asked him to immediately design a trial to test this,” says Bernards. “Eight months after our paper, we saw the first clinical responses to the drug combination, which led to a Phase 3 trial that resulted in an FDA approval in 2020. This is now a standard treatment for colorectal cancer,” he says.

Promising New Drug

Bernards’ research has so far resulted in 16 drug combinations that have undergone or are undergoing clinical trials. In his Inaugural Article, Bernards describes a promising new drug combination (1). “What we describe is a gene—MAP2K4—that if you co-inhibit it with a member of the MAP kinase pathway, we get spectacular responses,” he says. “The MAP kinase pathway is one of the central pathways in cancer, and the pharmaceutical industry has made a lot of drugs that act at all the different levels in the pathway,” says Bernards. Individually, however, many of these drugs are stymied by resistance and toxicity, he says.

Bernards showed that a small-molecule MAP2K4-inhibitor was potent in combination with specific MAP kinase pathway inhibitors that by themselves fail to show lasting responses (1). “Our data in animals show that we can get complete tumor regressions when we combine the drugs, and only modest responses when we use those other inhibitors alone,” he says.

Looking back at his career, Bernards says he is satisfied with the therapies he has helped develop, including the FDA-approved drug combination for colorectal cancer and another drug combination for liver cancer that he expects will be clinically relevant. He hopes that the MAP kinase combination could be a third therapy. “If I bring three drug combinations to the clinic, that would be pretty amazing,” says Bernards.