By Deborah Borfitz

April 24, 2025 | Pharma companies and academic institutions are key players in drug development but operate in disconnected ecosystems. Universities are constantly developing highly innovative drug screening models, while industry has many promising molecules and drug compounds, yet the two worlds more often collide than collaborate to get needed medicines to patients faster, according to Annette Bakker, Ph.D., CEO of the Children's Tumor Foundation (CTF). 

“In academia researchers need to publish to get funding and to be recognized and in industry one needs to keep things secret as much as possible because that’s how you are differentiating yourself from your competitors,” says Bakker. 

Earlier in her career, when Bakker was heading a neurooncology department in a biotech, the cell lines commercially available to her for drug screening purposes had genetically drifted so much that they were no longer reliable for glioblastoma drug selection. “No wonder that today we still have so few novel treatments for glioblastoma... we keep using the same cells for drug selection.”  

Bakker says she learned about the development of many highly innovative glioblastoma cell and animal models, but up until 2012 she worked on the industry side and back then academic researchers “wouldn’t even pick up the phone” when she called. That level of inefficiency is why she pivoted to the nonprofit sector where “you are the nexus between patients and providers, and you have the same sense of urgency as the patients you are working for.” 

At CTF, Bakker’s dream and mission is to “showcase a new role for not-for-profits in the R&D ecosystem,” she says. “We can do things that nobody else can do; we are truly unconflicted but highly impatient. Today we can talk to patients, tomorrow to regulators, the day after to pharma, and then to clinicians and researchers.” 

‘Real R&D Partner’

Resolving the “shelved asset” problem is high on Bakker’s priority list because if current trends continue (about a five-fold increase in clinical trial assets over the past decade) “we are going to trash a lot of great drugs,” she says. “There have been huge investments made in these drugs that are now shelved, so it’s just a waste of energy and time.” It is also “our ethical obligation as a healthcare community to identify a system that gets patients the treatments that could benefit them.”  

Pharma companies are not only throwing away drugs with potential commercial value when they fail to meet their commercial or strategic business goals, adds Bakker. “What I am seeing is a new era where large pharma companies buy a biotech for one drug and if that biotech happens to have three other drugs it will shelve those.” 

Bakker has been advocating heavily for the pharma industry to rethink the role of nonprofits not just for neurofibromatosis (NF)—the focus of CTF’s efforts—but for all diseases. The nonprofit sector might logically become a “real R&D partner,” rather than being viewed only as patient support and advocacy organizations, especially since so many of them are now being run by pharma veterans. 

“We know the disease that we are working on very well, we know the community really well, so between those two we can really add value to the ecosystem,” Bakker says. Nonprofits like CTF are now partnering with academic institutions and other nonprofits (e.g., Global Coalition for Adaptive Research) to run patient-centric platform trials that simultaneously evaluate multiple interventions under a single master protocol. 

Apart from just cash (venture philanthropy), foundations like CTF bring an immense amount of “intel” to the table, says Bakker. They therefore ought to “get a little piece of the cake” when providing the intel that leads to winning, money-making projects. As it is, nonprofits are putting in many hours, often on nights and weekends, “all out of the goodness of their heart. The problem is that’s an unsustainable model.” 

Creating a ‘Drug Vault’

The industry is abuzz about “drug repurposing,” but to ramp up its potential for accelerating drug development is going to require new tactics. That was the topic of discussion during a panel session Bakker moderated involving a healthcare executive Freda C. Lewis-Hall, former chief medical officer for Pfizer and now a “highly respected” board member on many biotech boards; finance professor Andrew Lo, MIT Sloan School of Management, and health and policy experts Tanisha Carino of the Duke-Margolis Institute for Health Policy, and Rena Conti of Boston University during this week's World Orphan Drug Congress (WODC) in Boston. 

Particularly distressing to Bakker is when drug candidates are abandoned, and the data gets dismantled with nobody having either the time or the interest in finding and cleaning up the data. When companies shelve a drug candidate, it’s hard for people outside to even know, she says. 

At the WODC, Carino advocated for companies to transparently report their shelved assets. Lo liked the idea of creating a secure, centralized “drug vault” where companies could instead be incentivized to deposit those assets. 

An unsuccessful attempt to create something similar happened in the UK two decades ago, Bakker believes because it was so broad as to become “everybody and nobody’s problem.” She instead argues for choosing two or three diseases to focus on initially (e.g., NF and NF type 2-related schwannomatosis, or SWN) and later expanding the model to other diseases.  

Currently, when caring people come together to rescue a discontinued drug, it can be a Herculean effort. Consider the tale of Gomekli (mirdametinib), which just received approval by the U.S. Food and Drug Administration (FDA) in February for treating adults and children with NF type 1 who have symptomatic plexiform neurofibromas not amenable to complete resection.  

It started out as a Pfizer asset, but in 2017 SpringWorks Therapeutics was created and the team successfully brought the NF and desmoid tumor (aggressive fibromatosis) assets all the way to FDA approval. But it took two years of commitment from 200 volunteers within Pfizer—with the support and encouragement of Lewis-Hall, the company’s then-CMO—to get the drug out of the one company and into the other. 

In addition to championing that heroic level of comradery, Bakker took on the job of getting a dozen clinicians seated around the table to design the trial to help accelerate the process. But things would have gone a lot faster, and required less work, if big pharma companies like Pfizer had a standardized process for managing data once a clinical project stops. 

What the experience with Gomekli showed her, says Bakker, is that “the way we spun out [the asset] from Pfizer is not scalable.” 

What matters is having champions within the pharma industry with decision-making power who recognize the potential of a drug for patients and care enough to decisively say “let’s do this,” Bakker says. “I’ve seen that at many companies,” she adds, including AstraZeneca, GSK, and Novartis as well as Pfizer.  

Patient-Centric Platform Trials

CTF has built a pair of R&D accelerators, including a preclinical hub resulting from a public-private partnership between contract research organizations and academic labs. That initiative, overseen by Irene Morganstern, Ph.D., proactively seeks permission from companies to conduct preclinical work on one of their drug assets on the condition that if it looks promising in treating NF the company commits to putting it in a clinical trial.    

This has only been done once thus far, and the drug didn’t pan out, but the model provides a means to stop the stall in drug development, says Bakker. On the clinical trial side, the accelerator is use of patient-centric platform trials “where patients are actually at the table when we design the trials.” 

Thirty percent of clinical trials in rare diseases “never make it because it takes too long to recruit the patients,” she points out. As has been repeatedly documented, unnecessary participation burdens are a key reason. 

Designing a study that requires 2-year-olds to go into an MRI machine every two or three months under anesthesia probably isn’t going to cut it with parents, Bakker offers as an example. But they might be agreeable to having them undergo the procedure twice a year and, if the trial reflects that, when it is eventually publicized those parents would more readily sign up their kids. 

“The reason we have these platform trials is that they stay open for 10 years,” says Bakker. “With your usual [regulatory] trial, you have to design a completely new trial for every drug,” meaning new protocol, new sites, and a bunch of new contracts to negotiate—all of which can take years.  

In contrast, CTF has co-funded two open platform trials for NF2 and NF2-related SWN. The clinicians’ team, led by Scott Plotkin, M.D., Ph.D., “agreed up front what the endpoints should be, which patients should be part of the trial, and the sites are signed on,” reports Bakker. Since the master protocols are in place, sponsors can use the existing protocol framework when adding a new drug to the trial rather than building one from scratch.  

More broadly, platform trials have hit a few adoption road bumps related to the upfront planning required to launch collaborative studies of this nature. But Bakker holds up several success stories—the I-SPY 2 trial for breast cancer (Current Breast Cancer Reports, DOI: 10.1007/s12609-019-00334-2), the AGILE trial for glioblastoma (Neuro-Oncology, DOI: 10.1093/neuonc/noae144.079), and another in France for idiopathic nephrotic syndrome in children (Pediatric Nephrology, DOI: 10.1007/s00467-025-06676-7)—suggesting the required effort can be well worth the rewards. 

“If you were to ask me, 10 years from now platform trials should be the standard for everything,” says Bakker. The rare disease sector is probably the best sector for testing and optimizing the model before rolling it out to the bigger indications, she adds. 

Platform trials are invaluable for rare diseases like NF because “you have no [other] choice,” says Bakker. Enrollment targets of traditional one-drug trials can be impossibly hard to hit due to low prevalence of the condition being treated and the geographic dispersal of affected individuals. 

‘Pipeline of Investments’ 

Bakker also has a few ideas about how to better inject capital into early-stage biotechs focused on rare disease, including the need to build a “financial continuum” to reward their progress step by step—along with their nonprofit partner. As it is, philanthropic money is being 100% invested in discovery with 0% return, she notes.   

For CTF, she more immediately imagines a move “from pure philanthropy to venture philanthropy where we are still investing in risk... but if something comes out of our investment in an early-stage biotech [a certain] amount of money goes back to the foundation,” Bakker explains. That’s precisely what other major nonprofits, such as the Cystic Fibrosis and Alzheimer’s Drug Discovery foundations, have been doing for many years now. 

“Once we get out of venture philanthropy, I see an opportunity to move slowly into the venture capital [arena],” continues Bakker. The idea here is to create partnerships between a foundation and various investors (e.g., seed funder, Series A and B rounds) for different stages of a biotech’s R&D program. “I think we could save a lot of biotechs this way.” 

The problem with the venture philanthropy model is that a foundation might invest a quarter or half a million dollars in a biotech, but it can be a “dead end” because that only carries a young company so far, she says. She’d instead like to see nonprofits do the “handoffs” from one round of investors to the next who might put in an initial $2 million, followed by $50 million, and then $100 million—effectively creating a “pipeline of investments.” 

Forward Momentum

The Congressionally Directed Medical Research Program, which was just hit with a significant cut in funding, is one reason rare disease clinical trials have been conducted for a fraction of the cost of traditional trials, says Bakker. It has been supporting the NF Clinical Trials Consortium, a group of 20 centers efficiently running signal-finding clinical trials together with a single operations center and one data center.  

The other cost- and time-cutter has been platform trials, thanks in large part to the efforts of the EU Patient-Centric Clinical Trial Platforms (EU-PEARL), a public-private partnership funded by the Innovative Medicines Initiative. EU-PEARL is devoted to the development of integrated research platforms multiple companies can use to test their drugs simultaneously against a shared placebo group. The project focuses initially on four disease areas, one of which is NF.  

As CTF’s CEO, Bakker’s goal is to help bring at least five new NF treatments to market in the next decade. Currently two drugs are on the market—Gomekli as well as Koselugo (selumetinib) for children with NF1 who have symptomatic, inoperable plexiform neurofibromas.  

She says she is currently in talks with about 28 companies that have expressed interest in NF about possibly tackling other manifestations of NF, including NF2-related SWN, non-NF2-related SWN, cutaneous neurofibromas, and glioma. Validated, clinically usable biomarkers are also needed for malignant peripheral nerve sheath tumors, which often begin as nonmalignant plexiform neurofibromas. 

Bakker adds that she is also laser-focused on schwannomatosis, which can cause excruciating pain with no good way of measuring the suffering. She is on the lookout for better options than the NRS-11 score, a numerical assessment tool for quantifying pain intensity that can’t effectively capture changes in pain over time, fluctuations in pain levels, or the complexity of a pain experience. 

A wearable product out of Australia that gauges pain more universally but normalizes its measurement to the same individual will be showcased at the upcoming NF Conference in Washington, D.C. Perhaps it could be used for building a protype specific to NF, she says. “We are kind of looking at everything.”