The New Cancer Models, Part 1: The Tumor Organoid Biobank

December 4, 2013

By Aaron Krol 

We know that cancer is a personal disease, with each case displaying a unique genetic makeup that demands uniquely targeted therapy. Yet even as private companies like Foundation Medicine rush to capitalize on personalized cancer treatment, the basic research that supports these efforts still relies on flawed models: animal cancers, or human cancer cell lines, which may not map appropriately to live human tumors at all, let alone to a specific patient’s disease. This week, Bio-IT World is taking a look at three groups who are trying to update cancer models for modern drug discovery with a personal touch. 

December 4, 2013 | At the University Medical Center Utrecht (UMCU), a hub for biomedical research located in one of the busiest cities in the Netherlands, a remarkable resource is being created – or perhaps more accurately, grown – under the auspices of a multimillion dollar research grant. A collection of so-called “mini-guts,” organized into around 25 pairs so far and increasing, is flourishing in a specially developed culture, recreating with impressive faithfulness the normal growth process of the human colon.

Or rather, half of them are: the half grown from healthy cell samples harvested from patient volunteers at the Medical Center. The other half, the mirror cell colonies that represent one of every mini-gut pair, are growing into thriving colon tumors in the lab. The cell samples that gave rise to these disembodied tumors were drawn from the same two dozen or so patients who produced the healthy mini-guts, all of whom are suffering from difficult-to-treat colon cancers. These patients are hoping that the strange, divorced organs surviving in their absence will soon provide the key to their treatments.

How to Grow a Mini-Gut 

Strictly, these are not organs but “organoids,” superb models of natural organ growth that can be generated from a single stem cell if cared for under the right conditions. They are a somewhat tangential product of the long and winding career of Dr. Hans Clevers, president of the Royal Netherlands Academy of Arts and Sciences, and a leading member and former director of the Hubrecht Institute affiliated with UMCU.

Back when Dr. Clevers first formed his lab at the Hubrecht Institute, creating these tumorous organoids would not have seemed like an inevitable extension of his research, which focuses on the growth of the small intestine. His lab was interested in the Wnt signaling pathway, crucial in organs’ embryonic development, as it relates to the gut. But about six years ago, Dr. Clevers and his team discovered that a protein involved in that pathway, Lgr5, could be used as a highly sensitive marker for intestinal stem cells, and was stimulated by a novel growth factor called R-spondin 1. Several speculative experiments later, the lab found that by isolating stem cells using Lgr5 as a marker, and stimulating them with R-spondin 1, they could grow organoids more or less indefinitely where other groups had always hit a brick wall in keeping these proto-organs alive.

This research has expanded to other organ systems since, with Dr. Charles Sawyer of Memorial Sloan-Kettering Cancer Center growing prostate organoids using the same methods, and Dr. David Tuveson of the Lustgarten Foundation following suit with the pancreas. In fact, Dr. Clevers told Bio-IT World, “It looks like we can take stem cells from any adult organ – lung, stomach, colon, small intestine, prostate, liver, pancreas – grow them in a cocktail that contains this growth factor, and essentially grow these cells forever.”


 organoid transplant  

A graphic rendering of an organoid-based transplant produced by Dr. Clevers' lab. Image credit: Hubrecht Institute 

This faithful proliferation of micro-organs could have serious implications for a number of medical fields, and at first Dr. Clevers went right for the most obvious. His lab started cultivating mouse colon organoids around 2009, and later began using the resulting tissue for transplants. “From a single cell, we can transplant many, many mice,” he says, “and the tissue that we transplant is actually healthy and functional. This is a bit of a breakthrough.” The hope is to eventually develop a new method of tissue transplant that could repair a patient’s damaged organ using organoids grown from the same patient’s cells. 

But when Dr. Clevers chanced to mention his lab’s work to a group of American cancer specialists, their imaginations went elsewhere. “They asked me, ‘Well, if you can do this, can you also do this for cancer?’” Clevers remembers. “ I said, ‘Well yeah, that’s easy, because cancer cells tend to grow more easily than normal cells.’” This conversation proved to be the genesis for an ambitious project in which tumor organoids would stand in for patients’ own bodies in a battery of drug tests, to see which therapies can best reverse the progress of a specific cancer.

How to Grow Dozens of Mini-Guts 

The project would not be an easy one to get off the ground. Expensive, international in scope, and highly speculative, the creation and validation of this “tumor organoid biobank” would struggle to find support using ordinary, small-bore funding models. “It’s not easy to finds grants this size in Europe that can be spent in such a dedicated way,” says Clevers. So he turned to the United States, where by a happy coincidence, Stand Up To Cancer (SU2C) was just looking to expand its reach overseas. A nontraditional grant-giving organization, SU2C favors widely dispersed collaborations and game-changing research, and insists that cost be no obstacle to the initiatives it funds. In return, its leadership has one overarching demand: real clinical impact, for real patients, within three years of funding.

Dr. Clevers’ “Dream Team,” as the research collaboratives that apply for SU2C grants are called, was part of a wave of around ten Dutch groups who approached the organization when it opened its doors to the Netherlands. Still, Dr. Arnold Levine, vice chair of the Science Advisory Board that awards SU2C grants, felt that Clevers’ group had little trouble standing out. “This was by far, I think, the most imaginative [application], and could have in a short time the biggest impact on patient care,” Dr. Levine told Bio-IT World. Rather than relying on generic drug trials with unreliable cancer cell lines, patients could have their own genetic makeup inform their therapies.

“Notoriously there’s a problem of testing drugs against cell lines,” says Dr. Levine. “Cell lines don’t give you as much information as you like. Even tumors in animals… don’t give you as much information as you like.” Cancer cell lines have sometimes diverged significantly from their original tumors in the years they’ve spent in the lab, and because they are not really representative of organ growth, the full spectrum of important cancer phenotypes is not expressed in their development.

Dr. Clevers’ organoids, on the other hand, display “the closest possible relationship between a cell culture system and the animal, or human in this case, herself,” Dr. Levine says. Impressed by the Dream Team’s potential for rapid clinical intervention, Levine and his colleagues awarded a grant of €6 million (over $8 million), dispersed over a four-year period, to a multinational team consisting of the Hubrecht Institute, UMCU, the Netherlands Cancer Institute, and the Wellcome Trust Sanger Institute, a genomic research center located in Cambridge, UK, whose role would be to sequence the whole exome of each healthy and tumor organoid created. Dr. Clevers is the team’s leader, and Dr. Johannes Bos of UMCU is the co-leader.

Drs. Sawyer and Tuveson, who pioneered growing organoid models for prostate and pancreatic cancers, were disqualified from formal membership in the Dream Team due to prior ties to SU2C, but as unpaid collaborators they extend the team into the United States as well.


clevers and bos 
Drs. Johannes Bos (L) and Hans Clevers celebrating their grant. Image credit: Dutch Cancer Society 

The SU2C grant will cover colon, prostate, and pancreatic tumors, both because these are the systems for which organoid culturing has been most thoroughly studied, and because the need for better models for these cancers is particularly dire. “For pancreas cancer,” says Dr. Clevers, “where we now have a collection, there’s only probably two or three available cell lines that people trust to represent the cancer… What we are growing is much more representative of real tumors in patients than these few cells lines that pharma has had to work with.”

Early indications are that the tumor organoids will retain their close ties to their parent tumors. Because the relevant patients are known – not always the case with ordinary cell lines – the organoids can be sequenced alongside their tumors of origin, and these screens have revealed the same spectrum of mutations in both samples. Dr. Clevers also expects to expand from whole exome to whole genome sequencing, and take into account copy number variations and other difficult-to-capture abnormalities. In the meantime, a set of around one hundred compounds has been selected for the first round of drug screenings, derived from Dr. Michael Stratton’s work at the Sanger Institute running pharmaceuticals against traditional cancer cell lines.

Bankable Research 

“If this works,” says Dr. Levine, “and it really is a great new way to test drugs outside of the human being for their efficacy, this could become a standard procedure in any hospital. When a tumor’s removed, an organoid would be made – it can be made rather rapidly, within a week or two – and drugs would be tested against it, and then a profile for treatment could be formed.”

Yet even cancer patients without the privilege of having custom organoids grown stand to benefit from the tumor biobank. The organoids are much more faithful cancer models than undifferentiated cells that have adapted to live in plastic, and the volume of patients represented – eighty in the initial terms of the grant – ensures that new combinations of mutations will be represented in drug trials, better narrowing down which therapy is indicated for a given cancer’s profile.

Nor does the Dream Team intend to limit the biobank’s impact to this single round of research. “The bank is owned by [UMCU],” says Clevers, “but will be [managed] by a foundation which also has my IP. So it’s a not-for-profit organization, and this will maintain the bank, and will actually make this living biobank available for academic researchers in collaborations, but also for [the pharmaceutical] industry.” If academics, or pharmaceutical companies, want to run new drug screens, or perform drug discovery, or consider different applications altogether, they can apply for access to the organoids, which are easy to replicate for use in expanded research.

As one example, Dr. Levine looks forward to basic research into how cancers naturally grow. “There are whole new sets of questions,” he says, “that this allows one to bring up: getting the conditions for what hormones are important, what kinds of cells are important, whether metastatic cells are very different in their organoid cultures than are non-metastatic stem cells.” These are questions that existing cancer models were never equipped to handle, even if they faithfully maintained every mutation found in their tumors of origin.

The politics of maintaining the biobank are tricky, as Dr. Clevers is meticulously careful about patient consent. “We have to be able to destroy the tissue at any moment that the patient or the family asks for this,” he says. “We don’t want to turn these things into HeLa cells.” But the reward for navigating these ethical concerns is a new generation of thoroughly sequenced cancer models, with real patient histories, which will grow like real tumors in the lab. The biobank can also embrace more types of cancer if research on the first organoids seems promising. Protocols have already been developed for growing lung organoids.

The international approach of the SU2C grant has already laid the groundwork for growing the biobank project outwards. Now it only remains to be seen if the independent organs growing at UMCU can save the lives of the human beings they came from – and where they travel once they do. If some of these organoids become the mainstays of future cancer research that certain cell lines are today, they could be destined to long and fruitful lives in the lab, even as their progenitors live on in the world outside.

Read Part 2: A Fly of One's Own 
Read Part 3: The Cell Line Critics