May 26, 2019
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Companies tracking mutations in cancer cells can provide a key to unlocking better therapies

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Investors and entrepreneurs are beginning to bring new diagnostic tools to market that promise better results for cancer patients through the identification of mutations in cancer cells that can create more targeted therapies.

Earlier this month, research using technology developed by the startup Mission Bio helped identify cellular mutations in acute myeloid leukemia cancer cells that could be indicators of potential relapse or recurrence of the cancer after therapy.

In the study, which was presented at the American Society for Hematology’s recent conference, a team from the MD Anderson cancer research institute in Texas, including Dr. Koishi Takahashi, sequenced more than 500,000 cells across 70 patients using Mission Bio’s “Tapestri” platform.

“These results demonstrate the power of analyzing heterogeneity for the study and treatment of cancer patients,” said Dr. Takahashi, in a statement. “Tapestri’s ability to precisely identify cancer subclones throughout treatment and disease progression brings us closer to delivering on the promise of precision medicine.”

Increasingly, researchers are coming to the conclusion that genetic mutations of individual cancer cells can lead to the persistence of minimal residual disease and therapy resistance. Other leading cancer centers at  universities including the University of California, San Francisco, University of Pennsylvania, and Stanford University have also released papers on the viability of Mission Bio’s approach.

That research may help explain why Mission Bio was able to land $30 million in new funding from a slew of investors including Agilent Technologies, Cota Capital, LabCorp, LAM Capital, and Mayfield.

The company said it will use the cash to increase the work it’s doing in blood cancer research while expanding its business into the analysis of CRISPR applications and potential mutations that can occur through the use of that gene editing technology.

“Cancer will kill 10 million people this year alone. We can beat cancer with more effective, dynamic therapies, but we first need to precisely understand its biology, starting with the varying genetic composition of each and every cancerous cell,” explained Charlie Silver, CEO of Mission Bio. “Minimal residual disease is a major cause of cancer relapse; overlooking even one cell could put a life at risk. With the Tapestri Platform, we can track every cell, every mutation, to better guide treatments and save patient lives.”

That mutation tracking is also what brought Agilent on board as the company takes its initial steps into monitoring the intended and unintended consequences of using CRISPR technology to edit genes.

“The Tapestri platform’s unique quality control capabilities are strenghtening our CRISPR R&D programs,” remarked Darlene Solomon, Senior Vice President and Chief Technology Officer of Agilent Technologies. “Agilent’s commitment to innovation and precision medicine are well matched with Mission Bio’s Tapestri platform as it has the potential to improve patient outcomes in the fight against cancer — and that’s the most meaningful benchmark of all.”

Mission Bio isn’t the only company making strides when it comes to cancer treatments and new targeted monitoring technologies.

Cambridge Cancer Genomics is another startup company working on bringing new technologies to blood sample analysis that can better identify cancer and target personalized therapies for the disease.

The company has raised $4.5 million to build what it’s calling one of the largest datasets of longitudinal cancer in the world

Like Mission Bio, CCG is hoping that its data can help map the ways cancer cells evolve in response to treatments and suggest new therapies to doctors.

Financing the companies rollout are investors including AME Cloud Ventures, Refactor Capital, Romulus Capital and Y Combinator. Additional capital has come from the company’s early partner, the Comprehensive Blood and Cancer Center in Bakersfield, Calif. who invested not only cash but provided 4,000 clinical samples for CCG to analyze and develop their monitoring and predictive solution.

Both companies are trying to tackle the “one-size-fits-all” approach to cancer therapy that exists for most patients around the world.

First line cancer treatment fails two-thirds of all patients and the realization that treatments aren’t working can take up to six months to recognize. Like Mission Bio, CCG is also working to identify whether a patient is at risk of relapse — something the company claims it can do 7 months earlier than standard practices.

“When you drill down into the DNA changes behind cancer, you quickly find that no two tumors are the same. To apply cancer therapies more successfully to any given tumor, we need a deeper understanding of what exactly has gone wrong in each case at a molecular level,” says Dr. Harry Clifford, a co-founder and chief technology officer at Cambridge Cancer Genomics. “This starts with effective tools to capture that information. The approaches we’re developing at CCG will have widespread applications, from identifying targets for new therapy development, to deciding which personalized approach is best for a given patient.”

That echoes the thinking of companies like Mission Bio, and like Mission Bio, CCG has published results from recent trials of its technology.

The company applied its predictive technology to the outcome of different therapies in over 2,500 breast cancer patients and used its machine learning technology to identify the same kind of variants that Mission Bio is working to call out in an attempt to understand when and how relapses can occur.


1) Interlacing Personal and Reference Genomes for Machine Learning Disease-Variant Detection

Summary: Differences in our DNA underlie many aspects of human health; from rare genetic diseases to cancer. In this paper, we build a new class of software for detecting DNA variants. Based on the same principles behind facial recognition, our technique can identify cancer variants with unparalleled accuracy. We hope that releasing this software for non-commercial use will lead to more successful targeted therapy and personalized cancer medicine. 

Cambridge Cancer Genomics offers a better way to gauge effective cancer treatments

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John Cassidy’s family has been at the forefront of cancer research for three generations now.

The Cambridge-educated co-founder and Chief Executive Officer of cancer diagnostics company Cambridge Cancer Genomics was just following in his father’s and grandfather’s footsteps when he took up researching the disease in college.

Cassidy’s father was head of cancer therapies at Glasgow University and his grandfather was also a professor researching cancer there.

Joined by three other phDs from Oxford, Cambridge, and Kings College, Cassidy thought it was his turn to take up the mantle.

What Cambridge Cancer Genomics has done, through a combination of new sensing technology and machine learning, is develop a technique that can identify how well cancer treatments are working. That’s incredibly important for getting different therapies to market faster, and for ensuring that targeted therapies are working the way they’re supposed to — ultimately driving down the overall cost for cancer treatments.

“You can detect when people should be off of treatment 7 months earlier than traditional means of analysis,” using the CCG technology, says Cassidy.

That’s incredibly significant for patients diagnosed with the types of cancers that Cassidy and his colleagues are working with — cancers like colorectal cancer, pancreatic cancer, and lung cancer.

Joining Cassidy in the journey to create better, more effective cancer therapies are Harry Clifford, a former cancer bioinformatics phD at Oxford University who serves as Chief Scientific Officer; Evaline Tsai; the chief technology officer who has a BSE in chemical and biological engineering from Princeton; and Nirmesh Patel, the company’s chief medical officer, whose background is in translational cancer medicine, which he studied at Kings College London.

“Two of us come from the same lab in Cambridge,” says Cassidy. “We knew that Evaline was doing a phD in biosesnsors at the same time. The other guy was doing a phD in translational genomics,” Cassidy said.

The company now has a clinical partnership with the Comprehensive Blood and Cancer Center in Bakersfield, Calif. to pilot its technology.

For Cassidy and his compatriots, the decision to launch CCG was all about the patient experience. While amazing work is being done in research centers around the world on cancer therapies and novel treatments, the clinical experience remained relatively unchanged, Cassidy said.

“How patients were being treated was stuck in the 80s,” he said.

“When you think about something like targeted therapies… they’re super expensive,” Cassidy explained. “The reason they’re expensive is that it’s very difficult to figure out who the drug is going to work for. If you can tell whether the drug is working or not.. there’s implications for getting drugs through clinical trials faster.”

CCG tracks mutations in cancer cells, Cassidy explains. “The mutations are easily pinpointed changes in base pairs in DNA. We look for these changes in a patient’s blood,” he said.

The company, which graduated alongside Y Combinator’s recent batch of startups, has already received some pre-seed funding on its way to a $1.3 million targeted seed round.

Featured Image: Ed Uthman/Flickr UNDER A CC BY 2.0 LICENSE

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