Clinical OMICS

JUL-AUG 2019

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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www.clinicalomics.com July/August 2019 Clinical OMICs 13 is also developing a synthetic biology diagnostic platform, called Internal Splint-Pairing Expression Cassette Transla- tion Reaction, or INSPECTR, that would be stable at room temperature. At the Chan Zuckerberg BioHub—a collaborative effort by Berkeley, Stanford, and the University of California, San Francisco—researchers have created a CRISPR-based diag- nostic tool that can rapidly identify common drug-resistant microbes. Called FLASH (Finding Low Abundance Sequences by Hybridization), the tool uses CRISPR-Cas9 enzyme to search through a patient's metagenomic sample and cuts its target DNA on either side, separating the drug-resistant sequences from the rest of the microbial genome. Emily Crawford, Ph.D., a scientist at the CZ Biohub Infec- tious Disease Initiative and adjunct assistant professor of microbiology and immunology at UCSF, said the test can be used to identify drug-resistant microbes in 24 hours. Stan- dard culture-based methods take 48 to 72 hours or longer for slower-growing microbes. While metagenomic sequenc- ing of microbial nucleic acid sequences is now being done in research settings, it's not yet widely available. The benefit of FLASH, Crawford said, is that it can be mul- tiplexed to detect and reveal thousands of antimicrobial-re- sistant genes at once. In that sense, she said FLASH is highly complementary to the DETECTR and SHERLOCK system. Her group is currently collaborating with the Doudna lab to use FLASH and DETECTR in tandem for tuberculosis detection. Cancer diagnostics and beyond Both companies also want to use their platforms in oncology, though neither indicated what specific mutations they are tar- geting. The tests could potentially look for multiple mutations at once—and be faster and cheaper than tumor sequencing. Crawford said she also hopes FLASH will be used to find mutations in cancer. "Imagine if you had to download all the information on the Internet and search it every time you wanted to find something online," said Michael Heltzen, CEO of Cardea Bio, which has partnered with researchers at Berkeley and the Keck Graduate Institute to build a graphene-based CRISPR detector. "That's essentially what whole-genome sequencing is." M e a n w h i l e , I s r a e l i biotech NovellusDx is developing a functional annotation for cancer treat- ment (FACT) assay that uses CRISPR technology licensed from the Christi- ana Care Health System in New Jersey. The test is not meant to replace tumor sequencing, but rather sup- plement it. Using Cas12a, scientists were able to reproduce the genetic features of an individual patient's tumor in a human DNA sample. "What we developed was a way to take that DNA as if it were a blank canvas and recreate the mutagenic profile of the patient using CRISPR," said Eric Kmiec, director of the Gene Editing Institute at Christiana Care. That information is then put into computer algorithms that identify which signaling pathways are being activated or deactivated in a person's tumor. The assay can also screen through can- cer drugs and drug combinations to predict clinical results based on a patient's results. Kmiec thinks CRISPR diagnostics are more likely to come to market before CRISPR-based therapeutics. "I'm more opti- mistic right now about CRISPR influencing patient health through the diagnostic portal," he said. "Of course, we and others want to develop gene editing as therapy. But the hur- dles to get to patients are large and, in some cases, not known." Before that happens, companies will need to validate their CRISPR tests in randomized control trials against tra- ditional diagnostics. Neither company provided details on when they plan to do that. Where CRISPR-based diagnos- tics could come to the market first is in a different industry altogether. Both companies plan to develop agriculture and manufacturing diagnostics, to test for contamination in food and water. "Our goal is to make sure this is used as broadly as pos- sible in as many settings as possible," Sherlock Biosciences' Dhanda said. Trevor Martin, co-founder and CEO of Mammoth Biosciences Jennifer Doudna (second from right) and the Mammoth Biosciences team.

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