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Faster, better, cheaper: the rise of CRISPR in disease detection

Powerful gene-editing tool could help to diagnose illnesses such as Lassa fever early and rein in the spread of infection.

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Grad students using one of the CRISPR tests in Nigeria.

Fehintola Ajogbasile, a graduate student at the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria, uses a CRISPR diagnostic test to look for Lassa virus in a blood sample.Credit: Amy Maxmen

An epidemic of Lassa fever in Nigeria that has killed 69 people this year is on track to be the worst ever recorded anywhere. Now, in the hope of reducing deaths from Lassa in years to come, researchers in Nigeria are trying out a new diagnostic test based on the gene-editing tool CRISPR.

The test relies on CRISPR’s ability to hunt down genetic snippets ― in this case, RNA from the Lassa virus ― that it has been programmed to find. If the approach is successful, it could help to catch a wide range of viral infections early so that treatments can be more effective and health workers can curb the spread of infection.

Scientists in Honduras and California are testing CRISPR diagnostics for dengue viruses, Zika viruses and strains of human papillomavirus (HPV) associated with cancer. And a study to explore a CRISPR test for the Ebola virus is pending in the Democratic Republic of the Congo.

A robust, user-friendly test could reduce the death rates from Lassa fever, which can be as high as 60%, says Jessica Uwanibe, a molecular biologist developing a Lassa diagnostic at Redeemer’s University in Ede, Nigeria. “I’m working on something that could save a lot of lives.”

Trial runs

For most infectious diseases, diagnosis requires specialized expertise, sophisticated equipment and ample electricity ― all of which are in short supply in many places where illnesses such as Lassa fever occur. The CRISPR tests offer the tantalizing possibility of diagnosing infections as accurately as conventional methods, and almost as simply as an at-home pregnancy test. And because CRISPR is engineered to target specific genetic sequences, researchers hope to develop a tool based on the technology that can be fine-tuned to identify, within a week, whatever viral strain is circulating.

“This is a very exciting direction for the CRISPR field to go in,” says Jennifer Doudna, a biochemist at the University of California, Berkeley, who is developing some of these tools.

Uwanibe and her team are running trials of a CRISPR diagnostic developed by researchers at the Broad Institute of MIT and Harvard in Cambridge, who had paired CRISPR with the Cas13 protein1. Unlike Cas9 — the enzyme originally used in CRISPR gene editing — Cas13 cuts the genetic sequence that it’s been told to target, and then starts slicing up RNA indiscriminately. This behaviour presents a problem when trying to edit genes, but it’s a boon for diagnostics because all that cutting can serve as a signal.

In 2018, the Broad team updated its test, called SHERLOCK, by adding RNA molecules that signal when they've been sliced by Cas13. The cut RNA triggers the formation of a dark band on a paper strip — similar to the visual cues in a pregnancy test — that indicates the presence of whatever genetic sequence CRISPR was engineered to find2.

The team in Nigeria is now testing how accurately a version of this diagnostic, engineered to find the Lassa virus, flags people whose infections have previously been confirmed with the conventional lab-based approach, called polymerase chain reaction (PCR).

SHERLOCK is roughly half the price of PCR tests in Nigeria and takes half the time to return results ― around two hours compared with four, says Kayla Barnes, a geneticist at the Broad who is collaborating with the group in Nigeria. Both diagnostics require electricity to process samples, but SHERLOCK isn’t as sensitive to power outages — which are ubiquitous across Nigeria ― as PCR is. “We want to be able to rely on just a heat block that you can run off a car generator,” says Barnes.

Expanding the toolkit

Other CRISPR tests developed by Doudna and her team at Berkeley use Cas proteins with different properties and patents to target various illnesses. Their diagnostic for HPV uses the Cas12a protein, instead of Cas13. Cas12a also cuts indiscriminately after locking onto its target, but it slices DNA instead of RNA. The test distinguishes between two types of HPV that studies have linked to cervical or anal cancer3.

Doudna hopes it will be able to help curb the rising death toll from cervical cancer in African countries where the disease is frequently diagnosed too late for treatment. She co-founded a San Francisco-based startup called Mammoth Biosciences last year to further develop the diagnostic. The company is testing it on blood samples from people in California.

The Berkeley and Mammoth researchers are looking to expand their CRISPR toolkit by adding newly discovered Cas14 and CasX proteins, whose small size makes them easier to incorporate into diagnostic technologies4,5.

Market forces

“These are exciting innovations,” says Dhamari Naidoo, a technical officer at the World Health Organization, based in Nigeria. But she adds that for CRISPR tests to have the impact in low-income countries that their developers hope they will, researchers must ensure that the technology is licensed, manufactured and priced affordably.

Researchers often fail to think about this side of the equation, Naidoo says. For instance, about a dozen diagnostic tests for Ebola have been developed, but only two have been deployed in the current outbreak in the Democratic Republic of the Congo. The rest have been held up because of economic obstacles, including the lack of a market large enough for manufacturers to justify the expense of making and distributing the tests.

In light of the ongoing patent battles between Berkeley and the Broad, CRISPR-based diagnostics could be particularly troublesome from an economic standpoint. But Doudna and Pardis Sabeti, who leads the SHERLOCK project at the Broad, say they’re committed to licensing their tools so that the people who need these diagnostics can use them.

For Uwanibe, that day cannot come soon enough. “I wish we could do this even faster,” she says.

Nature 566, 437 (2019)

doi: 10.1038/d41586-019-00601-3

References

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    Gottenberg, J.S. et al. Science 356, 438-442 (2017).

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    Gootenberg, J.S. et al. Science 360, 439–444 (2018)

  3. 3.

    Chen, J.S. et al. Science 360, 436-439 (2018).

  4. 4.

    Harrington, L.B. et al. Science 362, 839-842 (2018).

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    Liu, J. J. et al. Nature 566, 218–223 (2019).

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