New gene drive platform uncovers genetic networks in Candida

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Candida albicans is a leading cause of fungal infections; however, its diploid nature has made complex genetic interaction analysis a challenge, leading to little understanding of the genetic factors underlying pathogenesis. A new study has reported a CRISPR–Cas9-based ‘gene drive array’ platform, which can be used to create diploid mutant strains and facilitate genetic analysis in this fungal pathogen.

The study, published recently in Nature Microbiology, utilized mating-competent haploid forms of C. albicans to create homozygous double-deletion mutants, as author George Church (Harvard Medical School, MA, USA) explained: “We used haploid C. albicans strains and replaced genes that we wanted to eliminate with a ‘gene drive’ that we previously developed and had adjusted to the specific biology of C. albicans. After mating, these ‘selfish genetic elements’ proceed to replace the normal copy of the gene in the diploid fungi.

“The approach worked so efficiently that it enabled us to even delete pairs of different genes simultaneously with higher throughput and to explore whether their functions are related.”

By applying this gene-deletion approach the team could then identify combinations of genes that act synergistically in fungi to facilitate processes such as biofilm formation or drug resistance.

First author, Rebecca Shapiro (Massachusetts Institute of Technology, MA, USA), gave more detail: “For example, deleting either the two efflux pump-encoding genes CDR1 and CDR2, or TPO3 and CDR2 together, rendered C. albicans highly sensitive to fluconazole and other antifungal drugs, suggesting that targeting two mechanisms at the same time could help overcome drug resistance. In biofilm formation assays, we also found that loss of the ALS3 adhesion factor gene synergizes with the loss of several other adhesion factor genes, which makes it a highly interconnected hub of biofilm adhesion and an interesting candidate to further explore.”

The team hope this new method could be used to uncover more about C. albicans pathogenesis, in addition to identifying drug targets and combination therapies in the future.

Author James Collins (Massachusetts Institute of Technology), concluded: “We can now get a much better handle on how genetic networks that underlie the virulence of C. albicans are organized, see how they respond to specific environmental and drug perturbations, and thereby uncover new vulnerabilities, that in the future may lead to new drug targets and combination therapies. Moreover, our gene drive array platform can be a blueprint for similar approaches in other fungal pathogens, such as the newly emerging Candida auris, which is highly drug resistant and has already been marked as a threat by the Centers for Disease Control and Prevention (GA, USA).”

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Sources: Shapiro RS, Chavez A, Porter CBM et al. A CRISPR–Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nat. Microbiol.  doi:10.1038/s41564-017-0043-0 (2017) (Epub ahead of print); www.eurekalert.org/pub_releases/2017-10/wifb-ddr102717.php

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