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1. Development of CRISPR/Cas13a-based assays for the diagnosis of SchistosomiasisResearch in context

Author

Skye R. MacGregor, Donald P. McManus, Haran Sivakumaran, Thomas G. Egwang, Moses Adriko, Pengfei Cai, Catherine A. Gordon, Mary G. Duke, Juliet D. French, Natasha Collinson, Remigio M. Olveda, Gunter Hartel, Carlos Graeff-Teixeira, Malcolm K. Jones, and Hong You

Subjects
Schistosomiasis, Schistosoma japonicum, Schistosoma mansoni, Diagnostics, CRISPR, Cas13a, Medicine, Medicine (General), R5-920
Abstract

Summary: Background: Schistosomiasis is a disease that significantly impacts human health in the developing world. Effective diagnostics are urgently needed for improved control of this disease. CRISPR-based technology has rapidly accelerated the development of a revolutionary and powerful diagnostics platform, resulting in the advancement of a class of ultrasensitive, specific, cost-effective and portable diagnostics, typified by applications in COVID-19/cancer diagnosis. Methods: We developed CRISPR-based diagnostic platform SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) for the detection of Schistosoma japonicum and S. mansoni by combining recombinase polymerase amplification (RPA) with CRISPR-Cas13a detection, measured via fluorescent or colorimetric readouts. We evaluated SHERLOCK assays by using 150 faecal/serum samples collected from Schistosoma-infected ARC Swiss mice (female), and 189 human faecal/serum samples obtained from a S. japonicum-endemic area in the Philippines and a S. mansoni-endemic area in Uganda. Findings: The S. japonicum SHERLOCK assay achieved 93–100% concordance with gold-standard qPCR detection across all the samples. The S. mansoni SHERLOCK assay demonstrated higher sensitivity than qPCR and was able to detect infection in mouse serum as early as 3 weeks post-infection. In human samples, S. mansoni SHERLOCK had 100% sensitivity when compared to qPCR of faecal and serum samples. Interpretation: These schistosomiasis diagnostic assays demonstrate the potential of SHERLOCK/CRISPR-based diagnostics to provide highly accurate and field-friendly point-of-care tests that could provide the next generation of diagnostic and surveillance tools for parasitic neglected tropical diseases. Funding: Australian Infectious Diseases Research Centre seed grant (2022) and National Health and Medical Research Council (NHMRC) of Australia (APP1194462, APP2008433).

Published
2023
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2. eQTL Colocalization Analyses Identify NTN4 as a Candidate Breast Cancer Risk Gene

Author

Kristine M. Hillman, Stacey L. Edwards, Mahdi Moradi Marjaneh, Sunyoung Ham, Haran Sivakumaran, Jonathan Beesley, Siddhartha Kar, Georgia Chenevix-Trench, Nehal Hussein, Andreas Möller, Luize G. Lima, Wei Shi, Susanne Kaufmann, and Juliet D. French

Subjects
Risk, Quantitative Trait Loci, Mice, Nude, Genome-wide association study, Breast Neoplasms, Biology, Quantitative trait locus, 03 medical and health sciences, Mice, 0302 clinical medicine, Breast cancer, Report, Cell Line, Tumor, Genetics, medicine, Animals, Humans, Genetic Predisposition to Disease, Gene, Genetics (clinical), Alleles, 030304 developmental biology, Genetic association, 0303 health sciences, Gene Expression Profiling, Cancer, Genomics, medicine.disease, Neoplasm Proteins, Gene Expression Regulation, Neoplastic, Enhancer Elements, Genetic, Phenotype, Cancer Genome Project, 030220 oncology & carcinogenesis, Expression quantitative trait loci, MCF-7 Cells, Heterografts, Female, Netrins, Genome-Wide Association Study
Abstract

Breast cancer genome-wide association studies (GWASs) have identified 150 genomic risk regions containing more than 13,000 credible causal variants (CCVs). The CCVs are predominantly noncoding and enriched in regulatory elements. However, the genes underlying breast cancer risk associations are largely unknown. Here, we used genetic colocalization analysis to identify loci at which gene expression could potentially explain breast cancer risk phenotypes. Using data from the Breast Cancer Association Consortium (BCAC) and quantitative trait loci (QTL) from the Genotype-Tissue Expression (GTEx) project and The Cancer Genome Project (TCGA), we identify shared genetic relationships and reveal novel associations between cancer phenotypes and effector genes. Seventeen genes, including NTN4, were identified as potential mediators of breast cancer risk. For NTN4, we showed the rs61938093 CCV at this region was located within an enhancer element that physically interacts with the NTN4 promoter, and the risk allele reduced NTN4 promoter activity. Furthermore, knockdown of NTN4 in breast cells increased cell proliferation in vitro and tumor growth in vivo. These data provide evidence linking risk-associated variation to genes that may contribute to breast cancer predisposition.

Published
2020
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