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Article ; Online: Allelic imbalance in human breast cancer.

French, Juliet D / Edwards, Stacey L

2017 Volume 8, Issue 7, Page(s) 10763–10764

Language	English
Publishing date	2017-03-16
Publishing country	United States
Document type	News
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.14648
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Article ; Online: Redefining normal breast cell populations using long noncoding RNAs.

Bitar, Mainá / Rivera, Isela Sarahi / Almeida, Isabela / Shi, Wei / Ferguson, Kaltin / Beesley, Jonathan / Lakhani, Sunil R / Edwards, Stacey L / French, Juliet D

Nucleic acids research

2023 Volume 51, Issue 12, Page(s) 6389–6410

Abstract: Single-cell RNAseq has allowed unprecedented insight into gene expression across different cell populations in normal tissue and disease states. However, almost all studies rely on annotated gene sets to capture gene expression levels and sequencing ... ...

Abstract	Single-cell RNAseq has allowed unprecedented insight into gene expression across different cell populations in normal tissue and disease states. However, almost all studies rely on annotated gene sets to capture gene expression levels and sequencing reads that do not align to known genes are discarded. Here, we discover thousands of long noncoding RNAs (lncRNAs) expressed in human mammary epithelial cells and analyze their expression in individual cells of the normal breast. We show that lncRNA expression alone can discriminate between luminal and basal cell types and define subpopulations of both compartments. Clustering cells based on lncRNA expression identified additional basal subpopulations, compared to clustering based on annotated gene expression, suggesting that lncRNAs can provide an additional layer of information to better distinguish breast cell subpopulations. In contrast, these breast-specific lncRNAs poorly distinguish brain cell populations, highlighting the need to annotate tissue-specific lncRNAs prior to expression analyses. We also identified a panel of 100 breast lncRNAs that could discern breast cancer subtypes better than protein-coding markers. Overall, our results suggest that lncRNAs are an unexplored resource for new biomarker and therapeutic target discovery in the normal breast and breast cancer subtypes.
MeSH term(s)	Female ; Humans ; Breast/cytology ; Breast/metabolism ; Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Breast Neoplasms/pathology ; Gene Expression Regulation, Neoplastic ; RNA, Long Noncoding
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2023-05-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad339
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Zs.A 1067: Show issues

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Article: Lentiviral Transduction-based CRISPR/Cas9 Editing of

Du, Xiaofeng / McManus, Donald P / French, Juliet D / Sivakumaran, Haran / Johnston, Rebecca L / Kondrashova, Olga / Fogarty, Conor E / Jones, Malcolm K / You, Hong

Current genomics

2023 Volume 24, Issue 3, Page(s) 155–170

Abstract: Background: Recent studies on CRISPR/Cas9-mediated gene editing in : Methods: To improve the efficiency of CRISPR/Cas9 genome editing in schistosomes, we used lentivirus, which has been effectively used for gene editing in mammalian cells, to deliver ...

Abstract	Background: Recent studies on CRISPR/Cas9-mediated gene editing in Methods: To improve the efficiency of CRISPR/Cas9 genome editing in schistosomes, we used lentivirus, which has been effectively used for gene editing in mammalian cells, to deliver plasmid DNA encoding Cas9 nuclease, a sgRNA targeting acetylcholinesterase ( Results: MCherry fluorescence was observed in transduced eggs, schistosomula, and adult worms, indicating that the CRISPR components had been delivered into these parasite stages by lentivirus. In addition, clearly changed phenotypes were observed in Conclusion: Taken together, electroporation is more efficient than lentiviral transduction in the delivery of CRISPR/Cas9 into schistosomes for programmed genome editing. The exploration of tactics for enhancing CRISPR/Cas9 gene editing provides the basis for the future improvement of programmed genome editing in
Language	English
Publishing date	2023-12-21
Publishing country	United Arab Emirates
Document type	Journal Article
ZDB-ID	2033677-9
ISSN	1875-5488 ; 1389-2029
ISSN (online)	1875-5488
ISSN	1389-2029
DOI	10.2174/1389202924666230823094608
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Zs.A 5571: Show issues

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Article ; Online: CRISPR/Cas9: A new tool for the study and control of helminth parasites.

Du, Xiaofeng / McManus, Donald P / French, Juliet D / Jones, Malcolm K / You, Hong

BioEssays : news and reviews in molecular, cellular and developmental biology

2020 Volume 43, Issue 1, Page(s) e2000185

Abstract: Recent reports of CRISPR/Cas9 genome editing in parasitic helminths open up new avenues for research on these dangerous pathogens. However, the complex morphology and life cycles inherent to these parasites present obstacles for the efficient application ...

Abstract	Recent reports of CRISPR/Cas9 genome editing in parasitic helminths open up new avenues for research on these dangerous pathogens. However, the complex morphology and life cycles inherent to these parasites present obstacles for the efficient application of CRISPR/Cas9-targeted mutagenesis. This is especially true with the trematode flukes where only modest levels of gene mutation efficiency have been achieved. Current major challenges in the application of CRISPR/Cas9 for study of parasitic worms thus lie in enhancing gene mutation efficiency and overcoming issues involved in host passage so that mutated parasites survive. Strategies developed for CRISPR/Cas9 studies on Caenorhabditis elegans, protozoa and mammalian cells, including novel delivery methods, the choice of selectable markers, and refining mutation precision represent novel tactics whereby these impediments can be overcome. Furthermore, employing CRISPR/Cas9-mediated gene drive to interfere with vector transmission represents a novel approach for the control of parasitic worms that is worthy of further exploration.
MeSH term(s)	Animals ; CRISPR-Cas Systems/genetics ; Caenorhabditis elegans/genetics ; Gene Editing ; Mutagenesis ; Parasites
Language	English
Publishing date	2020-11-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.202000185
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Article ; Online: CRISPR interference for sequence-specific regulation of fibroblast growth factor receptor A in

Du, Xiaofeng / McManus, Donald P / French, Juliet D / Collinson, Natasha / Sivakumaran, Haran / MacGregor, Skye R / Fogarty, Conor E / Jones, Malcolm K / You, Hong

Frontiers in immunology

2023 Volume 13, Page(s) 1105719

Abstract: Employing the flatworm ... ...

Abstract	Employing the flatworm parasite
MeSH term(s)	Animals ; Mice ; Gene Expression ; Parasites ; Receptors, Fibroblast Growth Factor ; Schistosoma mansoni ; Stem Cells ; CRISPR-Cas Systems
Chemical Substances	Receptors, Fibroblast Growth Factor
Language	English
Publishing date	2023-01-13
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.1105719
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Article ; Online: Development of CRISPR/Cas13a-based assays for the diagnosis of Schistosomiasis.

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

EBioMedicine

2023 Volume 94, Page(s) 104730

Abstract: 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 ... ...

Abstract	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).
MeSH term(s)	Humans ; Female ; Animals ; Mice ; Sensitivity and Specificity ; Australia ; COVID-19 ; Schistosomiasis/diagnosis ; Schistosoma japonicum ; COVID-19 Testing
Language	English
Publishing date	2023-07-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2023.104730
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Article ; Online: CRISPR screens identify gene targets at breast cancer risk loci.

Genome biology

2023 Volume 24, Issue 1, Page(s) 59

Abstract: Background: Genome-wide association studies (GWAS) have identified > 200 loci associated with breast cancer risk. The majority of candidate causal variants are in non-coding regions and likely modulate cancer risk by regulating gene expression. However, ...

Abstract	Background: Genome-wide association studies (GWAS) have identified > 200 loci associated with breast cancer risk. The majority of candidate causal variants are in non-coding regions and likely modulate cancer risk by regulating gene expression. However, pinpointing the exact target of the association, and identifying the phenotype it mediates, is a major challenge in the interpretation and translation of GWAS. Results: Here, we show that pooled CRISPR screens are highly effective at identifying GWAS target genes and defining the cancer phenotypes they mediate. Following CRISPR mediated gene activation or suppression, we measure proliferation in 2D, 3D, and in immune-deficient mice, as well as the effect on DNA repair. We perform 60 CRISPR screens and identify 20 genes predicted with high confidence to be GWAS targets that promote cancer by driving proliferation or modulating the DNA damage response in breast cells. We validate the regulation of a subset of these genes by breast cancer risk variants. Conclusions: We demonstrate that phenotypic CRISPR screens can accurately pinpoint the gene target of a risk locus. In addition to defining gene targets of risk loci associated with increased breast cancer risk, we provide a platform for identifying gene targets and phenotypes mediated by risk variants.
MeSH term(s)	Animals ; Mice ; Genome-Wide Association Study ; Clustered Regularly Interspaced Short Palindromic Repeats ; Genetic Predisposition to Disease ; Neoplasms ; Phenotype ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2023-03-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-023-02898-w
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Article ; Online: eQTL Colocalization Analyses Identify NTN4 as a Candidate Breast Cancer Risk Gene.

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

American journal of human genetics

2020 Volume 107, Issue 4, Page(s) 778–787

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 ... ...

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.
MeSH term(s)	Alleles ; Animals ; Breast Neoplasms/diagnosis ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Cell Line, Tumor ; Enhancer Elements, Genetic ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genomics/methods ; Heterografts ; Humans ; MCF-7 Cells ; Mice ; Mice, Nude ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Netrins/genetics ; Netrins/metabolism ; Phenotype ; Quantitative Trait Loci ; Risk
Chemical Substances	NTN4 protein, human ; Neoplasm Proteins ; Netrins
Language	English
Publishing date	2020-08-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	219384-x
ISSN	1537-6605 ; 0002-9297
ISSN (online)	1537-6605
ISSN	0002-9297
DOI	10.1016/j.ajhg.2020.08.006
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Article ; Online: CRISPR/Cas9-mediated genome editing of Schistosoma mansoni acetylcholinesterase.

You, Hong / Mayer, Johannes U / Johnston, Rebecca L / Sivakumaran, Haran / Ranasinghe, Shiwanthi / Rivera, Vanessa / Kondrashova, Olga / Koufariotis, Lambros T / Du, Xiaofeng / Driguez, Patrick / French, Juliet D / Waddell, Nicola / Duke, Mary G / Ittiprasert, Wannaporn / Mann, Victoria H / Brindley, Paul J / Jones, Malcolm K / McManus, Donald P

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

2021 Volume 35, Issue 1, Page(s) e21205

Abstract: CRISPR/Cas9-mediated genome editing shows cogent potential for the genetic modification of helminth parasites. We report successful gene knock-in (KI) into the genome of the egg of Schistosoma mansoni by combining CRISPR/Cas9 with single-stranded ... ...

Abstract	CRISPR/Cas9-mediated genome editing shows cogent potential for the genetic modification of helminth parasites. We report successful gene knock-in (KI) into the genome of the egg of Schistosoma mansoni by combining CRISPR/Cas9 with single-stranded oligodeoxynucleotides (ssODNs). We edited the acetylcholinesterase (AChE) gene of S. mansoni targeting two guide RNAs (gRNAs), X5 and X7, located on exon 5 and exon 7 of Smp_154600, respectively. Eggs recovered from livers of experimentally infected mice were transfected by electroporation with a CRISPR/Cas9-vector encoding gRNA X5 or X7 combining with/ without a ssODN donor. Next generation sequencing analysis of reads of amplicon libraries spanning targeted regions revealed that the major modifications induced by CRISPR/Cas9 in the eggs were generated by homology directed repair (HDR). Furthermore, soluble egg antigen from AChE-edited eggs exhibited markedly reduced AChE activity, indicative that programed Cas9 cleavage mutated the AChE gene. Following injection of AChE-edited schistosome eggs into the tail veins of mice, an significantly enhanced Th2 response involving IL-4, -5, -10, and-13 was detected in lung cells and splenocytes in mice injected with X5-KI eggs in comparison to control mice injected with unmutated eggs. A Th2-predominant response, with increased levels of IL-4, -13, and GATA3, also was induced by X5 KI eggs in small intestine-draining mesenteric lymph node cells when the gene-edited eggs were introduced into the subserosa of the ileum of the mice. These findings confirmed the potential and the utility of CRISPR/Cas9-mediated genome editing for functional genomics in schistosomes.
MeSH term(s)	Acetylcholinesterase/genetics ; Acetylcholinesterase/metabolism ; Animals ; CRISPR-Cas Systems ; Female ; Gene Editing ; Helminth Proteins/genetics ; Helminth Proteins/metabolism ; Mice ; Schistosoma mansoni/enzymology ; Schistosoma mansoni/genetics ; Schistosomiasis mansoni/genetics ; Schistosomiasis mansoni/metabolism
Chemical Substances	Helminth Proteins ; Acetylcholinesterase (EC 3.1.1.7)
Language	English
Publishing date	2021-06-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	639186-2
ISSN	1530-6860 ; 0892-6638
ISSN (online)	1530-6860
ISSN	0892-6638
DOI	10.1096/fj.202001745RR
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Zs.A 2266: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Long-range transcriptional regulation of breast cancer genes.

Betts, Joshua A / French, Juliet D / Brown, Melissa A / Edwards, Stacey L

Genes, chromosomes & cancer

2013 Volume 52, Issue 2, Page(s) 113–125

Abstract: Breast cancer is a major health problem and understanding the genetic basis of this disease is crucial for predicting risk and developing effective targeted therapeutics. Several breast cancer predisposing genes have been identified, but mutations in the ...

Abstract	Breast cancer is a major health problem and understanding the genetic basis of this disease is crucial for predicting risk and developing effective targeted therapeutics. Several breast cancer predisposing genes have been identified, but mutations in the coding regions of these genes only accounts for a small proportion of risk. Research now suggests that combinations of multiple non-coding changes in breast cancer susceptibility genes, which cause moderate alterations in gene expression, will be responsible for the remaining inherited risk. These non-coding changes will include variants in proximal and distal transcriptional and post-transcriptional regulatory elements and may affect the levels and function of trans-acting factors, including proteins and RNAs, which act on these elements. Somatic changes in such elements and factors have also been associated with breast cancer progression. With the recent advent of techniques allowing the detection of long-range DNA interactions spanning the human genome, it has become increasingly clear that long-range regulatory elements constitute an important mechanism for gene regulation. Recent studies have identified several such elements that are important for regulating genes involved in breast cancer, raising the possibility that defects in these sequences may contribute to breast cancer predisposition and progression. In this review, we discuss the emerging functions of cis-regulatory elements and a subset of trans-acting factors in breast tumorigenesis. We also discuss some recent progress in our understanding of how dysregulation in these transcriptional components may contribute to breast cancer, and the potential implications for molecular diagnosis, prognosis prediction, and the treatment of this disease.
MeSH term(s)	Breast Neoplasms/genetics ; Female ; Gene Expression Regulation, Neoplastic ; Genetic Predisposition to Disease/genetics ; Humans ; Models, Genetic ; Mutation ; Protein Binding ; Regulatory Elements, Transcriptional/genetics ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors
Language	English
Publishing date	2013-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1018988-9
ISSN	1098-2264 ; 1045-2257
ISSN (online)	1098-2264
ISSN	1045-2257
DOI	10.1002/gcc.22020
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