1
|
Yamamoto S, Kanca O, Wangler MF, Bellen HJ. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans. Nat Rev Genet 2024; 25:46-60. [PMID: 37491400 DOI: 10.1038/s41576-023-00633-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/27/2023]
Abstract
Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.
Collapse
Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
2
|
Cevik S, Zhao P, Zorluer A, Pir MS, Bian W, Kaplan OI. Matching variants for functional characterization of genetic variants. G3 (BETHESDA, MD.) 2023; 13:jkad227. [PMID: 37933433 PMCID: PMC10700107 DOI: 10.1093/g3journal/jkad227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/06/2023] [Indexed: 11/08/2023]
Abstract
Rapid and low-cost sequencing, as well as computer analysis, have facilitated the diagnosis of many genetic diseases, resulting in a substantial rise in the number of disease-associated genes. However, genetic diagnosis of many disorders remains problematic due to the lack of interpretation for many genetic variants, especially missenses, the infeasibility of high-throughput experiments on mammals, and the shortcomings of computational prediction technologies. Additionally, the available mutant databases are not well-utilized. Toward this end, we used Caenorhabditis elegans mutant resources to delineate the functions of eight missense variants (V444I, V517D, E610K, L732F, E817K, H873P, R1105K, and G1205E) and two stop codons (W937stop and Q1434stop), including several matching variants (MatchVar) with human in ciliopathy associated IFT-140 (also called CHE-11)//IFT140 (intraflagellar transport protein 140). Moreover, MatchVars carrying C. elegans mutants, including IFT-140(G680S) and IFT-140(P702A) for the human (G704S) (dbSNP: rs150745099) and P726A (dbSNP: rs1057518064 and a conflicting variation) were created using CRISPR/Cas9. IFT140 is a key component of IFT complex A (IFT-A), which is involved in the retrograde transport of IFT along cilia and the entrance of G protein-coupled receptors into cilia. Functional analysis of all 10 variants revealed that P702A and W937stop, but not others phenocopied the ciliary phenotypes (short cilia, IFT accumulations, mislocalization of membrane proteins, and cilia entry of nonciliary proteins) of the IFT-140 null mutant, indicating that both P702A and W937stop are phenotypic in C. elegans. Our functional data offered experimental support for interpreting human variants, by using ready-to-use mutants carrying MatchVars and generating MatchVars with CRISPR/Cas9.
Collapse
Affiliation(s)
- Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| | - Pei Zhao
- School of Applied Science and Engineering, Fuzhou Institute of Technology, Fuzhou 350014, China
- SunyBiotech Co., Ltd., Fuzhou 35000, China
| | - Atiyye Zorluer
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| | - Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| | | | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| |
Collapse
|
3
|
Brandel-Ankrapp KL, Arey RN. Uncovering novel regulators of memory using C. elegans genetic and genomic analysis. Biochem Soc Trans 2023; 51:161-171. [PMID: 36744642 PMCID: PMC10518207 DOI: 10.1042/bst20220455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/20/2022] [Accepted: 01/19/2023] [Indexed: 02/07/2023]
Abstract
How organisms learn and encode memory is an outstanding question in neuroscience research. Specifically, how memories are acquired and consolidated at the level of molecular and gene pathways remains unclear. In addition, memory is disrupted in a wide variety of neurological disorders; therefore, discovering molecular regulators of memory may reveal therapeutic targets for these disorders. C. elegans are an excellent model to uncover molecular and genetic regulators of memory. Indeed, the nematode's invariant neuronal lineage, fully mapped genome, and conserved associative behaviors have allowed the development of a breadth of genetic and genomic tools to examine learning and memory. In this mini-review, we discuss novel and exciting genetic and genomic techniques used to examine molecular and genetic underpinnings of memory from the level of the whole-worm to tissue-specific and cell-type specific approaches with high spatiotemporal resolution.
Collapse
Affiliation(s)
- Katie L. Brandel-Ankrapp
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, U.S.A
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, U.S.A
| | - Rachel N. Arey
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, U.S.A
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, U.S.A
| |
Collapse
|
4
|
Ma J, Ma X, Lin K, Huang R, Bi X, Ming C, Li L, Li X, Li G, Zhao L, Yang T, Gao Y, Zhang T. Genetic screening of a Chinese cohort of children with hearing loss using a next-generation sequencing panel. Hum Genomics 2023; 17:1. [PMID: 36597107 PMCID: PMC9811745 DOI: 10.1186/s40246-022-00449-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND At present, the hereditary hearing loss homepage, ( https://hereditaryhearingloss.org/ ), includes 258 deafness genes and more than 500 genes that have been reported to cause deafness. With few exceptions, the region-specific distributions are unclear for many of the identified variants and genes. METHODS Here, we used a custom capture panel to perform targeted sequencing of 518 genes in a cohort of 879 deaf Chinese probands who lived in Yunnan. Mutation sites of the parents were performed by high-throughput sequencing and validated by Sanger sequencing. RESULTS The ratio of male to female patients was close to 1:1 (441:438) and the age of onset was mainly under six. Most patients (93.5%) were diagnosed with moderate to severe deafness. Four hundred and twenty-eight patients had variants in a deafness gene, with a detection rate of 48.7%. Pathogenic variants were detected in 98 genes and a number of these were recurrent within the cohort. However, many of the variants were rarely observed in the cohort. In accordance with the American College of Medical Genetics and Genomics, pathogenic, likely pathogenic and variants of uncertain significance accounted for 34.3%, 19.3% and 46.4% of all detected variants, respectively. The most common genes included GJB2, SLC26A4, MYO15A, MYO7A, TMC1, CDH23, USH2A and WFS1, which contained variants in more than ten cases. The two genes with the highest mutation frequency were GJB2 and SLC26A4, which accounted for 28.5% (122/428) of positive patients. We showed that more than 60.3% of coding variants were rare and novel. Of the variants that we detected, 80.0% were in coding regions, 17.9% were in introns and 2.1% were copy number variants. CONCLUSION The common mutation genes and loci detected in this study were different from those detected in other regions or ethnic groups, which suggested that genetic screening or testing programs for deafness should be formulated in accordance with the genetic characteristics of the region.
Collapse
Affiliation(s)
- Jing Ma
- grid.415549.8Yunnan Key Laboratory of Children’s Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children’s Hospital, Kunming, China
| | - Xiuli Ma
- grid.415549.8Yunnan Key Laboratory of Children’s Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children’s Hospital, Kunming, China ,grid.415549.8Yunnan Institute of Pediatrics, Kunming Children’s Hospital, Kunming, China
| | - Ken Lin
- grid.415549.8Yunnan Key Laboratory of Children’s Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children’s Hospital, Kunming, China
| | - Rui Huang
- grid.415549.8Yunnan Key Laboratory of Children’s Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children’s Hospital, Kunming, China
| | - Xianyun Bi
- grid.415549.8Yunnan Key Laboratory of Children’s Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children’s Hospital, Kunming, China
| | - Cheng Ming
- grid.415549.8Yunnan Key Laboratory of Children’s Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children’s Hospital, Kunming, China
| | - Li Li
- grid.415549.8Yunnan Institute of Pediatrics, Kunming Children’s Hospital, Kunming, China
| | - Xia Li
- grid.415549.8Yunnan Key Laboratory of Children’s Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children’s Hospital, Kunming, China
| | - Guo Li
- grid.415549.8Yunnan Key Laboratory of Children’s Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children’s Hospital, Kunming, China
| | - Liping Zhao
- grid.415549.8Yunnan Key Laboratory of Children’s Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children’s Hospital, Kunming, China
| | - Tao Yang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yingqin Gao
- Yunnan Key Laboratory of Children's Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming, China.
| | - Tiesong Zhang
- Yunnan Key Laboratory of Children's Major Disease Research, Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming, China.
| |
Collapse
|
5
|
Wu X, Nagasawa S, Muto K, Ueda M, Suzuki C, Abe T, Higashitani A. Mitochonic Acid 5 Improves Duchenne Muscular Dystrophy and Parkinson's Disease Model of Caenorhabditis elegans. Int J Mol Sci 2022; 23:9572. [PMID: 36076995 PMCID: PMC9455831 DOI: 10.3390/ijms23179572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/09/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022] Open
Abstract
Mitochonic Acid 5 (MA-5) enhances mitochondrial ATP production, restores fibroblasts from mitochondrial disease patients and extends the lifespan of the disease model "Mitomouse". Additionally, MA-5 interacts with mitofilin and modulates the mitochondrial inner membrane organizing system (MINOS) in mammalian cultured cells. Here, we used the nematode Caenorhabditis elegans to investigate whether MA-5 improves the Duchenne muscular dystrophy (DMD) model. Firstly, we confirmed the efficient penetration of MA-5 in the mitochondria of C. elegans. MA-5 also alleviated symptoms such as movement decline, muscular tone, mitochondrial fragmentation and Ca2+ accumulation of the DMD model. To assess the effect of MA-5 on mitochondria perturbation, we employed a low concentration of rotenone with or without MA-5. MA-5 significantly suppressed rotenone-induced mitochondria reactive oxygen species (ROS) increase, mitochondrial network fragmentation and nuclear destruction in body wall muscles as well as endogenous ATP levels decline. In addition, MA-5 suppressed rotenone-induced degeneration of dopaminergic cephalic (CEP) neurons seen in the Parkinson's disease (PD) model. Furthermore, the application of MA-5 reduced mitochondrial swelling due to the immt-1 null mutation. These results indicate that MA-5 has broad mitochondrial homing and MINOS stabilizing activity in metazoans and may be a therapeutic agent for these by ameliorating mitochondrial dysfunction in DMD and PD.
Collapse
Affiliation(s)
- Xintong Wu
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Satoi Nagasawa
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Kasumi Muto
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Maiko Ueda
- Biomedical Research Core, Tohoku University Graduate School of Medicine, Sendai 980-0872, Japan
| | - Chitose Suzuki
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai 980-0872, Japan
| | - Takaaki Abe
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai 980-0872, Japan
| | | |
Collapse
|
6
|
Weinkove D, Zavagno G. Applying C. elegans to the Industrial Drug Discovery Process to Slow Aging. FRONTIERS IN AGING 2022; 2:740582. [PMID: 35821999 PMCID: PMC9261450 DOI: 10.3389/fragi.2021.740582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/29/2021] [Indexed: 01/29/2023]
Abstract
The increase in our molecular understanding of the biology of aging, coupled with a recent surge in investment, has led to the formation of several companies developing pharmaceuticals to slow aging. Research using the tiny nematode worm Caenorhabditis elegans was the first to show that mutations in single genes can extend lifespan, and subsequent research has shown that this model organism is uniquely suited to testing interventions to slow aging. Yet, with a few notable exceptions, C. elegans is not in the standard toolkit of longevity companies. Here we discuss the paths to overcome the barriers to using C. elegans in industrial drug discovery. We address the predictive power of C. elegans for human aging, how C. elegans research can be applied to specific challenges in the typical drug discovery pipeline, and how standardised and quantitative assays will help C. elegans fulfil its potential in the biotech and pharmaceutical industry. We argue that correct application of this model and its knowledge base will significantly accelerate progress to slow human aging.
Collapse
Affiliation(s)
- David Weinkove
- Department of Biosciences, Durham University, Durham, United Kingdom.,Magnitude Biosciences Ltd., NETpark Plexus, Sedgefield, United Kingdom
| | - Giulia Zavagno
- Department of Biosciences, Durham University, Durham, United Kingdom.,Magnitude Biosciences Ltd., NETpark Plexus, Sedgefield, United Kingdom
| |
Collapse
|
7
|
Wittes J, Greenwald I. Genetic analysis of DAF-18/PTEN missense mutants for the ability to maintain quiescence of the somatic gonad and germ line in Caenorhabditis elegans dauer larvae. G3 (BETHESDA, MD.) 2022; 12:jkac093. [PMID: 35451467 PMCID: PMC9157151 DOI: 10.1093/g3journal/jkac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022]
Abstract
The mammalian tumor suppressor PTEN has well-established lipid phosphatase and protein phosphatase activities. DAF-18, the Caenorhabditis elegans ortholog of PTEN, has a high degree of conservation in the catalytic domain, and human PTEN complements a null allele of daf-18, suggesting conserved protein function. Insights gleaned from studies of mammalian PTEN have been applied to studies of DAF-18 in C. elegans, including predicted enzymatic properties of mutants. Here, we characterize DAF-18 missense mutants previously treated as selectively disrupting either protein or lipid phosphatase activity in genetic assays to connect distinct phenotypes to specific enzymatic activities of DAF-18/PTEN. We analyze the ability of these mutants to maintain quiescence of the somatic gonad and germ line in dauer larvae, a state of diapause during which development is suspended. We show that transgenes expressing either the putative lipid phosphatase-deficient or putative protein phosphatase-deficient form fail to complement a daf-18 null allele, and that the corresponding homozygous endogenous missense mutant alleles fail to maintain developmental quiescence. We also show that the endogenous daf-18 missense alleles fail to complement each other, suggesting that one or both of the missense forms are not activity-selective. Furthermore, homozygous daf-18 missense mutants have a more severe phenotype than a daf-18 null mutant, suggesting the presence of functionally compromised mutant DAF-18 is more deleterious than the absence of DAF-18. We discuss how these genetic properties complicate the interpretation of genetic assays to associate specific enzymatic activities with specific phenotypes.
Collapse
Affiliation(s)
- Julia Wittes
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| |
Collapse
|
8
|
Kepler LD, McDiarmid TA, Rankin CH. Rapid assessment of the temporal function and phenotypic reversibility of neurodevelopmental disorder risk genes in Caenorhabditis elegans. Dis Model Mech 2022; 15:dmm049359. [PMID: 35363276 PMCID: PMC9092656 DOI: 10.1242/dmm.049359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
Recent studies have indicated that some phenotypes caused by decreased function of select neurodevelopmental disorder (NDD) risk genes can be reversed by restoring gene function in adulthood. However, few of the hundreds of risk genes have been assessed for adult phenotypic reversibility. We developed a strategy to rapidly assess the temporal requirements and phenotypic reversibility of NDD risk gene orthologs using a conditional protein degradation system and machine-vision phenotypic profiling in Caenorhabditis elegans. We measured how degrading and re-expressing orthologs of EBF3, BRN3A and DYNC1H1 at multiple periods throughout development affect 30 morphological, locomotor, sensory and learning phenotypes. We found that phenotypic reversibility was possible for each gene studied. However, the temporal requirements of gene function and degree of rescue varied by gene and phenotype. This work highlights the critical need to assess multiple windows of degradation and re-expression and a large number of phenotypes to understand the many roles a gene can have across the lifespan. This work also demonstrates the benefits of using a high-throughput model system to prioritize NDD risk genes for re-expression studies in other organisms.
Collapse
Affiliation(s)
- Lexis D. Kepler
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Troy A. McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
- Department of Genome Sciences, University of Washington School of Medicine, Foege Building S-250 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Catharine H. Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
- Department of Psychology, University of British Columbia, 2136 West Mall, Vancouver, BC V6T 1Z4, Canada
| |
Collapse
|
9
|
Macaisne N, Touzon MS, Rajkovic A, Yanowitz JL. Modeling primary ovarian insufficiency-associated loci in C. elegans identifies novel pathogenic allele of MSH5. J Assist Reprod Genet 2022; 39:1255-1260. [PMID: 35437714 DOI: 10.1007/s10815-022-02494-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/11/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE In women under the age of 40, primary ovarian insufficiency (POI) is a devastating diagnosis with significant prevalence of 1-4% (Rajkovic and Pangas, Semin Reprod Med. 35(3):231-40, 2017). POI is characterized by amenorrhea with elevated levels of follicle stimulating hormone (FSH) and reduced estrogen levels, mimicking the menopausal state. Genetic determinants account for just over 10% of POI cases, yet determining whether particular single nucleotide polymorphisms (SNPs) are pathogenic is challenging. METHODS We performed exome sequencing on a cohort of women with POI. CRISPR mutagenesis was employed to create a mutation in a conserved amino acid in the nematode protein. Functional relevance was assessed by analysis of bivalents and aberrant DNA morphologies in diakinesis nuclei. RESULTS We identified a nonsynonymous c.C1051G; p.R351G variant, in a conserved region of the MSH5 protein. Mutation of this conserved amino acid in the C. elegans homolog, msh-5, revealed defective crossover outcomes in the homozygous and hemizygous states. CONCLUSIONS These studies further implicate MSH5 as a POI gene and c.C1051G; p.R351G variant as likely playing a functional role in mammalian meiosis. This approach also highlights the ability of model organisms, such as C. elegans, to rapidly and inexpensively identify alleles of interest for further studies in mammalian models.
Collapse
Affiliation(s)
- Nicolas Macaisne
- Magee-Womens Research Institute, Pittsburgh, PA, 15217, USA.,Université de Paris, CNRS, Institut Jacques Monod, 75013, Paris, France
| | - Maria Sol Touzon
- Endocrinology Department, Research Unit Garrahan Consejo Nacional de Investigaciones Cientificas Y Tecnologicas, Hospital de Pediatr a Garrahan, 1245, Ciudad Autonoma de Buenos Aires, Argentina
| | - Aleksander Rajkovic
- Department of Pathology, Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94158, USA
| | - Judith L Yanowitz
- Magee-Womens Research Institute, Pittsburgh, PA, 15217, USA. .,Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA. .,Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA. .,Department of Microbiology and Molecular Genetics and the Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA. .,Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA.
| |
Collapse
|
10
|
Kropp PA, Bauer R, Zafra I, Graham C, Golden A. Caenorhabditis elegans for rare disease modeling and drug discovery: strategies and strengths. Dis Model Mech 2021; 14:dmm049010. [PMID: 34370008 PMCID: PMC8380043 DOI: 10.1242/dmm.049010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although nearly 10% of Americans suffer from a rare disease, clinical progress in individual rare diseases is severely compromised by lack of attention and research resources compared to common diseases. It is thus imperative to investigate these diseases at their most basic level to build a foundation and provide the opportunity for understanding their mechanisms and phenotypes, as well as potential treatments. One strategy for effectively and efficiently studying rare diseases is using genetically tractable organisms to model the disease and learn about the essential cellular processes affected. Beyond investigating dysfunctional cellular processes, modeling rare diseases in simple organisms presents the opportunity to screen for pharmacological or genetic factors capable of ameliorating disease phenotypes. Among the small model organisms that excel in rare disease modeling is the nematode Caenorhabditis elegans. With a staggering breadth of research tools, C. elegans provides an ideal system in which to study human disease. Molecular and cellular processes can be easily elucidated, assayed and altered in ways that can be directly translated to humans. When paired with other model organisms and collaborative efforts with clinicians, the power of these C. elegans studies cannot be overstated. This Review highlights studies that have used C. elegans in diverse ways to understand rare diseases and aid in the development of treatments. With continuing and advancing technologies, the capabilities of this small round worm will continue to yield meaningful and clinically relevant information for human health.
Collapse
Affiliation(s)
| | | | | | | | - Andy Golden
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
11
|
Reiss AP, Rankin CH. Gaining an understanding of behavioral genetics through studies of foraging in Drosophila and learning in C. elegans. J Neurogenet 2021; 35:119-131. [PMID: 34151727 DOI: 10.1080/01677063.2021.1928113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The pursuit of understanding behavior has led to investigations of how genes, the environment, and the nervous system all work together to produce and influence behavior, giving rise to a field of research known as behavioral neurogenetics. This review focuses on the research journeys of two pioneers of aspects of behavioral neurogenetic research: Dr. Marla Sokolowski and Dr. Catharine Rankin as examples of how different approaches have been used to understand relationships between genes and behavior. Marla Sokolowski's research is centered around the discovery and analysis of foraging, a gene responsible for the natural behavioral polymorphism of Drosophila melanogaster larvae foraging behavior. Catharine Rankin's work began with demonstrating the ability to learn in Caenorhabditis elegans and then setting out to investigate the mechanisms underlying the "simplest" form of learning, habituation. Using these simple invertebrate organisms both investigators were able to perform in-depth dissections of behavior at genetic and molecular levels. By exploring their research and highlighting their findings we present ways their work has furthered our understanding of behavior and contributed to the field of behavioral neurogenetics.
Collapse
Affiliation(s)
- Aaron P Reiss
- Department of Psychology, University of British Columbia, Vancouver, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | - Catharine H Rankin
- Department of Psychology, University of British Columbia, Vancouver, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| |
Collapse
|
12
|
Vicencio J, Cerón J. A Living Organism in your CRISPR Toolbox: Caenorhabditis elegans Is a Rapid and Efficient Model for Developing CRISPR-Cas Technologies. CRISPR J 2021; 4:32-42. [PMID: 33538637 DOI: 10.1089/crispr.2020.0103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Cas9 nuclease from Streptococcus pyogenes (SpCas9) is the most popular enzyme for CRISPR technologies. However, considering the wide diversity of microorganisms (discovered and still unknown), a massive number of CRISPR effectors are being and will be identified and characterized in the search of optimal Cas variants for each of the many applications of CRISPR. In this context, a versatile and efficient multicellular system for CRISPR editing such as Caenorhabditis elegans would be of great help in the development of these effectors. Here, we highlight the benefits of using C. elegans for the rapid evaluation of new CRISPR effectors, and for optimizing CRISPR efficiency in animals in several ways such as by modulating the balance between repair pathways, modifying chromatin accessibility, or controlling the expression and activity of nucleases and guide RNAs.
Collapse
Affiliation(s)
- Jeremy Vicencio
- Modeling human diseases in C. elegans Group, Genes, Disease and Therapy Program, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Julián Cerón
- Modeling human diseases in C. elegans Group, Genes, Disease and Therapy Program, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| |
Collapse
|
13
|
Lange KI, Tsiropoulou S, Kucharska K, Blacque OE. Interpreting the pathogenicity of Joubert syndrome missense variants in Caenorhabditis elegans. Dis Model Mech 2021; 14:dmm.046631. [PMID: 33234550 PMCID: PMC7859701 DOI: 10.1242/dmm.046631] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/13/2020] [Indexed: 12/26/2022] Open
Abstract
Ciliopathies are inherited disorders caused by defects in motile and non-motile (primary) cilia. Ciliopathy syndromes and associated gene variants are often highly pleiotropic and represent exemplars for interrogating genotype-phenotype correlations. Towards understanding disease mechanisms in the context of ciliopathy mutations, we have used a leading model organism for cilia and ciliopathy research, Caenorhabditis elegans, together with gene editing, to characterise two missense variants (P74S and G155S) in mksr-2/B9D2 associated with Joubert syndrome (JBTS). B9D2 functions within the Meckel syndrome (MKS) module at the ciliary base transition zone (TZ) compartment and regulates the molecular composition and sensory/signalling functions of the cilium. Quantitative assays of cilium/TZ structure and function, together with knock-in reporters, confirm that both variant alleles are pathogenic in worms. G155S causes a more severe overall phenotype and disrupts endogenous MKSR-2 organisation at the TZ. Recapitulation of the patient biallelic genotype shows that compound heterozygous worms phenocopy worms homozygous for P74S. The P74S and G155S alleles also reveal evidence of a very close functional association between the B9D2-associated B9 complex and MKS-2/TMEM216. Together, these data establish C. elegans as a model for interpreting JBTS mutations and provide further insight into MKS module organisation. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Karen I Lange
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Katarzyna Kucharska
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
14
|
Hahnel SR, Dilks CM, Heisler I, Andersen EC, Kulke D. Caenorhabditis elegans in anthelmintic research - Old model, new perspectives. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:237-248. [PMID: 33249235 PMCID: PMC7704361 DOI: 10.1016/j.ijpddr.2020.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/13/2022]
Abstract
For more than four decades, the free-living nematode Caenorhabditis elegans has been extensively used in anthelmintic research. Classic genetic screens and heterologous expression in the C. elegans model enormously contributed to the identification and characterization of molecular targets of all major anthelmintic drug classes. Although these findings provided substantial insights into common anthelmintic mechanisms, a breakthrough in the treatment and control of parasitic nematodes is still not in sight. Instead, we are facing increasing evidence that the enormous diversity within the phylum Nematoda cannot be recapitulated by any single free-living or parasitic species and the development of novel broad-spectrum anthelmintics is not be a simple goal. In the present review, we summarize certain milestones and challenges of the C. elegans model with focus on drug target identification, anthelmintic drug discovery and identification of resistance mechanisms. Furthermore, we present new perspectives and strategies on how current progress in C. elegans research will support future anthelmintic research.
Collapse
Affiliation(s)
| | - Clayton M Dilks
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
| | | | - Erik C Andersen
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
| | | |
Collapse
|
15
|
Hunt PR, Camacho JA, Sprando RL. Caenorhabditis elegans for predictive toxicology. CURRENT OPINION IN TOXICOLOGY 2020. [DOI: 10.1016/j.cotox.2020.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
16
|
McDiarmid TA, Au V, Moerman DG, Rankin CH. Peel-1 negative selection promotes screening-free CRISPR-Cas9 genome editing in Caenorhabditis elegans. PLoS One 2020; 15:e0238950. [PMID: 32960926 PMCID: PMC7508457 DOI: 10.1371/journal.pone.0238950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023] Open
Abstract
Improved genome engineering methods that enable automation of large and precise edits are essential for systematic investigations of genome function. We adapted peel-1 negative selection to an optimized Dual-Marker Selection (DMS) cassette protocol for CRISPR-Cas9 genome engineering in Caenorhabditis elegans and observed robust increases in multiple measures of efficiency that were consistent across injectors and four genomic loci. The use of Peel-1-DMS selection killed animals harboring transgenes as extrachromosomal arrays and spared genome-edited integrants, often circumventing the need for visual screening to identify genome-edited animals. To demonstrate the applicability of the approach, we created deletion alleles in the putative proteasomal subunit pbs-1 and the uncharacterized gene K04F10.3 and used machine vision to automatically characterize their phenotypic profiles, revealing homozygous essential and heterozygous behavioral phenotypes. These results provide a robust and scalable approach to rapidly generate and phenotype genome-edited animals without the need for screening or scoring by eye.
Collapse
Affiliation(s)
- Troy A. McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vinci Au
- Department of Zoology, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Donald G. Moerman
- Department of Zoology, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Catharine H. Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychology, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
17
|
Kepler LD, McDiarmid TA, Rankin CH. Habituation in high-throughput genetic model organisms as a tool to investigate the mechanisms of neurodevelopmental disorders. Neurobiol Learn Mem 2020; 171:107208. [DOI: 10.1016/j.nlm.2020.107208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 03/02/2020] [Indexed: 10/24/2022]
|
18
|
Wong WR, Brugman KI, Maher S, Oh JY, Howe K, Kato M, Sternberg PW. Autism-associated missense genetic variants impact locomotion and neurodevelopment in Caenorhabditis elegans. Hum Mol Genet 2020; 28:2271-2281. [PMID: 31220273 DOI: 10.1093/hmg/ddz051] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 01/17/2023] Open
Abstract
Autism spectrum disorder (ASD) involves thousands of alleles in over 850 genes, but the current functional inference tools are not sufficient to predict phenotypic changes. As a result, the causal relationship of most of these genetic variants in the pathogenesis of ASD has not yet been demonstrated and an experimental method prioritizing missense alleles for further intensive analysis is crucial. For this purpose, we have designed a pipeline that uses Caenorhabditis elegans as a genetic model to screen for phenotype-changing missense alleles inferred from human ASD studies. We identified highly conserved human ASD-associated missense variants in their C. elegans orthologs, used a CRISPR/Cas9-mediated homology-directed knock-in strategy to generate missense mutants and analyzed their impact on behaviors and development via several broad-spectrum assays. All tested missense alleles were predicted to perturb protein function, but we found only 70% of them showed detectable phenotypic changes in morphology, locomotion or fecundity. Our findings indicate that certain missense variants in the C. elegans orthologs of human CACNA1D, CHD7, CHD8, CUL3, DLG4, GLRA2, NAA15, PTEN, SYNGAP1 and TPH2 impact neurodevelopment and movement functions, elevating these genes as candidates for future study into ASD. Our approach will help prioritize functionally important missense variants for detailed studies in vertebrate models and human cells.
Collapse
Affiliation(s)
- Wan-Rong Wong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Katherine I Brugman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shayda Maher
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jun Young Oh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Mihoko Kato
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| |
Collapse
|
19
|
McDiarmid TA, Belmadani M, Liang J, Meili F, Mathews EA, Mullen GP, Hendi A, Wong WR, Rand JB, Mizumoto K, Haas K, Pavlidis P, Rankin CH. Systematic phenomics analysis of autism-associated genes reveals parallel networks underlying reversible impairments in habituation. Proc Natl Acad Sci U S A 2020; 117:656-667. [PMID: 31754030 PMCID: PMC6968627 DOI: 10.1073/pnas.1912049116] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A major challenge facing the genetics of autism spectrum disorders (ASDs) is the large and growing number of candidate risk genes and gene variants of unknown functional significance. Here, we used Caenorhabditis elegans to systematically functionally characterize ASD-associated genes in vivo. Using our custom machine vision system, we quantified 26 phenotypes spanning morphology, locomotion, tactile sensitivity, and habituation learning in 135 strains each carrying a mutation in an ortholog of an ASD-associated gene. We identified hundreds of genotype-phenotype relationships ranging from severe developmental delays and uncoordinated movement to subtle deficits in sensory and learning behaviors. We clustered genes by similarity in phenomic profiles and used epistasis analysis to discover parallel networks centered on CHD8•chd-7 and NLGN3•nlg-1 that underlie mechanosensory hyperresponsivity and impaired habituation learning. We then leveraged our data for in vivo functional assays to gauge missense variant effect. Expression of wild-type NLG-1 in nlg-1 mutant C. elegans rescued their sensory and learning impairments. Testing the rescuing ability of conserved ASD-associated neuroligin variants revealed varied partial loss of function despite proper subcellular localization. Finally, we used CRISPR-Cas9 auxin-inducible degradation to determine that phenotypic abnormalities caused by developmental loss of NLG-1 can be reversed by adult expression. This work charts the phenotypic landscape of ASD-associated genes, offers in vivo variant functional assays, and potential therapeutic targets for ASD.
Collapse
Affiliation(s)
- Troy A McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Manuel Belmadani
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joseph Liang
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Fabian Meili
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Eleanor A Mathews
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Gregory P Mullen
- Biology Program, Oklahoma City University, Oklahoma City, OK 73106
| | - Ardalan Hendi
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Wan-Rong Wong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - James B Rand
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Kota Mizumoto
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kurt Haas
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Paul Pavlidis
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Catharine H Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada;
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| |
Collapse
|
20
|
|
21
|
Abstract
Using neXtProt release 2019-01-11, we manually curated a list of 1837 functionally uncharacterized human proteins. Using OrthoList 2, we found that 270 of them have homologues in Caenorhabditis elegans, including 60 with a one-to-one orthology relationship. According to annotations extracted from WormBase, the vast majority of these 60 worm genes have RNAi experimental data or mutant alleles, but manual inspection shows that only 15% have phenotypes that could be interpreted in terms of a specific function. One third of the worm orthologs have protein-protein interaction data, and two of these interactions are conserved in humans. The combination of phenotypic, protein-protein interaction, and gene expression data provides functional hypotheses for 8 uncharacterized human proteins. Experimental validation in human or orthologs is necessary before they can be considered for annotation.
Collapse
Affiliation(s)
- Paula Duek
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland
| | - Lydie Lane
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland
| |
Collapse
|
22
|
CRISPR editing of sftb-1/SF3B1 in Caenorhabditis elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing. PLoS Genet 2019; 15:e1008464. [PMID: 31634348 PMCID: PMC6830814 DOI: 10.1371/journal.pgen.1008464] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/05/2019] [Accepted: 10/05/2019] [Indexed: 12/23/2022] Open
Abstract
SF3B1 is the most frequently mutated splicing factor in cancer. Mutations in SF3B1 likely confer clonal advantages to cancer cells but they may also confer vulnerabilities that can be therapeutically targeted. SF3B1 cancer mutations can be maintained in homozygosis in C. elegans, allowing synthetic lethal screens with a homogeneous population of animals. These mutations cause alternative splicing (AS) defects in C. elegans, as it occurs in SF3B1-mutated human cells. In a screen, we identified RNAi of U2 snRNP components that cause synthetic lethality with sftb-1/SF3B1 mutations. We also detected synthetic interactions between sftb-1 mutants and cancer-related mutations in uaf-2/U2AF1 or rsp-4/SRSF2, demonstrating that this model can identify interactions between mutations that are mutually exclusive in human tumors. Finally, we have edited an SFTB-1 domain to sensitize C. elegans to the splicing modulators pladienolide B and herboxidiene. Thus, we have established a multicellular model for SF3B1 mutations amenable for high-throughput genetic and chemical screens.
Collapse
|
23
|
Meneely PM, Dahlberg CL, Rose JK. Working with Worms:Caenorhabditis elegansas a Model Organism. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/cpet.35] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | | | - Jacqueline K. Rose
- Behavioral Neuroscience Program, Department of PsychologyWestern Washington University Bellingham Washington
| |
Collapse
|
24
|
Vicencio J, Martínez-Fernández C, Serrat X, Cerón J. Efficient Generation of Endogenous Fluorescent Reporters by Nested CRISPR in Caenorhabditis elegans. Genetics 2019; 211:1143-1154. [PMID: 30696716 PMCID: PMC6456308 DOI: 10.1534/genetics.119.301965] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/25/2019] [Indexed: 12/27/2022] Open
Abstract
CRISPR-based genome-editing methods in model organisms are evolving at an extraordinary speed. Whereas the generation of deletion or missense mutants is quite straightforward, the production of endogenous fluorescent reporters is more challenging. We have developed Nested CRISPR, a cloning-free ribonucleoprotein-driven method that robustly produces endogenous fluorescent reporters with EGFP, mCherry or wrmScarlet in Caenorhabditis elegans This method is based on the division of the fluorescent protein (FP) sequence in three fragments. In the first step, single-stranded DNA (ssDNA) donors (≤200 bp) are used to insert the 5' and 3' fragments of the FP in the locus of interest. In the second step, these sequences act as homology regions for homology-directed repair using a double-stranded DNA (dsDNA) donor (PCR product) containing the middle fragment, thus completing the FP sequence. In Nested CRISPR, the first step involving ssDNA donors is a well-established method that yields high editing efficiencies, and the second step is reliable because it uses universal CRISPR RNAs (crRNAs) and PCR products. We have also used Nested CRISPR in a nonessential gene to produce a deletion mutant in the first step and a transcriptional reporter in the second step. In the search for modifications to optimize the method, we tested synthetic single guide RNAs (sgRNAs), but did not observe a significant increase in efficiency. To streamline the approach, we combined all step 1 and step 2 reagents in a single injection and were successful in three of five loci tested with editing efficiencies of up to 20%. Finally, we discuss the prospects of this method in the future.
Collapse
Affiliation(s)
- Jeremy Vicencio
- Genes, Diseases, and Therapies Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Carmen Martínez-Fernández
- Genes, Diseases, and Therapies Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Xènia Serrat
- Genes, Diseases, and Therapies Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Julián Cerón
- Genes, Diseases, and Therapies Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| |
Collapse
|
25
|
Memar N, Schiemann S, Hennig C, Findeis D, Conradt B, Schnabel R. Twenty million years of evolution: The embryogenesis of four Caenorhabditis species are indistinguishable despite extensive genome divergence. Dev Biol 2019; 447:182-199. [DOI: 10.1016/j.ydbio.2018.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022]
|
26
|
Hmeljak J, Justice MJ. From gene to treatment: supporting rare disease translational research through model systems. Dis Model Mech 2019; 12:12/2/dmm039271. [PMID: 30819728 PMCID: PMC6398488 DOI: 10.1242/dmm.039271] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Individual rare diseases may affect only a few people, making them difficult to recognize, diagnose or treat by studying humans alone. Instead, model organisms help to validate genetic associations, understand functional pathways and develop therapeutic interventions for rare diseases. In this Editorial, we point to the key parameters in face, construct, predictive and target validity for accurate disease modelling, with special emphasis on rare disease models. Raising the experimental standards for disease models will enhance successful clinical translation and benefit rare disease research. Summary: This Editorial discusses the importance of model systems with accurate face, construct, target and predictive validity for rare disease research.
Collapse
Affiliation(s)
- Julija Hmeljak
- Disease Models & Mechanisms, The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
| | - Monica J Justice
- Program in Genetics and Genome Biology, The Hospital for Sick Children, and Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5G 0A4 Canada
| |
Collapse
|