1
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Meyer KJ, Fingert JH, Anderson MG. Lack of evidence for GWAS signals of exfoliation glaucoma working via monogenic loss-of-function mutation in the nearest gene. Hum Mol Genet 2024:ddae088. [PMID: 38770563 DOI: 10.1093/hmg/ddae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/29/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
PURPOSE Exfoliation syndrome (XFS) is a systemic disease of elastin-rich tissues involving a deposition of fibrillar exfoliative material (XFM) in the anterior chamber of the eye, which can promote glaucoma. The purpose of this study was to create mice with CRISPR/Cas9-induced variations in candidate genes identified from human genome-wide association studies (GWAS) and screen them for indices of XFS. METHODS Variants predicted to be deleterious were sought in the Agpat1, Cacna1a, Loxl1, Pomp, Rbms3, Sema6a, and Tlcd5 genes of C57BL/6J mice using CRISPR/Cas9-based gene editing. Strains were phenotyped by slit-lamp, SD-OCT imaging, and fundus exams at 1-5 mos of age. Smaller cohorts of 12-mos-old mice were also studied. RESULTS Deleterious variants were identified in six targets; Pomp was recalcitrant to targeting. Multiple alleles of some targets were isolated, yielding 12 strains. Across all genotypes and ages, 277 mice were assessed by 902 slit-lamp exams, 928 SD-OCT exams, and 358 fundus exams. Homozygosity for Agpat1 or Cacna1a mutations led to early lethality; homozygosity for Loxl1 mutations led to pelvic organ prolapse, preventing aging. Loxl1 homozygotes exhibited a conjunctival phenotype of potential relevance to XFS. Multiple other genotype-specific phenotypes were variously identified. XFM was not observed in any mice. CONCLUSIONS This study did not detect XFM in any of the strains. This may have been due to species-specific differences, background dependence, or insufficient aging. Alternatively, it is possible that the current candidates, selected based on proximity to GWAS signals, are not effectors acting via monogenic loss-of-function mechanisms.
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Affiliation(s)
- Kacie J Meyer
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Rd, Iowa City, IA 52242, United States
- Institute for Vision Research, University of Iowa, 375 Newton Rd, Iowa City, IA 52242, United States
| | - John H Fingert
- Institute for Vision Research, University of Iowa, 375 Newton Rd, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, United States
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Rd, Iowa City, IA 52242, United States
- Institute for Vision Research, University of Iowa, 375 Newton Rd, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, United States
- Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, 601 Hwy 6 W, Iowa City, IA 52246, United States
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2
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De Pablo-Moreno JA, Miguel-Batuecas A, Rodríguez-Merchán EC, Liras A. Treatment of congenital coagulopathies, from biologic to biotechnological drugs: The relevance of gene editing (CRISPR/Cas). Thromb Res 2023; 231:99-111. [PMID: 37839151 DOI: 10.1016/j.thromres.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/09/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023]
Abstract
Congenital coagulopathies have, throughout the history of medicine, been a focus of scientific study and of great interest as they constitute an alteration of one of the most important and conserved pathways of evolution. The first therapeutic strategies developed to address them were aimed at restoring the blood components lost during hemorrhage by administering whole blood or plasma. Later on, the use of cryoprecipitates was a significant breakthrough as it made it possible to decrease the volumes of blood infused. In the 1970' and 80', clotting factor concentrates became the treatment and, from the 1990's to the present day, recombinant factors -with increasingly longer half-lives- have taken over as the treatment of choice for certain coagulopathies in a seamless yet momentous transition from biological to biotechnological drugs. The beginning of this century, however, saw the emergence of new advanced (gene and cell) treatments, which are currently transforming the therapeutic landscape. The possibility to use cells and viruses as well as specific or bispecific antibodies as medicines is likely to spark a revolution in the world of pharmacology where therapies will be individualized and have long-term effects. Specifically, attention is nowadays focused on the development of gene editing strategies, chiefly those based on CRISPR/Cas technology. Rare coagulopathies such as hemophilia A and B, or even ultra-rare ones such as factor V deficiency, could be among those deriving the greatest benefit from these new developments.
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Affiliation(s)
- Juan A De Pablo-Moreno
- Department of Genetic, Physiology and Microbiology, Biology School, Complutense University of Madrid, Spain
| | - Andrea Miguel-Batuecas
- Department of Genetic, Physiology and Microbiology, Biology School, Complutense University of Madrid, Spain
| | - E Carlos Rodríguez-Merchán
- Osteoarticular Surgery Research, Hospital La Paz Institute for Health Research-IdiPAZ (La Paz University Hospital-Autonomous University of Madrid), Spain
| | - Antonio Liras
- Department of Genetic, Physiology and Microbiology, Biology School, Complutense University of Madrid, Spain.
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3
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Fabo T, Khavari P. Functional characterization of human genomic variation linked to polygenic diseases. Trends Genet 2023; 39:462-490. [PMID: 36997428 PMCID: PMC11025698 DOI: 10.1016/j.tig.2023.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
The burden of human disease lies predominantly in polygenic diseases. Since the early 2000s, genome-wide association studies (GWAS) have identified genetic variants and loci associated with complex traits. These have ranged from variants in coding sequences to mutations in regulatory regions, such as promoters and enhancers, as well as mutations affecting mediators of mRNA stability and other downstream regulators, such as 5' and 3'-untranslated regions (UTRs), long noncoding RNA (lncRNA), and miRNA. Recent research advances in genetics have utilized a combination of computational techniques, high-throughput in vitro and in vivo screening modalities, and precise genome editing to impute the function of diverse classes of genetic variants identified through GWAS. In this review, we highlight the vastness of genomic variants associated with polygenic disease risk and address recent advances in how genetic tools can be used to functionally characterize them.
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Affiliation(s)
- Tania Fabo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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4
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Richardson C, Kelsh RN, J. Richardson R. New advances in CRISPR/Cas-mediated precise gene-editing techniques. Dis Model Mech 2023; 16:dmm049874. [PMID: 36847161 PMCID: PMC10003097 DOI: 10.1242/dmm.049874] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Over the past decade, CRISPR/Cas-based gene editing has become a powerful tool for generating mutations in a variety of model organisms, from Escherichia coli to zebrafish, rodents and large mammals. CRISPR/Cas-based gene editing effectively generates insertions or deletions (indels), which allow for rapid gene disruption. However, a large proportion of human genetic diseases are caused by single-base-pair substitutions, which result in more subtle alterations to protein function, and which require more complex and precise editing to recreate in model systems. Precise genome editing (PGE) methods, however, typically have efficiencies of less than a tenth of those that generate less-specific indels, and so there has been a great deal of effort to improve PGE efficiency. Such optimisations include optimal guide RNA and mutation-bearing donor DNA template design, modulation of DNA repair pathways that underpin how edits result from Cas-induced cuts, and the development of Cas9 fusion proteins that introduce edits via alternative mechanisms. In this Review, we provide an overview of the recent progress in optimising PGE methods and their potential for generating models of human genetic disease.
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Affiliation(s)
- Chris Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Robert N. Kelsh
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Rebecca J. Richardson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
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5
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Kat M, Margadant C, Voorberg J, Bierings R. Dispatch and delivery at the ER-Golgi interface: how endothelial cells tune their hemostatic response. FEBS J 2022; 289:6863-6870. [PMID: 35246944 PMCID: PMC9790534 DOI: 10.1111/febs.16421] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 01/13/2023]
Abstract
Von Willebrand factor (VWF) is a glycoprotein that is secreted into the circulation and controls bleeding by promoting adhesion and aggregation of blood platelets at sites of vascular injury. Substantial inter-individual variation in VWF plasma levels exists among the healthy population. Prior to secretion, VWF polymers are assembled and condensed into helical tubules, which are packaged into Weibel-Palade bodies (WPBs), a highly specialized post-Golgi storage compartment in vascular endothelial cells. In the inherited bleeding disorder Von Willebrand disease (VWD), mutations in the VWF gene can cause qualitative or quantitative defects, limiting protein function, secretion, or plasma survival. However, pathogenic VWF mutations cannot be found in all VWD cases. Although an increasing number of genetic modifiers have been identified, even more rare genetic variants that impact VWF plasma levels likely remain to be discovered. Here, we summarize recent evidence that modulation of the early secretory pathway has great impact on the biogenesis and release of WPBs. Based on these findings, we propose that rare, as yet unidentified quantitative trait loci influencing intracellular VWF transport contribute to highly variable VWF levels in the population. These may underlie the thrombotic complications linked to high VWF levels, as well as the bleeding tendency in individuals with low VWF levels.
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Affiliation(s)
- Marije Kat
- Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdam University Medical CenterUniversity of AmsterdamThe Netherlands
| | - Coert Margadant
- Angiogenesis laboratoryCancer Center AmsterdamAmsterdam University Medical Center location VUmcThe Netherlands
| | - Jan Voorberg
- Molecular HematologySanquin Research and Landsteiner LaboratoryAmsterdam University Medical CenterUniversity of AmsterdamThe Netherlands,Experimental Vascular MedicineAmsterdam University Medical CenterUniversity of AmsterdamThe Netherlands
| | - Ruben Bierings
- Hematology, Erasmus University Medical CenterRotterdamThe Netherlands
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6
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Finding the “switch” in platelet activation prediction of key mediators involved in reversal of platelet activation using a novel network biology approach. J Proteomics 2022; 261:104577. [DOI: 10.1016/j.jprot.2022.104577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/24/2022] [Accepted: 03/23/2022] [Indexed: 11/15/2022]
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7
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Siew WS, Tang YQ, Kong CK, Goh BH, Zacchigna S, Dua K, Chellappan DK, Duangjai A, Saokaew S, Phisalprapa P, Yap WH. Harnessing the Potential of CRISPR/Cas in Atherosclerosis: Disease Modeling and Therapeutic Applications. Int J Mol Sci 2021; 22:8422. [PMID: 34445123 PMCID: PMC8395110 DOI: 10.3390/ijms22168422] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 12/26/2022] Open
Abstract
Atherosclerosis represents one of the major causes of death globally. The high mortality rates and limitations of current therapeutic modalities have urged researchers to explore potential alternative therapies. The clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) system is commonly deployed for investigating the genetic aspects of Atherosclerosis. Besides, advances in CRISPR/Cas system has led to extensive options for researchers to study the pathogenesis of this disease. The recent discovery of Cas9 variants, such as dCas9, Cas9n, and xCas9 have been established for various applications, including single base editing, regulation of gene expression, live-cell imaging, epigenetic modification, and genome landscaping. Meanwhile, other Cas proteins, such as Cas12 and Cas13, are gaining popularity for their applications in nucleic acid detection and single-base DNA/RNA modifications. To date, many studies have utilized the CRISPR/Cas9 system to generate disease models of atherosclerosis and identify potential molecular targets that are associated with atherosclerosis. These studies provided proof-of-concept evidence which have established the feasibility of implementing the CRISPR/Cas system in correcting disease-causing alleles. The CRISPR/Cas system holds great potential to be developed as a targeted treatment for patients who are suffering from atherosclerosis. This review highlights the advances in CRISPR/Cas systems and their applications in establishing pathogenetic and therapeutic role of specific genes in atherosclerosis.
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Affiliation(s)
- Wei Sheng Siew
- School of Biosciences, Taylor’s University, Subang Jaya 47500, Malaysia; (W.S.S.); (Y.Q.T.)
| | - Yin Quan Tang
- School of Biosciences, Taylor’s University, Subang Jaya 47500, Malaysia; (W.S.S.); (Y.Q.T.)
- Centre for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences (FHMS), Taylor’s University, Subang Jaya 47500, Malaysia
| | - Chee Kei Kong
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Bey-Hing Goh
- Biofunctional Molecule Exploratory (BMEX) Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Serena Zacchigna
- Centre for Translational Cardiology, Department of Medicine, Surgery and Health Sciences and Cardiovascular Department, Azienda Sanitaria Universitaria Giuliano Isontina, Strada di Fiume 447, 34149 Trieste, Italy;
- International Center for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University (IMU), Bukit Jalil 57000, Malaysia;
| | - Acharaporn Duangjai
- Unit of Excellence in Research and Product Development of Coffee, Division of Physiology, School of Medical Sciences, University of Phayao, Phayao 56000, Thailand; (A.D.); (S.S.)
- Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao 56000, Thailand
- Unit of Excellence on Clinical Outcomes Research and IntegratioN (UNICORN), School of Pharmaceutical Sciences, University of Phayao, Phayao 56000, Thailand
| | - Surasak Saokaew
- Unit of Excellence in Research and Product Development of Coffee, Division of Physiology, School of Medical Sciences, University of Phayao, Phayao 56000, Thailand; (A.D.); (S.S.)
- Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao 56000, Thailand
- Unit of Excellence on Clinical Outcomes Research and IntegratioN (UNICORN), School of Pharmaceutical Sciences, University of Phayao, Phayao 56000, Thailand
- Unit of Excellence on Herbal Medicine, School of Pharmaceutical Sciences, University of Phayao, Phayao 56000, Thailand
- Department of Pharmaceutical Care, Division of Pharmacy Practice, School of Pharmaceutical Sciences, University of Phayao, Phayao 56000, Thailand
| | - Pochamana Phisalprapa
- Department of Medicine, Division of Ambulatory Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wei Hsum Yap
- School of Biosciences, Taylor’s University, Subang Jaya 47500, Malaysia; (W.S.S.); (Y.Q.T.)
- Centre for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences (FHMS), Taylor’s University, Subang Jaya 47500, Malaysia
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8
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Antao AM, Karapurkar JK, Lee DR, Kim KS, Ramakrishna S. Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems. Comput Struct Biotechnol J 2020; 18:3649-3665. [PMID: 33304462 PMCID: PMC7710510 DOI: 10.1016/j.csbj.2020.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
CRISPR/Cas systems are popular genome editing tools that belong to a class of programmable nucleases and have enabled tremendous progress in the field of regenerative medicine. We here outline the structural and molecular frameworks of the well-characterized type II CRISPR system and several computational tools intended to facilitate experimental designs. The use of CRISPR tools to generate disease models has advanced research into the molecular aspects of disease conditions, including unraveling the molecular basis of immune rejection. Advances in regenerative medicine have been hindered by major histocompatibility complex-human leukocyte antigen (HLA) genes, which pose a major barrier to cell- or tissue-based transplantation. Based on progress in CRISPR, including in recent clinical trials, we hypothesize that the generation of universal donor immune-engineered stem cells is now a realistic approach to tackling a multitude of disease conditions.
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Affiliation(s)
- Ainsley Mike Antao
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | | | - Dong Ryul Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, South Korea.,CHA Stem Cell Institute, CHA University, Seoul, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.,College of Medicine, Hanyang University, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.,College of Medicine, Hanyang University, Seoul, South Korea
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9
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Zhang Y, Karakikes I. Translating genomic insights into cardiovascular medicine: Opportunities and challenges of CRISPR-Cas9. Trends Cardiovasc Med 2020; 31:341-348. [PMID: 32603681 DOI: 10.1016/j.tcm.2020.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/13/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
The growing appreciation of human genetics and genomics in cardiovascular disease (CVD) accompanied by the technological breakthroughs in genome editing, particularly the CRISPR-Cas9 technologies, has presented an unprecedented opportunity to explore the application of genome editing in cardiovascular medicine. The ever-growing genome editing toolbox includes an assortment of CRISPR-Cas systems with increasing efficiency, precision, flexibility, and targeting capacity. Over the past decade, the advent of large-scale genotyping technologies and genome-wide association studies (GWAS) has provided numerous genotype-phenotype associations for diseases with complex traits. Notably, a growing number of loss-of-function mutations have been associated with favorable CVD risk-factor profiles that may confer protection. Combining the newly gained insights of human genetics with recent breakthrough technologies, such as the CRISPR-Cas9 technologies, holds great promise in elucidating novel disease mechanisms and transforming genes into medicines. Nonetheless, translating genetic insights into novel therapeuties remains challenging. Applications of "in body" genome editing for CVD treatment and engineering cardioprotection remain mostly theoretical. Here we highlight the recent advances of the CRISPR-based genome editing toolbox and discuss the potential and challenges of CRISPR-based technologies for translating GWAS findings into genomic medicines.
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Affiliation(s)
- Yuan Zhang
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 300 Pasteur Dr, Suite 1347, Stanford, CA 94305-5515, USA; Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ioannis Karakikes
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, 300 Pasteur Dr, Suite 1347, Stanford, CA 94305-5515, USA; Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
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10
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Li F, Shi J, Lu HS, Zhang H. Functional Genomics and CRISPR Applied to Cardiovascular Research and Medicine. Arterioscler Thromb Vasc Biol 2019; 39:e188-e194. [PMID: 31433696 DOI: 10.1161/atvbaha.119.312579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Fang Li
- From the Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York (F.L., J.S., H.Z.)
| | - Jianting Shi
- From the Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York (F.L., J.S., H.Z.)
| | - Hong S Lu
- Department of Physiology, Saha Cardiovascular Research Center, University of Kentucky, Lexington (H.S.L.)
| | - Hanrui Zhang
- From the Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York (F.L., J.S., H.Z.)
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11
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Interaction networks of Weibel-Palade body regulators syntaxin-3 and syntaxin binding protein 5 in endothelial cells. J Proteomics 2019; 205:103417. [PMID: 31201948 DOI: 10.1016/j.jprot.2019.103417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/17/2019] [Accepted: 06/11/2019] [Indexed: 12/27/2022]
Abstract
The endothelium stores the hemostatic protein Von Willebrand factor (VWF) in endothelial storage organelles called Weibel-Palade bodies (WPBs). During maturation, WPBs recruit a complex of Rab GTPases and effectors that associate with components of the SNARE machinery that control WPB exocytosis. Recent genome wide association studies have found links between genetic variations in the SNAREs syntaxin-2 (STX2) and syntaxin binding protein 5 (STXBP5) and VWF plasma levels, suggesting a role for SNARE proteins in regulating VWF release. Moreover, we have previously identified the SNARE proteins syntaxin-3 and STXBP1 as regulators of WPB release. In this study we used an unbiased iterative interactomic approach to identify new components of the WPB exocytotic machinery. An interactome screen of syntaxin-3 identifies a number of SNAREs and SNARE associated proteins (STXBP2, STXBP5, SNAP23, NAPA and NSF). We show that the VAMP-like domain (VLD) of STXBP5 is indispensable for the interaction with SNARE proteins and this capacity of the VLD could be exploited to identify an extended set of novel endothelial SNARE interactors of STXBP5. In addition, an STXBP5 variant with an N436S substitution, which is linked to lower VWF plasma levels, does not show a difference in interactome when compared with WT STXBP5. SIGNIFICANCE: The hemostatic protein Von Willebrand factor plays a pivotal role in vascular health: quantitative or qualitative deficiencies of VWF can lead to bleeding, while elevated levels of VWF are associated with increased risk of thrombosis. Tight regulation of VWF secretion from WPBs is therefore essential to maintain vascular homeostasis. We used an unbiased proteomic screen to identify new components of the regulatory machinery that controls WPB exocytosis. Our data expand the endothelial SNARE protein network and provide a set of novel candidate WPB regulators that may contribute to regulation of VWF plasma levels and vascular health.
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12
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Lu HS, Schmidt AM, Hegele RA, Mackman N, Rader DJ, Weber C, Daugherty A. Reporting Sex and Sex Differences in Preclinical Studies. Arterioscler Thromb Vasc Biol 2019; 38:e171-e184. [PMID: 30354222 DOI: 10.1161/atvbaha.118.311717] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hong S Lu
- From the Department of Physiology, Saha Cardiovascular Research Center, University of Kentucky, Lexington (H.S.L., A.D.)
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, New York University Langone Medical Center, New York, NY (A.M.S.)
| | - Robert A Hegele
- Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada (R.A.H.)
| | - Nigel Mackman
- Department of Medicine, University of North Carolina at Chapel Hill (N.M.)
| | - Daniel J Rader
- Department of Medicine (D.J.R.), Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Department of Genetics (D.J.R.), Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Christian Weber
- Department of Medicine, Institute for Cardiovascular Prevention, Ludwig-Maximilians-Universität, Munich, Germany (C.W.).,German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany (C.W.)
| | - Alan Daugherty
- From the Department of Physiology, Saha Cardiovascular Research Center, University of Kentucky, Lexington (H.S.L., A.D.)
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13
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Satoh K, Shimokawa H. Recent Advances in the Development of Cardiovascular Biomarkers. Arterioscler Thromb Vasc Biol 2019; 38:e61-e70. [PMID: 29695533 DOI: 10.1161/atvbaha.118.310226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kimio Satoh
- From the Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroaki Shimokawa
- From the Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.
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14
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CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases. Semin Cell Dev Biol 2019; 96:32-43. [PMID: 31112800 DOI: 10.1016/j.semcdb.2019.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022]
Abstract
Recent developments in the nucleic acid editing technologies have provided a powerful tool to precisely engineer the genome and epigenome for studying many aspects of immune cell differentiation and development as well as several immune mediated diseases (IMDs) including autoimmunity and cancer. Here, we discuss the recent technological achievements of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based RNA-guided genome and epigenome editing toolkit and provide an insight into how CRISPR/Cas9 (CRISPR Associated Protein 9) toolbox could be used to examine genetic and epigenetic mechanisms underlying IMDs. In addition, we will review the progress in CRISPR/Cas9-based genome-wide genome and epigenome screens in various cell types including immune cells. Finally, we will discuss the potential of CRISPR/Cas9 in defining the molecular function of disease associated SNPs overlapping gene regulatory elements.
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15
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Cong Z, Li Q, Yang Y, Guo X, Cui L, You T. The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells. Biochem Biophys Res Commun 2019; 514:734-741. [PMID: 31078271 DOI: 10.1016/j.bbrc.2019.04.190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/28/2019] [Indexed: 12/01/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) identified by Genome-Wide Association Studies (GWASs) have been determined to closely connect with multiple diseases. Previous studies revealed one underlying mechanism that SNPs located within the regulatory elements could affect the encoding gene expression through long-range regulation. SNP rs6854845 was suggested to be a risk of colon cancer in human population. Nevertheless, the underlying molecular mechanism for colon carcinogenesis remains largely unknown. In present study, rs6854845 with G > T mutation in situ in FHC, HCT-116 and SW-480 cells were generated by Crispr/Cas9. The nearby chromatin organization was investigated by chromatin conformation capture (3C). And the expression of coding gene regulated by super-enhancer (SE) was detected by real-time PCR. We observed a significantly different pattern of the genome organization upon rs6854845 generation in colon epithelial cells but not in colon cancer cells. Moreover, we observed the shifted enrichment of H3K4me1 and H3K27ac at the SE (chr4:75.7M-76.0 M) where rs6854845 located. Furthermore, we observed that the transcription of the gene clusters regulated by SE were affected by rs6854845 in colon cells. Overall, our results demonstrated that SNP rs6854845 located in SE could destroy the long-range chromosomal interaction between SE and target gene clusters thereby affecting the transcription of these genes.
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Affiliation(s)
- Zhuangzhi Cong
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, Shanghai 200438, PR China
| | - Qinghua Li
- Department of Hepatobiliary Surgery, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji-Mo Road, Shanghai, 200120, PR China
| | - Yongkang Yang
- Department of Hepatobiliary Surgery, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji-Mo Road, Shanghai, 200120, PR China
| | - Xinlai Guo
- Department of Hepatobiliary Surgery, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji-Mo Road, Shanghai, 200120, PR China
| | - Longjiu Cui
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, Shanghai 200438, PR China
| | - Tiangeng You
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, Shanghai 200438, PR China.
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16
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Zarei A, Razban V, Hosseini SE, Tabei SMB. Creating cell and animal models of human disease by genome editing using CRISPR/Cas9. J Gene Med 2019; 21:e3082. [DOI: 10.1002/jgm.3082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/02/2019] [Accepted: 02/02/2019] [Indexed: 12/26/2022] Open
Affiliation(s)
- Ali Zarei
- Department of Molecular Genetics, Marvdasht BranchIslamic Azad University Marvdasht Iran
- Department of Molecular Genetics, Science and Research BranchIslamic Azad University Fars Iran
| | - Vahid Razban
- Department of Molecular medicine, School of Advanced Medical Sciences and Technologies Shiraz Iran
- Stem Cell and Transgenic Technology Research CenterShiraz University of Medical Sciences Shiraz Iran
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17
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Miano JM, Long X, Lyu Q. CRISPR links to long noncoding RNA function in mice: A practical approach. Vascul Pharmacol 2019; 114:1-12. [PMID: 30822570 PMCID: PMC6435418 DOI: 10.1016/j.vph.2019.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/29/2022]
Abstract
Next generation sequencing has uncovered a trove of short noncoding RNAs (e.g., microRNAs) and long noncoding RNAs (lncRNAs) that act as molecular rheostats in the control of diverse homeostatic processes. Meanwhile, the tsunamic emergence of clustered regularly interspaced short palindromic repeats (CRISPR) editing has transformed our influence over all DNA-carrying entities, heralding global CRISPRization. This is evident in biomedical research where the ease and low-cost of CRISPR editing has made it the preferred method of manipulating the mouse genome, facilitating rapid discovery of genome function in an in vivo context. Here, CRISPR genome editing components are updated for elucidating lncRNA function in mice. Various strategies are highlighted for understanding the function of lncRNAs residing in intergenic sequence space, as host genes that harbor microRNAs or other genes, and as natural antisense, overlapping or intronic genes. Also discussed is CRISPR editing of mice carrying human lncRNAs as well as the editing of competing endogenous RNAs. The information described herein should assist labs in the rigorous design of experiments that interrogate lncRNA function in mice where complex disease processes can be modeled thus accelerating translational discovery.
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Affiliation(s)
- Joseph M Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America.
| | - Xiaochun Long
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, United States of America
| | - Qing Lyu
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
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18
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Gong W, Liu Y, Qu H, Liu A, Sun P, Wang X. The effect of CTCF binding sites destruction by CRISPR/Cas9 on transcription of metallothionein gene family in liver hepatocellular carcinoma. Biochem Biophys Res Commun 2019; 510:530-538. [PMID: 30738580 DOI: 10.1016/j.bbrc.2019.01.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 01/24/2019] [Indexed: 01/20/2023]
Abstract
Chromatin spatial organization is essential for transcriptional modulation and stabilization. The pattern of DNA distal interplay form the multiple topological associating domains (TADs), and further assemble the functional compartmentalization with open and expression-active chromatin ("A" compartments) or closed and expression-inactive chromatin ("B" compartments) in genome, whose boundaries were defined by the high enrichment of CCCTC-binding factor (CTCF). Nevertheless, As a potential therapeutic strategy, changing the local chromatin architecture via adding or removing the CTCF binding sites in situ to regulate the transcription activity of genes within one TAD in cancer cells is poorly explored. In present study, we observed that the metallothionein (MT) family were all remarkably decreased in HCC of TCGA database, and MT genes family were located within a TAD of 1.2 Mb at 16q13 in order, and CTCF binding sites were distributed at the both sites of MT gene clusters. Furthermore, CRISPR/Cas9 was employed to destroy the CTCF binding sites at the vicinity of the MT family in human liver hepatocellular carcinoma (HCC) cell lines Huh-7 and HepG2. And the presence of up-regulated transcription of MTs were observed in Huh-7 and HepG2 cells compared to normal liver CRL-12461 cells. Moreover, the presence of the varying DNA interplay as well as H3K4me3 and H3K9me3 modification on different MT genes were observed after CTCF binding domain destruction compared to the control using chromosome conformation capture (3C) and chromatin immunoprecipitation (ChIP). Our results determined a potential way to regulate the transcription of a series of genes via changing the local genomic organization for diseases treatment.
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Affiliation(s)
- Wenjing Gong
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China
| | - Youde Liu
- Department of Hepatology, Yantai Infectious Disease Hospital, Yantai, Shandong, 264001, China
| | - Huajun Qu
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China
| | - Aina Liu
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China
| | - Ping Sun
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China
| | - Xiumei Wang
- Department of Oncology, Yantai Yuhuangding Hospital, Yantai, Shandong, 264001, China.
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19
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Memi F, Ntokou A, Papangeli I. CRISPR/Cas9 gene-editing: Research technologies, clinical applications and ethical considerations. Semin Perinatol 2018; 42:487-500. [PMID: 30482590 DOI: 10.1053/j.semperi.2018.09.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gene therapy carries the potential to treat more than 10,000 human monogenic diseases and benefit an even greater number of complex polygenic conditions. The repurposing of CRISPR/Cas9, an ancient bacterial immune defense system, into a gene-editing technology has armed researchers with a revolutionary tool for gene therapy. However, as the breadth of research and clinical applications of this technology continues to expand, outstanding technical challenges and ethical considerations will need to be addressed before clinical applications become commonplace. Here, we review CRISPR/Cas9 technology and discuss its benefits and limitations in research and the clinical context, as well as ethical considerations surrounding the use of CRISPR gene editing.
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Affiliation(s)
- Fani Memi
- Department of Cell and Developmental Biology, University College London, 21 University Street, WC1E 6DE London, UK.
| | - Aglaia Ntokou
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine, 300 George, 7(th) Floor, New Haven, CT 06511, United States.
| | - Irinna Papangeli
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine, 300 George, 7(th) Floor, New Haven, CT 06511, United States.
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20
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Abstract
Prokaryotic type II adaptive immune systems have been developed into the versatile CRISPR technology, which has been widely applied in site-specific genome editing and has revolutionized biomedical research due to its superior efficiency and flexibility. Recent studies have greatly diversified CRISPR technologies by coupling it with various DNA repair mechanisms and targeting strategies. These new advances have significantly expanded the generation of genetically modified animal models, either by including species in which targeted genetic modification could not be achieved previously, or through introducing complex genetic modifications that take multiple steps and cost years to achieve using traditional methods. Herein, we review the recent developments and applications of CRISPR-based technology in generating various animal models, and discuss the everlasting impact of this new progress on biomedical research.
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Affiliation(s)
- Xun Ma
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Avery Sum-Yu Wong
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Hei-Yin Tam
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Samuel Yung-Kin Tsui
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Dittman Lai-Shun Chung
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Bo Feng
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Guangdong 510530, China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen Guangdong 518057, China
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21
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Maney DL. Polymorphisms in sex steroid receptors: From gene sequence to behavior. Front Neuroendocrinol 2017; 47:47-65. [PMID: 28705582 PMCID: PMC6312198 DOI: 10.1016/j.yfrne.2017.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/05/2017] [Accepted: 07/08/2017] [Indexed: 01/09/2023]
Abstract
Sex steroid receptors have received much interest as potential mediators of human behaviors and mental disorders. Candidate gene association studies have identified about 50 genetic variants of androgen and estrogen receptors that correlate with human behavioral phenotypes. Because most of these polymorphisms lie outside coding regions, discerning their effect on receptor function is not straightforward. Thus, although discoveries of associations improve our ability to predict risk, they have not greatly advanced our understanding of underlying mechanisms. This article is intended to serve as a starting point for psychologists and other behavioral biologists to consider potential mechanisms. Here, I review associations between polymorphisms in sex steroid receptors and human behavioral phenotypes. I then consider ways in which genetic variation can affect processes such as mRNA transcription, splicing, and stability. Finally, I suggest ways that hypotheses about mechanism can be tested, for example using in vitro assays and/or animal models.
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Affiliation(s)
- Donna L Maney
- Department of Psychology, 36 Eagle Row, Emory University, Atlanta, GA 30322, USA.
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22
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Dron JS, Ho R, Hegele RA. Recent Advances in the Genetics of Atherothrombotic Disease and Its Determinants. Arterioscler Thromb Vasc Biol 2017; 37:e158-e166. [DOI: 10.1161/atvbaha.117.309934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jacqueline S. Dron
- From the Department of Biochemistry (J.S.D, R.H., R.A.H.), Robarts Research Institute (J.S.D., R.H., R.A.H.), and Department of Medicine (R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Rosettia Ho
- From the Department of Biochemistry (J.S.D, R.H., R.A.H.), Robarts Research Institute (J.S.D., R.H., R.A.H.), and Department of Medicine (R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A. Hegele
- From the Department of Biochemistry (J.S.D, R.H., R.A.H.), Robarts Research Institute (J.S.D., R.H., R.A.H.), and Department of Medicine (R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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23
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Birling MC, Herault Y, Pavlovic G. Modeling human disease in rodents by CRISPR/Cas9 genome editing. Mamm Genome 2017; 28:291-301. [PMID: 28677007 PMCID: PMC5569124 DOI: 10.1007/s00335-017-9703-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/21/2017] [Indexed: 02/08/2023]
Abstract
Modeling human disease has proven to be a challenge for the scientific community. For years, generating an animal model was complicated and restricted to very few species. With the rise of CRISPR/Cas9, it is now possible to generate more or less any animal model. In this review, we will show how this technology is and will change our way to obtain relevant disease animal models and how it should impact human health.
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Affiliation(s)
- Marie-Christine Birling
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Guillaume Pavlovic
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France
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