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Gene Editing for Disease Modeling and Therapeutics
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Gene Editing for Disease Modeling and Therapeutics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 February 2025 | Viewed by 16861

Special Issue Editor

Dr. Rivka Ofir

E-Mail Website1 Website2
Guest Editor
Regenerative Medicine & Stem Cell Research Center, Ben-Gurion University and Dead Sea & Arava Science Center, Beer Sheva 84105, Israel
Interests: reprogramming; differentiation; Brain Blood Barrier (BBB); iPSC; drug discovery; disease in a dish model
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This issue will accept manuscripts that use genome-edited, human-induced pluripotent stem cells (hiPSCs) as models for monogenic/complex diseases and as cells relevant for therapeutics.

The gene editing methodology can be used for fixing mutations, creating mutations, and knocking out repressors or enhancers, etc., and as such can serve to generate disease models and their controls for both the studying of diseases and for their therapeutic potential (including issues of off target).

Original research papers, reviews, and methodology papers on these topics and related topics are encouraged. They can deal with any issue relevant to genome editing.

Dr. Rivka Ofir
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gene editing methodology
  • CRISPR
  • iPSC
  • knockout
  • activation
  • off target
  • differentiation
  • drug discovery

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Published Papers (6 papers)

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Research

Jump to: Review, Other

18 pages, 18651 KiB  
Article
GAL3ST1 Deficiency Reduces Epithelial–Mesenchymal Transition and Tumorigenic Capacity in a Cholangiocarcinoma Cell Line
by Lin Chen, Montserrat Elizalde, Ludwig J. Dubois, Anjali A. Roeth, Ulf P. Neumann, Steven W. M. Olde Damink, Frank G. Schaap and Gloria Alvarez-Sola
Int. J. Mol. Sci. 2024, 25(13), 7279; https://doi.org/10.3390/ijms25137279 - 2 Jul 2024
Viewed by 3976
Abstract
Cholangiocarcinoma (CCA), or bile duct cancer, is the second most common liver malignancy, with an increasing incidence in Western countries. The lack of effective treatments associated with the absence of early symptoms highlights the need to search for new therapeutic targets for CCA. [...] Read more.
Cholangiocarcinoma (CCA), or bile duct cancer, is the second most common liver malignancy, with an increasing incidence in Western countries. The lack of effective treatments associated with the absence of early symptoms highlights the need to search for new therapeutic targets for CCA. Sulfatides (STs), a type of sulfoglycosphingolipids, have been found in the biliary tract, with increased levels in CCA and other types of cancer. STs are involved in protein trafficking and cell adhesion as part of the lipid rafts of the plasma membrane. We aimed to study the role of STs in CCA by the genetic targeting of GAL3ST1, an enzyme involved in ST synthesis. We used the CRISPR-Cas9 system to generate GAL3ST1-deficient TFK1 cells. GAL3ST1 KO cells showed lower proliferation and clonogenic activity and reduced glycolytic activity compared to TFK1 cells. Polarized TFK1 GAL3ST1 KO cells displayed increased transepithelial resistance and reduced permeability compared to TFK1 wt cells. The loss of GAL3ST1 showed a negative effect on growth in 30 out of 34 biliary tract cancer cell lines from the DepMap database. GAL3ST1 deficiency partially restored epithelial identity and barrier function and reduced proliferative activity in CCA cells. Sulfatide synthesis may provide a novel therapeutic target for CCA. Full article
(This article belongs to the Special Issue Gene Editing for Disease Modeling and Therapeutics)
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21 pages, 8875 KiB  
Article
Identification of the Efficient Enhancer Elements in FVIII-Padua for Gene Therapy Study of Hemophilia A
by Rou Xiao, Yan Chen, Zhiqing Hu, Qiyu Tang, Peiyun Wang, Miaojin Zhou, Lingqian Wu and Desheng Liang
Int. J. Mol. Sci. 2024, 25(7), 3635; https://doi.org/10.3390/ijms25073635 - 24 Mar 2024
Viewed by 1410
Abstract
Hemophilia A (HA) is a common X-linked recessive hereditary bleeding disorder. Coagulation factor VIII (FVIII) is insufficient in patients with HA due to the mutations in the F8 gene. The restoration of plasma levels of FVIII via both recombinant B-domain-deleted FVIII (BDD-FVIII) and [...] Read more.
Hemophilia A (HA) is a common X-linked recessive hereditary bleeding disorder. Coagulation factor VIII (FVIII) is insufficient in patients with HA due to the mutations in the F8 gene. The restoration of plasma levels of FVIII via both recombinant B-domain-deleted FVIII (BDD-FVIII) and B-domain-deleted F8 (BDDF8) transgenes was proven to be helpful. FVIII-Padua is a 23.4 kb tandem repeat mutation in the F8 associated with a high F8 gene expression and thrombogenesis. Here we screened a core enhancer element in FVIII-Padua for improving the F8 expression. In detail, we identified a 400 bp efficient enhancer element, C400, in FVIII-Padua for the first time. The core enhancer C400 extensively improved the transcription of BDDF8 driven by human elongation factor-1 alpha in HepG2, HeLa, HEK-293T and induced pluripotent stem cells (iPSCs) with different genetic backgrounds, as well as iPSCs-derived endothelial progenitor cells (iEPCs) and iPSCs-derived mesenchymal stem cells (iMSCs). The expression of FVIII protein was increased by C400, especially in iEPCs. Our research provides a novel molecular target to enhance expression of FVIII protein, which has scientific value and application prospects in both viral and nonviral HA gene therapy strategies. Full article
(This article belongs to the Special Issue Gene Editing for Disease Modeling and Therapeutics)
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12 pages, 4415 KiB  
Article
A Digital PCR Method Based on Highly Specific Taq for Detecting Gene Editing and Mutations
by Bo Li, Junhao Liu and Qilai Huang
Int. J. Mol. Sci. 2023, 24(17), 13405; https://doi.org/10.3390/ijms241713405 - 29 Aug 2023
Viewed by 2183
Abstract
Digital PCR (dPCR) has great potential for assessing gene editing or gene mutation due to its ability to independently inspect each DNA template in parallel. However, current dPCR methods use a fluorescence-labeled probe to detect gene variation events, and their ability to distinguish [...] Read more.
Digital PCR (dPCR) has great potential for assessing gene editing or gene mutation due to its ability to independently inspect each DNA template in parallel. However, current dPCR methods use a fluorescence-labeled probe to detect gene variation events, and their ability to distinguish variated sequences from the wild-type sequence is limited by the probe’s tolerance to mismatch. To address this, we have developed a novel dPCR method that uses a primer instead of a probe to sense gene variation. The enhanced Taq DNA polymerase in the PCR system has a high mismatch sensitivity, which enables our dPCR method to distinguish gene mutations from wild-type sequences. Compared to current dPCR methods, our method shows superior precision in assessing gene editing efficiency and single-base DNA mutation. This presents a promising opportunity to advance gene editing research and rare gene mutation detection. Full article
(This article belongs to the Special Issue Gene Editing for Disease Modeling and Therapeutics)
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Review

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15 pages, 683 KiB  
Review
Applications of Genome-Editing Technologies for Type 1 Diabetes
by Rana El Nahas, Mohammad Ameen Al-Aghbar, Laura Herrero, Nicholas van Panhuys and Meritxell Espino-Guarch
Int. J. Mol. Sci. 2024, 25(1), 344; https://doi.org/10.3390/ijms25010344 - 26 Dec 2023
Cited by 2 | Viewed by 3112
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by the destruction of insulin-producing pancreatic β-cells by the immune system. Although conventional therapeutic modalities, such as insulin injection, remain a mainstay, recent years have witnessed the emergence of novel treatment approaches encompassing [...] Read more.
Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by the destruction of insulin-producing pancreatic β-cells by the immune system. Although conventional therapeutic modalities, such as insulin injection, remain a mainstay, recent years have witnessed the emergence of novel treatment approaches encompassing immunomodulatory therapies, such as stem cell and β-cell transplantation, along with revolutionary gene-editing techniques. Notably, recent research endeavors have enabled the reshaping of the T-cell repertoire, leading to the prevention of T1D development. Furthermore, CRISPR–Cas9 technology has demonstrated remarkable potential in targeting endogenous gene activation, ushering in a promising avenue for the precise guidance of mesenchymal stem cells (MSCs) toward differentiation into insulin-producing cells. This innovative approach holds substantial promise for the treatment of T1D. In this review, we focus on studies that have developed T1D models and treatments using gene-editing systems. Full article
(This article belongs to the Special Issue Gene Editing for Disease Modeling and Therapeutics)
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11 pages, 792 KiB  
Review
The Development, Optimization and Future of Prime Editing
by Irina O. Petrova and Svetlana A. Smirnikhina
Int. J. Mol. Sci. 2023, 24(23), 17045; https://doi.org/10.3390/ijms242317045 - 1 Dec 2023
Cited by 2 | Viewed by 3960
Abstract
Prime editing is a rapidly developing method of CRISPR/Cas-based genome editing. The increasing number of novel PE applications and improved versions demands constant analysis and evaluation. The present review covers the mechanism of prime editing, the optimization of the method and the possible [...] Read more.
Prime editing is a rapidly developing method of CRISPR/Cas-based genome editing. The increasing number of novel PE applications and improved versions demands constant analysis and evaluation. The present review covers the mechanism of prime editing, the optimization of the method and the possible next step in the evolution of CRISPR/Cas9-associated genome editing. The basic components of a prime editing system are a prime editor fusion protein, consisting of nickase and reverse transcriptase, and prime editing guide RNA, consisting of a protospacer, scaffold, primer binding site and reverse transcription template. Some prime editing systems include other parts, such as additional RNA molecules. All of these components were optimized to achieve better efficiency for different target organisms and/or compactization for viral delivery. Insights into prime editing mechanisms allowed us to increase the efficiency by recruiting mismatch repair inhibitors. However, the next step in prime editing evolution requires the incorporation of new mechanisms. Prime editors combined with integrases allow us to combine the precision of prime editing with the target insertion of large, several-kilobase-long DNA fragments. Full article
(This article belongs to the Special Issue Gene Editing for Disease Modeling and Therapeutics)
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Other

Jump to: Research, Review

11 pages, 1181 KiB  
Brief Report
Generation of a Well-Characterized Homozygous Chromodomain-Helicase-DNA-Binding Protein 4G1003D Mutant hESC Line Using CRISPR/eCas9 (ULIEGEe001-A-1)
by Ilyas Chohra, Subhajit Giri and Brigitte Malgrange
Int. J. Mol. Sci. 2023, 24(13), 10543; https://doi.org/10.3390/ijms241310543 - 23 Jun 2023
Viewed by 1276
Abstract
The chromatin remodeler Chromodomain-helicase-DNA-binding protein 4 (CHD4) is crucial for the development of multiple organ systems. Functional mutations of CHD4 have recently been described in a developmental disorder, namely Siffrim-Hitz-Weiss syndrome (SIHIWES). Herein, we have generated a homozygous CHD4G1003D hESC line (WAe025-A-1) using [...] Read more.
The chromatin remodeler Chromodomain-helicase-DNA-binding protein 4 (CHD4) is crucial for the development of multiple organ systems. Functional mutations of CHD4 have recently been described in a developmental disorder, namely Siffrim-Hitz-Weiss syndrome (SIHIWES). Herein, we have generated a homozygous CHD4G1003D hESC line (WAe025-A-1) using CRISPR/eCas9-based gene editing in the WA-25 hESC line. The edited hESC line maintains normal karyotype, pluripotency, and ability to differentiate into three germ layers. This cell line will be a valuable resource for studying the functional role of CHD4 during the development and disease modeling of SIHIWES in vitro. Full article
(This article belongs to the Special Issue Gene Editing for Disease Modeling and Therapeutics)
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