Pub Date : 2024-10-31eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1481443
Yihan Wang, Gary C Hon
Large scale cancer genomic studies in patients have unveiled millions of non-coding variants. While a handful have been shown to drive cancer development, the vast majority have unknown function. This review describes the challenges of functionally annotating non-coding cancer variants and understanding how they contribute to cancer. We summarize recently developed high-throughput technologies to address these challenges. Finally, we outline future prospects for non-coding cancer genetics to help catalyze personalized cancer therapy.
{"title":"Towards functional maps of non-coding variants in cancer.","authors":"Yihan Wang, Gary C Hon","doi":"10.3389/fgeed.2024.1481443","DOIUrl":"10.3389/fgeed.2024.1481443","url":null,"abstract":"<p><p>Large scale cancer genomic studies in patients have unveiled millions of non-coding variants. While a handful have been shown to drive cancer development, the vast majority have unknown function. This review describes the challenges of functionally annotating non-coding cancer variants and understanding how they contribute to cancer. We summarize recently developed high-throughput technologies to address these challenges. Finally, we outline future prospects for non-coding cancer genetics to help catalyze personalized cancer therapy.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1481443"},"PeriodicalIF":4.9,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11560456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-16eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1426228
Ioanna Angelioudaki, Ana Ruxandra Badea, Martina Bodo, Daniel Fernández-Soto, Emmanouela Sevasti Karyampa, Adam Kokkinakis, Nikolaos Kolisis, Xenia Kominea, Sandra Ozáez Armijos, Simon Vogel, Oliver Feeney
Over 40 years ago, the 1982 Splicing Life report outlined the two distinctions that have orientated much of the normative and legal landscape of genetic intervention or genome editing since - that of somatic versus germline (or heritable interventions) and medical versus non-medical (or enhancement) applications. During this time, these distinctions have been used to ethically prioritize some areas of research and potential application, such as somatic treatments, while considering others for prohibition, such as germline enhancements. Nevertheless, somatic interventions may also be done for controversial enhancement purposes while some germline interventions may be done with greater prima facie justification (e.g., the enhancement of athletic ability versus the avoidance of Tay-Sachs disease). Even with new somatic treatments that are generally lauded, exemplified with the case of Casgevy, many issues still arise - such as cost and access, particularly salient on a global level. The concerns over a dystopian future of genetic haves and have nots, as a result of enhancement and/or germline interventions, that perhaps may happen, should not distract us from a greater attention to what is happening in the here and now. In this paper, we will highlight the limits of the two distinctions in terms of moving from questions of "should a technology be used" to "how should a technology be used." We argue that an additional focus on vulnerability and marginalization can be useful to support the attempt to better prioritize which interventions should be permitted or prohibited. We show how this can better dovetail with calls for effective (global) governance and reasonable consensus by focusing on the most urgent issues and developing policy accordingly, while leaving aside more abstract issues for further discussion.
{"title":"Beyond the traditional distinctions of genome editing: evaluating a vulnerability framework.","authors":"Ioanna Angelioudaki, Ana Ruxandra Badea, Martina Bodo, Daniel Fernández-Soto, Emmanouela Sevasti Karyampa, Adam Kokkinakis, Nikolaos Kolisis, Xenia Kominea, Sandra Ozáez Armijos, Simon Vogel, Oliver Feeney","doi":"10.3389/fgeed.2024.1426228","DOIUrl":"https://doi.org/10.3389/fgeed.2024.1426228","url":null,"abstract":"<p><p>Over 40 years ago, the 1982 Splicing Life report outlined the two distinctions that have orientated much of the normative and legal landscape of genetic intervention or genome editing since - that of somatic versus germline (or heritable interventions) and medical versus non-medical (or enhancement) applications. During this time, these distinctions have been used to ethically prioritize some areas of research and potential application, such as somatic treatments, while considering others for prohibition, such as germline enhancements. Nevertheless, somatic interventions may also be done for controversial enhancement purposes while some germline interventions may be done with greater <i>prima facie</i> justification (e.g., the enhancement of athletic ability versus the avoidance of Tay-Sachs disease). Even with new somatic treatments that are generally lauded, exemplified with the case of Casgevy, many issues still arise - such as cost and access, particularly salient on a global level. The concerns over a dystopian future of genetic haves and have nots, as a result of enhancement and/or germline interventions, that perhaps may happen, should not distract us from a greater attention to what is happening in the here and now. In this paper, we will highlight the limits of the two distinctions in terms of moving from questions of \"should a technology be used\" to \"how should a technology be used.\" We argue that an additional focus on vulnerability and marginalization can be useful to support the attempt to better prioritize which interventions should be permitted or prohibited. We show how this can better dovetail with calls for effective (global) governance and reasonable consensus by focusing on the most urgent issues and developing policy accordingly, while leaving aside more abstract issues for further discussion.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1426228"},"PeriodicalIF":4.9,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11556113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-14eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1455761
Muhammad Jawad Akbar Awan, Imran Amin, Awais Rasheed, Nasir A Saeed, Shahid Mansoor
Recent advances allow the deployment of cluster regularly interspaced short palindromic repeats (CRISPR)-associated endonucleases (Cas) system for the targeted mutagenesis in the genome with accuracy and precision for trait improvement in crops. CRISPR-Cas systems have been extensively utilized to induce knockout or frameshift mutations in the targeted sequence of mostly negative regulating genes for wheat improvement. However, most of the reported work has been done in non-commercial varieties of wheat and introgression of edited alleles into breeding population comes with the penalty of unwanted linkage-drag. Wheat yield is controlled by various genes such as positive and negative regulators. The TaD27 gene is described as a negative regulator of shoot branching or tillering and involved in the biosynthesis of strigolactones. In this study, we developed Tad27 knockout mutant lines of an elite wheat cultivar that showed a twofold increase in the number of tillers and 1.8-fold increase in the number of grains per plant. Subsequently, enhancing the grain yield without any morphological penalty in the architecture of the plants. The co-transformation of regeneration enhancing growth regulator, Growth Regulating Factor 4 (GRF4) and its cofactor GRF-Interacting Factor 1 (GIF1), under single T-DNA cassette improved the regeneration efficiency up to 6% of transgenic events from mature embryos of wheat. Our results indicate that the CRISPR-mediated targeted mutagenesis confers the potential to knockout yield-related negative regulators in elite cultivars of wheat that can substantially enhance grain yield per plant and this strategy can be harnessed for the improvement of future wheat.
{"title":"Knockout mutation in <i>TaD27</i> enhances number of productive tillers in hexaploid wheat.","authors":"Muhammad Jawad Akbar Awan, Imran Amin, Awais Rasheed, Nasir A Saeed, Shahid Mansoor","doi":"10.3389/fgeed.2024.1455761","DOIUrl":"10.3389/fgeed.2024.1455761","url":null,"abstract":"<p><p>Recent advances allow the deployment of cluster regularly interspaced short palindromic repeats (CRISPR)-associated endonucleases (Cas) system for the targeted mutagenesis in the genome with accuracy and precision for trait improvement in crops. CRISPR-Cas systems have been extensively utilized to induce knockout or frameshift mutations in the targeted sequence of mostly negative regulating genes for wheat improvement. However, most of the reported work has been done in non-commercial varieties of wheat and introgression of edited alleles into breeding population comes with the penalty of unwanted linkage-drag. Wheat yield is controlled by various genes such as positive and negative regulators. The <i>TaD27</i> gene is described as a negative regulator of shoot branching or tillering and involved in the biosynthesis of strigolactones. In this study, we developed <i>Tad27</i> knockout mutant lines of an elite wheat cultivar that showed a twofold increase in the number of tillers and 1.8-fold increase in the number of grains per plant. Subsequently, enhancing the grain yield without any morphological penalty in the architecture of the plants. The co-transformation of regeneration enhancing growth regulator, G<i>rowth Regulating Factor 4</i> (<i>GRF4</i>) and its cofactor <i>GRF-Interacting Factor 1</i> (<i>GIF1</i>), under single T-DNA cassette improved the regeneration efficiency up to 6% of transgenic events from mature embryos of wheat. Our results indicate that the CRISPR-mediated targeted mutagenesis confers the potential to knockout yield-related negative regulators in elite cultivars of wheat that can substantially enhance grain yield per plant and this strategy can be harnessed for the improvement of future wheat.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1455761"},"PeriodicalIF":4.9,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11513295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-14eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1427322
Najmeh Heshmatpour, S Maryam Kazemi, Niklas D Schmidt, Sarita R Patnaik, Patrick Korus, Bodo G C Wilkens, Arturo Macarrón Palacios
Diffuse large B cell lymphomas (DLBCL) are highly aggressive tumors. Their genetic complexity and heterogeneity have hampered the development of novel approaches for precision medicine. Our study aimed to develop a personalized therapy for DLBCL by utilizing the CRISPR/Cas system to induce knockouts (KO) of driver genes, thereby causing cancer cell death while minimizing side effects. We focused on OCI-LY3 cells, modeling DLBCL, and compared them with BJAB cells as controls. Analysis of whole exome sequencing revealed significant mutations in genes like PAX5, CD79B, and MYC in OCI-LY3 cells. CRISPR/Cas9-mediated KO of these genes resulted in reduced cancer cell viability. Subsequent single and dual gRNA targeting of PAX5 mutations inhibited proliferation specifically in OCI-LY3 cells. Moreover, dual gRNA targeting of PAX5 and MYC induced chromosomal rearrangements, reducing cell proliferation substantially. However, targeting single intronic mutations did not affect cell viability, highlighting the importance of disrupting protein function. Targeting multiple mutations simultaneously addresses intra-tumoral heterogeneity, and the transient delivery of CRISPR/Cas9 allows for permanent gene disruption. While challenges such as incomplete editing efficiency and delivery limitations exist, further optimization may enhance therapeutic efficacy. Overall, our findings demonstrate the efficacy of CRISPR/Cas9 in targeting oncogenic mutations, opening avenues for precision medicine in DLBCL treatment.
{"title":"Targeting DLBCL by mutation-specific disruption of cancer-driving oncogenes.","authors":"Najmeh Heshmatpour, S Maryam Kazemi, Niklas D Schmidt, Sarita R Patnaik, Patrick Korus, Bodo G C Wilkens, Arturo Macarrón Palacios","doi":"10.3389/fgeed.2024.1427322","DOIUrl":"10.3389/fgeed.2024.1427322","url":null,"abstract":"<p><p>Diffuse large B cell lymphomas (DLBCL) are highly aggressive tumors. Their genetic complexity and heterogeneity have hampered the development of novel approaches for precision medicine. Our study aimed to develop a personalized therapy for DLBCL by utilizing the CRISPR/Cas system to induce knockouts (KO) of driver genes, thereby causing cancer cell death while minimizing side effects. We focused on OCI-LY3 cells, modeling DLBCL, and compared them with BJAB cells as controls. Analysis of whole exome sequencing revealed significant mutations in genes like <i>PAX5</i>, <i>CD79B</i>, and <i>MYC</i> in OCI-LY3 cells. CRISPR/Cas9-mediated KO of these genes resulted in reduced cancer cell viability. Subsequent single and dual gRNA targeting of <i>PAX5</i> mutations inhibited proliferation specifically in OCI-LY3 cells. Moreover, dual gRNA targeting of <i>PAX5</i> and <i>MYC</i> induced chromosomal rearrangements, reducing cell proliferation substantially. However, targeting single intronic mutations did not affect cell viability, highlighting the importance of disrupting protein function. Targeting multiple mutations simultaneously addresses intra-tumoral heterogeneity, and the transient delivery of CRISPR/Cas9 allows for permanent gene disruption. While challenges such as incomplete editing efficiency and delivery limitations exist, further optimization may enhance therapeutic efficacy. Overall, our findings demonstrate the efficacy of CRISPR/Cas9 in targeting oncogenic mutations, opening avenues for precision medicine in DLBCL treatment.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1427322"},"PeriodicalIF":4.9,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11513324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1467449
Zhi Q Yao, Madison B Schank, Juan Zhao, Mohamed El Gazzar, Ling Wang, Yi Zhang, Addison C Hill, Puja Banik, Jaeden S Pyburn, Jonathan P Moorman
Hepatitis B virus (HBV) infection is a common cause of liver disease worldwide. The current antiviral treatment using nucleotide analogues (NAs) can only suppress de novo HBV replication but cannot eliminate chronic HBV infection due to the persistence of covalently closed circular (ccc) DNA that sustains viral replication. The CRISPR/Cas9 system is a novel genome-editing tool that enables precise gene disruption and inactivation. With high efficiency and simplicity, the CRISPR/Cas9 system has been utilized in multiple studies to disrupt the HBV genome specifically, eliciting varying anti-HBV effects both in vitro and in vivo. Additionally, multi-locus gene targeting has shown enhanced antiviral activity, paving the way for combination therapy to disrupt and inactivate HBV cccDNA as well as integrated HBV DNA. Despite its promising antiviral effects, this technology faces several challenges that need to be overcome before its clinical application, i.e., off-target effects and in vivo drug delivery. As such, there is a need for improvement in CRISPR/Cas9 efficiency, specificity, versatility, and delivery. Here, we critically review the recent literature describing the tools employed in designing guide RNAs (gRNAs) targeting HBV genomes, the vehicles used for expressing and delivering CRISPR/Cas9 components, the models used for evaluating CRISPR-mediated HBV gene disruption, the methods used for assessing antiviral and off-target effects induced by CRISPR/Cas9-mediated HBV gene disruption, and the prospects of future directions and challenges in leveraging this HBV gene-editing approach, to advance the HBV treatment toward a clinical cure.
{"title":"The potential of HBV cure: an overview of CRISPR-mediated HBV gene disruption.","authors":"Zhi Q Yao, Madison B Schank, Juan Zhao, Mohamed El Gazzar, Ling Wang, Yi Zhang, Addison C Hill, Puja Banik, Jaeden S Pyburn, Jonathan P Moorman","doi":"10.3389/fgeed.2024.1467449","DOIUrl":"https://doi.org/10.3389/fgeed.2024.1467449","url":null,"abstract":"<p><p>Hepatitis B virus (HBV) infection is a common cause of liver disease worldwide. The current antiviral treatment using nucleotide analogues (NAs) can only suppress <i>de novo</i> HBV replication but cannot eliminate chronic HBV infection due to the persistence of covalently closed circular (ccc) DNA that sustains viral replication. The CRISPR/Cas9 system is a novel genome-editing tool that enables precise gene disruption and inactivation. With high efficiency and simplicity, the CRISPR/Cas9 system has been utilized in multiple studies to disrupt the HBV genome specifically, eliciting varying anti-HBV effects both <i>in vitro</i> and <i>in vivo</i>. Additionally, multi-locus gene targeting has shown enhanced antiviral activity, paving the way for combination therapy to disrupt and inactivate HBV cccDNA as well as integrated HBV DNA. Despite its promising antiviral effects, this technology faces several challenges that need to be overcome before its clinical application, i.e., off-target effects and <i>in vivo</i> drug delivery. As such, there is a need for improvement in CRISPR/Cas9 efficiency, specificity, versatility, and delivery. Here, we critically review the recent literature describing the tools employed in designing guide RNAs (gRNAs) targeting HBV genomes, the vehicles used for expressing and delivering CRISPR/Cas9 components, the models used for evaluating CRISPR-mediated HBV gene disruption, the methods used for assessing antiviral and off-target effects induced by CRISPR/Cas9-mediated HBV gene disruption, and the prospects of future directions and challenges in leveraging this HBV gene-editing approach, to advance the HBV treatment toward a clinical cure.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1467449"},"PeriodicalIF":4.9,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11496132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-26eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1471720
Song Hee Jeong, Ho Joung Lee, Sang Jun Lee
The paired nickases approach, which utilizes clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) nickase and dual guide RNA, has the advantage of reducing off-target effects by being able to double the target sequence. In this study, our research utilized the Cas9-NG nickase variant to minimize PAM sequence constraints, enabling the generation of paired nicks at desired genomic loci. We performed a systematic investigation into the formation sites for double nicks and the design of donor DNA within a bacterial model system. Although we successfully identified the conditions necessary for the effective formation of double nicks in vivo, achieving single-nucleotide level editing directly at the target sites in the genome proved challenging. Nonetheless, our experiments revealed that efficient editing at the single-nucleotide level was achievable on target DNA sequences that are hybridized with 5'-end-truncated dual single-guide RNAs (sgRNAs). Our findings contribute to a deeper understanding of the paired nickases approach, offering a single-mismatch intolerance design strategy for accurate nucleotide editing. This strategy not only enhances the precision of genome editing but also marks a significant step forward in the development of nickase-derived genome editing technologies.
配对切口酶方法利用聚类规则间隔短回文重复序列(CRISPR)-CRISPR相关蛋白(Cas)切口酶和双引导RNA,其优点是能够加倍靶序列,从而减少脱靶效应。在本研究中,我们利用Cas9-NG切口酶变体最大程度地减少了PAM序列限制,从而在所需的基因组位点上生成了成对的切口。我们在细菌模型系统中对双缺口的形成位点和供体 DNA 的设计进行了系统研究。虽然我们成功地确定了在体内有效形成双缺口的必要条件,但直接在基因组的目标位点实现单核苷酸水平的编辑证明具有挑战性。不过,我们的实验表明,在与 5'-end-truncated 双单导 RNA(sgRNA)杂交的目标 DNA 序列上,可以实现单核苷酸水平的高效编辑。我们的研究结果有助于加深对成对缺口酶方法的理解,为精确的核苷酸编辑提供了一种单错配不容忍设计策略。这一策略不仅提高了基因组编辑的精确度,而且标志着镍酶衍生基因组编辑技术的发展向前迈出了重要一步。
{"title":"Use of paired Cas9-NG nickase and truncated sgRNAs for single-nucleotide microbial genome editing.","authors":"Song Hee Jeong, Ho Joung Lee, Sang Jun Lee","doi":"10.3389/fgeed.2024.1471720","DOIUrl":"10.3389/fgeed.2024.1471720","url":null,"abstract":"<p><p>The paired nickases approach, which utilizes clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) nickase and dual guide RNA, has the advantage of reducing off-target effects by being able to double the target sequence. In this study, our research utilized the Cas9-NG nickase variant to minimize PAM sequence constraints, enabling the generation of paired nicks at desired genomic loci. We performed a systematic investigation into the formation sites for double nicks and the design of donor DNA within a bacterial model system. Although we successfully identified the conditions necessary for the effective formation of double nicks <i>in vivo</i>, achieving single-nucleotide level editing directly at the target sites in the genome proved challenging. Nonetheless, our experiments revealed that efficient editing at the single-nucleotide level was achievable on target DNA sequences that are hybridized with 5'-end-truncated dual single-guide RNAs (sgRNAs). Our findings contribute to a deeper understanding of the paired nickases approach, offering a single-mismatch intolerance design strategy for accurate nucleotide editing. This strategy not only enhances the precision of genome editing but also marks a significant step forward in the development of nickase-derived genome editing technologies.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1471720"},"PeriodicalIF":4.9,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11464485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-25eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1464531
Shivani Goolab, Janine Scholefield
The designer nuclease, CRISPR-Cas9 system has advanced the field of genome engineering owing to its programmability and ease of use. The application of these molecular scissors for genome engineering earned the developing researchers the Nobel prize in Chemistry in the year 2020. At present, the potential of this technology to improve global challenges continues to grow exponentially. CRISPR-Cas9 shows promise in the recent advances made in the Global North such as the FDA-approved gene therapy for the treatment of sickle cell anaemia and β-thalassemia and the gene editing of porcine kidney for xenotransplantation into humans affected by end-stage kidney failure. Limited resources, low government investment with an allocation of 1% of gross domestic production to research and development including a shortage of skilled professionals and lack of knowledge may preclude the use of this revolutionary technology in the Global South where the countries involved have reduced science and technology budgets. Focusing on the practical application of genome engineering, successful genetic manipulation is not easily accomplishable and is influenced by the chromatin landscape of the target locus, guide RNA selection, the experimental design including the profiling of the gene edited cells, which impacts the overall outcome achieved. Our assessment primarily delves into economical approaches of performing efficient genome engineering to support the first-time user restricted by limited resources with the aim of democratizing the use of the technology across low- and middle-income countries. Here we provide a comprehensive overview on existing experimental techniques, the significance for target locus analysis and current pitfalls such as the underrepresentation of global genetic diversity. Several perspectives of genome engineering approaches are outlined, which can be adopted in a resource limited setting to enable a higher success rate of genome editing-based innovations in low- and middle-income countries.
{"title":"Making gene editing accessible in resource limited environments: recommendations to guide a first-time user.","authors":"Shivani Goolab, Janine Scholefield","doi":"10.3389/fgeed.2024.1464531","DOIUrl":"10.3389/fgeed.2024.1464531","url":null,"abstract":"<p><p>The designer nuclease, CRISPR-Cas9 system has advanced the field of genome engineering owing to its programmability and ease of use. The application of these molecular scissors for genome engineering earned the developing researchers the Nobel prize in Chemistry in the year 2020. At present, the potential of this technology to improve global challenges continues to grow exponentially. CRISPR-Cas9 shows promise in the recent advances made in the Global North such as the FDA-approved gene therapy for the treatment of sickle cell anaemia and β-thalassemia and the gene editing of porcine kidney for xenotransplantation into humans affected by end-stage kidney failure. Limited resources, low government investment with an allocation of 1% of gross domestic production to research and development including a shortage of skilled professionals and lack of knowledge may preclude the use of this revolutionary technology in the Global South where the countries involved have reduced science and technology budgets. Focusing on the practical application of genome engineering, successful genetic manipulation is not easily accomplishable and is influenced by the chromatin landscape of the target locus, guide RNA selection, the experimental design including the profiling of the gene edited cells, which impacts the overall outcome achieved. Our assessment primarily delves into economical approaches of performing efficient genome engineering to support the first-time user restricted by limited resources with the aim of democratizing the use of the technology across low- and middle-income countries. Here we provide a comprehensive overview on existing experimental techniques, the significance for target locus analysis and current pitfalls such as the underrepresentation of global genetic diversity. Several perspectives of genome engineering approaches are outlined, which can be adopted in a resource limited setting to enable a higher success rate of genome editing-based innovations in low- and middle-income countries.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1464531"},"PeriodicalIF":4.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11461239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-24eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1467080
Diane Wray-Cahen, Eric Hallerman, Mark Tizard
Genome editing (GnEd) has the potential to provide many benefits to animal agriculture, offering a means for achieving rapid growth, disease resistance, and novel phenotypes. The technology has the potential to be useful for rapidly incorporating traits into existing selectively bred animals without the need for crossbreeding and backcrossing. Yet only four products from animals created via biotechnology, all growth-enhanced fishes, have reached commercialization and only on a limited scale. The past failure of genetically engineered (or GM) products to reach conventional producers can largely be attributed to the high cost of meeting GMO regulatory requirements. We review the history of GMO regulations internationally, noting the influence of Codex Alimentarius on the development of many existing regulatory frameworks. We highlight new regulatory approaches for GnEd organisms, first developed by Argentina, and the adoption of similar approaches by other countries. Such new regulatory approaches allow GnEd organisms that could have been developed by conventional means to be regulated under the same rules as conventional organisms and in the future is likely to enhance the opportunity for biotech animals to enter production. Treating certain GnEd products as conventional has had a large impact on the variety of biotechnological innovations successfully navigating regulatory processes. We suggest that for the full potential of GnEd technologies to be realized, enabling public policies are needed to facilitate use of GnEd as a breeding tool to incorporate new traits within existing animal breeding programs, rather than only a tool to create distinct new products.
{"title":"Global regulatory policies for animal biotechnology: overview, opportunities and challenges.","authors":"Diane Wray-Cahen, Eric Hallerman, Mark Tizard","doi":"10.3389/fgeed.2024.1467080","DOIUrl":"https://doi.org/10.3389/fgeed.2024.1467080","url":null,"abstract":"<p><p>Genome editing (GnEd) has the potential to provide many benefits to animal agriculture, offering a means for achieving rapid growth, disease resistance, and novel phenotypes. The technology has the potential to be useful for rapidly incorporating traits into existing selectively bred animals without the need for crossbreeding and backcrossing. Yet only four products from animals created via biotechnology, all growth-enhanced fishes, have reached commercialization and only on a limited scale. The past failure of genetically engineered (or GM) products to reach conventional producers can largely be attributed to the high cost of meeting GMO regulatory requirements. We review the history of GMO regulations internationally, noting the influence of Codex Alimentarius on the development of many existing regulatory frameworks. We highlight new regulatory approaches for GnEd organisms, first developed by Argentina, and the adoption of similar approaches by other countries. Such new regulatory approaches allow GnEd organisms that could have been developed by conventional means to be regulated under the same rules as conventional organisms and in the future is likely to enhance the opportunity for biotech animals to enter production. Treating certain GnEd products as conventional has had a large impact on the variety of biotechnological innovations successfully navigating regulatory processes. We suggest that for the full potential of GnEd technologies to be realized, enabling public policies are needed to facilitate use of GnEd as a breeding tool to incorporate new traits within existing animal breeding programs, rather than only a tool to create distinct new products.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1467080"},"PeriodicalIF":4.9,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11459211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1401088
Muhammad Sulyman Saleem, Sultan Habibullah Khan, Aftab Ahmad, Iqrar Ahmad Rana, Zunaira Afzal Naveed, Azeem Iqbal Khan
Cotton is globally known for its high-priority cellulose-rich natural fiber. In addition to providing fiber for the textile industry, it is an important source material for edible oil, livestock feed, and fuel products. Global warming and the growing population are the major challenges to the world's agriculture and the potential risks to food security. In this context, improving output traits in cotton is necessary to achieve sustainable cotton production. During the last few years, high throughput omics techniques have aided in identifying crucial genes associated with traits of cotton fiber, seed, and plant architecture which could be targeted with more precision and efficiency through the CIRPSR/Cas-mediated genome editing technique. The various CRISPR/Cas systems such as CRISPR/Cas9, CRISPR/nCas9, and CRISPR/Cas12a have been employed to edit cotton genes associated with a wide range of traits including fiber length, flowering, leaf colour, rooting, seed oil, plant architecture, gossypol content, somatic embryogenesis, and biotic and abiotic stresses tolerance, highlighting its effectiveness in editing the cotton genome. Thus, CRISPR/Cas-mediated genome editing has emerged as a technique of choice to tailor crop phenotypes for better yield potential and environmental resilience. The review covers a comprehensive analysis of cotton phenotypic traits and their improvement with the help of the latest genome editing tools to improve fiber, food, feed, and fuel-associated genes of cotton to ensure food security.
{"title":"The 4Fs of cotton: genome editing of cotton for fiber, food, feed, and fuel to achieve zero hunger.","authors":"Muhammad Sulyman Saleem, Sultan Habibullah Khan, Aftab Ahmad, Iqrar Ahmad Rana, Zunaira Afzal Naveed, Azeem Iqbal Khan","doi":"10.3389/fgeed.2024.1401088","DOIUrl":"https://doi.org/10.3389/fgeed.2024.1401088","url":null,"abstract":"<p><p>Cotton is globally known for its high-priority cellulose-rich natural fiber. In addition to providing fiber for the textile industry, it is an important source material for edible oil, livestock feed, and fuel products. Global warming and the growing population are the major challenges to the world's agriculture and the potential risks to food security. In this context, improving output traits in cotton is necessary to achieve sustainable cotton production. During the last few years, high throughput omics techniques have aided in identifying crucial genes associated with traits of cotton fiber, seed, and plant architecture which could be targeted with more precision and efficiency through the CIRPSR/Cas-mediated genome editing technique. The various CRISPR/Cas systems such as CRISPR/Cas9, CRISPR/nCas9, and CRISPR/Cas12a have been employed to edit cotton genes associated with a wide range of traits including fiber length, flowering, leaf colour, rooting, seed oil, plant architecture, gossypol content, somatic embryogenesis, and biotic and abiotic stresses tolerance, highlighting its effectiveness in editing the cotton genome. Thus, CRISPR/Cas-mediated genome editing has emerged as a technique of choice to tailor crop phenotypes for better yield potential and environmental resilience. The review covers a comprehensive analysis of cotton phenotypic traits and their improvement with the help of the latest genome editing tools to improve fiber, food, feed, and fuel-associated genes of cotton to ensure food security.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1401088"},"PeriodicalIF":4.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11424549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-23eCollection Date: 2024-01-01DOI: 10.3389/fgeed.2024.1458037
Chiara Simoni, Elena Barbon, Andrés F Muro, Alessio Cantore
The liver is an essential organ of the body that performs several vital functions, including the metabolism of biomolecules, foreign substances, and toxins, and the production of plasma proteins, such as coagulation factors. There are hundreds of genetic disorders affecting liver functions and, for many of them, the only curative option is orthotopic liver transplantation, which nevertheless entails many risks and long-term complications. Some peculiar features of the liver, such as its large blood flow supply and the tolerogenic immune environment, make it an attractive target for in vivo gene therapy approaches. In recent years, several genome-editing tools mainly based on the clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) system have been successfully exploited in the context of liver-directed preclinical or clinical therapeutic applications. These include gene knock-out, knock-in, activation, interference, or base and prime editing approaches. Despite many achievements, important challenges still need to be addressed to broaden clinical applications, such as the optimization of the delivery methods, the improvement of the editing efficiency, and the risk of on-target or off-target unwanted effects and chromosomal rearrangements. In this review, we highlight the latest progress in the development of in vivo liver-targeted genome editing approaches for the treatment of genetic disorders. We describe the technological advancements that are currently under investigation, the challenges to overcome for clinical applicability, and the future perspectives of this technology.
{"title":"<i>In vivo</i> liver targeted genome editing as therapeutic approach: progresses and challenges.","authors":"Chiara Simoni, Elena Barbon, Andrés F Muro, Alessio Cantore","doi":"10.3389/fgeed.2024.1458037","DOIUrl":"10.3389/fgeed.2024.1458037","url":null,"abstract":"<p><p>The liver is an essential organ of the body that performs several vital functions, including the metabolism of biomolecules, foreign substances, and toxins, and the production of plasma proteins, such as coagulation factors. There are hundreds of genetic disorders affecting liver functions and, for many of them, the only curative option is orthotopic liver transplantation, which nevertheless entails many risks and long-term complications. Some peculiar features of the liver, such as its large blood flow supply and the tolerogenic immune environment, make it an attractive target for <i>in vivo</i> gene therapy approaches. In recent years, several genome-editing tools mainly based on the clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) system have been successfully exploited in the context of liver-directed preclinical or clinical therapeutic applications. These include gene knock-out, knock-in, activation, interference, or base and prime editing approaches. Despite many achievements, important challenges still need to be addressed to broaden clinical applications, such as the optimization of the delivery methods, the improvement of the editing efficiency, and the risk of on-target or off-target unwanted effects and chromosomal rearrangements. In this review, we highlight the latest progress in the development of <i>in vivo</i> liver-targeted genome editing approaches for the treatment of genetic disorders. We describe the technological advancements that are currently under investigation, the challenges to overcome for clinical applicability, and the future perspectives of this technology.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"6 ","pages":"1458037"},"PeriodicalIF":4.9,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11378722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142157203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}