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• Published: 27 March 2023

Thermostable enzyme research advances: a bibliometric analysis

• Che Haznie Ayu Che Hussian   ORCID: orcid.org/0000-0001-8798-9840 1 &
• Wai Yie Leong 1  

Journal of Genetic Engineering and Biotechnology volume  21 , Article number:  37 ( 2023 ) Cite this article

3349 Accesses

11 Citations

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Thermostable enzymes are enzymes that can withstand elevated temperatures as high as 50 °C without altering their structure or distinctive features. The potential of thermostable enzymes to increase the conversion rate at high temperature has been identified as a key factor in enhancing the efficiency of industrial operations. Performing procedures at higher temperatures with thermostable enzymes minimises the risk of microbial contamination, which is one of the most significant benefits. In addition, it helps reduce substrate viscosity, improve transfer speeds, and increase solubility during reaction operations. Thermostable enzymes offer enormous industrial potential as biocatalysts, especially cellulase and xylanase, which have garnered considerable amount of interest for biodegradation and biofuel applications. As the usage of enzymes becomes more common, a range of performance-enhancing applications are being explored. This article offers a bibliometric evaluation of thermostable enzymes. Scopus databases were searched for scientific articles. The findings indicated that thermostable enzymes are widely employed in biodegradation as well as in biofuel and biomass production. Japan, the United States, China, and India, as along with the institutions affiliated with these nations, stand out as the academically most productive in the field of thermostable enzymes. This study’s analysis exposed a vast number of published papers that demonstrate the industrial potential of thermostable enzymes. These results highlight the significance of thermostable enzyme research for a variety of applications.

Recent developments in biological based materials for a variety of applications have begun to penetrate the industrial sector [ 1 , 2 ]. As a result, several industries are now taking steps to transition from chemical-based manufacturing to clean biological manufacturing. [ 3 , 4 , 5 ]. Enzymes are proteins that operate as biological catalysts in biological systems, speeding up reactions and catalyzing chemical reaction functions [ 6 , 7 , 8 ]. Enzymes are increasingly being used in a wide range of industrial processes due to their great specificity of action. Their benefits include their efficiency in speeding chemical reactions and their selectivity in distinguishing between potential substrates [ 6 , 9 , 10 ]. Enzymes may aid in the development of environmentally friendly processes by displacing toxic chemicals used in industrial manufacturing [ 11 , 12 , 13 ].

Enzymes can be utilized in many industrial production processes, enabling the creation of environmentally friendly technology processes without creation of waste and production of hazardous chemicals such as detergent formulations, cheese production, the leather industry and pharmaceuticals industry [ 8 , 14 , 15 , 16 , 17 ]. However, the most major difficulty to the widespread commercial deployment of enzymes is their intrinsic fragility under rigorous industrial operations conditions, one of which is that they cannot sustain the process's high temperature. The majority of enzymes lose activity at higher temperatures, which are typically between 25 °C and 37 °C [ 18 ]. Enzymes derived from thermophiles have affected the interest of numerous businesses, including the pharmaceutical, detergent, textile, food, feed industries, leather, and paper, as well as biorefineries [ 19 , 20 ]. The term for these enzymes is “thermostable enzymes”.

Thermostable enzymes are enzymes that can resist high temperatures, typically between 45 °C and 120 °C [ 2 ]. These enzymes not only survive at high temperatures, but they also work in severe environments where humans cannot exist. Thermostable enzymes provide numerous benefits to the industrial sector, including a rapid growth rate, a reduced risk of contamination, a reduction in liquid viscosity, and improved solubility in polymeric substrates and oil [ 21 ]. The resistance of thermostable enzymes to proteolysis and chemical denaturation is greater. With these benefits, it is possible to slow down the process of denaturation, which is essential for commercial preparations, and to store them at room temperature for a longer half-life. Many different enzymes have been identified from thermophiles, including cellulases, amylases, xylanases, pectinases, proteases, and lipases [ 22 , 23 , 24 , 25 ].

Numerous thermophilic microbial taxa, such as Bacillus , Clostridium , Pyrococcus , Thermus, Thermotoga , and Aquifex , produce unique enzymes including α-amylase, lipase, cellulase, xylanase, alkaline phosphatase, polymerase and ligase [ 18 ]. Taq polymerase was the first thermostable enzyme to be reported in 1976 [ 26 ]. It was discovered from thermal springs of Yellowstone National Park in 1969 and was isolated from Thermus Aquaticus . The ideal temperature for activity was determined to be 75–80 °C, with a half-life of 2 h at 92.5 °C, 40 min at 95 °C, and 9 min at 97.5 °C [ 27 ]. Formerly, DNA polymerases obtained from Escherichia coli were used in polymerase chain reaction (PCR) methods [ 28 ]. Nevertheless, they lost their enzymatic activity at high temperatures, necessitating the addition of a new polymerase enzyme after each cycle of denaturation and primer hybridization, which was time-consuming and costly. As a result, the availability of thermostable Taq DNA polymerase has an impact on the PCR development process since it can survive the 95 °C required for DNA strand separation without denaturing. Thermophilic microorganisms are occupying several biological niches, including hot springs, deep marine, volcanic sites, compost and deep organic landfills [ 29 ]. However, they have been widely investigated in hot springs around the world and are abundant in nature [ 30 ]. Hot springs have been identified as natural habitats that are ideal for thermophile colonization.

Since 1970, numerous studies have been undertaken on thermostable enzymes. As this protein differs from mesophilic enzymes in its structural properties and adaptations to the harsh environment, the majority of the studies have been oriented to studying these characteristics [ 25 , 31 ]. Thermophiles have rigid cell walls, a high G + C concentration of DNA contents that ultimately alters these protein structure [ 32 ]. This component causes these enzymes to have distinct hydrogen bonds, electrostatic interactions, hydrophilic contacts, metal binding and loop deletion or shortening, which eventually results in a superior conformational shape. Enzyme thermostability is typically an intrinsic feature determined by the primary protein structure. The thermostable enzymes were more stable than the mesophilic enzymes because they had larger levels of non-polar amino acids [ 33 ]. These amino acids increase the hydrophobicity of proteins, which is directed towards the catalytic pocket and increases the rigidity of proteins [ 34 ]. Furthermore, the higher charged of amino acids also enhance the electrostatic interactions in the outer part of protein leading greater ion pair interaction [ 35 ]. Studies also revealed that thermostable enzymes contain higher disulphide bonds and hydrophobic bonds [ 36 ]. These criteria make the structure of the enzymes more rigid and lead to better folding of the conformational.

Technologies for data extraction and synthesis are currently essential due to the abundance of data available. Bibliometric analysis is a statistical methodology that use [ 37 , 38 ] to analyze and evaluate a significant number of scientific research articles in various fields of knowledge. Bibliometric is very important for uncovering developing trends in a specific topic or field by identifying the relationship of core research or authors across all publications, journal performance, collaboration patterns, and research constituents [ 39 ]. The findings of academic publishing analysis have proven to be an excellent method of measuring the impact of research trends [ 40 ]. As a result, the researcher can find knowledge gaps concerning the issue and develop new original ideas for investigation and contribution to the specific research topic. Through bibliometric analysis, it is possible to gain a comprehensive understanding of a certain topic and its relationship to specific databases. Utilizing interaction charts, this popular method provides a simple and easy assessment of selected works. The publication year, the most-cited articles, journals, authors, and fields of study were all examined in this study's bibliometric analysis of thermostable enzymes. Current trends in thermostable enzymes are examined in light of relevant research.

Scientific literature research

The Scopus database ( www.scopus.com ) was recovered in September 2022 using the search terms "thermostable enzyme" AND "thermostable" AND "enzymes" (Fig.  1 ), with only research publications and review studies included. There were no time restrictions placed on the search, and all publications up to the search year (1970–2022). This allows us to estimate the global research output on thermostable enzymes from a large number of high-quality journal papers. The "analyze results" feature of Scopus's search tools displays the publication year and topic matter of the chosen work. The articles we gathered were examined using VOSviewer version 1.6.15, which was used to import all data into a Microsoft Excel spreadsheet (csv) ( www.vosviewer.com ). VOSviewer is a software tool used in bibliometric analysis by constructing and visualising the networks of publications, documents, sources, authors, organizations, and countries. These networks can be built via citation, bibliographic coupling, co-citation, or co-authorship relationships. It also provides network mapping of the relationships between bibliometric networks and the topic of interest. In this study, the data were collected to determine the most productive countries, the most highly referenced journals, authors, publications and research trends based on keyword analysis. Several different types and units of analysis were used to construct the results.

Flowchart of bibliometric search strategy

Analysis of publications

General analysis.

The aforementioned search method accumulates 1090 articles, which were divided into 11 categories of research topics (Fig.  2 ). The search for articles and reviews was narrowed down to 1010 publications. 97% ( n  = 3925) of them were written in English, 1.03% ( n  = 42) in Chinese and 1.97% in other languages. The first study on thermostable enzymes published was the purification of thermostable isoleucyl-tRNA synthetase from Bacillus stearothermophilus in 1972 [ 41 ]. After 1995, the number of articles increased each year, finally surpassing 20 and going over 40. The distribution of articles by study area from 1970 to 2022 is shown in Fig.  3 . Qualitative trend analysis for each study area with more than 100 publications between 2017 and 2022 was conducted to examine the most common use of thermostable enzymes during the preceding five years (biochemistry, genetic and molecular biology, immunology and microbiology, chemical engineering, chemistry and agricultural and biological sciences).

The main research topic related to thermostable enzymes (Scopus)

Annual scientific production of articles on thermostable enzymes

Biochemistry, genetics and molecular biology

Study on the isolation and characterization [ 42 , 43 , 44 , 45 ], expression and purification [ 46 , 47 , 48 , 49 , 50 ], gene cloning, structural function analysis, improving catalytic efficiency, site-directed mutagenesis, protein crystallization, computational simulations, rational engineering to improve enzymes activity [ 51 , 52 , 53 , 54 , 55 , 56 ] preservation of enzymes, indigenous thermophilic exploration, cell-free enzymatic, polymerase synthesis, marine thermophiles, enzymatic purification and biodegradation [ 57 , 58 , 59 ]. The most important enzymes: Cellulose, xylanase, lipase and amylase.

Immunology and microbiology

Study on immunogenicity of subunit vaccine [ 60 ], biosensor, detection of organic pollutants [ 61 ], enzymatic bioreceptor [ 62 ], applications to in vitro biosynthesis, substrate specificity, improvement catalytic performance, biomedical, preparation of pharmacologically active icaritin, in vitro antioxidant activity, cancer prodrug-mediated therapies or gene therapy applications [ 63 , 64 , 65 ]. The most important enzymes: Esterase-2, endoglucanase, aldehyde dehydrogenase, cellulose, xylanase and laccase.

Chemical engineering

Study on dye-linked L-lactate dehydrogenase [ 66 ], lignification [ 67 ], dishwashing machine [ 68 ], degradation of lignocellulose [ 69 ], biodegradable polymer, biotransformation, fine chemical industry, bio-bleaching and dye decolorizing agent [ 70 ], renewable bioethanol [ 71 ] and enzyme immobilization for the hydrolysis reaction [ 72 ]. The most important enzymes: Lipase, cellulase, xylanase, glucosidase and amylase.

Agricultural and biological sciences

Study on class III peroxidases (POX) plants [ 73 ], Calotropis procera root peroxidase (CPrP) [ 74 ], oxidoreductive enzymes, microalgal and cyanobacterial [ 75 ] and bioremediate phenol from petroleum effluent [ 57 ]. The most important enzymes: Amylase, peroxidase, esterase.

Enzymes-based sensor [ 76 ], Flavoenzyme dye-linked L-lactate dehydrogenase (Dye-LDH) [ 66 ], degradation of poly (lactic acid), PLA, biodegradation of xenobiotics [ 77 ], aromatic compounds and lactic acid, enzyme immobilization on carboxymethyl cellulose (CMC)-hydrogel, organic chemistry, synthetic catalyst and bioremediation—dimethylformamidase (DMFase) [ 78 ]. The most important enzymes: Dehydrogenase, peroxidases, phosphatase and pectate lyse.

• Research trends

According to the results of a general analysis, most research on thermostable enzymes has been carried out in the fields of biochemistry, genetics and molecular biology [ 79 , 80 ]. All studies on this topic, were focuses more on strategies used to enhance thermostable enzymes, such as molecular, characterization, genetic alteration to improve catalytic activity and purification. Although the quest for thermophiles began 40 years ago, the discovery of important and novel thermostable enzymes continues to rise, making the search for and isolation of thermophiles an essential topic of research. However, based on the industrial potential of thermostable enzymes, the majority of research focuses on lignocellulosic biodegradation for biofuel production. The biodegradable process requires severe conditions for the hydrolysis of lignocellulosic biomass [ 67 , 79 ]. Enzymatic degradation is the most effective and environmentally safe method for converting complex lignocellulose polymers into fermentable monosaccharides, compared to chemical and physical procedures. Cellulase and xylanase are the thermostable enzymes that are involved in this industrial sector [ 4 , 5 , 12 ]. The usefulness of thermostable cellulases and xylanases is primarily determined by their productivity, thermostability, specific activity, broad pH range and broad substrate specificity. Using genetic engineering, expression control and enzyme immobilization, the thermostability of thermophile cellulase and xylanase has been increased in order to expand their industrial applications. Most approaches involve site-directed mutagenesis, whereas cloning was used to increase the enzymes' stability.

Top research institutions and countries

A review of publications by nation revealed that the top 10 countries represented 79.90% ( n  = 807) of all articles (Fig.  4 ). Japan came in first with 15.6% of all papers produced, followed by the United States (15%), China (11.88%) and India (9.10%). The top 10 institutions with the most publications included three Chinese universities and five Japanese universities. Other countries, such as India, Germany, South Korea and the United States (US), did not have any institutions in the top 10, while the US had just one. From search results analysis based on document affiliations, Osaka University Japan was the top research institution for the study of thermostable enzymes with 25 documents followed by the Consiglio Nazionale delle Ricerche Italy, the Russian Academy of Sciences, Kyoto University and the Ministry of Education, China (Fig. 5 ).

Collaborative networks between the 20 most productive countries in the research of thermostable enzymes according to a bibliometric analysis of the Scopus database

Number of publications per country and top research institutions on thermostable enzyme research based on the Scopus database

Most global cited documents

We examined the number of citations of articles published between 1976 and 2022 to identify the most cited articles of recent times and determined that highly referred publications are often older. As indicated in Table 1 , Holland (1991) [ 81 ] had the most referenced articles throughout this time span, with 2,147 citations. The 5'-3' exonuclease activity of Taq DNA polymerase from Thermus aquaticus was used by the authors to create a simple and effective approach for identifying PCR products. This enzyme is frequently employed for PCR amplification because of its exceptional heat resistance. At 72 °C, nucleotides are integrated at a rate of 2 and 4 kb/min, while their half-life at 95 °C is 40 min.

The second most cited review article, ‘Developments in Industrially Significant Thermostable Enzymes: A Review ‘ by Haki and Rakshit [ 82 ], with 883 citations. The authors are connected to the Thai Asian Institute of Technology's Bioprocess Technology Program (AIT). The number of applications for enzymes has increased as a result of the creation of thermostable enzymes, as this review article explains. Due to their inherent stability, thermophilic organisms have discovered a variety of economic applications as a result of the numerous studies that have been conducted to identify them. The food industry (which synthesizes amino acids), the petroleum, chemical and paper sectors are the next largest users of thermostable enzymes in the starch sector [ 91 , 92 , 93 ].

Barany is the author of third most cited article which published in the same journal as Holland 1991, Journal of Proceeding Natl Acad Sci USA . Barany is a researcher from the Cornell University Medical College, New York has conducted a study on genetic disease detection and DNA amplification using cloned thermostable ligase from Thermus aquaticus [ 83 ].

Fernandez-Lafuente is the fourth most cited review article with total citation about 449. Fernandez-Lafuente is a researcher from the Instituto de Catálisis-CSIC, Spain. The most cited article in 2010 is specific for thermostable lipase from Thermomyces laguginosus which available in both soluble and immobilized form [ 84 ].

Most relevant authors

Rossi Mosè E, a researcher at the Consiglio Nazionale delle Ricerche in Rome, Italy, is the most cited and notable author. His 445 papers were cited 11,991 times in 6737 different documents. The author has written 13 articles on the study of thermostable enzymes, and the paper titled "Crystal structure of the most catalytically effective carbonic anhydrase enzyme, SazCA from the thermophilic bacterium Sulfurihydrogenibium azorense " has received the most citations, with 62 citations [ 52 ]. Oh Deokkun, a scholar at Konkuk University in Seoul, South Korea, is the second most cited author (8286 citations). The most recent publication, which has 74 citations, was released in 2011 where the research was conducted on cloning and expression of thermostable cellobiose 2-epimerase, a from Caldicellulosiruptor saccharolyticus into Escherichia coli as expression host [ 44 ].

The collaborative network among authors has been analyzed. From the VOSviewer bibliometric analysis in Fig. 6 , there are seven clusters of authors that connected with each other on thermostable enzyme research, but Rossi Mosè and Oh Deokkun were not included in the collaborative network. However, Ohshima, T (Cluster 3) is the third most cited author (3315 citations) and a researcher from Osaka Institute of Technology, Japan. He has connections with the fourth most cited author, Soda. K (Cluster 4) who is from the Institute of Chemical Research, Kyoto University. Both of them published a review paper together in 1989 with the title’Thermostable amino acid dehydrogenases: applications and gene cloning ‘ which was cited by 33 authors [ 94 ]. Cluster 1 consists of eight connected authors, which are Gao, R., Wang, Y., Wang, Xiaojuan, Wang, Zhongyu (Jilin University, China). They are members of the same research group at Key Laboratory for Molecular Enzymology and Engineering.

The top 30 most productive authors collaborate in thermostable lipase research according to a bibliometric analysis of the Scopus database

Recent research

Recent research on thermostable lipase was analyzed in the Scopus database from 2018–2022 (5 years). From the results, Febbraio Ferdinando from Consiglio Nazionale delle Ricerche, Rome, Italy (same affiliations with the most relevant authors, Rossi Mosè) have much more research on enzyme-based biosensor by using thermostable lipase. The most recent research paper on biosensor fluorescent detection of organophosphate pesticides using the thermostable enzyme esterase-2 from Alicyclobacillus acidocaldarius (EST2) with a lipase-like Ser-His-Asp catalytic triad was published in 2022, and is a promising candidate as a bioreceptor for the development of biosensor [ 62 ].

Huiying Luo, a researcher at the Chinese Academy of Agricultural Sciences in Beijing, China, studies thermostable xylanase and cellulase, which are commonly used to decompose lignocellulosic biomass and have potential applications in the feed and fuel industries [ 95 , 96 ]. This study sheds light on the underlying mechanism and methods of modifying xylanase for commercial use.

Most relevant journals

The Journal of Applied Microbiology and Biotechnology , published by Springer Nature, ranked first, with 43 papers and 1066 citations. Table 2 shows that 20% of all publications on the subject may be attributed to the top 10 journals. From 43 documents, the highest cited paper is written by Bragger (1989) with research on extremely thermophilic archaebacteria and eubacteria with 101 citations [ 97 ]. This article demonstrated the isolation of 36 thermophilic eubacteria for extracellular amylase, hemicellulase (xylanase), cellulase, protease, pectinase and lipase activities. As shown in Table 3 , the journal had an impact factor of 3.3 and a CiteScore of 8.8 in 2019; thus, it received an average of 8.8 citations per article published. This publication is of tremendous relevance in the field since, as its title suggests, it focuses primarily on the application of microorganism-derived enzymes in biotechnology.

The Journal of Enzyme and Microbial Technology , with 36 articles, is the second most relevant publication in the field. Its publications had to do with technological advancements. Bioresource Technology is the most prominent journal on the subject, with an impact factor of 11.889 and 13 articles. This journal published Haki & Rakshit (2003), which is one of the top 10 most referenced papers with 885 citations. Their principal fields of publication were Bioscience, Biotechnology, and Biochemistry ranked third among the most cited journals with twenty citations for 18 published publications. 33% of the top ten journals were published in the United States, 30% in the United Kingdom, 21% in Germany, and 16% in the Netherlands. Thus, 67% of the journals were European and 33% were North American.

Keyword trends analysis

The purpose of keyword co-occurrence analysis is to identify emerging trends and hot subjects, and it is an important method for tracking scientific progress. The findings of the trend analysis for the time periods utilising keywords with at least 30 occurrences are displayed in Fig.  7 and Table 3 . The result revealed that there were 7996 keywords in the 1,010 articles, and 135 keywords appeared 30 times or more. For better interpretation of results, the terms used for the literature search were omitted from Fig.  7 . From the results, 5 clusters were obtained from total keywords. Analysis of the keyword trend revealed that studies were associated with amylase, beta glucosidase, biofuel, cellulase, and cellulose are included in cluster 1 (Table 3 ). We highlight the fact that research on thermostable enzymes and biofuel production began to emerge strongly in this time range.

Keyword trend analysis of scientific publications on thermostable enzymes in the Scopus collections database (1976-2022)

Conclusions

This study has detailed the current research status on thermostable enzymes that has increased throughout the years. We detected a trend toward the application of thermostable enzymes in several industrial research domains, notably for ecologically friendly approaches to address pollution and bioremediation. Enzymatic production of biodiesel is expected to be a trend in the coming years, encouraged by the increasing interest in natural components and green technologies. The usage of thermostable enzymes in industrial applications is expected to increase especially in biodegradable of lignocellulosic biomass for biofuel production. However, we noticed weak collaboration links between researchers from different nations, and organizations which have to be developed to increase knowledge diffusion. There has been an increasing amount of study and Japan remains ahead in both the sum of publications and total citation frequency in this sector. Thus, it is not difficult to forecast that this area of research is expected to continue to rapidly increase and that more papers will be published in the coming years. For future research, it will be necessary to create strategies for developing thermostable enzymes that can be employed extensively in the biofuel, biodegradation, food, pharmaceutical, textile, bio-based, and animal feed industries. Enzymes are frequently denatured by high temperatures, strong acids and bases, organic solvents, and other harsh conditions, compromising their catalytic capabilities and limiting their applicability in industrial processes. Discovering new thermostable enzymes in extreme environments or performing molecular modification of existing enzymes with poor thermostability using emerging protein engineering technology are now effective methods for getting new thermostable enzymes.

Availability of data and materials

All research manuscripts and review data utilised in this study were retrieved in CSV format from the Scopus database (attached in supplementary materials). This link yielded all of the evaluated search results.https://www.scopus.com/term/analyzer.uri?sid=4e9621c056d6ac82d181afb073c5e641&origin=resultslist&src=s&s=TITLE-ABS-KEY%28thermostable-enzymes%2c+thermostable%2c+enzymes%29&sort=plf-f&sdt=cl&sot=b&sl=58&count=1022&analyzeResults=Analyze+results&cluster=scosubtype%2c%22ar%22%2ct%2c%22re%22%2ct%2bscopubstage%2c%22aip%22%2cf%2bscosrctype%2c%22d%22%2cf&txGid=12bdad479e4e1e91daabb8fc725d2e54

Abbreviations

Comma Separated Value (CSV)

Ribonucleic acid

Deoxyribonucleic acid

Polymerase chain reaction

Peroxidases

Calotropis procera root peroxidase

L-lactate dehydrogenase

Poly lactic acid

Carboxymethyl cellulose

Carnonic anhydrase

Dimethylformamidase

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Che Hussian, C.H.A., Leong, W.Y. Thermostable enzyme research advances: a bibliometric analysis. J Genet Eng Biotechnol 21 , 37 (2023). https://doi.org/10.1186/s43141-023-00494-w

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Historic Overview of Genetic Engineering Technologies for Human Gene Therapy

Ryota tamura1.

1 Department of Neurosurgery, Keio University School of Medicine, Tokyo, Japan

Masahiro TODA

The concepts of gene therapy were initially introduced during the 1960s. Since the early 1990s, more than 1900 clinical trials have been conducted for the treatment of genetic diseases and cancers mainly using viral vectors. Although a variety of methods have also been performed for the treatment of malignant gliomas, it has been difficult to target invasive glioma cells. To overcome this problem, immortalized neural stem cell (NSC) and a nonlytic, amphotropic retroviral replicating vector (RRV) have attracted attention for gene delivery to invasive glioma. Recently, genome editing technology targeting insertions at site-specific locations has advanced; in particular, the clustered regularly interspaced palindromic repeats/CRISPR-associated-9 (CRISPR/Cas9) has been developed. Since 2015, more than 30 clinical trials have been conducted using genome editing technologies, and the results have shown the potential to achieve positive patient outcomes. Gene therapy using CRISPR technologies for the treatment of a wide range of diseases is expected to continuously advance well into the future.

Introduction

Gene therapy is a therapeutic strategy using genetic engineering techniques to treat various diseases. 1 , 2) In the early 1960s, gene therapy first progressed with the development of recombinant DNA (rDNA) technology, 1) and was further developed using various genetic engineering tools, such as viral vectors. 3 – 5) More than 1900 clinical trials have been conducted with gene therapeutic approaches since the early 1990s. In these procedures, DNA is randomly inserted into the host genome using conventional genetic engineering tools. In the 2000s, genome editing tootls, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the recently established clustered regularly interspaced palindromic repeats/CRISPR-associated-9 (CRISPR/Cas9) technologies, were developed, which induce genome modifications at specific target sites. 5) Genome editing tools are efficient for intentional genetic engineering, which has led to the development of novel treatment strategies for a wide range of diseases, such as genetic diseases and cancers. Therefore, gene therapy has again became a major focus of medical research. However, because gene therapy involves changing the genetic background, it raises important ethical concerns. In this article, we review the brief history of gene therapy and the development of genetic engineering technologies.

History of Genetic Engineering Technologies

Ethical issues.

In 1968, the initial proof-of-concept of virus- mediated gene transfer was made by Rogers et al. 6) who showed that foreign genetic material could be transferred into cells by viruses. In the first human gene therapy experiment, Shope papilloma virus was transduced into two patients with genetic arginase deficiency, because Rogers et al. hypothesized that the Shope papilloma virus genome contained a gene that encodes arginase. However, this gene therapy produced little improvement in the arginase levels in the patients. 7) Sequencing of the Shope papilloma virus genome revealed that the virus genome did not contain an arginase gene. 7)

This experiment prompted public concerns about the risks and ethical issues of gene therapy. In 1972, Friedman et al. 8) proposed ethical standards for the clinical application of gene therapy to prevent premature application in human. However, in 1980, genetic engineering was unethically performed in patients with thalassemia without the approval of the institutional review board. 9) The patients’ bone marrow cells were harvested and returned into their bone marrow after transduction with the plasmid DNA containing an integrated b-globin gene. 9) This treatment showed no effects, and the experiments were regarded as morally dubious. The gene therapy report of the President's Commission in the United States, Splicing Life , emphasized the distinction between somatic and germline genome editing in humans, and between medical treatment and non-medical enhancement. 10) An altered gene inserted into sperm or egg cells (germ cells) would lead to changes not only in the individual receiving the treatment but also in their future offspring. Interventions aimed at enhancing “normal” people also are problematic because they might lead to attempts to make “perfect” human beings.

Beginning of gene therapy using viral vector

In 1980, only nonviral methods, such as microinjection and calcium-phosphate precipitation, were used for gene delivery. Nonviral methods showed some advantages compared with viral methods, such as large-scale production and low host immunogenicity. However, nonviral methods yielded lower levels of transfection and gene expression, resulting in limited therapeutic efficacy. 11) In 1989, the rDNA Advisory Committee of the National Institutes of Health proposed the first guidelines for the clinical trials of gene therapy. In 1990, retroviral infection, which is highly dependent on host cell cycle status, was first performed for the transduction of the neomycin resistance marker gene into tumor-infiltrating lymphocytes that were obtained from patients with metastatic melanoma. 3 , 4) Then, the lymphocytes were cultured in vitro and returned to the patients’ bodies. 3 , 4) The first Food and Drug Administration (FDA)- approved gene therapy using a retroviral vector was performed by Anderson et al. in 1990; the adenosine deaminase (ADA) gene was transduced into the white blood cells of a patient with ADA deficiency, resulting in temporary improvements in her immunity. 2 , 12)

First severe complications

A recombinant adenoviral (AV) vector was developed after advances in the use of the retroviral vector. In 1999, a clinical trial was performed for ornithine transcarbamylase (OTC) deficiency. A ubiquitous DNA AV vector (Ad5) containing the OTC gene was delivered into the patient. Four days after administration, the patient died from multiple organ failure that was caused by a cytokine storm. 13 , 14) In 1999, of the 20 patients enrolled in two trials for severe combined immunodeficiency (SCID)-X1, T-cell leukemia was observed in five patients at 2–5.5 years after the treatment. Hematopoietic stem cells with a conventional, amphotropic, murine leukemia virus-based vector and a gibbon-ape leukemia virus-pseudotyped retrovirus were used for gene transduction in those trials. 15 , 16) Although four patients fully recovered after the treatment, one patient died 15 , 16) because oncogene activation was mediated by viral insertion. 15 , 16)

Development of viral vectors

Viral vectors continued to be crucial components in the manufacture of cell and gene therapy. Adeno- associated viral (AAV) vectors were applied for many genetic diseases including Leber’s Congenital Amaurosis (LCA), and reverse lipoprotein lipase deficiency (LPLD). In 2008, remarkable success was reported for LCA type II in phase I/II clinical trials. 17) LCA is a rare hereditary retinal degeneration disorder caused by mutations in the RPE65 gene (Retinoid Isomerohydrolase RPE65), which is highly expressed in the retinal pigment epithelium and encodes retinoid isomerase. 17) These trials confirm that RPE65 could be delivered into retinal pigment epithelial cells using recombinant AAV2/2 vectors, resulting in clinical benefits without adverse events. 17) Recently, the FDA approved voretigene neparvovec-rzyl (Luxturna, Spark Therapeutics, Philadelphia, PA, USA) for patients with LCA type II. Alipogene tiparvovec Glybera (uniQure, Lexington, MA, USA) is the first gene-therapy-based drug to reverse LPLD to be approved in Europe in 2012. The AAV1 vector delivers an intact LPL gene to the muscle cells. 18) To date, more than 200 clinical trials have been performed using AAV vectors for several genetic diseases, including spinal muscular atrophy, 19) retinal dystrophy, 20) and hemophilia. 21)

Retrovirus is still one of the mainstays of gene therapeutic approaches. Strimvelis (GlaxoSmithKline, London, UK) is an FDA-approved drug consisting of an autologous CD34 (+)-enriched cell population that includes a gammaretrovirus containing the ADA gene that was used as the first ex-vivo stem cell gene therapy in patients with SCID because of ADA deficiency. 22) Subsequently, retroviral vectors were often used for other genetic diseases, including X-SCID. 23)

Lentivirus belongs to a family of viruses that are responsible for diseases, such as aquired immunodeficiency syndrome caused by the human immunodeficiency virus (HIV) that causes infection by inserting DNA into the genome of their host cells. 24) The lentivirus can infect non-dividing cells; therefore, it has a wider range of potential applications. Successful treatment of the patients with X-linked adrenoleukodystrophy was demonstrated using a lentiviral vector with the deficient peroxisomal adenosine triphosphate–binding cassette D1. 25) Despite the use of a lentiviral vector with an internal viral long terminal repeat, no oncogene activation was observed. 25)

A timeline showing the history of scientific progress in gene therapy is highlighted in Table 1 .

ADA: adenosine deaminase, ALD: adrenoleukodystrophy, B-ALL: B cell acute lymphoblastic leukemia, CAR: chimeric antigen receptor-modified, DLBCL: diffuse large B-cell lymphoma, GT: gene therapy, LCA: Leber’s congenital amaurosis, LPL: lipoprotein lipase deficiency, OTC: ornithine transcarbamylase, SCID: severe combined immunodeficiency, SMA: spinal muscular atrophy, TCR: T cell receptor, TIL: tumor infiltrating lymphocyte

Gene Therapeutic Strategies for Brain Tumor

A variety of studies were performed to apply gene therapy to malignant tumors. The concept of gene therapy for tumors is different from that for genetic diseases, in which new genes are added to a patient's cells to replace missing or malfunctioning genes. In malignant tumors, the breakthrough in gene therapeutic strategy involved designing suicide gene therapy, 26) which was first applied for malignant glioma in 1992. 26 , 27) The first clinical study was performed on 15 patients with malignant gliomas by Ram et al (phase I/II). 27) Stereotactic intratumoral injections of murine fibroblasts producing a replication-deficient retrovirus vector with a suicide gene (herpes simplex virus-thymidine kinase [HSV-TK]) achieved anti-tumor activity in four patients through bystander killing effects. 27) Subsequently, various types of therapeutic genes have been used to treat malignant glioma. Suicide genes (cytosine deaminase [CD]), genes for immunomodulatory cytokines (interferon [IFN]-β, interleukin [IL]-12, granulocyte- macrophage colony-stimulating factor [GM-CSF]), and genes for reprogramming (p53, and phosphatase and tensin homolog deleted from chromosome [PTEN]) have been applied to the treatment of malignant glioma using viral vectors. 28 , 29)

Recently, a nonlytic, amphotropic retroviral replicating vector (RRV) and immortalized human neural stem cell (NSC) line were used for gene delivery to invasive glioma. 30 – 32) In 2012, a nonlytic, amphotropic RRV called Toca 511 was developed for the delivery of a suicide gene (CD) to tumors. 32) A tumor-selective Toca 511 combined with a prodrug (Toca FC) was evaluated in patients with recurrent high-grade glioma in phase I clinical trial. 30) The complete response rate was 11.3% in 53 patients. 30) In addition, the sub-analysis of this clinical trial revealed that the objective response was 21.7% in the 23-patient phase III eligible subgroup. 33) However, in the recent phase III trial, treatment with Toca 511 and Toca FC did not improve overall survival compared with standard therapy in patients with recurrent high-grade glioma. A further combinational treatment strategy using programmed cell-death ligand 1 (PD-L1) checkpoint blockade delivered by TOCA-511 was evaluated in experimental models, which may lead to future clinical application. 34) Since 2010, intracranial administration of allogeneic NSCs containing CD gene (HB1.F3. CD) has been performed by a team at City of Hope. Autopsy specimens indicate the HB1.F3. CD migrates toward invaded tumor areas, suggesting a high tumor-trophic migratory capacity of NSCs. 31) No severe toxicities were observed in the trial. Generally, it is difficult to obtain NSCs derived from human embryonic or fetal tissue. The use of human embryos for research on embryonic stem cells is ethically controversial because it involves the destruction of human embryos, and the use of fetal tissue associated with abortion also raises ethical considerations. 35) Recently, the tumor-trophic migratory activity of NSCs derived from human-induced pluripotent stem cells (hiPSCs) was shown using organotypic brain slice culture. 36) Moreover, hiPSC-derived NSCs with the HSV-TK suicide gene system demonstrated considerable therapeutic potential for the treatment of experimental glioma models. 36) Furthermore, iPSCs have the ability to overcome ethical and practical issues of NSCs in clinical application.

New Genetic Engineering Technologies for Gene Therapy

Genetic engineering technologies using viral vectors to randomly insert therapeutic genes into a host genome raised concerns about insertional mutagenesis and oncogene activation. Therefore, new technology to intentionally insert genes at site-specific locations was needed. Genome editing is a genetic engineering method that uses nucleases or molecular scissors to intentionally introduce alterations into the genome of living organisms. 6) As of 2015, three types of engineered nucleases have been used: ZFNs, TALENs, and CRISPR/Cas ( Table 2 ). 6)

CRISPR/Cas9: clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins 9, PAM: protospacer adjacent motif, TALENs: transcription activator-like effector nucleases, ZFNs: zinc finger nucleases

Genome editing tools

ZFNs are fusions of the nonspecific DNA cleavage domain of the Fok I restriction endonuclease and zinc-finger proteins that lead to DNA double-strand breaks (DSBs). Zinc-finger domains recognize a trinucleotide DNA sequence ( Fig. 1 ). However, design and selection of zinc-finber arrays is difficult and time-consuming. 37)

Genome editing tools. Three types of genome editing tools including ZFNs, TALENs, and CRISPR/Cas9 are shown. ZFNs are hybrid proteins using zinc-finger arrays and the catalytic domain of FokI endonuclease. TALENs are hybrid proteins containing the TAL effector backbone and the catalytic domain of FokI endonuclease. The CRISPR/Cas9 system is composed of Cas9 endonuclease and sgRNA. Cas9: CRISPR-associated-9, CRISPR: clustered regularly interspaced palindromic repeats, sgRNA: single-guide RNA, TALENs: transcription activator-like effector nucleases, ZFNs: zinc-finger nucleases.

TALENs are fusions of the Fok I cleavage domain and DNA-binding domains derived from TALE proteins. TALEs have multiple 33–35 amino acid repeat domains that recognizes a single base pair, leading to the targeted DSBs, similar to ZFNs ( Fig. 1 ). 38)

The CRISPR/Cas9 system consists of Cas9 nuclease and two RNAs (CRISPR RNA [crRNA] and trans- activating CRISPR RNA [tracrRNA]). 39) The crRNA/tracrRNA complex (gRNA) induces the Cas9 nuclease and cleaves DNA upstream of a protospacer-adjacent motif (PAM, 5’-NGG-3’ for S. pyogenes ) ( Fig. 1 ). 40) Currently, Cas9 from S. pyogenes (SpCas9) is the most popular tool for genome editing. 40)

Critical issues in geneome editing

Several studies have demonstrated the off-target effects of Cas9/gRNA complexes. 41) It is important to select unique target sites without closely homologous sequences, resulting in minimum off-target effects. 42) Additionally, other CRISPR/Cas9 gene editing tools were developed to mitigate off-target effects, including gRNA modifications (slightly truncated gRNAs with shorter regions of target complementarity <20 nucleotides) 43) and SpCas9 variants, such as Cas9 paired nickases (a Cas9 nickase mutant or dimeric Cas9 proteins combined with pairs of gRNAs). 44) The type I CRISPR-mediated distinct DNA cleavage (CRISPR/Cas3 system) was developed recently in Japan to decrease the risk of off-target effets. Cas3 triggered long-range deletions upstream of the PAM (5'-ARG). 45)

A confirmatory screening of off-target effects is necessary for ensuring the safe application of genome editing technologies. 46) Although off-target mutations in the genome, including the noncoding region, can be evaluated using whole genome sequencing, this method is expensive and time-consuming. With the development of unbiased genome-wide cell-based methods, GUIDE-seq (genome-wide, unbiased identification of DSBs enabled by sequencing) 47) and BLESS (direct in situ breaks labeling, enrichment on streptavidin; next-generation sequencing) 48) were developed to detect off-target cleavage sites, and these methods do not require high sequencing read counts.

Applications of Genome Editing Technologies

Gene therapy has in- vivo and ex- vivo strategies. For the in- vivo strategy, vectors containing therapeutic genes are directly delivered into the patients, and genetic modification occurs in situ . For the ex- vivo strategy, the harvested cells are modified by the appropriate gene delivery tools in vitro (e.g., recombinant viruses and genome editing technologies). The modified cells are then delivered back to the patient via autologous or allogeneic transplantation after the evaluation of off-target effects ( Fig. 2 ).

In- vivo and ex- vivo strategies of gene therapy. In- vivo and ex- vivo gene transfer strategies are shown. For in- vivo gene transfer, genetic materials containing therapeutic genes, such as viral vectors, nanoparticles, and ribosomes, are delivered directly to the patient, and genetic modification occurs in situ . For ex- vivo gene transfer, the harvested cells are modified by the appropriate gene delivery tools in vitro (e.g., recombinant viruses genome editing technologies). The modified cells are then delivered back to the patient via autologous or allogeneic transplantation after the evaluation of off-target effects.

HIV-resistant T cells were established by ZFN- mediated disruption of the C-C chemokine receptor (CCR) 5 coreceptor for HIV-I, which is being evaluated as an ex- vivo modification in early-stage clinical trials. 49 , 50) Disruption of CCR5 using ZFNs was the first-in-human application of a genome editing tool. Regarding hematologic disorders, since 2016, clinical trials have attempted the knock-in of the factor IX gene using AAV/ZFN-mediated genome editing approach for patients with hemophilia B. 51)

In addition to these promising ongoing clinical trials for genetic diseases, CRISPR/Cas9 and TALEN technologies have improved the effect of cancer immunotherapy using genome-engineered T cells. Engineered T cells express synthetic receptors (chimeric antigen receptors, CARs) that can recognize epitopes on tumor cells. The FDA approved two CD19-targeting CAR-T-cell products for B-cell acute lymphoblastic leukemia and diffuse large B-cell lymphoma. 52 , 53) Engineered CARs target many other antigens of blood cancers, including CD30 in Hodgkin's lymphoma as well as CD33, CD123, and FLT3 of acute myeloid leukemia. 54) Recent research has shown that Cas9-mediated PD-1 disruption in the CAR-T cells improved the anti-tumor effect observed in in- vitro and in- vivo experimental models, leading to the performance of a clinical trial. 55 , 56) All other ongoing clinical trials using genome-editing technologies are highlighted in Table 3 .

AAV: adeno-associated virus, CAR: chimeric antigen receptor, CRISPR/Cas9: clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 proteins, HIV: human immunodeficiency virus, HPV: human papillovirus, MPS: mucopolysaccharidosis, N/A: not available, PD-1: programmed cell death-1, TALEN: transcription activator-like effector nucleases, ZFN: zinc finger nucleases

Future Direction

Gene therapy has advanced treatments for patients with congenital diseases and cancers throughout recent decades by optimizating various types of vectors and the introduction of new techniques including genome editing tools. The CRISPR/Cas9 system is considered one of the most powerful tools for genetic engineering because of its high efficiency, low cost, and ease of use. CRISPR technologies have progressed and are expected to continuously advance. Although there are still many challenging obstacles to overcome to achieve safe clinical application, these methods provide the possibility of treatment for a wide variety of human diseases.

Acknowledgement

We thank Lisa Kreiner, PhD, from Edanz Group (https://en-author-services.edanzgroup.com/) for editing a draft of this manuscript.

Conflicts of Interest Disclosure

The authors declare no conflicts of interest associated with this manuscript. This work was supported in part by grants from the Japan Society for the Promotion of Science (JSPS) (18K19622 to M.T.). All authors have registered online Self-reported COI Disclosure Statement Forms through the website for JNS members.

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Enhancing photosynthesis and plant productivity through genetic modification.

1. Introduction

2. chloroplast component modifications, 2.1. optimization of light harvesting and pigment content, 2.2. photosystem ii, 2.3. c. cytochrome b 6 f complex, 2.4. photosystem i, 2.5. electron transport chain, 2.6. chloroplast atp synthase, 3. carbon assimilation efficiency, 3.1. rubisco as a target to improve carbon assimilation efficiency, 3.2. rubisco assembly factors, 3.3. sedoheptulose-1,7-bisphosphatase, 3.4. genes involved in c4-type photosynthesis, 3.5. photorespiratory, 4. cellular transport and regulation, 4.1. sucrose transporters, 4.2. aquaporins, 4.3. carbonic anhydrase, 5. gene regulation, 5.1. high pigment epistasis 1, 5.2. transcription factors, 5.3. micrornas, 6. environmental stressors limiting photosynthesis, 6.1. temperature stress, 6.2. light stress, 6.3. water and salt stresses, 6.4. biotic stress, 6.5. cross-adaptation, 7. conclusions, author contributions, institutional review board statement, informed consent statement, data availability statement, acknowledgments, conflicts of interest.

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Nazari, M.; Kordrostami, M.; Ghasemi-Soloklui, A.A.; Eaton-Rye, J.J.; Pashkovskiy, P.; Kuznetsov, V.; Allakhverdiev, S.I. Enhancing Photosynthesis and Plant Productivity through Genetic Modification. Cells 2024 , 13 , 1319. https://doi.org/10.3390/cells13161319

Nazari M, Kordrostami M, Ghasemi-Soloklui AA, Eaton-Rye JJ, Pashkovskiy P, Kuznetsov V, Allakhverdiev SI. Enhancing Photosynthesis and Plant Productivity through Genetic Modification. Cells . 2024; 13(16):1319. https://doi.org/10.3390/cells13161319

Nazari, Mansoureh, Mojtaba Kordrostami, Ali Akbar Ghasemi-Soloklui, Julian J. Eaton-Rye, Pavel Pashkovskiy, Vladimir Kuznetsov, and Suleyman I. Allakhverdiev. 2024. "Enhancing Photosynthesis and Plant Productivity through Genetic Modification" Cells 13, no. 16: 1319. https://doi.org/10.3390/cells13161319

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Genetic Engineering and Society Center

Study analyzes potato-pathogen ‘arms race’ after irish famine.

August 5, 2024 | newswire

Researchers examine both the pathogen’s effector genes and the plant’s resistance genes simultaneously in a first-of-its-kind analysis.

August 5, 2024 |  Mick Kulikowski  at CALS News | 5 -min. read

Historic potato plant affected by pathogen.

In an examination of the genetic material found in historic potato leaves, North Carolina State University researchers reveal more about the tit-for-tat evolutionary changes occurring in both potato plants and the pathogen that caused the 1840s Irish potato famine.

The study used a targeted enrichment sequencing approach to simultaneously examine both the plant’s resistance genes and the pathogen’s effector genes – genes that help it infect hosts – in a first-of-its-kind analysis.

“We use small pieces of historic leaves with the pathogen and other bacteria on them; the DNA is fragmented more than a normal tissue sample,” said Allison Coomber , an NC State former graduate student researcher and lead author of the paper. “We use small 80 base-pair chunks like a magnet to fish out similar pieces in this soup of DNA. These magnets are used to find resistance genes from the host and effector genes from the pathogen.”

“This is a first for looking at both potato and pathogen changes at the same time; usually researchers look at one or the other,” says Jean Ristaino , William Neal Reynolds Distinguished Professor of Plant Pathology at North Carolina State University and corresponding author of a paper in Nature Communications that describes the study. “The dual enrichment strategy employed here allowed us to capture targeted regions of genomes of both sides of the host-pathogen relationship, even when host and pathogen were present in unequal amounts. We couldn’t have done this work 15 years ago because the genomes weren’t sequenced.”

The study’s results show that the pathogen, Phytophthora infestans , is very adept at fighting off potato late blight disease resistance. For example, the study shows that the FAM-1 strain of the pathogen had the ability to defeat the resistance provided by the plant’s R1 resistance gene – even before plant breeders deployed it in potato.

“The pathogen would have been able to resist this R1 resistance gene even if it had been deployed years earlier, probably because it was exposed to a potato with that resistance gene in the wild,” Coomber said.

The study also shows that many of the pathogen’s effector genes have remained stable, although different mutations have occurred to increase its infection prowess as plant breeders attempted to breed resistance – specifically after 1937 when more structured potato breeding programs commenced in the United States and other parts of the globe.

The study also shows that the pathogen added a set of chromosomes between 1845 and 1954, the period of time in which the study’s plant samples were collected.

“We show in this work that after 100 years of human intervention, there are some genes that haven’t changed much in the pathogen,” Coomber said. “They are very stable potentially because they haven’t been selected on, or because they are really important to the pathogen. Targeting those genes would make it really hard for the pathogen to evolve an opposing response.”

“It’s hard to do effective plant breeding when we don’t know enough about the pathogen. Now that we know what effectors have changed over time, breeders may be able use resistance genes that are more stable or pyramid multiple resistance genes from different wild hosts,” Ristaino said.

“That’s where I see the future for this type of study – applying it to slow changes in pathogen virulence or other traits such as fungicide resistance.”

Amanda C. Saville, a research and laboratory specialist in Ristaino’s lab, also co-authored the paper. Funding was provided by a seed grant from the Triangle Center for Evolutionary Medicine, by National Science Foundation AgBioFews Training Grant Number 2018-1966 and by Grip4PSI Grant Number 557299.

-kulikowski-

Note to editors : The abstract of the paper follows.

“Evolution of Phytophthora infestans on its Potato Host Since the Irish Potato Famine”

Authors : Allison Coomber , Amanda Saville and Jean B Ristaino , NC State University

Published : Aug. 5, 2024 in Nature Communications

DOI : 10.1038/s41467-024-50749-4

Abstract : Since the Irish Potato Famine of 1845-1852, late blight caused by the plant pathogen Phytophthora infestans has continued to plague potato ( Solanum tuberosum ) fields worldwide. In the years after the famine, plant breeders deployed potato varieties with resistance (R) genes to the pathogen. These R genes allow the host plant to recognize pathogen effector genes which are responsible for virulence, and after recognition, shut down disease progression. The host and pathogen began an arms race that resulted in the pathogen overcoming many R genes that were deployed. How these gene families evolved over time in tandem is not well understood. Herein, we show that that currently relevant pathogen effector genes have historically been present in P. infestans but with alternative alleles compared to the modern reference genome. We found that the historic FAM-1 lineage had the virulent allele for Avr1 and the ability to break the R1 resistance gene, before plant breeders had deployed it in potato. The pathogen also underwent an increase in chromosome number, from diploid to triploid after the famine. Our results show that both pathogen virulence genes and host resistance genes have undergone significant changes since the Famine, likely both from natural and artificial selection.

This post was originally published in NC State News.

THIS ARTICLE ORIGINALLY APPEARED IN NC State CALS News at https://cals.ncsu.edu/news/study-analyzes-potato-pathogen-arms-race-after-irish-famine/

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New genetic editing technique can modify wild populations with less risk

by Macquarie University

A new technique developed by researchers from Macquarie University and the California Institute of Technology could allow scientists to more safely alter the genetic makeup of wild populations. The study is published in the journal Nature Communications .

The researchers have proposed a new technique that aims to address some of the regulatory challenges and public concerns associated with existing genetic modification methods.

Lead author Dr. Maciej Maselko from Applied Biosciences at Macquarie University says the technique, called an Allele Sail, would allow beneficial genetic changes to spread through a population without leaving "foreign DNA" behind.

"Allele Sail offers a way to change the traits and fates of wild populations in ways that may be more acceptable, as the genetically modified part is introduced at low frequencies and usually won't last forever," he says.

Breaking down the gene-editing barriers

Genetic engineering could address major global challenges by altering the genetic makeup of certain wild populations—for example, to combat mosquito-borne illnesses such as malaria, or stop the spread of environmentally harmful invasive pests like cane toads.

But there is genuine public concern about introducing genetic modification into wild populations, and many regulatory constraints.

People are worried that modified organisms could contain foreign DNA that cause unpredictable ecological consequences over time; they worry that engineered genes could spread to other species with unknown impacts on ecosystems; and they also fear that once genetic modifications are introduced, they may not be able to be reversed.

Traditional methods of genetic modification can also see a rapid spread of engineered genes within a population, raising both ecological and ethical questions.

In response, many regulatory frameworks have been introduced to address genetic modification, presenting further challenges.

Current regulations often distinguish between genetically modified organisms (GMOs) and those with edited existing genes, creating barriers for approval and implementation.

"The Allele Sail system uses a gene editor to make specific DNA changes to an organism's genome—but unlike other genetic modification methods, the editor is inherited normally and does not increase in the population," says Dr. Maselko.

"However, the edits it creates can spread rapidly, potentially making desirable traits common."

Modeling Allele Sail

The Allele Sail is different from other genetic modification techniques like gene drives, which quickly spread engineered genes through a population.

In contrast, an Allele Sail introduces genetic changes using an editor that remains at low levels and could potentially be removed from the population completely.

The researchers used computer models to test how an Allele Sail system would work under different scenarios. They found that releasing even a small number of organisms carrying the editor, could make the edited genes very common in a population.

This approach could be used to help conserve endangered species, control invasive species or reduce the spread of insect-borne diseases.

For example, it might let scientists add genes for disease resistance or heat tolerance to threatened species. It could also potentially make mosquitoes less able to spread diseases like malaria.

"Current regulations often treat transgenic organisms as genetically modified, but their edited offspring as non-GMO. In this context, an Allele Sail provides a way to alter wild populations that may be more acceptable."

How Allele Sail works

The genome editor, referred to as the "Wind," could use CRISPR-based systems to make targeted changes at specific DNA sequences. The resulting edits, called the "Sail," then increase as the editor encounters unmodified versions of the target genes in future generations.

Importantly, organisms with two copies of the edited genes would need to survive and reproduce for the system to work effectively.

The researchers explored using the technique both to modify populations—like adding beneficial traits—and to reduce them in some cases.

Computer simulations showed the system could make edited genes very common across various scenarios with different costs or benefits.

"We believe Allele Sails will be especially useful to help endangered species and reduce harm from pests, while also offering a powerful way to suppress some populations," Dr. Maselko says.

The approach uses recent advances in gene editing that allow very precise DNA changes. Even small edits can sometimes significantly affect an organism's traits.

Examples in the paper include single genetic changes that can give heat resistance to mussels and cattle, or disease resistance to some plants.

Such small changes may be more likely to be approved by regulators compared to adding entirely new genes.

Meeting the regulators with Allele Sail systems

The researchers note that some regulatory systems are starting to treat certain gene edits as similar to natural changes—such as the 2021 statement defining genetically modified organisms, by Australia's Office of the Gene Technology Regulator.

An Allele Sail that introduces such edits via a low-level, non-lasting transgene, could therefore be easier to approve than other genetic modification approaches.

"Any genetic modification of wild populations is going to be controversial and would need careful study of potential environmental impacts," says Dr. Maselko.

He points out that, while most research into genetic modification is focused on eliminating pest species, these tools can also have a positive effect on threatened species or ecosystems.

"Our research shows that the Allele Sail technique is a subtle and potentially reversible genetic tool for modifying populations, and as the technology for gene editing improves, this approach will be increasingly viable."

The researchers have published their computer simulation code to allow further research into ways that Allele Sail systems could be applied to different scenarios.

Journal information: Nature Communications

Provided by Macquarie University

This content was originally published on The Macquarie University Lighthouse .

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ORIGINAL RESEARCH article

Semaphorin 3a promotes the long-term persistence of human svfderived microvascular networks in engineered grafts.

• 1 Department of Biomedicine, University of Basel, Basel, Switzerland
• 2 Department of Plastic, Reconstructive, Aesthetic and Hand Surgery, University Hospital of Basel, Basel, Basel-Stadt, Switzerland
• 3 Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States
• 4 Department of General and Visceral Surgery, University of Freiburg, Freiburg, Baden-Wurttemberg, Germany

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The stromal vascular fraction (SVF) of human adipose tissue is an attractive cell source for engineering grafts with intrinsic vascularization potential, as it is rich in vasculogenic progenitors.However, in order to maintain their functional perfusion it is important to promote the in vivo stabilization of newly assembled microvascular networks. We previously found that Semaphorin 3A (Sema3A) promotes the rapid stabilization of new blood vessels induced by VEGF overexpression in skeletal muscle. Here we investigated whether Sema3A could promote the assembly, connection to circulation and persistence of human SVF-derived microvascular networks in engineered grafts.Recombinant Sema3A was engineered with a transglutaminase substrate sequence (TG-Sema3A) to allow cross-linking into fibrin hydrogels. Grafts were prepared with freshly isolated human SVF cells in fibrin hydrogels decorated with 0, 0.1 or 100 µg/ml TG-Sema3A and implanted subcutaneously in immune-deficient mice. After 1 week in vivo, the assembly of human-derived networks was similar in all conditions. The outer part of the grafts was populated by blood vessels of both human and mouse origin, which formed abundant hybrid structures within a common basal lamina. About 90% of human-derived blood vessels were functionally connected to the host circulation in all conditions. However, in the control samples human vessels were unstable. In fact, they significantly regressed by 6 weeks and could no longer be found by 12 weeks. In contrast, a low Sema3A dose (0.1 µg/ml) promoted further human vascular expansion by about 2-fold at 6 weeks and protected them from regression until 12 weeks. From a mechanistic point of view, the stabilization of SVF-derived vessels by 0.1 µg/ml of Sema3A correlated with the recruitment of a specific population of monocytes expressing its receptor Neuropilin-1. In conclusion, Sema3A is a potent stimulator of in vivo longterm persistence of microvascular networks derived from human SVF. Therefore, decoration of matrices with Sema3a can be envisioned to promote the functional support of tissue engineered grafts.

Keywords: Stromal-vascular fraction, Adipose Tissue, Angiogenesis, Semaphorin 3A, Vessel stabilization, Fibrin

Received: 05 Mar 2024; Accepted: 07 Aug 2024.

Copyright: © 2024 Schwager, Di Maggio, Grosso, Rasadurai, Minder, Hubbell, Kappos, Schaefer, Briquez, Banfi and Burger. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Andrea Banfi, Department of Biomedicine, University of Basel, Basel, 4001, Switzerland

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.