keyword
https://read.qxmd.com/read/38457474/preclinical-toxicity-analyses-of-lentiviral-vectors-expressing-the-hiv-1-ltr-specific-designer-recombinase-brec1
#21
JOURNAL ARTICLE
Niklas Beschorner, Paul Künzle, Maike Voges, Ilona Hauber, Daniela Indenbirken, Jacqueline Nakel, Sanamjeet Virdi, Peter Bradtke, Niels Christian Lory, Michael Rothe, Maciej Paszkowski-Rogacz, Frank Buchholz, Adam Grundhoff, Axel Schambach, Christian Thirion, Hans-Willi Mittrücker, Julian Schulze Zur Wiesch, Joachim Hauber, Jan Chemnitz
Drug-based antiretroviral therapies (ART) efficiently suppress HIV replication in humans, but the virus persists as integrated proviral reservoirs in small numbers of cells. Importantly, ART cannot eliminate HIV from an infected individual, since it does not target the integrated provirus. Therefore, genome editing-based strategies that can inactivate or excise HIV genomes would provide the technology for novel curative therapies. In fact, the HIV-1 LTR-specific designer-recombinase Brec1 has been shown to remove integrated proviruses from infected cells and is highly efficacious on clinical HIV-1 isolates in vitro and in vivo, suggesting that Brec1 has the potential for clinical development of advanced HIV-1 eradication strategies in people living with HIV...
2024: PloS One
https://read.qxmd.com/read/38456839/genetic-modification-of-candida-maltosa-a-non-pathogenic-ctg-species-reveals-efg1-function
#22
JOURNAL ARTICLE
Marco Chávez-Tinoco, Luis F García-Ortega, Eugenio Mancera
Candida maltosa is closely related to important pathogenic Candida species, especially C. tropicalis and C. albicans, but it has been rarely isolated from humans. For this reason, through comparative studies, it could be a powerful model to understand the genetic underpinnings of the pathogenicity of Candida species. Here, we generated a cohesive assembly of the C. maltosa genome and developed genetic engineering tools that will facilitate studying this species at a molecular level. We used a combination of short and long-read sequencing to build a polished genomic draft composed of 14 Mbp, 45 contigs and close to 5700 genes...
March 2024: Microbiology
https://read.qxmd.com/read/38453184/fashion-meets-science-how-advanced-breeding-approaches-could-revolutionize-the-textile-industry
#23
REVIEW
Santosh Gudi, Pavan M, Praveenkumar Alagappan, Om Prakash Raigar, Priyanka Halladakeri, Rakshith S R Gowda, Pradeep Kumar, Gurjeet Singh, Meenakshi Tamta, Pusarla Susmitha, Amandeep, Dinesh Kumar Saini
Natural fibers have garnered considerable attention owing to their desirable textile properties and advantageous effects on human health. Nevertheless, natural fibers lag behind synthetic fibers in terms of both quality and yield, as these attributes are largely genetically determined. In this article, a comprehensive overview of the natural and synthetic fiber production landscape over the last 10 years is presented, with a particular focus on the role of scientific breeding techniques in improving fiber quality traits in key crops like cotton, hemp, ramie, and flax...
March 7, 2024: Critical Reviews in Biotechnology
https://read.qxmd.com/read/38447046/long-noncoding-rna-gata2as-influences-human-erythropoiesis-by-transcription-factor-and-chromatin-landscape-regulation
#24
JOURNAL ARTICLE
Guoyou Liu, Juhyun Kim, Nicole Han Nguyen, Lecong Zhou, Ann Dean
LncRNAs are extensively expressed in eukaryotic cells and have been revealed to be important for regulating cell differentiation. Many lncRNAs have been found to regulate erythroid differentiation in the mouse. However, given the low sequence conservation of lncRNAs between mouse and human, our understanding of lncRNAs in human erythroid differentiation remains incomplete. LncRNAs are often transcribed opposite to protein coding genes and regulate their expression. Here we characterized a human erythrocyte-expressed lncRNA, GATA2AS, which is transcribed opposite to erythroid transcription regulator GATA2...
March 6, 2024: Blood
https://read.qxmd.com/read/38440883/epigenome-editing-for-targeted-dna-de-methylation-a-new-perspective-in-modulating-gene-expression
#25
REVIEW
Karishma Seem, Simardeep Kaur, Suresh Kumar, Trilochan Mohapatra
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression...
March 5, 2024: Critical Reviews in Biochemistry and Molecular Biology
https://read.qxmd.com/read/38434025/hiv-1-proviral-dna-in-purified-peripheral-blood-cd34-stem-and-progenitor-cells-in-individuals-with-long-term-haart-paving-the-way-to-hiv-gene-therapy
#26
JOURNAL ARTICLE
Boonrat Tassaneetrithep, Angsana Phuphuakrat, Ekawat Pasomsub, Kanit Bhukhai, Wasinee Wongkummool, Thongkoon Priengprom, Wannisa Khamaikawin, Sujittra Chaisavaneeyakorn, Usanarat Anurathapan, Nopporn Apiwattanakul, Suradej Hongeng
Human immunodeficiency virus (HIV)-1 infection is an important public health problem worldwide. After primary HIV-1 infection, transcribed HIV-1 DNA is integrated into the host genome, serving as a reservoir of the virus and hindering a definite cure. Although highly active antiretroviral therapy suppresses active viral replication, resulting in undetectable levels of HIV RNA in the blood, a viral rebound can be detected after a few weeks of treatment interruption. This supports the concept that there is a stable HIV-1 reservoir in people living with HIV-1...
February 29, 2024: Heliyon
https://read.qxmd.com/read/38431844/engineered-cbes-based-on-macaca-fascicularis-a3a-with-improved-properties-for-precise-genome-editing
#27
JOURNAL ARTICLE
Chun-Yan Ren, Yan-Shan Liu, Yu-Shan He, Lin-Pei Zhang, Jun-Hua Rao, Yijian Rao, Jian-Huan Chen
Cytidine deaminase defines the properties of cytosine base editors (CBEs) for C-to-T conversion. Replacing the cytidine deaminase rat APOBEC1 (rA1) in CBEs with a human APOBEC3A (hA3A) improves CBE properties. However, the potential CBE application of macaque A3A orthologs remains undetermined. Our current study develops and evaluates engineered CBEs based on Macaca fascicularis A3A (mA3A). Here, we demonstrate that BE4-mA3A and its RNA-editing-derived variants exhibit improved CBE properties, except for DNA off-target activity, compared to BE3-rA1 and BE4-rA1...
March 1, 2024: Cell Reports
https://read.qxmd.com/read/38430734/generation-of-a-tmem43-knockout-human-induced-pluripotent-stem-cell-line-hdzi003-a-1-using-crispr-cas9
#28
JOURNAL ARTICLE
Sandra Ratnavadivel, Joline Dammeier, Anna Gaertner, Marcelo A Szymanski de Toledo, Martin Zenke, Jan Gummert, Torsten Bloch Rasmussen, Nora Klinke, Kai Jürgens, Heiko Meyer, Achim Paululat, Hendrik Milting
TMEM43 (LUMA) is a ubiquitously expressed protein with unknown function. The protein is phylogenetically highly conserved and also found in Drosophila melanogaster (Klinke et al., 2022). TMEM43-p.S358L is a rare, fully penetrant mutation that leads to arrhythmogenic right ventricular cardiomyopathy type 5 (ARVC5). To understand the function of the ARVC5-associated mutation it is first important to understand the function of the TMEM43 protein. Therefore, a TMEM43 knockout induced pluripotent stem cell (iPSC) line was generated using the CRISPR/Cas9 genome editing system...
February 17, 2024: Stem Cell Research
https://read.qxmd.com/read/38428389/past-present-and-future-of-crispr-genome-editing-technologies
#29
REVIEW
Martin Pacesa, Oana Pelea, Martin Jinek
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them...
February 29, 2024: Cell
https://read.qxmd.com/read/38427245/quantitative-measurement-of-tau-aggregation-in-genetically-modified-rats-with-neurodegeneration
#30
JOURNAL ARTICLE
YouJin Lee, Eric M Morrow
Animal models of neurodegenerative diseases have helped us to better understand the pathogenesis of neurodegenerative diseases. However, recent failure to translate pre-clinical model studies to the clinic urges us to develop more rigorous and faithful animal models in neurodegenerative diseases. As genetic manipulation of rats becomes much more accessible due to availability of CRISPR-Cas9 and other genomic editing toolboxes, rats have been emerging as a new model system for neurodegenerative diseases. Even though mouse models have been dominant over the last decades, rats may provide advantages over mice...
2024: Methods in Molecular Biology
https://read.qxmd.com/read/38424152/generation-of-fel-d-1-chain-2-genome-edited-cats-by-crispr-cas9-system
#31
JOURNAL ARTICLE
Sang Ryeul Lee, Kyung-Lim Lee, Seok-Hwan Song, Myeong-Don Joo, Seo-Hyun Lee, Ji-Su Kang, Seon-Min Kang, Muhammad Idrees, Jae-Wook Kim, Il-Keun Kong
Allergens from domestic cats (Felis catus) cause allergy-related health problems worldwide. Fel d 1 is a major allergen that causes severe allergic reactions in humans, including rhinitis, conjunctivitis, and life-threatening asthma. Therefore, patients with cat allergies anticipate hypoallergenic cats. We successfully generated Fel d 1 chain 2 (CH2) genome-edited cats using the CRISPR-Cas9 system in this study. T7 endonuclease 1 assay and Sanger sequencing were used to confirm the mutation in CH2 genome-edited cats...
February 29, 2024: Scientific Reports
https://read.qxmd.com/read/38421879/first-in-human-study-with-lis1-a-next-generation-porcine-low-immunogenicity-antilymphocyte-immunoglobulin-in-kidney-transplantation
#32
JOURNAL ARTICLE
Ondrej Viklicky, Janka Slatinska, Libor Janousek, Juliette Rousse, Pierre-Joseph Royer, Pierre-Louis Toutain, Emanuele Cozzi, Cesare Galli, Gwenaelle Evanno, Odile Duvaux, Jean-Marie Bach, Jean-Paul Soulillou, Magali Giral, Bernard Vanhove, Gilles Blancho
BACKGROUND: Polyclonal rabbit antithymocyte globulins (ATGs) are commonly used in organ transplantation as induction. Anti-N-glycolylneuraminic acid carbohydrate antibodies which develop in response to rabbit carbohydrate antigens might lead to unwanted systemic inflammation. LIS1, the first new generation of antilymphocyte globulins (ALGs) derived from double knockout swine, lacking carbohydrate xenoantigens was already tested in nonhuman primates and rodent models. METHODS: This open-label, single-site, dose escalation, first-in-human, phase 1 study evaluated the safety, T cell depletion, pharmacokinetics, and pharmacodynamics of LIS1...
February 29, 2024: Transplantation
https://read.qxmd.com/read/38420804/a-comprehensive-prognostic-and-immune-infiltration-analysis-of-rbm4-in-pan-cancer
#33
JOURNAL ARTICLE
Jia-Jun Ding, Jie Wu, Hai-Lei Bian, Yi Zong, Bing Lu, Li Ni
BACKGROUND: Aberrant splicing has been closely associated with human cancer, though the precise underlying mechanisms linking the two remain not fully understood. Investigating the role of splicing factors in cancer progression may aid in the development of targeted therapies for dysregulated splicing, thereby opening up new avenues for cancer treatment. RNA-binding motif 4 (RBM4) has been identified as a critical participant in the condensin II complex, which is involved in chromosome condensation and stabilization during mitosis...
February 23, 2024: Frontiers in Bioscience (Landmark Edition)
https://read.qxmd.com/read/38418907/programmable-rna-base-editing-via-targeted-modifications
#34
REVIEW
Jinghui Song, Yuan Zhuang, Chengqi Yi
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editors are powerful tools in biology and hold great promise for the treatment of human diseases. Advanced DNA base editing tools, such as cytosine base editor and adenine base editor, have been developed to correct permanent mistakes in genetic material. However, undesired off-target edits would also be permanent, which poses a considerable risk for therapeutics. Alternatively, base editing at the RNA level is capable of correcting disease-causing mutations but does not lead to lasting genotoxic effects...
February 28, 2024: Nature Chemical Biology
https://read.qxmd.com/read/38412306/an-engineered-baculoviral-protein-and-dna-co-delivery-system-for-crispr-based-mammalian-genome-editing
#35
JOURNAL ARTICLE
Julien Capin, Alexandra Harrison, Renata A Raele, Sathish K N Yadav, Dominique Baiwir, Gabriel Mazzucchelli, Loic Quinton, Timothy J Satchwell, Ashley M Toye, Christiane Schaffitzel, Imre Berger, Francesco Aulicino
CRISPR-based DNA editing technologies enable rapid and accessible genome engineering of eukaryotic cells. However, the delivery of genetically encoded CRISPR components remains challenging and sustained Cas9 expression correlates with higher off-target activities, which can be reduced via Cas9-protein delivery. Here we demonstrate that baculovirus, alongside its DNA cargo, can be used to package and deliver proteins to human cells. Using protein-loaded baculovirus (pBV), we demonstrate delivery of Cas9 or base editors proteins, leading to efficient genome and base editing in human cells...
February 27, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38411120/the-dcas9-based-genome-editing-in-plasmodium-yoelii
#36
JOURNAL ARTICLE
Chao Zhang, Shijie Yang, Elvis Quansah, Ziyu Zhang, Weiran Da, Bingjie Wang
Genetic editing is a powerful tool for functional characterization of genes in various organisms. With its simplicity and specificity, the CRISPR-Cas9 technology has become a popular editing tool, which introduces site-specific DNA double-strand breaks (DSBs), and then leverages the endogenous repair pathway for DSB repair via homology-directed repair (HDR) or the more error-prone non-homologous end joining (NHEJ) pathways. However, in the Plasmodium parasites, the lack of a typical NHEJ pathway selects for DSB repair through the HDR pathway when a homologous DNA template is available...
February 27, 2024: MSphere
https://read.qxmd.com/read/38410490/a-polr3b-variant-reveals-a-pol-iii-transcriptome-response-dependent-on-la-protein-ssb
#37
Sandy Mattijssen, Kyra Kerkhofs, Joshi Stephen, Acong Yang, Chen G Han, Yokoyama Tadafumi, James R Iben, Saurabh Mishra, Rima M Sakhawala, Amitabh Ranjan, Mamatha Gowda, William A Gahl, Shuo Gu, May C Malicdan, Richard J Maraia
RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B :c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B . Genome-edited POLR3B 1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E ...
February 5, 2024: bioRxiv
https://read.qxmd.com/read/38409211/dna-and-rna-base-editors-can-correct-the-majority-of-pathogenic-single-nucleotide-variants
#38
JOURNAL ARTICLE
Ariel Dadush, Rona Merdler-Rabinowicz, David Gorelik, Ariel Feiglin, Ilana Buchumenski, Lipika R Pal, Shay Ben-Aroya, Eytan Ruppin, Erez Y Levanon
The majority of human genetic diseases are caused by single nucleotide variants (SNVs) in the genome sequence. Excitingly, new genomic techniques known as base editing have opened efficient pathways to correct erroneous nucleotides. Due to reliance on deaminases, which have the capability to convert A to I(G) and C to U, the direct applicability of base editing might seem constrained in terms of the range of mutations that can be reverted. In this evaluation, we assess the potential of DNA and RNA base editing methods for treating human genetic diseases...
February 26, 2024: NPJ Genomic Medicine
https://read.qxmd.com/read/38409199/precise-genome-editing-in-human-diseases-mechanisms-strategies-and-applications
#39
REVIEW
Yanjiang Zheng, Yifei Li, Kaiyu Zhou, Tiange Li, Nathan J VanDusen, Yimin Hua
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications...
February 26, 2024: Signal Transduction and Targeted Therapy
https://read.qxmd.com/read/38409124/engineering-self-deliverable-ribonucleoproteins-for-genome-editing-in-the-brain
#40
JOURNAL ARTICLE
Kai Chen, Elizabeth C Stahl, Min Hyung Kang, Bryant Xu, Ryan Allen, Marena Trinidad, Jennifer A Doudna
The delivery of CRISPR ribonucleoproteins (RNPs) for genome editing in vitro and in vivo has important advantages over other delivery methods, including reduced off-target and immunogenic effects. However, effective delivery of RNPs remains challenging in certain cell types due to low efficiency and cell toxicity. To address these issues, we engineer self-deliverable RNPs that can promote efficient cellular uptake and carry out robust genome editing without the need for helper materials or biomolecules. Screening of cell-penetrating peptides (CPPs) fused to CRISPR-Cas9 protein identifies potent constructs capable of efficient genome editing of neural progenitor cells...
February 26, 2024: Nature Communications
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