2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
January 21st, 2025
Version: 1
University of WA/Fred Hutchinson Cancer Research Center
molecular biology
biorxiv

Minimization of gene editing off-target effects by tissue restriction of expression

Kim, N.-G.Open in Google Scholar•Aubert, M.Open in Google Scholar•Haick, A. K.Open in Google Scholar•Massa, P. A.Open in Google Scholar•Loprieno, M. A.Open in Google Scholar•Walter, M.Open in Google Scholar•Kim, H. G.Open in Google Scholar•Nunley, B. E.Open in Google Scholar•Xie, H.Open in Google Scholar•Stensland, L.Open in Google Scholaret al.

Therapeutic in vivo gene editing with highly specific nucleases has the potential to revolutionize treatment for a wide range of human diseases, including genetic disorders and latent viral infections like herpes simplex virus (HSV). However, challenges regarding specificity, efficiency, delivery, and safety must be addressed before its clinical application. A key concern is the risk of off-target effects, which can cause unintended and potentially harmful genetic changes. We previously developed a curative in vivo gene editing approach to eliminate latent HSV using HSV-specific meganuclease delivered by an AAV vector. In this study, we investigate off-target effects of meganuclease by identifying potential off-target sites through GUIDE-tag analysis and assessing genetic alterations using amplicon deep sequencing in tissues from meganuclease treated mice. Our results show that meganuclease expression driven by a ubiquitous promoter leads to high off-target gene editing in the mouse liver, a non-relevant target tissue. However, restricting the meganuclease expression with a neuron-specific promoter and/or a liver-specific miRNA target sequence efficiently reduces off-target effects in both liver and trigeminal ganglia. These findings suggest that incorporation of regulatory DNA elements for tissue-specific expression in viral vectors can reduce off-target effects and improve the safety of therapeutic in vivo gene editing.

Similar Papers

biorxiv
Wed Jan 22 2025
Comparison of Activities of Transcription Factor NF-κB from Two Jellyfish Models
Herein, transcription factor NF-{kappa}B is characterized from two model jellyfish, Aurelia aurita (Aa) and Clytia hemisphaerica (Ch). Both jellyfish NF-{kappa}B proteins consist primarily of the N-terminal DNA-binding/dimerization domain, and they lack the C-terminal ankyrin repeat inhibitory domain found in vertebrate NF-{kappa}B proteins. Both jellyfish NF-{kappa}B proteins can bind to a consen...
Williams, L. M.
•
Wang, W.
•
Grigoryeva, A. V.
•
Navarro-Rosado, A.
...•
Gilmore, T. D.
biorxiv
Tue Jan 21 2025
Multi-omics reveals global signaling rewiring and identifies Activin A-induced dysregulation of FOS/Activator Protein 1 as a novel target in Fibrodysplasia ossificans progressiva
Background: Fibrodysplasia ossificans progressiva (FOP) is caused by an activating mutation (p.R206H) in the type I BMP receptor ALK2, leading to heterotopic ossification (HO) in soft connective tissues. While aberrant Activin A-induced SMAD signaling is central in FOP pathogenesis, global signaling alterations remain poorly understood. Methods: We performed phosphoproteomics, transcriptomics and ...
Wits, M.
•
Gomez-Suarez, N.
•
Lopez, A. D.
•
Farfan, N.
...•
Sanchez-Duffhues, G.
biorxiv
Tue Jan 21 2025
Local nucleolar surveillance mechanisms maintain rDNA stability
The nucleoli are subdomains of the nucleus that form around actively transcribed ribosomal RNA (rRNA) genes. The highly repetitive and transcribed nature of the rRNA genes (rDNA) by RNA polymerase I (Pol I) poses a challenge for DNA repair and replication machineries. Here, we profile the nucleolar proteome and the chromatin landscape of stalled replication sites upon rDNA damage tocharacterize th...
Liu, R.
•
Xuan, J.
•
Pan, J.
•
Sundramurthi Chelliah, S.
...•
Sanij, E.
biorxiv
Tue Jan 21 2025
Density-dependent expression of epitranscriptomic, stress, and appetite regulating genes in Atlantic salmon
Intraspecific competition due to e.g., density, has substantial influence on fitness dynamics and life histories, but the underlying physiological mechanisms are often complex, and the molecular basis unclear. Further, designing laboratory experiments to measure physiological responses that reflect natural conditions is challenging. Here, we reared Atlantic salmon juveniles in semi-wild conditions...
Frapin, M.
•
Quispe, L.
•
Troka, J.
•
Prokkola, J. M.
...•
Ahi, E. P.
biorxiv
Tue Jan 21 2025
Description of a novel extremophile green algae, Chlamydomonas pacifica, and its potential as a biotechnology host
We present the comprehensive characterization of a newly identified microalga, Chlamydomonas pacifica, originally isolated from a soil sample in San Diego, CA, USA. This species showcases remarkable biological versatility, including a broad pH range tolerance (6-11.5), high thermal tolerance (up to 42 degree celsius), and salinity resilience (up to 2% NaCl). Its amenability to genetic manipulation...
Dutra Molino, J. V.
•
Oliver, A.
•
Sethuram, H.
•
Kang, K.
...•
Mayfield, S.
biorxiv
Tue Jan 21 2025
The Specific Genetic Markers to Diagnose Xanthomonads Infecting Pepper and Tomato Plants
We have improved a marker system to examine the genetic diversity in Xanthomonads species by using whole genome sequence analysis and repetitive regions in the bacterial genome. Specifically, we amplified microsatellite regions using PCR, and the resulting fragments were digested with specific enzymes. These fragment profiles served as molecular markers. Consequently, a more precise marker for bac...
Can, A.
•
Abdul-Baasit, A.-N.
•
Belen, I. N.
•
Capar, U.
...•
Baysal, O.
biorxiv
Mon Jan 20 2025
Chameau (HBO1) regulates starvation in a temperature-dependent manner in Drosophila melanogaster
The body temperature of Drosophila melanogaster depends on the extrinsic temperature. Numerous studies in fruit flies have shown that environmental temperature has an effect on metabolism, lifespan and starvation resilience. We have previously shown that Chameau (Chm), a MYST-domain acetyltransferase, promotes aging but also increases starvation resilience. As starvation resilience is highly tempe...
Venkatasubramani, A. V.
•
Ichinose, T.
•
Forne, I.
•
Tanimoto, H.
...•
Imhof, A.
biorxiv
Sun Jan 19 2025
KIDINS220 and InsP8 safeguard the stepwise regulation of phosphate exporter XPR1
XPR1 is emerging as the only known inorganic phosphate (Pi) exporter in humans, critical for Pi homeostasis, with its activity stimulated by inositol pyrophosphate InsP8 and regulated by neuronal scaffold protein KIDINS220. Our structural studies reveal InsP8 specifically activates XPR1 in a stepwise manner, involving profound SPX domain movements. Each XPR1 subunit functions with four gating stat...
Wang, X.
•
Bai, Z.
•
Wallis, C.
•
Wang, H.
...•
Zhang, Y.
biorxiv
Sun Jan 19 2025
H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation
Heterochromatin is a key architectural feature of eukaryotic chromosomes, essential for cell type-specific gene expression and genome stability. In the mammalian nucleus, heterochromatin is segregated from transcriptionally active euchromatic regions (A compartments), forming large, condensed, and inactive nuclear compartments (B compartments). However, the mechanisms underlying its spatial organi...
Fukuda, K.
•
Shimura, C.
•
Shinkai, Y.