Transcriptome-Wide Off-Target Effects of Steric-Blocking Oligonucleotides

Abstract

Steric-blocking oligonucleotides (SBOs) are short, single-stranded nucleic acids designed to modulate gene expression by binding to mRNA and blocking access from cellular machinery such as splicing factors. SBOs have the potential to bind to near-complementary sites in the transcriptome, causing off-target effects. In this study, we used RNA-seq to evaluate the off-target differential splicing events of 81 SBOs and differential expression events of 46 SBOs. Our results suggest that differential splicing events are predominantly hybridization-driven, while differential expression events are more common and driven by other mechanisms. We further evaluated the performance of in silico screens for off-target events, and found an edit distance cutoff of three to result in a sensitivity of 14% and false discovery rate of 99%. A machine learning model incorporating splicing predictions substantially improved the ability to prioritize low edit distance hits, increasing sensitivity from 4% to 26% at a fixed FDR. Despite these large improvements in performance, the approach does not detect the majority of events at a false discovery rate below 99%. Our results suggest that in silico methods are currently of limited use for predicting the off-target effects of SBOs.

Innate immunity and microbial dysbiosis in hidradenitis suppurativa – vicious cycle of chronic inflammation

“…This review has summarized the potential contributions of innate immune system activation and microbial dysbiosis to HS pathogenesis. While studies utilizing single cell omics approaches have already revealed insight into HS pathology and deregulation of host responses (189)(190)(191) advancements in spatial transcriptomics and proteomics should be utilized to further understanding of deregulated innate immunity at the host-pathogen interphase. Future longitudinal studies simultaneously evaluating the focal genetic makeup, innate immunity, microbial dysbiosis and bacterial biofilms will provide detailed insights in HS pathogenesis and progression.…”

Sub‐lineages of the SARS‐CoV‐2 Omicron variants: Characteristics and prevention

“…Omicron can enter cells effectively through the endosomal pathway independent of TMPRSS2 and is weak in inducing syncytial formation. 33,[35][36][37][38][39] Variants preceding Omicron tended to adopt the TMPRSS2-mediated membrane fusion route to infect host cells, but only a low proportion of upper respiratory tract cells expressed both ACE2 and TMPRSS2. This explains why Omicron infects the upper respiratory tract more frequently than its predecessors.…”

“…50 The proximity of H655Y, N679K, P681H, and D796Y to the furin cleavage site in the spike protein has been hypothesized to be associated with increased infectivity 51 ; however, cellular-level experiments have demonstrated these mutations may contribute to a weakening in facilitating S1/S2 cleavage. 33,[37][38][39] The NTD contains four mutations, three deletions and one insertions: A67V, del69/70, T95I, G142D, del143/145, N211I, del212, and ins214EPE. Del69/70 also existed in Alpha and can be recognized by a useful detection method called s-gene target failure (SGTF).…”

“…The proximity of H655Y, N679K, P681H, and D796Y to the furin cleavage site in the spike protein has been hypothesized to be associated with increased infectivity 51 ; however, cellular‐level experiments have demonstrated these mutations may contribute to a weakening in facilitating S1/S2 cleavage 33,37–39 …”

“…Differences in the pattern of Omicron infection generated by abundant mutations were strongly associated with changes in the transmission rate and clinical severity. Omicron can enter cells effectively through the endosomal pathway independent of TMPRSS2 and is weak in inducing syncytial formation 33,35–39 . Variants preceding Omicron tended to adopt the TMPRSS2‐mediated membrane fusion route to infect host cells, but only a low proportion of upper respiratory tract cells expressed both ACE2 and TMPRSS2.…”