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Atkins, J.

Publications and source records attributed to Atkins, J..

6 recordsLinked to original sources

Expanding the Ligandable Chemical Space of OTUB1 through Discovery of a Four-Membered-Ring Recruiter Chemotype

Deubiquitinase-targeting chimeras (DUBTACs) have emerged as a promising strategy for targeted protein stabilization, but their broader application remains limited by the scarcity of ligandable deubiquitinase recruiters. Here, we report a previously unexplored four-membered-ring OTUB1 recruiter chemotype. Through systematic structure-activity relationship studies, we identified compound 21 (MS2159) as a potent and selective covalent OTUB1 ligand. Biochemical and intact protein mass spectrometric analyses demonstrated that MS2159 selectively engages the non-catalytic C23 residue of OTUB1, shows minimal reactivity toward other tested proteins, and preserves OTUB1 deubiquitinase activity. Conjugation of MS2159 with the CFTR ligand lumacaftor yielded compound 25 (MS2134), which effectively stabilized {Delta}F508-CFTR. Collectively, these findings establish a new OTUB1 recruiter scaffold, expand the ligandable chemical space of OTUB1, and provide additional opportunities for developing next-generation DUBTACs.

biochemistry↗

Delivery of defective interfering RNA antivirals to the lungs using hyperbranched poly(beta-amino ester) nanoparticles

Hyperbranched poly(beta-amino ester) (hPBAE) nanoparticles represent a promising platform for nucleic acid delivery, particularly to the lungs. In this study, we evaluate the potential of hPBAE nanoparticles to deliver defective interfering RNA (diRNA) antivirals targeting betacoronaviruses under a range of formulations and storage conditions. hPBAE-diRNA nanoparticles demonstrated efficient cellular uptake of functional diRNA across diverse cell types, conferred protection against nuclease-mediated degradation, and exhibited low in vitro cytotoxicity. In vivo, these nanoparticles enabled effective delivery of functional diRNA to the lungs of golden hamsters without inducing adverse physiological effects. Collectively, these findings support hPBAE nanoparticles as a safe and effective platform for diRNA delivery for the treatment of respiratory viral infections. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/721911v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@2fc386org.highwire.dtl.DTLVardef@1cda4f9org.highwire.dtl.DTLVardef@9f61borg.highwire.dtl.DTLVardef@1fc8461_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO Defective interfering RNA was mixed with hyperbranched poly(beta-amino ester) nanoparticles and delivered to cells in vitro and to golden hamsters in vivo, to measure toxicity and the replication potential of the RNA. C_FIG

microbiology↗

A 667-nucleotide sequence in the SARS-CoV-2 nsp15 coding region promotes genome encapsidation

Coronavirus genome encapsidation depends on cis-acting RNA elements that interact with viral structural proteins. While such packaging signals have been characterized in several coronaviruses, their definition in SARS-CoV-2 remains incomplete. Using synthetic defective SARS-CoV-2 genomes, we identify a 667-nucleotide region within the nsp15 coding sequence that preferentially binds SARS-CoV-2 nucleoprotein and enhances the accumulation of defective viral genomes both in vitro and in vivo. Sequential and targeted deletion analyses further delineate candidate RNA secondary structures within this region that contribute to this enrichment. These structures show similarity to elements within the putative packaging signal of SARS-CoV but are not conserved across other coronaviruses. Together, these findings support the presence of a structured RNA element within nsp15 that contributes to SARS-CoV-2 genome encapsidation and provide a framework for further structural and functional dissection of coronavirus packaging signals. IMPORTANCEThis study identifies a 667-nt region within the SARS-CoV-2 nsp15 coding sequence that binds nucleoprotein and promotes accumulation of defective viral genomes, revealing a previously unrecognized contributor to genome encapsidation. Mapping of candidate RNA structures within this region links SARS-CoV-2 packaging activity to conserved structural features observed in SARS-CoV, while highlighting key differences from other coronaviruses. These findings refine understanding of cis-acting packaging signals in SARS-CoV-2 and provide a foundation for further structural and functional analysis of coronavirus genome encapsidation. O_FIG O_LINKSMALLFIG WIDTH=177 HEIGHT=200 SRC="FIGDIR/small/721935v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1b64611org.highwire.dtl.DTLVardef@1b21b7borg.highwire.dtl.DTLVardef@2a68b5org.highwire.dtl.DTLVardef@405fe1_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHICAL ABSTRACTC_FLOATNO A part of the nsp15 coding sequence of SARS-CoV-2 promotes efficient transmission of defective viral genomes in vitro and in vivo. Using a sequential deletion library and targeted deletions within this region we identify RNA structures that may function as packaging signals. C_FIG

microbiology↗

Comprehensive analysis of yeast +1 ribosomal frameshifting unveils a novel stimulator affirming two distinct frameshifting mechanisms

Ribosomal frameshifting is an important, albeit rare, mRNA decoding mechanism that generally allows the synthesis of a single protein from two different reading frames. For most +1 frameshifting cases, the mechanism is commonly presumed to involve dissociation of the P-site tRNA from its cognate codon followed by its movement to the +1 codon, setting the new +1 frame for incoming tRNAs. This movement is stabilized by P-site tRNA pairing with the +1 codon. However, in several occurrences in the yeast Saccharomyces cerevisiae, P-site tRNA re-pairing with the +1 codon is impossible. Two alternative hypotheses exist explaining this observation. One model suggests that +1 frameshifting occurs according to a common mechanism involving P-site movement, while its re-pairing with +1 codon is not essential. The alternative model suggests a distinct mechanism in which the A-site tRNA acceptance at the +1 codon occurs in the absence of P-site tRNA movement relative to mRNA. Here we set out to perform a comprehensive comparative analysis of all known +1 ribosomal frameshifting sites in S. cerevisiae. This included a novel case of +1 ribosomal frameshifting that we discovered during this study. It is required for the expression of LLP1 gene encoding dolichol-linked oligosaccharide pyrophosphatase. During the analysis of all frameshifting contexts, we identified a conserved RNA secondary structure located almost immediately upstream of the ABP140 frameshifting site. This structure substantially increases +1 frameshifting efficiency. The RNA stimulators location suggests that mRNA exiting the ribosome forms this structure, creating an mRNA pulling effect, thus favouring positioning of the +1 codon in the P-site. Placing the stimulator upstream of various known frameshifting sites, revealed that its stimulatory action is selective to those frameshifting sites where P-site tRNA re-pairing is possible, reinforcing the idea of two distinct mechanisms of ribosomal frameshifting.

molecular biology↗

Characterisation of native human pancreatic mesenchymal stromal cells in type 1 diabetes

Aims/hypothesisCulture-expanded mesenchymal stromal cells (MSCs) reduce immune cell activation and improve islet functional survival. However, little is known about native human pancreatic MSCs (npMSCs) in health or how they are altered in type 1 diabetes. Here, we determined the number, density and islet-protective phenotype of npMSCs in situ in control individuals and those with type 1 diabetes. MethodsMultiplex immunohistochemistry was used to identify npMSCs (CD90+/CD105+/CD73+/CD31-/CD45-/CD34-) in human pancreas sections from 38 donors (Network for Pancreatic Organ Donors with Diabetes and Exeter Archival Diabetes Biobank). Donors were categorised as either < 13 years at type 1 diabetes diagnosis (n = 8) or [&ge;] 13 years at type 1 diabetes diagnosis (n = 11) or were age- and sex-matched individuals without diabetes. Consecutive sections were immunostained with antisera against insulin, glucagon, and the established islet-protective and immunomodulatory factors Annexin A1 (ANXA1) and indoleamine 2,3-Dioxygenase-1. Whole-slide scans were acquired and npMSCs either inside or at the periphery (within 10 {micro}m) of islets were quantified on an individual-islet basis. We identified 53,375 npMSCs and performed an analysis of 26,376 individual islets. Culture-expanded MSCs were exposed to cytokines and viability and proliferation was assessed by flow cytometry. ResultsnpMSC were identified in situ in the human pancreas where they wrap around the islet periphery in an expected spindle-like morphology. ANXA1 was expressed by 33.2% of npMSCs and was expressed constitutively among individuals with or without diabetes. The density of both intraislet npMSCs and npMSCs within 10 {micro}m of the islet periphery was increased for insulin-containing islets in individuals with type 1 diabetes compared to individuals without diabetes (p < 0.001). npMSC density within 10 {micro}m of the islet periphery was preferentially increased in individuals [&ge;] 13 years at type 1 diabetes diagnosis compared to individuals < 13 years at type 1 diabetes diagnosis (p < 0.001). npMSC density was reduced around insulin-deficient islets compared to insulin-containing islets in individuals with diabetes (p < 0.001), consistent with an islet-protective role for npMSCs. Exposure of culture-expanded MSCs to an aggressive cytokine combination led to increased cell death and reduced proliferation. Conclusion/interpretationnpMSCs express ANXA1 constitutively suggesting an islet-protective role in health. The density of npMSCs was increased around insulin-containing islets and lost around insulin-deficient islets in individuals with type 1 diabetes which aligns with this hypothesis. npMSC density at the periphery of insulin-containing islets was preferentially higher in individuals with later onset type 1 diabetes, correlating with a less intense immune cell infiltration. The reduced ability of npMSCs to survive in the more intense pro-inflammatory environment around islets in younger onset type 1 diabetes may contribute to the rapid rate of beta cell loss in these individuals. Research in context What is already known about the subject?* Culture-expanded mesenchymal stromal cells (MSCs) reduce immune cell activation and improve islet functional survival. * Therapeutically administered MSCs migrate to sites of injury and preserve endogenous C-peptide in individuals with newly diagnosed type 1 diabetes. What is the key question?* Is the number, distribution and/or cytoprotective and immunomodulatory phenotype of native pancreatic MSCs (npMSCs) altered in type 1 diabetes? What are the new findings?* npMSCs express typical markers of isolated, culture-expanded MSCs and their number and density is increased within and at the periphery of insulin-containing islets in individuals with type 1 diabetes. * npMSCs are more abundant at the periphery of islets in individuals with later onset type 1 diabetes, correlating with a less intense immune cell infiltration. * MSCs are less able to survive an aggressive inflammatory environment such as that arising from the enhanced islet immune cell infiltration in individuals with younger onset type 1 diabetes How might this impact on clinical practice in the foreseeable future?* Therapeutically administered MSCs are likely to be more effective at preserving endogenous beta cell mass in individuals with later onset type 1 diabetes where MSCs have a greater ability to survive and exert their therapeutic functions.

physiology↗

Evidence for the pairing of mRNA exiting ribosomes acting as a Driver of unidirectional forward bypassing: Its cessation permits Backwards scanning

Efficient translational avoidance of a 50 nucleotide non-coding insert in phage T4 gene 60 sequence involves dissociation of peptidyl-tRNA pairing from the mRNA take-off codon, GGA. This tRNA is retained in the ribosomal P-site during bypassing. Its anticodon does not scan the 5 part of the non-coding sequence, which contains a cognate GGG codon, but it does scan the main and 3 part of the coding gap for potential complementarity. Re-pairing to a matched GGA landing site codon occurs exclusively 48-50 nt after take-off. Coding resumption ensues. Here we analyze proteins synthesized from mutants that abrogate the potential for re-pairing at the canonical landing site. The results show that some ribosomes move backwards 39 nt allowing re-pairing to the initially hidden GGG or forwards at least 56 additional nt before resumed anticodon: codon pairing at a downstream matched codon. We discuss the nature of the driving force for the initial unidirectional movement and why it becomes dissipated when the site of landing in WT is reached. Also presented is an analysis of the relative importance of recoding signals located 6 nucleotides upstream (5) and close downstream (3) of the WT landing site, for re-pairing to mRNA and coding resumption.

molecular biology↗