Author: Stanley Crooke, M.D., Ph.D.

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Unravelling why some PS ASOs activate the innate immune system

Working out the step by step molecular mechanism to explain why some PS ASOs of all chemical classes are cytotoxic led directly to medicinal chemical solutions that are enhancing the therapeutic index  of many PS ASOs significantly by dramatically reducing their potential cytotoxic effects without materially altering their potency (Shen, W., et.al., NAR, 2018; Migawa, M., et.al., NAR, 2019; Vasquez, G., et.al., NAR, 2021; Anderson, … Continue reading Unravelling why some PS ASOs activate the innate immune system »

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Insights into innate immune activation via PS-ASO-Protein-TLR9 Interactions

July 15, 2022 : Pollak,A.J., et al, NAR https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac618/6644951 It has long been known that nucleic acids that have CpG motifs can activate the immune system and that DNA like nucleic acids do that by interacting with TLR9 located in late endosomes. It has also been shown that PS ASOs that do not have CpG motifs can activate the innate immune system in a TLR9 … Continue reading Insights into innate immune activation via PS-ASO-Protein-TLR9 Interactions »

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Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey

In the fall of last year, I received a very unusual request from two associated editors, David Corey, Ph.D. and Helle Ulrich, Ph.D. for Nucleic Acid Research (NAR), a highly regarded and highly cited scientific journal. They asked if I would be willing to provide a manuscript describing how I established a rigorous scientific environment at Ionis. I was pleased to have two scientists for whom I … Continue reading Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey »

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RNA modifications can affect RNase H1-mediated PS-ASO activity

Thanks to decades of work, we have a great deal of detailed knowledge about how various chemical modifications of a PS ASO can affect hybridization to target RNAs and how those modifications affect the interactions of the heteroduplex with RNAseH1, including binding, catalytic rate and sites of cleavage of the target RNA. However, it is now clear that cellular RNAs may be modified post-transcriptionally with … Continue reading RNA modifications can affect RNase H1-mediated PS-ASO activity »

Blogs

COVID-19 Post-Mortem 1

Throughout the COVID-19 epidemic and the unprecedented response to it, I have tried to express a number of concerns about the response that I think have to a large extent proven to be valid, despite the death toll in the US due to COVID-19 being much larger than I expected it to be. Today, with the benefit of hindsight and a growing number of scholarly … Continue reading COVID-19 Post-Mortem 1 »

Blogs

Effects of PS ASOs on the conformations of RNAse H1 and P54.

Nucleic Acid Research Journal

Over the past several years, my group has systematically identified cellular proteins that bind PS ASOs, defined the roles of many of the proteins bound by PS ASOs, assessed the effects of PS ASO binding on those proteins and developed a thorough appreciation of the biochemistry of PS ASO protein interactions. We have also shown that PS ASO induce the formation of numerous PS ASO/protein/RNA … Continue reading Effects of PS ASOs on the conformations of RNAse H1 and P54. »

Blogs

PS ASO Induced Aggregates Undergo Phase separations.

Work from my group has demonstrated that proteins determine the fate of PS ASOs in all biological systems, identified the key proteins involved in cellular pharmacodynamics, pharmacokinetics and toxicology, characterized the binding of PS ASO to many of the critical proteins and demonstrated that most cytotoxic PS ASOs in all cells and organs studied are to interactions with paraspeckle proteins and RNAse H1 that delocalize … Continue reading PS ASO Induced Aggregates Undergo Phase separations. »

Blogs

The Role of HSC 70 in Endosomal Release of PS ASOs.

In the HSC 70 paper in Nucleic Acid Therapeutics (Laing, NAT 2021, ahead of print), we add another protein that plays an important role. HSC 70 is a heat shock protein that we showed binds to PS ASOs and that reducing HSC 70 reduced the potency of PS ASOs delivered by free cellular uptake. In the current manuscript, we delineate the molecular mechanisms by which … Continue reading The Role of HSC 70 in Endosomal Release of PS ASOs. »

Blogs

Perspectives paper published in Journal of the American Chemical Society (JACS)

One of the more important recent advances in antisense technology has been the demonstration the importance of protein binding to the pharmacological effects of ASOs or siRNAs that contain phophorothioates. Said simply: proteins determine the fate of PS ASOs (and siRNAs) in biological systems and PS ASOs (and siRNAs) can affect the fates of many of the proteins with which they interact. This means that … Continue reading Perspectives paper published in Journal of the American Chemical Society (JACS) »

Blogs

Proteins determine the fate of PS ASOs in biological systems

Though we have known that PS ASOs bind to proteins since 1989 and, in fact, one of the reasons we chose phosphorothioate to replace the phosphodiester inter-nucleotide linkage was the belief that they would bind to plasma proteins thereby preventing rapid clearance in urine via glomerular filtration, the focus of ASO medicinal chemistry was on the language of ASO-nucleic acid interaction. That is, we focused on … Continue reading Proteins determine the fate of PS ASOs in biological systems »