SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in the presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy.

Viruses are parasites, relying on the cells they infect to make more of themselves. In doing so they change how an infected cell turns its genes on and off, forcing it to build new virus particles and turning off the immune surveillance that would allow the body to intervene. This is how SARS-CoV-2, the virus that causes COVID, survives with a genome that carries instructions to make just 29 proteins.

One of these proteins, known as Nsp14, is involved in both virus reproduction and immune escape. Previous work has shown that it interacts with IMPDH2, the cellular enzyme that controls the production of the building blocks of the genetic code. The impact of this interaction is not clear.

To find out more, Zaffagni et al. introduced 26 of the SARS-CoV-2 proteins into human cells one at a time. Nsp14 had the most dramatic effect, dialing around 4,000 genes up or down and changing how the cell interprets over 1,000 genes. Despite being just one protein, it mimicked the genetic changes seen during real SARS-CoV-2 infection. Blocking IMPDH2 partially reversed the effects, which suggests that the interaction of Nsp14 with the enzyme might be responsible for the effects of SARS-CoV-2 on the genes of the cell.

Understanding how viral proteins affect cells can explain what happens during infection. This could lead to the discovery of new treatments designed to counteract the effects of the virus. Further work could investigate whether interfering with Nsp14 helps cells to overcome infection.

Intra-epithelial non-canonical Activin A signaling safeguards prostate progenitor quiescence

The healthy prostate is a relatively quiescent tissue. Yet, prostate epithelium overgrowth is a common condition during aging, associated with urinary dysfunction and tumorigenesis. For over thirty years, TGF-β ligands have been known to induce cytostasis in a variety of epithelia, but the intracellular pathway mediating this signal in the prostate, and its relevance for quiescence, have remained elusive. Here, using mouse prostate organoids to model epithelial progenitors, we find that intra-epithelial non-canonical Activin A signaling inhibits cell proliferation in a Smad-independent manner. Mechanistically, Activin A triggers Tak1 and p38 ΜAPK activity, leading to p16 and p21 nuclear import. Spontaneous evasion from this quiescent state occurs upon prolonged culture, due to reduced Activin A secretion, a condition associated with DNA replication stress and aneuploidy. Organoids capable to escape quiescence in vitro are also able to implant with increased frequency into immunocompetent mice. This study demonstrates that non-canonical Activin A signaling safeguards epithelial quiescence in the healthy prostate, with potential implications for the understanding of cancer initiation, and the development of therapies targeting quiescent tumor progenitors.

SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1,000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy.

SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs

Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our strategy involves two steps: annotation of validated circRNAs followed by a quantification step. We show that SRCP is more sensitive than other individual pipelines and allows for more comprehensive quantification of a larger number of differentially expressed circRNAs. To facilitate the use of SRCP, we generate a comprehensive collection of validated circRNAs in five different organisms, including humans. We then utilize our approach and identify a subset of circRNAs bound to the miRNA-effector protein AGO2 in human brain samples.

Craving for Introns

Parenteau et al. (2019) and Morgan et al. (2019) showed that a subset of introns can work as non-coding RNAs that trap the spliceosome and decrease global splicing upon nutrient depletion in yeast, providing a new example of the functionality of introns, molecules that were previously assumed to be useless.

Abstract 1670: Discovery of novel water-soluble derivatives of mebendazole as selective CLK1/4 kinase inhibitors and their anticancer cancer activity

Metastatic cancers remain clinically challenging and account for more than 90% of all cancer deaths. Drugs used to treat advanced metastatic cancers often generate drug resistance and relapse. Therefore, there is a critical need for novel therapeutic approaches for patients with advanced stage cancers that do not respond to any currently available anticancer therapies. Mebendazole and structurally related benzimidazole analogues, which are FDA approved compounds used to treat helminthic infections in the gastrointestinal track, are effective in inhibiting in vitro cancer cell proliferation. Unfortunately, their therapeutic applications in metastatic cancer are limited by their extremely low solubility and poor bioavailability. Further, the mechanism of the anticancer activities of this class of compounds is poorly defined. Here, we report the design and synthesis of water-soluble benzimidazoles as novel anticancer agents. Among them, the novel oxetanyl substituted compound, OBD9 (Methyl (5-(4-(methyl(oxetan-3-yl)amino)benzoyl)-1H-benzo[d]imidazol-2-yl)carbamate), demonstrated potent cytotoxicity towards a variety of highly aggressive cancer lines including prostate, lung, and ovarian cancers (IC50: 0.9-3.8 μM). In the NCI60 cancer cell panel screen, OBD9 broadly inhibited the proliferation of leukemia, melanoma, and breast and colon cancers. The aqueous solubility of OBD9 achieved 361 μM vs <1μM for mebendazole. In a mouse xenograft model of the highly metastatic human prostate cancer PC3MLN4, OBD9 (30 mg/kg/day, three times/week for two weeks) significantly inhibited the growth of established tumors (treatment-to-control ratio: 0.36) without noticeable toxicity. We performed broad kinase screening (KINOMEscan, DiscoverX) to explore the mechanism of action and discovered OBD9 as a potent and highly selective inhibitor of Cdc-like kinase 1 and 4 (CLK1 and 4). The Selectivity Score of OBD9 at 10 μM concentration in the 403 non-mutant kinases is 0.002; and its IC50 is 1.5 and 1.2 μM for CLK1 and CLK4, respectively. CLKs are nuclear serine/threonine (S/T) kinases that regulate gene splicing and are frequently over activated in cancers. Our results suggest that OBD9 impedes cancer growth at least in part by inhibiting CLK1/4.

Citation Format: Lijun Sun, Jae Eun Cheong, Michela Zaffagni, Kun Zhou, Bruce Zetter. Discovery of novel water-soluble derivatives of mebendazole as selective CLK1/4 kinase inhibitors and their anticancer cancer activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1670.