Inflammatory bowel disease (IBD) are heterogenous disorders of the gastrointestinal tract caused by a spectrum of genetic and environmental factors. In mice, overlapping regions of chromosome 3 have been associated with susceptibility to IBD-like pathology, including a locus called Hiccs. However, the specific gene that controls disease susceptibility remains unknown. Here we identify a Hiccs locus gene, Alpk1 (encoding alpha kinase 1), as a potent regulator of intestinal inflammation. In response to infection with the commensal pathobiont Helicobacter hepaticus (Hh), Alpk1-deficient mice display exacerbated interleukin (IL)-12/IL-23 dependent colitis characterized by an enhanced Th1/interferon(IFN)-γ response. Alpk1 controls intestinal immunity via the hematopoietic system and is highly expressed by mononuclear phagocytes. In response to Hh, Alpk1−/− macrophages produce abnormally high amounts of IL-12, but not IL-23. This study demonstrates that Alpk1 promotes intestinal homoeostasis by regulating the balance of type 1/type 17 immunity following microbial challenge.

Background & Aims: The efficacy of NS5A inhibitors against several less common subtypes of hepatitis C virus (HCV) is poorly characterised. Some subtypes including 3b, 3g, 6u and 6v commonly harbour amino acid residues as wild type in NS5A that may confer resistance to direct acting antivirals (DAAs) in other common subtypes. Data from patients also suggest that 1l and 4r with amino acid substitutions at positions 28-31 and 93 in NS5A are relatively resistant to DAA therapy.Methods: In this study, we tested the efficacy of daclatasvir, elbasvir, ledipasvir, pibrentasvir and velpatasvir against these subtypes using the SGR-JFH1 replicon backbone. Results: NS5A inhibitors showed different levels of efficacy with only pibrentasvir effective against all tested subtypes. Daclatasvir and ledipasvir were ineffective against 6u and 6v (half maximal effective concentration [EC50] values of 239-321 nM) while 3b and 3g were only susceptible to pibrentasvir. Analysis of effects of individual mutations indicated that Q30R in 1l increased the EC50 of ledipasvir by 18 fold, conferring intermediate resistance, while those of L31M and Y93H in 4r induced increases in EC50s of 2100-and 3575-fold (high level resistance). Conclusion:The high ledipasvir EC50 values of 1l with the Q30R substitution, 4r L31M and 4r Y93H may explain the treatment failure in patients who were infected with these viruses and treated with ledipasvir + sofosbuvir. This study also shows the ineffectiveness of the first generation NS5A inhibitors against 6u and 6v, and confirms the inherent resistance of 3b and 3g to most NS5A inhibitors. Clinical studies to confirm in vivo sensitivity to NS5A inhibitors are urgently needed so that rational, effective treatment strategies may be developed for unusual subtypes. Lay summaryLittle is known about the efficacy of NS5A inhibitors against some "unusual" HCV subtypes including 1l, 3b, 3g, 4r, 6u and 6v. In this study, we manufactured HCV replicons which express the NS5A protein from the unusual HCV subtypes 1l, 3b, 3g, 4r, 6u, 6v. We then tested the effect of the NS5A inhibitors daclatasvir, elbasvir, ledipasvir, pibrentasvir and velpatasvir on blocking replication on these replicons. We show that these replicons are resistance at some level to all NS5A inhibitors other than pibrentasvir.

Human immunodeficiency virus 1 (HIV-1) is a life-threatening pathogen that still lacks a curative therapy or vaccine. Despite the reduction in AIDS-related deaths achieved by current antiretroviral therapies, drawbacks including drug resistance and the failure to eradicate infection highlight the need to identify new pathways to target the infection. Circadian rhythms are endogenous 24-h oscillations which regulate physiological processes including immune responses to infection, and there is an emerging role for the circadian components in regulating viral replication. The molecular clock consists of transcriptional/translational feedback loops that generate rhythms. In mammals, BMAL1 and CLOCK activate rhythmic transcription of genes including the nuclear receptor REV-ERBα, which represses BMAL1 and plays an essential role in sustaining a functional clock. We investigated whether REV-ERB activity regulates HIV-1 replication and found REV-ERB agonists inhibited HIV-1 promoter activity in cell lines, primary human CD4 T cells and macrophages, whilst antagonism or genetic disruption of REV-ERB increased promoter activity. The REV-ERB agonist SR9009 inhibited promoter activity of diverse HIV-subtypes and HIV-1 replication in primary T cells. This study shows a role for REV-ERB synthetic agonists to inhibit HIV-1 LTR promoter activity and viral replication, supporting a role for circadian clock components in regulating HIV-1 replication. All life forms have evolved under a rhythmically changing light/dark cycle due to the Earth's rotation. From bacteria to man, all organisms possess an internal clock that oscillates in a 24-h manner to anticipate environmental changes. The central clock and peripheral oscillators share a common molecular architecture and consist of transcriptional/translational feedback loops that regulate rhythmic gene expression 1. In mammals, BMAL1 and CLOCK dimerize and the complex can bind E-box motifs in the promoter/enhancer of various clock genes, including Per and Cry, to activate their transcription. In turn, the PER and CRY proteins repress BMAL1/CLOCK function and thereby shut down their own transcription. An additional feedback loop involves the nuclear receptors REV-ERBα and RORα. RORα competes with REV-ERBα for binding to the Bmal1 promoter ROR element (RORE) site and activates Bmal1 transcription. REV-ERBα and RORα coordinate a regulatory loop which is crucial for stabilizing the core clock machinery 2 (Fig. 1). The circadian system regulates host innate and adaptive immune responses to microbial pathogens 3-5 and host susceptibility to an infectious agent is not only dependent on the inoculum size, transmission route and length of exposure, but on the time of day when the pathogen is encountered 6. Recent clinical studies show that the time of vaccination can influence host immune responses and vaccine efficacy 7. Viruses are obligate parasites that rely on host cell synthesis machinery for their replication, survival and dissemination. The potential for circadian pathways to regulat...

Human induced pluripotent stem cells (iPSCs) and macrophages derived from them are increasingly popular tools for research into both infectious and degenerative diseases. However, as the field strives for greater modeling accuracy, it is becoming ever more challenging to justify the use of undefined and proprietary media for the culture of these cells. Here, we describe a defined, serum-free, open-source medium for the differentiation of iPSC-derived macrophages. This medium is equally capable of maintaining these cells compared with commercial alternatives. The macrophages differentiated in this medium display improved terminally differentiated cell characteristics, reduced basal expression of induced antiviral response genes, and improved polarization capacity. We conclude that cells cultured in this medium are an appropriate and malleable model for tissue-resident macrophages, on which future differentiation techniques can be built.

The authors would like to make two corrections to the supplemental information for this manuscript. First, the formulation of XVIVO medium is stated to be the same as previously published by van Wilgenburg et al. (2013), and OXM is subsequently based on this formulation. In van Wilgenburg et al. (2013) the concentration of M-CSF used was 100 ng/mL; however, in the originally published version of our supplemental information, 50 ng/mL M-CSF was reportedly used. This value was incorrect as written, and the concentration was in fact 100 ng/mL, the same as in Wilgenburg et al. (2013). Therefore, Table S2 in the supplemental information has been corrected to reflect this, stating a final concentration of 100 ng/mL M-CSF in both OXM and XVIVO media. Secondly, in the originally published version of this paper, OXM Macrophage medium is described to be the same as OXM differentiation medium with only Tropolone and IL-3 omitted. However, in the originally published version of Table S2 in the supplemental information, the composition of OXM Macrophage medium is listed as 96.5% Advanced DMEM/F-12, 2mM GlutaMAX, 15mM HEPES, 10 ng/mL M-CSF, and 1% Penicillin-Streptomycin. The correct formulation is 96.5% Advanced DMEM/F-12, 2mM GlutaMAX, 15mM HEPES, 5 mg/mL human recombinant Insulin solution, 100 ng/mL M-CSF, and 1% Penicillin-Streptomycin. The supplemental information has now been corrected with the manuscript online and the authors sincerely apologize for any confusion these errors may have caused.