UTX promotes CD8+ T cell-mediated antiviral defenses but reduces T cell durability

Persistent virus infections can cause pathogenesis that is debilitating or lethal. During these infections, virus-specific T cells fail to protect due to weakened antiviral activity or failure to persist. These outcomes are governed by histone modifications, although it is unknown which enzymes contribute to T cell loss or impaired function over time. In this study, we show that T cell receptor-stimulated CD8⁺ T cells increase their expression of UTX (ubiquitously transcribed tetratricopeptide repeat, X chromosome) to enhance gene expression. During chronic lymphocytic choriomeningitis virus (LCMV) infection in mice, UTX binds to enhancers and transcription start sites of effector genes, allowing for improved cytotoxic T lymphocyte (CTL)-mediated protection, independent of its trimethylation of histone 3 lysine 27 (H3K27me3) demethylase activity. UTX also limits the frequency and durability of virus-specific CD8⁺ T cells, which correspond to increased expression of inhibitory receptors. Thus, UTX guides gene expression patterns in CD8⁺ T cells, advancing early antiviral defenses while reducing the longevity of CD8⁺ T cell responses.

T cells fail to eliminate chronic virus infections due to alterations in gene expression that undermine their activity. In this study, Mitchell et al. identify a histone-modifying enzyme that promotes effector gene expression and CTL activity early on yet reduces T cell survival, leading to infection persistence.

IL22 Inhibits Epithelial Stem Cell Expansion in an Ileal Organoid Model

Background & Aims

Crohn's disease is an inflammatory bowel disease that affects the ileum and is associated with increased cytokines. Although interleukin (IL)6, IL17, IL21, and IL22 are increased in Crohn's disease and are associated with disrupted epithelial regeneration, little is known about their effects on the intestinal stem cells (ISCs) that mediate tissue repair. We hypothesized that ILs may target ISCs and reduce ISC-driven epithelial renewal.

Methods

A screen of IL6, IL17, IL21, or IL22 was performed on ileal mouse organoids. Computational modeling was used to predict microenvironment cytokine concentrations. Organoid size, survival, proliferation, and differentiation were characterized by morphometrics, quantitative reverse-transcription polymerase chain reaction, and immunostaining on whole organoids or isolated ISCs. ISC function was assayed using serial passaging to single cells followed by organoid quantification. Single-cell RNA sequencing was used to assess Il22ra1 expression patterns in ISCs and transit-amplifying (TA) progenitors. An IL22-transgenic mouse was used to confirm the impact of increased IL22 on proliferative cells in vivo.

Results

High IL22 levels caused decreased ileal organoid survival, however, resistant organoids grew larger and showed increased proliferation over controls. Il22ra1 was expressed on only a subset of ISCs and TA progenitors. IL22-treated ISCs did not show appreciable differentiation defects, but ISC biomarker expression and self-renewal-associated pathway activity was reduced and accompanied by an inhibition of ISC expansion. In vivo, chronically increased IL22 levels, similar to predicted microenvironment levels, showed increases in proliferative cells in the TA zone with no increase in ISCs.

Conclusions

Increased IL22 limits ISC expansion in favor of increased TA progenitor cell expansion.

Discussion of “Attitude of Physi -cians Towards Automatic Alerting in Computerized Physician Order Entry Systems”

With these comments on the paper “Attitude of Physicians Towards Automatic Alerting in Computerized Physician Order Entry Systems”, written by Martin Jung and co authors, with Dr. Elske Ammenwerth as senior author [1], the journal wants to stimulate a broad discussion on computerized physi cian order entry systems. An international group of experts have been invited by the editor of Methods to comment on this paper. Each of the invited commentaries forms one section of this paper.

Discussion of "Attitude of physicians towards automatic alerting in computerized physician order entry systems"

With these comments on the paper "Attitude of Physicians Towards Automatic Alerting in Computerized Physician Order Entry Systems", written by Martin Jung and co-authors, with Dr. Elske Ammenwerth as senior author [1], the journal wants to stimulate a broad discussion on computerized physician order entry systems. An international group of experts have been invited by the editor of Methods to comment on this paper. Each of the invited commentaries forms one section of this paper.

Predicting Shine-Dalgarno sequence locations exposes genome annotation errors

In prokaryotes, Shine-Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis. The location of SD sequences relative to start codons and the stability of the hybridization between the mRNA and the rRNA correlate with the rate of synthesis. Thus, accurate characterization of SD sequences enhances our understanding of how an organism's transcriptome relates to its cellular proteome. We implemented the Individual Nearest Neighbor Hydrogen Bond model for oligo-oligo hybridization and created a new metric, relative spacing (RS), to identify both the location and the hybridization potential of SD sequences by simulating the binding between mRNAs and single-stranded 16S rRNA 3' tails. In 18 prokaryote genomes, we identified 2,420 genes out of 58,550 where the strongest binding in the translation initiation region included the start codon, deviating from the expected location for the SD sequence of five to ten bases upstream. We designated these as RS+1 genes. Additional analysis uncovered an unusual bias of the start codon in that the majority of the RS+1 genes used GUG, not AUG. Furthermore, of the 624 RS+1 genes whose SD sequence was associated with a free energy release of less than -8.4 kcal/mol (strong RS+1 genes), 384 were within 12 nucleotides upstream of in-frame initiation codons. The most likely explanation for the unexpected location of the SD sequence for these 384 genes is mis-annotation of the start codon. In this way, the new RS metric provides an improved method for gene sequence annotation. The remaining strong RS+1 genes appear to have their SD sequences in an unexpected location that includes the start codon. Thus, our RS metric provides a new way to explore the role of rRNA-mRNA nucleotide hybridization in translation initiation.

Sequestered chemistry of the Arminacean nudibranch Leminda millecra in Algoa Bay, South Africa

Extracts of the endemic nudibranch Leminda millecra collected in Algoa Bay, South Africa, yielded four known metabolites, millecrones A (1) and B (2), isofuranodiene (5), and (+)-8-hydroxycalamenene (9), and nine new compounds, algoafuran (7), cubebenone (8), and a series of seven triprenylquinones and hydroquinones (21-27). A subsequent GC-MS survey of extracts of 21 of L. millecra's possible octocoral prey species in Algoa Bay identified the soft coral Alcyonium fauri as the source of 1 and the gorgonian Leptogorgia palma as the species producing 2 and 8.