Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy.

The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences in autologously derived T cells are a major contributor to therapy failure. To interrogate the molecular determinants of clinical CAR T-cell persistence, we extensively characterized the premanufacture T cells of 71 patients with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy. We performed RNA-sequencing analysis on sorted T-cell subsets from all 71 patients, followed by paired Cellular Indexing of Transcriptomes and Epitopes (CITE) sequencing and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on T cells from six of these patients. We found that chronic IFN signaling regulated by IRF7 was associated with poor CAR T-cell persistence across T-cell subsets, and that the TCF7 regulon not only associates with the favorable naïve T-cell state, but is maintained in effector T cells among patients with long-term CAR T-cell persistence. These findings provide key insights into the underlying molecular determinants of clinical CAR T-cell function. SIGNIFICANCE: To improve clinical outcomes for CAR T-cell therapy, there is a need to understand the molecular determinants of CAR T-cell persistence. These data represent the largest clinically annotated molecular atlas in CAR T-cell therapy to date, and significantly advance our understanding of the mechanisms underlying therapeutic efficacy.This article is highlighted in the In This Issue feature, p. 2113.

Antioxidant and Genotoxic Effects of Aqueous and Methanol Extracts from Two Edible Mushrooms from Turkey in Human Peripheral Lymphocytes.

This study reported the genetic and oxidative effects of aqueous and methanol extracts from two edible mushrooms, Lepista nuda (Bull.) Cooke and Pleurotus ostreatus (Jacq.) P. Kummer, in cultured human lymphocytes. Chromosome aberration (CA) and micronucleus (MN) assays were used for genotoxic influences estimation. In addition, the changes of total antioxidant capacity (TAC) and total oxidative stress (TOS) in the cells were monitored. The fungal extracts at all applied concentrations did not indicate significant differences (p > 0.05) in CA and MN analyses. Furthermore, while the treatments with maximum concentration of aqueous extract of L. nuda statistically (p < 0.05) increased TAC especially, TOS levels in the cells were reduced by them in comparison with negative control. Based on TAC analysis, low IC50 values belonging to aqueous (5.43 mg/L) and methanol (10.88 mg/L) extracts of L. nuda were remarkable. Our data demonstrated that the extracts obtained from P. ostreatus and especially L. nuda can be a new resource for therapeutics with their nonmutagenic and antioxidant features.

Risk variants disrupting enhancers of TH1 and TREG cells in type 1 diabetes.

Genome-wide association studies (GWASs) have revealed 59 genomic loci associated with type 1 diabetes (T1D). Functional interpretation of the SNPs located in the noncoding region of these loci remains challenging. We perform epigenomic profiling of two enhancer marks, H3K4me1 and H3K27ac, using primary TH1 and TREG cells isolated from healthy and T1D subjects. We uncover a large number of deregulated enhancers and altered transcriptional circuitries in both cell types of T1D patients. We identify four SNPs (rs10772119, rs10772120, rs3176792, rs883868) in linkage disequilibrium (LD) with T1D-associated GWAS lead SNPs that alter enhancer activity and expression of immune genes. Among them, rs10772119 and rs883868 disrupt the binding of retinoic acid receptor α (RARA) and Yin and Yang 1 (YY1), respectively. Loss of binding by YY1 also results in the loss of long-range enhancer-promoter interaction. These findings provide insights into how noncoding variants affect the transcriptomes of two T-cell subtypes that play critical roles in T1D pathogenesis.