Dataset of proinflammatory cytokine and cytokine receptor gene expression in rainbow trout (Oncorhynchus mykiss) measured using a novel GeXP multiplex, RT-PCR assay
DATA IN BRIEF
Authors: Kutyrev, Ivan; Cleveland, Beth; Leeds, Timothy; Wiens, Gregory D.
Abstract
A GeXP multiplex, RT-PCR assay was developed and optimized that simultaneously measures expression of a suite of immune-relevant genes in rainbow trout (Oncorhynchus mykiss), concentrating on tumor necrosis factor and interleukin-1 ligand/receptor systems and acute phase response genes. The dataset includes expression values for drpt, il11a, il1b1, il1b2, il1b3, il1r-like-1(e3-5), il1r-like-1 (e9-11), il1r1-like-a, il1r1-like-b, il1r2, saa, tnfa1, tnfa2, tnfa3, tnfrsf1a, trifrsf1a-like-a, tnfrsf1a-like-b, tnfrsf5, and tnfrsf9. Gene expression was measured at four time-points post-challenge in both a resistant line (ARS-Fp-R) and a susceptible line (ARS-Fp-S) of rainbow trout. In addition, fish body weight, spleen index and the Flayobacterium psychrophilum load are reported. These data are an extension of information presented and discussed in "Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with Flayobacteriurn psychrophilum in resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)" (Kutyrev et al., 2016) [1]. Published by Elsevier Inc.
Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing
NATURE MEDICINE
Authors: Guo, Xinyi; Zhang, Yuanyuan; Zheng, Liangtao; Zheng, Chunhong; Song, Jintao; Zhang, Qiming; Kang, Boxi; Liu, Zhouzerui; Jin, Liang; Xing, Rui; Gao, Ranran; Zhang, Lei; Dong, Minghui; Hu, Xueda; Ren, Xianwen; Kirchhoff, Dennis; Roider, Helge Gottfried; Yan, Tiansheng; Zhang, Zemin
Abstract
Cancer immunotherapies have shown sustained clinical responses in treating non-small-cell lung cancer(1-3), but efficacy varies and depends in part on the amount and properties of tumor infiltrating lymphocytes(4-6). To depict the baseline landscape of the composition, lineage and functional states of tumor infiltrating lymphocytes, here we performed deep single-cell RNA sequencing for 12,346 T cells from 14 treatment-naive non-small-cell lung cancer patients. Combined expression and T cell antigen receptor based lineage tracking revealed a significant proportion of inter-tissue effector T cells with a highly migratory nature. As well as tumor-infiltrating CD8(+) T cells undergoing exhaustion, we observed two clusters of cells exhibiting states preceding exhaustion, and a high ratio of "pre-exhausted" to exhausted T cells was associated with better prognosis of lung adenocarcinoma. Additionally, we observed further heterogeneity within the tumor regulatory T cells (Tregs), characterized by the bimodal distribution of TNFRSF9, an activation marker for antigen-specific Tregs. The gene signature of those activated tumor Tregs, which included IL1R2, correlated with poor prognosis in lung adenocarcinoma. Our study provides a new approach for patient stratification and will help further understand the functional states and dynamics of T cells in lung cancer.