Journal: Nature

Article Title: Identification of essential genes for cancer immunotherapy

doi: 10.1038/nature23477

Figure Lengend Snippet: a–c, Kaplan-Meier survival plots of patient overall survival with the expression of antigen presentation genes B2M (a), TAP1 (b) and TAP2 (c) after ipilimumab immunotherapy. Patients were categorized into ‘High’ and ‘Low’ groups according to the highest and the lowest quartiles of each individual gene expression (RPKM). Reported P-values have been penalized by multiplying the unadjusted P-value by 3 to account for the comparison of the two extreme quartiles. Hazard ratio (HR) was calculated using Mantel-Haenszel test; with HR ranges: B2M (0.02–0.31), TAP1 (0.04–0.52) and TAP2 (0.12–1.07). Data is derived from 42 melanoma patients from the Van-Allen et al. cohort3. d, Schematic of the 2CT-CRISPR assay to identify essential genes for EFT. e, NY-ESO-1 antigen specific lysis of melanoma cells after 24 h of co-culture of ESO T cells with NY-ESO-1− SK23, NY-ESO-1+ SK23 and NY-ESO-1+ Mel624 cells (n = 3 biological replicates) at E:T ratio of 1. f, Survival of Mel624 cells modified through lentiviral CRISPR targeting of MHC class I antigen presentation/processing genes after introduction of ESO T cells. CRISPR-modified Mel624 cells were co-cultured with ESO T cells at E:T ratio of 0.5 for 12 h. Live cell survival (%) was calculated from control cells unexposed to T cell selection. Data is from 3 independent infection replicates. All values are mean ± s.e.m. ***P < 0.001 as determined by Student’s t-test.

Article Snippet: Gene expression was quantified using TaqMan RNA-to-Ct 1-Step Kit (Thermo Fisher) and Taqman assay probes (Invitrogen): Aplnr (Mm00442191_s1), Actb (Mm00607939_s1), APLN (Hs00936329), ACTB (Hs01060665_g1), IRF1 (Hs00971965_m1), IFI30 (Hs00173838_m1), TAP1 (Hs00388675_m1), TAP2 (Hs00241060_m1), TAPBP (Hs00917451_g1) and JAK1 (Hs01026983_m1).

Techniques: Expressing, Immunopeptidomics, Gene Expression, Comparison, Derivative Assay, CRISPR, Lysis, Co-Culture Assay, Modification, Cell Culture, Control, Selection, Infection

Journal: Behavioural brain research

Article Title: Prenatal stress-induced disruptions in microbial and host tryptophan metabolism and transport

doi: 10.1016/j.bbr.2021.113471

Figure Lengend Snippet: Taqman Mouse-Specific Gene Expression Assays.

Article Snippet: SLC7A5 , Mm00441516_m1.

Techniques: Gene Expression

Journal: Behavioural brain research

Article Title: Prenatal stress-induced disruptions in microbial and host tryptophan metabolism and transport

doi: 10.1016/j.bbr.2021.113471

Figure Lengend Snippet: SLC6A4 (SERT) is a transporter of 5-HT. Increased 5-HT induces AhR. SLC3A2 and SLC7A5 heterodimerize to form LAT-1 and act as a Trp transporter. Trp can be metabolized to indole, which can act as a ligand for AhR. AhR, when bound to a ligand such as indole, can induce expression of Cyp1 genes (Cyp1a1, Cyp1b1). This figure was created in BioRender.

Article Snippet: SLC7A5 , Mm00441516_m1.

Techniques: Expressing

Journal: Behavioural brain research

Article Title: Prenatal stress-induced disruptions in microbial and host tryptophan metabolism and transport

doi: 10.1016/j.bbr.2021.113471

Figure Lengend Snippet: (A) Distal colon Tdo2 (p < 0.05) was increased over the course of the assessment. (B) Cyp1a1 at PNW1 (p < 0.05), (C) 5-ht2br at PNW1 (p < 0.05), (D) Slc7a5 at PNW3 (p = 0.0556), and (E) Slc3a2 at PNW5 (p = 0.0655), were altered in PNS offspring compared to control. Data are mean ± SEM. All data are presented as 2−ΔΔCT (fold-change compared to control). For each time point, one male and one female were used from each litter, and then averaged after statistical testing for sex revealed no effects; n = 5–7. * = p < 0.05.

Article Snippet: SLC7A5 , Mm00441516_m1.

Techniques: Control