Frequency-dependent selection of neoantigens fosters tumor immune escape and predicts immunotherapy response Article Open access 25 June 2024 Genetic immune escape landscape in primary and metastatic cancer Article Open access 10 May 2023 Oncogenic context shapes the fitness landscape of tumor suppres...
Genome-wide expression profiling identified five biological BC subtypes36, namely luminal A/B, HER2-enriched, basal-like and normal breast-like, which differ by hormonal receptor status, proliferation, genomic instability, mutational signatures, treatment response and prognosis37,38,39,40,41. It has...
F1 pool data. Whole body RNA-Seq data for a selection of these intersected genes are plotted in Fig.7. Several of the AVR-upregulated genes shown are annotated as enzymes with hydrolase, glycosidase or peroxidase functions. Other annotations include a transcription factor and proteins of unknown...
All four alternatives are present throughout the study area, but the frequency of conservation-oriented and social alternatives being identified as the most suitable decreases in the north-western parts of Spain, while increases in the central area (Fig.6). On the other hand, the productive alte...
Memory B cells (MBCs) are long-lived sources of rapid, isotype-switched secondary antibody-forming cell (AFC) responses. Whether MBCs homogeneously retain the ability to self-renew and terminally differentiate or if these functions are compartmentalized into MBC subsets has remained unclear. It has ...
(C) Schematic summarizing experimental plan for testing effect of time-dependent downregulation of canonical Wnt signaling by CHIR withdrawal. (D and E) Retention of distal lung epithelial fate on day 29 of the experiment described in (C), measured by the frequency of cells expressing the (D)...
(F) Frequency and size (vesicle diameter in nm) distribution of vesicles from negative stain TEM in (E). The number of vesicles measured: SEV n = 118; MEV n = 51; LEV n = 30; and UC n = 291. The median size in nm for each category is indicated with an asterisk (∗). See...
First, the motif position frequency matrix was created using motif information from the JASPAR database (JASPAR2020 matrix for species 9606, homo sapiens). Next, chromvar was used to calculate a motif score per cell for each TF. Seurat’s FeaturePlot function was then used to visualize the ...
914 passed these filters. Donor-level genotype missingness rates were checked to exclude donors with genotype missingness rates > 10%. All 297 individuals passed this filter. Finally, variants with minor allele frequency (MAF) < 5%, missingness > 5%, and Hardy-Weinberg equilibriump-value ...
even for small subpopulations of low-frequency cells. Fine clustering of tumor-associated T cells based on RNA splicing heterogeneity We then used SCASL to delineate heterogeneous tumor-associated lymphocytes based on their RNA splicing landscapes. First, immune cells from different tissues of 6 ...