-
Article
Open AccessQuantification of cerebrospinal fluid tumor DNA in lung cancer patients with suspected leptomeningeal carcinomatosis
Cerebrospinal fluid tumor-derived DNA (CSF-tDNA) analysis is a promising approach for monitoring the neoplastic processes of the central nervous system. We applied a lung cancer-specific sequencing panel (CAPP...
-
Article
Sarcoma microenvironment cell states and ecosystems are associated with prognosis and predict response to immunotherapy
Characterization of the diverse malignant and stromal cell states that make up soft tissue sarcomas and their correlation with patient outcomes has proven difficult using fixed clinical specimens. Here, we emp...
-
Article
Open AccessHigh-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE,...
-
Article
p53 governs an AT1 differentiation programme in lung cancer suppression
Lung cancer is the leading cause of cancer deaths worldwide1. Mutations in the tumour suppressor gene TP53 occur in 50% of lung adenocarcinomas (LUADs) and are linked to poor prognosis1–4, but how p53 suppresses ...
-
Protocol
Profiling Cellular Ecosystems at Single-Cell Resolution and at Scale with EcoTyper
Tissues are composed of diverse cell types and cellular states that organize into distinct ecosystems with specialized functions. EcoTyper is a collection of machine learning tools for the large-scale delineat...
-
Article
Open AccessAuthor Correction: Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis
-
Article
Inferring gene expression from cell-free DNA fragmentation profiles
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles fr...
-
Article
Open AccessIntegrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis
Acral melanoma, the most common melanoma subtype among non-White individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we perform integrative genomic and clin...
-
Article
T cell characteristics associated with toxicity to immune checkpoint blockade in patients with melanoma
Severe immune-related adverse events (irAEs) occur in up to 60% of patients with melanoma treated with immune checkpoint inhibitors (ICIs). However, it is unknown whether a common baseline immunological state ...
-
Protocol
Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx
CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With this framework, single-cel...
-
Article
Open AccessFunctional significance of U2AF1 S34F mutations in lung adenocarcinomas
The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood. Here, we report a significant co-occurrence of U2AF1 S34F mutations with ROS1 translocations in LUADs. To...
-
Article
Determining cell type abundance and expression from bulk tissues with digital cytometry
Single-cell RNA-sequencing has emerged as a powerful technique for characterizing cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be applied to fixed specimens collec...
-
Article
Open AccessA functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPα expression
Prolonged exposure of CD8+ T cells to antigenic stimulation, as in chronic viral infections, leads to a state of diminished function termed exhaustion. We now demonstrate that even during exhaustion there is a su...
-
Article
Complex mammalian-like haematopoietic system found in a colonial chordate
Haematopoiesis is an essential process that evolved in multicellular animals. At the heart of this process are haematopoietic stem cells (HSCs), which are multipotent and self-renewing, and generate the entire...
-
Protocol
Profiling Tumor Infiltrating Immune Cells with CIBERSORT
Tumor infiltrating leukocytes (TILs) are an integral component of the tumor microenvironment and have been found to correlate with prognosis and response to therapy. Methods to enumerate immune subsets such as...
-
Chapter
Urochordata: Botryllus – Natural Chimerism and Tolerance Induction in a Colonial Chordate
Chimerism is defined as the coexistence of two or more genomes of separate origin within an individual. In placental mammals such as humans, natural chimerism develops during pregnancy between a mother and fet...
-
Article
Open AccessData normalization considerations for digital tumor dissection
In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The...
-
Article
Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens
Evidence for the abundant presentation of class II neoantigens by a human B-cell lymphoma.
-
Article
Open AccessCorrection: Corrigendum: Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients
Nature Communications 7: Article number: 11815 (2016); Published 10 June 2016; Updated 14 November 2016 Previous work by Del Re et al. describing the emergence of KRAS mutations following treatment of non-smal...
-
Article
Open AccessCirculating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients
Circulating tumour DNA (ctDNA) analysis facilitates studies of tumour heterogeneity. Here we employ CAPP-Seq ctDNA analysis to study resistance mechanisms in 43 non-small cell lung cancer (NSCLC) patients trea...
