Tools of the Trade

In this article, Efrat Shema describes EPINUC, a liquid biopsy method based on epigenetic profiling of nucleosomes from cell-free DNA in the plasma. EPINUC, combined with protein biomarker measurements, enables the accurate differentiation of samples from healthy volunteers and patients.

In this Tools of the Trade article, Francisco Barriga describes the development and use of MACHETE, a flexible deletion engineering strategy, which enables the functional characterization of the large genomic deletions that occur in cancer.

In this Tools of the Trade article, Susan Bullman describes the development and use of INVADEseq, a single-cell RNA sequencing approach that facilitates the simultaneous capture of both eukaryotic and bacterial transcripts in host cells to functionally understand the intratumoural microbiota.

In this Tools of the Trade article, Lee describes Select-seq, a novel method for generating epitranscriptomic data from microniches within the tumour. The author reveals how the method can be used to identify novel biomarkers from rare cell subpopulations such as cancer stem cells in tumours.

In this Tools of the Trade article, Venkataramani describes the development of in vivo imaging workflows that allow the acquisition of imaging data with improved signal-to-noise matched to single-cell RNA-sequencing data.

In this Tools of the Trade article, Luigi Ombrato describes the development of Cherry-niche, a cell labelling system, which enables the unbiased identification of cancer cell-neighbouring cells.

In this Tools of the Trade article, Daniela S. Thommen describes the development and use of a patient-derived tumour fragment (PDTF) platform wherein surgically resected tumour lesions are cultured ex vivo, which enables patients’ responses to immunotherapy to be more faithfully modelled.

In this Tools of the Trade article, Anne C. Rios describes the development of multispectral large-scale single-cell resolution three-dimensional (mLSR-3D) imaging and the analytical pipeline, segmentation analysis by parallelization of 3D datasets (STAPL-3D), which enables the extraction of hundreds of molecular, spatial and volumetric features from millions of cells imaged in 3D, revealing details of the structural organization of human tumours.

In this Tools of the Trade article, Amir Giladi describes the development and use of PIC-seq, which enables the direct enrichment and analysis of conjugates of physically interacting cells in the tumour microenvironment.

In this Tools of the Trade article, Yaara Oren describes the development and use of the Watermelon system to simultaneously track the lineage, transcriptional profile and proliferative state of each cancer cell in a population, which enables the characterization of rare cycling persister cells.

In this Tools of the Trade article, Ana Luísa Correia describes the development and use of a tracker of dormant disseminated tumour cells to investigate the distribution and dynamics of dormant reservoirs within and across distant sites.

In this Tools of the Trade article, Christian Umkehrer describes the development and use of CaTCH, which enables therapy-naive cancer cell clones to be isolated and compared to their resistant counterparts.

In this Tools of the Trade article, Alejandro E. Mayorca-Guiliani describes the development and use of in situ decellularization, which allows native extracellular matrix to be preserved to address both tumour deconstruction and reassembly.

In this Tools of the Trade article, Eunhee Yi describes the development and use of a method called ecTag, which allows imaging and tracking of extrachromosomal DNA in live cancer cells.