IL-21/IL-21R signaling renders acute myeloid leukemia stem cells more susceptible to cytarabine treatment and CAR T cell therapy.

Self-renewal programs in leukemia stem cells (LSCs) predict poor prognosis in patients with acute myeloid leukemia (AML). We identify CD4 T cell-derived interleukin (IL)-21 as an important negative regulator of self-renewal of LSCs. IL-21/IL-21R signaling favors asymmetric cell division and differentiation in LSCs through the activation of p38-MAPK signaling, resulting in reduced LSC numbers and significantly prolonged survival in murine AML models.

Microenvironmental reorganization in brain tumors following radiotherapy and recurrence revealed by hyperplexed immunofluorescence imaging.

The tumor microenvironment plays a crucial role in determining response to treatment. This involves a series of interconnected changes in the cellular landscape, spatial organization, and extracellular matrix composition. However, assessing these alterations simultaneously is challenging from a spatial perspective, due to the limitations of current high-dimensional imaging techniques and the extent of intratumoral heterogeneity over large lesion areas.

The thymocyte-specific RNA-binding protein Arpp21 provides TCR repertoire diversity by binding to the 3'-UTR and promoting Rag1 mRNA expression.

The regulation of thymocyte development by RNA-binding proteins (RBPs) is largely unexplored. We identify 642 RBPs in the thymus and focus on Arpp21, which shows selective and dynamic expression in early thymocytes. Arpp21 is downregulated in response to T cell receptor (TCR) and Ca signals.

The dynamic genetic determinants of increased transcriptional divergence in spermatids.

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify allele-specific expression during spermatogenic differentiation at single-cell resolution in an F1 hybrid mouse system, allowing for the comprehensive characterisation of cis- and trans-genetic effects, including their dynamics across cellular differentiation.

cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data.

Background: Highly multiplexed imaging enables single-cell-resolved detection of numerous biological molecules in their spatial tissue context. Interactive visualization of multiplexed imaging data is crucial at any step of data analysis to facilitate quality control and the spatial exploration of single cell features. However, tools for interactive visualization of multiplexed imaging data are not available in the statistical programming language R.

Dissecting viral infections, one cell at a time, by single-cell technologies.

The meteoric rise of single-cell genomic technologies, especially of single-cell RNA-sequencing (scRNA-seq), has revolutionized several fields of cellular biology, especially immunology, oncology, neuroscience and developmental biology. While the field of virology has been relatively slow to adopt these technological advances, many works have shed new light on the fascinating interactions of viruses with their hosts using single cell technologies. One clear example is the multitude of studies dissecting viral infections by single-cell sequencing technologies during the recent COVID-19 pandemic.

An end-to-end workflow for multiplexed image processing and analysis.

Multiplexed imaging enables the simultaneous spatial profiling of dozens of biological molecules in tissues at single-cell resolution. Extracting biologically relevant information, such as the spatial distribution of cell phenotypes from multiplexed tissue imaging data, involves a number of computational tasks, including image segmentation, feature extraction and spatially resolved single-cell analysis. Here, we present an end-to-end workflow for multiplexed tissue image processing and analysis that integrates previously developed computational tools to enable these tasks in a user-friendly and customizable fashion.

Multielement Z-tag imaging by X-ray fluorescence microscopy for next-generation multiplex imaging.

Rapid, highly multiplexed, nondestructive imaging that spans the molecular to the supra-cellular scale would be a powerful tool for tissue analysis. However, the physical constraints of established imaging methods limit the simultaneous improvement of these parameters. Whole-organism to atomic-level imaging is possible with tissue-penetrant, picometer-wavelength X-rays.

DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging.

Imaging mass cytometry (IMC) is a highly multiplexed, antibody-based imaging method that captures heterogeneous spatial protein expression patterns at subcellular resolution. Here we report the extension of IMC to low-abundance markers through incorporation of the DNA-based signal amplification by exchange reaction, immuno-SABER. We applied SABER-IMC to image the tumor immune microenvironment in human melanoma by simultaneous imaging of 18 markers with immuno-SABER and 20 markers without amplification.

an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data.

Highly multiplexed imaging enables single-cell-resolved detection of numerous biological molecules in their spatial tissue context. Interactive data visualization of multiplexed imaging data is necessary for quality control and hypothesis examination. Here, we describe , an R/Bioconductor package for interactive visualization and exploration of multi-channel images and segmentation masks.

A comprehensive single-cell map of T cell exhaustion-associated immune environments in human breast cancer.

Immune checkpoint therapy in breast cancer remains restricted to triple negative patients, and long-term clinical benefit is rare. The primary aim of immune checkpoint blockade is to prevent or reverse exhausted T cell states, but T cell exhaustion in breast tumors is not well understood. Here, we use single-cell transcriptomics combined with imaging mass cytometry to systematically study immune environments of human breast tumors that either do or do not contain exhausted T cells, with a focus on luminal subtypes.

Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation.

Recent advances in multiplexed imaging methods allow simultaneous detection of dozens of proteins and hundreds of RNAs, enabling deep spatial characterization of both healthy and diseased tissues. Parameters for the design of optimal multiplex imaging studies, especially those estimating how much area has to be imaged to capture all cell phenotype clusters, are lacking. Here, using a spatial transcriptomic atlas of healthy and tumor human tissues, we developed a statistical framework that determines the number and area of fields of view necessary to accurately identify all cell phenotypes that are part of a tissue.

Biology, vulnerabilities and clinical applications of circulating tumour cells.

In recent years, exceptional technological advances have enabled the identification and interrogation of rare circulating tumour cells (CTCs) from blood samples of patients, leading to new fields of research and fostering the promise for paradigm-changing, liquid biopsy-based clinical applications. Analysis of CTCs has revealed distinct biological phenotypes, including the presence of CTC clusters and the interaction between CTCs and immune or stromal cells, impacting metastasis formation and providing new insights into cancer vulnerabilities. Here we review the progress made in understanding biological features of CTCs and provide insight into exploiting these developments to design future clinical tools for improving the diagnosis and treatment of cancer.

Clinical and Biological Aspects of Disseminated Tumor Cells and Dormancy in Breast Cancer.

Progress in detection and treatment have drastically improved survival for early breast cancer patients. However, distant recurrence causes high mortality and is typically considered incurable. Cancer dissemination occurs circulating tumor cells (CTCs) and up to 75% of breast cancer patients could harbor micrometastatses at time of diagnosis, while metastatic recurrence often occurs years to decades after treatment.

Variability of Primary Sjögren's Syndrome Is Driven by Interferon-α and Interferon-α Blood Levels Are Associated With the Class II HLA-DQ Locus.

Objective: Primary Sjögren's syndrome (SS) is the second most frequent systemic autoimmune disease, affecting 0.1% of the general population. To characterize the molecular and clinical variabilities among patients with primary SS, we integrated transcriptomic, proteomic, cellular, and genetic data with clinical phenotypes in a cohort of 351 patients with primary SS.

Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy.

Intratumoral immune cells are crucial for tumor control and antitumor responses during immunotherapy. Immune cell trafficking into tumors is mediated by binding of specific immune cell receptors to chemokines, a class of secreted chemotactic cytokines. To broadly characterize chemokine expression and function in melanoma, we used multiplexed mass cytometry-based imaging of protein markers and RNA transcripts to analyze the chemokine landscape and immune infiltration in metastatic melanoma samples.

targeting of a variant causing vanishing white matter using CRISPR/Cas9.

Vanishing white matter (VWM) is a leukodystrophy caused by recessive variants in subunits of eIF2B. At present, no curative treatment is available and patients often die at young age. Due to its monogenic nature, VWM is a promising candidate for the development of CRISPR/Cas9-mediated gene therapy.

Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines.

Epithelial-mesenchymal transition (EMT) equips breast cancer cells for metastasis and treatment resistance. However, detection, inhibition, and elimination of EMT-undergoing cells is challenging due to the intrinsic heterogeneity of cancer cells and the phenotypic diversity of EMT programs. We comprehensively profiled EMT transition phenotypes in four non-cancerous human mammary epithelial cell lines using a flow cytometry surface marker screen, RNA sequencing, and mass cytometry.

BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data.

Cell-to-cell gene expression variability is an inherent feature of complex biological systems, such as immunity and development. Single-cell RNA sequencing is a powerful tool to quantify this heterogeneity, but it is prone to strong technical noise. In this article, we describe a step-by-step computational workflow that uses the BASiCS Bioconductor package to robustly quantify expression variability within and between known groups of cells (such as experimental conditions or cell types).

Grainyhead 1 acts as a drug-inducible conserved transcriptional regulator linked to insulin signaling and lifespan.

Aging is impacted by interventions across species, often converging on metabolic pathways. Transcription factors regulate longevity yet approaches for their pharmacological modulation to exert geroprotection remain sparse. We show that increased expression of the transcription factor Grainyhead 1 (GRH-1) promotes lifespan and pathogen resistance in Caenorhabditis elegans.

Replacing the Cas9 HNH domain by deaminases generates compact base editors with an alternative targeting scope.

Base editors are RNA-guided deaminases that enable site-specific nucleotide transitions. The targeting scope of these Cas-deaminase fusion proteins critically depends on the availability of a protospacer adjacent motif (PAM) at the target locus and is limited to a window within the CRISPR-Cas R-loop, where single-stranded DNA (ssDNA) is accessible to the deaminase. Here, we reason that the Cas9-HNH nuclease domain sterically constrains ssDNA accessibility and demonstrate that omission of this domain expands the editing window.

The Nrf2 transcription factor: A multifaceted regulator of the extracellular matrix.

The transcription factor nuclear factor-erythroid 2-related factor 2 (Nrf2) is widely recognized as a master regulator of the cellular stress response by facilitating the transcription of cytoprotective genes. As such, the Nrf2 pathway is critical in guarding the cell from the harmful effects of excessive reactive oxygen species/reactive nitrogen species (ROS/RNS) and in maintaining cellular redox balance. While excessive ROS/RNS are harmful to the cell, physiological levels of ROS/RNS play important roles in regulating numerous signaling pathways important for normal cellular function, including the synthesis of extracellular matrix (ECM).