Ivan Berest
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View article: Peroxisomes are critical for a unique metabolic demand and survival of alveolar macrophages
Peroxisomes are critical for a unique metabolic demand and survival of alveolar macrophages Open
Tissue-resident macrophages (TRMs) populate throughout various tissues, and their homeostatic metabolism is heavily influenced by these microenvironments. Peroxisomes are organelles that contribute to lipid metabolism. However, the involve…
View article: Tuft cell IL-17RB restrains IL-25 bioavailability and reveals context-dependent ILC2 hypoproliferation
Tuft cell IL-17RB restrains IL-25 bioavailability and reveals context-dependent ILC2 hypoproliferation Open
The tuft cell–group 2 innate lymphoid cell (ILC2) circuit orchestrates rapid type 2 responses upon detecting microbially derived succinate and luminal helminths. Our findings delineate key mechanistic steps involving IP3R2 engagement and C…
View article: IL-6 mediates defense against influenza virus by promoting protective antibody responses but not innate inflammation
IL-6 mediates defense against influenza virus by promoting protective antibody responses but not innate inflammation Open
Influenza virus infection is a leading cause of morbidity and mortality worldwide, posing a significant public health problem. The pro-inflammatory cytokine interleukin-6 (IL-6) has been shown to promote defense against respiratory viral i…
View article: Inflammatory Mediators Suppress FGFR2 Expression in Human Keratinocytes to Promote Inflammation
Inflammatory Mediators Suppress FGFR2 Expression in Human Keratinocytes to Promote Inflammation Open
Fibroblast growth factors (FGFs) are key orchestrators of development, tissue homeostasis and repair. FGF receptor (FGFR) deficiency in mouse keratinocytes causes an inflammatory skin phenotype with similarities to atopic dermatitis, but t…
View article: Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumourigenesis
Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumourigenesis Open
Cell fate plasticity enables development, yet unlocked plasticity is a cancer hallmark. Regulating cell identity requires gene activation and repression. While master regulators induce lineage-specific genes to restrict plasticity, it rema…
View article: Tuft cell IL-17RB restrains IL-25 bioavailability and reveals context-dependent ILC2 hypoproliferation
Tuft cell IL-17RB restrains IL-25 bioavailability and reveals context-dependent ILC2 hypoproliferation Open
The tuft cell–ILC2 circuit orchestrates rapid type 2 responses upon detecting microbe-derived succinate and luminal helminths. Our findings delineate key mechanistic steps, involving IP3R2 engagement and Ca 2+ flux, governing IL-25 product…
View article: Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in <scp>CLL</scp>
Drug‐microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in <span>CLL</span> Open
The tumour microenvironment and genetic alterations collectively influence drug efficacy in cancer, but current evidence is limited and systematic analyses are lacking. Using chronic lymphocytic leukaemia (CLL) as a model disease, we inves…
View article: Enhancer-priming in ageing human bone marrow mesenchymal stromal cells contributes to immune traits
Enhancer-priming in ageing human bone marrow mesenchymal stromal cells contributes to immune traits Open
Bone marrow mesenchymal stromal cells (BMSCs) can differentiate into adipocytes and osteoblasts, and are important regulators of the haematopoietic system. Ageing associates with an increased ratio of bone marrow adipocytes to osteoblasts …
View article: Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis Open
Regulation of hematopoiesis during human development remains poorly defined. Here we applied single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to over 8,000 human immu…
View article: Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF
Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF Open
Transcription factors (TFs) regulate many cellular processes and can therefore serve as readouts of the signaling and regulatory state. Yet for many TFs, the mode of action-repressing or activating transcription of target genes-is unclear.…
View article: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells Open
The epigenetic regulator TET2 is frequently mutated in hematological diseases. Mutations have been shown to arise in hematopoietic stem cells early in disease development and lead to altered DNA methylation landscapes and an increased risk…
View article: Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors:<i>diffTF</i>
Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors:<i>diffTF</i> Open
Transcription factor (TF) activity is an important read-out of cellular signalling pathways and thus to assess regulatory differences across conditions. However, current technologies lack the ability to simultaneously assess activity chang…
View article: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells Open
The epigenetic regulator TET2 is frequently mutated in hematological diseases. Mutations have been shown to arise in hematopoietic stem cells early in disease development, lead to altered DNA methylation landscapes and to an increased risk…