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Research Articles
CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq dataA systematic comparison of batch effect metrics for single cell data is performed. The new cell-specific mixing score from the R/Bioconductor CellMixS package performs well across various tasks.
Cancer-associated cells release citrate to support tumour metastatic progressionCancer-associated stroma is recruited by cancer cells to synthesise and release citrate necessary to support metastatic progression of the disease.
DGCR8 deficiency impairs macrophage growth and unleashes the interferon response to mycobacteriaLack of miRNA biosynthesis in DGCR8-deficient macrophages did not block macrophage differentiation but caused overshooting type I IFN responses to mycobacterial glycolipids.
RNA polymerase backtracking results in the accumulation of fission yeast condensin at active genesUsing both experiments and mathematical modelling, the authors show that RNA polymerase backtracking contributes to the accumulation of condensin in the termination zone of active genes.
Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophagesThis study uses biomaterial scaffolds to identify a macrophage gene signature defined by high expression of C1qa, C1qb, and Trem2 that is elevated systemically in mouse and human pancreatic cancer.
The AXL-PYK2-PKCα axis as a nexus of stemness circuits in TNBCA clinically relevant AXL-PYK2-PKCα axis where PYK2 and PKCα act as signaling nodes and functionally cooperate to converge stemness promoting pathways and regulate Oct4 and Nanog pluripotent TFs.
Replicated chromatin curtails 53BP1 recruitment in BRCA1-proficient and BRCA1-deficient cellsThis study demonstrates how single cell normalization to genome size provides insight into genome function, here in the context of DNA double-strand break repair by 53BP1 versus BRCA1–BARD1.
Mitochondrial Aurora kinase A induces mitophagy by interacting with MAP1LC3 and Prohibitin 2The multifunctional Ser/Thr kinase AURKA uses the Inner Mitochondrial Membrane receptor PHB2 and MAP1LC3 as a signalling platform to orchestrate the elimination of dysfunctional mitochondria.
Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenzaThe structure of extracellular domain of MSPL and inhibitor complex helps to understand the TTSP functions, including TMPRSS2, and provides the insights of the infection of influenza and SARS-CoV.
In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord bloodIn utero exposure to chlordecone affects chromatin and leads to activation of retroelements. This study shows the changes induced by chlordecone in human umbilical cord blood and blood-derived cell line.
NF-κB inhibition in keratinocytes causes RIPK1-mediated necroptosis and skin inflammationTNFR1 was found to cause skin inflammation in mice with epidermal keratinocyte-specific ablation of IKK2 or of both the NF-kB subunits RelA and cRel by triggering RIPK1-dependent, RIPK3-MLKL–mediated necroptosis of keratinocytes.
Single-cell RNA sequencing of mouse islets exposed to proinflammatory cytokinesSingle-cell RNA-seq was used to show that islet endocrine cells respond to acute cytokine exposure with an increase in the expression of protective genes and the absence of apoptotic gene expression.
Fast but not furious: a streamlined selection method for genome-edited cellsMagnetic-activated genome-edited cell sorting (MAGECS) allows a fast and easy generation of genetically modified cells.
On the relation of gene essentiality to intron structure: a computational and deep learning approachA deep learning classifier predicts gene essentiality by intron sequence. A unique set of intron features of essential genes was found and its importance demonstrated by a high-performing classifier.
Cell-free expression of the outer membrane protein OprF of Pseudomonas aeruginosa for vaccine purposesProduction of recombinant proteoliposomes containing OprF from P. aeruginosa promotes the active open conformation of the porin exposing native epitopes. These OprF proteoliposomes were used as vaccines to protect mice against a P. aeruginosa acute pulmonary infection model.
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Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiationL929 cell supernatant is commonly used to differentiate murine macrophages from bone marrow. The supernatant and its effect on macrophage phenotype was characterised by proteomics and the authors identified novel immunoregulatory proteins.
