Table of Contents
Research Articles
PD-L1 regulates inflammatory programs of macrophages from human pluripotent stem cellsThis study identified the novel role of immune checkpoint PD-L1 in inflammatory programs of macrophages.
Mechanisms of cellular crosstalk in the gastric tumor microenvironment are mediated by YAP1 and STAT3The study shows that Yap1 expression correlates with poor outcomes in human gastric cancer and causally contributes to disease progression in mice via cancer cell–intrinsic and –extrinsic mechanisms.
Visualization of conformational transition of GRP94 in solutionSAXS, nsEM, and HDX-MS reveal that one extended and two compact conformations of GRP94 coexist in solution and that the binding and hydrolysis of ATP only drives the transition between the two compact conformations while leaving the extended population unaffected.
Cristae dynamics is modulated in bioenergetically compromised mitochondriaLive-cell super-resolution nanoscopy reveals modulation of cristae dynamics in bioenergetically compromised mitochondria demonstrating that cristae morphology and dynamics are intricately connected.
DOCK1 insufficiency disrupts trophoblast function and pregnancy outcomes via DUSP4-ERK pathwayThis study reveals that decreased DOCK1 in placental villi affects trophoblast function via the DUSP4-ERK pathway, providing insights into adverse pregnancy outcomes.
Transgenerational epigenetic effects imposed by neonicotinoid thiacloprid exposureWe exposed pregnant female mice to neonicotinoid thiacloprid. We observed reproductive defects together with DNA methylation and histone H3K9me3 changes in the third-generation males.
Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9–mediated genome engineering in HAP1 cells mimicking cancer profilesThe unintended 10q23.31 deletion frequency rises in HAP1 cells stressed during CRISPR-Cas9 engineering, leading to aberrant molecular and cellular changes resembling common cancer patient deletions.
Chromatin priming elements direct tissue-specific gene activity before hematopoietic specificationThis study shows that signalling processes prime many enhancer elements at the chromatin level before the expression of their associated genes and that priming is essential for developmental stage-specific dynamic gene activation.
Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cellsThe study shows that estrogen activates transcription within pre-established chromosomal 3D architectures, strengthening enhancer interactions through local accumulation of the estrogen receptor α.
Megakaryocytes possess a STING pathway that is transferred to platelets to potentiate activationThis work reveals that megakaryocytes transfer cGAS and STING proteins to platelets during thrombopoiesis and that cGAS stimulation results in the activation and aggregation of platelets, suggesting a new role of cGAS in thromboinflammation.
Decline of DNA damage response along with myogenic differentiationIn postmitotic myotubes, DNA repair processes such as Base Excision Repair, and Non-Homologous End Joining are weakened compared with the proliferative precursors myoblasts.
Endothelial cells adopt a pro-reparative immune responsive signature during cardiac injuryscRNA-seq uncovers an endothelial cell (EC) subpopulation with immune responsive signatures in cardiac injury. Profiling of human heart failure samples reveals EC-specific immune responsive signatures in adult and pediatric heart failure. ECs can adopt immune responsive signatures during cardiac stress.
A dual-targeted drug inhibits cardiac ryanodine receptor Ca2+ leak but activates SERCA2a Ca2+ uptakeOur study identified a first multi-targeted compound (GM1869) inhibiting RyR2-mediated Ca2+ leak together with activating SERCA2a function that may represent a critical breakthrough for treatment of diastolic Ca2+ leak in heart failure.
2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibitionThis study investigates the genome-wide effects of 2-HG accumulation on chromatin and gene expression and identifies Rph1-dependent and H3K36me3-associated gene repression at silenced loci in yeast.
RNA helicase EIF4A1-mediated translation is essential for the GC responseConditional mouse knock-out models show that EIF4A1, but not its cofactors EIF4B or EIF4H, is essential in B cells for their development, the GC response, and increased translation after activation.
PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during developmentPARP-1 fine-tunes gene expression to control energy balance and development by selectively repressing and activating critical genes for developmental progression.
Analysis of the indispensable RAD51 cofactor BRCA2 in Naganishia liquefaciens, a Basidiomycota yeastIdentification of the BRCA2 homolog in the Basidiomycota yeast Naganishia liquefaciens reveals the general attributes of fungal BRCA2 and its essential role in Rad51-mediated homologous recombination.
Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifsPublished predictions of 5-methylcytosine at GCU sites inferred from direct RNA sequencing and the Tombo Alternative Model should be reconsidered unless further validated with orthogonal methods.
Proteomic-based stratification of intermediate-risk prostate cancer patientsThis study demonstrates the ability of a protein-based signature to risk-stratify prostate cancer patients with Gleason grade groups 2 and 3 and predict the risk of biochemical recurrence.
Structural maintenance of chromosomes (SMC) proteins are required for DNA elimination in ParameciumThis work focuses on two functionally distinct paralogues of SMC4 in Paramecium. SMC4-1 appears to have a classical function as a condensin subunit whereas SMC4-2 is required for developmental DNA elimination process.
IMPA1 dependent regulation of phosphatidylinositol 4,5-bisphosphate and calcium signalling by lithiumThis study demonstrates that lithium that is used to treat bipolar disorder acts via IMPA1 to regulate calcium signalling and neuronal excitability.
The AP-2 complex interacts with γ-TuRC and regulates the proliferative capacity of neural progenitorsThis study reveals a novel role of endocytic adaptor AP-2 in orchestrating centrosome function and cell cycle progression through its interaction with components of the γ-TuRC complex, providing valuable insights for addressing neurodevelopmental and neurodegenerative disorders linked to AP-2 dysfunction.
The structural basis for deubiquitination by the fingerless USP-type effector TssMThe structural characterization of the bacterial effector deubiquitinase TssM from Burkholderia pseudomallei, belonging to the USP family, reveals that TssM lacks the canonical “Fingers” subdomain of USP-type deubiquitinases and evolved instead the functionally analog “Littlefinger” loop for ubiquitin binding.
Methods
Patient-specific analysis of co-expression to measure biological network rewiring in individualsCosinet has the potential to empower personalized treatment by accurately quantifying the degree of rewiring in individual samples compared with reference conditions using mechanism-related differential co-expression sub-networks.
Mitochondria isolated from lipid droplets of white adipose tissue reveal functional differences based on lipid droplet sizeIn the current study, we show an optimized protocol using proteolytic treatment that enables the isolation of peridroplet mitochondria (PDM) from white adipose tissue (WAT), revealing a unique function of WAT PDM that depends on the heterogeneity of lipid droplet size.
RedRibbon: A new rank–rank hypergeometric overlap for gene and transcript expression signaturesRedRibbon is a comparative analysis tool of differential omics analyses to reveal overlapping features between two differential studies, with high performance, accuracy, and simplicity in use.
Resources
Mitochondrial phosphoproteomes are functionally specialized across tissuesThis study explores tissue-specific mitochondrial proteomes and phosphoproteomes in unprecedented depth, offering valuable insights into mitochondrial organization and specialization.
Corrections
- Correction: The coenzyme A precursor pantethine enhances antitumor immunity in sarcoma
VitB5 level becomes limiting in sarcomas. It is regulated by the pantetheinase activity of VNN1. VNN1 expression in sarcomas is associated with better prognosis and immune infiltration. In mice, complementation with pantethine, a vitB5 precursor, boosts antitumor immunity.
Correction: LACTB exerts tumor suppressor properties in epithelial ovarian cancer through regulation of SlugWe show the ability of LACTB to function as a tumor suppressor in ovarian cancer through down-regulation of Slug and induction of differentiation.
Reviewer Index
- 2023 Reviewer Index
The LSA Editors thank these scientists for sharing their time and expertise while reviewing manuscripts in 2023. We sincerely appreciate their support.
