cell-cell communication

Linking clinical border morphology to cell-scale growth mechanisms in melanoma: a segmentation-to-simulation alignment study

Across 1,581 ISIC 2018 lesions, melanoma borders differ from nevi mainly by coarse lobulation rather than fractal dimension; of six simulated mechanisms, only an imposed long-range growth-rate field reproduces this.

De novo lipogenesis controls antigen presentation and metastatic immune escape in triple-negative breast cancer.

FASN-driven lipogenesis sustains EGFR palmitoylation and PI3K-AKT-mTOR signaling, suppressing tumor MHC-I antigen presentation; blocking it curbs TNBC metastasis in mice via CD8 T cell recognition.

The epidermal growth factor (EGF) receptor family network in cardiac hypertrophy and heart failure

EGFR-family ligand mRNAs shift in failing human hearts; NRG1 and EGF drive distinct, differently ERBB2-dependent transcriptional programmes in rat cardiomyocytes; afatinib blunts mouse angiotensin II hypertrophy but worsens fibrosis.

Host response against SARS-CoV-2 infection is impacted by allosteric modulation of cholinergic and purinergic receptors

Ivermectin's protection in SARS-CoV-2-infected hamsters depended partly on both α7 nicotinic and P2X4 receptors; in co-cultures its effects were α7nAChR-independent, and P2X4 blockade prevented CXCL10 induction at 48 hpi.

Gut microbial interaction networks control autoimmunity to neuroretina

Akkermansia expansion reduces short-chain fatty acid-producing Firmicutes in human-flora uveitis mice, raising Th1 responses and disease; a Verrucomicrobia/Firmicutes ratio is elevated in uveitis, MS and Crohn's patients.

Illuminating dark genes and dark metabolites: calibrated functional association across kingdoms with autoencoders and correlation

VaLPAS pairs a bi-directional autoencoder with correlation for omics guilt-by-association with calibrated confidence; in L. starkeyi its autoencoder linked 176 unidentified metabolites to known-function proteins at ≥50% confidence.

Lipocalin-2-expressing red pulp macrophages link ischemic stroke to systemic immune reprogramming in mice and humans

Splenic Lcn2 is induced biphasically after mouse stroke and localizes to red pulp macrophages; recombinant LCN2 induces T cell and monocyte hyporesponsiveness and monocyte phagocytosis-ROS uncoupling, with human spleen support.

eIF4E and Ezrin cooperate in pseudopods to drive a localized migratory translation program in acute myeloid leukemia

In acute myeloid leukemia, Ezrin binds eIF4E and anchors active ribosomes in pseudopods for local translation of CD44 and hyaluronan pathway proteins; eIF4E loss impairs mouse engraftment.

Tfh dysfunction is associated with poor responses to HBV vaccination

HBV vaccine-draining lymph node biopsies tie low antibody titers to reduced, interferon-skewed GNG4+ germinal center T follicular helper cells; public B cell clonotypes did not track response.

TxCyto: A machine learning framework for estimating cytokine activity from whole transcriptome

A fully connected neural network trained on 9491 TCGA bulk tumor transcriptomes estimates activity of 645 cytokines and secreted proteins, checked against perturbation and protein data.

Human protein complex interfaces reveal candidate assembly roles for initiator methionine excision

N-terminal positions whose residue 2 permits methionine aminopeptidase cleavage are less often buried at human assembly interfaces (37.5% vs 47.5%), yet 175 such proteins stay engaged after boundary filtering.

A cortical basis for perception of internal gut sensations

Mice can report optogenetic activation of vagal gut mechanosensory neurons; insular cortex encodes perceptual report and causally affects detection only in a difficult psychophysics task, not simple detection.

Maternal-fetal immune conflict contributes to male-specific impairments in a mouse model of neurodevelopmental disorders

A poly(I:C) dose at E12.5 causes placental junctional-zone breakdown, amniotic inflammation and developmental defects in a male-only subset of embryos within 24 hours, dependent on maternal IL-6.

Cooperative CTCF-nucleosome oligomerization stabilizes chromatin loop anchors

CTCF dimerization on stacked nucleosomes is resolved by cryo-EM through a ZnF6-7-8 interface. Disrupting it in mouse stem cells weakens CTCF-cohesin loops more than insulation and impairs germline differentiation.

Chemotherapy-Induced Oral Mucosal Injury Is Defined by p53 Activation, Cell Cycle Arrest and Diverse Epithelial Progenitor Dynamics

In 5-FU-treated mice, oral and intestinal epithelial atrophy stems from p53-linked cell cycle arrest, not apoptosis, while a chemoresistant AP-1/p53 basal cluster expands in tongue.

SPP1+ Microglia Are Associated with Neuroimmune Rewiring and Glutamatergic Neuronal Injury in ART-Suppressed People Living with HIV

In ART-suppressed human brain, an SPP1+ activated microglial subset holds most detected HIV RNA and shows chronic interferon-I and MHC-I signatures, alongside complement signaling and neuronal loss.

EVd3x: A Bioinformatics Platform for Evidence-aware Interpretation of EV Cargo

EVd3x integrates over 22 million records from 28 public resources so one fixed molecule set can be traced from reported EV cargo through disease, pathway, cell and interaction evidence.

Adaptive immunity is dispensable for salamander appendage regeneration

Rag1-knockout newts lacking adaptive immunity regenerate larval limbs, tails and adult limbs without overt gross differences from controls; newt blastema tolerates allografts, and axolotl regenerating limbs show immunosuppressive transcriptional shifts.

A high-resolution blood immune cell doublet atlas via imaging spectral cytometry

Image-based gating on an imaging spectral cytometer resolves 12 high-purity immune doublet types in human blood; in tuberculosis, doublet frequencies are unchanged but tightly contacting T cell-monocyte doublets increase.

Granule cells reorient cortical trajectories to separate contexts

In mice learning two tasks, cerebellar granule cells kept the low-rank geometry of premotor cortical output within each task but rotated their population trajectories apart between tasks, while cortex generalized.

KSTITCH links cellular morphology and gene expression in spatial transcriptomics

STITCH pairs size-independent tangent-PCA contour shape modes with expression factors by canonical correlation, recovering keratinocyte, fibroblast and melanoma shape-expression links in Xenium and CosMx data.

C1Q-associated adaptive myeloid remodelling accompanies early response to BCMA CAR-T therapy in multiple myeloma

In a ten-patient multiple myeloma reanalysis, myeloid pseudobulk from day-30 BCMA CAR-T responders showed C1Q enrichment with interferon-γ signalling, not cholesterol efflux; patient-level composite scores stayed exploratory.

Daily Bowel Movements are Associated with Stronger Gut-Brain Phase-Amplitude Coupling and Better Cognitive Performance

In 76 healthy middle-aged women, daily bowel movements went with better composite cognitive scores, stronger gastric-phase to EEG-alpha coupling and higher faecal short-chain fatty acids than less-frequent ones.

MuSpAn: A Toolbox for Multiscale Spatial Analysis

MuSpAn, a Python library of over 100 spatial methods, quantifies multiscale tissue organisation and maps cancer-associated fibroblast subtypes to distinct immune niches in mouse colorectal tumours.

Invasion status stratifies the composition of the human pancreatic cancer perineural niche

Xenium and single-nucleus profiling of 14 human pancreatic tumors shows invaded nerve neighborhoods enriched for classical cancer cells, myCAFs and lipid-handling macrophages but depleted of lymphocytes.

Nutrient environments shape amino acid auxotrophy and cross-feeding

Across 40 carbon-nitrogen environments, six matched E. coli and B. subtilis amino acid auxotrophs show context-dependent auxotrophy, while auxotroph type predicts cross-feeding yield better than environment.

Cellular context restricts a promiscuous m6A reader IDR to a single functional effector interface for mRNA decay

Yeast m6A reader Pho92 uses one helical hydrophobic interface in its disordered region to engage Caf40; a single L35A substitution halts m6A-transcript decay in meiosis.

Impaired astrocyte-to-neuron cholesterol trafficking drives synaptic dysfunction in Rett syndrome

Mecp2 knock-out mouse astrocytes accumulate cholesterol yet release poorly lipidated ApoE; cholesterol supplementation restores synaptic puncta density in neurons exposed to their conditioned medium and in Mecp2 heterozygous neurons.

Preformed Fibril Seeding Reshapes the Phosphorylated α-Synuclein Proximal Proteome in the Olfactory Bulb

Proximity proteomics in PFF-seeded mouse olfactory bulb shows aggregated phospho-S129 alpha-synuclein mostly reprioritizes existing interactions toward axon-glia, myelin and proteostasis proteins, with a conserved 107-protein signature.

Statistical tests for bivariate spatial association across multi-omics data with disjoint coordinates

Autocorrelation-aware bivariate Moran's I, bivariate Gaussian process tests and generalized additive models (R package sbivar) test cross-modality colocalisation on disjoint coordinates; many existing permutation tests inflate false positives.