proteomics

Alzheimer's Disease-Associated Proteomic Changes in Olfactory Stem Cells Show Pathway-Level Transcriptomic Overlap

This study identifies proteomic and transcriptomic changes in olfactory stem cells from AD and MCI patients, revealing pathway-level overlaps and potential biomarkers.

Overcoming segmentation bottlenecks in brain tissue for spatial proteomic inference at population scale

The paper introduces SPInfer, a workflow for spatial proteomic inference that improves cell segmentation in human brain tissue, enabling better biological discovery at population scale.

Large-genome phages encode diverse proteins associated with host cell envelope functions

The paper identifies diverse phage-encoded proteins associated with bacterial cell envelope functions in huge phages, revealing potential roles in host interactions.

Temporal Proteomics Links the APP London Mutation to Early Cholesterol Remodeling Cell Programs in Human Neurons

The paper uses proteomic analysis of APP-London mutant neurons to show early cholesterol remodeling and altered A beta secretion without changes in total cholesterol.

Joining Two Perspectives of the Proteome with the Trypsin+HTA Protease Workflow

This paper evaluates the use of HTA protease in combination with trypsin for proteomic analysis, showing increased protein and modification identifications and improved quantification.

Two opposite failure modes in alignment-based conservation scores, one inflating and one concealing constraint, are computable before the score is used

The paper identifies two opposite failure modes in alignment-based conservation scores and shows how to correct them to improve score accuracy.

RNA viruses that exploit self-cleaving ribozymes for translation initiation

This study identifies self-cleaving ribozymes in RNA viruses, showing their role in translation initiation across fungi and plants.

Engineered proteins to restore and enhance neurotransmitter release

This paper engineers proteins to restore and enhance neurotransmitter release by reconstituting active zone functions in neurons.

Mucosal Inflammation as a Driver of Gd-IgA1 Production in IgA Nephropathy: Mechanistic Support for Targeted Therapies

This study shows mucosal cytokines drive Gd-IgA1 production in IgAN by expanding specific B cell populations, supporting therapies targeting mucosal immunity.

A clinically annotated proteomic and histological resource of 1,000 colorectal cancers

Deep proteomics of 997 treatment-naïve colorectal cancers defines six subgroups, splitting chromosomally unstable tumors into three and revealing a rare adverse subgroup, with H&E slide benchmarks.

Tipping the lipid scale: Sebaceous fatty acid ratios govern Malassezia antifungal susceptibility

The paper shows that host sebum fatty acid ratios influence Malassezia antifungal susceptibility, with palmitic acid counteracting oleic acid's antagonistic effect.

Mapping the THESEUS1 interactome links cell wall integrity and stress signalling in Arabidopsis

This study identifies THE1 interactors to elucidate its role in cell wall integrity and stress signaling in Arabidopsis.

The mannose 6-phosphate receptor system is ancient, widespread in eukaryotes, and functionally diversified in the human parasite Trichomonas vaginalis

The paper identifies the M6P pathway as ancient and widespread in eukaryotes, with functional diversification in Trichomonas vaginalis.

SNX13 and SNX14 interorganelle tethers suppress lysosome membrane damage and neurodegeneration

This study identifies SNX13 and SNX14 as proteins that maintain lysosome membrane integrity and prevent neurodegeneration by supporting lipid homeostasis and repair mechanisms.

Orai1α and Orai1β more potently promote NFAT activation and transcription than Orai2 and Orai3

The paper compares the ability of different Orai isoforms to promote NFAT activation and transcription, finding Orai1α and Orai1β are more potent than Orai2 and Orai3.

Disruption of cAMP Signalling and RNA Regulation Confers Cefiderocol Resistance in Acinetobacter baumannii

This study identifies two mechanisms of cefiderocol resistance in Acinetobacter baumannii: cAMP signalling disruption and Hfq RNA-binding domain truncation, both linked to iron homeostasis and reduced drug activity.

Relaxed evolutionary constraints on mitochondrial electron-transfer-associated variants in human cancers

The paper predicts how MT-CYB mutations affect electron transfer in cancer and finds they are depleted in germline but enriched in tumors.

AI-guided discovery of natural pocket proteins for portable small-molecule sensing

The paper develops an AI-guided workflow to identify natural pocket proteins for small-molecule sensing, achieving 43.8% binding response in tested pairs and demonstrating portable device performance with low serum LODs.

Mycobacterium tuberculosis suppresses protective Th17 responses during infection

This study identifies factors by which Mycobacterium tuberculosis suppresses Th17 responses during infection, showing that ESX-1 and PDIM inhibit IL-23 production in dendritic cells.

ANO6 Scaffolds ER Mitochondria Contacts to Govern Spatial Lipid Compartmentalization and Ferroptosis Evasion in Chemoresistant Breast Cancer

This study identifies ANO6 as a scaffold at ER-mitochondria contacts that facilitates lipid sequestration and ferroptosis evasion in chemoresistant breast cancer.

Functional and acid-stability constraints on the Junin virus glycoprotein complex

This study uses deep mutational scanning to analyze how amino-acid mutations affect the pH stability and cell entry function of the Junin virus glycoprotein complex.

Once in a blue moon: an unexpected evolutionary route to blue floral pigmentation in orchids

The paper investigates the genetic basis of blue floral pigmentation in orchids, finding an unexpected pathway involving duplicated genes and regulatory changes rather than the expected CYP75A pathway.

Sequential invasion under disturbance drives functional homogenisation of lake benthos

The paper examines how sequential invasion under different disturbance histories affects functional diversity in lake benthos, finding that non-native species dominate and reduce native functional richness.

Expanding the HIF-2α proteomic interactome with TurboID proximity labeling.

This study expands the HIF-2α proteomic interactome using TurboID proximity labeling, identifying 329 novel interactors and linking some to poor patient survival in breast cancer.

RiboDFM: Robust RNA sequence design using backbone-conditioned discrete flow matching

RiboDFM designs RNA sequences that fold into target 3D structures using a backbone-conditioned discrete flow-matching framework, achieving high sequence recovery and tertiary-structure consistency.

Single-nucleus transcriptomics and phosphoproteomics identify misregulated sperm components in mice carrying a selfish supergene

The paper identifies misregulated sperm components in mice with a selfish supergene using single-nucleus transcriptomics and phosphoproteomics, revealing dysregulated phosphorylation and gene expression related to sperm motility.

Novel 3D Mature Osteocyte Perfusion Platform Reveals Subtype-Dependent and Radiation-Sensitive Disruption of Mechanotransduction by Breast Cancer Secretomes

This study shows that breast cancer subtype and radiation affect osteocyte mechanosensing, with ER+ tumors being more sensitive to radiation-induced secretome changes.

Cytoplasmic localization of 5hmC reveals RNA hydroxymethylation in breast cancer

The paper identifies cytoplasmic 5hmC in breast cancer tissues and cell lines, linking it to TET3 expression and RNA processing, with implications for triple-negative breast cancer.

Infection drives localised and individualised antibody repertoires, whereas immunisation promotes repertoire convergence in pig

This study compares antibody repertoires in pigs after infection and immunisation, finding infection drives compartmentalised, individualised responses while immunisation promotes convergent, public repertoires.

Sample preparation for direct nanopore based protein identification via tryptic peptide recognition

This paper introduces a sample preparation workflow (SP3) that enables nanopore-based protein identification by decoupling proteolysis from interfering components, demonstrating its effectiveness with tryptic digests of myelin basic protein.