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Biology subjects

Liang, Z.

Publications and source records attributed to Liang, Z..

At least 55 records · Page 3Linked to original sources

Mitofusin agonists enhances long-term engraftment and potency of cultured hematopoietic stem cells

Umbilical cord blood (CBU) is a valuable source of hematopoietic stem cells (HSCs) due to lower incidence of graft-versus-host disease. However, limited HSC counts restrict use in adults, necessitating improved methods for ex vivo expansion and improved HSC function. Mitofusin 2 (MFN2), a mitochondrial membrane fusion protein, is necessary for preserving HSC function and mitofusin agonists have been characterized. We report ex vivo culture of CBU HSCs with mitofusin agonists (MAs) enhances long-term repopulating activity by over five-fold in both primary and secondary transplantation assays without changes of total nucleated cells or phenotypic HSCs. Mechanistically, MA-treated HSCs show suppressed protein synthesis, increased autophagic flux, and elevated lysosomal mass. Transcriptomic analysis implicates downregulation of MTOR signaling, and immunoprecipitation studies suggest MFN2 interacts with MTOR. These data support a model in which fusion-competent MFN2 sequesters MTOR, promoting a catabolic state that preserves HSC potency. Our findings suggest a novel MFN2-MTOR regulatory axis that enhances the function of human HSCs cultured ex vivo for potential therapeutic application.

cell biology↗

Proteomic characterization of neuronal extracellular vesicle interactomes in Alzheimer's disease mouse model through TurboID-based proximity labeling

Extracellular vesicles (EVs) are critical mediators of neuronal communication and have been implicated in propagating pathological processes in neurodegenerative diseases, including Alzheimers disease (AD). However, the molecular interactome of neuronal EVs in vivo remains poorly defined. Here, we employed TurboID-CD9-based proximity biotinylation to label and capture EV-interacting proteins in the hippocampus of wild-type (WT) and APPNLGF knock-in AD mouse models. Adeno-associated viral delivery of hSyn1 promoter-driven TurboID-CD9 enabled neuron-specific EV tagging, followed by in vivo biotinylation and affinity purification of labeled proteins. Proteomic analysis using data independent acquisition liquid chromatography - mass spectrometry identified 5,502 proteins, with enriched pathways involving synaptic transmission, vesicle trafficking, and inhibitory neurotransmission. Comparative analyses revealed robust enrichment of GABAergic signaling components, including GABAA receptor subunits (Gabrb3, Gabra1, Gabbr2), Ncam1, and chloride transporters, in both WT and APPNLGF EV interactomes, with additional disease-associated proteins (Mapt, Snca) and potassium channel enrichment observed in APPNLGF mice. Proximity ligation assays validated direct EV-associated biotinylation of Ncam1, Gabrb3, and Gad1, with Gad1 showing significant upregulation in the APPNLGF cohort. In silico HADDOCK docking supported stable interactions between CD9 and these target proteins, revealing plausible EV-protein interfaces. These findings define the in vivo neuronal EV interactome and its remodeling in amyloid pathology, implicating EV-associated GABAergic and ion channel proteins in network excitability regulation. This work establishes a proteomic and structural framework for understanding EV-mediated signaling in health and disease, providing candidate targets for therapeutic modulation of excitatory / inhibitory balance in AD.

neuroscience↗

Impaired store-operated Ca2+ entry in mouse epidermis leads to reduced epidermal barrier function via Klk activation.

Store-operated Ca2+ entry (SOCE) is a mechanism by which STIM1/2 detect calcium depletion in the endoplasmic reticulum (ER) and activate ORAI1/TRPC channels on the cell membrane to induce calcium influx into the cytoplasm. This study aimed to investigate SOCEs role in the skin epidermis in vivo, using female mice with epithelial tissue-specific Stim1 and Stim2 knockout (Stim1/2 cKO) and control mice (Stim1/2fl/fl). Keratinocytes from Stim1/2 cKO mice exhibited reduced Stim1 and Stim2 gene expression levels and impaired SOCE function compared with the controls. Histological analysis revealed hyperkeratosis in the Stim1/2 cKO tissues; however, no significant changes were observed in the proliferation or migration of keratinocytes or wound healing of the back skin. RNA-seq analysis indicated altered keratinization and cell-to-cell adhesion in the Stim1/2 cKO mice. Additionally, transepidermal water loss (TEWL) was increased significantly, and a biotinylated reagent diffused from the subcutaneous area into the granular layer, signifying compromised barrier function in the Stim1/2 cKO mice. The Stim1/2 cKO mice exhibited alterations in desmoglein 1 (Dsg1) and elevated levels of Kallikrein-related peptidase (Klk) 6 and Klk7, leading to increased trypsin- and chymotrypsin-like serine protease activities, respectively. These results suggest that SOCE dysfunction leads to hyperkeratosis and impaired epidermal barrier function via Klk activation without affecting skin cell proliferation in vivo. These novel findings improve understanding of the molecular mechanisms underlying calcium signaling in the epidermis barrier and suggest potential avenues for investigating related skin pathologies linked to calcium homeostasis, such as Hailey-Hailey disease (HHD) and Darier disease (DD).

cell biology↗

ADAR1p150 RNA binding, independent of A-to-I RNA editing, buffers immunogenicity from the tonic type I IFN induced transcriptome in vivo.

ADAR1 edits adenosine to inosine (A-to-I) in double-stranded RNA to prevent MDA5 sensing of cellular transcripts, its key physiological role. However, editing-independent functions of ADAR1 remain poorly understood. Using a series of Adar1 mutant mice rescued by loss of MDA5 and PKR, we investigated isoform-specific, editing-independent roles of ADAR1 in vivo. We found that the cytoplasmic ADAR1p150 isoform is essential for maintaining peripheral T cell numbers and differentiation of hematopoietic stem and progenitor cells (HSPCs). In bone marrow transplants, ADAR1p150 protein, but not its editing activity, was crucial for T cell regeneration and HSPC repopulation, demonstrating a cell-intrinsic function in hematopoiesis. Experiments with IFN{beta}-treatment of purified HSPCs in vitro and in vivo IFNAR1 neutralization revealed hypersensitivity to tonic type I interferon (IFN) in the absence of ADAR1p150. Using cell lines, we demonstrate that type I IFN activates the OAS-RNaseL pathway, leading to cell death. This study shows that tonic type I IFN induces immunogenic cellular RNAs in sterile conditions. ADAR1p150 suppresses immune sensing of self-dsRNAs through both editing-dependent (MDA5) and editing-independent (PKR, OAS-RNaseL) mechanisms. Thus, ADAR1p150 protein levels and activity combine to set the threshold for tolerance to self-derived dsRNAs.

immunology↗

Disrupted Regional Dynamics of Structure-Function Connectivity Coupling in Euthymic Bipolar Disorder

BackgroundBipolar disorder (BD) is characterized by persistent disturbances in emotional regulation and cognitive function, even during euthymia, yet its neural mechanisms remain unclear. Given evidence of structural and dynamic functional connectivity (dFC) abnormalities in BD, investigating dynamic structure-function connectivity coupling (SC-FC coupling) may provide insights into the pathophysiology of the disorder. MethodsDiffusion tensor imaging and resting-state fMRI data were collected from 61 euthymic BD-I patients and 54 healthy controls (HC). Structural connectivity was derived using probabilistic tractography, and dFC was estimated with a sliding-window approach. SC-FC coupling was quantified as the extent to which structural features predicted dFC using multivariate linear regression. Abnormal SC-FC coupling in BD was assessed at both the network and regional levels, relative to HC. Over time, SC-FC coupling was categorized into high- and low-coupling states, and dynamic state analyses of dwell time, occurrence rate, and transition probabilities were performed in the affected brain regions. ResultsNetwork-level analyses indicated that BD exhibits lower SC-FC coupling in subcortical regions compared with HC. Regional analyses revealed significantly reduced dynamic SC-FC coupling in two thalamic subregions (medial posterior and rostral temporal) and in the right primary somatosensory cortex in BD compared to HC. Dynamic analyses further demonstrated thalamic instability: BD showed shorter dwell times in high-coupling states, increased occurrence of low-coupling states, and more frequent high-to-low coupling transitions than HC. These abnormalities suggest that BD is characterized by disrupted structure-function integration and unstable thalamocortical dynamics. ConclusionOur findings reveal regional abnormalities in SC-FC coupling dynamics in BD, indicating persistent dysfunction of structure-function integration during euthymia. Dynamic coupling measures may provide preliminary insights into potential biomarkers for disease monitoring.

neuroscience↗

A Low-dimensional Manifold Representation of the Human Brain Aging Continuum

Brain aging involves complex structural changes that challenge traditional analytical methods and hinder personalized assessment of brain health. Integrating regional brain alterations into a unified, interpretable representation is difficult due to the high dimensionality of neuroimaging data. Here, we projected regional brain volumes from the Human Connectome Project Aging Dataset onto a low-dimensional manifold that reflects underlying neuroanatomical constraints. We then built a transparent framework on the manifold to estimate brain age and identify key regional drivers of the estimate. By analyzing local neighborhoods on the manifold, we identified distinct structural aging trajectories, including pronounced frontal atrophy occurring predominantly in males. This approach provides a biologically interpretable means of characterizing individual brain-aging patterns, reveals heterogeneous aging pathways, and supports more personalized assessments and insights into the aging process. TeaserA manifold representation can map brain aging patterns across regions and reveal distinct trajectories

bioengineering↗

A neural circuit for female-specific defensive homeostasis in risk assessment

HighlightsSC CB1R+ neurons encode visual survival threats and initiate risk assessment in both sexes CB1R+ SC-LHb GABAergic circuit maintains defensive homeostasis in risk assessment in females eCBs gate this circuit by disinhibiting presynaptic GABA release exclusively in females Disruption of this mechanism female-specifically impairs risk assessment and stress coping In BriefLiu et al. identify a female-specific subcortical circuit in which eCB signaling, via CB1R on GABAergic terminals in the SC, suppresses transmission to the LHb to maintain precise defensive homeostasis in risk assessment. These findings uncover the circuit and neuronal mechanisms that contribute to the sexually dimorphic maintenance of defensive homeostasis. Risk assessment in defensive behavior is an adaptive mechanism shaped by natural selection, enabling individuals to evaluate potential threats and thereby maintain defensive homeostasis. However, it remains unknown whether specific neural circuits maintain their behavioral homeostasis in a sex-specific manner. To address this, we investigated its neural basis by hierarchical behavior analysis framework with neural circuit dissection. In mice of both sexes, visual survival threats activated cannabinoid 1 receptor (CB1R)-expressing neurons in the superior colliculus (SC) to initiate consistent risk assessment. Deletion of CB1R in SC GABAergic neurons female-specifically impairs risk assessment by disinhibiting GABA release in SC-lateral habenula (LHb) projections, resulting in shortened risk assessment. This disruption furthermore increases the occurrence of abnormal spontaneous behavior following chronic stress exclusively in females. We identified a female-specific SC-LHb GABAergic circuit gated by CB1R maintains defensive homeostasis in risk assessment. Our findings reveal how a conserved neuromodulatory system sex-specifically gates a subcortical circuit to orchestrate distinct survival strategies.

neuroscience↗

Mapping Human Survivability at Extreme Wet-Bulb Temperatures 32-35°C

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/677706v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@70b72dorg.highwire.dtl.DTLVardef@9fbfeorg.highwire.dtl.DTLVardef@17f05a5org.highwire.dtl.DTLVardef@4b977b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG HighlightsWe report the first empirical human survival map across wet-bulb temperatures of 32-35{degrees}C. HydraAon and behavior cooling extend survival beyond the 6-hour theoreAcal limit. Females consistently tolerate extreme humid heat longer than males in controlled trials. Our findings refine heat-health models and inform equitable climate adaptaAon strategies. In briefExtreme humid heat, measured by wet-bulb temperature (Tw), is nearing the threshold of human survivability under climate change. In controlled trials with 36 adults, we provide the first empirical survival map across Tw=32-35{degrees}C, showing that hydration and behavioral adaptations extend endurance beyond the theoretical 6-hour limit, with women tolerating heat longer than men. These findings refine human heat tolerance thresholds and inform equitable climate adaptation and heat-health strategies. SCIENCE FOR SOCIETYAs climate change accelerates, extreme humid heat events--measured by wet-bulb temperature (Tw)--pose a growing threat to human survival. This study provides the first empirical benchmarks of human survivability across Tw=32-35{degrees}C, clarifying how long healthy adults can endure these conditions under full hydration and minimal activity. We find that while the theoretical 6-hour survival limit at Tw=35{degrees}C is partly supported, both men and women can withstand these conditions for 7-8 hours when hydrated, with women demonstrating greater tolerance. At Tw=34{degrees}C, projected heatstroke onset extends beyond 12-16 hours, while conditions at Tw=32-33{degrees}C remain largely compensable for more than 30 hours. These results challenge prevailing heat tolerance models, underscore the role of behavioral and physiological adaptations, and provide critical data for designing equitable heat-health policies and early warning systems that account for sex differences and vulnerable populations. Climate change-driven extreme heat events increasingly threaten human health. Here, we provide the first empirical map of human survivability across four extreme wet-bulb temperatures (Tw=32- 35{degrees}C) in controlled trials. Thirty-six healthy young adults (20 males, 16 females) were exposed to twelve dry-bulb temperature and relative humidity combinations in shaded indoor settings under full hydration. Participants remained seated and performed light office tasks until core temperature (Tcore) reached 39{degrees}C or exposures lasted 8 hours. Clinical heatstroke threshold (Tcore=40.5{degrees}C) were projected by extrapolating from our direct Tcore measurements during controlled exposure trials. At Tw=35{degrees}C, males and females reached heatstroke in approximately 7.1-7.7 and 8.3-8.6 hours, respectively--partly supporting the 6-hour theoretical limit while revealing enhanced short-duration resilience when hydrated. At Tw=34{degrees}C, projected times are 12.5-12.9 hours (males) and 15.5-16.2 hours (females). Conditions at Tw=32{degrees}C and 33{degrees}C remained (quasi-)compensable, with projected heatstroke onset after 33-35 hours. Females consistently tolerated heat stress longer than males. These physiological benchmarks are critical for improving heat-health models and embedding sex-specific vulnerability in equitable adaptation strategies amid accelerating global warming.

physiology↗

KSHV-encoded vIRF3 Cooperates with Cellular IRF4 to Drive Super-Enhancer Activity through Complex DNA Elements

The Kaposis sarcoma-associated herpesvirus (KSHV) oncoprotein vIRF3 is essential for the survival of primary effusion lymphoma (PEL) cells. vIRF3 cooperates with cellular IRF4 to activate super-enhancers (SEs) driving oncogenes including MYC and IRF4 itself. However, the vIRF3/IRF4-responsive DNA sequences underlying this cooperation are unknown. Investigating the IRF4-SE, we mapped its vIRF3/IRF4-responsiveness to a complex [~]83 bp region, which retained cooperative activation by vIRF3 and IRF4 and was activated by vIRF3 but not IRF4 alone. vIRF3-mediated activation depended on an AP1 site, while the cooperation of vIRF3 with IRF4 required the DNA binding ability of IRF4 and IRF-related motifs that do not participate in canonical AP1-IRF (AICE) composite sites. These motifs are necessary but insufficient to confer responsiveness outside their native sequence context, suggesting that vIRF3/IRF4-mediated IRF4-SE activation requires an extended composite element. DNA pulldowns confirmed the importance of the identified motifs for association of vIRF3 and IRF4 with the IRF4-SE. A PEL MYC-SE similarly depended on an extended responsive element containing a critical AP1 site, within a functional AICE motif. Together, our results show that vIRF3 activates oncogenic SEs by co-opting complex genetic elements that may accommodate previously unknown IRF4 binding configurations, improving our understanding of vIRF3 and IRF4-dependent oncogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=59 SRC="FIGDIR/small/669493v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@8eb737org.highwire.dtl.DTLVardef@19ea21eorg.highwire.dtl.DTLVardef@1a5909dorg.highwire.dtl.DTLVardef@b947c0_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Protein Folding accompanied by disulfide bond formation drives glutenin polymerization into multidimensional gluten networks

Wheat flour dough, which is routinely used to make bread, pasta and noodles, can be stretched several thousand-fold without rupture. The molecular basis of this extraordinary property arises due to the ability to crosslink glutenin subunits, the major constituent of dough, into linear and branched elastic networks. The mechanism by which the glutenin subunits self-assemble and polymerize is unknown. Here, we show, using mass spectrometry, confocal imaging and molecular dynamics simulations that structuring of two hydrophobic residues, phenylalanine and tyrosine, in the core region of the monomeric glutenin 1Dx5 N-terminal domain (1Dx5-NTD) initiates inter molecular interactions and network formation. Upon folding of monomeric 1Dx5-NTD, two cysteine residues (Cys10 and Cys40) form an intramolecular disulfide bond and poises the third cysteine (Cys25) to engage in inter molecular crosslink with other glutenin subunits. Propagation of such a disulfide linkage pattern results in the formation of a cohesive linear gluten network. In alternate pathways, crosslinking of Cys10 with Cys25 with a third glutenin subunit results in the creation of a junction, which drives the formation of a three-dimensional network. The disulfide patterns in the networks accord well with the measured chemical reactivity of each cysteine residue and the solvent accessibility of the associated side chains during 1Dx5-NTD interactions. Our study shows that the diversity in the folding of a single glutenin subunit that exposes the third cysteine to the solvent is the key event that initiates polymerization and directs the formation of networks with differing architecture. Significance statementGlutenin proteins polymerize to form intricate molecular networks that support the expansion of dough by several thousand-fold. Although network formation occurs spontaneously, the polymerization mechanism is unknown. There are multiple cysteine residues in glutenin that can form intra and intermolecular disulfide bonds. Multiple experimental techniques and molecular dynamics simulations are used to show that folding of glutenin, initiated by two hydrophobic residues, exposes cysteines that are poised to form intermolecular disulfide bonds. The disulfide crosslinking pattern, determined by the initial folding process, dictates the creation of a linear or branched network. The study demonstrates that the propensity to form linear or branched networks is encoded by the diversity of the disulfide patterns created at the level of monomeric folding.

biophysics↗

Spatial Coordination between Leaf Gradient and Temperature Response in Barley

The linear shape of cereal leaves creates distinct longitudinal zones that coordinate tissue maturation and resource allocation. Under abiotic stress such as heat, these longitudinal zones may differentially activate protective pathways, revealing hidden heterogeneity in stress response that remains poorly understood. Barley (Hordeum vulgare), a cold-adapted crop particularly sensitive to elevated temperatures, can serve as an ideal model for studying region-specific heat responses in leaves. Using chlorophyll fluorescence imaging, we found that non-photochemical quenching (NPQ) kinetics captured additional physiological changes beyond those detected by SPAD, highlighting the added value of chlorophyll fluorescence-based assessments. NPQ kinetics traits displayed consistent spatial gradients from tip to base, with heat stress reducing NPQ induction across leaf gradients. Genome-wide association analysis of traits derived from chlorophyll fluorescence imaging across leaf gradients identified significant SNPs within multiple candidate genes, including HORVU.MOREX.r3.3HG0262630 that was consistently detected in over 90% resampling iterations under heat stress, suggesting its key role during heat responses. Transcriptomic profiling along the leaf axis revealed both conserved and region-specific heat responses between leaf regions. Conserved activations highlighted conserved heat response pathways, including the reactivation of the Arabidopsis thermomemory module FtsH6-HSP21. In contrast, the region-by-temperature interaction analysis identified 40 genes with spatial responses indicative of resource reallocation from growth to defense, including those involved in growth and transport. The integration between spatially resolved phenotyping and transcriptional profiling underscores region-specific variation in response to heat along the leaf axis, guiding targeted strategies to enhance heat resilience in barley and other cereal crops.

plant biology↗

Cetuximab increases LGR5 expression and augments LGR5-targeting antibody-drug conjugate efficacy in patient-derived colorectal cancer models

Colorectal cancer (CRC) remains the second-leading cause of cancer-associated deaths, indicating an urgent need for improved therapeutic options. We previously generated antibody-drug conjugates (ADCs) targeting the cancer stem-like cell marker leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5). However, tumor relapse due to LGR5 downregulation and suboptimal payload selection warranted strategies to improve ADC efficacy. Here we report cetuximab, an EGFR-targeting monoclonal antibody indicated for RASWT metastatic CRC, augments LGR5 expression independent of RAS/PIK3CA mutation status and promotes EGFR-LGR5 interactions. Furthermore, we describe the development of LGR5 ADCs incorporating a camptothecin-derived payload that is well-tolerated and significantly inhibits tumor growth. Importantly, cetuximab in combination with LGR5 ADCs results in enhanced tumor inhibition or regression versus single-agent treatment and extends survival in RASMUT patient-derived xenografts. These findings support growing evidence that ADC combination therapies may be more effective than monotherapies and suggests a broader clinical use for cetuximab in treating RASMUT CRC.

cancer biology↗

Sulindac Sulfide Suppresses Oncogenic Transformation Through let-7b-Mediated Repression of K-Ras Signaling

Cell transformation is a key early event in tumorigenesis, yet the molecular mechanisms underlying its chemoprevention remain poorly defined. Here, we show that sulindac sulfide (SS), the active metabolite of the NSAID sulindac, inhibits chemically induced transformation of NIH/3T3 cells through a COX-independent mechanism. SS treatment upregulates the tumor-suppressive microRNA let-7b, which directly targets K-Ras and suppresses downstream ERK signaling. Notably, K-Ras negatively regulates let-7b via activation of ERK and LIN28B, forming a reciprocal feedback loop that drives transformation. SS disrupts this loop by downregulating p-ERK and LIN28B, thereby restoring let-7b expression. Functional analyses confirmed that let-7b, but not let-7g, is required for SS-mediated inhibition of transformation. In human colon cancer tissues and cell lines, let-7b is downregulated, but restored upon SS treatment. These findings identify a novel let-7b/K-Ras/LIN28B/ERK regulatory axis targeted by SS and provide mechanistic insight into its role in early-stage cancer chemoprevention.

cell biology↗

Arabidopsis RabGDIs are essential for the asymmetric division of zygotes and embryonic patterning

An asymmetric division of zygotes sets up the apical-basal body axis and starts the life cycle of angiosperms. In addition to specific expression of transcription factors and polar distribution of auxin, vesicular trafficking-mediated endomembrane dynamics are critical for zygotic division and embryonic patterning. As key regulators of vesicular trafficking, whether Rab GTPases play a role in these processes is unclear. We report that Arabidopsis guanine nucleotide dissociation inhibitors for Rab (RabGDIs) are essential for the asymmetric division of zygotes and embryonic patterning likely through regulating the dynamic targeting of canonical Rab GTPases, especially Rab5. Arabidopsis RabGDIs specifically interact with canonical Rab GTPases. Functional loss of Arabidopsis RabGDI1 and RabGDI2 compromises the asymmetry of zygotic division, cell fate determination, and embryonic patterning. Polar distribution of vacuolar dynamics was disrupted in zygotes and 1-cell embryo of gdi1 gdi2, suggesting a key role of RabGDIs in vacuolar dynamics. Furthermore, genetic interference of canonical Rab5, a key regulator of vacuolar trafficking and biogenesis, in zygotes leads to similar defects, consistent with the disturbed localization of Rab5 in gdi1 gdi2 embryos. Results presented demonstrate the key role of RabGDIs through Rab GTPases in asymmetric division of zygotes and embryonic patterning.

plant biology↗

Bacteriophage diversity declines with COPD severity in the respiratory microbiome

Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterised the lung virome by re-analysing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. Whilst viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Phages infecting anaerobic oral bacteria showed disproportionately lower abundance--Porphyromonas phages were 40-fold less abundant despite only 4-fold lower bacterial abundance--whilst pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonised patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognised feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.

microbiology↗

obABPP-HT*: A Precision-Engineered Activity Proteomics Pipeline for the Streamlined Discovery of Deubiquitinase Inhibitors

Deubiquitinases (DUBs), and the dysregulation thereof, are implicated in human disease. The recent inclusion of selective DUB inhibitors in clinical trials has heightened interest in DUB-focused drug discovery. Current DUB screening methods remain constrained, however, as they often rely on recombinant proteins that are truncated or derived from non-human sources, typically necessitating extensive optimisation of initial hits. We introduce a high-throughput, endogenous human DUB-focused activity proteomics workflow designed for the simultaneous screening and profiling of small, targeted libraries of catalytic group-reactive compounds. In a proof-of-concept screen, this innovative platform expanded the repertoire of electrophilic groups targeting DUBs, leading to the discovery of potent and selective inhibitors for USP47, OTUD7B, and USP5. Remarkably, these inhibitors required minimal or no optimisation to confirm the previously reported biological roles of the three DUBs, underscoring the advantages of this methodology for drug discovery applications.

biochemistry↗

Microbially-mediated halogenation and dehalogenation cycling of organohalides in the ocean

Microbially mediated organohalide cycling in the ocean has profound implications for global element cycles and climate, but the phylogeny, coding potential, and distribution of the halogenation-dehalogenation cycling microorganisms remain unknown. Here, we construct an organohalide-cycling database (HaloCycDB) to explore the global atlas of halogenation-dehalogenation cycling genes and microorganisms in the ocean from 1,473 marine metagenomes. FlaHase and HyDase/RDase as predominant halogenase- and dehalogenase-encoding genes account for 80.24% of all potential organohalide-cycling activities. We identify 80.91% RDase and 91.35% RDase-containing prokaryotes as unknown organohalide-cycling genes and microorganisms, respectively, which greatly expand the diversity of dehalogenation phylogeny and coding potential. Further integration of microbial cultivation with protein structure prediction and molecular docking elucidates 4 unique "microorganism-enzyme-organohalide" patterns for organohalide dehalogenation in the ocean. Our results provide the first insight into microbial halogenation-dehalogenation cycling of organohalides and associated yet-to-be-explored resources in the ocean.

ecology↗

Sludge liquefaction and stratification enable ultra-high digestion rate and resource recovery for waste activated sludge treatment

Most of the energy, nitrogen/N and phosphorus/P entering wastewater treatment plants (WWTPs) accumulates in waste activated sludge (WAS). While these resources are theoretically recoverable through anaerobic digestion (AD), conventional sludge AD faces long-standing challenges of low organic loading rate and limited N/P recovery. Here, building on an innovative sludge liquefaction and stratification technique, we present a novel process entitled SPREAD that boasts 10 times higher organic loading rates and recovers 5 folds of N/P resources, relative to conventional sludge AD. We develop an anaerobic digestion database (ADDB) for multi-omics analyses of digestion microbiomes, and pinpoint the mechanism underlying the exceptionally high organic loading rate and remarkable N/P recovery in SPREAD. Importantly, we identify a negative correlation between the Gibbs free energy ({Delta}G) and the relative abundance of methanogens, enabling identification of bottleneck steps for stimulation and augmentation of methanogenic digestion. Our study provides a game-changing technology for the treatment and resource recovery from WAS and opens a new avenue for sustainable management and carbon/energy-neutrality of WWTPs.

bioengineering↗