Biology subjects

Wei, B.

Publications and source records attributed to Wei, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Multi-resolution humanness scoring of antibodies via a region-isolated language model

Antibodies recognized as foreign can elicit anti-drug antibodies that compromise efficacy and safety, making humanness scoring, estimating how human-like a sequence appears, an early, repeated step in antibody development. Widely used scores reduce a variable domain to a single framework-dominated number, leaving the complementarity-determining regions (CDRs) grafted during humanization, diversified by generative models weakly supervised and rarely audited. Here we introduce IgScope, a 23-million-parameter antibody language model trained from scratch that scores humanness at chain, IMGT-region, and residue resolution; a region-isolated attention module confines attention to within-region pairs, and chimeric-sequence training supplies region-level supervision. On 2.38 million held-out chains, masking all framework tokens leaves CDR accuracy unchanged, and back-mutated murine residues in human frameworks are detected at 93.4% accuracy. At chain level, IgScope matches the strongest published correlation with clinical anti-drug-antibody incidence (r = 0.567, n = 217) and outperforms a same-protocol recomputation. Region-level scoring exposes what chain-level scoring conceals: antibodies designed de novo by four generative models pass whole-chain humanness (0.966-0.988), while their CDRs score far below natural (P < 1e-30) in every chain class. Quality control turns the same resolution to the mirror-image question: in humanized-mouse platforms, whose domains are human by design, IgScope scores the domain as human and, in HUGO-Nano chimeric VHHs, isolates only the FR2 signal of four camelid hallmark residues deliberately retained to stabilize the VHH. IgScope gives antibody humanization a verified foundation and generative design an audit.

bioinformatics↗

bioRxiv2026

Chimeric Induced Cooperativity Opens the Design Space of Eukaryotic Gene Regulation

Predictive engineering of eukaryotic transcription is limited by the coupling of signal sensing, DNA binding, TF abundance and promoter output. Here we establish chimeric induced cooperativity (CIC), a modular architecture that separates LBD, DBD and AD functions and links them to promoters with tunable basal and maximal output. Module parameters can be recombined to predict new CIC-TF configurations and guide design before construction. Ligand-induced cooperativity reduces basal DNA occupancy while increasing induced occupancy, and effective DBDs combine low OFF-state activity with strong ON-state promoter occupancy rather than binding strength alone. Synthetic promoters independently control occupancy gain and output range. The same framework extends to repression and can be recalibrated with limited measurements in mammalian cells. In yeast, CIC-12 achieved a mean fold induction of 298-fold across 12 orthogonal sensors; an earlier CIC-10 chassis enabled model-guided optimization of an eight-gene vitamin B5 biosynthetic pathway. CIC establishes a programmable, model-guided design space for eukaryotic transcriptional control.

synthetic biology↗

bioRxiv2026

Cyanobacterial cohorts structure the diversity, abundance, and metabolism of heterotrophic bacteria in Lake Erie

Eutrophication and warming in Lake Erie create two microbial threats: cyanobacterial harmful algal blooms (cHABs) that can produce toxins, and seasonal hypoxia driven by microbial respiration. These phenomena are often studied separately, with cHABs research focused on the Western basin and hypoxia on the Central basin. We conducted lakewide microbial sampling at three time points in 2024 (May, August, and September), integrating physicochemical data, cyanotoxin quantification, amplicon sequencing, and flow cytometry. We demonstrate that cyanobacteria form spatially and seasonally distinct "cohorts" that act as hubs structuring abundant, diverse, and active communities across all basins. These cohorts display distinct relationships with heterotrophic communities, with colonial, bloom-forming cohorts (i.e., C1: Microcystis, C2: Pseudanabaena) associated with higher richness and evenness, the picocyanobacterium C3: Cyanobium with increased heterotrophic abundance, and C2: Pseudanabaena additionally associated with increased numbers of metabolically active cells. Neither temperature nor nutrient concentrations consistently explained these patterns, although total phosphorus correlated with bloom-forming C1 and C2 cohorts. The cohorts also formed structured "consortia" with heterotrophic taxa, with each cyanobacterial group associated with consistent sets of heterotrophic partners. Together, these results are consistent with a model in which cyanobacterial abundance increases heterotrophic growth and respiration, suggesting a lakewide pathway linking cHABs to oxygen demand and hypoxia. IMPORTANCECyanobacterial harmful algal blooms and hypoxia are two microbial processes shaping water quality in Lake Erie, yet they are typically studied separately and at basin-specific scales. We link cyanobacterial abundance to heterotrophic metabolism at a lakewide scale. We show that cyanobacterial abundance is associated with heterotrophic diversity, abundance, and metabolic activity, with contrasting patterns across cyanobacterial functional groups. These relationships were not explained by temperature nor consistently by nutrients, although cyanobacterial distribution in the Central basin is likely linked to nutrient availability as a result of upwellings and basin-wide gyres. Bloom-forming and picocyanobacterial cohorts play fundamentally different roles in structuring microbial diversity and biomass, with implications for how bloom management influences ecosystem metabolism. By identifying cyanobacteria as a major predictor of microbial biomass and activity, this work reveals a spatially-explicit pathway connecting cyanobacterial primary production to oxygen demand, suggesting that managing blooms may regulate oxygen depletion.

microbiology↗

bioRxiv2026

Benthic biodiversity hotspots in the Weddell Sea: Bridging geomorphology, biogeography, and oceanography across scales

Benthic ecosystems are shaped by seafloor structure, yet linking geomorphology and biology across environmental gradients remains challenging. Here, we integrate seafloor imagery, multiscale bathymetry, and predictive modelling to quantify benthic biodiversity and its environmental drivers along the Powell Basin flank of the Antarctic Peninsula. Steep geomorphological landforms (terraces and steep slopes) hosted maximal densities and distinct communities, with significant enrichment of corals, sponges, ophiuroids, and sea pens. The marked congruence of slope across bathymetric resolutions enabled regional upscaling, estimating a standing stock of [~]96 billion individuals across 7,400 km{superscript 2} of the basin flank. Decadal oceanographic models indicate that benthic densities peak in cold bottom water below -0.15 {degrees}C. We identified four biodiversity hotspots ([~]33 km2) with slopes >35{degrees} and depths >1,700 m, with up to threefold higher densities. Hotspots align with the pathway of Weddell Sea Deep Water, where thermal decoupling between bottom and overlying waters indicates dynamic hydrography along steep, biodiverse terrain. Furthermore, contrasting sea-ice cover and stratification regimes suggest distinct cryo-pelagic-benthic coupling around hotspots. The concentration of biodiversity through seafloor geomorphology and ocean circulation bridges Antarctic benthic ecology from habitat to biogeography, with implications for monitoring change and guiding conservation in the warming Weddell Sea.

ecology↗

bioRxiv2025

Revisiting Humidity Ramp Protocols for Assessing Human Heat Tolerance

BackgroundHumidity ramp protocols are widely used to estimate human heat tolerance limits, yet reported critical environmental limits (CELs) vary markedly across studies. Whether this variability reflects true physiological differences or systematic methodological artifacts related to ramp design remains unresolved. MethodsWe combined first-order thermal modeling with controlled physiological trials to examine how ramp temporal structure (step dwell time) influences apparent rectal temperature (Tcr) inflection points. Twenty-six healthy young adults completed randomized trials at 42 {degrees}C under two protocols: an aggressive-ramp (30-min equilibration followed by humidity increases every 5 min) and a slow-ramp (4-h equilibration followed by hourly humidity increments). CELs derived from ramp protocols were further evaluated using prolonged fixed-condition exposures in independent cohorts (n=14 per sex). ResultsShort-step dwell times ({Delta}t/{tau} <<1) prevented rectal temperature from approaching its step-specific equilibrium, resulting in kinetically constrained, non-equilibrium dynamics and earlier Tcr inflection points. Consequently, aggressive-ramp protocols yielded substantially lower CELs than slow-ramp protocols in both sexes ({approx}3.5 {degrees}C difference). CELs derived from the slow ramp closely matched those obtained from prolonged fixed-condition exposures, whereas aggressive ramps misclassified physiologically compensable conditions as uncompensable. ConclusionRapid humidity increments systematically underestimate heat tolerance because environmental forcing outpaces physiological response kinetics. Accurate CEL determination requires either prolonged fixed-condition exposures (benchmark approach) or sufficiently slow ramps that allow near-equilibrium responses ({Delta}t/{tau} {gtrsim}0.3-0.5).

physiology↗

bioRxiv2025

Cell-cell communication analysis demonstrates early-stage common pathways linking ageing, Alzheimers disease, and Type 2 diabetes-related brain dysfunction

Ageing promotes to the development of age-related diseases and cognitive decline. In this study, we integrated and analysed four single-cell RNA sequencing (scRNA-seq) datasets encompassing Alzheimers disease, type 2 diabetes, and ageing in mouse brain tissue to identify early pathological factors that may drive normal ageing toward disease through alterations in cell-cell communication (CCC). Building on our previously established CCC change modelling framework, we found that both Alzheimers disease and ageing were characterized by a loss of intercellular communication, whereas type 2 diabetes exhibited an overall gain of new communication pathways. Notably, vascular communication changes were more prominent in age-related diseases than in normal ageing. Furthermore, we identified a series of CCC molecules that play key roles in brain ageing and disease through pseudo covariance and conflicting resolving CCC algorithms. Among them, the LRP1 receptor on astrocytes emerged as a central CCC hub implicated in both ageing and disease pathology.

bioinformatics↗

bioRxiv2025

A Critical Rectal Temperature Defines Sex-Specific Leukocyte and Neutrophil Activation During Prolonged Passive Heat Exposure in Young Adults

BackgroundProlonged heat exposure disrupts immune homeostasis and can precipitate acute systemic inflammation. However, the core temperature threshold that triggers sex-specific leukocyte and neutrophil activation during passive heat stress remains undefined. MethodsWe studied 52 males and 58 females exposed to wet-bulb temperatures of 32-35 {degrees}C. Rectal temperature (Trec) was continuously monitored, and blood samples were collected at 0.5 {degrees}C increments up to 38.6 {degrees}C. Leukocyte and neutrophil counts were modeled using quadratic and segmented regression to identify inflection points of immune activation. ResultsBoth leukocytes and neutrophils increased nonlinearly with rising Trec (p < 0.05). A critical Trec of 38.1 {degrees}C--closely aligns with the 38.0 {degrees}C occupational core temperature limits--marked an inflection in leukocyte responses: below this point, females showed steeper increases; whereas above it, males showed accelerated activation. Neutrophils demonstrated consistently greater mobilization in males across the entire temperature range (36.9-38.6 {degrees}C). ConclusionsA distinct core temperature threshold ([~]38.1 {degrees}C) governs immune cell activation and reveals sex-dependent response patterns. This finding provides an immunological rationale for current occupational het limits and highlights the importance of integrating sex-specific considerations into protective guidelines under extreme heat. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/681783v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@9620dorg.highwire.dtl.DTLVardef@47beborg.highwire.dtl.DTLVardef@6396daorg.highwire.dtl.DTLVardef@44c890_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Macrophages display spatiotemporal specificity in intrahepatic cholangiocarcinoma and drive tumour progression via OSM and THBS1

Tumor-associated macrophages (TAMs) are abundant in intrahepatic cholangiocarcinoma (ICC) and correlate with poor prognosis, but their non-immunosuppressive roles remain unclear. This study aimed to define TAM transcriptional heterogeneity and map their interactions with ICC cells that promote malignancy beyond immune suppression. Single-cell and spatial transcriptome analysis with mouse and human ICC tissues revealed a TAM subpopulation, designated M{varphi}_VEGFA, that emerged as the major macrophage population from the intermediate stage of ICC development onward. Data from Gene Expression Omnibus (GEO) and spatial transcriptome indicate that M{varphi}_VEGFA was associated with poor prognosis and spatially localized to the ICC cells. Cell co-culture and cell-cell communication analyses revealed that M{varphi}_VEGFA promoted ICC cell proliferation via secreted OSM and downstream OSMR-STAT3-CCND1 axis, and enhanced ICC cell invasion through THBS1 and downstream CD47-mTOR/DBN1 signaling. Critically, multiplex immunofluorescence with human ICC tissue microarray indicated that OSM and THBS1 were co-elevated in human ICCs, and dual blockade of both targets inhibited ICC progression in mouse models. This study uncovers the direct and critical roles of M{varphi}_VEGFA in driving ICC progression with paracrine signaling and further highlights the potential of targeting macrophages in ICC treatment.

cancer biology↗

bioRxiv2025

Dissecting the epigenome dynamics in human immune cells upon viral and chemical exposure by multimodal single-cell profiling

Environmental and pathogen exposure can lead to profound remodeling of the gene-regulatory landscape across human immune cell populations. Here, we present a single-nucleus chromatin accessibility atlas of human immune cells comprising 271,299 cells and 319,420 candidate regulatory elements from individuals exposed to HIV-1, COVID-19, Influenza virus, organophosphates, as well as healthy controls. Our longitudinal HIV cohort reveals epigenetic signatures of T cell exhaustion manifested in changes in the accessibility at binding sites for the FOXP family transcription factors. Upon severe exposure to SARS-Cov2 we identified changes in chromatin accessibility manifesting in a regulatory switch in cytokine networks characterized by the downregulation of the NF-{kappa}B motif family, alongside concordant changes in AP-1 and IRF factor networks in CD14+ classical monocytes. By integrating single-cell profiles of DNA methylation from matched samples, we created a multimodal epigenome atlas of human immune cell states using the accessibility-derived candidate regulatory elements. Both modalities exhibit complementary epigenetic signatures at transcription factor binding sites associated with cell state, as exemplified in the process of memory formation in T-cells, where BATF, AP-1, and ETS motifs exhibit significant epigenetic covariance across both epigenomic layers. Finally, by linking potentially regulatory DNA methylation signatures to changes in chromatin accessibility in monocytes, we observe that severe COVID-19 involves selective, multiomics remodeling of epigenetic profiles at TF binding sites manifested in concordant DNA methylation and accessibility dynamics at inflammation-associated regulatory TFs.

bioinformatics↗

bioRxiv2025

Light-up nanostructures with allosteric DNA mimics of GFP

In this study, we present a systematic approach for the rational design of synthetic allosteric DNA aptamers. This methodology enables precise control over the allosteric ON-OFF transition in fluorescent DNA aptamers, allowing for the engineering of aptamers with highly tunable fluorescent properties. When combined with toehold-mediated strand displacement, we have developed a series of allosteric aptamers in which the target sequence functions as a specific allosteric modulator. Furthermore, these aptamers have been applied in synthetic DNA computing and in the construction of responsive nanostructures that light up upon activation.

synthetic biology↗

bioRxiv2025

Intranasal Dantrolene Nanoparticles for Treatment of Amyotrophic Lateral Sclerosis as a Disease-Modifying Drug

Calcium dysregulation, caused by pathological activation of ryanodine receptors, contributes to motor neuron degeneration, motor dysfunction, and muscle weakness in SOD1-G93A transgenic amyotrophic lateral sclerosis (ALS) mice. This study investigates the therapeutic efficacy of intranasally administered dantrolene nanoparticles, a ryanodine receptor antagonist, on motor neuron function, muscle strength, spinal cord degeneration, and survival outcomes. Male and female C57BL/6SJLF1 non-transgenic control and SOD1-G93A ALS transgenic mice were assigned to one of three experimental groups: 1) NO TX: No treatment control; 2) IN-DAN: Intranasal administration of dantrolene in the Ryanodex formulation vehicle (RFV), at a dosage of 5mg/kg, administered daily from ages 90-120 days; 3) IN-VEH: Intranasal administration of RFV alone (as a vehicle control), following the same dosing schedule as the IN-DAN condition. Body weight and general motor function were monitored weekly, with survival recorded daily throughout the treatment period. At the treatment conclusion, neurological function was comprehensively evaluated using a standardized neurological scoring system. Motor coordination and balance were assessed using the balance beam test (beam widths of 12 mm and 6 mm) and the rotarod test. Muscle strength was evaluated by measuring grip force using the Kondziela inverted screen test. After behavioral testing, spinal cord tissues were collected for analysis. The levels of neurofilament light chain (NFL), a skeletal neuron protein, and spinal cord weight were determined to measure spinal cord degeneration. Compared to non-transgenic control mice, SOD1-G93A mice exhibited significantly elevated neurological scores, indicating severely impaired neurological function. This deterioration was robustly and significantly ameliorated by IN-DAN treatment by 90% (P<0.0001). Similarly, ALS mice demonstrated impairments in motor coordination and balance on the beam balance test, with dramatic and significant increases in crossing time and the number of foot slips. These impairments were greatly and significantly mitigated by IN-DAN treatment, by 78% in crossing time (P<0.0001) and 84% in the number of slips (P<0.0001) on the 12 mm-wide beam, but not by the vehicle control. ALS mice demonstrated progressive body weight loss as well, which was similarly reversed by IN-DAN treatment, but not by the vehicle control. Muscle strength, as measured by grip force, was significantly reduced in ALS mice but robustly preserved IN-DAN treatment, which prevented the decrease by 213% (P<0.0001), while the vehicle control had no effect. Spinal cord weight was significantly reduced in ALS mice, a trend reversed by intranasal dantrolene nanoparticle treatment, but not by the vehicle control. Survival analysis revealed that 100% of control mice survived through the 30-day treatment period (up to 120 days of age), while survival in untreated or vehicle-treated ALS mice dropped to 67%. In contrast, ALS mice treated with intranasal dantrolene nanoparticles demonstrated a significantly improved survival rate of 89%. Thus, intranasal dantrolene nanoparticle treatment significantly and robustly improved neurological outcomes in SOD1-G93A ALS mice, inhibiting neurological impairment, motor dysfunction, balance deficits, and muscle weakness. These improvements were associated with a marked inhibition of spinal cord weight loss. Additionally, dantrolene treatment reversed body weight loss and significantly improved survival probability in ALS mice.

pharmacology and toxicology↗

bioRxiv2025

Patient-Derived Three-Dimensional Lung Tumor Models to Evaluate Response to Immunotherapy

Novel preclinical models that better mimic the in vivo tumor microenvironment are needed for advanced understanding of tumor biology and resistance/response to therapy. Herein, we report development of a novel ex vivo patient-derived three-dimensional lung tumor model (3D-LTM), that maintains features of human extracellular matrix, cell-cell interactions, and tissue architecture to evaluate a rapid response to immune checkpoint inhibitors (ICI). Within this model system, we recapitulated the heterogeneity of response to immunotherapy observed in non-small cell lung cancer (NSCLC) patients and defined signatures associated with response for predicting early response of ICI in patients. Spatial transcriptomics of the 3D-LTMs identified positive correlation of CD8+ T cell populations, CD4+ memory T cells, mast cells, NK cells, endothelial cells and non-classical monocytes with response status, whereas macrophages negatively correlated with response status. Pathway analysis of gene expression showed that chemokine signaling related pathways were activated in responder 3D-LTM tissues, whereas suppression of antigen presentation-related pathways and activation of Treg differentiation-related pathways was associated with 3D-LTMs that were not considered responders. This model system has utility for rapid testing of novel immune directed therapy outcomes and for developing biomarkers of ICI response in NSCLC.

cancer biology↗

bioRxiv2024

Identification of Stress-induced miRNA of Microbial flora, networking, expression with chronic rhinosinusitis (CRS)

All age groups are affected by one of the most prevalent chronic medical disorders globally: chronic rhinosinusitis (CRS). Its estimated incidence is 10.9% in Europe, 13% in China, and 12.3% in the United States. For many years, the 16S rRNA gene has been the backbone of sequence-based bacterial study. Still, it is only recently that the possibility of high-throughput sequencing the entire gene has been feasible. A unique gene regulation mechanism known as "RNA silencing" limits the transcript level by either starting specific RNA degradation or blocking translation. RNA interference (RNAi) is commonly induced by viruses or exogenously produced small interfering RNAs. Small RNAs like these have been utilized in biomedical research to specifically silence genes. The purpose of a short hairpin RNA is to create interference by inserting an artificial RNA molecule with a hairpin or loop-like structure into a specially designed siRNA. Every stage of life, including cell development, metabolism, the cell cycle, and signal transmission, depends on gene regulatory networks. Total fifteen mRNAs of 16SrRNA gene examined, siRNA regions is unique and isolated through 3 to 5 position nucleotide. Networking of both genes lies varieties of path in human being, so early to utilized siRNA technique to silence the effect of 16SrRNA gene in CRS illness. The gene encoding 16S rRNA has around ten target sites that siRNAs can attach to. The siRNAs are made to be complementary sequences to each of the target sites. Verify the 16S rRNA gene expression in CRS illness and other types across the body. Since a cystic fibrosis transmembrane conductance regulator (CFTR) mutation causes CRS illness, we isolated a mutant form of CFTR with an accession ID of 1XMJ and 16S rRNA protein quotes in 8SR6. Examine the two proteins interaction (1xmj, 8sr6) describe the inhibition of CRS illness through new way. Utilizing in-vitro exploratory approaches, both this computational study of siRNA and protein-protein interaction may be employed further to verify efficacy and appropriateness.

bioinformatics↗

bioRxiv2024

Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity

Rapid and comprehensive analysis of complex proteomes across large sample sets is vital for unlocking the potential of systems biology. We present UFP-MS, an ultra-fast mass spectrometry (MS) proteomics method that integrates narrow-window data-independent acquisition (nDIA) with short-gradient micro-flow chromatography, enabling profiling of >240 samples per day. This optimized MS approach identifies 6,201 and 7,466 human proteins with 1- and 2-min gradients, respectively. Our streamlined sample preparation workflow features high-throughput homogenization, adaptive focused acoustics (AFA)-assisted proteolysis, and Evotip-accelerated desalting, allowing for the processing of up to 96 tissue samples in 5 h. As a practical application, we analyzed 507 samples from 13 mouse tissues treated with the enzyme-drug L-asparaginase (ASNase) or its glutaminase-free Q59L mutant, generating a quantitative profile of 11,472 proteins following drug treatment. The MS results confirmed the impact of ASNase on amino acid metabolism in solid tissues. Further analysis revealed broad suppression of anticoagulants and cholesterol metabolism and uncovered numerous tissue-specific dysregulated pathways. In summary, the UFP-MS method greatly accelerates the generation of biological insights and clinically actionable hypotheses into tissue-specific vulnerabilities targeted by ASNase.

systems biology↗

bioRxiv2024

Innate immune epigenomic landscape following controlled human influenza virus infection

Viral infections can induce changes in innate immunity that persist after virus clearance. Here, we used blood samples from a human influenza H3N2 challenge study to perform comprehensive multi-omic analyses. We detected remodeling of immune programs in innate immune cells after resolution of the infection that was proportional in magnitude to the level of prior viral load. We found changes associated with suppressed inflammation including decreased cytokine and AP-1 gene expression as well as decreased accessibility at AP-1 targets and interleukin-related gene promoter regions. We also found decreased histone deacetylase gene expression, increased MAP kinase gene expression, and increased accessibility at interferon-related gene promoter regions. Genes involved in inflammation and epigenetic-remodeling showed modulation of gene-chromatin site regulatory circuit activity. These results reveal a coordinated rewiring of the epigenetic landscape in innate immune cells induced by mild influenza virus infection.

immunology↗

bioRxiv2024

Inflammatory Neuropathy in Mouse and Primate Models of Colorectal Cancer

Colorectal cancer survivors are at increased risk of developing neurological issues, particularly peripheral neuropathy and chronic pain. Although pre-existing neuropathy is a risk factor for chronic pain, tumor-induced neuropathy has not been firmly established in pre-clinical models. Consistent with clinical observations, we show that mice with colorectal cancer develop peripheral neuropathy, which was associated with subtle locomotor deficits, without overt hypersensitivity. We detected widespread differences in pro-inflammatory cytokines and lipid metabolites in peripheral nerves from tumor-bearing mice. Macrophage accumulation, myelin decompaction and ryanodine receptor oxidation were associated with dysfunctional calcium homeostasis and reduced spike amplitude in sensory neurons. Inflammatory neuropathy and macrophage accumulation were also observed in peripheral nerves of rhesus macaques with colorectal cancer. These findings suggest colorectal cancer is causally linked to a subacute form of chronic inflammatory demyelinating polyneuropathy across species, which may represent an under-reported, yet important risk factor for neurological dysfunction in colorectal cancer survivors.

neuroscience↗

bioRxiv2024

Colorectal ALOX15 as a host factor determinant of EPA and DHA effects on colorectal carcinogenesis

Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), omega-3 polyunsaturated fatty acids ({omega}-3 PUFAs) derived from fish oil, are widely used as dietary supplements and FDA-approved treatments for hypertriglyceridemia. However, studies investigating the effects of EPA and DHA on colorectal carcinogenesis (CRC) have yielded conflicting results. The factors that determine these discrepant results remain unknown. Resolvins, oxidative metabolites of EPA and DHA, inhibit key pro-tumorigenic cytokine and chemokine signaling of colorectal cancer (e.g., IL-6, IL-1{beta}, and CCL2). 15-lipoxygenase-1 (ALOX15), a critical enzyme for resolvin generation is commonly lost during human CRC. Whether ALOX15 expression, as a host factor, modulates the effects of EPA and DHA on CRC remains unknown. Therefore, we evaluated the effects of ALOX15 transgenic expression in colonic epithelial cells on resolvin generation by EPA and DHA and CRC in mouse models representative of human CRC. Our results revealed that 1) EPA and DHA effects on CRC were diverse, ranging from suppressive to promotive, and these effects were occasionally altered by the formulations of EPA and DHA (free fatty acid, ethyl ester, triglyceride); 2) EPA and DHA uniformly suppressed CRC in the presence of intestinal ALOX15 transgenic expression, which induced the production of resolvins, decreased colonic CCL3-5 and CXCL-5 expression and tumor associated macrophages while increasing CD8 T cell abundance in tumor microenvironment; and 3) RvD5, the predominant resolvin produced by ALOX15, inhibited macrophage generation of pro-tumorigenic cytokines. These findings demonstrate the significance of intestinal ALOX15 expression as a host factor in determining the effects of EPA and DHA on CRC. SignificanceEicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are widely used as dietary supplements and FDA-approved treatments for hypertriglyceridemia. Studies of EPA and DHA effects on colorectal carcinogenesis (CRC) have revealed inconsistencies; factors determining the direction of their impact on CRC have remained unidentified. Our data show that EPA and DHA effects on CRC were divergent and occasionally influenced by their formulations. More importantly, intestinal 15-lipoxgenase-1 (ALOX15) expression modulated EPA and DHA effects on CRC, leading to their consistent suppression of CRC. ALOX15 promoted EPA and DHA oxidative metabolism to generate resolvins, which inhibited key pro-tumorigenic inflammatory cytokines and chemokines, including IL-6. IL-1{beta}, and CCL2. ALOX15 is therefore an important host factor in determining EPA and DHA effects on CRC.

cancer biology↗

bioRxiv2024

NLRP3, NLRP6, and NLRP12 are inflammasomes with distinct expression patterns

Inflammasomes are sensors that detect cytosolic microbial molecules or cellular damage, and in response they initiate a form of lytic regulated cell death called pyroptosis. Inflammasomes signal via homotypic protein-protein interactions where CARD or PYD domains are crucial for recruiting downstream partners. Here, we screened these domains from NLR family proteins, and found that the PYD domain of NLRP6 and NLRP12 could activate caspase-1 to induce cleavage of IL-1{beta} and GSDMD. Inflammasome reconstitution verified that full length NLRP6 and NLRP12 formed inflammasomes in vitro, and NLRP6 was more prone to auto-activation. NLRP6 was highly expressed in intestinal epithelial cells (IEC), but not in immune cells. Molecular phylogeny analysis found that NLRP12 was closely related to NLRP3, but the activation mechanisms are different. NLRP3 was highly expressed in monocytes and macrophages, and was modestly but appreciably expressed in neutrophils. In contrast, NLRP12 was specifically expressed in neutrophils and eosinophils, but was not detectable in macrophages. NLRP12 mutations cause a periodic fever syndrome called NLRP12 autoinflammatory disease. We found that several of these patient mutations caused spontaneous activation of caspase-1 in vitro, which likely causes their autoinflammatory disease. Different cell types have unique cellular physiology and structures which could be perturbed by a pathogen, necessitating expression of distinct inflammasome sensors to monitor for signs of infection.

immunology↗