Biology subjects

Liang, H.

Publications and source records attributed to Liang, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Lipid acyl chain remodeling governs KRAS nanoclustering and oncogenic functions through membrane composition control

KRAS signaling is spatially organized within the dynamic proteolipid nanoclusters on the plasma membrane (PM) that selectively concentrate anionic phospholipids, yet the molecular determinants governing this lipid sorting remain incompletely defined. Here we identify phospholipid acyl chain composition as a critical regulator of KRAS spatial organization and signal output. Using genetic and pharmacological perturbation of lysophosphatidylcholine acyltransferase 3 (LPCAT3), a key enzyme that incorporates polyunsaturated fatty acids into phospholipids, we demonstrate that remodeling of membrane acyl chain unsaturation alters the phosphatidylserine (PS) lipidome without changing total PS abundance. Loss of LPCAT3 depletes polyunsaturated PS species, disrupts KRAS PM association and nanoclustering, and attenuates downstream MAPK signaling and oncogenic activity across multiple KRAS mutant contexts. Acute restoration of polyunsaturated, but not saturated, lipids rescue KRAS nanoclustering, establishing a direct requirement for lipid unsaturation in sustaining signaling-competent assemblies. Mechanistically, these findings define membrane acyl chain composition as a determinant of proteolipid organization that encodes KRAS signaling capacity. Consistent with this model, LPCAT3 inhibition selectively impairs KRAS-dependent proliferation and sensitizes tumor cells to direct KRAS inhibition. Together, this work uncovers lipid acyl chain remodeling as a fundamental regulator of membrane-associated signaling and identifies membrane composition as an exploitable vulnerability in oncogenic KRAS systems.

cancer biology↗

bioRxiv2026

Balancing receptor engagement and payload catalytic activity broadens the therapeutic window of immunotoxins

Immunotoxins (ITs) are potent targeted cancer therapeutics that couple tumor-selective receptor binding with efficient intracellular delivery and cytotoxic enzymatic activity of bacterial toxins. While ITs have shown impressive efficacy in hematologic malignancies, dose-limiting toxicity remains a major barrier to their broader clinical application, particularly in solid tumors. The exceptional potency of immunotoxin payloads contributes to off-tumor toxicity because even limited uptake by receptor-low cells can be sufficient to cause cell death. Here, we systematically investigated how receptor-binding domain (RBD) affinity and avidity interact with catalytic payload activity to determine IT selectivity. Using CD123-, HER3-, and HER2-targeted ITs, we found that increasing receptor-binding affinity or avidity altered potency but provided limited control over the selectivity between receptor-high and receptor-low cells. In contrast, attenuating catalytic activity produced profound gains in selectivity when payload potency was appropriately matched to receptor engagement. The optimal level of attenuation varied with receptor context and toxin scaffold, demonstrating that maximal selectivity emerges from balancing cellular delivery with catalytic activity rather than maximizing either property alone. In vivo, payload attenuation increased the maximum tolerated dose of a HER2-targeted IT by 400-fold and enabled robust antitumor activity well below its toxicity limit, whereas the WT counterpart showed no detectable efficacy at tolerated doses. Together, these findings uncover and establish payload activity as a tunable determinant of immunotoxin selectivity and provide a framework for matching receptor engagement with catalytic potency to develop safer and more broadly applicable targeted toxins.

pharmacology and toxicology↗

bioRxiv2026

Dissecting context-dependent cancer vulnerabilities using Perturb-seq

Background CRISPR-mediated viability assays in diverse cancer cell lines have informed cancer biology and precision medicine, but cell fitness is not the only cancer-relevant phenotype. Gene expression profiling provides insight into cellular stress, inflammation, and differential state, while still identifying activation of cell-death pathways. Perturb-seq allows scalable functional genomics screening of expression phenotypes at single-cell resolution, however existing datasets cover only a small number of work-horse cell lines. Results We produced a proof-of-concept Perturb-seq dataset targeting 100 genes in 16 diverse cancer cell lines. In the process, we established methods to address single-cell technical artifacts, identified Cas9-mediated chromosomal aberrations and assessed screen quality. Even with a limited library, we observed common signatures of deleting essential genes as well as context-specific responses based on intrinsic genomic properties of the models. For example, we inferred a previously undescribed relationship between dependence on the ER-golgi transport gene immediate early response 3 interacting protein 1 (IER3IP1) and oxidative stress, demonstrating the potential of integrated Perturb-seq for hypothesis generation. Conclusions We established a framework for building a comprehensive map of post-perturbational transcriptional phenotypes using parallel Perturb-seq experiments across multiple cell lines. We demonstrated that integrated Perturb-seq experiments spanning diverse contexts enable hypotheses about gene function specific to tissue types or cancer subtypes - suggesting large-scale, genome-wide datasets would offer invaluable insight into the highly context-dependent nature of cancer biology.

cancer biology↗

bioRxiv2026

A leakage-controlled benchmark shows apparent codon-language-model advantages in synonymous-variant prediction are evaluation artifacts

Synonymous codon choices shape mRNA stability, translation, and folding, and codon language models (cLMs) are increasingly reported to read this biology from sequence. However, when a true signal is thin relative to a confounding one, standard evaluation protocols can manufacture the reported gain rather than measure it--and we show this is what has happened for cLMs on synonymous-variant prediction. Under random splits, the codon advantage is large: tokenization gaps of +2.3-14.3 percentage points (pp) and pretrained codon leads of +2.9 pp over the strongest protein model (ESM-1b) and up to +4.9 pp over ESM-2. We find these numbers are properties of the measurement, not the models. A memorization baseline outscores every neural model; the advantage collapses under gene-held-out evaluation; the sole surviving residual dissolves into six defensible probe defaults; and the synonym-randomization drop that appeared to confirm true signal is itself variance under pooled analysis (0.3 pp, p = 0.49). No advantage survives leakage-controlled evaluation with pooled statistics. We release CodonBench, a leakage-controlled benchmark with an emergent audit cascade, and characterize how artifacts accumulate at every pipeline step. A thin signal (I({sigma}; Y |A) {approx} 0.04 bits) may exist but is not reliably detectable at current sample sizes; we specify what detecting it would require.

bioinformatics↗

bioRxiv2026

COMPASS: Component-Wise Inference of Shared and Gene-Specific Perturbation Response

Predicting how a genetic perturbation reshapes a cells transcriptome is a central goal of computational biology. Previous studies report that the mean response across training perturbations rivals specialized models on standard accuracy metrics, even though it cannot distinguish which perturbation occurred. Across 2,270 CRISPRi perturbations measured in each of six cell lines, we show that this apparent paradox reflects a conserved organization of perturbation responses. Perturbations span a continuum from responses strongly aligned with the mean to more targeted responses that depart from it. Crucially, a perturbations position along this continuum is conserved across cell lines (Kendalls W = 0.59) and predictable from STRING protein-interaction embeddings (R2 = 0.35). We formalize this structure with COMPASS, an interpretable linear model that decomposes each response into shared and gene-specific components and estimates them separately. The shared-response component is modeled as a cell-line-wide response scaled by a perturbation-specific coefficient. This coefficient is strongly conserved across cell lines. The residual gene-specific component--which is moderately conserved across cell lines--recovers pathway-level programs. COMPASS outperforms scGPT, CPA, GEARS, GenePert, and SO_SCPLOWTATEC_SCPLOW in both response accuracy (de-biased Pearson delta 0.34 vs. [≤] 0.32) and perturbation discrimination (cosine PDS gain 0.23 vs. [≤] 0.08). These results recast perturbation prediction across cellular contexts as component-wise inference, with each component estimated from the evidence best suited to it.

bioinformatics↗

bioRxiv2026

PFOS aggravates atherosclerosis via Bacteroides caecimuris expansion-driven bile acid remodeling and subsequent intestinal FXR-TLR3 signaling cascade

BACKGROUNDPerfluorooctane sulfonate (PFOS) is a widely distributed persistent organic pollutant in the environment and has been associated with an increased risk of atherosclerosis. However, the underlying pathogenic mechanisms remain largely unclear. This study aimed to investigate the effects of PFOS on atherosclerosis and its associated gut-vascular axis. METHODSPseudo-germ-free mouse models and fecal microbiota transplantation (FMT) were used to determine the role of the gut microbiota in PFOS-induced atherosclerosis. Metagenomic sequencing was performed to characterize alterations in gut microbial composition following PFOS exposure, and targeted metabolomics was used to assess bile acid profiles in the ileum and plasma. Transcriptomic analysis of Bacteroides caecimuris (B.caecimuris) was conducted to explore the reasons for the increased abundance of B.caecimuris after PFOS exposure. In addition, intestinal transcriptomics and ChIP-qPCR were performed to validate transcriptional regulation within the FXR-TLR3 signaling axis. RESULTSAmong 127 participants with paired serum and fecal samples, including 82 patients undergoing coronary angiography with Gensini scores (GS score), fecal PFOS levels were significantly associated with lipid profiles and GS score, whereas serum PFOS showed no such association.Mechanistically, PFOS exposure promotes intestinal enrichment of B.caecimuris by upregulating its tolC gene, thereby enhancing efflux capacity.This microbial shift was accompanied by reduced levels of tauro-ursodeoxycholic acid (TUDCA) and aberrant activation of intestinal FXR signaling.Further analyses demonstrated that FXR activation upregulated TLR3 expression and promoted inflammatory responses and atherosclerosis progression via the TLR3-NF-{kappa}B signaling axis. Both intestinal epithelial-specific FXR deficiency (Fxr{Delta}IE) and TUDCA supplementation significantly suppressed pathway activation and alleviated disease phenotypes.Functional experiments identified TLR3 as a key downstream effector of FXR. Overexpression of TLR3 abolished the protective effects observed in Fxr{Delta}IE mice. Moreover, pharmacological inhibition of TLR3 using CU CPT-4a significantly improved established atherosclerotic lesions in vivo. CONCLUSIONSThis study identifies a gut microbiota-driven FXR-TLR3 signaling axis that mediates PFOS-induced atherosclerosis. These findings provide new mechanistic insights into environmentally induced cardiovascular disease and suggest potential targets for risk assessment and therapeutic intervention.

pathology↗

bioRxiv2026

Comprehensive Complete-Genome Analysis of Lactobacillaceae and Bifidobacteriaceae Reveals Strain-Specific Metabolic Interactions in Chinese Gut Microbiota

Bifidobacteriaceae and Lactobacillaceae are key probiotic families and widely used in food production, yet a comprehensive understanding of strain functions and their gut microbial interactions based on complete genomes remain understudied. Here we constructed a complete-genome dataset of 3,300 strains from these two families, including 1,151 newly isolated from China. Compared with draft assemblies, complete genomes substantially recovered a gene functional landscape encompassing stress tolerance, surface exopolysaccharide synthesis, nutrient utilization, and mobile genetic elements. Major species from both families exhibited a prevalence >60% in the Chinese population, far higher than that in US/Dutch cohorts. Notably, as a core probiotic species with remarkable genomic plasticity and gut-adaptive potential, Lactiplantibacillus plantarum stood out in our dataset for its enriched functional profile and was particularly abundant in the Chinese population. Moreover, compared with non-Chinese genomes, our isolates of key species displayed less metabolic complementarity and stronger competition with potentially pathogenic keystone species in the gut, thereby linking strain origin to enhanced probiotic potential and ecological fitness to benefit human gut health.

microbiology↗

bioRxiv2026

The abscopal effect of Combination IRE with anti-PD-1 achieves local ablation and systemic control of PDAC

Irreversible electroporation (IRE) has shown promise for treating pancreatic ductal adenocarcinoma (PDAC), but whether IRE can induce an abscopal effect is not established. We demonstrated that the combination of IRE and anti-PD-1 antibody could trigger robust abscopal effects in preclinical models of metastatic PDAC. Data from multiple in vivo models, RNA-seq, scRNA-seq, and spatial immunofluorescence provide compelling evidence that IRE induced mitochondrial dysfunction and cellular stress, which triggered activation of the cGAS-STING pathway and subsequent systemic antitumor effects. IRE also led to inflammatory response characterized by tumor infiltration of myeloid cells and their polarization toward M1 state, turning immunologically "cold" tumors into "hot" tumors. Moreover, the presence of T cell/B cell clusters in tumors from mice treated with IRE plus PD-1 and the lack of antitumor efficacy in B cell knockout mice bearing orthotopic murine PDAC tumors indicate that B cells play an important role in IRE-mediated systemic antitumor immunity. SignificanceThis study shows that IRE plus a checkpoint inhibitor represents a promising therapeutic strategy for PDAC and supports advancing this treatment toward clinical translation. Our data also support potential combination strategies with immunomodulatory agents that can recruit and reprogram B cells to support T cell activation and cytotoxic effector functions.

immunology↗

bioRxiv2026

FOXA1 preserves cell polarity and restrains lysosome biogenesis in non-small cell lung adenocarcinoma

BackgroundThis study investigates the role of the pioneer transcription factor FOXA1 as a master gene in sustaining epithelial cell polarization in early-stage lung adenocarcinoma. The partial loss of FOXA1 is explored to determine if it will affect plasticity and progression of lung adenocarcinoma. The study also addresses the transcriptional circuitry that links polarity defects to lysosome homeostasis. MethodsA multiomics approach was used to define the status of the chromatin in epithelial and mesenchymal states of A549 adenocarcinoma cells obtained with a newly synthetized TGF-{beta} receptor inhibitor or TGF-{beta} respectively. The study leveraged ATAC-seq, RNA sequencing, Cut&Tag sequencing of FOXA1 and histone marks profiling. The functional impact of FOXA1 was examined by partial silencing in vitro and by heterozygous FOXA1 deletion in a KrasG12D mouse model. Three-dimensional organoid culture, high-resolution electron microscopy, spatial transcriptomics and multiplex immunohistochemistry assessed carcinoma cell polarity, proliferation, the tumor microenvironment and organelle content. Group differences were evaluated with two-tailed t tests or one-way analysis of variance. ResultsFOXA1 binding and expression were highest in cells harboring an epithelial phenotype. In mouse KrasG12D LUAD tumors FOXA1 marked polarized, CDH1-positive cells; heterozygous loss diminished CDH1, disrupted apical-basal architecture, lowered organoid-forming efficiency and remodeled the immune microenvironment. Spatial transcriptomics and ultrastructural analyses showed that FOXA1-deficient carcinoma cells accumulated lysosomes, down-regulated vesicle fusion genes of the SNARE family and activated the lysosomal CLEAR gene network. FOXA1 occupied enhancers of lysosome-associated genes and competed with the transcription factor TFE3, thereby suppressing transcription of cathepsin B and cathepsin C and restricting lysosome biogenesis. ConclusionsFOXA1 is a central regulator that preserves epithelial cell polarity and limits lysosome formation in lung adenocarcinoma. Targeting the FOXA1-TFE3-lysosome axis may affect tumor plasticity and provide new therapeutic opportunities.

cancer biology↗

bioRxiv2026

STDrug enables spatially informed personalized drug repurposing from spatial transcriptomics

Drug repurposing offers a scalable route to accelerate therapeutic discovery, yet existing approaches based on single-cell RNA sequencing (scRNA-seq) often overlook spatial tissue context, limiting their ability to capture microenvironment-dependent drug responses. Here we present STDrug, a spatially informed computational framework that integrates spatial transcriptomics, graph-based modeling, and multimodal learning to enable patient-specific therapeutic prioritization. STDrug identifies and aligns disease and control spatial domains using graph convolutional networks and coherent point drift, and prioritizes candidate drugs through an integrative scoring scheme combining tumor-reversible gene signatures, perturbation-based reversal scores, and knowledge-guided gene weighting within a machine learning framework. By modeling spatial domain interactions alongside predicted drug efficacy and toxicity, STDrug generates robust patient-level drug scores. Across hepatocellular carcinoma and prostate cancer datasets, STDrug outperforms existing single-cell and spatial transcriptomics-based drug repurposing methods, achieving signficantly improved predictive accuracy (AUCs=0.81-0.82) across patients. Validation using large-scale electronic health records and in vitro assays further supports the translational relevance of top-ranked candidates. Taking together, STDrug establishes a generalizable framework for incorporating spatial omics into therapeutic discovery, advancing spatially informed and personalized drug repurposing.

bioinformatics↗

bioRxiv2026

Complete genome-derived metabolic interactions reveal impact of gut ecology on human health

Metabolic interactions govern gut microbiome assembly, yet functional rules remain obscured by genomic incompleteness and fragmentation. Here, we leverage 1,150 complete genomes to construct genome-scale metabolic models, demonstrating that draft genomes introduce systemic artifacts missing critical transport functions. We observe that metabolic interactions are intrinsically driven by genomic traits and niche specialization rather than random association. We stratifies strains into four ecological groups, including active players, resource predators, utilizers, and contributors, each of which exhibits distinct metabolite exchange/competition signatures. This functional architecture is strongly coupled to secondary metabolism. Applying this framework to inflammatory bowel disease revealed distinct temporal dynamics of ecological groups across disease subtypes, where group-specific dysbiosis predicted clinical phenotypes better than whole community profiles. Furthermore, integrating metabolic and co-occurrence networks to identify keystone for classifiers as features significantly improved disease diagnosis. Our study provides novel insights into gut metabolic interaction landscape, bridging the gap between genomic potential and clinical utility for precision microbiome therapeutics.

microbiology↗

bioRxiv2026

Complete Genomes of Cultivated Gut Bacteria Reveal Mobile Genetic Element-Driven Functional Diversity with Therapeutic Implications

Cultivated bacterial isolates are essential for elucidating gut microbiota functions, yet reliance on fragmented draft genomes and limited mobile genetic element (MGE) annotation has constrained high-resolution analyses. Here, we present the Cultivated Complete Genome Reference (CCGR), a comprehensive compendium of 1,150 fully circularized human gut bacterial genomes. Overcoming draft limitations, CCGR achieves chromosome-scale resolution and reveals distinct evolutionary strategies shaping gene topological organization in response to bacterial growth. Furthermore, we decode the dynamic landscape of MGEs, demonstrating that broad-host-range phages follow strict positional patterns by integrating at conserved chromosomal hotspots flanked by nutrient transporter loci. Importantly, we provide mechanistic in vivo evidence that accessory genomic elements drive strain-level functional heterogeneity. Specifically, the plasmid-encoded scrK gene in Levilactobacillus brevis involved in fructose catabolism is required to mitigate fructose-diet-exacerbated colitis. Collectively, CCGR establishes a framework linking chromosomal architecture and MGEs to bacterial evolution and host health, enabling precise, strain-resolved functional investigations.

microbiology↗

bioRxiv2026

Bacillus velezensis-derived muropeptide promotes growth of zebrafish via NOD2-mediated induction of IGF1 signaling

The role of gut microbiome in regulating vertebrate metabolism has been well-recognized. However, the effects of gut bacteria on growth have been less studied. Bacillus is a prevalent genus in the gut microbiota of human and animals. In this study, the effect of gut-derived Bacillus velezensis T23 on growth was investigated in zebrafish. B. velezensis T23 improved the growth of zebrafish and promoted IGF1 production in the liver and muscle, with a concomitant activation of the AKT/mTOR signaling pathway. The growth-promoting effect of B. velezensis T23 was not dependent on lipopeptides and polyketides. Cell wall peptidoglycan isolated from B. velezensis T23, as well as muramyl dipeptide (MDP), was sufficient to stimulate IGF1 signaling and growth. Further, the effect of B. velezensis T23 on growth and IGF1 production was abrogated in nod2-/- zebrafish, confirming that B. velezensis T23 promoted growth via MDP-NOD2 signaling. Gut transcriptomic analysis indicated that B. velezensis T23 promoted renewal and differentiation of intestinal cells, suggesting an involvement of gut-liver axis in the effect of B. velezensis T23 on systemic IGF1 production. Together, our results revealed an effect of gut Bacillus-derived muropeptide on growth via NOD2-IGF1 signaling, and provided novel mechanistic insights in the beneficial effect of Bacillus spp. as probiotics.

microbiology↗

bioRxiv2026

CEACAM5/6+ Tumor Cells and IL-1β+ Macrophages Drive Resistance to Chemo-immunotherapy in Gastric Cancer

Chemo-immunotherapy is a first-line treatment for advanced gastric cancer, yet response rates remain limited and resistance mechanisms are poorly defined. Here we generate a single-cell atlas of 542,121 cells from 35 patients treated with anti-PD-1 plus chemotherapy, profiling pre- and post-treatment tumors linked to clinical response. Integrating spatial transcriptomics, immunohistochemistry, and bulk RNA sequencing, we identify two temporally distinct resistance programs. Intrinsic resistance in pre-treatment non-responders is marked by enrichment of CEACAM5/6 tumor cells that form immune-excluded spatial niches characterized by macrophage recruitment and CD8 T-cell exhaustion. Acquired resistance in post-treatment non-responders is driven by expansion of IL-1{beta} macrophages, which induces coordinated NF-{kappa}B activation across tumor and stromal compartments, promoting PD-L1 upregulation, epithelial-mesenchymal transition, and chronic inflammation. These findings delineate an evolutionary trajectory of resistance and nominate CEACAM5/6 and IL-1{beta} as predictive biomarkers and therapeutic targets to improve anti-PD-1-based combination strategies.

cancer biology↗

bioRxiv2026

Co-evolution of Oncogenic KRAS Signaling and LILRBhigh Macrophages Drives Pancreatic Cancer Recurrence

Pancreatic ductal adenocarcinoma (PDAC) frequently recurs after surgical resection, indicating that residual disease is sustained by coordinated tumor-microenvironment interactions. To define the biological basis of recurrence, we leverage large-scale clinical data from 2,710 patients, deeply characterized multi-omics profiling (whole-exome, bulk RNA, and single-nucleus sequencing) of 36 matched primary and locally recurrent PDACs, an in-house multiplex spatial imaging cohort of 190 patients, and extensive public datasets. Recurrent tumors were characterized by increased KRAS mutant allele dosage and reinforced KRAS signaling, accompanied by expansion of basal-like malignant cell states. In parallel, we identified an immunosuppressive macrophage population marked by high LILRB expression that spatially co-localized with KRAS-activated tumor cells. Functional studies showed that LILRB4+ macrophages enhanced tumor cell plasticity and progression, whereas inhibition of macrophage LILRB4 suppressed these phenotypes. Notably, a first-in-class human anti-LILRB4 antibody reduced macrophage-driven tumor traits, and dual targeting of KRAS signaling and LILRB4 achieved superior tumor control in macrophage-containing mouse models. These findings reveal a co-evolved tumor-immune niche underlying PDAC recurrence and nominate the KRAS-LILRB4 axis as a therapeutic vulnerability.

cancer biology↗

bioRxiv2026

Epigenomic profiling of cerebrospinal fluid cells identifies immune regulatory alterations and implicates protocadherins in multiple sclerosis

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS), where DNA methylation may play a role by connecting genetic and environmental risk factors. We performed whole-genome DNA methylation profiling of cerebrospinal fluid (CSF) cells from relapsing-remitting MS patients and matched controls, identifying 2,710 differentially methylated positions (DMPs) and 4,330 regions (DMRs). These changes were enriched in immune signaling, adhesion and migration processes, and were accompanied by corresponding RNA expression changes. MS-associated methylation changes enriched in the cohesin chromatin regulation pathway mapped to enhancers of T helper 17 (Th17) cells, whereas in other T cell types they were mapping to bivalent enhancers and repressed chromatin. Notably, this pathway comprised multiple Protocadherin (PCDH) genes, typically expressed in neuronal cells, that displayed consistent methylation and expression changes in CSF cells. Expression of shared intracellular domain of PCDH{gamma} cluster proteins was confirmed in peripheral blood T cells by flow cytometry as well as expression of PCDH{gamma} cluster genes in memory CD4+ T cell subsets. Moreover, co-expression analysis suggests a role of PCDH genes in aryl hydrocarbon receptor (AHR) signaling. In summary, DNA methylation changes in CSF resident cells reflect dysregulated T cell activation and migration in MS and suggest a novel role of protocadherin molecules in MS pathogenesis.

immunology↗

bioRxiv2026

NRF2 pathway activation and SPP1⁺TREM2⁺ macrophages drive chemoradiotherapy resistance in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is among the most aggressive cancers, with low rates of durable response to chemoradiotherapy and limited therapeutic options for relapsed disease. To uncover mechanisms of treatment resistance and relapse, we performed comprehensive multi-omics profiling of >100 pre-treatment and post-relapse ESCC tumors from a prospective clinical trial (NCT04694391), integrating whole-exome/genome sequencing, bulk RNA-sequencing, single-cell RNA sequencing, and spatial transcriptomics. We identify somatic alterations in NFE2L2/KEAP1 in nearly 40% of relapsed patients, which are associated with upregulation of NRF2 signaling targets in resistant tumors and cell line models. At single-cell and spatial resolution, relapsed tumors are enriched for NRF2-activated epithelial cells that physically co-localize with immunosuppressive SPP1TREM2 macrophages. This co-localization suggests a synergistic interaction between NRF2-driven tumor programs and macrophage-mediated immune suppression that promotes relapse after chemoradiotherapy. Our findings nominate NFE2L2/KEAP1 mutations as predictive biomarkers for patient stratification and highlight therapeutic targeting of NRF2 signaling and SPP1TREM2 macrophages as rational strategies to overcome resistance in ESCC.

cancer biology↗

bioRxiv2026

Elucidating Odorant Masking Effects in Food Matrices Through Olfactory Receptor-Based Profiling

Dynamic interactions among aroma compounds, especially odorant masking, constitute a key determinant of the intricate flavor profiles of thermally processed foods. However, the molecular and receptor-level mechanisms governing mutual odor suppression remain largely unclear. This study investigated the reciprocal sensory masking between 2,3,5-trimethylpyrazine and L-menthol via systematic sensory evaluation. Olfactory receptor screening identified OR5K1 as the responsive receptor for 2,3,5-trimethylpyrazine (EC50 = 27.67 {+/-} 2.02 mol/L) and OR2W1 as the functional receptor for L-menthol (EC50 = 22.69 {+/-} 3.85 mol/L). Consistently, quantitative cellular response assays further validated that 2,3,5-trimethylpyrazine and L-menthol exert mutual inhibitory effects on their respective receptors, as evidenced by the significant inhibition of receptor signaling. Moreover, molecular modeling predicted that 2,3,5-trimethylpyrazine and L-menthol competitively occupy the same orthosteric pocket via analogous binding conformations. These results provide novel receptor-level insights into odorant inhibitory effects, connecting sensory perception to molecular recognition, and deepen mechanistic understanding of flavor perception.

cell biology↗