Biology subjects

Miao, T.

Publications and source records attributed to Miao, T..

10 recordsLinked to original sources

bioRxiv2026

Decoding antibody-antigen recognition: the BL8 language and its application in calibrating deep learning predictions

Antibodies are central to immunology and therapeutics, and understanding how they recognize antigens is essential to rational drug design. This recognition depends on the interplay of interface geometry, physicochemical interactions, sequence context, and complementarity-determining region (CDR) conformation. However, traditional analyses often oversimplify this complexity, which becomes particularly problematic when evaluating the massive and frequently overconfident structural hypotheses generated by modern deep learning models. Here, we introduce BL8, an interpretable, eight-view structural language that comprehensively parameterizes interfaces across topology, shape, interaction, CDR conformation, flexibility, interfacial area, amino-acid-pair composition, and sequence background. Using 15,396 experimental interface records from the Structural Antibody Database (SAbDab), we built a fixed reference atlas containing 1,498 discrete BL8 signatures. The atlas shows that natural interfaces occupy a diverse, long-tailed structural space in which similar geometric scaffolds can be associated with different chemical and sequence features. Furthermore, we projected 28,501 predicted complexes involving programmed death-ligand 1 (PD-L1), the SARS-CoV-2 receptor-binding domain (RBD), and programmed cell death protein 1 (PD-1), generated using AlphaFold 3 (AF3), Protenix-v2, and OpenDDE, into the reference space. Acting as a robust underlying calibration layer, BL8 successfully decoupled physical viability from native confidence illusions, revealing cross-target hallucinations and filtering out 15.3% to 20.1% of highly deceptive false-positive predictions. Crucially, by benchmarking distinct generative behaviors across models, it enabled the extraction of highly reliable, multi-model consensus out-of-distribution binding paradigms. Together, BL8 bridges foundational biophysics with large-scale computational predictions, providing an essential benchmarking framework for discovering novel mechanisms in the era of artificial intelligence.

immunology↗

bioRxiv2026

Endogenous nucleophilic scavengers of reactive acyl-species neutralize carbon stress

Aberrant protein acylation by reactive acyl species (RAS)--termed carbon stress--is a major driver of aging and metabolic disease. While enzymatic deacylases such as sirtuins counteract aberrant acylation, whether endogenous metabolites can directly neutralize RAS remains unclear. Here, we report that nucleophilic metabolites--taurine, spermidine, and ethanolamine--react with acyl-CoAs, preventing aberrant protein acylation and potentially extending lifespan. We demonstrate that spermidine scavenges acetyl-CoA within the catalytic pocket of p300, a histone acetyltransferase, and extends lifespan in Drosophila. Taurine supplementation in mice fed a high-fat diet promotes N-fatty acyl taurine formation, confirming in vivo scavenging of RAS. These findings identify endogenous nucleophilic metabolites as scavengers that neutralize carbon stress, with implications for combating aging and metabolic disease. SummaryProtein homeostasis is constantly challenged by reactive metabolic intermediates that drive aberrant post-translational modifications, contributing to aging and metabolic disease. While the antioxidant systems that neutralize reactive oxygen species (ROS) are well characterized, whether analogous defenses exist against reactive acyl species (RAS)--the metabolic drivers of non-enzymatic protein acylation, termed carbon stress--has remained unknown. Here we show that three abundant endogenous nucleophilic metabolites--taurine, spermidine, and ethanolamine--directly intercept reactive acyl-CoA species through nucleophilic attack, preventing aberrant protein acylation. We demonstrate that spermidine scavenges acetyl-CoA within the catalytic pocket of the histone acetyltransferase p300, effectively buffering p300-mediated hyperacetylation of muscle, cytosolic, and mitochondrial proteins and extending lifespan in a Drosophila model of p300-driven toxicity. In mice fed a high-fat diet, taurine supplementation promotes the formation of N-fatty acyl taurines, providing direct in vivo evidence for nucleophilic scavenging of diet-derived RAS. Our findings reveal a previously unrecognized metabolite-based defense system--parallel to classical antioxidant defenses against ROS--that neutralizes carbon stress, with broad implications for understanding the molecular mechanisms of aging and the long-observed but mechanistically unexplained health benefits of taurine and spermidine.

biochemistry↗

bioRxiv2025

Phage display-mediated immuno-PCR to detect low-abundance secreted proteins in Drosophila

Circulating hormones, that mediate communications across organs to maintain physiological balance, are commonly detected and quantified using enzyme-linked immunosorbent assays (ELISAs). However, while ELISA is well-suited for organisms where sample blood can be readily obtained, its application is considerably more challenging in smaller organisms, particularly Drosophila, which has gained widespread use in recent years for physiological studies. Here, we present sensitive phage display-mediated immuno-PCR (PD-iPCR) to detect Drosophila hemolymph proteins via two approaches: 1) by identifying high-affinity nanobodies through phage-display library screening and subsequent affinity maturation and 2) by generating a knock-in fly line producing secreted proteins tagged with tandem NanoTags composed of VHH05 and 127D01. Using these approaches, we successfully established PD-iPCR to detect insulin-binding ImpL2 protein in fly hemolymph. Notably, the tandem NanoTag-based sandwich PD-iPCR enabled highly sensitive detection of tagged antigens, allowing us to quantify elevated ImpL2 levels in the hemolymph of starved flies and those bearing Yki-induced gut tumors. Collectively, our results demonstrate that PD-iPCR enables detection of endogenous, low-abundance circulating hormones in Drosophila, providing a powerful tool for studying interorgan communication. Significance statementHormones and other secreted factors orchestrate organism-wide physiology, yet their routine quantification in Drosophila has been limited by the limited volume of hemolymph available for assays like enzyme-linked immunosorbent assay (ELISA). Here, we present phage display-mediated immuno-PCR (PD-iPCR) as a novel sensitive platform for quantifying secreted proteins in flies in vivo. Using ImpL2 as an example, we successfully detected nanomolar level of circulating ImpL2 and monitored its physiological changes during starvation and tumorigenesis using PD-iPCR. This approach can be readily expanded to multiplexed quantification of secreted proteins in vivo by leveraging the multiple available nanobodies and the vast collection of epitope-tagged Drosophila lines. This work opens the door to systematic endocrine phenotyping across developmental stages and diverse physiological conditions.

genetics↗

bioRxiv2025

Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer

Paraneoplastic syndromes arise when tumor-derived cytokines reprogram distant organs. Although mediators such as Interleukin-6 have been implicated, how these signals impair host organ function remains incompletely defined. Here, we identify a cytokine-lipid axis that drives hepatic autophagy dysfunction. Specifically, in Drosophila, the gut tumor-derived interleukin-like cytokine Upd3 induces the expression of the triglyceride lipase CG5SCC, which we named "cancer-associated lipid mobilizer (calm)", and the ceramide synthase schlank in the fat body. This upregulation rewires fat body lipid metabolism, resulting in an autophagic-flux blockade. Genetic reduction of either CG5SCC or schlank restores organelle homeostasis and mitigates paraneoplastic phenotypes. This mechanism is conserved in mammals: in mice, IL-6 upregulates the lipoprotein lipase Lpl and ceramide synthases which in turn trigger a hepatic autophagy-flux blockade; in humans, hepatic LPL and ceramide synthases expression correlates with poorer survival in hepatocellular carcinoma. Our findings position hepatic lipid metabolism rewiring, especially ceramide synthesis as a critical, conserved node coupling systemic inflammation to organelle dysfunction, and suggest this pathway as a possible therapeutic entry point for cancer-associated liver disorders.

genetics↗

bioRxiv2025

Renal Coenzyme A (CoA) Production Fuels Stem Cell Proliferation and Tumor Growth

Coenzyme A (CoA), derived from Vitamin B5 (VB5; also called pantothenate), is essential for lipid metabolism, energy production, and cell proliferation. While the intracellular functions of CoA are well-characterized, much less is known about its tissue-specific regulation and systemic physiological roles. Here, using Drosophila melanogaster, we uncover a gut-renal circuit in which dietary VB5 fuels CoA biosynthesis specifically in the Malpighian tubules (MTs, the fly kidney), non-autonomously impacting gut homeostasis. We show that, in the MTs, Myc boosts renal CoA production by directly upregulating the pantothenate kinase Fbl (human PANK1-3 ortholog) and downregulating CG5828, which we characterize as the functional ortholog of the metabolite phosphatase and CoA synthesis suppressor PANK4 (dPANK4). Elevated CoA biosynthesis enhances the mevalonate-isoprenoid pathway activity in the gut, promoting intestinal stem cell proliferation. We further demonstrate that renal CoA production is required for gut tumor growth in a fly model. Consistently, MYC and genes within the CoA-isoprenoid axis display strong association with clinical outcomes in human cancers. Together, our findings establish that Myc-driven CoA metabolism generates an inter-organ signal that couples VB5 availability to stem cell control and tumor growth, and identify the CoA-isoprenoid axis as a targetable metabolic vulnerability in cancer.

genetics↗

bioRxiv2025

Lipid metabolism of hepatocyte-like cells supports intestinal tumor growth by promoting tracheogenesis

Tumors reprogram lipid metabolism in distant tissues to support their growth. In adult Drosophila, gut tumors secrete the PDGF/VEGF-like factor Pvf1, which activates the TORC1-Hnf4 pathway in hepatocyte-like oenocytes. This drives production of very long-chain fatty acids and wax esters essential for tracheal growth around the tumor. Blocking Hnf4 or the elongase mElo in oenocytes strongly suppresses tracheogenesis, tumor progression, and cachexia-like organ wasting, while extending host lifespan. The same pathway also controls tracheal development in healthy flies. Lipoprotein receptor LpR2 depletion in oenocytes rescues the observed tumor induced tracheal tracheal remodeling. This tumor-host interaction is conserved: VEGF-A induces lipid metabolism genes in human hepatocytes, and lung tumor-bearing mice show elevated hepatic Hnf4 and Elovl7. The study reveals a non-autonomous role of the TORC1-Hnf4 axis in lipid-mediated tumor progression and identifies potential therapeutic targets for cancer-associated metabolic dysfunction.

cell biology↗

bioRxiv2025

Heterogeneous T cell response patterns within established clinical phases of Hepatitis B infection revealed through the rapid functional characterization of HBV-specific T cells in whole blood

Background & AimsThere is an unmet need for immunological biomarkers in chronic hepatitis B (CHB), where patient management relies on virological and biochemical markers despite the crucial role of virus-specific T cells in controlling viral replication and disease progression. To address this, we developed the HBV-cytokine release assay (HBV-CRA), a rapid, point-of-care test that measures multiple cytokines in whole blood after HBV-peptide stimulation. MethodsWe first assessed the assays sensitivity by spiking whole blood with engineered HBV-specific T cells. Next, we compared sensitivity and consistency of HBV-CRA to ex vivo IFN-{gamma} ELISpot assays. We then applied the assay in a cross-sectional study of 235 CHB patients and longitudinally in acute HBV patients during HBsAg sero-clearance. ResultsThe HBV-CRA detected T cell function in 80% of CHB cases and showed that elevated IL-2 and IFN-{gamma} levels after Core peptide stimulation were associated with HBsAg clearance. Importantly, unsupervised clustering identified distinct immune response patterns independent of established clinical and virological classifications. The assay also demonstrated the functional impact of NUC treatment on HBV-specific T cell responses. ConclusionsThe HBV-CRA is a rapid and easy-to-use assay that identifies immune profiles associated with HBsAg clearance and differentiates CHB patients based on antiviral T cell function. Its application in a large CHB cohort revealed that traditional disease phase classifications, based on viral and clinical parameters, cannot predict HBV-specific T cell profiles. The HBV-CRA has the potential to guide patient stratification for immunotherapeutic interventions.

immunology↗

bioRxiv2023

Ptth regulates lifespan through innate immunity pathway in Drosophila

The prothoracicotropic hormone (PTTH) is a well-known neuropeptide that regulates insect metamorphosis (the juvenile-to-adult transition) by inducing the biosynthesis of steroid hormones. However, the role of PTTH in adult physiology and longevity is largely unexplored. Here, we show that Ptth loss-of-function mutants are long-lived and exhibit increased resistance to oxidative stress in Drosophila. Intriguingly, we find that loss of Ptth blunt age-dependent upregulation of NF-{kappa}B signaling specifically in fly hepatocytes (oenocytes). We further show that oenocyte-specific overexpression of Relish/NF-{kappa}B blocks the lifespan extension of Ptth mutants, suggesting that PTTH regulates lifespan through oenocyte-specific NF-{kappa}B signaling. Surprisingly, adult-specific knockdown of Ptth did not prolong lifespan, indicating that PTTH controls longevity through developmental programs. Indeed, knockdown of PTTH receptor Torso in prothoracic gland (PG) during fly development prolongs lifespan. To uncover the developmental processes underlying PTTH-regulated lifespan, we perform a developmental transcriptomic analysis and identify an unexpected activation of NF-{kappa}B signaling in developing oenocytes during fly metamorphosis, which is blocked in Ptth mutants. Importantly, knockdown of Relish/NF-{kappa}B specifically in oenocytes during early pupal stages significantly prolongs the lifespan of adult flies. Thus, our findings uncover an unexpected role of PTTH in controlling adult lifespan through temporal and spatial activation of NF-{kappa}B signaling in developing hepatocytes and highlight the vital role of developmental NF-{kappa}B signaling in shaping adult physiology. Significance StatementDespite the strong link between animal development and adult lifespan, we know little about how developmental programs impact adult longevity, and when and where such programs are activated during development. Here, we demonstrate that loss of insect hormone PTTH prolongs lifespan and healthspan by repressing chronic inflammation in Drosophila. Intriguingly, we demonstrate that PTTH regulates adult lifespan through temporal and spatial activation of NF-{kappa}B signaling in developing hepatocytes during insect metamorphosis. These findings provide novel insights into the developmental programs that impact adult longevity.

physiology↗

bioRxiv2022

Acetyl-CoA mediated autoacetylation of fatty acid synthase in de novo lipogenesis

De novo lipogenesis (DNL) is a highly regulated metabolic process, which is known to be activated through transcriptional regulation of lipogenic genes, including fatty acid synthase (FASN). Unexpectedly, we find that the expression of FASN protein remains unchanged during Drosophila larval development when lipogenesis is hyperactive. Instead, acetylation modification of FASN is highly upregulated in fast-growing larvae. We further show that lysine K813 is highly acetylated in developing larvae, and its acetylation is required for upregulated FASN activity, body fat accumulation, and normal development. Intriguingly, K813 is rapidly autoacetylated by acetyl-CoA in a dosage-dependent manner, independent of known acetyltransferases. Furthermore, the autoacetylation of K813 is mediated by a conserved P-loop-like motif (N-xx-G-x-A). In summary, this work uncovers a novel role of acetyl-CoA-mediated autoacetylation of FASN in developmental lipogenesis and reveals a self-regulatory system that controls metabolic homeostasis by linking acetyl-CoA, lysine acetylation, and DNL. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/475252v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@db2042org.highwire.dtl.DTLVardef@22dde8org.highwire.dtl.DTLVardef@116b3a5org.highwire.dtl.DTLVardef@16c2dc9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAcetylation modification of FASN, but not protein expression, positively correlates with de novo lipogenesis during Drosophila larval development C_LIO_LISite-specific acetylation at K813 residue enhances FASN enzymatic activity C_LIO_LIK813 residue is autoacetylated by acetyl-CoA, independent of KATs C_LIO_LIA novel N-xx-G-x-A motif is required for autoacetylation of K813 C_LI

developmental biology↗

bioRxiv2019

Impaired peroxisomal import in Drosophila hepatocyte-like cells induces cardiac dysfunction through the pro-inflammatory cytokine Upd3

Age is a major risk factor for cardiovascular diseases. Currently, the non-autonomous regulation of age-related cardiac dysfunction is poorly understood. In the present study, we discover that age-dependent induction of cytokine unpaired 3 (Upd3) in Drosophila oenocytes (hepatocyte-like cells), due to a dampened peroxisomal import function, is the primary non-autonomous mechanism for elevated arrhythmicity in old hearts. We show that Upd3 is significantly up-regulated (52-fold) in aged oenocytes. Oenocyte-specific knockdown of Upd3 is sufficient to block aging-induced cardiac arrhythmia. We further show that the age-dependent induction of Upd3 is triggered by impaired peroxisomal import and elevated JNK signaling in aged oenocytes. Intriguingly, oenocyte-specific over-expression of Pex5, the key peroxisomal import receptor, restores peroxisomal import, blocks age-related Upd3 induction, and alleviates aging- and paraquat-induced cardiac arrhythmicity. Thus, our studies identify an important role of the evolutionarily conserved pro-inflammatory cytokine signaling and hepatocyte-specific peroxisomal import in mediating non-autonomous regulation of cardiac aging.

physiology↗