Yong Huang

Objective: This study aimed to identify clinically relevant regulators of pancreatic ductal adenocarcinoma (PDAC), a disease characterized by stromal remodeling and immune suppression, and to define their links to malignant progression and microenvironmental reprogramming. Methods: We integrated multi-cohort bulk, single-cell, and spatial transcriptomic datasets and subsequently validated bulk differential expression and network analyses with machine learning-based prioritization in an independent combined cohort (TCGA-PAAD plus GSE62452). Single-cell mapping was used to assess cell-type specificity, positioning candidates along inferCNV- and pseudotime-defined malignant continua. In Visium sections, a DKK1-associated program score quantified intratumoral spatial heterogeneity and informed our analyses of ligand–receptor communication. Bulk immune deconvolution linked gene levels to immune infiltration patterns, and functional assays were used to test the impact of DKK1 knockdown on migration, proliferation, clonogenic growth, and apoptosis in PDAC cells. Results: Four reproducible tumor-associated genes—DKK1, COL10A1, SULF1, and SLC24A3—were prioritized and validated externally. DKK1 was predominantly expressed by epithelial tumor cells and tracked along a malignant progression continuum. Spatially, the DKK1 program localized to epithelial-dominant regions, revealed pronounced intratumoral heterogeneity, and highlighted epithelial–endothelial and endothelial–immune signaling in high-score areas. Immune deconvolution associated higher DKK1 expression with increased myeloid infiltration and reduced cytotoxic lymphocyte signatures. Functionally, DKK1 knockdown impaired migration, proliferation, and clonogenicity while increasing apoptosis. Conclusions: We demonstrate that DKK1 is an epithelial-derived regulator linked to malignant progression and tumor–stroma–immune remodeling, supporting its potential as a biomarker and therapeutic target in PDAC treatment, including rational combinations with stroma-modulating strategies and immunotherapy.

KasA and KasB are promising drug targets against Mycobacterium tuberculosis and infectious nontuberculous mycobacteria, while most lead compounds are in the preclinical development stage. Herein, a platensimycin (PTM) analogue library consisting of 340 members was first screened to identify 46 PTM thioethers with superior activity compared to that of PTM against Mycobacterium smegmatis. Next, 19 PTM thioethers were chosen and semisynthesized from PTM oxirane (7), together with seven PTM ether derivatives and 6-ido, 6-bromo-, and 6-thiocyanato PTM. Most of them showed stronger antimycobacterial activity than PTM. In particular, one thioether Ec42 exhibited superior antimycobacterial activity to INH in M. smegmatis-infected mouse model. Molecular docking analysis revealed that Ec42 may bind to the active sites of KasA and KasB. Our study revealed that these PTM derivatives significantly expand dual inhibitors for KasA and KasB, and suggest that late-stage functionalization of natural antibiotics targeting mycolic acid biosynthesis remains fruitful for antimycobacterial drug discovery.

Background: Dithiolopyrrolones (DTPs), such as holomycin and thiolutin, exhibit potent antibacterial activities. DTPs contain a disulfide within a unique bicyclic scaffold, which may chelate metal ions and disrupt metal-dependent cellular processes once the disulfide is reductively transformed to thiols. However, the contribution of the intrinsic redox mechanism of DTPs to their antibacterial activity remains unclear. Herein we used pyrroloformamide (Pyf) A, a DTP with a unique formyl substituent, as a prototype to study the antibacterial potential and mechanism against ESKAPE pathogens, in particular carbapenem-resistant Klebsiella pneumoniae (CRKP). Methods: The antibacterial and anti-biofilm activities of Pyf A were mainly assessed against clinical CRKP isolates. Propidium iodide staining, scanning electron microscopy, glutathione (GSH) quantification, and reactive oxygen species (ROS) analysis were utilized to infer its anti-CRKP mechanism. The synergistic antibacterial effects of Pyf A and AgNO₃ were evaluated through checkerboard and time-kill assays, as well as in vivo murine wound and catheter biofilm infection models. Results: Pyf A exhibited broad-spectrum antibacterial activity against ESKAPE pathogens with minimum inhibitory concentrations ranging from 0.25 to 4 μg/mL. It also showed potent anti-biofilm effects against CRKP. Pyf A disrupted the cell membranes of CRKP and markedly depleted intracellular GSH without triggering ROS accumulation. Pyf A and AgNO₃ showed synergistic anti-CRKP activities in vitro and in vivo, by disrupting both GSH- and thioredoxin-mediated redox homeostasis. Conclusions: Pyf A acts as a GSH-depleting agent and, when combined with AgNO₃, achieves dual-targeted disruption of bacterial thiol redox systems. This dual-targeting strategy enhances antibacterial efficacy of Pyf A and represents a promising therapeutic approach to combat CRKP infections.

Cancer cells rely on lipogenesis in addition to exogenous lipid uptake, and fatty acid synthase (FASN) is aberrantly overexpressed in myeloid leukemia. However, the precise role of FASN in leukemogenesis in vivo remains elusive. Here, we demonstrated that FASN is essential for leukemogenesis. Ablation of FASN impeded leukemic cell growth, survival, clonogenicity in vitro , and the leukemic burden in vivo . Conditional knockout of FASN barely affected hematopoiesis but significantly attenuated the leukemic progression of MLL-AF9 transplants. By screening a library of platensimycin derivatives, we identified compound MS-C19 as a potent FASN inhibitor. Pharmacological targeting of FASN by MS-C19 suppressed leukemic cell growth and clonogenicity in clinical AML blasts. Mechanistically, both MS-C19 treatment and FASN deficiency triggered the activation of lysosomal and inflammatory gene expression. Loss of FASN led to lysosomal membrane permeabilization and subsequent lysosome-associated cell death, but not lysosome biogenesis. We further identified that GRN , a lysosomal and neuroinflammatory gene, was potently transcribed by TFEB upon FASN loss. Depletion of GRN significantly reversed the inhibitory effects caused by FASN knockdown. Our work demonstrates that FASN is a therapeutic target for myeloid leukemia, and inactivation of FASN by the lead compound MS-C19 provides an alternative approach for leukemic intervention. Key Points: Genetic ablation of FASN induces apoptosis, impedes leukemia cell growth, and improves the survival of leukemic xenografts. Targeting FASN by the compound MS-C19, a derivative of the natural microbe antibiotic platensimycin, reduces the cell survival of leukemic cell lines, the clinical leukemic blasts, and MLL-AF9 transformed murine leukemic cells. FASN inhibition induces lysosome-dependent cell death that relies on Progranulin ( GRN ) expression.

Strain robustness and titer improvement are major challenges faced in the industrial development of natural products from Streptomyces. Tiancimycins (TNMs) produced by Streptomyces sp. CB03234 are promising anticancer payloads for antibody-drug conjugates, but further development is severely limited by the low titer of TNMs. Despite many efforts to generate various TNMs overproducers, the mechanisms underlying high TNMs production remain to be explored. Herein, genome resequencing and genomic comparisons of different TNMs overproducers were conducted to explore the unique genotypes in CB03234-GS26. Four target genes were selected for further bioinformatic analyses and genetic validations. The results indicated that the inactivation of histidine ammonia-lyase (HAL) showed the most significant effect by blocking the intracellular degradation of histidine to facilitate relevant enzymatic catalysis and thus improve the production of TNMs. Additionally, the potassium/proton antiporter (P/PA) was crucial for intracellular pH homeostasis, and its deficiency severely impaired the alkaline tolerance of the cells. Subsequent pan-genomic analysis suggested that HAL and P/PA are core enzymes that are highly conserved in Streptomyces. Therefore, HAL and P/PA represented novel targets to regulate secondary metabolism and enhance strain robustness and could become potential synthetic biological modules to facilitate development of natural products and strain improvement in Streptomyces.

Chalkophomycin is a novel chalkophore with antibiotic activities isolated from Streptomyces sp. CB00271, while its potential in studying cellular copper homeostasis makes it an important probe and drug lead. The constellation of N-hydroxylpyrrole, 2H-oxazoline, diazeniumdiolate, and methoxypyrrolinone functional groups into one compact molecular architecture capable of coordinating cupric ions draws interest to unprecedented enzymology responsible for chalkophomycin biosynthesis. To elucidate the biosynthetic machinery for chalkophomycin production, the chm biosynthetic gene cluster from S. sp. CB00271 was identified, and its involvement in chalkophomycin biosynthesis was confirmed by gene replacement. The chm cluster was localized to a ~31 kb DNA region, consisting of 19 open reading frames that encode five nonribosomal peptide synthetases (ChmHIJLO), one modular polyketide synthase (ChmP), six tailoring enzymes (ChmFGMNQR), two regulatory proteins (ChmAB), and four resistance proteins (ChmA′CDE). A model for chalkophomycin biosynthesis is proposed based on functional assignments from sequence analysis and structure modelling, and is further supported by analogy to over 100 chm-type gene clusters in public databases. Our studies thus set the stage to fully investigate chalkophomycin biosynthesis and to engineer chalkophomycin analogues through a synthetic biology approach.

Dynemicin A has been the sole prototypical anthraquinone-fused enediyne (AFE) explored since its discovery in 1989. This study investigates the distinct DNA binding and cleavage mechanisms of emerging AFEs, represented by tiancimycins and yangpumicins, along with semisynthetic analogues. Our findings reveal their potent cytotoxicity against various tumor cell lines, while 18-methoxy tiancimycin A treatment could significantly suppress breast tumor growth with minimal toxicity. One of the most potent AFEs, i.e., tiancimycin A, preferentially targets DNA sequences 5'-ATT, 5'-CTT, 5'-GAA, 5'-GAT, and 5'-TTA. Molecular dynamics simulations suggest that emerging AFEs intercalate deeper into AT-rich DNA base pairs compared to dynemicin A. Importantly, tiancimycin A may equilibrate between insertional and intercalative modes without deintercalation, enabling selective cleavage of T and A bases. This study underscores how subtle structural variations among AFEs significantly influence their DNA recognition and cleavage, facilitating future design of novel AFEs as potent and selective payloads for antibody-drug conjugates.

Chalkophomycin is a novel chalkophore with antibiotic activities isolated from Streptomyces sp. CB00271, while its potential in studying cellular copper homeostasis makes it an important probe and drug lead. The constellation of N -hydroxylpyrrole, 2 H -oxazoline, diazeniumdiolate, and methoxypyrrolinone functional groups into one compact molecular architecture capable to coordinate cupric ion draws interest to unprecedented enzymology responsible for chalkophomycin biosynthesis. To elucidate the biosynthetic machinery for chalkophomycin production, the chm biosynthetic gene cluster from S. sp. CB00271 was identified, and its involvement in chalkophomycin biosynthesis was confirmed by gene replacement. The chm cluster was localized to a ∼31 kb DNA region, consisting of 19 open reading frames that encode five non-ribosomal peptide synthetase (ChmHIJLO), one modular polyketide synthases (ChmP), six tailoring enzymes (ChmFGMNQR), two regulatory proteins (ChmAB), and four resistance proteins (ChmA′CDE). A model for chalkophomycin biosynthesis is proposed based on functional assignments from sequence analysis and structure modelling, and is further supported by analogy to over 100 chm -type gene clusters in public databases. Our studies thus set the stage to fully investigate chalkophomycin biosynthesis and to engineer chalkophomycin analogues through a synthetic biology approach.

The purpose of this study was to evaluate the efficacy of ethanol extracts from Torreya grandis seed (EST) as a functional food in hyperuricemia mice. We investigated EST by analyzing its chemical composition. Using a mouse model of hyperuricemia induced by potassium oxonate (PO), we evaluated the effects of EST on uric acid (UA) production, inflammation-related cytokines, and gut microbiota diversity. The primary constituents of EST consist of various flavonoids and phenolic compounds known for their antioxidant and anti-inflammatory properties in vitro. Notably, our findings demonstrate that EST significantly reduced UA levels in hyperuricemia mice by 71.9%, which is comparable to the effects observed with xanthine treatment. Moreover, EST exhibited an inhibitory effect on xanthine oxidase activity in mouse liver, with an IC₅₀ value of 20.90 μg/mL (36%). EST also provided protective effects to the mouse kidneys by modulating oxidative stress and inflammation in damaged tissues, while also enhancing UA excretion. Finally, EST influenced the composition of the intestinal microbiota, increasing the relative abundance of beneficial bacteria such as Akkermansia muciniphila, Corynebacterium parvum, Enterorhabdus, Muribaculaceae, Marvinbryantia, and Blautia. In summary, our research unveils additional functions of Torreya grandis and offers new insights into the future of managing hyperuricemia.