Biology subjects

Zhou, L.

Publications and source records attributed to Zhou, L..

At least 127 records · Page 7Linked to original sources

bioRxiv2024

Epithelial heme oxygenase-1 enhances colonic tumorigenesis by inhibiting ferroptosis

Induction of heme oxygenase-1 (HO-1/Hmox1) is broadly considered cytoprotective, but the role of colonic epithelial HO-1 in colitis-associated tumorigenesis is poorly defined. HO-1 catabolizes heme, releasing ferrous iron, a key driver of oxidative stress and lipid peroxidation. We observed that colonic epithelial HO-1 is induced during colitis and tumorigenesis. We also found that HO-1 is upregulated in ferroptosis-inducing conditions in murine and human colonic epithelial organoids, and correlated with lipid peroxidation and ferroptosis markers in colonic tumors. In colonic epithelial organoids exposed to heme, deletion of Hmox1 amplified a compensatory oxidative stress and detoxification transcriptional program, likely reflecting unresolved oxidative and non-oxidative toxicity from heme. In vivo, epithelial HO-1 deficient mice developed significantly fewer and smaller tumors compared to littermate controls in a colitis-associated tumorigenesis model, despite similar inflammatory injury. Tumors from knockout mice exhibited reduced iron levels, decreased lipid peroxidation, lower oxidative DNA damage, and decreased proliferation. Single-cell RNA sequencing of tumor epithelial cells revealed a shift from a proliferative to a stress-adaptive program with loss of HO-1. These findings identify epithelial HO-1 as a context-dependent regulator of tumorigenesis: protective against acute heme toxicity, but promoting iron-dependent oxidative damage and proliferation in the setting of chronic inflammation.

cancer biology↗

bioRxiv2024

Heterogeneous hybrid immunity against Omicron variant JN.1 at 11 months following breakthrough infection

A highly transmissible SARS-CoV-2 variant JN.1 is rapidly spreading throughout the nation, becoming the predominant strain in China and worldwide. However, the current immunity against the circulating JN.1 at population level has yet to be fully evaluated. We recruited representative cohorts with stratified age groups and diverse combinations of vaccination and/or infection in recent months, and promptly assessed humoral immunity for these subjects predominantly exhibiting hybrid immunity. We report that at 11 months following BA.5-wave breakthrough infection (BTI), these vaccinated individuals generally showed above-the-threshold yet low level of neutralizing activity against JN.1, with slightly greater potency observed in children and adolescents compared to adults and seniors. Meanwhile, XBB/EG.5-wave reinfection post-BTI significantly boosted the neutralizing antibodies against Omicron variants, including JN.1 in both adults (13.4-fold increase) and seniors (24.9-fold increase). To better understand respiratory mucosal protection against JN.1 over an extended period of months post-BTI, we profiled the humoral immunity in bronchoalveolar lavage samples obtained from vaccinated subjects with or without BTI, and revealed increased potency of neutralizing activity against the BA.5 and JN.1 variants in the respiratory mucosa through natural infection. Notably, at 11 months post-BTI, memory B cell responses against prototype and JN.1 were detectable in both blood and respiratory mucosa, displaying distinct memory features in the circulation and airway compartments. XBB/EG.5-wave reinfection drove the expansion of JN.1-specific B cells, along with the back-boosting of B cells responding to the ancestral viral strain, suggesting the involvement of immune imprinting. Together, this study indicates heterogeneous hybrid immunity over 11 months post-BTI, and underscores the vulnerability of individuals, particularly high-risk seniors, to JN.1 breakthrough infection. An additional booster with XBB-containing vaccine may greatly alleviate the onward transmission of immune-evasive SARS-CoV-2 variants.

immunology↗

bioRxiv2024

Gut microbes of the cecum versus the colon drive more severe lethality and multi-organ damage

An intestinal perforation or puncture leads to a high risk of sepsis-associated morbidity. A perforation initiates the transfer of the intestinal contents (ICs) to the peritoneal cavity, leading to abdominal infections and varying with different prognoses. However, the mechanisms associated with different perforations in the cecum and colon remain unknown. We sought to examine how different gut flora contribute to prognoses in different intestinal perforation sites. We compared the microbiome of the ICs in the cecum and colon in a fecal-induced peritonitis mouse model. The results showed that cecum ICs developed more severe sepsis than colon ICs, including a shorter median survival time, increased biochemical indicators, more pathological changes in multiple organs and overwhelmed systematic inflammation. Moreover, our results demonstrated that cecum ICs hold more bacterial burden in unit weight than colon ICs, and the microbial communities differed between the ICs from the cecum and colon. A more detailed comparison of the two microbiome groups showed that the abundance of potentially pathogenic bacteria increased in the cecum ICs. Our data suggest that the sepsis severity developed by perforation was associated with bacterial burden and increased abundance of potentially pathogenic bacteria in the cecum. Our findings first compared the differences in the lethality associated with the ICs of the cecum and colon, which pointed out that the site of perforation could help providers predict the severity of sepsis.

immunology↗

bioRxiv2024

Diaminopurine in Nonenzymatic RNA Template Copying

In the primordial RNA World, before the advent of ribozymes, nonenzymatic template copying would have been essential for the transmission of genetic information. However, the products of chemical copying with the canonical nucleotides are heavily biased towards the incorporation of G and C. Diaminopurine (D) can form a D:U base pair that is almost as strong as a G:C base pair. We therefore asked whether replacing A with D might lead to more efficient and less biased nonenzymatic template copying. As expected, primer extension substrates containing D bind to U in the template more tightly than substrates containing A. However, primer extension with D exhibited elevated reaction rates on a C template, leading to concerns about fidelity. To investigate the nature of the D:C mismatch, we solved the crystal structure of RNA duplexes containing D:C mismatches, and showed that D can form a wobble-type base pair with C. We then asked whether competition with G would decrease mismatched primer extension. We performed nonenzymatic primer extension with all four activated nucleotides on randomized RNA templates containing all four letters, and used deep sequencing to analyze the products. We found that the DUCG genetic system exhibited a more even product distribution and a lower mismatch frequency than the canonical AUCG system. Furthermore, primer extension is greatly reduced following all mismatches, including the D:C mismatch. Our study suggests that diaminopurine deserves further attention for its possible role in the RNA World, and as a potentially useful component of artificial nonenzymatic RNA replication systems.

biochemistry↗

bioRxiv2024

Development of an orthotopic medulloblastoma zebrafish model for rapid drug testing.

Medulloblastoma (MB) is one of the most common malignant brain tumors in children. Current preclinical in vivo model systems for MB have increased our understanding of molecular mechanisms regulating MB development; however, they may not be suitable for high-throughput screening efforts. We demonstrate here that transplantation of seven different MB cell lines or patient-derived cells into the blastula stage of zebrafish embryos leads to orthotopic tumor cell growth that can be observed within 24 hours after transplantation. Importantly, the homing of transplanted cells to the hindbrain region and the aggressiveness of tumor growth are enhanced by pre-culturing cells in a neural stem cell-like medium. The change in culture conditions rewires the transcriptome towards a more migratory and neuronal progenitor phenotype, including the expression of guidance molecules SEMA3A and EFNB1, both of which correlate with lower overall survival in MB patients. Furthermore, we highlight that the orthotopic zebrafish MB xenograft model has the potential to be used for high-throughput drug screening. Key pointsO_LIMedulloblastoma cells home to the hindbrain region in developing zebrafish embryos. C_LIO_LINeural stem cell culture conditions improve the homing capacity of MB tumor cells. C_LIO_LIMedulloblastoma-transplanted zebrafish embryos can be used as a high-throughput in vivo model for drug screening. C_LI Importance of the StudyOne of the challenges of accurately modeling medulloblastoma is the large heterogeneity in tumor characteristics. To accurately model this heterogeneous disease, patient-derived xenograft mouse models are currently the standard. However, such mouse models are labor intensive, time-consuming, and not suitable for high-throughput studies. Here, we describe a quick and straightforward zebrafish xenograft model that provides a promising alternative to these existing mouse models. We demonstrate that this model can be utilized to study tumor cell growth of several major medulloblastoma subgroups. More importantly, our model facilitates high-throughput drug testing, providing a scalable opportunity for in vivo drug screenings that will support the discovery of novel therapeutic compounds against medulloblastoma.

cancer biology↗

bioRxiv2024

Structure-based design of a soluble human cytomegalovirus glycoprotein B antigen stabilized in a prefusion-like conformation

Human cytomegalovirus (HCMV) glycoprotein B (gB) is a class III membrane fusion protein required for viral entry. HCMV vaccine candidates containing gB have demonstrated moderate clinical efficacy, but no HCMV vaccine has been FDA-approved. Here, we used structure-based design to identify and characterize amino acid substitutions that stabilize gB in its metastable prefusion conformation. One variant containing two engineered interprotomer disulfide bonds and two cavity-filling substitutions (gB-C7), displayed increased expression and thermostability. A 2.8 [A] resolution cryo-electron microscopy structure shows that gB-C7 adopts a prefusion-like conformation, revealing additional structural elements at the membrane-distal apex. Unlike previous observations for several class I viral fusion proteins, mice immunized with postfusion or prefusion-stabilized forms of soluble gB protein displayed similar neutralizing antibody titers, here specifically against an HCMV laboratory strain on fibroblasts. Collectively, these results identify initial strategies to stabilize class III viral fusion proteins and provide tools to probe gB-directed antibody responses. TeaserA structure-based design campaign leads to stabilization of the class III viral fusion protein from HCMV in a prefusion-like conformation.

molecular biology↗

bioRxiv2024

High-throughput neural stem cell-based drug screening identifies S6K1 inhibition as a selective vulnerability in SHH-medulloblastoma

BackgroundMedulloblastoma (MB) is one of the most common malignant brain tumors in children. Current treatments have increased overall survival but can lead to devastating side effects and late complications in survivors, emphasizing the need for new, improved targeted therapies that specifically eliminate tumor cells while sparing the normally developing brain. MethodsHere, we used a SHH-MB model based on a patient-derived neuroepithelial stem (NES) cell system for an unbiased high-throughput screen with a library of 172 compounds with known targets. Compounds were evaluated in both healthy neural stem cells and tumor cells derived from the same patient. Based on the difference of cell viability and drug sensitivity score between normal cells and tumor cells, hit compounds were selected and further validated in vitro and in vivo. ResultsWe identified PF4708671 (S6K1 inhibitor) as a potential agent that selectively targets Sonic Hedgehog (SHH) driven MB tumor cells while sparing neural stem cells and differentiated neurons. Subsequent validation studies confirmed that PF4708671 inhibited the growth of SHH-MB tumor cells both in vitro and in vivo, and that knockdown of S6K1 resulted in reduced tumor formation. ConclusionOverall, our results suggest that inhibition of S6K1 specifically affects tumor growth, whereas it has less effect on non-tumor cells. Our data also show that the NES cell platform can be used to identify potentially effective new therapies and targets for SHH-MB. Key pointsO_LIHigh-throughput screening system using the NES model identifies efficient compounds and targets against SHH-MB. C_LIO_LIS6K1 inhibition shows selectivity toward tumor cells while having less effect on normal neural stem cells and neurons. C_LI Importance of the studyCurrent treatment modalities for medulloblastoma have improved overall survival but also come with detrimental side effects for survivors. Therefore, novel treatment options need to be developed which will specifically target the tumor cells while sparing the healthy brain. In this study, we tested a library of compounds targeting commonly dysregulated oncogenic pathways on both normal neural stem cells and SHH-MB tumor cells derived from the same patients. Interestingly, we found that most compounds including commonly used targeted therapy such as PI3K or mTOR inhibition, albeit effective, affected tumor cells and normal cells similarly. However, inhibition of the downstream effector S6K1 preferentially targeted tumor cells both in vitro and in vivo. These results thus reveal potential targets for translational studies of novel therapies that specifically target medulloblastoma tumor cells.

cancer biology↗

bioRxiv2024

nanoBERT: A deep learning model for gene agnostic navigation of the nanobody mutational space

Nanobodies are a subclass of immunoglobulins, whose binding site consists of only one peptide chain, bestowing favorable biophysical properties. Recently, the first nanobody therapy was approved, paving the way for further clinical applications of this antibody format. Further development of nanobody-based therapeutics could be streamlined by computational methods. One of such methods is infilling - positional prediction of biologically feasible mutations in nanobodies. Being able to identify possible positional substitutions based on sequence context, facilitates functional design of such molecules. Here we present nanoBERT, a nanobody-specific transformer to predict amino acids in a given position in a query sequence. We demonstrate the need to develop such machine-learning based protocol as opposed to gene-specific positional statistics since appropriate genetic reference is not available. We benchmark nanoBERT with respect to human-based language models and ESM-2, demonstrating the benefit for domain-specific language models. We also demonstrate the benefit of employing nanobody-specific predictions for fine-tuning on experimentally measured thermostability dataset. We hope that nanoBERT will help engineers in a range of predictive tasks for designing therapeutic nanobodies. Availabilityhttps://huggingface.co/NaturalAntibody/

bioinformatics↗

bioRxiv2024

Restricted intake of sulfur-containing amino acids reversed the hepatic injury induced by excess Desulfovibrio through gut-liver axis

Gut-liver axis has been a study focus for liver diseases. Diet is a key player in influencing the gut microbiota. However, the effect of different dietary patterns on gut microbiota and liver functions remains unclear. Here, we used mouse standard chow and purified diet to mimic two common human dietary patterns: healthy grain and planted-based diet and Western style diet, respectively and explored their impacts on the gut microbiota and liver. Gut microbiota experienced a great shift with notable increase in Desulfovibrio, gut bile acid (BA) concentration elevated significantly, and liver inflammation was observed in mice fed with the purified diet. Liver inflammation due to translocation of toxic lipopolysaccharides (LPS) and hydrophobic BAs from the damaged gut barrier was also observed in mice fed with the chow diet after receiving Desulfovibrio desulfuricans ATCC 29577 (DSV). Restricted intake of sulfur-containing amino acids reversed the liver injury due to excess Desulfovibrio through lowering the gut BA concentration and enhancing the hepatic antioxidant and detoxifying ability. Ex vivo fermentation of human fecal microbiota with primary BAs also demonstrated that DSV enhanced production of secondary BAs. Germ-free mice had higher concentration of both conjugated and unconjugated primary BAs in their gut after receiving DSV.

microbiology↗

bioRxiv2024

The ESCRT protein CHMP5 promotes T cell leukemia by controlling BRD4-p300-dependent transcription

Oncogene activity rewires cellular transcription, creating new transcription networks to which cancer cells become addicted, by mechanisms that are still poorly understood. Using human and mouse models of T cell acute lymphoblastic leukemia (T-ALL), we identify an essential nuclear role for CHMP5, a cytoplasmic endosomal sorting complex required for transport (ESCRT) protein, in establishing and maintaining the T-ALL transcriptional program. Nuclear CHMP5 promoted the T-ALL gene program by augmenting recruitment of the co-activator BRD4 by the histone acetyl transferase p300 selectively at enhancers and super-enhancers, an interaction that potentiated H3K27 acetylation at these regulatory enhancers. Consequently, loss of CHMP5 diminished BRD4 occupancy at enhancers and super-enhancers and impaired RNA polymerase II pause release, which resulted in downregulation of key T-ALL genes, notably MYC. Reinforcing its importance in T-ALL pathogenesis, CHMP5 deficiency mitigated chemoresistance in human T-ALL cells and abrogated T-ALL induction by oncogenic NOTCH1 in vivo. Thus, the ESCRT protein CHMP5 is an essential positive regulator of the transcriptional machinery promoting T-ALL disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/577409v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@191e10dorg.highwire.dtl.DTLVardef@4e5093org.highwire.dtl.DTLVardef@18c0a08org.highwire.dtl.DTLVardef@e6a887_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIIdentification of a nuclear role for the cytosolic ESCRT protein CHMP5 in transcription C_LIO_LICHMP5 mediates BRD4-dependent Pol II pause release and transcription of T-ALL genes C_LIO_LIP300-BRD4 induced enhancer and super-enhancer H3K27 acetylation requires CHMP5 C_LIO_LICHMP5 depletion mitigates chemoresistance and abrogates T-ALL initiation in vivo C_LI

cancer biology↗

bioRxiv2024

Computation-aided Design of Rod-Shaped Janus Base Nanopieces for Improved Tissue Penetration and Therapeutics Delivery

Despite the development of various drug delivery technologies, there remains a significant need for vehicles that can improve targeting and biodistribution in "hard-to-penetrate" tissues. Some solid tumors, for example, are particularly challenging to penetrate due to their dense extracellular matrix (ECM). In this study, we have formulated a new family of rod-shaped delivery vehicles named Janus base nanopieces (Rod JBNps), which are more slender than conventional spherical nanoparticles, such as lipid nanoparticles (LNPs). These JBNp nanorods are formed by bundles of DNA-inspired Janus base nanotubes (JBNts) with intercalated delivery cargoes. To develop this novel family of delivery vehicles, we employed a computation-aided design (CAD) methodology that includes molecular dynamics and response surface methodology. This approach precisely and efficiently guides experimental designs. Using an ovarian cancer model, we demonstrated that JBNps markedly improve penetration into the dense ECM of solid tumors, leading to better treatment outcomes compared to FDA-approved spherical LNP delivery. This study not only successfully developed a rod-shaped delivery vehicle for improved tissue penetration but also established a CAD methodology to effectively guide material design.

bioengineering↗

bioRxiv2024

Constraints on the Emergence of RNA through Non-Templated Primer Extension with Mixtures of Potentially Prebiotic Nucleotides

The emergence of RNA on the early Earth is likely to have been influenced by a series of chemical and physical processes that acted to filter out various alternative nucleic acids. For example, UV photostability is thought to have favored the survival of the canonical nucleotides. In a recent proposal for the prebiotic synthesis of the building blocks of RNA, ribonucleotides share a common pathway with arabino- and threo-nucleotides. We have therefore investigated non-templated primer extension with 2-aminoimidazole-activated forms of these alternative nucleotides to see if the synthesis of the first oligonucleotides might have been biased in favor of RNA. We show that non-templated primer extension occurs predominantly through 5'-5' imidazolium bridged dinucleotides, echoing the mechanism of template-directed primer extension. Ribo- and arabino-nucleotides exhibited comparable rates and yields of non-templated primer extension, whereas threo-nucleotides showed lower reactivity. Competition experiments with mixtures of nucleotides confirmed the bias against the incorporation of threo-nucleotides into oligonucleotides. This bias, coupled with selective prebiotic synthesis and templated copying favoring ribonucleotides, provides a plausible model for the exclusion of threo-nucleotides from primordial oligonucleotides. In contrast, the exclusion of arabino-nucleotides may have resulted primarily from biases in synthesis and in template-directed primer extension.

biochemistry↗

bioRxiv2024

Shared Transcriptomic Signatures of Inflammaging Among Diverse Strains of Drosophila melanogaster

BackgroundA prominent hallmark of aging is inflammaging--the increased expression of innate immune genes without identifiable infection. Model organisms with shorter lifespans, such as the fruit fly, provide an essential platform for probing the mechanisms of inflammaging. Multiple groups have reported that, like mammalian models, old flies have significantly higher levels of expression of anti-microbial peptide genes. However, whether some of these genes--or any others--can serve as reliable markers for assessing and comparing inflammaging in different strains remains unclear. Methods and ResultsWe compared RNA-Seq datasets generated by different groups. Although the fly strains used in these studies differ significantly, we found that they share a core group of genes with strong aging-associated expression. In addition to anti-microbial peptide genes, we identified other genes that have prominently increased expression in old flies, especially SPH93. We further showed that machine learning models can be used to predict the "inflammatory age" of the fruit fly. ConclusionA core group of genes may serve as markers for studying inflammaging in Drosophila. RNA-Seq profiles, in combination with machine-learning models, can be applied to measure the acceleration or deceleration of inflammaging.

immunology↗

bioRxiv2024

CellDemux: coherent genetic demultiplexing in single-cell and single-nuclei experiments.

Multiplexed single-cell experiment designs are superior in terms of reduced batch effects, increased cost-effectiveness, throughput and statistical power. However, current computational strategies using genetics to demultiplex single-cell (sc) libraries are limited when applied to single-nuclei (sn) sequencing data (e.g., snATAC-seq and snMultiome). Here, we present CellDemux: a computational framework for genetic demultiplexing within and across data modalities, including single-cell, single-nuclei and paired snMultiome measurements. CellDemux uses a consensus approach, leveraging modality-specific tools to robustly identify non-empty oil droplets and singlets, which are subsequently demultiplexed to donors. Notable, CellDemux demonstrates good performance in demultiplexing snMultiome data and is generalizable to single modalities, i.e. snATAC-seq and sc/snRNA-seq libraries. We benchmark CellDemux on 187 genetically multiplexed libraries from 800 samples (scRNA-seq, snATAC-seq, CITE-seq and snMultiome), confidently identifying and assigning cells to 88% of donors. In paired snMultiome libraries, CellDemux achieves consistent demultiplexing across data modalities. Moreover, analysis of 38 snATAC libraries from 149 samples shows that CellDemux retains more genetically demultiplexed nuclei for downstream analyses compared to existing methods. In summary, CellDemux is a modular and robust framework that deconvolves donors from genetically multiplexed single-cell and single-nuclei RNA/ATAC/Multiome libraries.

genomics↗

bioRxiv2024

Single-cell RNA sequencing reveals recruitment of the M2-like CCL8high macrophages in Lewis lung carcinoma-bearing mice following hypofractionated radiotherapy

Tumor-associated macrophages (TAMs) are a crucial factor in reprogramming the tumor microenvironment following radiotherapy. The mechanisms underlying this process remain to be elucidated. Here, we seek to investigate the effects of hypofractionated radiotherapy on macrophages dynamics in a subcutaneous Lewis lung carcinoma murine model. Utilizing single-cell RNA sequencing, we identified a distinct M2-like population of macrophages with high Ccl8 expression level post-hypofractionated radiotherapy. Remarkbly, hypofractionated radiotherapy promoted CCL8high macrophages infiltration and reprogrammed them by upregulating immunosuppressive genes and downregulating antigen-presenting genes, leading to an immunosuppressive tumor microenvironment. Further, we demonstrated that hypofractionated radiotherapy amplified the CCL signaling pathway, enhancing the pro-tumorigenic functions of CCL8high macrophages and promoting macrophages recruitment. The combination therapy of hypofractionated radiotherapy with the CCL signal inhibitor Bindarit was effective in reducing M2 macrophages infiltration and extending the duration of local tumor control. This research highlights the potential of targeting TAMs and introduces a novel combination to improve the efficacy of hypofractionated radiotherapy.

immunology↗

bioRxiv2024

Neuronal polyunsaturated fatty acids are protective in FTD/ALS

We report a conserved transcriptomic signature of reduced fatty acid and lipid metabolism gene expression in human post-mortem ALS spinal cord and a Drosophila model of the most common genetic cause of FTD/ALS, a repeat expansion in C9orf72. To investigate lipid alterations, we performed lipidomics on C9FTD/ALS iPSC-neurons and post-mortem FTLD brain tissue. This revealed a common and specific reduction in phospholipid species containing polyunsaturated fatty acids (PUFAs). To determine whether this PUFA deficit contributes to neurodegeneration, we fed C9FTD/ALS flies PUFAs, which yielded a modest increase in survival. However, increasing PUFA levels specifically in neurons of the C9orf72 flies, by overexpressing fatty acid desaturase enzymes, led to a substantial extension of lifespan. Neuronal overexpression of fatty acid desaturases also suppressed stressor induced neuronal death in C9FTD/ALS patient iPSC-neurons. These data implicate neuronal fatty acid saturation in the pathogenesis of FTD/ALS and suggest that interventions to increase PUFA levels specifically within neurons will be beneficial.

neuroscience↗

bioRxiv2024

Inhibition of Alpha Interferon-Induced miR-873 Negatively Affects the Hepatitis B Virus Expression

BackgroundAlpha interferon (IFN-)-based therapy can effectively treat chronic hepatitis B virus (HBV) infection, which remains a serious public health problem. This study aims to identify the potential biomarker of IFN treatment and investigate the effects of miR-873 on chronic hepatitis B (CHB). MethodsWe utilized the random forest to screen core differentially expressed miRNAs (DEmiRNAs) based on the miRNA (GSE29911) dataset. DEmiRNAs expressions were determined in clinical samples from CHB patients and normal controls. HBV-transfected hepatoma cell lines were constructed for vitro study. Quantitative real-time reverse transcription PCR (RT-qPCR) was used to determine miRNA mRNA expressions. ELISA assays were used to detect the secretion levels of HBsAg and HBeAg. ResultsBoruta feature selection revealed miR-873 hinting at a predictive marker for IFN response. MiR-873 was significantly up-regulated in the CHB patients, as compared with normal controls (P<0.001). Increased expression of miR-873 was also found in HBV-infected cells (P<0.001). With IFN- treatment, miR-873 was significantly down-regulated in HBV-infected Huh-7 and HepG-NTCP cells (P<0.05). IFN- treatment and miR-873 inhibitor significantly reduced HBsAg and HBeAg level (P<0.05). The inhibitory effect was enhanced by blocking the IFN--induced miR-873 downregulation by inhibitor transfection (P<0.05). In miR-873 mimic-treated cells, the inhibitory effect was greatly supressed by blocking the IFN--induced miR-873 downregulation by mimic transfection (P< 0.01). ConclusionWe provide evidence that inhibition of miR-873 by IFN- enhances the antiviral effects of IFN-. Our study provides a potential strategy to enhance the anti-HBV effect of IFN- by inhibiting miR-873 expression.

molecular biology↗

bioRxiv2024

Target-aware Molecule Generation for Drug Design Using a Chemical Language Model

Generative drug design facilitates the creation of compounds effective against pathogenic target proteins. This opens up the potential to discover novel compounds within the vast chemical space and fosters the development of innovative therapeutic strategies. However, the practicality of generated molecules is often limited, as many designs focus on a narrow set of drug-related properties, failing to improve the success rate of subsequent drug discovery process. To overcome these challenges, we develop TamGen, a method that employs a GPT-like chemical language model and enables target-aware molecule generation and compound refinement. We demonstrate that the compounds generated by TamGen have improved molecular quality and viability. Additionally, we have integrated TamGen into a drug discovery pipeline and identified 7 compounds showing compelling inhibitory activity against the Tuberculosis ClpP protease, with the most effective compound exhibiting a half maximal inhibitory concentration (IC50) of 1.9 M. Our findings underscore the practical potential and real-world applicability of generative drug design approaches, paving the way for future advancements in the field.

biochemistry↗