Biology subjects

Ni, A.

Publications and source records attributed to Ni, A..

6 recordsLinked to original sources

bioRxiv2026

Ex vivo glioblastoma migration phenotypes define clinical recurrence and tumor heterogeneity

Glioblastoma's pronounced migratory capacity underlies its diffuse invasion, presenting a formidable barrier to successful treatment. Ex vivo characterization of glioblastoma cells isolated from freshly resected clinical samples under physiologically relevant conditions revealed two distinct migratory phenotypes, Fast Migrating (FM) and Slow Migrating (SM). These phenotypes reflect distinct mechanosensitivity profiles and are associated with pharmacological responses that support the motor clutch model of cell migration. Analysis of genes associated with these phenotypes revealed a transcriptomic signature that closely associated with in vitro cell migration, histological invasion in patient specimens, and clinical survival. Single-nucleus RNA sequencing revealed that FM and SM cells coexist within a single glioblastoma, with FM cells enriched at the periphery and SM cells localized to the tumor core. Collectively, our study demonstrates the utility of ex vivo glioblastoma characterization, allowing decoding of tumor heterogeneity and clinical prognostication as well as providing a framework for deconvoluting the complex cancer phenotype.

cancer biology↗

bioRxiv2025

Screening and structural characterization of a nanobody targeting the thermostable green fluorescent protein

Nanobody-fluorescent protein pairs are powerful tools in imaging, protein purification, and structural biology studies. While thermostable GFP (TGP) offers improved characteristics over conventional GFP, nanobodies that specifically recognize TGP remain relatively limited. Here, we report the screening and identification of a synthetic nanobody, Sb32, that binds TGP with nanomolar affinity using the ribosome technique. The crystal structure of the Sb32-TGP complex, solved at 1.82 [A] resolution, revealed an unusual binding mode in which Complementarity Determining Region 2 (CDR2) provides the major contribution, rather than the typically dominant CDR3. Moreover, the interface is stabilized by an extensive hydration network, which compensates for relatively few direct contacts and may explain the fast association and dissociation kinetics observed for this complex. These findings expand the repertoire of TGP-specific nanobodies and highlight an alternative strategy by which nanobodies achieve high affinity. Sb32 provides a new reagent for TGP-based applications, with potential utility in membrane protein purification and structural studies.

biophysics↗

bioRxiv2024

Structure-Based Design of Covalent Nanobody Binders for a Thermostable Green Fluorescence Protein

Green fluorescence protein (GFP) lights up almost every aspects of life sciences. An ultra thermostable GFP (TGP), engineered from a coral GFP, offers potential advantages over traditional jellyfish-derived GFP due to its high stability. However, owing to its later discovery, TGP lacks the extensive toolsets available for GFP, such as heavy chain-only antibody binders known as nanobodies. In this study, we have structurally characterized TGP in complex with Sb92, a synthetic nanobody identified from a previous in vitro screening, revealing its precise three-dimensional epitope. This structural insight, alongside the previously characterized Sb44-TGP complex, have allowed us to rationally design disulfide bonds between antigen and antibody for tighter interactions. Using biochemical analyses, we identify two bridged complexes (TGP A18C-Sb44 V100C, TGP E118C-Sb92 S57C), with the TGP-Sb92 disulfide pair showing high resistance to reducing agents. Our study expands the toolkit available for TGP and should encourage its wider applications.

biochemistry↗

bioRxiv2024

Biomolecular condensates can function as inherent catalysts

We report the discovery that chemical reactions can be catalyzed by condensates formed by intrinsically disordered proteins (IDPs). The proteins themselves lack any catalytic activities. Catalytic functions of condensates emerge as a consequence of sequence-dependent mesoscale electrochemical microenvironments created by phase separation. Stimulated Raman spectroscopy suggests that the catalytic behaviors of condensates are attributable to the spatial variations of water activities across condensate interiors and interfaces. We show that condensates are capable of catalyzing diverse cellularly relevant hydrolysis reactions. Through sequence design, the electrochemical properties of condensates can be programmed to exert control over catalytic behaviors. Incorporation of synthetic condensates into live cells alters transcription profiles and enables the activation of gene circuits that depend on products of hydrolysis reactions catalyzed by condensates. Our discovery of suggests that condensates, depending on their composition-dependent electrochemical properties, can be "Condenzymes", which contribute unexpected emergent chemical functions in cells.

biophysics↗

bioRxiv2021

Combined oncolytic adenovirus carrying MnSOD and mK5 genes both regulated by survivin promoter has synergistic inhibitory effect on gastric cancer

Gastric cancer (GC) is one of the major causes of cancer related mortality. The use of oncolytic virus for cancer gene-virotherapy is a new approach for the treatment of human cancers. In this study, a novel Survivin promoter driven recombinant oncolytic adenovirus carrying mK5 or MnSOD gene was constructed, which was modified after deletion of E1B gene. Human plasminogen Kringle 5 mutant (mK5) and manganese superoxide dismutase (MnSOD) are both potential tumor suppressor genes. To construct Ad-Surp-mK5 and Ad-Surp-MnSOD oncolytic adenovirus, we hypothesized that the combination of the two viruses would enhance the therapeutic efficacy of GC as compared to the virus alone. The results of the in vitro experiments revealed that the combination of adenovirus carrying mK5 and MnSOD gene exhibited stronger cytotoxicity to GC cell lines as compared to the virus alone, Additionally, the virus could selectively kill cancer cells and human somatic cells. Cell staining, flow cytometry and western blot analysis showed that the combination of two adenovirus containing therapeutic genes could promote the apoptosis of cancer cells. In vivo experiments further verified that Ad-Surp-mK5 in combination with Ad-Surp-MnSOD exhibited significant inhibitory effect on the growth of GC tumor xenograft as compared to the virus alone, and no significant difference was observed in the body weight of treatment and the normal mice. In conclusion, the combination of our two newly constructed recombinant oncolytic adenovirus containing mK5 or MnSOD therapeutic genes could significantly inhibit gastric cancer growth by inducing apoptosis, suggestive of its potential for GC therapy.

cancer biology↗

bioRxiv2020

Acquisition of Oral Microbiota is Driven by Environment, Not Host Genetics

The human oral microbiota is acquired early in an organized pattern, but the factors driving this acquisition are not well understood. Microbial "heritability" could have far-reaching consequences for health, yet no studies have specifically examined the fidelity with which the oral microbiota are passed from parents to offspring. Some previous studies comparing monozygotic (MZ) and dizygotic (DZ) twins had suggested that host genetics has a role in shaping oral microbial communities, and also identified so called "heritable" taxa. However, these findings are likely to be confounded by shared environmental factors resulting from the well-established greater behavioral similarity among MZ twins. In addition, MZ and DZ twins share an equal portion of their parents genome, and so this model is not informative for studying direct parent to offspring transmission. To specifically examine the contribution of genetics to the fidelity of transmission of bacteria from parents to offspring, we used a novel study design comparing fraction of shared species and strains between our genetically related group consisting of children and their biological mothers, with that of children and their adoptive mothers, constituting our genetically unrelated group. Fifty-five biological and 50 adoptive mother-child pairs were recruited along with 23 biological fathers and 16 siblings. Subjects were carefully selected to ensure the two groups were matched on childs age. Three distinct habitats within the oral cavity: the saliva/soft tissue surface, supragingival biofilm, and subgingival biofilm, were sampled to comprehensively profile the oral microbiome. Our recently developed strategy for subspecies level characterization of bacterial communities by targeted sequencing of the ribosomal 16-23S intergenic spacer region (ISR) was utilized in the present study to track strain sharing between subjects, in addition to 16S rRNA gene sequencing for species analysis. Results showed that oral bacterial community profiles of adoptive and biological mother-child pairs were equally similar, indicating no effect of host genetics on the fidelity of transmission. This was consistent at both species and strain level resolutions, and across all three habitats sampled. We also found that all children more closely resembled their own mother as compared to unrelated women, suggesting that contact and shared environment were the major factors shaping the oral microbiota. Individual analysis of the most abundant species also did not detect any effect of host genetics on strain sharing between mother and child. Mother-child strain similarity increased with the age of the child, ruling out early effects that are lost over time. No effect on the fidelity of mother-child strain sharing from vaginal birth or breast feeding was seen. Analysis of extended families showed that fathers and mothers were equally similar to their children. Cohabitating couples showed even greater strain similarity than mother-child pairs, further supporting the role of age, contact and shared environment as determinants of microbial similarity. Based on these findings we suggest that the genetic effects on oral microbial acquisition observed in twin studies are more likely the result of confounding environmental factors based on greater behavioral similarity among MZ twins. Our findings suggest that these host mechanisms are universal to humans, since no effect of genetic relatedness on fidelity of microbial transmission could be detected. Instead, our findings point toward contact and shared environment being the driving factors of microbial transmission, with a unique combination of these factors ultimately shaping a highly personalized human oral microbiome.

microbiology↗