Biomedical subjects

Xiaoyue Zhu

Publications and source records attributed to Xiaoyue Zhu.

11 recordsLinked to original sources

PubMed2026

Pan-cancer single-cell atlas of immunotherapy response identifies ZNF385A as a regulator of immune evasion in small cell lung cancer.

Although immune checkpoint inhibitors (ICIs) have revolutionized the treatment landscape of solid tumors, response rates in patients with small cell lung cancer (SCLC) remain limited, and acquired resistance is highly prevalent. The underlying mechanisms of this immunotherapy resistance remain to be fully elucidated. Clinically, SCLC typically manifests as an "immune-cold" tumor, characterized by a low abundance of CD8+ T cell infiltration and the rare formation of tertiary lymphoid structures (TLS). While DNA damage repair (DDR) is closely linked to innate immune responses, how DDR networks orchestrate the SCLC immune microenvironment remains obscure. In this study, we integrated single-cell transcriptomic data (comprising 344,447 high-quality cells) from six cancer types (BCC, CRC, HCC, HNSCC, iCCA, and SCLC). Our comparative analysis revealed a fundamental depletion of TLS-associated cellular subpopulations (e.g., CXCL13+ CD8+ T cells, HLA-DRB5+ B cells, and CXCL9+ dendritic cells) in SCLC, which was significantly correlated with aberrant DDR activity. Through high-dimensional weighted gene co-expression network analysis (hdWGCNA), we identified ZNF385A as the core hub gene within the DDR-associated module. ZNF385A is highly expressed in SCLC and is associated with poorer prognosis. In vitro, ZNF385A depletion suppressed SCLC cell proliferation and induced apoptosis, accompanied by R-loop accumulation and activation of cGAS-STING signaling, indicating a potential link between ZNF385A, genomic stability and tumor-intrinsic innate immune signaling. Collectively, these findings identify ZNF385A as a potential regulator associated with TLS deficiency and immune evasion in SCLC.

Immunotherapy resistance↗

PubMed2026

R-loops and D-loops: a delicate balance in genomic stability and instability.

R-loops and D-loops are three-stranded nucleic acid structures that have emerged as central regulators of genome stability, gene expression, and DNA metabolism. R-loops form co-transcriptionally or post-transcriptionally when nascent RNA re-anneals with the template DNA strand, generating an RNA: DNA hybrid that displaces the non-template strand into a single-stranded state. These structures are enriched at CpG island promoters, transcription termination sites, and immunoglobulin class-switch regions, where they coordinate transcription regulation, chromatin remodeling, and DNA damage signaling. D-loops are formed when a single-stranded DNA segment pairs with one strand of a duplex and displaces the other, arising through context-dependent mechanisms that include RAD51- or DMC1-mediated strand invasion in homologous recombination, shelterin-assisted invasion at telomeres, and replication-coupled strand displacement at the mitochondrial DNA origin. They serve as indispensable intermediates in double-strand break repair, telomere maintenance, and mitochondrial DNA replication. Recent cryo-electron microscopy studies have resolved the stepwise RAD51-mediated strand exchange mechanism at near-atomic resolution, substantially advancing structural understanding of D-loop biogenesis. Despite their differences in molecular composition, both structures remodel Watson-Crick base pairing and, when dysregulated, are associated with replication fork stalling, transcription-replication conflicts, and aberrant recombination. This review systematically compares the structural features, formation mechanisms, regulatory networks, and biological functions of R-loops and D-loops, with emphasis on their convergent roles in safeguarding genome integrity. We further discuss rapidly evolving detection technologies and emerging therapeutic strategies targeting these structures in cancer and neurodegeneration, identifying key unresolved questions for future investigation.

Genomic Instability↗

PubMed2025

Efficient site-specific integration of kilobase-length DNA fragments in plant cells via Kp03 recombinase.

Targeted insertion of large DNA sequences into plant genomes remains a major challenge in synthetic biology. Here, we evaluate the large serine recombinase Kp03 for site-specific integration of DNA fragments in rice and Arabidopsis. In transient protoplast assays, Kp03 mediates efficient insertion of donor DNA up to 27.3 kilobases (kb), with plasmid integration efficiencies reaching 99.1% for fragments up to 3.4 kb. Truncation experiments reveal that a minimal 15-bp attB sequence is necessary for integration. As a proof of concept, Kp03 successfully incorporates a 3.4-kb donor DNA into the rice genome at a locus containing this minimal attB sequence. Moreover, in rice callus, combining Kp03 with the NM-PE genome editing system to install a 26-bp attB site enables targeted integration of a 3.4-kb donor at the desired genomic locus. These findings establish Kp03 as a versatile tool for plant genome engineering, with broad applications for synthetic biology.

Oryza↗

PubMed2006

The effect of continuous wavy micropatterns on silicone substrates on the alignment of skeletal muscle myoblasts and myotubes.

Tissue-engineered muscle is a viable option for tissue repair, though presently technologies are not developed enough to produce tissue in vitro identical to that in vivo. One important step in generating accurate engineered muscle is to mimic natural muscle architecture. Skeletal muscle is composed of fibrils whose organization defines functionality. In musculoskeletal myogenesis, aligning myoblasts in preparation for myotube formation is a crucial step. The ability to efficiently organize myoblasts to form aligned myotubes in vitro would greatly benefit efforts in muscle tissue engineering. This paper reports alignment of prefused and differentiated skeletal muscle cells in vitro by use of continuous micropatterned wavy silicone surfaces, with features sized 3, 6 and 12 microm in periodicity. Wave features with 6 microm periodicity produced the most healthy, aligned myoblasts. Alignment was found to be a function of plating density. Further growth on these substrates with aligned myoblasts promoted fusion, yielding healthy aligned myotubes. This method will be useful for applications in which differentiated myogenic cells need to be aligned unidirectionally as in the development of engineered muscle.

Animals↗

PubMed2006

Microscale integrated sperm sorter.

This chapter describes the design and fabrication of a passively driven microfluidic sperm sorter using soft lithographic microfabrication techniques. This self-contained device can separate motile sperm from nonmotile sperm and other cellular debris. The sorting system is small (coin sized) and structurally simple. It comprises two inlets; two outlets; a sorting channel; and arrays of horizontally oriented reservoirs that function as passively driven, constant-flow-rate pumps. Sperm with higher motility are sorted out from the rest of the semen samples based on their ability to swim through interfaces between adjacent laminar streams into separate streamlines, whereas the nonmotile sperm and debris remain in their initial streamlines. The device, which we call a microscale integrated sperm sorter, does not rely on any external power sources or controllers and incorporates all sample loading and sorting functions necessary to prepare high-quality sperm for in vitro fertilization. This self-contained, inexpensive, and portable device may also be useful for developing convenient sperm motility assays that can be used at the point of care or at home.

Cell Separation↗

PubMed2005

IVF within microfluidic channels requires lower total numbers and lower concentrations of sperm.

BACKGROUND: Microfluidic technology has been utilized in numerous biological applications specifically for miniaturization and simplification of laboratory techniques. We sought to apply microfluidic technology to murine IVF. METHODS: Microfluidic devices measuring 500 microm wide, 180 microm deep, and 2.25 cm in length were designed and fabricated using poly(dimethylsiloxane) (PDMS). Controls were standard centre-well culture dishes with 500 microl of media, half of which also contained PDMS as a material control. Denuded mouse oocytes were placed into microchannels or centre-well dish controls in groups of 10, then co-incubated overnight with epididymal mouse sperm at various concentrations. Fertilization was assessed and Fisher's exact test was used for statistical analysis (P < 0.05 significant). RESULTS: Fertilization rates between the two control groups (42%, no PDMS; 41%, with PDMS; not significant) were similar. Fertilization rates for denuded oocytes at standard mouse insemination sperm concentration (1 degrees 10(6) sperm/ml) was poorer in microchannels (12%) than controls (43%; P < 0.001). As insemination concentrations decreased, fertilization rates improved in microchannels with a plateau between 8 degrees 10(4) and 2 degrees 10(4) sperm/ml (4000-1000 total sperm). At these concentrations, combined fertilization rate for denuded oocytes was significantly higher in microchannels than centre-well dishes (27 versus 10%, respectively; P < 0.001), and was not significantly different from corresponding controls with a sperm concentration of 1 degrees 10(6) (37%; P = 0.06). CONCLUSIONS: Murine IVF can be conducted successfully within microfluidic channels. Lower total numbers and concentrations of sperm are required. Microfluidic devices may ultimately be useful in clinical IVF.

Animals↗

PubMed2005

Fabrication of reconfigurable protein matrices by cracking.

The interface between extracellular matrices and cells is a dynamic environment that is crucial for regulating important cellular processes such as signal transduction, growth, differentiation, motility and apoptosis. In vitro cellular studies and the development of new biomaterials would benefit from matrices that allow reversible modulation of the cell adhesive signals at a scale that is commensurate with individual adhesion complexes. Here, we describe the fabrication of substrates containing arrays of cracks in which cell-adhesive proteins are selectively adsorbed. The widths of the cracks (120-3,200 nm) are similar in size to individual adhesion complexes (typically 500-3,000 nm) and can be modulated by adjusting the mechanical strain applied to the substrate. Morphology of cells can be reversibly manipulated multiple times through in situ adjustment of crack widths and hence the amount of the cell-adhesive proteins accessible to the cell. These substrates provide a new tool for assessing cellular responses associated with exposure to matrix proteins.

Animals↗

PubMed2004

Computerized microfluidic cell culture using elastomeric channels and Braille displays.

Computer-controlled microfluidics would advance many types of cellular assays and microscale tissue engineering studies wherever spatiotemporal changes in fluidics need to be defined. However, this goal has been elusive because of the limited availability of integrated, programmable pumps and valves. This paper demonstrates how a refreshable Braille display, with its grid of 320 vertically moving pins, can power integrated pumps and valves through localized deformations of channel networks within elastic silicone rubber. The resulting computerized fluidic control is able to switch among: (i) rapid and efficient mixing between streams, (ii) multiple laminar flows with minimal mixing between streams, and (iii) segmented plug-flow of immiscible fluids within the same channel architecture. The same control method is used to precisely seed cells, compartmentalize them into distinct subpopulations through channel reconfiguration, and culture each cell subpopulation for up to 3 weeks under perfusion. These reliable microscale cell cultures showed gradients of cellular behavior from C2C12 myoblasts along channel lengths, as well as differences in cell density of undifferentiated myoblasts and differentiation patterns, both programmable through different flow rates of serum-containing media. This technology will allow future microscale tissue or cell studies to be more accessible, especially for high-throughput, complex, and long-term experiments. The microfluidic actuation method described is versatile and computer programmable, yet simple, well packaged, and portable enough for personal use.

Audiovisual Aids↗

PubMed2004

Arrays of horizontally-oriented mini-reservoirs generate steady microfluidic flows for continuous perfusion cell culture and gradient generation.

This paper describes the use of arrays of horizontally-oriented reservoirs to deliver liquids through microchannels at a constant flow rate over extended periods of time (hours to days). The horizontal orientation maintains a constant hydraulic pressure drop across microfluidic channels even as the volumes of liquids within the reservoirs change over time. For a given channel-reservoir system, the magnitude of the flow velocity depends linearly on the height difference between reservoirs. The simple structure and operation mechanism make this pumping system versatile. A one-inlet-one-outlet system was used to continuously deliver media for perfusion cell culture, and an array of inlet reservoirs coupled to an outlet reservoir via microchannels was used to drive flows of multiple laminar streams. The parallel pumping scheme conveniently generated various smooth and step concentration gradients, and allowed evaluation of the effect of colchicine on myoblasts. Since the reservoir arrays are configured to be compatible with commercialized multichannel pipettors designed for 96 well plate handling, this simple pumping scheme is envisioned to be broadly useful for medium to high throughput microfluidic perfusion cell culture assays, cell migration assays, multiple laminar flow drug tests, and any other applications needing multiple microfluidic streams.

Cell Culture Techniques↗

PubMed2003

Passively driven integrated microfluidic system for separation of motile sperm.

This paper describes a self-contained integrated microfluidic system that can separate motile sperm from small samples that are difficult to handle using conventional sperm-sorting techniques. The device isolates motile sperm from nonmotile sperm and other cellular debris, based on the ability of motile sperm to cross streamlines in a laminar fluid stream. The device is small, simple, and disposable yet is an integrated system complete with sample inlets, outlets, sorting channel, and a novel passively driven pumping system that provides a steady flow of liquid; it requires no external power source or controls. The device fulfills a need in clinical settings where small amounts of sperm need to be sorted. It also opens the way for convenient bioassays based on sperm motility including at-home motile sperm tests.

Cell Separation↗

PubMed2003

Micro- and nanotechnologies for studying cellular function.

The study of complex biological systems requires methods to perturb the system in complex yet controlled ways to elucidate mechanisms and dynamic interactions, and to recreate in vivo conditions in flexible in vitro set-ups. This paper reviews recent advances in the use of micro- and nanotechnologies in the study of complex biological systems and the advantages they provide in these two areas. Particularly useful for controlling the chemical and mechanical microenvironments of cells is a set of techniques called soft lithography, whereby elastomeric materials are used to transfer and generate micro- and nanoscale patterns. Examples of some of the capabilities of soft lithography include the use of elastomeric stamps to generate micropatterns of protein and the use of elastomeric channels to localize chemicals with subcellular spatial resolutions. These types of biological micro- and nanotechnologies combined with mathematical modeling will propel our understandings of cellular and subcellular physiology to new heights.

Animals↗