Biology subjects

Tsai, M.-H.

Publications and source records attributed to Tsai, M.-H..

9 recordsLinked to original sources

bioRxiv2026

Kif2C safeguards radial glial integrity to prevent cortical malformation

Radial glial cells (RGCs) generate cortical neurons and guide radial neuronal migration, yet how microtubule (MT) regulators coordinate progenitor maintenance, mitotic fidelity, and cortical architecture remains unclear. Here, we identify the MT depolymerase Kif2C/MCAK as an essential regulator of RGC integrity with relevance to human neurodevelopmental disorders. Kif2C is enriched in developing cortical RGCs and localizes to radial fibers, basal endfeet, and mitotic structures. Acute Kif2C depletion in embryonic mouse cortices disrupts RG fiber organization, impairs neuronal migration, reduces the RGC pool, and induces mitotic defects, chromosome segregation errors, DNA damage, and cell-cycle arrest. Kif2C-deficient cortices further exhibit focal pial basement membrane disruption and neuronal overmigration, resulting in a cobblestone-like cortical malformation. We identify two individuals with neurodevelopmental disorders carrying rare deleterious KIF2C variants and show that a patient-derived truncating variant fails to rescue Kif2C-deficient cortical phenotypes, implicating KIF2C dysfunction in human neurodevelopmental disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/726143v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@1970844org.highwire.dtl.DTLVardef@9fe29eorg.highwire.dtl.DTLVardef@d72ddcorg.highwire.dtl.DTLVardef@103f729_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2024

CORNICHON HOMOLOG 5-dependent ER export of membrane cargoes in phosphate-starved Arabidopsis root as revealed by membrane proteomic analysis

Developing plants tolerant of low phosphate (Pi) availability is essential to reduce reliance on fertilizers and achieve agricultural sustainability. One strategy is to enhance the endoplasmic reticulum (ER) export of cargoes associated with Pi starvation and their trafficking to final destinations. However, the mechanisms underlying this process are underexplored. We recently discovered that Arabidopsis thaliana CORNICHON HOMOLOG 5 (AtCNIH5) encodes a Pi deficiency-induced ER cargo receptor that regulates Pi homeostasis. To find potential membrane cargoes of AtCNIH5, we applied the UV-cleavable 4-hexylphenylazosulfonate (Azo)-solubilized microsomal protein extraction for iTRAQ-based proteomic analysis. We identified 4,317 proteins in Pi-limited Arabidopsis roots, with 372 upregulated and 106 downregulated proteins in cnih5. Besides PHOSPHATE TRANSPORTER 1 proteins (PHT1s), downregulation of the biosynthetic or modifying enzymes for cell wall polysaccharides, very long-chain fatty acids, and their derivative extracellular aliphatic compounds is over-represented. Using the yeast split-ubiquitin and the in-planta tripartite split-GFP assays, we verified the interaction of AtCNIH5 with various downregulated transporters in cnih5, including AtPHT1s, AtOCT1, AtURGT6, AtDTX21, and AtDTX35. In addition, we demonstrated that the C-terminal acidic residue of AtCNIH5 is required for interaction with AtOCT1 but not with AtPHT1;1 or AtDTX21, indicating distinct cargo selection mechanisms. More importantly, enhancing in-situ AtCNIH5 expression/activity enhances plant growth. By analogy with transcriptional factors that govern gene expression, we propose that AtCNIH5 acts as a low Pi-responsive hub to facilitate ER export of specific membrane cargoes, providing a potential engineering strategy to improve plant fitness under suboptimal Pi supply.

plant biology↗

bioRxiv2024

Renal outcomes of combination therapy with sodium-glucose cotransporter 2 inhibitors plus renin-angiotensin system blockers in patients with type 2 diabetes mellitus: A population-based cohort study

BackgroundSodium-glucose cotransporter 2 inhibitors (SGLT2i) can benefit patients with type 2 diabetes mellitus by reducing hazardous renal outcomes. This study aimed to evaluate whether the combination of sodium-glucose cotransporter 2 inhibitors (SGLT2i) and conventional renin-angiotensin system blockers (RASB) provides a synergistic effect on renal outcomes in patients with type 2 diabetes mellitus, compared to the combination of RASB and dipeptidyl peptidase 4 inhibitors (DPP4i). MethodsThis is a retrospective cohort study. The study utilized data from the Taiwan National Health Insurance Research Database (NHIRD), including patients with type 2 diabetes mellitus enrolled between January 1, 2016, and December 31, 2016. Participants were divided into two groups: the case group (n = 3,622) receiving RASB plus SGLT2i and the comparison group (n = 3,622) receiving RASB plus DPP4i. The groups were matched 1:1 based on gender, age, and Charlson comorbidity index. Additionally, TriNetX was used for external validation. ResultsPrior to matching, unadjusted hazard ratios (HRs) showed significant differences favoring the SGLT2i group for chronic kidney disease (CKD) (HR: 0.66; 95% CI, 0.58-0.74), advanced kidney failure (HR: 0.64; 95% CI, 0.44-0.93), and initiation of long-term dialysis (HR: 0.61; 95% CI, 0.38-0.97). These differences remained significant post-matching: CKD (HR: 0.74; 95% CI, 0.65-0.84), advanced kidney failure (HR: 0.62; 95% CI, 0.42-0.92), and commencement of long-term dialysis (HR: 0.53; 95% CI, 0.32-0.87). The renal benefits of the combination therapy were consistently observed in the TriNetX dataset. LimitationsNHIRD lacks key clinical factors (e.g., physical features, lab data), potential baseline disparities due to retrospective design, and limited generalizability beyond Taiwanese patients, despite TriNexT validation. ConclusionsIn patients with type 2 diabetes mellitus, combination therapy with SGLT2i and RASB yielded better renal outcomes.

pharmacology and toxicology↗

bioRxiv2024

Phosphate Starvation-Induced CORNICHON HOMOLOG 5 as Endoplasmic Reticulum Cargo Receptor for PHT1 Transporters in Arabidopsis

Inorganic phosphate (Pi) is essential for plant growth and is acquired and distributed by the plasma membrane PHOSPHATE TRANSPORTER 1 proteins (PHT1s). Enhancing the abundance of PHT1s at the cell surface thus ensures plant productivity and sustainable agriculture. CORNICHON HOMOLOG proteins (CNIHs) are conserved eukaryotic cargo receptors that mediate the selective endoplasmic reticulum (ER) export of membrane proteins. In this study, we identified the Arabidopsis thaliana CNIH5 (AtCNIH5) as a Pi starvation-inducible gene, preferentially expressed in vascular tissues and outer root cell layers above the meristem. AtCNIH5 co-localizes to the AtSAR1A/AtSEC16A/AtSEC24A-labeled ER exit sites and interacts with AtPHT1;1. Loss of AtCNIH5 confers reduced shoot Pi levels under Pi sufficiency due to the reduced translocation of Pi from roots to shoots, as well as decreased Pi uptake under Pi deficiency. The cnih5 mutant exhibits decreased abundance of AtPHT1s but increased PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 (AtPHF1), which enables the ER exit of PHT1s. The cnih5 mutant also shows a lower plasma membrane targeting efficiency of split-GFP tagged-AtPHT1;1 in the root hair and the epidermis within the root transition/elongation zone. Consistently, dysfunctional AtCNIH5 exerts a suppressive effect on the growth of phf1 and alleviates Pi toxicity in the Pi overaccumulator pho2. However, the in vivo protein-protein interaction and degradation assays indicated that AtCNIH5 is not a direct target of AtPHO2. Our findings unveil that AtCNIH5 is a low Pi-responsive ER cargo receptor that interplays with AtPHF1 to promote the plasma membrane targeting of AtPHT1s in a cell-type-dependent manner.

plant biology↗

bioRxiv2024

Image-based Strain Analysis Reveals Intracellular Strain Controlled by Nucleo-Cytoskeletal Coupling

Cells can sense and transduce mechanical forces, such as stretching, and convert these signals into diverse cell biological events. While much effort has been devoted to identifying the downstream biochemical and cellular responses, it is equally crucial to pinpoint the mechanical stimuli within a cell driving these responses. Specifically, much remains unknown about how intracellular strains are distributed and controlled during mechanical deformation. In this study, we developed a microscopy-based intracellular strain measurement technique. Utilizing the intrapopulation mechanical heterogeneity of epithelial monolayers, we observed an inverse relationship between cytoplasmic and nuclear strains. We found that this anti-correlation is abolished by the inhibition of Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, suggesting that nucleo-cytoskeletal coupling controls intracellular strain distribution. We discovered a direct connection between cytoplasmic strain and stretch-induced nucleus size changes, implying that molecular events arising from cytoplasmic deformation may drive nuclear remodeling during stretching. By conducting multivariable analyses, we found that the intracellular strain can be inferred from cell morphology. Overall, our experimental platform and findings provide a foundation for unraveling the relationship between mechanotransduction pathways and upstream intracellular strain. SIGNIFICANCEMechanical stimuli exert influence on epithelial cells, not only orchestrating embryogenesis and regeneration, but also regulating cancer progression and inflammatory conditions. Despite efforts to identify mechanically activated molecular events, understanding how deformation is distributed within cells to induce subcellular responses remains limited. Specifically, the control of subcellular strain distribution during mechanical stretch is unclear. In this study, we developed a microscopy-based method to measure subcellular strain and observed an inverse relationship between cytoplasmic and nuclear strains. Disrupting nucleo-cytoplasmic coupling abolished this relationship, suggesting its role in controlling strain distribution. Additionally, we found that cytoplasmic strain correlates with nucleus size changes during stretching, indicating cytoplasmic events influence nucleus remodeling.

biophysics↗

bioRxiv2023

Structural and functional analysis of vaccinia viral fusion complex component protein A28 through NMR and molecular dynamic simulations

Host cell entry of vaccinia virus (a poxvirus) proceeds through multiple steps that involve many viral proteins to mediate cell infection. Upon binding to cells, vaccinia virus membrane fuses with host membranes via a viral entry fusion protein complex comprising 11 proteins: A16, A21, A28, F9, G3, G9, H2, J5, L1, L5 and O3. Despite vaccinia virus having two infectious forms, mature and enveloped, that have different membrane layers, both forms require an identical viral entry fusion complex for membrane fusion. Components of the poxvirus entry fusion complex that have been structurally assessed to date share no known homology with all other type I, II and III viral fusion proteins, and the large number of fusion protein components renders it a unique system to investigate poxvirus-mediated membrane fusion. Here, we determined the NMR structure of a truncated version of vaccinia A28 protein. We also expressed a soluble H2 protein and showed that A28 interacts with H2 protein at a 1:1 ratio in vitro. Furthermore, we performed extensive in vitro alanine mutagenesis to identify A28 protein residues that are critical for H2 binding, entry fusion complex formation, and virus-mediated membrane fusion. Finally, we used molecular dynamic simulations to model full-length A28-H2 subcomplex in membranes. In summary, we characterized vaccinia virus A28 protein and determines residues important in its interaction with H2 protein and membrane components. We also provide a structural model of the A28-H2 protein interaction to illustrate how it forms a 1:1 subcomplex on a modeled membrane.

microbiology↗

bioRxiv2022

MicroRNA-4776-5p acts as a radiosensitizer and predicts the prognosis of patients with head and neck cancer receiving radiotherapy

Head and neck cancer is the leading cancer worldwide. Radiation therapy plays important role of treatment for head and neck cancer. MicroRNAs have been shown to be related to tumor progression and radiosensitivity. However, the mechanisms are still largely unknown and evidence are still limited. In the current study, we sought to identify the miRNA related the radiosensitivity of head and neck tumor cell, which leading to the disappointed prognosis of patients with head and neck cancer receiving radiation therapy. The miRNA expression profiles and clinical information of patients with head and neck cancer were obtained from The Cancer Genome Atlas. The identification of miRNA was carried out through an integrated bioinformatics analysis. The miRNA identified in previous approach was validated through in vitro and in vivo studies. MiR-4776-5p was finally identified as the role of radio-sensitizer and predicts the prognosis of patients with head and neck cancer receiving radiotherapy. 11 of 16 genes targeted by the miR-4776-5p have been discovered to regulate the mechanisms related to radiosensitivity using functional annotation.

cancer biology↗

bioRxiv2020

COVID-19: Variant screening, an important step towards precision epidemiology

Precision epidemiology using genomic technologies allows for a more targeted approach to COVID-19 control and treatment at individual and population level, and is the urgent need of the day. It enables identification of patients who may be at higher risk than others to COVID-19-related mortality, due to their genetic architecture, or who might respond better to a COVID-19 treatment. The COVID-19 virus, similar to SARS-CoV, uses the ACE2 receptor for cell entry and employs the cellular serine protease TMPRSS2 for viral S protein priming. This study aspires to present a multi-omics view of how variations in the ACE2 and TMPRSS2 genes affect COVID-19 infection and disease progression in affected individuals. It reports, for both genes, several variant and gene expression analysis findings, through (i) comparison analysis over single nucleotide polymorphisms (SNPs), that may account for the difference of COVID-19 manifestations among global sub-populations; (ii) calculating prevalence of structural variations (copy number variations (CNVs) / insertions), amongst populations; and (iii) studying expression patterns stratified by gender and age, over all human tissues. This work is a good first step to be followed by additional studies and functional assays towards informed treatment decisions and improved control of the infection rate.

genomics↗

bioRxiv2019

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

RNA-Seq analysis has revolutionized researchers understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the underlying biological impact of transcription. RNA-Seq analysis requires multiple processing steps and huge computational capabilities. There are many well-developed R packages for individual steps; however, there are few R/Bioconductor packages that integrate existing software tools into a comprehensive RNA-Seq analysis and provide fundamental end-to-end results in pure R environment so that researchers can quickly and easily get fundamental information in big sequencing data. To address this need, we have developed the open source R/Bioconductor package, RNASeqR. It allows users to run an automated RNA-Seq analysis with only six steps, producing essential tabular and graphical results for further biological interpretation. The features of RNASeqR include: six-step analysis, comprehensive visualization, background execution version, and the integration of both R and command-line software. RNASeqR provides fast, light-weight, and easy-to-run RNA-Seq analysis pipeline in pure R environment. It allows users to efficiently utilize popular software tools, including both R/Bioconductor and command-line tools, without predefining the resources or environments. RNASeqR is freely available for Linux and macOS operating systems from Bioconductor (https://bioconductor.org/packages/release/bioc/html/RNASeqR.html).

bioinformatics↗