Biology subjects

wu, c.

Publications and source records attributed to wu, c..

4 recordsLinked to original sources

bioRxiv2025

Single-cell copy number alteration signature analysis reveals masked patterns and potential biomarkers for cancer

Copy number alteration (CNA) is a major type of cancer genome alteration that drives cancer progression. CNA signature analysis can reveal underlying etiology and provide biomarkers for cancer treatment, and existing CNA signature analyzes are all performed using bulk tissue samples. However CNA usually affect large proportion of genome, and the CNA profile of bulk sample does not reflect the actual CNA profiles of the individual cancer cells of the sample, especially in tumors with high heterogeneity, such as hepatocellular carcinoma (HCC). Furthermore, the evolutionary trajectory of CNA mutational processes still remain elusive. Here we build a method to comprehensively analyze the CNA signatures of HCC from single-cell and bulk sample perspective, revealing patterns and potential noise signals from the usually performed bulk tissue CNA signature analysis. Single-cell signature analysis delineated the evolutionary trajectory of HCC CNA signatures, and different CNA signatures consistently emerge in different HCC evolution stages. Single-cell CNA signatures show robust performance in patient prognosis and drug sensitivity prediction. This work not only reveals specific considerations in analyzing CNA signature derived from bulk tissue but also depicts CNA evolution process and provides potential biomarkers for the prognosis and treatment of HCC patients. HighlightSingle-cell analysis reveals CNA signatures masked in bulk tissue. Single-cell analysis delineates the evolutionary trajectory of CNA signature. Small CNAs occur early and large CNAs happens late in HCC evolution. Single-cell CNA signatures show robust performance in guiding cancer clinical treatment.

genomics↗

bioRxiv2023

Photosynthetic CO2 response characteristics in canopy of Larix principis-rupprechtii Mayr. tree and practicability of three Models

Accurately predicting the crown photosynthesis of trees is important to understand the tree growth status and carbon circle in terrestrial ecosystem. However, modeling the photosynthetic carbon dioxide (CO2) response curves for individual tree are still challenging due to the complex canopy structure and changeable environmental conditions. Therefore, taking 16-old year Larix principis-rupprechtii Mayr. as the research material, the dynamic CO2 response models of photosynthesis, including rectangular hyperbolic model (RHM), the non-rectangular hyperbolic model (NRHM) and the modified rectangular hyperbolic model (MRHM), were used to simulate CO2 response curves of the crown. The fitting accuracy of the models depend on the comparison of determinants coefficients (R2), mean square errors (MSE) and Akaike information criterion (AIC). The results showed that the mean value of R2 (R2=0.9939 [~] 0.9964) of MRHM was the highest, whereas MSE value (MSE=0.2185[~]0.2627) and AIC value (AIC=-13.18[~]-8.03) were the lowest. The CO2-saturated gross photosynthetic rate (Amax) and the saturation point (CiSP) obtained by MRHM were closest to the measured value respectively. Therefore, the MRHM fitted the CO2 response data well, and calculated the photosynthetic parameters directly and accurately, the fitted result showed , Amax, CiSP, CiCP and RP were 0.04, 7.51 mol{middle dot}m-2s-1, 938.97 mol{middle dot}m-2, 67.54 mol{middle dot}m-2 and 0.60 mol{middle dot}m-2s-1, respectively. In addition, the difference on the photosynthetic CO2 response parameters values showed somewhat among different layers and orientations. In all, all data suggested that the modified rectangular hyperbolic model (MRHM) was an ideal model to fit the crown photosynthetic CO2 response curve of Larix principis-rupprechtii Mayr. These results are of great significance for parameter calibration of photosynthetic model and robust prediction of photosynthetic response in forest.

ecology↗

bioRxiv2023

Molecular cloning and characterization of an AP2/ERF protein gene in cotton (Gossypium hirsutum L.)

Upland cotton (Gossypium hirsutum L.) is one of the most economically important crops worldwide due to the significant source of natural fiber, feed, oil and biofuel products. Cottonseed can also serve as an excellent source of edible protein and oil. However,the presence of gossypol in pigment gland has limited it utilization In the past few decades, some progress has been made in the understanding molecular mechanism of the formation of the pigment gland. However, little is known about the specific mechanism of pigment gland formation in cotton. In this study, the cDNA sequence of a ethylene transcription factor gene, designated GhERF105a, was cloned from upland cotton CCRI12. Sequence alignment revealed that GhERF105a gene contained a typical AP2/ERF domain of 61 amino acids, and belonged to the ERF subgroup of the ERF supfamily. It was highly expressed in the leaves and stems of glanded plants but had substantially lower expression of the glandless plants. GhERF105a, localized to the nucleus, could bind to GCC-box and DRE. Some development, phytohormone and stress related cis-elements were enriched in the promoters of GhERF105a/d. Split ubiquitin assays in yeast and BiFC experiments showed extensive interactions between GhERF105a and Gh_A07G1044. In addition, GhERF105a was highly similar with GhERF105d in the gene length, molecular weight, protein molecule, gene structure and expression pattern. The overall results suggested that GhERF105a might participate in the pigment gland formation and stree-response processes.

bioengineering↗

bioRxiv2023

Amino acid transporter SLC7A5 regulates Paneth cell function to affect the intestinal inflammatory response

The intestine is critical for not only processing and resorbing nutrients but also protecting the organism from the environment. These functions are mainly carried out by the epithelium, which is constantly being self-renewed. Many genes and pathways can influence intestinal epithelial cell proliferation. Among them is mTORC1, whose activation increases cell proliferation. Here, we report the first intestinal epithelial cell-specific knockout ({Delta}IEC) of an amino acid transporter capable of activating mTORC1. We show that the transporter, SLC7A5, is highly expressed in mouse intestinal crypt and Slc7a5{Delta}IEC reduces mTORC1 signaling. Surprisingly, Slc7a5{Delta}IEC mice have increased cell proliferation but reduced secretory cells, particularly mature Paneth cells. scRNA-seq and electron microscopic analyses revealed dedifferentiation of Paneth cells in Slc7a5{Delta}IEC mice, leading to markedly reduced secretory granules with little effect on Paneth cell number. We further show that Slc7a5{Delta}IEC mice are prone to experimental colitis. Thus, SLC7A5 regulates secretory cell differentiation to affect stem cell niche and/or inflammatory response to regulate cell proliferation.

immunology↗