Genomics, proteomics & bioinformatics最新文献

Although xenotransplantation has been revolutionized by the development of genome-edited pigs, it is still unknown whether these pigs and their offspring remain genomically stable. Here, we showed that GGTA1-knockout (GTKO) pigs accumulated an average of 1205 genome-wide genetic mutations, and their filial 1 (F1) offspring contained an average of 18 de novo mutations compared with wild-type controls and their parents. The majority of mutations were in regions annotated as intergenic without altering protein functions, and none were located at predicted off-target sites. RNA sequencing analysis and phenotypic observations indicated that the accumulated mutations may have only a limited influence on GTKO pigs, and most of the mutations in the GTKO pigs could be attributed to the electrotransfection of plasmids into cells. This is the first report demonstrating that genetic mutations in genome-edited pigs are inherited stably by the next generation, providing a reference for the safe application and a standard approach to breed genome-edited pigs for xenotransplantation.

Overweight-related hypertension (OrH), defined by the coexistence of excess body weight and hypertension (HTN), is an increasing health concern elevating cardiovascular disease risks. In this study, we evaluated the prediction performance of polygenic risk scores (PRSs) and methylation risk scores (MRSs) for OrH in 7605 Chinese participants from two cohorts: the Chinese Academy of Sciences (CAS) and the National Survey of Physical Traits (NSPT). In the CAS cohort, which predominantly consists of academics, males showed significantly higher prevalence of obesity, HTN, and OrH, along with worse metabolic syndrome indicators, compared to females. This disparity was less pronounced in the NSPT cohort and in broader Chinese epidemiological studies. Among ten PRS methods, PRS-CSx was the most effective, enhancing prediction accuracy for obesity [area under the curve (AUC) = 0.75], HTN (AUC = 0.74), and OrH (AUC = 0.75), compared to baseline models using only age and sex (AUC = 0.55-0.71). Similarly, least absolute shrinkage and selection operator (LASSO)-based MRS models improved prediction accuracy for obesity (AUC = 0.70), HTN (AUC = 0.73), and OrH (AUC = 0.78). Combining PRS and MRS further boosted prediction accuracy, achieving AUC values of 0.77, 0.76, and 0.80 for obesity, HTN, and OrH, respectively. These models stratified individuals into high (> 0.6) or low (< 0.1) risk categories, covering 59.95% for obesity, 31.75% for HTN, and 43.89% for OrH. Our findings highlight a higher OrH risk among male academics, emphasize the influence of metabolic and lifestyle factors on MRS predictions, and highlight the value of multi-omics approaches in enhancing risk stratification.

With global aging, the prevalence of calcific aortic valve stenosis (CAVS) has significantly increased, and even mild CAVS elevates mortality risk, highlighting an urgent need for preventive strategies. In this study, we analyzed 153,312 participants from the UK Biobank. We found that a higher Life's Essential 8 (LE8) score was independently associated with a decreased CAVS risk [hazard ratio (HR)/standard deviation (SD): 0.72, 95% confidence interval (CI): 0.68-0.76, P < 2E-16], whereas a higher genetic risk score was independently associated with an increased CAVS risk (HR/SD: 1.63, 95% CI: 1.54-1.71, P < 2E-16). Restricted cubic spline analysis revealed approximately linear inverse associations between LE8 score and CAVS risk across all genetic risk groups. Although no multiplicative interaction was found between cardiovascular health (CVH) and genetic risk for CAVS, a significant additive interaction was identified (relative excess risk due to interaction: 3.77, 95% CI: 1.30-8.50). Among participants with high genetic risk, those with ideal CVH had a lower 10-year cumulative CAVS incidence rate than those with poor CVH (0.33% vs. 1.80%, P < 0.001). Besides, a significant multiplicative interaction was observed between LE8 score and age (P = 0.007). Similar trends were also observed for early-onset and late-onset CAVS. In conclusion, regardless of genetic risk groups, a higher LE8 score was associated with a lower CAVS risk in an approximately linear pattern. In particular, high genetic risk and poor CVH had a synergistic effect on CAVS risk, meaning that participants with high genetic risk and poor CVH would amplify their CAVS risk. Therefore, early and sustained optimization of CVH, particularly among those with high genetic risk, is essential to mitigate the risk of CAVS and its subtypes.

More than 50 repeat expansion disorders have been identified, with long-read sequencing marking a new milestone in the diagnosis of these disorders. Despite these major achievements, the comprehensive characterization of short tandem repeats in a pathological context remains challenging, primarily due to their inherent characteristics such as motif complexity, high GC content, and variable length. In this study, our aim was to thoroughly characterize repeat expansions in two neuromuscular diseases: myotonic dystrophy type 1 (DM1) and oculopharyngodistal myopathy (OPDM) using CRISPR/Cas9-targeted long-read sequencing (Oxford Nanopore Technologies, ONT). We conducted precise analyses of the DM1 and OPDM loci, determining repeat size, repeat length distribution, expansion architecture, and DNA methylation, using three different basecalling strategies (MinKnow software, Dorado, and Bonito). We demonstrated the importance of the basecalling strategy in repeat expansion characterization. We proposed guidelines to perform CRISPR-Cas9 targeted long-read sequencing (no longer supported by ONT), from library preparation to bioinformatical analyses. Finally, we showed, for the first time, somatic mosaicism, hypermethylation of LRP12 locus in OPDM symptomatic patients and changes in the repeat tract structure of these patients. We propose a strategy based on CRISPR/Cas9-enrichment long-read sequencing for repeat expansion diseases, which can be readily applicable not only in research but also in diagnostic settings.

Cancer is a major global health threat, and early detection is crucial for improving patient outcomes. DNA methylation in circulating cell-free DNA (cfDNA) has emerged as a promising biomarker for non-invasive cancer diagnosis. However, the integration and utilization of existing cfDNA methylation data have been limited, hindering comprehensive research efforts, particularly in the discovery of cfDNA methylation biomarkers. To address this challenge, we introduce cfMethDB, a comprehensive database dedicated to cfDNA methylation in cancer that encompasses 4828 publicly available datasets. Through standardized analysis, we identified 1,048,770 differentially methylated cytosines (DMCs) as candidate biomarkers across seven cancer types. With cfMethDB, we not only identified known cfDNA methylation biomarkers, but also discovered several genes, such as ZIC4, that could be novel biomarkers. Moreover, cfMethDB offers a suite of user-friendly tools, including biomarker evaluation, pan-cancer search, and end motif analysis. We hope that cfMethDB will serve as a valuable platform for the discovery of novel cancer cfDNA methylation biomarkers and will facilitate cancer research and clinical applications. cfMethDB is publicly available at: https://cfmethdb.hzau.edu.cn/home.

While most T cells exclusively express a single T cell receptor (TCR), a distinct subpopulation exhibits dual types of TCR expression (dual-TCR). Although the functional implications of dual-TCR T cells in autoimmunity and immune protection have been documented, their isolation and characterization remain technically challenging, resulting in incomplete characterization of dual-TCR properties. To address this gap, we developed DeRR (Detection of dual T cell Receptors), a computational pipeline specifically designed to identify dual-TCRs in both single-cell TCR and RNA sequencing data (scTCR-seq and scRNA-seq, respectively). Evaluation of extensive datasets validated DeRR's robust performance. Analysis of over 600,000 single T cells from 147 samples revealed the first systematic characterization of dual-TCR T cells, with approximately 17% carrying dual TCR α-chains and 12% displaying dual TCR β-chains. Notably, dual-TCR frequency in cancer was elevated compared to other conditions and demonstrated a positive association with disease duration in autoimmune disorders. However, dual-TCR T cells were uniformly distributed across all T cell subtypes and exhibited greater cross-reactivity than conventional single-TCR T cells, particularly through their secondary TCR chains. Interestingly, the relative expression levels of the two TCRs varied dynamically within dual-TCR T cells. This study provides the first dedicated tool for dual-TCR detection and offers a comprehensive landscape of dual-TCR, significantly advancing our understanding of T cell immunology. The DeRR source code is publicly accessible under the following repositories: GitHub (https://github.com/GuoBioinfoLab/DeRR) and BioCode (https://ngdc.cncb.ac.cn/biocode/tool/7789).

The human decidua establishes immune tolerance at the maternal-fetal interface and is essential for successful embryo implantation and development. Here, we conducted a spatial transcriptomic analysis of human decidua from early pregnancies in both healthy donors and patients with recurrent pregnancy loss (RPL). Our analysis revealed two distinct spatial domains, named implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the layers of decidua compacta and spongiosa, respectively. The decidual natural killer cell subset (dNK1) and the macrophage subset (dM2), both associated with growth promotion and immune regulation, were predominantly localized in the healthy IZ but were significantly reduced in RPL patients. In contrast, cytotoxic CD8+ T cells, sparsely distributed in the healthy decidual domains, were elevated in both domains under RPL conditions. Spatial cell-cell interaction analysis indicated a broad exhibition but a marked downregulation of immunoregulatory interactions in the IZ of RPL patients. Through integrated single-cell chromatin accessibility and transcription factor occupancy analyses, we identified FOSL2 as a pivotal regulator orchestrating the spatial transformation of dNK1 cells. Decreased FOSL2 expression correlated with compromised IL-15-induced dNK1 cell transformation and diminished immunoregulatory capabilities. Our findings delineate the intricate spatial and regulatory architecture of immune tolerance within the human decidua, providing new insights into immune tolerance dysregulation in RPL.

It is now well established that an understanding of the chromatin structure is essential to delineate the mechanisms underlying genomic processes. However, while methods to obtain this information from cells in vitro are widely available, there is presently a significant lack of techniques that can acquire this data from cells in the tissue. Such a capability is critical to determine the dependence of the local tissue environment on cell functioning. Further, this ability is particularly necessary for cells that are a significant minority of the total tissue population, which are often obscured in data dominated by more abundant tissue cells. Here we have developed Histological Laser Capture Microdissection Hi-C (Histo-LCM-Hi-C) to enable the characterization of chromatin architecture of phenotype-defined, spatially localized cells within intact tissue sections from as few as about 300 cells. We demonstrate the effectiveness of this approach with the generation of the first 3D Hi-C map of the tissue-resident macrophages of the liver, the Kupffer cells (KC), which are a minor cell population in the normal liver. As expected, owing to their relative rarity, these KC maps are significantly different from those obtained from whole liver, revealing distant contacts between putative enhancers and genes involved in key KC functions as well as significant differences with that of in vitro induced bone-marrow derived macrophages. We anticipate that this method will prove to be an indispensable technique in the growing repertoire of methodologies used for the characterization of the genomic properties of cells within their native environment.

Indigo, a plant-originated blue dye, has a long and well-documented history of extensive human use. The Isatis genus has long been a key source for indigo production, however, the biosynthetic pathway responsible for indigo within Isatis has remained elusive. Here, we conducted phylogenetic and metabolic analyses of various Isatis taxa, revealing that the capacity to produce indigo was apparently lost in some of these taxa. Following de novo genome sequencing, assembly, and comparative genomic analysis between Isatis indigotica and Isatis cappadocica, we delved into the origins and evolution of indigo biosynthesis. Homologous expression of candidate genes in Nicotiana benthamiana identified multiple oxidase families, including flavin-containing monooxygenase (FMO) and cytochrome P450 (CYP) protein that catalyze the oxidation steps leading to the indigo biosynthesis, indicating a metabolic innovation derived from the oxime pathway in plants. The evolutionary aspects concerning the neofunctionalization of CYPs-catalyzed biosynthesis of glucosides and FMOs-catalyzed oxime in Isatis taxa provide new insights into the evolution of these metabolic pathways in plants.