Genomics最新文献_第4页

Microbial community differences between healthy and Ustilago-infected oats 健康燕麦与黑穗病菌感染燕麦的微生物群落差异

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-10 DOI: 10.1016/j.ygeno.2026.111202

Chao Cheng , Songhe Xu , Zhiguo Liu , Hui Zhang , Yuening Yang , Yiheng Zhang , Ermeng Ge , Jiaming Xu , Qingze Zhu , Xinru Li , Bo Yu , Mengqi Liu , Yan Guo

Ustilago, a pathogenic fungus, poses a serious threat to oat growth and yield. However, the species composition, abundance, and distribution of microbial communities in Ustilago-infected oats remain poorly characterized. In this study, we conducted 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing and biochemical assays to compare microbial profiles and physiological traits between healthy (n = 60) and Ustilago-infected oats (n = 60). Our analyses revealed higher bacterial diversity in healthy oats, particularly in the spikes and stems. Significant shifts in microbial community structure were observed across all tissues in diseased plants. While the microbiome of healthy oats predominantly comprised beneficial bacteria, including Exiguobacterium indicum, infected plants were largely colonized by pathogens, including Ustilago hordei, Pyrenophora chaetomioides, and Curtobacterium flaccumfaciens pv. flaccumfaciens, suggesting the occurrence of disease-driven microbial restructuring. Functional predictions indicated that enriched pathways were primarily associated with metabolism, followed by genetic information processing and environmental signal transduction. Malondialdehyde content was significantly lower in most healthy oat tissues compared to Ustilago-infected oats, whereas the activities of the antioxidant enzymes superoxide dismutase and peroxidase were markedly higher. These results implied that Ustilago infection induced severe oxidative damage to membrane systems, likely compromising the plant's ability to scavenge superoxide ions and hydrogen peroxide, thereby reducing overall plant health.

黑穗病菌是一种严重威胁燕麦生长和产量的病原菌。然而，在黑穗病感染的燕麦中，微生物群落的种类组成、丰度和分布特征仍然很差。在这项研究中，我们通过16S rRNA和ITS扩增子测序和生化分析来比较健康燕麦（n = 60）和ustilago感染燕麦（n = 60）的微生物特征和生理性状。我们的分析显示，健康燕麦的细菌多样性更高，尤其是在穗和茎中。在患病植物的所有组织中都观察到微生物群落结构的显著变化。虽然健康燕麦的微生物组主要由有益细菌组成，包括肠外革杆菌，但受感染的植物主要由病原体定殖，包括黑穗病菌、毛状芽孢杆菌和flaccumfaciens pv。flacfaciens，提示发生了疾病驱动的微生物重组。功能预测表明，富集的通路主要与代谢相关，其次是遗传信息处理和环境信号转导。与黑穗病菌感染的燕麦相比，大多数健康燕麦组织中丙二醛含量显著降低，而抗氧化酶超氧化物歧化酶和过氧化物酶活性显著升高。这些结果表明，黑穗病菌感染对膜系统造成了严重的氧化损伤，可能损害了植物清除超氧离子和过氧化氢的能力，从而降低了植物的整体健康。

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引用次数: 0

Comprehensive epigenetic analysis on 5-methylcytosine modification of circRNAs in the mouse cerebral ischemia model 小鼠脑缺血模型中5-甲基胞嘧啶修饰环状rna的综合表观遗传学分析。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-09 DOI: 10.1016/j.ygeno.2026.111199

Dan Xiong , Chao Zhang , Jian Xia

A growing body of research suggests that circular RNAs (circRNAs) and 5-methylcytosine (m⁵C) play crucial roles in the onset and progression of stroke. This includes their potential regulation of neuronal damage and repair under cerebral ischemic conditions. However, the specific features of m⁵C modification in circRNAs associated with stroke remain unclear. In this study, we established a mouse model of cerebral ischemia (MCAO) and utilized methylated RNA immunoprecipitation sequencing (MeRIP-Seq) to identify m⁵C peaks. In comparison to the control group, MCAO exhibited significant changes in 1982 m5C peaks, with 1096 peaks upregulated and 886 peaks downregulated. Differentially expressed genes in m5C were identified to have significant involvement in the MAPK signaling pathway, GABAergic synapse, and foxO signaling pathway. Additionally, through integrated analysis of MeRIP-Seq and RNA-Seq data, we identified 24 circRNAs that underwent significant changes in both methylation and expression. This suggests a potential association between stroke and circRNA m⁵C modification, providing insights into the prognosis of stroke patients and the identification of novel intervention targets.

越来越多的研究表明，环状rna （circRNAs）和5-甲基胞嘧啶（m5C）在中风的发生和发展中起着至关重要的作用。这包括它们在脑缺血条件下对神经元损伤和修复的潜在调节。然而，与卒中相关的circrna中m5C修饰的具体特征仍不清楚。在这项研究中，我们建立了脑缺血（MCAO）小鼠模型，并利用甲基化RNA免疫沉淀测序（MeRIP-Seq）鉴定m5C峰。与对照组相比，MCAO在1982个m5C峰发生了显著变化，其中1096个峰上调，886个峰下调。m5C中差异表达的基因与MAPK信号通路、gaba能突触和foxO信号通路相关。此外，通过MeRIP-Seq和RNA-Seq数据的综合分析，我们确定了24个circrna在甲基化和表达方面都发生了显著变化。这表明卒中与circRNA m5C修饰之间存在潜在关联，为卒中患者的预后和确定新的干预靶点提供了见解。

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引用次数: 0

Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis 时间过程与多组学显示高脂血症失调的昼夜节律在肠-肝轴。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-08 DOI: 10.1016/j.ygeno.2026.111198

Jinxing Su , Shangquan Jiang , Min Chu , Xiang Dong , Caiyun Zhang , Xiaoxing Li , Kan He

Background

Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by diurnal rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Diurnal rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.

Results

Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes—including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1—that are regulated by the hepatic circadian clock and modulate metabolites via the gut–liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.

Discussion

Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the diurnal rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind to hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut–liver axis—a key mechanism in hyperlipidemia pathogenesis.

Conclusions

This study identifies critical temporal windows and core microbial taxa involved in microbiota–metabolite–gene crosstalk via the gut–liver axis, offering a theoretical foundation for diurnal rhythm-targeted interventions in metabolic diseases.

背景：长期过量食用高脂肪饮食会导致肥胖，高脂血症是一种常见的合并症。心血管系统受昼夜节律的强烈影响，昼夜节律调节内皮活性、血栓形成和血压等关键功能。昼夜节律是代谢和生理过程的中心调节器，饮食模式的改变会破坏代谢系统内部时钟的同步。结果：使用高脂血症小鼠模型，我们通过转录组学、宏基因组学和代谢组学分析研究了昼夜节律对肝脏和肠道的影响。我们发现了几个关键基因，包括CD36、Hmgcs1、Ehhadh、Cyp4a12b、Ifi27l2b、Ugt2b1、Ces2a、Cyp3a11、Selenbp2和gal3st1，它们受肝脏生物钟调节，并通过肠肝轴调节代谢物。肠道微生物群表现出昼夜节律性，协调肠道消化和代谢，形成协同的昼夜节律代谢网络。高脂血症破坏肝脏和肠道的正常昼夜调节，影响脂质合成、运输、积累和分解代谢。讨论：我们的肝脏转录组学分析显示，高脂肪饮食诱导脂质代谢基因在夜间的异常表达。这种饮食也扰乱了肠道微生物群的昼夜节律，导致肠道代谢失调。进入门静脉循环的代谢物作为结合肝脏受体的信号分子，直接调控脂质代谢基因的转录。节律性代谢物分泌的丧失破坏了昼夜节律基因表达，通过肠-肝轴导致肝脏脂质失调，这是高脂血症发病的关键机制。结论：本研究通过肠-肝轴确定了参与微生物-代谢物-基因串扰的关键时间窗口和核心微生物类群，为代谢性疾病的昼夜节律靶向干预提供了理论基础。

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引用次数: 0

Evaluation of CNV detection tools for prenatal diagnosis using amniotic fluid clinical whole-exome sequencing data 利用羊水临床全外显子组测序数据评估产前诊断CNV检测工具。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-08 DOI: 10.1016/j.ygeno.2026.111196

Qi Guo , Yue Zhang , Xin Gui , Lijuan Zhong , Rong Zhong , Yan Jiang , Hongbo Qi

Background

Copy number variations (CNVs) are significant contributors to genetic disorders, making their accurate detection crucial for prenatal diagnosis. While clinical whole exome sequencing (cWES) is increasingly used to identify sequence variants in prenatal samples, the feasibility of using the same cWES data to detect CNVs remains underexplored, particularly in amniotic fluid samples.

Methods

We systematically evaluated seven CNV detection tools (CANOES, CODEX2, CLAMMS, ExomeDepth, XHMM, CNVkit, and GATK/gCNV) across various experimental conditions. Using 132 amniotic fluid (AF) samples, we assessed the impact of control sample type (AF and PB), CNV characteristics (including exon coverage and length), and tool integration strategies on detection accuracy. Performance was evaluated against CNV-seq results as the gold standard, with special focus on detecting pathogenic CNVs.

Results

The choice of control sample substantially influenced detection performance, with PB generally yielding better results than AF. CNV characteristics, particularly exon coverage, clearly affected detection rates, with multi-exon CNVs being more reliably detected than single-exon variants. Individual tools demonstrated varying capabilities, with CANOES achieving the highest recall rate for pathogenic CNVs (70.3%) but all tools showing limited precision (highest 3.4%). Integration of multiple tools appeared to improve overall detection capability for pathogenic variations. This study suggests that effective optimization of WES-based CNV detection should consider control-sample selection, CNV characteristics, and multi-tool integration. While the current precision limitations indicate that WES-based CNV detection cannot yet replace dedicated CNV-seq testing, the findings may inform strategies to streamline prenatal diagnostic workflows by using WES data as an initial CNV screening step, potentially helping to reduce unnecessary additional testing in selected cases.

Conclusion

These findings contribute to developing more effective and efficient genetic testing strategies in prenatal clinical settings, offering a foundation for future improvements in WES-based CNV detection methods.

背景：拷贝数变异（CNVs）是遗传疾病的重要因素，其准确检测对产前诊断至关重要。尽管临床全外显子组测序（cWES）越来越多地用于鉴定产前样本中的序列变异，但使用相同的cWES数据检测CNVs的可行性仍未得到充分探索，特别是在羊水样本中。方法：我们在不同的实验条件下系统地评估了七种CNV检测工具（CANOES、CODEX2、CLAMMS、ExomeDepth、XHMM、CNVkit和GATK/gCNV）。利用132份羊水（AF）样本，我们评估了对照样本类型（AF和PB）、CNV特征（包括外显子覆盖率和长度）以及工具集成策略对检测精度的影响。以CNV-seq结果作为金标准对性能进行评估，特别关注检测致病性cnv。结果：对照样本的选择极大地影响了检测性能，PB通常比AF产生更好的结果。CNV特征，特别是外显子覆盖率，明显影响检出率，多外显子CNV比单外显子变异更可靠。单个工具表现出不同的能力，CANOES对致病性CNVs的召回率最高（70.3%），但所有工具的精确度都有限（最高 3.4%）。多种工具的整合似乎提高了对致病变异的整体检测能力。该研究表明，基于wes的CNV检测的有效优化应考虑控制样本选择、CNV特性和多工具集成。虽然目前的精度限制表明，基于WES的CNV检测还不能取代专门的CNV-seq检测，但研究结果可以通过使用WES数据作为初始CNV筛查步骤来简化产前诊断工作流程，可能有助于减少选定病例中不必要的额外检测。结论：这些发现有助于在产前临床环境中开发更有效和高效的基因检测策略，为未来基于wes的CNV检测方法的改进提供基础。

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引用次数: 0

Genetic insights into large and small body size variation in Diqing Tibetan pigs: A comparative genomic analysis 迪庆藏猪大、小体型变异的遗传学见解：比较基因组分析。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-08 DOI: 10.1016/j.ygeno.2026.111200

Siqi Jin , Xinxing Dong , Chunlu Zhou , Jinyu Chu , Xinpeng Li , Wangjiao Li , Wenjun Dong , Yunlong Ma , Dawei Yan

In Diqing Prefecture, we identified two Tibetan pig groups that exhibit a significant difference in body size at six months of age, with the large-bodied pigs weighing 55.00 kg and the small-bodied pigs weighing 28.00 kg. To elucidate the genetic distance and relatedness between these two groups, we employed whole-genome resequencing and constructed a genomic dataset containing 247 pigs, including 60 newly sequenced individuals and 187 publicly available samples. We first assessed their phylogenetic relationships through population genetic differentiation analyses, and further explored their genome-wide differences using methods such as nucleotide diversity (θπ), integrated haplotype score (iHS), allele frequency difference (ΔAF), and genome-wide association analysis (GWAS). The results showed that both groups belong to the Diqing Tibetan pig population, and they can be classified as large-bodied and small-bodied Diqing Tibetan pigs, respectively. Combined analyses of selective sweep signals and GWAS revealed that the genomic regions with significant divergence between the two groups mainly contain genes involved in skeletal development, muscle growth, energy metabolism, and endocrine regulation. This study is the first to demonstrate, at the genomic level, that the Diqing Tibetan pig population contains distinct large- and small-bodied types. Although both belong to the same breed, their marked difference in body size leads to substantial variation in meat production capacity. Future studies may employ multi-omics approaches—including transcriptomics, proteomics, and metabolomics—using the two types as comparative models under the same genetic background to systematically identify key genes, proteins, and metabolites that influence meat production performance. The findings of this study not only provide valuable material for further elucidating the mechanisms underlying skeletal and muscle development, but also establish a foundation for breeding Diqing Tibetan pigs with improved meat production traits.

在迪庆地区，我们发现了两个6月龄体重差异显著的藏猪群体，大体猪体重55.00 kg，小体猪体重28.00 kg。为了阐明这两个群体之间的遗传距离和亲缘关系，我们采用全基因组重测序方法，构建了包含247头猪的基因组数据集，其中包括60只新测序的个体和187个公开样本。我们首先通过群体遗传分化分析评估了它们的系统发育关系，并使用θπ、iHS、ΔAF和全基因组关联分析（GWAS）等方法进一步探索了它们的全基因组差异。结果表明，这两个类群均属于迪庆藏猪种群，可分为大体和小体迪庆藏猪。结合选择性扫描信号和GWAS分析发现，两组差异显著的基因组区域主要包含与骨骼发育、肌肉生长、能量代谢和内分泌调节相关的基因。本研究首次在基因组水平上证明了迪庆藏猪种群包含明显的大体型和小体型。虽然两者属于同一品种，但它们在体型上的显著差异导致了它们在肉类生产能力上的巨大差异。未来的研究可能会采用多组学方法，包括转录组学、蛋白质组学和代谢组学，在相同的遗传背景下，使用这两种类型作为比较模型，系统地识别影响肉类生产性能的关键基因、蛋白质和代谢物。本研究结果不仅为进一步阐明骨骼肌发育机制提供了有价值的材料，也为培育具有改良肉品性状的迪庆藏猪奠定了基础。

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引用次数: 0

GC–TOF–MS-based metabolomic and whole-transcriptomic analyses reveal the molecular mechanism of primary metabolite changes in pear fruit after methyl jasmonate treatment 基于gc - tof - ms的代谢组学和全转录组学分析揭示了茉莉酸甲酯处理后梨果实初级代谢物变化的分子机制。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-07 DOI: 10.1016/j.ygeno.2026.111195

Yubo Yuan , Yangyang Chen , Lisha Luo , Yuanyuan Jia , Kaijie Qi , Zhihua Xie , Hao Yin , Shaoling Zhang , Xiao Wu

Background

Methyl jasmonate (MeJA) regulates plant development and reproductive processes and significantly influences metabolism. Pears are important economic fruits, but there is still limited research on the changes in primary metabolites in pears after MeJA treatment, and their molecular mechanisms are not yet clear.

Results

This study employed GC–TOF–MS to analyze primary metabolite changes in the peel and flesh of ‘Nanguo’ pears after MeJA treatment. The results showed that 174 and 156 metabolites were detected in the peel and flesh respectively, from which 7 and 2 differentially altered metabolites were subsequently screened out. We analysed the combined whole-transcriptome data and constructed relevant competitive endogenous RNA (ceRNA) and miRNA–target transcription factor regulatory networks for each differentially expressed compound.

Conclusions

Our results provide an informative insight to the molecular regulatory network by which MeJA treatment changes the primary metabolism in pears, providing a theoretical basis for improving fruit quality during storage.

背景：茉莉酸甲酯（Methyl jasmonate, MeJA）调节植物的发育和生殖过程，并显著影响植物的代谢。梨是重要的经济水果，但对MeJA处理后梨初级代谢物变化的研究仍然有限，其分子机制尚不清楚。结果：本研究采用气相色谱- tof - ms分析了MeJA处理后“南果”梨果皮和果肉中主要代谢物的变化。结果表明，在果皮和果肉中分别检测到174种和156种代谢物，从中筛选出7种和2种差异代谢物。我们分析了综合的全转录组数据，并为每种差异表达的化合物构建了相关的竞争性内源RNA （ceRNA）和mirna靶转录因子调控网络。结论：我们的研究结果揭示了MeJA处理改变梨初级代谢的分子调控网络，为提高果实贮藏品质提供了理论依据。

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引用次数: 0

Identification and functional prediction of ceRNA networks regulating ATP levels in boar spermatozoa treated with non-thermal plasma 非热等离子体处理的猪精子中调节ATP水平的ceRNA网络的鉴定和功能预测。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-07 DOI: 10.1016/j.ygeno.2026.111197

Yihan Li , Jiangwei Liu , Qian Wang , Yin Li , Xianzhong Wang , Jiaojiao Zhang

Adenosine triphosphate (ATP) is essential for sperm motility. We previously found that optimized non-thermal dielectric barrier discharge (DBD) plasma treatment enhanced boar sperm quality by increasing ATP levels. However, the molecular mechanisms underlying this process, particularly the role of competing endogenous RNA (ceRNA) networks, remain unclear. In this study, a total of 266 mRNAs, 163 miRNAs, and 37 circRNAs were identified as differentially expressed in boar spermatozoa treated with optimized DBD plasma. Functional enrichment analysis revealed that ATP-related pathways, including AMPK, mTOR, and cAMP signaling, were significantly enriched. A circRNA–miRNA–mRNA regulatory network was constructed, and two key ceRNA axes, circRNA7761–miR-7-3p–TECRL/CYP24A1/LOC100515741 and circRNA7508–miR-202-5p–CYP2A19/HHIP/WNT2, were identified in the network. These axes are predicted to enhance ATP production by regulating mitochondrial function and energy homeostasis, thereby improving sperm quality. This study provides novel mechanistic insights into the modulation of sperm energy metabolism by DBD plasma through ceRNA networks, thereby offering new theoretical foundations and potential molecular targets for improving male fertility and treating male infertility.

三磷酸腺苷（ATP）对精子的活力至关重要。我们之前发现，优化的非热介质阻挡放电（DBD）等离子体处理通过提高ATP水平来提高猪精子质量。然而，这一过程的分子机制，特别是内源性RNA （ceRNA）网络的竞争作用仍不清楚。在本研究中，共鉴定出266个mrna、163个mirna和37个circrna在经过优化的DBD血浆处理的猪精子中差异表达。功能富集分析显示，包括AMPK、mTOR和cAMP信号在内的atp相关通路显著富集。构建了一个circRNA-miRNA-mRNA调控网络，并在该网络中鉴定出两个关键的ceRNA轴circrna7761 - mir -7- 3d - tecrl /CYP24A1/LOC100515741和circRNA7508-miR-202-5p-CYP2A19/ hip /WNT2。预计这些轴通过调节线粒体功能和能量稳态来提高ATP的产生，从而提高精子质量。本研究为DBD血浆通过ceRNA网络调控精子能量代谢提供了新的机制见解，从而为提高男性生育能力和治疗男性不育症提供了新的理论基础和潜在的分子靶点。

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引用次数: 0

Comprehensive analysis of multiple species identifies novel molecular signatures and pathways involved in aging 对多个物种的综合分析发现了与衰老有关的新的分子特征和途径。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-01 Epub Date: 2025-11-28 DOI: 10.1016/j.ygeno.2025.111161

Weijuan Cai , Kunying Chong , Bo Zhou , Yanni Zhao , Binchang Lao , Liang Yin

Aging is an important pathological basis of age-related diseases. However, the similarities and differences among different types of senescent cells of different species and their role in normal homeostasis are poorly understood. Herein, in order to comprehensively map age-related transcriptome changes in multiple tissues of vertebrates during the ageing process, we analyzed 581 samples from 54 aging transcriptome datasets spanning 4 species including Homo sapiens, Mus musculus, Rattus norvegicus and Danio rerio, and identified the novel age-related differentially expressed genes, and obtained specific enriched expression of age-related pathways. Protein-protein interactions of differentially expressed genes in different species with the PTPRC or CD45 as the core were predicted. Through this study, we screened the key biomarkers and signaling pathways that regulate the aging process of tissues and organs in multiple species, which is of great significance for improving age-related tissues and organs by identifying senescent cells.

衰老是老年性疾病发生的重要病理基础。然而，不同物种的不同类型衰老细胞之间的异同及其在正常体内平衡中的作用尚不清楚。为了全面绘制脊椎动物衰老过程中多个组织的年龄相关转录组变化图谱，我们分析了包括智人、小家鼠、褐家鼠和丹尼奥在内的4个物种的54个衰老转录组数据集的581个样本，发现了新的年龄相关差异表达基因，并获得了年龄相关通路的特异性富集表达。预测以PTPRC或CD45为核心的不同物种差异表达基因的蛋白-蛋白相互作用。通过本研究，我们筛选了多个物种中调节组织器官衰老过程的关键生物标志物和信号通路，这对于通过识别衰老细胞来改善与年龄相关的组织器官具有重要意义。

引用次数: 0

TOGAR: Token-gated generative refinement for high-fidelity spatial transcriptomics and robust spatial domain clustering 用于高保真空间转录组学和鲁棒空间域聚类的令牌门控生成改进。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-01 Epub Date: 2025-12-19 DOI: 10.1016/j.ygeno.2025.111179

Dachen Liu , Hua Shi , Yihang Lin , Zhen Chen , Quan Zou

Spatial transcriptomics maps gene expression across tissues, yet data sparsity and noise challenge long-range dependency modeling, limiting accurate spatial domain delineation. In this study, we present TOGAR, a token-gated generative refinement model that unifies denoising, spatial enhancement, and clustering for spatial transcriptomics. Firstly, the model combines a graph convolutional network loss with a loss based on the zero-inflated negative binomial distribution to reduce noise and enhance signal clarity in sparse count data. It then employs a UGate-based diffusion backbone, which integrates token gating, gated linear attention, and rotary positional embedding for generative spatial refinement. Finally, similarity-guided averaging along diffusion trajectories provides stable spot-level estimates, and clustering of the refined representations produces spatial domains with sharp boundaries suitable for downstream analyses. We evaluate TOGAR across three spatial transcriptomics platforms. In benchmarks on twelve slices against seven popular methods, TOGAR consistently achieves or exceeds clustering accuracy, demonstrating superior stability. TOGAR effectively recovers coherent cortical layer organization, delineates fine-grained tumor subdomains associated with immune activity and extracellular matrix remodeling, and generates clearer, biologically interpretable domain boundaries. Notably, TOGAR excels in detecting extremely small and rare spatial structures, successfully identifying biologically important regions that other methods completely miss, while maintaining boundary integrity in complex multi-cluster structures and avoiding issues of over-connectivity or incomplete detection.

空间转录组学绘制跨组织的基因表达，但数据稀疏性和噪声挑战了远程依赖建模，限制了准确的空间域描绘。在这项研究中，我们提出了TOGAR，一个统一了去噪、空间增强和空间转录组聚类的标记门控生成细化模型。首先，该模型将图卷积网络损失与基于零膨胀负二项分布的损失相结合，以降低稀疏计数数据中的噪声，提高信号清晰度。然后，它采用基于gate的扩散主干，该主干集成了令牌门控、门控线性注意和旋转位置嵌入，用于生成空间细化。最后，沿着扩散轨迹的相似性引导平均提供了稳定的点水平估计，并且精细表示的聚类产生具有适合下游分析的明确边界的空间域。我们通过三个空间转录组学平台评估TOGAR。在针对7种常用方法的12个切片的基准测试中，TOGAR始终达到或超过聚类精度，显示出优越的稳定性。TOGAR有效地恢复了连贯的皮质层组织，描绘了与免疫活性和细胞外基质重塑相关的细粒度肿瘤亚域，并产生了更清晰、生物学上可解释的区域边界。值得注意的是，TOGAR在检测极小和罕见的空间结构方面表现出色，成功识别了其他方法完全遗漏的重要生物区域，同时保持了复杂多簇结构的边界完整性，避免了过度连接或检测不完整的问题。

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引用次数: 0

Comprehensive small non-coding RNA profiling reveals novel diagnostic biomarkers for primary open-angle glaucoma 全面的小非编码RNA分析揭示了原发性开角型青光眼的新诊断生物标志物。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2026-01-01 DOI: 10.1016/j.ygeno.2025.111187

Juntao Zhang , Hengqian He , Fang Wang , Huilei Yu , Bowen Liu , Jingwen Yang , Qinkang Lu

Primary open-angle glaucoma (POAG) is the most prevalent type of glaucoma, and early-stage optic neuropathy may cause visual field defects. As these early defects have minimal effects on vision, they are often overlooked, resulting in the loss of optimal treatment timing. Urgent identification of novel early diagnostic biomarkers is needed. In this study, blood samples from 30 POAG patients and 30 healthy controls were analyzed for Small Non-Coding RNAs (sncRNAs) transcriptomics and validated. We performed PANDORA-seq to profile quantitative sncRNAs signature, and a total of 169 differentially expressed sncRNAs were identified, including 147 PIWI-interacting RNAs, 10 microRNAs, and 12 transfer RNA-derived small RNAs. Functional enrichment analysis of sncRNAs target genes revealed significant involvement in key pathological processes, including apoptosis, inflammation, and intraocular pressure homeostasis. Regulatory network analysis demonstrated substantial functional overlap among different sncRNAs groups, suggesting potential cooperative roles in POAG pathogenesis. The expressions of 6 candidate sncRNAs were validated by quantitative real-time polymerase chain reaction, confirming the downregulation of tsRNA-5009b-ValCAC (p < 0.05), piR-hsa-767,596 (p < 0.05), piR-hsa-731,834 (p < 0.01) and hsa-miR-451a (p < 0.05) in POAG patients. Besides, receiver operating characteristic (ROC) curve analysis demonstrated that individual sncRNAs exhibited moderate diagnostic performance, with hsa-miR-451a showing good performance (AUC = 0.83).Our study provides novel insights into the role of sncRNAs in POAG and highlights their potential as diagnostic biomarkers for early disease detection and monitoring.

原发性开角型青光眼（POAG）是最常见的青光眼类型，早期视神经病变可引起视野缺损。由于这些早期缺陷对视力的影响很小，它们经常被忽视，导致失去最佳治疗时机。迫切需要识别新的早期诊断生物标志物。在这项研究中，对30名POAG患者和30名健康对照者的血液样本进行了小分子非编码rna （sncRNAs）转录组学分析和验证。我们通过PANDORA-seq分析了sncRNAs的定量特征，共鉴定了169个差异表达的sncRNAs，包括147个piwi相互作用rna， 10个microRNAs和12个转移rna衍生的小rna。sncRNAs靶基因的功能富集分析显示，sncRNAs靶基因参与细胞凋亡、炎症和眼压稳态等关键病理过程。调控网络分析显示，不同sncRNAs组之间存在大量功能重叠，提示在POAG发病机制中潜在的协同作用。通过实时定量聚合酶链反应验证了6个候选sncrna的表达，证实了tsRNA-5009b-ValCAC的下调(p

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