Molecular phenotyping of malignant canine mammary tumours: Detection of high-risk group and its relationship with clinicomolecular characteristics

Canine mammary gland tumours (CMTs) constitute the most common cancer in female dogs and comprise approximately 50% of all canine cancers. With the advent of high-throughput technologies such as microarray and next-generation sequencing, the molecular phenotyping (classification) of various cancers has been extensively developed. The present study used a canine RNA-sequencing dataset, namely GSE119810, to classify 113 malignant CMTs and 64 matched normal samples via an unsupervised hierarchical algorithm with a view to evaluating the association between the resulting subtypes (clusters) (n = 4) and clinical and molecular characteristics. Finally, a molecular classifier was developed, and it detected 1 high-risk molecular subtype in the training dataset (GSE119810) and 2 independent validation datasets (GSE20718 and GSE22516). Our results revealed four molecular subtypes (C2–C5) in malignant CMTs. Furthermore, the normal samples constituted a distinct group in the clustering analysis. Marked significant associations were observed between the molecular subtypes (especially C5) and clinical/molecular features, including positive lymphatic invasion, high tumour grades, histopathology diagnoses, short survival and high TP53 mutation rates (ps <.05). The high-risk subtype (C5) was further characterized through the development of a cell cycle-based gene signature, which comprised 37 proliferation-related genes according to the support vector machine algorithm. This signature identified the high-risk group in both training and validation datasets (ps <.001). In the validation analysis, our potential classifier robustly predicted patients with positive lymphatic invasion, metastases and short survival.     

多效唑影响朱顶红植株生长的转录组分析

朱顶红具有较高观赏价值,但其高花茎和叶太长成为其发展盆栽的限制因素.本研究应用不同浓度的多效唑(paclobutrazol,PBZ)对朱顶红进行处理,观测其表型性状的特征,并应用RNA-seq技术进行转录本分析.结果 表明,PBZ对朱顶红的株高及叶片长度具有抑制作用,随着PBZ浓度的增加,其株高越矮,叶长逐渐变短,各处...     

基于转录组分析ABA促进葡萄花青苷积累相关基因

[目的]分析参与调控ABA促进葡萄着色的相关基因,探讨ABA促进葡萄果实花青苷积累的分子机制.[方法]以'红巴拉多'葡萄为试材,在转色前期(约花后6周)使用300 mg·L-1 ABA对果穗进行浸果处理,以清水处理为对照.观察表型,并利用超高液相色谱质谱联用仪(UPLC-MS)测定花青苷组分及含量,再利用转录组测序技术...     

基于链特异性RNA-seq的禾谷镰刀菌全生活史转录组分析

为明确植物病原真菌禾谷镰刀菌Fusarium graminearum全生活史的转录组特征和基因表达模式,采用生物信息学技术对其生活史不同阶段15个时期或组织的链特异性RNA-seq数据进行分析。结果表明,共有8 106个基因在所有时期均有表达,为禾谷镰刀菌生活史核心基因,占总基因数的47.2%;有性生殖和侵染过程中表达的基因数相对较多,其中有性生殖后期表达的基因数最多,达15 221个;无性产孢和侵染小麦穗过程中基因表达水平整体较高,而分生孢子中基因表达水平最低。在燕麦培养基上禾谷镰刀菌气生菌丝的基因表达模式与侵染过程中的基因表达模式较为相似,而与营养生长菌丝的基因表达模式差异较大。该菌次生代谢物合成特征酶基因和分泌蛋白基因的表达模式均分成3类,即分别在侵染、营养生长和有性生殖过程上调表达,暗示其在生活史不同阶段的特异性功能。     

Transcriptome sequencing reveals two subtypes of cortisol-secreting adrenocortical tumours in dogs and identifies CYP26B1 as a potential new therapeutic target

Cushing's syndrome (CS) is a serious endocrine disorder that is relatively common in dogs, but rare in humans. In ~15%–20% of cases, CS is caused by a cortisol-secreting adrenocortical tumour (csACT). To identify differentially expressed genes that can improve prognostic predictions after surgery and represent novel treatment targets, we performed RNA sequencing on csACTs (n = 48) and normal adrenal cortices (NACs; n = 10) of dogs. A gene was declared differentially expressed when the adjusted p-value was <.05 and the log₂ fold change was >2 or < −2. Between NACs and csACTs, 98 genes were differentially expressed. Based on the principal component analysis (PCA) the csACTs were separated in two groups, of which Group 1 had significantly better survival after adrenalectomy (p = .002) than Group 2. Between csACT Group G1 and Group 2, 77 genes were differentially expressed. One of these, cytochrome P450 26B1 (CYP26B1), was significantly associated with survival in both our canine csACTs and in a publicly available data set of 33 human cortisol-secreting adrenocortical carcinomas. In the validation cohort, CYP26B1 was also expressed significantly higher (p = .012) in canine csACTs compared with NACs. In future studies it would be interesting to determine whether CYP26B1 inhibitors could inhibit csACT growth in both dogs and humans.     

基于RNA-seq的谷子萌芽期抗旱相关基因挖掘与分析

为了明确响应干旱胁迫的关键基因,解析谷子抗旱机制,本研究以谷子抗旱品种山西2010和干旱敏感品种K359*M4-1为材料,应用RNA-seq技术对两个品种干旱胁迫前后萌发期种子进行转录组测定。结果表明,在山西2010和K359*M4-1中分别鉴定出2 300个和3 652个差异表达基因(DEG),包括编码类锌诱导的促进因子、类萌发素蛋白、蛋白磷酸化酶、转运蛋白、胚胎发育晚期丰富蛋白(LEA)、转录因子、过氧化物酶等基因。通过对鉴定到的DEG进行GO和KEGG代谢途径富集分析,发现山西2010和K359*M4-1中的DEG分别富集在52个和21个生物学过程。KEGG 富集分析发现,DEG主要富集在淀粉和蔗糖代谢, 植物激素信号转导,光合作用-天线蛋白,苯丙素生物合成,角质、亚氨酸和蜡生物合成,次生代谢物生物合成等途径。本研究结果为挖掘谷子抗旱关键基因、解析谷子抗旱机制奠定了基础。     

泡泡刺高通量转录组鉴定及其黄酮类代谢途径初步分析

[目的]为了更好的了解泡泡刺黄酮类生物合成途径及其潜在的抗逆作用,[方法]应用高通量RNA-seq测序技术对泡泡刺当年生新叶进行了转录组测序及相关生物信息学分析。[结果]表明:泡泡刺当年生叶中获得了13 013 444 total reads,总核苷酸数为1 171 209 960 bp(1.09 Gb),组装拼接后得到48 921条unigene序列;Nr、Swiss-Prot、COG、GO、KEGG等数据库分析显示,有30 407个Nr注释,19 671个Swissprot注释,9 273个COG功能注释,46 153个GO功能注释,13 654个KEGG注释,并从KEGG通路中找到参与黄酮类化合物合成途径的关键基因片段186个。[结论]本研究获得了较好的泡泡刺转录组序列信息,并且其中富含黄酮类化合物代谢途径的相关基因,这为其抗逆机制、药用价值的研究及开发利用提供宝贵资源。