Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature

Background

Non-small cell lung cancer (NSCLC) represents more than about 80% of the lung cancer. The early stages of NSCLC can be treated with complete resection with a good prognosis. However, most cases are detected at late stage of the disease. The average survival rate of the patients with invasive lung cancer is only about 4%. Adenocarcinoma in situ (AIS) is an intermediate subtype of lung adenocarcinoma that exhibits early stage growth patterns but can develop into invasion.

Methods

In this study, we used RNA-seq data from normal, AIS, and invasive lung cancer tissues to identify a gene module that represents the distinguishing characteristics of AIS as AIS-specific genes. Two differential expression analysis algorithms were employed to identify the AIS-specific genes. Then, the subset of the best performed AIS-specific genes for the early lung cancer prediction were selected by random forest. Finally, the performances of the early lung cancer prediction were assessed using random forest, support vector machine (SVM) and artificial neural networks (ANNs) on four independent early lung cancer datasets including one tumor-educated blood platelets (TEPs) dataset.

Results

Based on the differential expression analysis, 107 AIS-specific genes that consisted of 93 protein-coding genes and 14 long non-coding RNAs (lncRNAs) were identified. The significant functions associated with these genes include angiogenesis and ECM-receptor interaction, which are highly related to cancer development and contribute to the smoking-free lung cancers. Moreover, 12 of the AIS-specific lncRNAs are involved in lung cancer progression by potentially regulating the ECM-receptor interaction pathway. The feature selection by random forest identified 20 of the AIS-specific genes as early stage lung cancer signatures using the dataset obtained from The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples. Of the 20 signatures, two were lncRNAs, BLACAT1 and CTD-2527I21.15 which have been reported to be associated with bladder cancer, colorectal cancer and breast cancer. In blind classification for three independent tissue sample datasets, these signature genes consistently yielded about 98% accuracy for distinguishing early stage lung cancer from normal cases. However, the prediction accuracy for the blood platelets samples was only 64.35% (sensitivity 78.1%, specificity 50.59%, and AUROC 0.747).

Conclusions

The comparison of AIS with normal and invasive tumor revealed diseases-specific genes and offered new insights into the mechanism underlying AIS progression into an invasive tumor. These genes can also serve as the signatures for early diagnosis of lung cancer with high accuracy. The expression profile of gene signatures identified from tissue cancer samples yielded remarkable early cancer prediction for tissues samples, however, relatively lower accuracy for boold platelets samples.

     

Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method

Background

Human cancers are complex ecosystems composed of cells with distinct molecular signatures. Such intratumoral heterogeneity poses a major challenge to cancer diagnosis and treatment. Recent advancements of single-cell techniques such as scRNA-seq have brought unprecedented insights into cellular heterogeneity. Subsequently, a challenging computational problem is to cluster high dimensional noisy datasets with substantially fewer cells than the number of genes.

Methods

In this paper, we introduced a consensus clustering framework conCluster, for cancer subtype identification from single-cell RNA-seq data. Using an ensemble strategy, conCluster fuses multiple basic partitions to consensus clusters.

Results

Applied to real cancer scRNA-seq datasets, conCluster can more accurately detect cancer subtypes than the widely used scRNA-seq clustering methods. Further, we conducted co-expression network analysis for the identified melanoma subtypes.

Conclusions

Our analysis demonstrates that these subtypes exhibit distinct gene co-expression networks and significant gene sets with different functional enrichment.

     

润楠属植物叶片和枝条水力特征的协同关系

以润楠属(Machilus) 7种植物成年个体为材料,对其进行生理指标测定,并对它们的叶片水分供需关系以及木质部纹孔特征和导水效率之间的关联进行分析。结果显示,润楠属7种植物相比原始被子植物具有更高的叶脉密度(VD),叶脉密度为9.8～14.1 mm/mm~2;气孔密度(SD)与叶脉密度呈显著正相关,说明叶片水分供需存在协同关系;气孔密度与气孔大小(GLC)呈负相关;气孔越大的叶片其膨压丧失点(TLP)的绝对值越低。枝条边材比导率(Ks)较低,为0.13～1.87 kg·m~(-1)·s~(-1)·MPa~(-1),且种间差异较大。叶脉和气孔密度均与边材比导率呈正相关。边材比导率与纹孔膜面积、纹孔口面积以及纹孔口长短轴比例相关性不显著。研究结果表明润楠属植物虽然叶脉密度较高,且木质部水分供应和叶片结构具有协同关系,但木质部解剖结构较为原始,导管多具梯形穿孔板,导水效率低,只能适应比较湿润的生境。     

Molecular evolution of maize catalases and their relationship to other eukaryotic and prokaryotic catalases

We have compared the nucleotide and protein sequences of the three maize catalase genes with other plant catalases to reconstruct the evolutionary relationship among these catalases. These sequences were also compared with other eukaryotic and prokaryotic catalases. Phylogenies based on distances and parsimony analysis show that all plant catalases derive from a common ancestral catalase gene and can be divided into three distinct groups. The first, and major, group includes maizeCatl, barleyCat1, riceCatB and most of the dicot catalases. The second group is an apparent dicot-specific catalase group encompassing the tobaccoCat2 and tomatoCat. The third is a monocot-specific catalase class including the maize Cat3, barley Cat2, and riceCatA. The maize Cat2 gene is loosely related to the first group. The distinctive features of monocot-specific catalases are their extreme high codon bias at the third position and low degree of sequence similarity to other plant catalases. Similarities in the intron positions for several plant catalase genes support the conclusion of derivation from a common ancestral gene. The similar intron position between bean catalases and human catalase implies that the animal and plant catalases might have derived from a common progenitor gene sequence. Correspondence to: J.G. Scandalios     

红细胞内翻外囊泡带3蛋白活性测试方法的研究

从人血中提取红细胞膜,用注射器加压推打的方法首次获得了包含80mmol/L吡啶二羧酸(DPA)的封闭完好的内翻外囊泡(IOVs).离心除去囊泡外DPA,即可按Newton法测其阴离子转运活性.此法在红细胞膜内翻外囊泡体系上成功地建立了带3蛋白(Band 3)测活方法,具有简便迅速,重复性好等优点.     

卵巢激素对肺泡巨噬细胞趋化活性的影响

为探讨卵巢激素对非性器官肺脏的防御功能有无影响,本研究以肺泡巨噬细胞（ＡＭ）趋化活性为指标,观察了卵巢激素对成年雄性大鼠离体ＡＭ的趋化活性的作用。结果显示：不同浓度的酵母多糖激活血清与ＡＭ在体外培养３．５ｈ,对ＡＭ趋化性有良好的线性关系。雌二醇能抑制ＡＭ的趋化活性,量效关系显著（ｒ＝－０．９２８０,Ｐ＜０．０１）;而孕酮则促进ＡＭ的趋化活性,亦具有剂量依从性（ｒ＝０．９９７５,Ｐ＜０．０１）。提示：卵巢激素除参与性器官功能的调节外,对于非性器官肺脏的防御功能亦具有一定的调控作用。     

毛喉萜抑制人胃癌细胞BGC－823增殖与ras基因表达相关性研究

毛喉萜（ｆｏｒｓｋｏｌｉｎ）对人胄癌细胞ＢＧＣ－８２３增殖有明显抑制作用,具药物剂量和作用时间之依赖性。剂量为２×１０~（－５）ｍｏｌ／Ｌ之毛喉萜使胃癌细胞在软琼脂中形成集落的能力显著降低;癌基因ｃ－Ｈａ－ｒａｓ之表达明显被抑制,细胞核中与ｒａｓ基因上游调控区２．５ｋｂ片段结合的三种蛋白结合能力下降。联系到以同样浓度药物处理胃癌细胞７２ｈ,细胞质、膜与细胞核中蛋白激酶Ｃ（ＰＫＣ）活性均下降的现象,可能ＰＫＣ活性下降与Ｈａ－ｒａｓ基因上游片段２．５ｋｂ结合蛋白之结合能力下降存在相关性,ＰＫＣ可能通过影响ＤＮＡ结合蛋白的磷酸化作用,导致了Ｈａ－ｒａｓ基因表达之被阻抑。而ｒａｓ基因表达下降可能是毛喉萜抑制胃癌细胞增殖的一个重要分子事件。     

Isolation of YAC insert sequences by representational difference analysis.

We present a method for the isolation of YAC insert sequences by representational difference analysis (RDA). To achieve maximal representation of the sequences, the amplicons were generated from a Mbol digestion product. RDA was performed using a 970 kb insert YAC clone. After two rounds of re-association and selective amplification 92% of the difference product represented sequences derived from the YAC insert. Twenty insert-specific sequence-tagged sites were readily defined. The difference product was also successfully used to isolate microsatellite markers, to identify clones from a human PAC library and as a chromosome painting probe in fluorescence in situ hybridization.     

FACTORS AFFECTING CORPORA ALLATA ACTIVITY IN THE ADULT LADY BEETLE COCCINELLA SEPTEMPUNCTATA L.

Abstract Corpora allata are the defined site of juvenile hormone (JH) biosynthesis in reproductive adult insects and their activity is regulated by intrinsic and extrinsic factors. In the adult lady beetle Coccinella septempunctata , it has been well established that the development of ovaries is controlled by JH (Guan 1987). The present study aims at the elucidation of the influence of some factors regulating reproduction of the lady beetle. They include topical application of JH analogues, presence of neuropeptides in the extract from the brain, as well as the development of ovary and type of food on CA activity. JH synthesis in CA is monitored with radiochemical assay and immunoelectrophoresis.