Transcriptional profiling of exosomes derived from plasma of canine with mammary tumor by RNA-seq analysis

Canine mammary tumor (CMT) are the second most common tumor in dogs. Exosomes can act as biomarkers for the early diagnosis of tumors, and also be involved in the pathogenesis and metastasis mechanism of tumors. The expression profile of exosomal RNA revealed that there were a total of 5547 differentially expressed mRNAs, and 196 differentially expressed lncRNAs. GO and KEGG enrichment analysis found that the differentially expressed mRNAs and lncRNA target genes were associated with metabolic processes, DNA replication, cell proliferation, cell junction, and cell adhesion. In conclusion, this study revealed lncRNA and mRNA expression profiles in exosomes derived from plasma of CMT and further annotated their potential functions. The data obtained in this study will also provide valuable resources for understanding lncRNA information in plasma exosomes of dogs with CMT, and contribute to the study of early diagnostic markers and pathogenesis of CMT.     

基于单细胞转录组的视网膜母细胞瘤进展特征分析

视网膜母细胞瘤（retinoblastoma,RB）是婴幼儿最常见的眼内恶性肿瘤。在RB进展过程中的关键致病因素目前尚不十分清楚。因此,识别与RB进展密切相关的基因能为病情诊断及基因治疗提供重要信息。然而,肿瘤组织具有很强的细胞异质性,不同病理状态下的细胞,其功能及基因表达都可能呈现显著的差异。本研究从公共基因表达数据库（gene expression omnibus,GEO）下载了1例4个月肿瘤患者和1例2年患者的肿瘤及癌旁组织的单细胞转录组测序数据,从单细胞水平解析不同患病时长的RB肿瘤转录图谱,鉴定与RB进展有潜在关联的细胞亚群及基因集。结果显示,肿瘤组织与癌旁组织在单细胞转录图谱上具有整体的一致性,但视锥前体G1期细胞群、G2期细胞群以及小胶质细胞群在肿瘤与癌旁组织中的分布比例存在明显差异。进一步分析了这3种细胞群在RB肿瘤进展过程中的作用。研究发现,在RB肿瘤的早期阶段,视锥前体细胞在G1期异常增殖,随着RB肿瘤的进展,视锥前体G2期细胞比例显著增加。同时,RB进展过程的小胶质细胞群差异分析结果显示,主要参与免疫应答的关键基因包括RPL23、B2M、HLA家族基因。本研究可为RB发病机制及进展研究提供更多新视角和数据资源。     

Human neuroblastoma tumor cell lines correspond to the arrested differentiation of chromaffin adrenal medullary neuroblasts

We have examined the hypothesis that nonhematopoietic malignancies may contain cells corresponding to those which occur during the differentiation of tissue precursors. Neuroblastoma, an embryonal tumor of the adrenal medulla, was studied because of its well described ability to differentiate both in vivo and in vitro. We examined the expression of four genes during development of the human adrenal medulla: tyrosine hydroxylase, chromagranin A, pG2, and beta-2-microglobulin. The sequential expression of these genes by adrenal neuroblasts marks successive stages during maturation of the chromaffin lineage. We also observed a population of neuroblasts during adrenal medullary development that did not express any of these four genes, suggestive of adrenal medullary cells differentiating along nonchromaffin lineage(s). We then evaluated 27 neuroblastoma cell lines for the expression of these genes and found that 24 expressed chromaffin markers, with 19 of these mimicking the pattern of gene expression found during development. Three cell lines did not express tyrosine hydroxylase, chromogranin A, or pG2, consistent with either a very undifferentiated neural crest cell or maturation along a nonchromaffin lineage. These data indicate that neuroblastoma tumor cells correspond to adrenal neuroblasts arrested during morphogenesis of the adrenal medulla and raise the possibility that malignant transformation of cells at different stages of tissue maturation may contribute to the diversity that characterizes tumors of solid tissues.     

Comparing solid tumors with cell lines: implications for identifying drug resistance genes in cancer

Gene expression arrays allow researchers to profile the differences between cell lines or tissues and they may identify genetic markers of development, organ maturation, or tumor progression. Although a primary tumor that grows in a host and a tumor-cell-line derived from that primary tumor and grown in vitro share similar gene expression profiles, there are, not unexpectedly, some important differences. In fact, Stein and colleagues have found that genes that are differentially expressed in primary tumors as compared to the specific genes expressed in their cell-line derivatives are more reliably predictive of tumor tractability. Thus, sensitivity in vitro might not reflect sensitivity in vivo. Because anti-tumor compounds are largely evaluated in cell culture assays, these compounds' therapeutic utility must be judged in light of genes described by Stein et al. that better predict tractability.     

The Relationship of Immune Cell Signatures to Patient Survival Varies within and between Tumor Types

Enhancing pre-existing anti-tumor immunity leads to therapeutic benefit for some patients, but why some tumors are more immunogenic than others remains unresolved. We took a unique systems approach to relate patient survival to immune gene expression in >3,500 tumor RNAseq profiles from a dozen tumor types. We found significant links between immune gene expression and patient survival in 8/12 tumor types, with tumors partitioned by gene expression comprising distinct molecular subtypes. T/NK cell genes were most clearly survival-related for melanoma, head and neck, and bladder tumors, whereas myeloid cell genes were most clearly survival-related with kidney and breast tumors. T/NK or myeloid cell gene expression was linked to poor prognosis in bladder and kidney tumors, respectively, suggesting tumor-specific immunosuppressive checkpoints. Our results suggest new biomarkers for existing cancer immunotherapies and identify targets for new immunotherapies.     

Average rank-based score to measure deregulation of molecular pathway gene sets

Background

Deregulation of biological pathways has been shown to be involved in the turmorigenesis of a variety of cancers. The co-regulation of pathways in tumor and normal tissues has not been studied in a systematic manner.

Results

In this study we propose a novel statistic named AR-score (average rank based score) to measure pathway activities based on microarray gene expression profiles. We calculate and compare the AR-scores of pathways in microarray datasets containing expression profiles for a wide range of cancer types as well as the corresponding normal tissues. We find that many pathways undergo significant activity changes in tumors with respect to normal tissues. AR-scores for a small subset of pathways are capable of distinguishing tumor from normal tissues or classifying tumor subtypes. In normal tissues many pathways are highly correlated in their activities, whereas their correlations reduce significantly in tumors and cancer cell lines. The co-expression of genes in the same pathways was also significantly perturbed in tumors.

Conclusions

The co-regulation of genes in the same pathways and co-regulation of different pathways are significantly perturbed in tumors versus normal tissues. Our method provides a useful tool for better understanding the mechanistic changes in tumors, which can also be used for exploring other biological problems.     

基于SVM和平均影响值的人肿瘤信息基因提取

基于基因表达谱的肿瘤分类信息基因选取是发现肿瘤特异表达基因、探索肿瘤基因表达模式的重要手段。借助由基因表达谱获得的分类信息进行肿瘤诊断是当今生物信息学领域中的一个重要研究方向,有望成为临床医学上一种快速而有效的肿瘤分子诊断方法。鉴于肿瘤基因表达谱样本数据维数高、样本量小以及噪音大等特点,提出一种结合支持向量机应用平均影响值来寻找肿瘤信息基因的算法,其优点是能够搜索到基因数量尽可能少而分类能力尽可能强的多个信息基因子集。采用二分类肿瘤数据集验证算法的可行性和有效性,对于结肠癌样本集,只需3个基因就能获得100%的留一法交叉验证识别准确率。为避免样本集的不同划分对分类性能的影响,进一步采用全折交叉验证方法来评估各信息基因子集的分类性能,优选出更可靠的信息基因子集。与基它肿瘤分类方法相比,实验结果在信息基因数量以及分类性能方面具有明显的优势。     

Determination of stromal signatures in breast carcinoma

Many soft tissue tumors recapitulate features of normal connective tissue. We hypothesize that different types of fibroblastic tumors are representative of different populations of fibroblastic cells or different activation states of these cells. We examined two tumors with fibroblastic features, solitary fibrous tumor (SFT) and desmoid-type fibromatosis (DTF), by DNA microarray analysis and found that they have very different expression profiles, including significant differences in their patterns of expression of extracellular matrix genes and growth factors. Using immunohistochemistry and in situ hybridization on a tissue microarray, we found that genes specific for these two tumors have mutually specific expression in the stroma of nonneoplastic tissues. We defined a set of 786 gene spots whose pattern of expression distinguishes SFT from DTF. In an analysis of DNA microarray gene expression data from 295 previously published breast carcinomas, we found that expression of this gene set defined two groups of breast carcinomas with significant differences in overall survival. One of the groups had a favorable outcome and was defined by the expression of DTF genes. The other group of tumors had a poor prognosis and showed variable expression of genes enriched for SFT type. Our findings suggest that the host stromal response varies significantly among carcinomas and that gene expression patterns characteristic of soft tissue tumors can be used to discover new markers for normal connective tissue cells.     

Gene expression profiling in a renal cell carcinoma cell line: dissecting VHL and hypoxia-dependent pathways

The von Hippel-Lindau tumor suppressor, pVHL, is a key player in one of the best characterized hypoxia signaling pathways, the VHL-hypoxia-inducible factor (VHL-HIF) pathway. To better understand the role of VHL in the hypoxia signaling pathways of tumor cells, we used serial analysis of gene expression (SAGE) to investigate hypoxia-regulated gene expression in renal carcinoma cells (786-0), with and without VHL. The gene expression profiles of the cancer cells were compared to SAGE profiles from normal renal proximal tubule cells grown under both normoxia and hypoxia. The data suggest that the role of VHL as a tumor suppressor may be more complex than previously thought. Further, the data reveal that renal carcinoma cells have evolved an alternative hypoxia signaling pathway(s) compared with normal renal cells. These alternative hypoxia pathways demonstrate VHL-dependent and VHL-independent regulation. The genes involved in such pathways include those with potential importance in the physiological and pathological regulation of tumor growth and angiogenesis. Some of the genes identified as showing overexpression in the cancer cells, particularly those encoding secreted or membrane-bound proteins, could be potential biomarkers for tumors or targets for rational therapeutics that are dependent on VHL status.     

A Conditional Mouse Mutant in the Tumor Suppressor SdhD Gene Unveils a Link between p21WAF1/Cip1 Induction and Mitochondrial Dysfunction

Mutations in mitochondrial complex II (MCII; succinate dehydrogenase, Sdh) genes cause familiar pheochromocytoma/paraganglioma tumors. Several mechanisms have been proposed to account for Sdh-mutation-induced tumorigenesis, the most accepted of which is based on the constitutive expression of the hypoxia-inducible factor 1α (Hif1α) at normal oxygen tension, a theory referred to as “pseudo-hypoxic drive”. Other molecular processes, such as oxidative stress, apoptosis, or chromatin remodeling have been also proposed to play a causative role. Nevertheless, the actual contribution of each of these mechanisms has not been definitively established. Moreover, the biological factors that determine the tissue-specificity of these tumors have not been identified. In this work, we made use of the inducible SDHD-ESR mouse, a conditional mutant in the SdhD gene, which encodes the small subunit of MCII, and that acts as a tumor suppressor gene in humans. The analysis of the Hif1α pathway in SDHD-ESR tissues and in two newly derived cell lines after complete SdhD loss -a requirement for hereditary paraganglioma type-1 tumor formation in humans- partially recapitulated the “pseudo-hypoxic” response and rendered inconsistent results. Therefore, we performed microarray analysis of adrenal medulla and kidney in order to identify other early gene expression changes elicited by SdhD deletion. Our results revealed that each mutant tissue displayed different variations in their gene expression profiles affecting to different biological processes. However, we found that the Cdkn1a gene was up-regulated in both tissues. This gene encodes the cyclin-dependent kinase inhibitor p21^WAF1/Cip1, a factor implicated in cell cycle, senescence, and cancer. The two SDHD-ESR cell lines also showed accumulation of this protein. This new and unprecedented evidence for a link between SdhD dysfunction and p21^WAF1/Cip1 will open new avenues for the study of the mechanisms that cause tumors in Sdh mutants. Finally, we discuss the actual role of Hif1α in tumorigenesis.     

Classifying human cancer by analysis of gene expression

With the development and application of DNA microarrays, the expression of almost all human genes can now be systematically examined in human malignancies. This can lead to the identification of candidate molecular targets for therapeutic intervention and biomarkers for early detection of these diseases. However, perhaps the most exciting result to come from this research has been the demonstration that patterns of gene expression can distinguish between tumors of different anatomical origin, and define new subgroups of cancer with similar histological appearance, but distinct molecular profiles. Some of these new molecular subclasses of tumor appear to correlate with clinical behavior. If substantiated in larger studies, this might form a basis for stratifying patients so that they receive optimal therapeutic treatment and follow-up.