Identification of Putative Biomarkers for the Early Stage of Porcine Spermatogonial Stem Cells Using Next-Generation Sequencing

To identify putative biomarkers of porcine spermatogonial stem cells (pSSCs), total RNA sequencing (RNA-seq) analysis was performed on 5- and 180-day-old porcine testes and on pSSC colonies that were established under low temperature culture conditions as reported previously. In total, 10,184 genes were selected using Cufflink software, followed by a logarithm and quantile normalization of the pairwise scatter plot. The correlation rates of pSSCs compared to 5- and 180-day-old testes were 0.869 and 0.529, respectively and that between 5- and 180-day-old testes was 0.580. Hierarchical clustering data revealed that gene expression patterns of pSSCs were similar to 5-day-old testis. By applying a differential expression filter of four fold or greater, 607 genes were identified between pSSCs and 5-day-old testis, and 2118 genes were identified between the 5- and 180-day-old testes. Among these differentially expressed genes, 293 genes were upregulated and 314 genes were downregulated in the 5-day-old testis compared to pSSCs, and 1106 genes were upregulated and 1012 genes were downregulated in the 180-day-old testis compared to the 5-day-old testis. The following genes upregulated in pSSCs compared to 5-day-old testes were selected for additional analysis: matrix metallopeptidase 9 (MMP9), matrix metallopeptidase 1 (MMP1), glutathione peroxidase 1 (GPX1), chemokine receptor 1 (CCR1), insulin-like growth factor binding protein 3 (IGFBP3), CD14, CD209, and Kruppel-like factor 9 (KLF9). Expression levels of these genes were evaluated in pSSCs and in 5- and 180-day-old porcine testes. In addition, immunohistochemistry analysis confirmed their germ cell-specific expression in 5- and 180-day-old testes. These finding may not only be useful in facilitating the enrichment and sorting of porcine spermatogonia, but may also be useful in the study of the early stages of spermatogenic meiosis.     

Learning Biomarkers of Pluripotent Stem Cells in Mouse

Pluripotent stem cells are able to self-renew, and to differentiate into all adult cell types. Many studies report data describing these cells, and characterize them in molecular terms. Machine learning yields classifiers that can accurately identify pluripotent stem cells, but there is a lack of studies yielding minimal sets of best biomarkers (genes/features). We assembled gene expression data of pluripotent stem cells and non-pluripotent cells from the mouse. After normalization and filtering, we applied machine learning, classifying samples into pluripotent and non-pluripotent with high cross-validated accuracy. Furthermore, to identify minimal sets of best biomarkers, we used three methods: information gain, random forests and a wrapper of genetic algorithm and support vector machine (GA/SVM). We demonstrate that the GA/SVM biomarkers work best in combination with each other; pathway and enrichment analyses show that they cover the widest variety of processes implicated in pluripotency. The GA/SVM wrapper yields best biomarkers, no matter which classification method is used. The consensus best biomarker based on the three methods is Tet1, implicated in pluripotency just recently. The best biomarker based on the GA/SVM wrapper approach alone is Fam134b, possibly a missing link between pluripotency and some standard surface markers of unknown function processed by the Golgi apparatus.     

Development of On-Chip Multi-Imaging Flow Cytometry for Identification of Imaging Biomarkers of Clustered Circulating Tumor Cells

An on-chip multi-imaging flow cytometry system has been developed to obtain morphometric parameters of cell clusters such as cell number, perimeter, total cross-sectional area, number of nuclei and size of clusters as “imaging biomarkers”, with simultaneous acquisition and analysis of both bright-field (BF) and fluorescent (FL) images at 200 frames per second (fps); by using this system, we examined the effectiveness of using imaging biomarkers for the identification of clustered circulating tumor cells (CTCs). Sample blood of rats in which a prostate cancer cell line (MAT-LyLu) had been pre-implanted was applied to a microchannel on a disposable microchip after staining the nuclei using fluorescent dye for their visualization, and the acquired images were measured and compared with those of healthy rats. In terms of the results, clustered cells having (1) cell area larger than 200 µm² and (2) nucleus area larger than 90 µm² were specifically observed in cancer cell-implanted blood, but were not observed in healthy rats. In addition, (3) clusters having more than 3 nuclei were specific for cancer-implanted blood and (4) a ratio between the actual perimeter and the perimeter calculated from the obtained area, which reflects a shape distorted from ideal roundness, of less than 0.90 was specific for all clusters having more than 3 nuclei and was also specific for cancer-implanted blood. The collected clusters larger than 300 µm² were examined by quantitative gene copy number assay, and were identified as being CTCs. These results indicate the usefulness of the imaging biomarkers for characterizing clusters, and all of the four examined imaging biomarkers—cluster area, nuclei area, nuclei number, and ratio of perimeter—can identify clustered CTCs in blood with the same level of preciseness using multi-imaging cytometry.     

间充质干细胞与肿瘤转移

间充质干细胞是一类能够自我更新、具有多向分化潜能的成体干细胞。近年来,有证据认为间充质干细胞是肿瘤组织中基质细胞的祖先,因此间充质干细胞微环境与肿瘤转移的关系逐渐成为研究热点,但间充质干细胞对肿瘤转移是促进还是抑制,目前的研究并不一致。我们简要综述了间充质干细胞参与肿瘤转移的研究进展。     

应用蛋白质组学的方法筛选胰腺干细胞标记物

探索利用蛋白质组学的方法筛选胰腺干细胞的标记物.通过大鼠胰腺大部分切除(Px)的方法建立胰腺增生模型,采用双向电泳(2DE)分离比较Px术后第3天大鼠增生胰腺组织与假手术(Sx)非增生胰腺组织蛋白质的表达谱差异,用基质辅助激光解吸离子化飞行时间质谱(MALDI-TOF-MS)和肽质量指纹图谱(PMF)的方法对差异蛋白进行鉴定,进一步经生物信息学检索,筛选与胚胎发育和细胞分化相关的蛋白质分子.蛋白质印迹分析蛋白质HSP47、Vimentin在Px大鼠胰腺组织中的表达,以验证2DE的结果.2DE显示Sx和Px大鼠胰腺组织平均蛋白质点数分别为(1369±31)和(1315±28)个,其中共有91个蛋白质点出现1.5倍以上的表达差异.所有差异蛋白质点PMF鉴定出53种蛋白质,其中Vimentin,cytokeratin8(CK8),lymphocytecytosolicprotein1(L-plastin),heterogeneousnuclearribonucleoproteinA2/B1(hnRNPA2/B1)和L-arginine:glycineamidinotransferase(AGAT)与胚胎发育和细胞分化有关,这些蛋白质可能是胰腺干细胞潜在的候选标记物.总之,蛋白质组学的方法利用其高通量的特点能有效发现潜在的胰腺干细胞生物学标记物.     

Phosphoprotein Secretome of Tumor Cells as a Source of Candidates for Breast Cancer Biomarkers in Plasma

Breast cancer is a heterogeneous disease whose molecular diversity is not well reflected in clinical and pathological markers used for prognosis and treatment selection. As tumor cells secrete proteins into the extracellular environment, some of these proteins reach circulation and could become suitable biomarkers for improving diagnosis or monitoring response to treatment. As many signaling pathways and interaction networks are altered in cancerous tissues by protein phosphorylation, changes in the secretory phosphoproteome of cancer tissues could reflect both disease progression and subtype. To test this hypothesis, we compared the phosphopeptide-enriched fractions obtained from proteins secreted into conditioned media (CM) derived from five luminal and five basal type breast cancer cell lines using label-free quantitative mass spectrometry. Altogether over 5000 phosphosites derived from 1756 phosphoproteins were identified, several of which have the potential to qualify as phosphopeptide plasma biomarker candidates for the more aggressive basal and also the luminal-type breast cancers. The analysis of phosphopeptides from breast cancer patient plasma and controls allowed us to construct a discovery list of phosphosites under rigorous collection conditions, and second to qualify discovery candidates generated from the CM studies. Indeed, a set of basal-specific phosphorylation CM site candidates derived from IBP3, CD44, OPN, FSTL3, LAMB1, and STC2, and luminal-specific candidates derived from CYTC and IBP5 were selected and, based on their presence in plasma, quantified across all cell line CM samples using Skyline MS1 intensity data. Together, this approach allowed us to assemble a set of novel cancer subtype specific phosphopeptide candidates for subsequent biomarker verification and clinical validation.Breast cancer (BC)¹ is a heterogeneous disease whose molecular complexity and diversity is not well reflected in current clinical and pathological markers. Therefore, there is a critical need to increase the number of clinically suitable biomarkers that better reflect the many molecular subtypes of BC (1–3). BC can be categorized by gene expression profiling and molecular pathology into three major clinical types, each with different natural histories and therapeutic recommendations, and exhibiting significant molecular and clinical heterogeneity. First, luminal estrogen receptor (ER) positive breast cancers exist in luminal A and B subtypes; they are the most numerous and clinically diverse of all breast cancers, with luminal A tumors having the more favorable prognosis because of their responsiveness to targeted endocrine therapy compared with the more proliferative luminal B tumors. Second, human epidermal growth factor receptor-2 (HER2/ErbB2) amplified breast cancers, despite having poor prognosis in the absence of any systemic adjuvant therapy, can now be successfully treated with HER2-targeted agents. Third, basal-like breast cancers are among the most aggressive tumors, and are further subdivided. Those with BRCA1-like features are modeled by basal-A breast cancer cell lines, and those with mesenchymal and stem/progenitor-cell features are modeled by basal-B breast cancer cell lines (4). This latter subtype of basal-like tumors include triple negative breast cancers (TNBC), lacking expression of ER, progesterone receptor (PR), and HER2, and therefore not susceptible to more advanced targeted treatment options and requiring aggressive chemotherapy with otherwise very poor prognosis (5).BC is the leading cause of adult female mortality worldwide, caused by recurrent spread of metastatic disease that is thought to have seeded prior to the time of primary tumor excision (6). Thus, blood-based biomarkers that are highly specific as well as capable of detecting BC prior to primary tumor diagnosis offer the potential to decrease BC morbidity as well as identify the most appropriate treatment options (7). As cancer cells are known to secrete proteins into the extracellular microenvironment that modify cell adhesion, intercellular communication, motility, and invasiveness (8), it is expected that some will enter the blood stream and become suitable targets for early noninvasive diagnosis or monitoring of treatment progression.It is well recognized that blood contains hormones, cytokines, and other nonhormonal proteins, as well as a tissue leakage products and secretions from diseased tissues and tumors (9). Secreted proteins are often in the low abundance range of plasma protein concentrations, and likely contain proteins specific for distinct tumor and/or tissue types. Because tumorogenesis is known to involve changes in cellular signaling pathways involving protein kinases, protein phosphorylation is a particularly promising target for the detection of such activated pathways in BC (10). For example, almost half of the tyrosine kinases of the human “kinome” are implicated in human cancers (11) as well as numerous serine-threonine kinases, including Akt and mTOR (12, 13). Kinases participating in signal transduction pathways phosphorylate their substrates altering their conformation, localization, and activity, which in turn modulates downstream protein effectors and alters cellular processes. Like other posttranslational modifications, changes in the phosphorylation status of a protein do not directly correlate with changes in expression, and are therefore not accounted for in most gene expression or protein array analyses (14). Therefore, we hypothesized that phosphoproteins secreted or shed by cancer cells constitute a largely overlooked source of biomarker candidates that could be correlated with BC subtypes and/or disease status (15, 16).To test this hypothesis, we analyzed the conditioned media (CM) from human cancer cell lines, a well-established model for the discovery of disease-specific biomarkers (17, 18). Breast cancer cell lines derived from primary tumors or pleural effusions are a good model of BC, mirroring molecular characteristics of primary breast tumors (19). The use of CM is also advantageous in that it provides sufficient amounts of sample to identify candidates that can subsequently be targeted in more limited breast cancer patient plasma samples. To examine the phosphorylation status of secreted proteins, we examined a panel of five luminal and five basal type BC cell lines thought to emulate the molecular characteristics of most primary breast tumor types, including four basal-B subtypes corresponding to TNBC (19). A mass spectrometry-based proteomic approach was used that employed HILIC fractionation, TiO₂ affinity enrichment of phosphopeptides, and final mass spectrometric analysis by reverse-phase liquid chromatography and label-free quantification (Fig. 1). MS1 Filtering in Skyline (20, 21) was used to quantify relative differences in site-specific protein phosphorylation between secretomes of BC cell lines derived from breast tumor subtypes to discern luminal or basal tumor specificity. Lastly, plasma obtained from breast cancer patients and controls were analyzed in an optimized workflow suitable to both preserve and identify phosphopeptides, and to qualify a subset of biomarker candidates selected from the CM analysis (Fig. 1). Overall, we identified 107 phosphorylation sites specific for basal-type tumors derived from 84 proteins and 95 phosphorylation sites specific for luminal-type tumors derived from 64 proteins. Moreover, we qualified the presence of seven basal type specific and two luminal specific phosphosites derived from eight phosphoproteins in BC patient and control plasma.

Table I

Luminal and basal breast cancer cell lines

Circulating Tumor DNA as Biomarkers for Cancer Detection

Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers. ctDNAs are detected and tracked primarily based on tumor-related genetic and epigenetic alterations. In this article, we reviewed the available studies on ctDNA detection and described the representative methods. We also discussed the current understanding of ctDNAs in cancer patients and their availability as potential biomarkers for clinical purposes. Considering the progress made and challenges involved in accurate detection of specific cell-free nucleic acids, ctDNAs hold promise to serve as biomarkers for cancer patients, and further validation is needed prior to their broad clinical use.     

Stochastic Dynamics of Hematopoietic Tumor Stem Cells

Many tumors derive from the transformation of normal stem cells into cancer stem-cells that retain their self-renewal capacity. This modern view of cancer has provided a natural explanation for the striking parallels which exist between these two different types of self-renewing cells. Here we develop a simple mathematical model to investigate the implications of this concept regarding the evolution of tumors in the hematopoietic system. Our results unequivocally demonstrate that stochastic effects related to the finite size of the active stem-cell population have a profound influence on the dynamics of cancer evolution. For input parameters compatible with both the natural history of human cancer and mouse models, our results show how stochastic dynamics alone may lead to both remission in some cases and rapid expansion in others.     

间充质干细胞与肿瘤的关系

最近的研究表明问充质干细胞(mesenchymal stem cells,MSCs)与多种肿瘤的发生发展有密切关系.MSCs对多种肿瘤具有趋向性,外源性(局部混合注射或静脉注射)MSCs可参与肿瘤间质的形成,同时MSCs的免疫抑制作用可以促进肿瘤在体内的生长.通过细胞因子介导或直接的细胞接触,MSCs与多种肿瘤细胞之间存在相互作用.MSCs可以抑制肿瘤细胞的的凋亡,促进肿瘤细胞的增殖及肿瘤的转移.由于MSCs易于分离、体外扩增及进行基因修饰,因此可以利用MSCs对肿瘤的趋向性,使MSCs携带抗肿瘤基因来实现对肿瘤的靶向治疗.     

颌突外胚间充质干细胞(EMSCs)的体外分离及鉴定

外胚间充质(ectomesenchyme)是一种胚胎发育早期颅面部出现的多能性结构(multipotentstructure),大多数颅面部结构和组织均由其衍生而来,这提示外胚间充质中存在一种干细胞,即外胚间充质干细胞(ectomesenchymalstemcells,EMSCs)。为了分离和鉴定EMSCs,对E125的SD大鼠颌突组织细胞进行了流式细胞学分析,发现其中的外胚间充质细胞表达多种神经谱系和中胚层谱系的标志,包括p75、CD57和nestin等。根据此特点,采用磁细胞分离技术对p75+的颌突外胚间充质细胞进行了分离和克隆培养。克隆分析表明,单个p75+细胞经过10～14d培养,可以形成由两种或两种以上细胞组成的多潜能性克隆(multipotentclone),提示该群外胚间充质细胞具有多潜能性。同时,亚克隆分析表明,多潜能性子克隆中的单个p75+细胞具有再次形成多潜能性克隆的能力,说明这些细胞在体外具有自我更新的能力。这些结果提示,p75+细胞同时具有多潜能性和自我更新能力,因此是外胚间充质干细胞。该干细胞的分离对于口腔颅面部的起源和发育研究无疑具有重要意义。此外,该干细胞的高度可塑性也预示它可以作为一种新的种子细胞,为组织工程皮肤、肌肉、软骨的研究提供新思路。     

MiR-138 Acts as a Tumor Suppressor by Targeting EZH2 and Enhances Cisplatin-Induced Apoptosis in Osteosarcoma Cells

Chemotherapeutic insensitivity remains a major obstacle to treating osteosarcoma effectively. Recently, increasing evidence has suggested that microRNAs (miRNAs) are involved in drug resistance. However, the effect of miR-138 on cisplatin chemoresistance in osteosarcoma has not been reported. We used real-time PCR to detect the expression of mature miR-138 in osteosarcoma tissues and cell lines. Cell proliferation, invasion, and migration assays were used to observe changes to the osteosarcoma malignant phenotype. MiR-138 was downregulated in osteosarcoma tissues and cell lines, and miR-138 overexpression negatively regulated osteosarcoma cell proliferation, migration, and invasion. We also verified that EZH2 is a direct target of miR-138. Furthermore, enhancing EZH2 expression reduced the inhibitory effects of miR-138 on osteosarcoma. Proliferation, apoptosis assays and caspase-3 activity assay confirmed that elevated miR-138 expression enhanced osteosarcoma cell chemosensitivity to cisplatin by targeting EZH2. In conclusion, the present study demonstrates that miR-138 acts as a tumor suppressor by enhancing osteosarcoma cell chemosensitivity and supports its potential application for treating osteosarcoma in the future.     

肿瘤干细胞起源及其生物学特性

肿瘤干细胞与正常成体干细胞在自我更新与增殖分化能力、表型标记和强耐药性等诸多方面存在着相类似的生物学特征,所以肿瘤干细胞被推测为肿瘤发生的细胞起源。基于肿瘤干细胞与正常干细胞之间的相似性质和肿瘤发生的分子机制,科学家建立了一系列从肿瘤组织或肿瘤细胞系分离肿瘤干细胞的实验方法和研究肿瘤干细胞起源的动物实验模型。现就目前在肿瘤干细胞起源和生物学特性领域的研究作概括阐述。     

肿瘤干细胞在肿瘤治疗中的研究进展

肿瘤干细胞(cancer stem cells,CSCs)学说的成熟发展和研究成为当前肿瘤治疗研究的热点之一,因其特殊的生物学特性在肿瘤防治中起重要作用。以CSCs为靶点为肿瘤治疗开辟了一条新思路。传统的治疗不能有效靶向CSC,开发针对CSC靶向治疗的新方法,将对肿瘤的耐药、复发、转移具有革新意义。     

肿瘤干细胞与肿瘤相关巨噬细胞的相互作用

肿瘤微环境(tumor microenvironment,TME)不仅促进了肿瘤的早期形成和远处转移,而且随着肿瘤的进展,其自身也不断地发生变化。作为TME的重要组成部分,肿瘤相关巨噬细胞(tumor associated macrophages,TAMs)可通过分泌多种细胞因子激活IL-6/STAT3、TGF-β、Wnt/β-catenin等信号通路促进肿瘤干细胞(cancer stem cells,CSCs)的存活、自我更新和化疗耐药等。同时,CSCs也可通过分泌多种细胞因子和趋化因子等募集巨噬细胞,并将其诱导为TAMs重塑CSCs特定的生态位,维持CSCs表型并促进肿瘤进展。TAMs与CSCs的相互作用在促进肿瘤生长、转移及化疗耐药等方面发挥了重要作用。本文对TME中CSCs与TAMs相互作用的研究进行综述,并总结了以CSCs与TAMs相互作用为靶点在新型癌症治疗以及增强化疗效果等方面的重要潜力。     

Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood

Covalently closed circular RNA molecules (circRNAs) have recently emerged as a class of RNA isoforms with widespread and tissue specific expression across animals, oftentimes independent of the corresponding linear mRNAs. circRNAs are remarkably stable and sometimes highly expressed molecules. Here, we sequenced RNA in human peripheral whole blood to determine the potential of circRNAs as biomarkers in an easily accessible body fluid. We report the reproducible detection of thousands of circRNAs. Importantly, we observed that hundreds of circRNAs are much higher expressed than corresponding linear mRNAs. Thus, circRNA expression in human blood reveals and quantifies the activity of hundreds of coding genes not accessible by classical mRNA specific assays. Our findings suggest that circRNAs could be used as biomarker molecules in standard clinical blood samples.     

LRH-1在肿瘤及干细胞中的功能研究进展

核受体(nuclear receptors,NRs)是转录因子家族中最大的成员,多以配体依赖的方式特异性调节其靶基因的表达,参与机体代谢、发育和生殖功能的调控。LRH-1(liver receptor homolog-1),也称为NR5A2(nuclear receptor subfamily 5,group A,member 2),是核受体家族的成员,作为转录共激活子调控相关基因的表达。LRH-1调控多种重要的生理功能,包括调节脂肪酸和胆固醇的代谢,另外在胚胎发育和分化中也起了重要作用。LRH-1在促进多种癌症的发生过程中扮演重要的角色,如结肠癌、胰腺癌、卵巢癌和乳腺癌。随着对LRH-1研究的深入,其在疾病和胚胎干细胞中的功能作用已备受关注,这也使得LRH-1成为了许多疾病的潜在治疗靶点。     

Tumor suppressor activity of CBX7 in lung carcinogenesis

The generation of knockout mice for the Cbx7 gene validates the tumor suppressor role of CBX7, whose expression is lost in several human malignancies. Indeed, these mice developed liver and lung adenomas and carcinomas. Cyclin E overexpression due to the lack of Cbx7 negative regulation of its expression likely accounts for the phenotype of the Cbx7-KO mice. A similar mechanism is likely involved in human lung carcinogenesis, since cyclin E upregulation associated with the loss of CBX7 expression has been observed in most of the human lung carcinomas analyzed.