Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer

Background

Structural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear.

Results

We used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. We find large and small chromothripsis events in nearly every colorectal tumor sample and show that several breakpoints of chromothripsis clusters and isolated rearrangements affect cancer genes, including NOTCH2, EXO1 and MLL3. We complemented the structural variation studies by sequencing the coding regions of a cancer exome in all colorectal tumor samples and found somatic mutations in 24 genes, including APC, KRAS, SMAD4 and PIK3CA. A pairwise comparison of somatic variations in primary and metastatic samples indicated that many chromothripsis clusters, isolated rearrangements and point mutations are exclusively present in either the primary tumor or the metastasis and may affect cancer genes in a lesion-specific manner.

Conclusions

We conclude that chromothripsis is a prevalent mechanism driving structural rearrangements in colorectal cancer and show that a complex interplay between point mutations, simple copy number changes and chromothripsis events drive colorectal tumor development and metastasis.     

Construction of preferential cDNA microarray specialized for human colorectal carcinoma: molecular sketch of colorectal cancer

cDNA microarray analyses can be used to identify candidate genes that play important roles in human carcinogenesis. To gain insight into the molecular sketch of colorectal cancer, we have constructed cDNA microarrays specialized for colorectal cancer, which we named "Colonochip" by selecting genes that are expressed in colorectal cancer, normal colonic mucosa, and liver metastatic cancer tissues. This microarray contained 4608 nonredundant cDNA clones from over 30,000 cDNA clones derived from the three types of human cDNA libraries, as well as clones from 170 additional conventional major genes suspected to be involved in colorectal carcinogenesis, according to literatures. Using this "Colonochip," we were able to identify 59 genes showing twofold or more differential expression between primary cancer and normal colonic mucosa, potent candidates for diagnosis, and therapy of colorectal cancer for further studies.     

大肠癌转移相关分子标签的筛选

目的:筛选与转移相关的大肠癌分子标签.方法:本文通过对大肠癌表达谱数据进行分析,按照表达谱中大肠癌转移情况,组织学分化程度以及患者生存时间进行显著性分析,将与大肠癌转移相关的具有显著性意义的基因群进行聚类,通过主成分分析以及自组织映射的方法计算出差异表达基因中,起着主体分类作用的基因群.结果:筛选出与肿瘤组织分化程度以及患者生存时间相关的差异表达基因,进行功能富集,并筛选出了一批与大肠癌转移密切相关的重要基因,这些基因对大肠癌早期诊断,及时治疗,预后评估有着重要意义.结论:细胞代谢,趋化因子信号通路和细胞因子受体等分子事件与大肠癌分化程度密切相关,是否发生转移与大肠癌的预后生存期密切相关.     

PDGF-D、MPO与CD15在大肠癌中的表达及临床相关性研究

目的：探讨血小板源性生长因子D（PDGF-D）、髓过氧化物酶（MPO）YL粒细胞相关抗原（CD15）在大肠癌组织中的表达及其与临床特征之间的关系。方法：采用免疫组化染色方法检测88例大肠癌组织、72例大肠腺瘤组织及50例正常大肠粘膜组织中PDGF-D、MPO及CD15的表达情况。结果：PDGF—D、MPO、CD15在大肠癌组织中的阳性表达率分别为85．23％、63．64％、61．36％。PDGF—D、MPO在正常组、大肠腺瘤组和大肠癌组三者之间的表达均有显著性差异（P〈0．05）。CD15在正常组、大肠腺瘤组中的阳性表达率与大肠癌组中的阳性表达率有显著性差异（P〈0．05）,但在正常组与大肠腺瘤组中的阳性表达率无显著性差异（P〉0．05）。PDGF—D、MPO、CD15的表达在有淋巴结转移组织中的阳性率分别为92_31％、75．00％,73．08％;在无淋巴结转移组织中的阳性率分别为75．00％、52．78％,47．22％,三者在有无淋巴结转移组织中的阳性率均有显著性差异（P〈0．05）。PDGF．D、MPO、CD15在大肠癌中的表达与性别、年龄及组织分化程度均无相关（P〉0．05）。经Spearman相关性分析,PDGF—D及MPO在大肠癌的表达具有相关性（P〈O．05）。大肠癌中CD15与PDGF—D、MPO的表达无明显相关性（P〉0．05）：结论：PDGF—D、MPO与CDl5在大肠癌中的高表达,提示均参与了大肠癌的发生发展,可作为大肠癌恶性程度和侵袭转移的分子生物学标志物。     

结直肠癌mP53 和PCNA 表达的相关性及临床意义

目的:探讨结直肠癌中突变型P53基因(mP53)和增殖细胞核抗原(PCNA)表达的相关性及临床意义。方法:应用免疫组化二步法,检测60例结直肠癌组织及20例正常肠粘膜中mP53、PCNA的表达,结合临床病理资料进行统计分析。结果:60例结直肠癌中mP53阳性表达率65.0%,PCNA阳性表达率78.3%,20例正常肠粘膜中mP53、PCNA表达均为阴性(P<0.05)。mP53和PCNA阳性表达率在低分化组、浆膜层浸润组、淋巴结转移组均较高(P均<0.05)。mP53和PCNA表达呈正相关(r=0.58,P<0.05)。结论:mP53和PCNA在结直肠癌中表达均增高,二者与结直肠癌病理学分级、浸润深度和淋巴结转移有关,可作为判断结直肠癌预后的参考指标。     

Clinical Significance of Frizzled Homolog 3 Protein in Colorectal Cancer Patients

Frizzled homolog 3 receptor was up-regulated in several gastrointestinal cancers such as esophageal and gastric cancers. Moreover, frizzled homolog 3 has recently reported to be expressed in colorectal adenoma specimens. In the present study, we investigated the clinical significance of frizzled homolog 3 protein in colorectal cancer patients. Using immunocytochemical staining, frizzled homolog 3 expression was examined in 186 colorectal cancer specimens, 79 colorectal adenoma specimens, 133 colorectal polyp specimens, 127 colorectal cancer specimens with lymph node and/or distant metastasis, 310 specimens of various non-colorectal cancer metastatic carcinomas and 40 specimens with simultaneous occurrence of colorectal cancer, colorectal adenoma and colorectal polyp. Statistical analysis was used to correlate frizzled homolog 3 protein expression to the clinicohistopathological factors, recurrence/metastasis and survival after follow-up for 42 months in colorectal cancer patients. Frizzled homolog 3 protein was expressed in 100% colorectal cancer specimens, 89% colorectal adenoma specimens, 75% colorectal polyp specimens and 69% normal colorectal epithelial tissues. Moreover, frizzled homolog 3 immunocytochemical scores were highly correlated with colorectal cancer progression. Furthermore, frizzled homolog 3 was expressed in a comparatively lower percentage of metastatic hepatocellular carcinoma and metastatic renal clear cell carcinoma with focal and very weak staining than other metastatic tumor types. On the other hand, the frizzled homolog 3 immunocytochemical scores of colorectal adenomas with synchronous colorectal carcinomas were significantly higher than those of pure colorectal adenomas. Statistical analysis showed that frizzled homolog 3 immunocytochemical scores were associated with Dukes stage and lymph node status. Finally, stratified groups of colorectal cancer patients had significant differences in their recurrence/metastasis and survival. In conclusion, the present large-scale study has clearly showed that frizzled homolog 3 protein can generate clinically important information for colorectal cancer patients.     

CREB5在大肠癌转移中的调控机制

大肠癌转移过程中所涉及的细胞信号调控网络非常复杂, 寻找调控网络中的关键调控点对阐明大肠癌转移机制以及寻找药物治疗靶点均具有重要意义。研究表明, CREB5 (cAMP responsive element binding protein 5)可能为大肠癌转移相关信号调控网络中的关键基因。文章基于大肠癌表达谱数据, 根据CREB5基因表达值的大小对大肠癌的相关分子事件进行了富集分析, 发现这些分子事件与肿瘤转移密切相关。根据CREB5能够和c-Jun结合成为异二聚体的特点, 联合分析转录因子AP-1结合位点的富集情况, 筛选出在CREB5基因高表达组中表达上调、具有AP-1结合位点、且属于癌症通路的基因16个, 这些基因所构成的分子网络与细胞迁移功能类相关度最高。细胞迁移功能类主要由5个基因——CSF1R、MMP9、PDGFRB、FIGF和IL6所构成, 因此CREB5可能是通过调控这5个关键基因进而促进大肠癌的转移。     

Plasma glycoprotein profiling for colorectal cancer biomarker identification by lectin glycoarray and lectin blot

Colorectal cancer (CRC) remains a major worldwide cause of cancer-related morbidity and mortality largely due to the insidious onset of the disease. The current clinical procedures utilized for disease diagnosis are invasive, unpleasant, and inconvenient; hence, the need for simple blood tests that could be used for the early detection of CRC. In this work, we have developed methods for glycoproteomics analysis to identify plasma markers with utility to assist in the detection of colorectal cancer (CRC). Following immunodepletion of the most abundant plasma proteins, the plasma N -linked glycoproteins were enriched using lectin affinity chromatography and subsequently further separated by nonporous silica reversed-phase (NPS-RP)-HPLC. Individual RP-HPLC fractions were printed on nitrocellulose coated slides which were then probed with lectins to determine glycan patterns in plasma samples from 9 normal, 5 adenoma, and 6 colorectal cancer patients. Statistical tools, including principal component analysis, hierarchical clustering, and Z-statistics analysis, were employed to identify distinctive glycosylation patterns. Patients diagnosed with colorectal cancer or adenomas were shown to have dramatically higher levels of sialylation and fucosylation as compared to normal controls. Plasma glycoproteins with aberrant glycosylation were identified by nano-LC-MS/MS, while a lectin blotting methodology was used to validate proteins with significantly altered glycosylation as a function of cancer progression. The potential markers identified in this study for diagnosis to distinguish colorectal cancer from adenoma and normal include elevated sialylation and fucosylation in complement C3, histidine-rich glycoprotein, and kininogen-1. These potential markers of colorectal cancer were subsequently validated by lectin blotting in an independent set of plasma samples obtained from 10 CRC patients, 10 patients with adenomas, and 10 normal subjects. These results demonstrate the utility of this strategy for the identification of N -linked glycan patterns as potential markers of CRC in human plasma, and may have the utility to distinguish different disease states.     

Linking stemness with colorectal cancer initiation,progression, and therapy

The discovery of cancer stem cells caused a paradigm shift in the concepts of origin and development of colorectal cancer. Several unresolved questions remain in this field though. Are colorectal cancer stem cells the cause or an effect of the disease? How do cancer stem cells assist in colorectal tumor dissemination to distant organs? What are the molecular or environmental factors affecting the roles of these cells in colorectal cancer? Through this review, we investigate the key findings until now and attempt to elucidate the origins, physical properties, microenvironmental niches, as well as the molecular signaling network that support the existence, self-renewal, plasticity, quiescence, and the overall maintenance of cancer stem cells in colorectal cancer. Increasing data show that the cancer stem cells play a crucial role not only in the establishment of the primary colorectal tumor but also in the distant spread of the disease. Hence, we will also look at the mechanisms adopted by cancer stem cells to influence the development of metastasis and evade therapeutic targeting and its role in the overall disease prognosis. Finally, we will illustrate the importance of understanding the biology of these cells to develop improved clinical strategies to tackle colorectal cancer.     

直肠癌组织中PTEN和Notch1的表达及其与临床病理参数的关系

目的:探究直肠癌组织中PTEN和Notch1的表达及其与临床病理参数的关系。方法:收集2014年1月~2015年4月,我院肿瘤外科确诊48例直肠癌病理组织标本与20例直肠癌患者癌旁正常组织标本为研究对象,应用免疫组化链霉菌抗生物素蛋白-过氧化物酶连结法(S-P法)分析PTEN和Notch1蛋白在直肠癌病理组织和正常组织中的表达情况。结果:PTEN和Notch1主要表达于直肠癌组织细胞质中,呈现棕黄色;Notch1在直肠癌病理组织中表达率显著高于正常组织(P0.05);PTEN在正常组织表达率显著高于在直肠癌组织(P0.05);Notch1在淋巴转移、中底分化及分期为C期患者病理组织中表达率较高(P0.05);PTEN在无淋巴转移、中底分化程度及A+B期患者病理组织表达率较高(P0.05);相关性分析显示,Notch1和PTEN在直肠癌病理组织中表达呈现负相关关系(r=-0.534,P=0.000)。结论:Notch1和PTEN表达失调在直肠癌的发生、发展和淋巴结转移中有重要作用;PTEN表达可能对直肠癌的发生、发展具有抑制作用,Notch1表达可能对直肠癌的发生、发展具有促进作用。     

Stem cell gene Girdin: a potential early liver metastasis predictor of colorectal cancer

The objective of this study is to investigate the liver's metastasis-related genes and the relationship between Girdin protein expression and clinical and pathological characteristics and prognosis in colorectal cancer. The differential expression of genes between tumor cells from cases with liver metastasis and those from cases without liver metastasis were detected using an RT(2) Profiler? PCR Array. The expression of the stem cell gene Girdin was analyzed using immunohistochemistry staining. Subsequently, the relationship between Girdin and clinicopathological parameters of colorectal cancer was determined. The Girdin protein was verified as a gene related to liver metastasis and was expressed positively in 161 (37.01 %) of the 435 cases examined. The expression of Girdin protein was related to histological grade and distant metastasis (P = 0.007 and 0.007, respectively). After analyzing survival rates, cases with highly expressed Girdin protein were shown to attain a significantly higher rate of liver metastasis and poorer postoperative, disease-specific survival than those with no or low expressed Girdin protein (P = 0.001). In the Cox regression test, the depth of tumor invasion, histological grade, duke's stage, distant metastasis, and the Girdin protein were detected as an independent prognostic factor (0.020, 0.032, 0.001, 0.001, and 0.010, respectively). The Girdin protein may be a potential new early liver metastasis biomarker of colorectal cancer.     

Robust consensus clustering for identification of expressed genes linked to malignancy of human colorectal carcinoma

Previous studies have been conducted in gene expression profiling to identify groups of genes that characterize the colorectal carcinoma disease. Despite the success of previous attempts to identify groups of genes in the progression of the colorectal carcinoma disease, their methods either require subjective interpretation of the number of clusters, or lack stability during different runs of the algorithms. All of which limits the usefulness of these methods. In this study, we propose an enhanced algorithm that provides stability and robustness in identifying differentially expressed genes in an expression profile analysis. Our proposed algorithm uses multiple clustering algorithms under the consensus clustering framework. The results of the experiment show that the robustness of our method provides a consistent structure of clusters, similar to the structure found in the previous study. Furthermore, our algorithm outperforms any single clustering algorithms in terms of the cluster quality score.     

Correlation of N-myc downstream-regulated gene 1 subcellular localization and lymph node metastases of colorectal neoplasms

In colorectal neoplasms, N-myc downstream-regulated gene 1 (NDRG1) is a primarily cytoplasmic protein, but it is also expressed on the cell membrane and in the nucleus. NDRG1 is involved in various stages of tumor development in colorectal cancer, and it is possible that the different subcellular localizations may determine the function of NDRG1 protein. Here, we attempt to clarify the characteristics of NDRG1 protein subcellular localization during the progression of colorectal cancer. We examined NDRG1 expression in 49 colorectal cancer patients in cancerous, non-cancerous, and corresponding lymph node tissues. Cytoplasmic and membrane NDRG1 expression was higher in the lymph nodes with metastases than in those without metastases (P < 0.01). Nuclear NDRG1 expression in colorectal neoplasms was significantly higher than in the normal colorectal mucosa, and yet the normal colorectal mucosa showed no nuclear expression. Furthermore, our results showed higher cytoplasmic NDRG1 expression was better for differentiation, and higher membrane NDRG1 expression resulted in a greater possibility of lymph node metastasis. These data indicate that a certain relationship between the cytoplasmic and membrane expression of NDRG1 in lymph nodes exists with lymph node metastasis. NDRG1 expression may translocate from the membrane of the colorectal cancer cells to the nucleus, where it is involved in lymph node metastasis. Combination analysis of NDRG1 subcellular expression and clinical variables will help predict the incidence of lymph node metastasis.     

Inhibitory effect of starfish polysaccharides on metastasis in HT-29 human colorectal adenocarcinoma

In the present study, we investigated the effects of starfish (Asterina pectinifera) polysaccharides on cancer proliferation and metastasis in HT-29 human colorectal adenocarcinoma. Cytokine-stimulated expression of inducible nitric oxide synthase (iNOS), which is closely associated with cancer proliferation, invasion and metastasis, was dose-dependently diminished by treatment with the starfish polysaccharides. 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced activity and expression of matrix metalloproteinase (MMP)-2, a major inducer of metastasis in colorectal cancer, were also down-regulated in a dose-dependent manner. In contrast, tissue inhibitor of matrix metalloproteinase (TIMP)-1 and -2 mRNA, which play critical roles in preventing metastasis, increased over the polysaccharides concentration range 10 ?? 120 ??g/mL. In the wound healing assay, HT-29 human colorectal adenocarcinoma migration activated by TPA was decreased by treatment with the starfish polysaccharides. These results indicate that the starfish polysaccharides inhibited human colorectal cancer proliferation and metastasis by preventing nitrogen oxide synthesis, which occurred via inhibition of iNOS and MMP-2 activity and expression and induction of TIMP-1 and -2 expressions. This report demonstrates that starfish polysaccharides may be used as an anti-proliferation and -metastatic material for the treatment of human colorectal cancer.     

沉默FOXQ1可逆转SW480细胞的上皮-间质转化

FOXQ1是FOX家族的的重要成员之一,其参与了多种人类肿瘤的上皮间质转化(epithelial- mesenchymal transition,EMT).本研究设计合成了FOXQ1基因的shRNA（short hairpin RNA）,用此转染SW480细胞,通过显微镜观察细胞形态,Transwell小室、细胞黏附试验检测转移能力及黏附能力,以探索FOXQ1与结直肠癌细胞EMT的关系.结果显示,沉默FOXQ1后,SW480细胞顶底极性及细胞间紧密连接增加,侵袭、迁移的细胞数目减少,同种黏附能力增加,异种黏附能力降低.进一步的机制研究表明,沉默FOXQ1基因可以导致SW480细胞的上皮标志因子E-cadherin表达显著增高,而间质细胞标志因子N-cadherin、Vimentin及MMP2表达均降低.以上结果表明,沉默FOXQ1基因可以逆转SW480细胞EMT,其机制可能与E-cadherin的上调和N cadherin、Vimentin、MMP2的下调有关,这为进一步研究FOXQ1在结直肠癌发生发展中的作用提供实验基础.     

PMEPA1 induces EMT via a non‐canonical TGF‐β signalling in colorectal cancer

Prostate transmembrane protein androgen induced 1 (PMEPA1) has been reported to promote cancer progression. Metastasis is the main factor leading to cancer progression and poor prognosis, and at the beginning of metastasis, epithelial‐to‐mesenchymal transition (EMT) is a crucial activation. However, the relationship between PMEPA1 and EMT in colorectal cancer metastasis is still poorly understood. In this study, we first testified that PMEPA1 expresses higher in tumour than normal tissue in Gene Expression Omnibus database, in the Cancer Genome Atlas (TCGA) as well as in the clinical data we collected. Moreover, the higher expression was associated with poor prognosis. We furthermore demonstrated PMEPA1 promotes colorectal cancer metastasis and EMT in vivo and in vitro. We found that PMEPA1 activates the bone morphogenetic proteins (BMP) signalling of TGF‐β signalling resulting in promoting EMT and accelerating the proliferation and metastasis of colorectal cancer.     

Prediction of human disease-related gene clusters by clustering analysis

Since genes associated with similar diseases/disorders show an increased tendency for their protein products to interact with each other through protein-protein interactions (PPI), clustering analysis obviously as an efficient technique can be easily used to predict human disease-related gene clusters/subnetworks. Firstly, we used clustering algorithms, Markov cluster algorithm (MCL), Molecular complex detection (MCODE) and Clique percolation method (CPM) to decompose human PPI network into dense clusters as the candidates of disease-related clusters, and then a log likelihood model that integrates multiple biological evidences was proposed to score these dense clusters. Finally, we identified disease-related clusters using these dense clusters if they had higher scores. The efficiency was evaluated by a leave-one-out cross validation procedure. Our method achieved a success rate with 98.59% and recovered the hidden disease-related clusters in 34.04% cases when removed one known disease gene and all its gene-disease associations. We found that the clusters decomposed by CPM outperformed MCL and MCODE as the candidates of disease-related clusters with well-supported biological significance in biological process, molecular function and cellular component of Gene Ontology (GO) and expression of human tissues. We also found that most of the disease-related clusters consisted of tissue-specific genes that were highly expressed only in one or several tissues, and a few of those were composed of housekeeping genes (maintenance genes) that were ubiquitously expressed in most of all the tissues.