Gene expression profiling of primary vitreoretinal lymphoma

The characteristics of tumor cells of primary vitreoretinal lymphoma (PVRL) have not been defined, although researches have shown that most cases are of diffuse large B‐cell lymphoma (DLBCL). To determine the subtype and biological characteristics of tumor cells of PVRL, we performed a gene expression profiling analysis. RNA was extracted from the vitreous fluid of 7 PVRL patients and from nodal samples of 10 DLBCL patients: 6 of germinal center B‐cell (GCB) type and 4 of activated B‐cell (ABC) type determined by Hans’ criteria. Six PVRL samples showed gene expression profiles that were similar to each other. The patterns were different from those of the ABC‐type nodular DLBCL but relatively close to those of the GCB‐type nodular DLBCL. Interestingly, all of the 6 examined PVRL samples had either MYD88^L265P or mutation in the immunoreceptor tyrosine‐based activation motif (ITAM) region of CD79B. Five PVRL patients with similar gene expression profiles were treated with a standardized regimen: intravitreal administration of methotrexate (MTX) followed by six courses of systemic high doses of MTX. As a result, 2 patients had CD79B mutations and showed early central nervous system (CNS) progression. Patients without CNS progression did not have this mutation. In conclusion, PVRL had unique genetic features: an expression pattern different from ABC‐type and relatively close to GCB‐type DLBCL. CD79B mutations showed potential to serve as prognostic markers for CNS progression.     

Gene expression profiling and clinical outcome in melanoma: in search of novel prognostic factors

To obtain insight into the mechanisms of tumor progression in cutaneous malignant melanoma (CMM), and in search of new prognostic markers, gene expression profiling on a series of CMMs with known follow-up was performed. We identified an expression signature of 254 genes with prognostic significance, with a predictive accuracy comparable to that obtainable from tumor thickness and ulceration. Most of these genes were correlated with thickness, thereby stressing the importance of thickness in the prognosis of CMM. On immunohistochemistry, eight new prognostic markers were identified, of which three (mini-chromosome maintenance proteins 3, 4 and 6) had independent prognostic value. These data provide new information regarding CMM progression. As several of the progression-related genes encode molecules that are the target of established or experimental therapies, our results may hopefully contribute to the treatment of end-stage CMM patients.     

A clinically relevant orthotopic xenograft model of ependymoma that maintains the genomic signature of the primary tumor and preserves cancer stem cells in vivo

Limited availability of in vitro and in vivo model systems has hampered efforts to understand tumor biology and test novel therapies for ependymoma, the third most common malignant brain tumor that occurs in children. To develop clinically relevant animal models of ependymoma, we directly injected a fresh surgical specimen from a 9-year-old patient into the right cerebrum of RAG2/severe complex immune deficiency (SCID) mice. All five mice receiving the initial transplantation of the patient tumor developed intracerebral xenografts, which have since been serially subtransplanted in vivo in mouse brains for 4 generations and can be cryopreserved for long-term maintenance of tumorigenicity. The xenograft tumors shared nearly identical histopathological features with the original tumors, harbored 8 structural chromosomal abnormalities as detected with spectral karyotyping, maintained gene expression profiles resembling that of the original patient tumor with the preservation of multiple key genetic abnormalities commonly found in human ependymomas, and contained a small population (<2.2%) of CD133⁺ stem cells that can form neurospheres and display multipotent capabilities in vitro. The permanent cell line (BXD-1425EPN), which was derived from a passage II xenograft tumor and has been passaged in vitro more than 70 times, expressed similar differentiation markers of the xenograft tumors, maintained identical chromosomal abnormalities, and formed tumors in the brains of SCID mice. In conclusion, direct injection of primary ependymoma tumor cells played an important role in the generation of a clinically relevant mouse model IC-1425EPN and a novel cell line, BXD-1425EPN. This cell line and model will facilitate the biological studies and preclinical drug screenings for pediatric ependymomas.     

Gene expression profiling for the diagnosis of acute leukaemia

An optimised diagnostic setting in acute leukaemias combines cytomorphology and cytochemistry, multiparameter immunophenotyping, cytogenetics, fluorescence in situ hybridisation, and polymerase chain reaction (PCR)-based assays. This allows classification and definition of biologically defined and prognostically relevant subtypes, and allows directed treatment in some sub-entities. Over the last years the microarray technology has helped to quantify simultaneously the expression status of ten thousands of genes in single experiments. This novel approach will hopefully become an essential tool for the molecular classification of acute leukaemias in the near future. It can be anticipated that new biologically defined and clinically relevant subtypes of leukaemia will be identified based on their unique gene expression profiles. This method may therefore guide therapeutic decisions and should be investigated in a diagnostic setting in parallel to established standard methods.     

肺腺癌患者淋巴转移的分子指纹鉴定

背景与目的：远处转移是肺癌患者的重要死因,癌转移可能与细胞内基因表达模式改变有关。急需运用新技术来筛选和分析这些基因,以便进一步阐明癌转移的机制并寻找新的治疗靶点。本研究旨在筛选肺腺癌患者淋巴转移差异表达基因。方法：原发癌组织及区域淋巴结取自22例接受根治性手术的肺腺癌患者。根据组织来源将标本分为三组：不伴淋巴转移的肺腺癌组织（TxN-,n=11）、伴有淋巴转移的肺腺癌组织（TxN＋,n=11）及相应转移淋巴结中的肺腺癌细胞（N＋,n=11）。对各组进行激光显微切割以获得纯净癌细胞,T7RNA线性扩增获取足够量的RNA,实验通道和参照通道分别标记以后与含6000个已知人类基因或表达序列标签的cDNA基因芯片杂交,扫描荧光信号以后进行数据分析。结果：TxN＋组与TxN-组共有17个差异表达基因,其中12个基因表达上调,5个基因表达下调。有53个基因可将N＋组与TxN＋组区分开,其中在N＋组高表达的基因有25个,在TxN＋组高表达的有28个。结论：早期癌形成中的遗传学变化和后期癌进展中的获得性分子学变异共同决定肺腺癌的淋巴转移。     

Gene expression profiling of human ovarian tumours

There is currently a lack of reliable diagnostic and prognostic markers for ovarian cancer. We established gene expression profiles for 120 human ovarian tumours to identify determinants of histologic subtype, grade and degree of malignancy. Unsupervised cluster analysis of the most variable set of expression data resulted in three major tumour groups. One consisted predominantly of benign tumours, one contained mostly malignant tumours, and one was comprised of a mixture of borderline and malignant tumours. Using two supervised approaches, we identified a set of genes that distinguished the benign, borderline and malignant phenotypes. These algorithms were unable to establish profiles for histologic subtype or grade. To validate these findings, the expression of 21 candidate genes selected from these analyses was measured by quantitative RT-PCR using an independent set of tumour samples. Hierarchical clustering of these data resulted in two major groups, one benign and one malignant, with the borderline tumours interspersed between the two groups. These results indicate that borderline ovarian tumours may be classified as either benign or malignant, and that this classifier could be useful for predicting the clinical course of borderline tumours. Immunohistochemical analysis also demonstrated increased expression of CD24 antigen in malignant versus benign tumour tissue. The data that we have generated will contribute to a growing body of expression data that more accurately define the biologic and clinical characteristics of ovarian cancers.     

Gene expression profiling of gliomas: merging genomic and histopathological classification for personalised therapy

The development of DNA microarray technologies over the past decade has revolutionised translational cancer research. These technologies were originally hailed as more objective, comprehensive replacements for traditional histopathological cancer classification systems, based on microscopic morphology. Although DNA microarray-based gene expression profiling (GEP) remains unlikely in the near term to completely replace morphological classification of primary brain tumours, specifically the diffuse gliomas, GEP has confirmed that significant molecular heterogeneity exists within the various morphologically defined gliomas, particularly glioblastoma (GBM). Herein, we provide a 10-year progress report on human glioma GEP, with focus on development of clinical diagnostic tests to identify molecular subtypes, uniquely responsive to adjuvant therapies. Such progress may lead to a more precise classification system that accurately reflects the cellular, genetic, and molecular basis of gliomagenesis, a prerequisite for identifying subsets uniquely responsive to specific adjuvant therapies, and ultimately in achieving individualised clinical care of glioma patients.     

Whole genome analysis for liver metastasis gene signatures in colorectal cancer

Liver metastasis is one of the major causes of death in colorectal cancer (CRC) patients. To understand this process, we investigated whether the gene expression profiling of matched colorectal carcinomas and liver metastases could reveal key molecular events involved in tumor progression and metastasis. We performed experiments using a cDNA microarray containing 17,104 genes with the following tissue samples: paired tissues of 25 normal colorectal mucosa, 27 primary colorectal tumors, 13 normal liver and 27 liver metastasis, and 20 primary colorectal tumors without liver metastasis. To remove the effect of normal cell contamination, we selected 4,583 organ-specific genes with a false discovery rate (FDR) of 0.0067% by comparing normal colon and liver tissues using significant analysis of microarray, and these genes were excluded from further analysis. We then identified and validated 46 liver metastasis-specific genes with an accuracy of 83.3% by comparing the expression of paired primary colorectal tumors and liver metastases using prediction analysis of microarray. The 46 selected genes contained several known oncogenes and 2 ESTs. To confirm that the results correlated with the microarray expression patterns, we performed RT-PCR with WNT5A and carbonic anhydrase II. Additionally, we observed that 21 of the 46 genes were differentially expressed (FDR=2.27%) in primary tumors with synchronous liver metastasis compared with primary tumors without liver metastasis. We scanned the human genome using a cDNA microarray and identified 46 genes that may play an important role in the progression of liver metastasis in CRC.     

Molecular classification of oral cancer by cDNA microarrays identifies overexpressed genes correlated with nodal metastasis

Our purpose was to classify OSCCs based on their gene expression profiles, to identify differentially expressed genes in these cancers and to correlate genetic deregulation with clinical and histopathologic data and patient outcome. After conducting proof-of-principle experiments utilizing 6 HNSCC cell lines, the gene expression profiles of 20 OSCCs were determined using cDNA microarrays containing 19,200 sequences and the BTSVQ method of data analysis. We identified 2 sample clusters that correlated with the T3-T4 category of disease (p = 0.035) and nodal metastasis (p = 0.035). BTSVQ analysis identified a subset of 23 differentially expressed genes with the lowest QE scores in the cluster containing more advanced-stage tumors. Expression of 6 of these differentially expressed genes was validated by quantitative real-time RT-PCR. Statistical analysis of quantitative real-time RT-PCR data was performed and, after Bonferroni correction, CLDN1 overexpression was significantly correlated with the cluster containing more advanced-stage tumors (p = 0.007). Despite the clinical heterogeneity of OSCC, molecular subtyping by cDNA microarray analysis identified distinct patterns of gene expression associated with relevant clinical parameters. Application of this methodology represents an advance in the classification of oral cavity tumors and may ultimately aid in the development of more tailored therapies for oral carcinoma.     

In vivo echographic evidence of tumoral vascularization and microenvironment interactions in metastatic orthotopic human neuroblastoma xenografts

Human neuroblastoma (NB) is the second most frequent solid tumor of childhood and represents a highly heterogeneous disease at clinical and biologic levels. Little progress has been made to improve the poor prognosis of patients with high-stage NB. Tumor progression and metastatic dissemination still represent major obstacles to the successful treatment of advanced stage disease. In order to develop and evaluate new, targeted, therapeutic strategies, fully defined and biologically relevant in vivo models of NB are strongly needed. We have developed an orthotopic model of metastatic human NB in the nude mouse, using 2 well-characterized NB cell lines. Tumor growth, vascular properties and metastatic patterns were investigated using a sensitive and newly developed in vivo echographic technology in addition to immunohistochemistry and PCR analyses. Results show that implantation of low numbers of NB cells directly into the adrenal gland of nude mice resulted in rapid and homogeneous tumor growth without tumor morbidity. Nude mice were shown to rapidly develop highly vascularized adrenal tumors that selectively metastasized to the liver and bone marrow. In addition, the newly formed mouse vessels in orthotopic but not in heterotopic tumors, were found to express the highly angiogenic alphavbeta3 integrin marker, indicating the development of a truly malignant neovasculature in orthotopic conditions only. This observation confirms the impact of the regional microenvironment on tumor biology and suggests the existence of cross-talk with the tumor cells. In conclusion, such model faithfully reproduces the growth, vascular and metastatic patterns as observed in patients. It therefore represents a powerful and biologically relevant tool to improve our understanding of the biology of NB and to develop and assess new antiangiogenic and metastasis-targeted therapies.     

Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases

Host cell reactions are a crucial determinant for tumor invasion. We analyzed on a genomewide scale gene expression differences between microdissected tissues taken from unaffected liver tissue of a human colorectal tumor (LS174) growing in the livers of nude mice and tissue from the host part of the invasive front. Due to the low degree of interspecies cross-hybridization of 15% as determined on Affymetrix microarrays, our xenograft model allowed for the distinction of genes of murine versus human origin even if the respective tissues could not be isolated separately. Using the gene ontology (GO) classification, we were able to determine patterns of up- and downregulated genes in the liver part of the invasive front. We observed a pronounced overrepresentation, e.g., of the GO terms "extracellular matrix," "cell communication," "response to biotic stimulus," "structural molecule activity" and "cell growth," indicating a very pronounced host cell response to tumor invasion. On the single gene level, hepatic stellate cell (HSC) activation markers were overrepresented in the liver part of the invasion front. Immunohistochemistry and qPCR confirmed an activation of HSC as well as an increased number of HSC in the invasive front as compared to the noninvaded liver tissue. In summary, our data demonstrate the feasibility of an interspecies differential gene expression approach on a genomewide scale.     

子宫内膜癌淋巴结转移相关基因的生物信息学分析

目的：基于芯片数据分析和生物信息学方法挖掘与子宫内膜癌淋巴结转移相关的潜在差异表达基因。方法：在GEO数据库中筛选子宫内膜癌淋巴结转移相关的mRNA表达谱芯片数据,分析mRNA表达谱,筛选差异表达基因;通过生物学过程注释、生物信号通路富集、文本挖掘及蛋白/基因相互作用等综合生物信息学方法再次分析,挖掘与子宫内膜癌淋巴结转移相关的信号通路和基因。结果：在GEO 数据库获得GSE2109、GSE39099 芯片数据,将共同差异表达基因及信号通路富集, 获得8 条与子宫内膜癌淋巴结转移显著相关的信号通路（type I interferon、interferon-gamma-mediated、PI3K-Akt、Rap1、TGF-beta、cGMP-PKG、Wnt、Ras）及调控这些信号通路的14 个差异表达基因,其中11 个基因与宫内膜癌淋巴结转移相关并且形成蛋白相互作用网络。PI3K-Akt 信号通路可能是子宫内膜癌淋巴结转移的重要信号通路,基因VEGFC、IRS1 可能是子宫内膜癌淋巴结转移相关的重要候选基因。结论：通过对芯片数据生物信息学分析,筛选出与子宫内膜癌淋巴结转移相关的8条信号通路及11个差异表达基因。     

Cost effectiveness of gene expression profiling for early stage breast cancer: A decision-analytic model

BACKGROUND:

Gene expression profiling (GEP) is being used increasingly for risk stratification to identify women with lymph node‐negative, estrogen receptor‐positive, early stage breast cancer who are most likely to benefit from adjuvant chemotherapy. The authors of this report evaluated the cost effectiveness of recurrence score‐guided treatment using 2 commercially available GEP tests, Oncotype DX (Genomic Health, Redwood City, Calif) and MammaPrint (Agendia Inc., Irvine, Calif), from a third‐party payer's perspective.

METHODS:

A 10‐year Markov model was developed to compare the costs and quality‐adjusted life‐years (QALYs) of treatment decisions guided by either Oncotype DX or MammaPrint in a hypothetical cohort of women with early stage, lymph node‐negative, estrogen receptor‐positive breast cancer who may experience recurrence. Outcomes included no recurrence, recurrence, and death. The costs considered included gene test costs, the costs of adjuvant chemotherapy and other chemotherapy (including premedication, oncology visits, and monitoring for adverse events), the cost of treating recurrence, costs associated with the treatment of adverse events, and end‐of‐life care costs.

RESULTS:

The model demonstrated that the patients who received the Oncotype DX test to guide treatment spent $27,882 (in US dollars) and gained 7.364 QALYs, whereas patients who received the MammaPrint test to guide treatment spent $21,598 and gained 7.461 QALYs. Sensitivity analyses demonstrated that the results were robust to changes in all parameters.

CONCLUSIONS:

The model suggested that MammaPrint is a more cost‐effective GEP test compared with Oncotype DX at a threshold willingness‐to‐pay of $50,000 per QALY. Because Oncotype DX is the most frequently used GEP in clinical practice in the United States, the authors concluded that the current findings have implications for health policy, particularly health insurance reimbursement decisions. Cancer 2012. © 2012 American Cancer Society.