Identification of genes associated with progression and metastasis of advanced cervical cancers after radiotherapy by cDNA microarray analysis

PURPOSE

To identify a set of genes related to the progression and metastasis of advanced cervical cancer after radiotherapy and to establish a predictive method.

METHODS AND MATERIALS

A total of 28 patients with cervical cancer (15 stage IIIB, 13 stage IVA patients) who underwent definitive radiotherapy between May 1995 and April 2001 were included in this study. All patients were positive for human papillomavirus infection and harbored the wild-type p53 gene. The expression profiles of 14 tumors with local failure and multiple distant metastasis and 14 tumors without metastasis (cancer free) obtained by punch biopsy were compared before treatment, using a cDNA microarray consisting of 23,040 human genes.

RESULTS

Sixty-three genes were selected on the basis of a clustering analysis, and the validity of these genes was confirmed using a cross-validation test. The most accurate prediction was achieved for 63 genes (sensitivity, 78.8%; specificity, 38.1%). Some of these genes were already known to be associated with metastasis via chromosomal instability (TTK, BUB1B), extracellular matrix components (matrix metalloproteinase 1 [MMP-1]), and carcinogenesis (protein phosphatase 1 regulatory subunit 7 [PPP1R7]). A "predictive score" system was developed that could predict the probability for development of metastases using leave-one-out cross-validation methods.

CONCLUSIONS

The present results may provide valuable information for identified predictive markers and novel therapeutic target molecules for progression and metastasis of advanced cervical cancer.

Optimizing the detection of hereditary non-polyposis colorectal cancer: An update

Hereditary non-polyposis colorectal cancer (HNPCC) is a dominant inherited disease and accounts for up to 5% of all colorectal cancer (CRC) patients. Despite the optimization of selection criteria and enhancements in molecular techniques for identifying more families with HNPCC, most cases are not recognized. Poor patient recollection of family history and inadequate family history-taking are main causative factors. We propose a new strategy for detecting HNPCC, one in which the pathologist selects patients for microsatellite instability (MSI) testing. Criteria for MSI analysis are: (1) CRC before the age of 50 years, (2) second CRC before 70 years, (3) CRC and HNPCC-associated cancer before 70 years, or (4) adenoma before 40 years. Additionally, patients with a positive MSI test and patients with a positive family history are offered referral for genetic counselling. With this strategy, at least twice the number of HNPCC patients will be identified among a population of CRC patients, and in a cost-effective, efficient and feasible way. The identification of patients with HNPCC is important because intensive surveillance can prevent death from CRC.

Impact of x chromosome genes in explaining the excess risk of cancer in males

The authors examined cancer incidence sex ratios in Denmark for 1943-2003 by age group. At nongenital/nonbreast sites, incidences were consistently higher in males. While environmental factors dominate cancer risk, the authors hypothesized that the higher risk in males might be explained by unspecified X chromosome genes' protecting female cells from genotoxic damage. If so, cancer susceptibility would be passed from parent to offspring differently by sex. The authors compared relative risks in offspring of parents with and without cancer histories. For all comparisons, relative risks were similar in offspring of fathers with cancer (relative risk (RR) = 1.14, 95% confidence interval: 1.08, 1.20). Risks in offspring were higher for parents diagnosed before age 50 years and for cancers at the same site rather than different sites. Genital cancer risks were increased in same-sex offspring of parents with genital cancers. Breast cancer risks were high in both daughters (RR = 2.37) and sons (RR = 4.63) of mothers with breast cancer and in daughters (RR = 5.96) of fathers with breast cancer. Thus, X chromosome genetic factors were not responsible for the excess risk of cancer in males. Susceptibility to genital cancer was increased in same-sex offspring, and breast cancer risks were increased in both sons and daughters when either parent had had breast cancer.

Surgical prophylaxis for inheritable malignant diseases: breast cancer and endocrine disease

Despite advances in modern medicine, cancer remains all too common and deadly. At its core, cancer is a disease of our DNA. As such, many cancers are passed from parents to children, making cancer one of the most commonly inherited diseases. Presently, we have no meaningful methods of "preventing" the malignant transformation that occurs as a result of an inherited gene, but investigators have identified several genetic mutations and subsequently developed risk-reduction strategies that sometimes involve surgery.

The cancer genome

All cancers arise as a result of changes that have occurred in the DNA sequence of the genomes of cancer cells. Over the past quarter of a century much has been learnt about these mutations and the abnormal genes that operate in human cancers. We are now, however, moving into an era in which it will be possible to obtain the complete DNA sequence of large numbers of cancer genomes. These studies will provide us with a detailed and comprehensive perspective on how individual cancers have developed.

A novel strategy of cancer gene therapy by transcriptional targeting of an allogeneic histocompatibility transgene

BACKGROUND

A drawback of cancer gene therapy is the failure of toxic gene introduction into a proportion of the tumor cells, resulting in re-progression of the disease. Cancer cell-specificity of the gene introduction has also been problematic.

MATERIALS AND METHODS

Previously defined promoter/enhancer DNA of Q5 tumor antigen gene was used for the purpose of transcriptional targeting. A replication defective adenovirus carrying H-2D(d) cDNA placed downstream of the Q5 promoter/enhancer (Ad/Q5-H-2D(d)) was constructed and administered systemically to C57Bl/6 (H-2(b)) mice bearing pre-established hepatic metastasis of the syngeneic M5076 tumor.

RESULTS

5 of the 10 mice showed complete regression of the tumor. Combination of the therapy with low dose cyclophosphamide (CY) administration augmented the therapeutic effect. The effect was brought about by tumor cell-specific allograft rejection reactions and by tumor antigen-specific reactions induced as "bystander effect" by the former reactions.

CONCLUSION

The results provide an experimental basis of a highly efficient novel strategy of cancer gene therapy.

Basic principles and technologies for deciphering the genetic map of cancer

The progress achieved in the field of genomics in recent years is leading medicine to adopt a personalized model in which the knowledge of individual DNA alterations will allow a targeted approach to cancer. Using pancreatic cancer as a model, we discuss herein the fundamentals that need to be considered for the high throughput and global identification of mutations. These include patient-related issues, sample collection, DNA isolation, gene selection, primer design, and sequencing techniques. We also describe the possible applications of the discovery of DNA changes to the approach of this disease and cite preliminary efforts where the knowledge has been translated into the clinical or preclinical setting.

Integrated genomic analysis implicates haploinsufficiency of multiple chromosome 5q31.2 genes in de novo myelodysplastic syndromes pathogenesis

Deletions spanning chromosome 5q31.2 are among the most common recurring cytogenetic abnormalities detectable in myelodysplastic syndromes (MDS). Prior genomic studies have suggested that haploinsufficiency of multiple 5q31.2 genes may contribute to MDS pathogenesis. However, this hypothesis has never been formally tested. Therefore, we designed this study to systematically and comprehensively evaluate all 28 chromosome 5q31.2 genes and directly test whether haploinsufficiency of a single 5q31.2 gene may result from a heterozygous nucleotide mutation or microdeletion. We selected paired tumor (bone marrow) and germline (skin) DNA samples from 46 de novo MDS patients (37 without a cytogenetic 5q31.2 deletion) and performed total exonic gene resequencing (479 amplicons) and array comparative genomic hybridization (CGH). We found no somatic nucleotide changes in the 46 MDS samples, and no cytogenetically silent 5q31.2 deletions in 20/20 samples analyzed by array CGH. Twelve novel single nucleotide polymorphisms were discovered. The mRNA levels of 7 genes in the commonly deleted interval were reduced by 50% in CD34+ cells from del(5q) MDS samples, and no gene showed complete loss of expression. Taken together, these data show that small deletions and/or point mutations in individual 5q31.2 genes are not common events in MDS, and implicate haploinsufficiency of multiple genes as the relevant genetic consequence of this common deletion.

Cancer genetics: a primer for surgeons

Contemporary ideas of carcinogenesis envisage a series of stochastic genetic changes that confer a selective growth advantage over healthy cells. These changes collectively lead to the disruption of coordinated networks of intercellular communication and cause a fundamental change in cellular behavior, which affects processes, such as proliferation, differentiation, and apoptosis. This progressive dysregulation of cellular function implies that cancer is not a morphologic entity, but a process in which the malignant phenotype is gradually acquired.

Management of colorectal cancer: a role for genetics in prevention and treatment?

Colorectal cancer remains one of the most common cancers in the Western world and amongst the top three causes of cancer morbidity and death. Cancer is caused by genetic mutations, but currently there is little use of genetic information in the clinic with the exception of establishing germline mutations for the uncommon predisposing syndromes. Rapid advances in technologies allowing high throughput analysis of germline and somatic mutations raises the possibility that genetics will find a major role in the clinic distinguishing individuals at low to high risk of cancer, allowing early intervention and stratification of cancers based on mutational pathways for therapeutic interventions. In the future, this will lead to treatment regimes tailored to the individuals and their tumor. Here, we summarize the genetics underlying colorectal cancer and the future role of genetics in prevention, diagnosis, classification and treatment.

[Effects of matrine on cgi-100 gene expression and proliferation in K562 cells]

This study was aimed to explore the expression level of the unknown cgi-100 gene in human leukemia K562 cells treated with matrine, and to investigate effect of cgi-100 on proliferation of K562 cells. The expression level of cgi-100 was detected by RT-PCR in K562 cells before and after being treated with matrine; pIRES2-EGFP/cgi-100 eukaryotic expression vector was constructed by DNA recombinant technique and was introduced into K562 cells by liposome-mediated DNA transfection. The cgi-100 gene expression level, growth-curve, and cell cycle of the modified K562-cgi-100 cells were detected by RT-PCR, Trypan blue staining and FCM. Morphological changes were observed under the optical and electron microscopes. The results indicated that the expression level of cgi-100 decreased in K562 cells treated with matrine. Heterochromatin decreased, euchromatin and the proportion of S phase in K562-cgi-100 cells increased, and cell proliferation enhanced. It is concluded that the expression of cgi-100 mRNA decreased in a dose- and time-dependent manner in the K562 cells treated with matrine and over-expression of cgi-100 elevates the proliferation and the immaturity level of K562-cgi-100 cells.

Intratumor genetic heterogeneity of breast carcinomas as determined by fine needle aspiration and TaqMan low density array

BACKGROUND

Gene expression profiling is thought to be an important tool in determining treatment strategies for breast cancer patients. Tissues for such analysis may at a preoperative stage be obtained, by fine needle aspiration (FNA) allowing initiation of neoadjuvant treatment. To evaluate the extent of the genetic heterogeneity within primary breast carcinomas, we examined whether a gene expression profile obtained by FNA was representative of the tumor.

METHODS

Tumors from 12 consecutive cases of early predominantly estrogen receptor positive (ER+) breast cancer patients undergoing primary surgery were split in halves and FNAs were obtained from each half. A tissue biopsy of the tumors was also snap-frozen for comparison. Non-amplified RNA was investigated by the novel qRT-PCR-based technique, Low Density Array (LDA) using 4 reference genes and 44 target genes.

RESULTS

Comparison of gene expression at the single gene level in the two FNA samples from each tumor demonstrated various degrees of heterogeneity. However, compared as gene expression profiles, intratumor correlations for 9/12 patients were high and these pairs could in a theoretical blinding of all the FNAs be correctly matched by statistical analysis. High correlations between the gene profiles of tumor FNAs and tissue biopsies from the same patient were observed for all patients. A cluster analysis identified clustering of both the two FNAs and the tissue biopsy of the same 9 patients.

CONCLUSION

The overall genetic heterogeneity of breast carcinomas, as sampled by FNA, does not prohibit generation of useful gene profiles for treatment decision making. However, sampling and analysis strategies should take heterogeneity within a tumor, and varying heterogeneity amongst the single genes, into account.

[Construction and screening of genomic library from Raji cells]

OBJECTIVE

To construct the genomic library of Raji cells and screen it by EBV DNA probe.

METHODS

High molecular weight genomic DNA of Raji cells was digested by restriction enzyme BamHI. DNA fragments ranging from 9 to 23 kb were recovered by agarose gel electrophoresis, which were ligated with Lambda DASH II vector BamHI arms pre-treated with calf intestine alkaline phosphatase (CIAP). Ligated DNA was packed in vitro using Gigapack III gold packaging extract. The library was plated on XL1-blue MRA (P2) host strain.Titering and screening of the Raji genomic library were performed.

RESULTS

The primary titer of the Raji genomic library was 1.8 x 10(5) pfu/mL, while that of the amplified library was 2.8 x 10(8) pfu/mL. Plaques (1 x 10(5)) were screened with (32)P-labeled EBV DNA probe(EBV genome 5-3271), 4 positive clones were obtained, and 1 of the 4 positive clones was picked out randomly for the second round of plaque screening. All the phage plaques were positive. DNA of the positive clone was extracted and was digested with BamHI. The length of the inserted fragment was 8.5 kb. Sequencing and BLAST analysis revealed that the inserted fragments consisted of the BamHI-W fragment at one end and clone RP11-665A22 on chromosome 15 at the other end.

CONCLUSION

The successfully established genomic library of Raji cells will provide a basis for cloning the sequences of the EBV junction sites and interpreting the mechanism of oncogenesis of EBV integration.

[F10 gene knock-down mediated by RNA interference induces apoptosis of KLE cells]

OBJECTIVE

To study the effect of short double-stranded RNA (dsRNA) on F10 gene expression in KLE cells and the effect of F10 knock-down on KLE cell apoptosis.

METHODS

The short dsRNA specifically targeting F10 gene prepared by in vitro transcription was transfected into KLE cells via lipofectamine 2000. The expression of F10 mRNA in the transfected KLE cells was detected by real-time quantitative RT-PCR, and the apoptosis of the cells was assayed by flow cytometry.

RESULTS

Real-time quantitative RT-PCR demonstrated that transfection of the KLE cells with the short dsRNA induced effective knock-down of F10 gene, and transfection of the cells with 20 nmol/L dsRNA for 48 h decreased the expression of F10 mRNA by 83%. Compared with the control, the apoptosis index of the transfected KLE cells increased from 0.36% to 8.91%.

CONCLUSION

F10 gene in KLE cells can be specifically knocked-down with dsRNA prepared by in vitro transcription, and the down-regulation of F10 gene induces apoptosis of KLE cells.

[Construction and identification of a stable eukaryotic expression system for F10 gene]

OBJECTIVE

To detect the transcriptional level of a novel gene F10 associated with the pathogenesis of hydatidiform mole in human cell lines and screen the cell lines with low F10 expression to construct a stable eukaryotic expression system for F10 gene.

METHODS

The expression level of F10 mRNA was detected with fluorescent quantitative PCR in A549, 16HBE, Bel7402, HIC, HepG2, 293, PC and MGC cell lines. A549 cell line was transfected with plasmid pRc-CMV2-F10 via electroporation to allow stable F10 expression, and the positive cell clones were selected by G418. The insertion and expression of F10 gene in the A549 cells was analyzed using fluorescent quantitative PCR.

RESULTS

F10 mRNA was expressed differentially in these cells lines, and the Bel7402 cells, PC and MGC cells showed the highest F10 mRNA expression, followed by HepG2 and HIC cells and further by 293 cells, and 16HBE and A594 cells had the lowest expression. After transfection, A594 cells showed genomic integration of F10 gene and high expression level of F10 mRNA.

CONCLUSION

The pulmonary carcinoma cell line A549 with stable expression of F10 gene has been established, which may facilitate further study of the biological functions of F10 gene.

New breast cancer genes-discovery at the intersection of complex data sets

The identification of genes that contribute to the oncogenic process, including those that determine risk of cancer onset, holds the key not only in understanding mechanisms of oncogenesis but also in the identification of new targets for therapeutic development. Traditional methods of genetics and molecular biology have been successful but are slow and laborious. The advent of genome technologies, leading to the generation of large data sets describing various properties of genes and proteins relevant to cancer phenotypes, has afforded a new opportunity for discovery. M. Vidal and colleagues have made use of this data, and in particular the integration of various forms of genome-scale data, to identify new genes involved in breast cancer.

Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network

Mutations or overexpression of signalling genes can result in cancer development and metastasis. In this study, we manually assembled a human cellular signalling network and developed a robust bioinformatics strategy for extracting cancer-associated single nucleotide polymorphisms (SNPs) using expressed sequence tags (ESTs). We then investigated the relationships of cancer-associated genes [cancer-associated SNP genes, known as cancer genes (CG) and cell mobility genes (CMGs)] in a signalling network context. Through a graph-theory-based analysis, we found that CGs are significantly enriched in network hub proteins and cancer-associated genes are significantly enriched or depleted in some particular network motif types. Furthermore, we identified a substantial number of hotspots, the three- and four-node network motifs in which all nodes are either CGs or CMGs. More importantly, we uncovered that CGs are enriched in the convergent target nodes of most network motifs, although CMGs are enriched in the source nodes of most motifs. These results have implications for the foundations of the regulatory mechanisms of cancer development and metastasis.

Characterization of microarray gene expression profiles of early stage thyroid tumours

BACKGROUND

Microarray analysis offers the opportunity of screening transcriptional expression profile of neoplastic cells on a genomic level. Defining consistent changes in gene expression pattern of tumours enables the detection of genes essential for tumorigenesis and might provide biomarkers to early recognition of malignant behaviour and new therapeutical targets.

PATIENTS AND METHODS

A high-density oligonucleotide array with 20,000 human gene-specific oligonucleotide was used to analyze benign and early-stage malignant thyroid tumours of epithelial origin: follicular adenoma, follicular carcinoma and papillary carcinoma, compared to normal thyroid tissue.

RESULTS

Significant expression differences of 279 genes -- underexpression of 252 and overexpression of 27 genes -- were found. The overlapping genes of the different histological types were examined extensively. Among these genes a limited set acting on the same transcriptional pathway, through NF-kappaB, were found.

CONCLUSION

The role of overlapping genes in histologically different tumours has not been clarified, but might represent early or pivotal steps of carcinogenesis. All investigated histiotypes of tumours contained significantly modulated genes acting on the NF-kappaB regulatory pathway. Our findings suggest that modulation of NF-kappaB signalling plays a crucial role in early thyroid carcinogenesis.

Genomic implications of H(2)O (2) for cell proliferation and growth of Caco-2 cells

Evidence indicates that oxidative stress inhibits cell proliferation in several cell systems. To determine whether the proliferation of Caco-2 cells is inhibited by oxidative stress and to identify any novel key regulatory factors involved in protecting or damaging the intestine from oxidative stress, Caco-2 cells were treated with an oxidizing agent and analyzed by transcriptomic oligonucleotide microarrays. Results indicated that expression of genes involved in cell proliferation and growth, including genes involved in lipid synthesis, cell cycle progression and cell division, angiogenesis, RNA processing and translation, cAMP metabolism, cytoskeleton and cell to cell adhesion, receptor tyrosine kinases, and intracellular and extracellular signaling, were repressed. If an oxidant-induced inhibition in cell proliferation is involved in the pathogenesis of intestinal disease, information gained could help explain the mechanisms contributing to the causes and consequences of intestinal disease and could aid in the elucidation of mechanisms by which intestinal cells protect against oxidative stress.

Quantitative expression profiling guided by common retroviral insertion sites reveals novel and cell type specific cancer genes in leukemia

Proviral insertional mutagenesis is a powerful tool for the discovery of cancer-associated genes. The ability of integrated proviruses to affect gene expression over long distances combined with the lack of methods to determine the expression levels of large numbers of genes in a systematic and truly quantitative manner have limited the identification of cancer genes by proviral insertional mutagenesis. Here, we have characterized a new model of proviral insertional mutagenesis-induced lymphoid tumors derived from Eed Polycomb group gene mutant mice and quantitatively determined the expression levels of all genes within 100 kb of 20 different retroviral common insertion sites (CISs) identified in these tumors. Using high-throughput quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR), we document an average of 13 CIS-associated genes deregulated per tumor, half of which are leukemia subtype-specific, while the others are coordinately deregulated in the majority of tumors analyzed. Interestingly, we find that genes located distantly from common proviral integration sites are as frequently deregulated as proximal genes, with multiple genes affected per integration. Our studies reveal an unsuspected conservation in the group of genes deregulated among phenotypically similar subtypes of lymphoid leukemias, and suggest that identification of common molecular determinants of this disease is within reach.

Biomarkers for lung cancer: clinical uses

PURPOSE OF REVIEW

Biomarkers for lung cancer may be used for risk stratification, early detection, treatment selection, prognostication and monitoring for recurrence. All these areas of clinical management would benefit from sensitive and specific, noninvasive, cost-effective biomarkers.

RECENT FINDINGS

Significant progress has been made in understanding the steps involved in lung carcinogenesis and in the development of novel technologies for biomarker discovery. Over the last 3 years research into prospective lung cancer biomarkers has proliferated, especially in the areas of early detection and prognostication. The most active areas of research have been in promoter methylation, proteomics and genomics. Many investigators are adopting panels of serum biomarkers in an attempt to increase sensitivity. The development of targeted lung cancer therapy has engendered interest in markers to identify the optimal candidates for these therapies.

SUMMARY

Much progress has been made in the last 3 years in the identification and validation of new biomarkers for the early diagnosis of lung cancer. The biomarkers require additional studies before they can be used clinically. Markers to identify lung cancer patients who may benefit from targeted therapy have been developed more rapidly and may be used now in some clinical situations.