Inherited predisposition to glioma

In gliomas, germline gene alterations play a significant role during malignant transformation of progenitor glial cells, at least for families with occurrence of multiple cancers or with specific hereditary cancer syndromes. Scientific evidence during the last few years has revealed several constitutive genetic abnormalities that may influence glioma formation. These germline abnormalities are manifested as either gene polymorphisms or hemizygous mutations of key regulatory genes that are involved either in DNA repair or in apoptosis. Such changes, among others, include hemizygous alterations of the neurofibromatosis 1 (NF1) and p53 genes that are involved in apoptotic pathways, and alterations in multiple DNA repair genes such as mismatch repair (MMR) genes, x-ray cross-complementary genes (XRCC), and O6-methylguanine-DNA methyltransferase (MGMT) genes. Subsequent cellular changes include somatic mutations in cell cycle regulatory genes and genes involved in angiogenesis and invasion, leading eventually to tumor formation in various stages. Future molecular diagnosis may identify new genomic regions that could harbor genes important for glioma predisposition and aid in the early diagnosis of these patients and genetic counseling of their families.     

Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses

Molecular mechanisms contributing to initiation and progression of head and neck squamous cell carcinoma are still poorly known. Numerous genetic alterations have been described, but molecular consequences of such alterations in most cases remain unclear. Here, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 20 laryngeal cancer cell lines and primary tumors. Our aim was to identify genetic alterations that play a key role in disease pathogenesis and pinpoint genes whose expression is directly impacted by these events. Integration of DNA level data from array-based comparative genomic hybridization with RNA level information from oligonucleotide microarrays was achieved with custom-developed bioinformatic methods. High-level amplifications had a clear impact on gene expression. Across the genome, overexpression of 739 genes could be attributed to gene amplification events in cell lines, with 325 genes showing the same phenomenon in primary tumors including FADD and PPFIA1 at 11q13. The analysis of gene ontology and pathway distributions further pinpointed genes that may identify potential targets of therapeutic intervention. Our data highlight genes that may be critically important to laryngeal cancer progression and offer potential therapeutic targets.     

Genetic analysis of cancer in families

Cancer is genetic, in the sense that it is caused by DNA alterations at the cellular level. On the other hand, the most important risk factors for the common cancers are environmental: cigarette smoking, environmental pollution, occupational exposures, poor diet, and so on. These two observations are not in conflict: the DNA alterations that lead to cancer are very likely to be caused by environmental mutagens. It would be valuable to know exactly what genes are altered to cause a specific cancer, because the effects of these alterations might then be reversible before cancer has a chance to develop. A key to identifying these cancer genes may lie with rare families at extremely high risk of a specific cancer. Unlike most cancer patients, members of these families may inherit an alteration that confers increased susceptibility to cancer. In these rare instances, cancer is a genetic disease at the level of the family, as well as at the level of the cell. Therefore, in these families, genes predisposing to cancer can be mapped in the same way as genes for purely genetic diseases like sickle cell anaemia, cystic fibrosis, and Huntington's disease. The hypothesis that underlies the mapping of cancer genes in families is that the genes inherited in altered form in these rare families are the same genes that are altered in somatic cells of individuals without a remarkable family history of cancer. This hypothesis has proved correct for retinoblastoma. Genes responsible for other rare cancers have been mapped in families as well: neurofibromatosis, multiple endocrine neoplasia, Wilms' tumour, and colon cancer following familial adenomatous polyps, among others. Genes responsible for common cancers are also being defined by genetic analysis, most notably breast cancer and colon cancer. This review summarizes why, how, and what genetic analysis of families can reveal about human cancers.     

The genetics of cancer survivorship

Constitutional (hereditary) genetic variation and somatic genetic alterations acquired during transformation to the neoplastic phenotype are both critical determinants of cancer outcome, and can ultimately have a significant effect on cancer survivorship. This article discusses the role of constitutional and somatic genetics in determining outcome and survivorship following a diagnosis of cancer using illustrative examples primarily from the hematologic malignancies.     

Genetic and epigenetic analysis of the VHL gene in gastric cancers

The von Hippel-Lindau tumor suppressor gene (VHL), which is located on chromosome 3p25, plays an important role in tumorigenesis, particularly in tumor growth and vascularization. Mutations of the VHL gene have been observed in the hereditary VHL syndrome and a variety of other sporadic cancers. In this study, in order to investigate whether the VHL gene is involved in gastric carcinogenesis, we have examined the genetic alterations, including somatic mutations and allelic loss, with the two microsatellite markers, D3S1038 and D3S1110, as well as promoter hypermethylation of the VHL gene in 88 sporadic gastric adenocarcinomas. No mutation was detected in the coding region of the VHL gene. Allelic loss was found in 20 (33.9%) of 59 informative cancer cases at one or both markers. In addition, promoter hypermethylation was not detected in the gastric cancer samples. This is the first investigation of the genetic and epigenetic alterations of the VHL gene in gastric cancers. Our results suggest that genetic and epigenetic alterations of the VHL gene may be not involved in the development or progression of gastric cancers. The findings also provide evidence for the presence of another gastric cancer specific tumor suppressor gene at the 3p25 region.     

RB and cyclin dependent kinase pathways: defining a distinction between RB and p16 loss in lung cancer

The genetic components of the RB:CDK:cyclin:p16 tumor suppressor pathway undergo mutational and epigenetic alterations in a wide range of human cancers and serve as critical targets for inactivation by the transforming oncoproteins of several DNA tumor viruses. Lung cancer has been a useful model system for these studies as it was the first tumor to demonstrate an important role for RB in the genesis of a common adult malignancy and was also the first human cancer to demonstrate genetic evidence for a multi-component RB:p16 tumor suppressor pathway. Lung tumorigenesis, however, is a complex disease process that requires longstanding carcinogen exposure in order to acquire somatic alterations at many distinct genetic loci. Understanding the multifunctional properties of RB to regulate cell proliferation, differentiation, and apoptosis and how they relate to the sequential accumulation of other clonal gene defects will be essential in order to understand the specific patterns of gene inactivation observed in different subtypes of lung cancer and to fulfill the promise of 'molecular target' therapeutics.     

Frequent somatic mutations of the beta-catenin gene in intestinal-type gastric cancer.

The increased level of cytoplasmic beta-catenin through the mutations to either beta-catenin or adenomatous polyposis coli (APC) has been proposed as an important oncogenic step in various tumors. Gastric cancer showed frequent genetic alterations of the APC gene, and the risk for gastric cancer in familial adenomatosus polyposis patients is 10 times higher than that in the general population. These findings raise the possibility that mutations of beta-catenin may also be associated with the development of gastric cancer. We detected seven somatic mutations in a portion of exon 3 encoding for the glycogen synthase kinase 3beta phosphorylation consensus region of the beta-catenin gene in 43 gastric cancers. All of these mutations were missense mutations, of which five are in the highly conserved aspartic acid 32 and two are in serine 29; all of these seven mutations were detected exclusively in intestinal-type gastric cancers (7 of 26; 26.9%), but not in the diffuse-type (0 of 17). We concluded that disruption of the APC/beta-catenin/T cell factor-lymphoid enhancer binding factor pathway might play an important role especially in the development of intestinal-type gastric cancer.     

Recall of Genomic Testing Results Among Patients with Cancer

BackgroundGenomic testing of somatic and germline DNA has transformed cancer care. However, low genetic knowledge among patients may compromise care and health outcomes. Given the rise in genomic testing, we sought to understand patients’ knowledge of their genetic test results.Materials and MethodsWe conducted a survey‐based study with 85 patients at a comprehensive cancer center. We compared self‐reported recall of (a) having had somatic/germline testing and (b) their specific somatic/germline results to the genomic test results documented in the medical record.ResultsApproximately 30% of patients did not recall having had testing. Of those who recalled having testing, 44% of patients with pathogenic/likely pathogenic germline mutations and 57% of patients with reported somatic alterations did not accurately recall their specific gene or variant‐level results.ConclusionGiven significant knowledge gaps in patients’ recall of genomic testing, there is a critical need to improve patient‐directed education and return‐of‐results strategies.     

Mutations in the tyrosine kinase domain of the epidermal growth factor receptor in non-small cell lung cancer.

We evaluated somatic genetic alterations in the kinase domain of the EGFR gene in the tumors of 219 non-small cell lung cancer patients of primarily Caucasian and African American origins. We identified 26 patients (12%) whose tumors had a mutation in the EGFR gene, and 11 (5%) patients carried novel genomic variations consistent with germ-line polymorphisms. All but one mutation were identified in Caucasian patients affected with adenocarcinoma. EGFR mutations were more frequent in women and in nonsmokers, but a significant portion of the affected patients were men (12 of 26) and current or past smokers accounted for half of the patients affected (13 of 26). Screening subjects with EGFR mutations may identify patients whose tumors could respond to targeted therapy using tyrosine kinase inhibitors.     

The role of extreme phenotype selection studies in the identification of clinically relevant genotypes in cancer research

The investigation of genetic alterations that may be related to the prognosis of patients with malignant disease has become a frequently used strategy in recent years. Although some conclusions have been reached in certain studies, the complexity and the multifactorial nature of most neoplastic diseases makes it difficult to identify clinically relevant information, and the results of some studies have been of borderline significance or have been conflicting. In contrast, the identification and the study of patients or families with very characteristic phenotypes have yielded outstanding results in the identification of the genetic characteristics underlying such phenotypes. Although, in most cases, the individuals who are selected for these types of studies are characterized by a negative phenotype (i.e., individuals who are at increased risk for developing a specific disease), a few studies have been directed toward individuals with phenotypes that imply an unusually good prognosis (i.e., individuals who present with a decreased risk for developing specific diseases despite an important exposure to well-known risk factors). Therefore, it seems logical to develop this strategy further as a valid methodology for the study of other diseases, such as cancer. The study of individuals with phenotypes that imply an extremely good prognosis, such as long-term survivors of theoretically incurable malignancies or individuals who seem to be protected against a certain neoplastic disorder despite having a markedly increased risk for its development, may unveil genetic alterations that explain such characteristic phenotypes and may provide potentially useful therapeutic targets against these diseases.     

Cancer epigenetics

Epigenetics refers to stable alterations in gene expression with no underlying modifications in the genetic sequence and is best exemplified by differentiation, in which multiple cell types diverge physiologically despite a common genetic code. Interest in this area of science has grown over the past decades, especially since it was found to play a major role in physiologic phenomena such as embryogenesis, imprinting, and X chromosome inactivation, and in disease states such as cancer. The latter had been previously thought of as a disease with an exclusive genetic etiology. However, recent data have demonstrated that the complexity of human carcinogenesis cannot be accounted for by genetic alterations alone, but also involves epigenetic changes in processes such as DNA methylation, histone modifications, and microRNA expression. In turn, these molecular alterations lead to permanent changes in the expression of genes that regulate the neoplastic phenotype, such as cellular growth and invasiveness. Targeting epigenetic modifiers has been referred to as epigenetic therapy. The success of this approach in hematopoietic malignancies validates the importance of epigenetic alterations in cancer, not only at the therapeutic level but also with regard to prevention, diagnosis, risk stratification, and prognosis.     

Human tumor antigens Tn and sialyl Tn arise from mutations in Cosmc

Neoplastic lesions typically express specific carbohydrate antigens on glycolipids, mucins, and other glycoproteins. Such antigens are often under epigenetic control and are subject to reversion and loss upon therapeutic selective pressure. We report here that two of the most common tumor-associated carbohydrate antigens, Tn and sialyl Tn (STn), result from somatic mutations in the gene Cosmc that encodes a molecular chaperone required for formation of the active T-synthase. Diverse neoplastic lesions, including colon cancer and melanoma-derived cells lines, expressed both Tn and STn antigen due to loss-of-function mutations in Cosmc. In addition, two human cervical cancer specimens that showed expression of the Tn/STn antigens were also found to have mutations in Cosmc and loss of heterozygosity for the cross-linked Cosmc locus. This is the first example of somatic mutations in multiple types of cancers that cause global alterations in cell surface carbohydrate antigen expression.     

DNA methylation markers in colorectal cancer

Colorectal cancer (CRC) arises as a consequence of the accumulation of genetic and epigenetic alterations in colonic epithelial cells during neoplastic transformation. Epigenetic modifications, particularly DNA methylation in selected gene promoters, are recognized as common molecular alterations in human tumors. Substantial efforts have been made to determine the cause and role of aberrant DNA methylation (“epigenomic instability”) in colon carcinogenesis. In the colon, aberrant DNA methylation arises in tumor-adjacent, normal-appearing mucosa. Aberrant methylation also contributes to later stages of colon carcinogenesis through simultaneous methylation in key specific genes that alter specific oncogenic pathways. Hypermethylation of several gene clusters has been termed CpG island methylator phenotype and appears to define a subgroup of colon cancer distinctly characterized by pathological, clinical, and molecular features. DNA methylation of multiple promoters may serve as a biomarker for early detection in stool and blood DNA and as a tool for monitoring patients with CRC. DNA methylation patterns may also be predictors of metastatic or aggressive CRC. Therefore, the aim of this review is to understand DNA methylation as a driving force in colorectal neoplasia and its emerging value as a molecular marker in the clinic.     

Carcinogenesis in Down syndrome: what can be learned from trisomy 21?

According to the currently prevailing perception, sporadic cancer arises as a result of somatic mutations in a cell that lead to its uncontrolled proliferation. It is generally accepted that somatic mutations occur randomly and that they are generally either "spontaneous" or due to various external agents (physical or chemical carcinogens). Constitutional genetic conditions, which modify cancer risk, may become instrumental in opening new concepts in carcinogenesis. For instance, evidence gathered from Down syndrome (DS) individuals has challenged the above perceived explanation since somatic mutations in these patients markedly differ from those arisen in the general population, and do not seem to occur at random. There is no global increase or decrease of somatic mutations in all genes in DS. Instead, specific mutations have been detected on particular loci, depending on the tissue type and the age of the DS person. In the context of constitutional trisomy 21, where cancer have a very particular and striking distribution, biochemical, physiological and architectural imbalances in specific tissues may be responsible for a vulnerable state leading to carcinogenesis. Conversely, in tissues of DS patients which seem resistant to cancer, the proliferative and maturation state of the cells would lead to a refractory state of neoplastic transformation. Experimentally, we observed that the proliferation of tumor cells in extracellular matrix produced by trisomic 21 fibroblasts appears to be inhibited when compared to that of those placed on an extracellular matrix produced by euploid fibroblasts. These observations challenge the current somatic mutation theory of carcinogenesis, and strongly suggest instead a critical role of cells and tissues in the microenvironment where carcinogenesis occurs.     

ras oncogene detection in pre-neoplastic lesions: possible applications for diagnosis and prevention.

The development of methodologies for the early detection of genetic mutations is an important issue in the prevention and treatment of malignancy. Current knowledge of the association of specific genetic alterations with the development of certain types of tumors enables us to approach the early detection of cancer long before histologic or pathologic evidence indicates the development of neoplastic tumor growth. The identification of genetic alterations as biological markers allows for early diagnosis, which in turn may dictate a particular regimen of treatment to prevent subsequent tumor development. This commentary presents an evaluation of the current status of procedures for the early detection of mutations in the ras oncogene family and their relevance to diagnosis and prevention of neoplastic disease.     

Gene Expression Profiling and Non–Small-Cell Lung Cancer: Where Are We Now?

Despite new developments in molecular techniques and better knowledge on lung cancer tumor biology, many genetic alterations associated with the development and progression of lung carcinogenesis still remain unclear. Although the development of targeted agents has improved response rates and survival, lung cancer has a very high mortality rate, even for early stages. Thus, there is a greater need for other mechanisms or technologies that may help us diagnose, predict, and treat patients with lung cancer in a more effective way. One of these technologies has been the use of genomics. Some of the available genomic technologies include single-nucleotide polymorphism analysis, high-throughput capillary sequencing, serial analysis of gene expression, and gene expression arrays. DNA microarray analysis is capable of discovering changes in DNA expression within the neoplastic tumor. Thus, gene expression array could help us to decipher the complexity and interaction of different oncogenic pathways and, hence, could contribute to the selection of better targeted agents on an individual basis rather than a general and nonspecific approach as it has been done for many decades. Several studies initiated a few years ago have started to produce fruitful results. Herein, we review the role of gene expression profiling in lung cancer as a diagnostic tool, predictive and prognostic biomarker, and its potential use for a “personalized” medicine in the years to come.     

Cytogenetic and molecular aspects of Philadelphia negative chronic myeloproliferative disorders: clinical implications

Chronic myeloproliferative disorders (CMPD) are clonal disorders of the hematopoietic stem cell. The myeloid lineage shows increased proliferation with effective maturation, while peripheral leukocytosis, thrombocytosis or elevated red blood cell mass are found. In Philadelphia negative CMPD recurrent cytogenetic abnormalities occur, but no specific abnormality has been defined to date. The spectrum of cytogenetic aberrations is heterogeneous ranging from numerical gains and losses to structural changes including unbalanced translocations. The most common chromosomal abnormalities are 20q-, 13q-, 12p-, +8, +9, partial duplication of 1q, balanced translocations involving 8p11 and gains in 9p. Cytogenetic analysis of CMPD by conventional or molecular techniques has an important role in establishing the diagnosis of a malignant disease, adding also more information for disease outcome. Molecular studies may detect the possible role of candidate genes implicated in the neoplastic process, addressing new molecular target therapies. FIP1L1/PDGFRalpha rearrangements, as well as alterations of PDGFRbeta or FGFR1 gene have been found to be associated with specific types of CMPD. Recently, a novel somatic mutation, JAK2V617F, has been reported in most of the polycthemia vera (PV) patients, as well as in a lower percentage in essential thrombocythemia (ET) or idiopathic myelofibrosis (IMF) patients. This finding represents the most important advance in understanding of the molecular mechanisms underlined the pathogenesis of CMPD, contributing to the classification and management of patients.     

Genetic and molecular aspects of human multigenerational carcinogenesis

The notion that cancer is a genetic disease has gained increasing credence from the now numerous studies in which specific alterations of chromosome and of gene structure and activity in a variety of cancers have been identified, and, in particular, with the increasing awareness of the heritability of factors that predispose to the development of early, specific cancers in the offspring of parents carrying these predisposing genes. That the inheritance of a single allele is a major causal factor in certain childhood cancers, e.g., retinoblastoma and Wilms' tumour, has long been known, and the locations of the genes predisposing to these tumours have been mapped and at least one has been isolated. Over the past year, using genetic analysis, a further five different loci have been mapped that are involved in five other inherited cancer predispositions. Moreover, in most of these cases the evidence again suggests that one of the pair of alleles at the locus linked to the predisposition undergoes somatic mutation (loss) within the cells that give rise to each of these tumours. A major factor in the origin of these tumours therefore is a loss of a tumour suppressing role of the loci in question. At the present time, seven such suppressor loci on six different chromosomes have been identified, and in a number of cases evidence has been presented for the occurrence of other specific genetic changes that may be necessary for the emergence of a neoplasm. Specific gene or chromosome loss is, however, not confined to cancers associated with the inheritance of a single gene but is increasingly being observed in various more common sporadic cancers, and these data are reviewed and some new data presented. Studies on sporadic cancers have revealed a wide range of different oncogenes in which mutation or abnormal regulation is a cardinal factor leading to a neoplastic state. The products of many of these oncogenes have homologies to growth factors, growth factor receptors or are signal or DNA binding proteins, and specific mutations have been characterized in a number of e-oncogenes in neoplastic human cells. In contrast to genes which may suppress neoplasia, the c-oncogenes act as positive factors, although the presence of a single mutated oncogene is not sufficient on its own to result in neoplastic transformation.(ABSTRACT TRUNCATED AT 400 WORDS)     

Pathway-based evaluation of 380 candidate genes and lung cancer susceptibility suggests the importance of the cell cycle pathway

Common genetic variation may play an important role in altering lung cancer risk. We conducted a pathway-based candidate gene evaluation to identify genetic variations that may be associated with lung cancer in a population-based case-control study in Xuan Wei, China (122 cases and 111 controls). A total of 1260 single-nucleotide polymorphisms (SNPs) in 380 candidate genes for lung cancer were successfully genotyped and assigned to one of 10 pathways based on gene ontology. Logistic regression was used to assess the marginal effect of each SNP on lung cancer susceptibility. The minP test was used to identify statistically significant associations at the gene level. Important pathways were identified using a test of proportions and the rank truncated product methods. The cell cycle pathway was found as the most important pathway (P = 0.044) with four genes significantly associated with lung cancer (PLA2G6 minP = 0.001, CCNA2 minP = 0.006, GSK3 beta minP = 0.007 and EGF minP = 0.013), after adjusting for multiple comparisons. Interestingly, most cell cycle genes that were associated with lung cancer in this analysis were concentrated in the AKT signaling pathway, which is essential for regulation of cell cycle progression and cellular survival, and may be important in lung cancer etiology in Xuan Wei. These results should be viewed as exploratory until they are replicated in a larger study.