The molecular genetics of cancer

Automatic segmentation and supervised learning-based selection of nuclei in cancer tissue images

Analysis of preferential localization of certain genes within the cell nuclei is emerging as a new technique for the diagnosis of breast cancer. Quantitation requires accurate segmentation of 100-200 cell nuclei in each tissue section to draw a statistically significant result. Thus, for large-scale analysis, manual processing is too time consuming and subjective. Fortuitously, acquired images generally contain many more nuclei than are needed for analysis. Therefore, we developed an integrated workflow that selects, following automatic segmentation, a subpopulation of accurately delineated nuclei for positioning of fluorescence in situ hybridization-labeled genes of interest. Segmentation was performed by a multistage watershed-based algorithm and screening by an artificial neural network-based pattern recognition engine. The performance of the workflow was quantified in terms of the fraction of automatically selected nuclei that were visually confirmed as well segmented and by the boundary accuracy of the well-segmented nuclei relative to a 2D dynamic programming-based reference segmentation method. Application of the method was demonstrated for discriminating normal and cancerous breast tissue sections based on the differential positioning of the HES5 gene. Automatic results agreed with manual analysis in 11 out of 14 cancers, all four normal cases, and all five noncancerous breast disease cases, thus showing the accuracy and robustness of the proposed approach.

Role of DLC1 tumor suppressor gene and MYC oncogene in pathogenesis of human hepatocellular carcinoma: potential prospects for combined targeted therapeutics (review)

Hepatocellular carcinoma (HCC) is the third leading cause of cancer death, and its incidence is increasing worldwide in an alarming manner. The development of curative therapy for advanced and metastatic HCC is a high clinical priority. The HCC genome is complex and heterogeneous; therefore, the identification of recurrent genomic and related gene alterations is critical for developing clinical applications for diagnosis, prognosis and targeted therapy of the disease. This article focuses on recent research progress and our contribution in identifying and deciphering the role of defined genetic alterations in the pathogenesis of HCC. A significant number of genes that promote or suppress HCC cell growth have been identified at the sites of genomic reorganization. Notwithstanding the accumulation of multiple genetic alterations, highly recurrent changes on a single chromosome can alter the expression of oncogenes and tumor suppressor genes (TSGs) whose deregulation may be sufficient to drive the progression of normal hepatocytes to malignancy. A distinct and highly recurrent pattern of genomic imbalances in HCC includes the loss of DNA copy number (associated with loss of heterozygosity) of TSG-containing chromosome 8p and gain of DNA copy number or regional amplification of protooncogenes on chromosome 8q. Even though 8p is relatively small, it carries an unusually large number of TSGs, while, on the other side, several oncogenes are dispersed along 8q. Compelling evidence demonstrates that DLC1, a potent TSG on 8p, and MYC oncogene on 8q play a critical role in the pathogenesis of human HCC. Direct evidence for their role in the genesis of HCC has been obtained in a mosaic mouse model. Knockdown of DLC1 helps MYC in the induction of hepatoblast transformation in vitro, and in the development of HCC in vivo. Therapeutic interventions, which would simultaneously target signaling pathways governing both DLC1 and MYC functions in hepatocarcinogenesis, could result in progress in the treatment of liver cancer.

Evolving models of tumor origin and progression

History of cancer disease models clearly illustrates the evolving nature of these concepts. Since such models undergo continual revisions and additions as a result of underlying medical research, they also tend to reorganize knowledge and allow perceiving previously unseen relationships. Growth of medical thought has been influenced for many centuries by an ancient Hippocratic concept of disease seen as a disturbance in bodily “humors.” True mechanisms of cell and tissue injury started to be elucidated only with the advent of postmortem pathological findings. Concerning cancer, when first disease-producing bacteria were identified in the nineteenth century, also neoplasms were treated as infectious diseases. Foreign organisms were thought to be present inside tumors. However, this hypothesis could not be confirmed by microscopic or histochemical studies. The latter suggested, instead, that tumors were rather formed by abnormal cells. Cancer was then started to be regarded as a disease of cells. This interpretation was radically altered by later developments in genetics which suggested that neoplasms can be treated as genetic diseases as pathologic cellular lesions are caused by mutations in specific genes. More recent models have compared carcinogenesis to evolutionary processes. Due to genetic instability, successive mutations, appearing in cells, lead to selection of cancer cells which feature specific phenotypic traits. The newest data indicate that there may be also a link between cancer and mutated stem cells. The review discusses main concepts of tumor origin forwarded since the beginnings of the nineteenth century.

DLC1 interaction with α-catenin stabilizes adherens junctions and enhances DLC1 antioncogenic activity

The DLC1 (for deleted in liver cancer 1) tumor suppressor gene encodes a RhoGAP protein that inactivates Rho GTPases, which are implicated in regulation of the cytoskeleton and adherens junctions (AJs), a cell-cell adhesion protein complex associated with the actin cytoskeleton. Malignant transformation and tumor progression to metastasis are often associated with changes in cytoskeletal organization and cell-cell adhesion. Here we have established in human cells that the AJ-associated protein α-catenin is a new binding partner of DLC1. Their binding was mediated by the N-terminal amino acids 340 to 435 of DLC1 and the N-terminal amino acids 117 to 161 of α-catenin. These proteins colocalized in the cytosol and in the plasma membrane, where together they associated with E-cadherin and β-catenin, constitutive AJ proteins. Binding of DLC1 to α-catenin led to their accumulation at the plasma membrane and required DLC1 GAP activity. Knocking down α-catenin in DLC1-positive cells diminished DLC1 localization at the membrane. The DLC1-α-catenin complex reduced the Rho GTP level at the plasma membrane, increased E-cadherin's mobility, affected actin organization, and stabilized AJs. This process eventually contributed to a robust oncosuppressive effect of DLC1 in metastatic prostate carcinoma cells. Together, these results unravel a new mechanism through which DLC1 exerts its strong oncosuppressive function by positively influencing AJ stability.

RNA-DNA differences are rarer in proto-oncogenes than in tumor suppressor genes

It has long been assumed that DNA sequences and corresponding RNA transcripts are almost identical; a recent discovery, however, revealed widespread RNA-DNA differences (RDDs), which represent a largely unexplored aspect of human genome variation. It has been speculated that RDDs can affect disease susceptibility and manifestations; however, almost nothing is known about how RDDs are related to disease. Here, we show that RDDs are rarer in proto-oncogenes than in tumor suppressor genes; the number of RDDs in coding exons, but not in 3′UTR and 5′UTR, is significantly lower in the former than the latter, and this trend is especially pronounced in non-synonymous RDDs, i.e., those cause amino acid changes. A potential mechanism is that, unlike proto-oncogenes, the requirement of tumor suppressor genes to have both alleles affected to cause tumor ‘buffers' these genes to tolerate more RDDs.

Genetic variations in multiple myeloma I: effect on risk of multiple myeloma

Few risk factors have been established for the plasma cell disorder multiple myeloma, but some of these like African American ethnicity and a family history of B-cell lymphoproliferative diseases suggest a genetic component for the disease. Genetic variation represents the genetic basis of variability in a population. The complex interplay between environment and genes for the development of cancer may therefore be influenced by genetic variations. A genetic variation may change the function of the gene, and if the genetic variation is associated with the risk of disease, that particular gene may be involved in the pathogenesis of disease. Genes of interest are genes involved in the normal development and function of the plasma cell and genes that protect us against exposures from the environment, for example, genes involved in the metabolism of xenobiotics, metabolism of folate and methionine, as well as genes involved in inflammation and DNA repair. Identification of genes with potential influence on cancer risk may help us to establish relevant laboratory studies on exposure and dose-response assessment and may help us to test the hypothesis in epidemiological studies. Knowledge of individual at high risk of cancer may offer promising insight for the prevention of cancer.

NIH-3T3 fibroblasts cultured with plasma from colorectal cancer patients generate poorly differentiated carcinomas in mice

The ability of cells to undergo cellular transitions, in particular, to switch between epithelial and mesenchymal states, might be highly advantageous during the progression of carcinoma. Using histological and immunohistochemical techniques, we here show that the injection into mice of spontaneously transformed NIH-3T3 cells generated fusocellular sarcomas, whereas NIH-3T3 cells that had been transformed by culturing with plasma from colorectal cancer patients gave rise to tumors that phenotypically resembled the carcinomas of the original cancer patients. Thus, plasma from cancer patients is able to transform NIH-3T3 fibroblasts into malignant epithelial-like cells, suggesting that such cells might undergo mesenchymal to epithelial transition during plasma-induced transformation.

[Cancer stem cells: a new target for lung cancer treatment]

Lung cancer remains the leading cause of cancer death. Understanding lung tumours physiopathology should provide opportunity to prevent tumour development or/and improve their therapeutic management. Cancer stem cell theory refers to a subpopulation of cancer cells also named tumour initiating cells that can drive cancer development. Cells presenting these characteristics have been identified and isolated from lung cancer. Exploring cell markers and signalling pathways specific to lung cancer stem cells may lead to progress in therapy and improve the prognosis of patients with lung cancer. Continuous efforts in developing in vitro and in vivo models may yield reliable tools to better understand cancer stem cell abilities and to test new therapeutic targets. Even if some data are in favour of a higher chemo and radioresistance of cancer stem cells this issue remains disputed. Preclinical data on putative cancer stem cell targets are emerging by now. These preliminary studies are critical for the next generation of lung cancer therapies.

Oral cancer: risk factors and molecular pathogenesis

INTRODUCTION

Oral cancer is one of the most common cancers and it constitutes a major health problem particularly in developing countries. It is one of the leading causes of death. Tobacco and alcohol consumption appears to be the major determinants of oral cancer.

MATERIALS AND METHODS

The literature search was carried out in NCBI Pubmed database using keywords "oral cancer", "risk factor", "epidemiology" and "patho*". Some basic information was also obtained from textbook and medical university websites.

RESULTS

Several risk factors have been well characterized to be associated with oral cancer with substantial evidences. The development of oral cancer is a multistep process involving the accumulation of genetic and epigenetic alterations in key regulatory genes. Experimental pathological studies of oral cancer in animal models and direct molecular genetic analysis of oral cancer subjects in recent times have revealed a substantial amount of knowledge on specific gene alterations or other genetic mechanisms involved in initiation and subsequent progression.

CONCLUSION

Considering known risk factors, oral cancer appears to be to a certain extent, a preventable disease. Recent development of molecular picture of pathoprogression and molecular genetic tools opens the avenue for easier diagnosis, better prognostication and efficient therapeutic management.

Protein folding, protein homeostasis, and cancer

Proteins fold into their functional 3-dimensional structures from a linear amino acid sequence. In vitro this process is spontaneous; while in vivo it is orchestrated by a specialized set of proteins, called chaperones. Protein folding is an ongoing cellular process, as cellular proteins constantly undergo synthesis and degradation. Here emerging links between this process and cancer are reviewed. This perspective both yields insights into the current struggle to develop novel cancer chemotherapeutics and has implications for future chemotherapy discovery.

Lung cancer stem cell: new insights on experimental models and preclinical data

Lung cancer remains the leading cause of cancer death. Understanding lung tumors physiopathology should provide opportunity to prevent tumor development or/and improve their therapeutic management. Cancer stem cell (CSC) theory refers to a subpopulation of cancer cells, also named tumor-initiating cells, that can drive cancer development. Cells presenting these characteristics have been identified and isolated from lung cancer. Exploring cell markers and signaling pathways specific to lung CSCs may lead to progress in therapy and improve the prognosis of patients with lung cancer. Continuous efforts in developing in vitro and in vivo models may yield reliable tools to better understand CSC abilities and to test new therapeutic targets. Preclinical data on putative CSC targets are emerging by now. These preliminary studies are critical for the next generation of lung cancer therapies.

Small molecule regulators of Rb-E2F pathway as modulators of transcription

The retinoblastoma tumor suppressor protein, Rb, plays a major role in the regulation of mammalian cell cycle progression. It has been shown that Rb function is essential for the proper modulation of G1/S transition and inactivation of Rb contributes to deregulated cell proliferation. Rb exerts its cell cycle regulatory functions mainly by targeting the E2F family of transcription factors and Rb has been shown to physically interact with E2Fs 1, 2 and 3, repressing their transcriptional activity. Multiple genes involved in DNA synthesis and cell cycle progression are regulated by E2Fs, and Rb prevents their expression by inhibiting E2F activity, inducing growth arrest. It has been established that inactivation of Rb by phosphorylation, mutation, or by the interaction of viral oncoproteins leads to a release of the repression of E2F activity, facilitating cell cycle progression. Rb-mediated repression of E2F activity involves the recruitment of a variety of transcriptional co-repressors and chromatin remodeling proteins, including histone deacetylases, DNA methyltransferases and Brg1/Brm chromatin remodeling proteins. Inactivation of Rb by sequential phosphorylation events during cell cycle progression leads to a dissociation of these co-repressors from Rb, facilitating transcription. It has been found that small molecules that prevent the phosphorylation of Rb prevent the dissociation of certain co-repressors from Rb, especially Brg1, leading to the maintenance of Rb-mediated transcriptional repression and cell cycle arrest. Such small molecules have anti-cancer activities and will also act as valuable probes to study chromatin remodeling and transcriptional regulation.

Cancer models, genomic instability and somatic cellular Darwinian evolution

The biology of cancer is critically reviewed and evidence adduced that its development can be modelled as a somatic cellular Darwinian evolutionary process. The evidence for involvement of genomic instability (GI) is also reviewed. A variety of quasi-mechanistic models of carcinogenesis are reviewed, all based on this somatic Darwinian evolutionary hypothesis; in particular, the multi-stage model of Armitage and Doll (Br. J. Cancer 1954:8;1-12), the two-mutation model of Moolgavkar, Venzon, and Knudson (MVK) (Math. Biosci. 1979:47;55-77), the generalized MVK model of Little (Biometrics 1995:51;1278-1291) and various generalizations of these incorporating effects of GI (Little and Wright Math. Biosci. 2003:183;111-134; Little et al. J. Theoret. Biol. 2008:254;229-238).

Discovery of novel fibroblast growth factor receptor 1 kinase inhibitors by structure-based virtual screening

Fibroblast growth factors (FGFs) play important roles in embryonic development, angiogenesis, wound healing, and cell proliferation and differentiation. In search of inhibitors of FGFR1 kinase, 2.2 million compounds were docked into the ATP binding site of the protein. A co-crystal structure, which shows two alternative conformations for the nucleotide binding loop, is reported. Docking was performed on both conformations and, ultimately, 23 diverse compounds were purchased and assayed. Following hit validation, two compounds 10 and 16, a benzylidene derivative of pseudothiohydantoin and a thienopyrimidinone derivative, respectively, were discovered that inhibit FGFR1 kinase with IC(50) values of 23 and 50 microM. Initial optimization of 16 led to the more unsaturated 40, which has significantly enhanced potency, 1.9 microM. The core structures represent new structural motifs for FGFR1 kinase inhibitors. The study also illustrates complexities associated with the choice of protein structures for docking, possible use of multiple kinase structures to seek selectivity, and hit identification.

Mixed lineage kinase 3 gene mutations in mismatch repair deficient gastrointestinal tumours

Mixed lineage kinase 3 (MLK3) is a serine/threonine kinase, regulating MAPkinase signalling, in which cancer-associated mutations have never been reported. In this study, 174 primary gastrointestinal cancers (48 hereditary and 126 sporadic forms) and 7 colorectal cancer cell lines were screened for MLK3 mutations. MLK3 mutations were significantly associated with MSI phenotype in primary tumours (P = 0.0005), occurring in 21% of the MSI carcinomas. Most MLK3 somatic mutations identified were of the missense type (62.5%) and more than 80% of them affected evolutionarily conserved residues. A predictive 3D model points to the functional relevance of MLK3 missense mutations, which cluster in the kinase domain. Further, the model shows that most of the altered residues in the kinase domain probably affect MLK3 scaffold properties, instead of its kinase activity. MLK3 missense mutations showed transforming capacity in vitro and cells expressing the mutant gene were able to develop locally invasive tumours, when subcutaneously injected in nude mice. Interestingly, in primary tumours, MLK3 mutations occurred in KRAS and/or BRAF wild-type carcinomas, although not being mutually exclusive genetic events. In conclusion, we have demonstrated for the first time the presence of MLK3 mutations in cancer and its association to mismatch repair deficiency. Further, we demonstrated that MLK3 missense mutations found in MSI gastrointestinal carcinomas are functionally relevant.

A new view of carcinogenesis and an alternative approach to cancer therapy

During the last few decades, cancer research has focused on the idea that cancer is caused by genetic alterations and that this disease can be treated by reversing or targeting these alterations. The small variations in cancer mortality observed during the previous 30 years indicate, however, that the clinical applications of this approach have been very limited so far. The development of future gene-based therapies that may have a major impact on cancer mortality may be compromised by the high number and variability of genetic alterations recently found in human tumors. This article reviews evidence that tumor cells, in addition to acquiring a complex array of genetic changes, develop an alteration in the metabolism of oxygen. Although both changes play an essential role in carcinogenesis, the altered oxygen metabolism of cancer cells is not subject to the high genetic variability of tumors and may therefore be a more reliable target for cancer therapy. The utility of this novel approach for the development of therapies that selectively target tumor cells is discussed.

Clinical significance of vascular endothelial growth factor expression in patients with carcinoma of the mouth floor and tongue

BACKGROUND/AIM

Although there are several types of malignant oral cancers, more than 90% of all diagnosed oral cancers are squamous cell carcinoma (OSCC). Angiogenesis is a cascade-like mechanism which is essential for tumor growth and metastasis. Therefore, vascular endothelial growth factor (VEGF) expression in OSCC and its effect on clinicopathological characteristics and prognosis is of major interest. So far researches have shown that increased expression of this gene, in other words enhanced sinthesis of this protein (VEGF), independently on other factors, increases a chance for local relapse, and distant metastasis. Consequently, patients with OSCC have poor disease-free survival, as well as poor overall survival. The aim of the study was to determine clinical significance of VEGF expression in patients with stage II and III OSCC.

METHODS

This retrospective study analysed 40 patients who had been operated for OSCC of their tongue and the mouth floor. Of these patients, some had stage II and III OSCC with histological grade, G1-G3 and nuclear grade Ng1-Ng3. Two high quality tissue samples were obtained and immunohistochemical expression of VEGF was quantitatively determined by using high microscope amplification. The value of VEGF expression of 20% was rated as significant expression, whereas tumor cells reactivation less than 20% was considered very low or no expression at all. The patients were followed up for a 3-year period.

RESULTS

The obtained results showed that 11 (17.5%) patients had VEGF expression less than 20% and 29 (82.5%) above 20%. A statistical significance was immanent with positive nodal status (p < 0.05) and disease stage (p < 0.05). No statistical correlation was found between the level of VEGF expression and histological and nuclear grade, tumor size, disease relapse or patients overall survival.

CONCLUSION

Inspite the controversy about the prognostic relevance of VEGF our results as well as the results of previous studies, suggest that the expression of VEGF is not reliable as a clinical parameter for the prognosis and disease outcome but it is one of the important factors for the disease progression.

Multiple hepatic arterial injections of recombinant adenovirus p53 and 5-fluorouracil after transcatheter arterial chemoembolization for unresectable hepatocellular carcinoma: a pilot phase II trial

This pilot phase II study was designed to determine the efficacy, toxicities, and biological activity of multiple hepatic arterial injections of recombinant adenovirus p53 (rAd-p53) and 5-fluorouracil (5-FU) after transcatheter arterial chemoembolization (TACE) when compared with TACE alone in patients with unresectable hepatocellular carcinoma (HCC). Forty-six patients with unresectable HCC were randomized in either group 1 [23 patients, multiple hepatic arterial injections of Ad-p53 (1x10 viral particles) and 5-FU (500-750 mg), after TACE] or group 2 (23 patients, TACE alone). In group 1, the number of Ad-p53/5-FU courses administered was 166 (median 7, range 3-12). In group 2, the number of TACE courses administered was 47 (median 2, range 1-3). Partial response and stable disease were 69.5% in group 1 and 65.2% in group 2. Times to progression were 9.6 months (range 2.1-21.7) in group 1 and 8.3 months (range 2.1-16.8) in group 2. Overall survivals were 12.8 months (range 2.7-26.2) in group 1 and 10.4 months (range 2.7-22.5) in group 2. Toxicities in both groups were generally mild and reversible. The most common Ad-p53-related toxicity was a transient fever. Specific p53 transgene expression was detected using reverse-transcriptase polymerase chain reaction in biopsied tumor tissues. Distribution studies revealed that the vector was detected in the plasma, but rarely in the gargle and urine. This study shows that multiple hepatic arterial injections of Ad-p53 and 5-FU after TACE can be active and safe as a treatment for patients with unresectable HCC.

Chromosome instability in lymphocytes of children with coeliac disease

Undiagnosed individuals with celiac disease (CD) or those who do not comply with gluten-free diet (GFD) are at a higher risk of developing malignancies. A possible origin of chromosomal alteration in autoimmune reaction could be mistakes in the rearrangement of V(D)J of the IgH gene. Our aim was to verify whether higher genomic instability was found in coeliac individuals and whether GFD reduced it. As marker of genomic instability we analysed the frequency of 2 translocations, t(14;18) and t(11;14), in peripheral blood by nested PCR, in 37 patients with CD at diagnosis, 27 patients with CD after 2 years on GFD, and 36 control individuals. No significant differences were found.

High mutability of the tumor suppressor genes RASSF1 and RBSP3 (CTDSPL) in cancer

Background

Many different genetic alterations are observed in cancer cells. Individual cancer genes display point mutations such as base changes, insertions and deletions that initiate and promote cancer growth and spread. Somatic hypermutation is a powerful mechanism for generation of different mutations. It was shown previously that somatic hypermutability of proto-oncogenes can induce development of lymphomas.

Methodology/Principal Findings

We found an exceptionally high incidence of single-base mutations in the tumor suppressor genes RASSF1 and RBSP3 (CTDSPL) both located in 3p21.3 regions, LUCA and AP20 respectively. These regions contain clusters of tumor suppressor genes involved in multiple cancer types such as lung, kidney, breast, cervical, head and neck, nasopharyngeal, prostate and other carcinomas. Altogether in 144 sequenced RASSF1A clones (exons 1–2), 129 mutations were detected (mutation frequency, MF = 0.23 per 100 bp) and in 98 clones of exons 3–5 we found 146 mutations (MF = 0.29). In 85 sequenced RBSP3 clones, 89 mutations were found (MF = 0.10). The mutations were not cytidine-specific, as would be expected from alterations generated by AID/APOBEC family enzymes, and appeared de novo during cell proliferation. They diminished the ability of corresponding transgenes to suppress cell and tumor growth implying a loss of function. These high levels of somatic mutations were found both in cancer biopsies and cancer cell lines.

Conclusions/Significance

This is the first report of high frequencies of somatic mutations in RASSF1 and RBSP3 in different cancers suggesting it may underlay the mutator phenotype of cancer. Somatic hypermutations in tumor suppressor genes involved in major human malignancies offer a novel insight in cancer development, progression and spread.

Advances in biology of multiple myeloma: cell kinetics, molecular biology and immunology

Bone marrow plasma cell proliferative activity has been evaluated in a large series of multiple myeloma (MM) patients. This kinetic parameter has been shown to be a useful tool for patient management, and contributes to a correct diagnosis and a selection of high-risk patients who can be offered high-dose chemotherapy. The role of ras oncogenes has been evaluated in the pathogenesis of MM. A point-mutated and activated H-ras oncogene, introduced in a human lymphoblastoid cell line, was able to induce neoplastic transformation and differentiation to plasma cell. Indeed, mutated alleles of ras genes have been detected in a high percentage of myeloma patients in relapse phase. Phenotypical and functional studies have been carried out in T-lymphocyte subsets and an impaired cellular immunity has been detected. Such an impairment was related to the disease status: marked alterations were detected in relapse phase, whereas a partial recovery was observed during remission phase.

Recurrent chemical reactivations of EBV promotes genome instability and enhances tumor progression of nasopharyngeal carcinoma cells

Nasopharyngeal carcinoma (NPC) is an endemic malignancy prevalent in South East Asia. Epidemiological studies have associated this disease closely with Epstein-Barr virus (EBV) infection. Previous studies also showed that EBV reactivation is implicated in the progression of NPC. Thus, we proposed that recurrent reactivations of EBV may be important for its pathogenic role. In this study, NPC cell lines latently infected with EBV, NA and HA, and the corresponding EBV-negative NPC cell lines, NPC-TW01 (TW01) and HONE-1, were treated with 12-O-tetradecanoylphorbol-13-acetate (TPA) and sodium n-butyrate (SB) for lytic cycle induction. A single treatment with TPA/SB revealed that DNA double-strand breaks and formation of micronuclei (a marker for genome instability) were associated with EBV reactivation in NA and HA cells. Examination of EBV early genes had identified several lytic proteins, particularly EBV DNase, as potent activators that induced DNA double-strand breaks and contribute to genome instability. Recurrent reactivations of EBV in NA and HA cells resulted in a marked increase of genome instability. In addition, the degree of chromosomal aberrations, as shown by chromosome structural variants and DNA copy-number alterations, is proportional to the frequency of TPA/SB-induced EBV reactivation. Whereas these DNA abnormalities were limited in EBV-negative TW01 cells with mock or TPA/SB treatment, and were few in mock-treated NA cells. The invasiveness and tumorigenesis assays also revealed a profound increase in both characteristics of the repeatedly reactivated NA cells. These results suggest that recurrent EBV reactivations may result in accumulation of genome instability and promote the tumor progression of NPC.

Evidence of ultraviolet type mutations in xeroderma pigmentosum melanomas

To look for a direct role of ultraviolet radiation (UV) exposure in cutaneous melanoma induction, we studied xeroderma pigmentosum (XP) patients who have defective DNA repair resulting in a 1000-fold increase in melanoma risk. These XP melanomas have the same anatomic distribution as melanomas in the general population. We analyzed laser capture microdissection samples of skin melanomas from XP patients studied at the National Institutes of Health. The tumor suppressor gene PTEN was sequenced and analyzed for UV-induced mutations. Samples from 59 melanomas (47 melanomas in situ and 12 invasive melanomas) from 8 XP patients showed mutations in the PTEN tumor suppressor gene in 56% of the melanomas. Further, 91% of the melanomas with mutations had 1 to 4 UV type base substitution mutations (occurring at adjacent pyrimidines) (P < 0.0001 compared to random mutations). We found a high frequency of amino-acid-altering mutations in the melanomas and demonstrated that these mutations impaired PTEN function; UV damage plays a direct role in induction of mutations and in inactivation of the PTEN gene in XP melanomas including in situ, the earliest stage of melanoma. This gene is known to be a key regulator of carcinogenesis and therefore these data provide solid mechanistic support for UV protection for prevention of melanoma.

Dysfunctional homologous recombination mediates genomic instability and progression in myeloma

A prominent feature of most if not all cancers is a striking genetic instability, leading to ongoing accrual of mutational changes, some of which underlie tumor progression, including acquisition of invasiveness, drug resistance, and metastasis. Thus, the molecular basis for the generation of this genetic diversity in cancer cells has important implications in understanding cancer progression. Here we report that homologous recombination (HR) activity is elevated in multiple myeloma (MM) cells and leads to an increased rate of mutation and progressive accumulation of genetic variation over time. We demonstrate that the inhibition of HR activity in MM cells by small inhibitory RNA (siRNAs) targeting recombinase leads to significant reduction in the acquisition of new genetic changes in the genome and, conversely, the induction of HR activity leads to significant elevation in the number of new mutations over time and development of drug resistance in MM cells. These data identify dysregulated HR activity as a key mediator of DNA instability and progression of MM, with potential as a therapeutic target.

QSAR study of p56(lck) protein tyrosine kinase inhibitory activity of flavonoid derivatives using MLR and GA-PLS

Quantitative relationships between molecular structure and p56(lck) protein tyrosine kinase inhibitory activity of 50 flavonoid derivatives are discovered by MLR and GA-PLS methods. Different QSAR models revealed that substituent electronic descriptors (SED) parameters have significant impact on protein tyrosine kinase inhibitory activity of the compounds. Between the two statistical methods employed, GA-PLS gave superior results. The resultant GA-PLS model had a high statistical quality (R(2) = 0.74 and Q(2) = 0.61) for predicting the activity of the inhibitors. The models proposed in the present work are more useful in describing QSAR of flavonoid derivatives as p56(lck) protein tyrosine kinase inhibitors than those provided previously.

RASSF1A expression inhibits the growth of hepatocellular carcinoma from Qidong County

BACKGROUND AND AIM

The tumor-suppressing role of Ras-association domain family 1A (RASSF1A) has been described in several systems. In this study, we tested its tumor-suppressing ability and the potential molecular mechanisms in hepatocellular carcinoma (HCC) from Qidong County.

METHODS

Reverse transcription polymerase chain reaction and Northern blotting were employed to detect the expression of RASSF1A in HCC. After establishing stable RASSF1A (wild type or mutant) expressing 'qi dong gan ai yan jiu suo' ([Qidong Institute of Liver Cancer] QGY)-7703 cell lines, we tested the effects of RASSF1A expression on cell growth by cell proliferation rate, cell colony formation, and cell cycle progression. We also tested the effects of RASSF1A expression on tumorigenesis in nude mice and on cellular sensitivity to mitomycin treatment.

RESULTS

The RASSF1A transcript was not found in 75% (three of four) of HCC cell lines and 67% (32/48) of HCC primary biopsies. The stepwise regression analyses indicated that the loss of RASSF1A expression was more frequent in patients who were hepatitis B virus surface antigen positive (HBsAg+) compared to those who were HBsAg(-), both in tumor and corresponding non-cancerous tissues. The wild-type (wt)-RASSF1A expression in the QGY-7703 cell line resulted in fewer and smaller clones, decreased xenograft tumor volume and weight, and G(1)/S arrest in vitro and in vivo. The wt-RASSF1A expression also decreased the cyclin D1 protein expression, which appeared to be at the level of post-transcriptional control. In addition, the wt-RASSF1A expression increased cell growth inhibition and the percentage of cells with sub-G(1) DNA content when the cells were treated with mitomycin.

CONCLUSION

RASSF1A is a tumor suppressor in HCC. The loss of RASSF1A expression may be related to HBsAg+ in hepatocarcinogenesis. Its inactivation may play an important role in the development of HCC.

MLPA mutation detection in Argentine HNPCC and FAP families

Colorectal cancer (CC) is the secondary cause of death in the Western countries of which approximately 15% are considered to be hereditary. The hereditary forms are Familial Adenomatous Polyposis (FAP) and Hereditary Non Polyposis Colorectal Cancer (HNPCC) which is the commonest form. The detection of mutations in the MMR and apc related genes, allows the development of health prevention strategies. Different molecular diagnostic strategies are available for the detection of mutations in these genes, i.e. DGGE, SSCP and direct sequencing. However, deletions and duplications of one or more consecutive exons, which account for around 50% of the total alterations in MMR genes, cannot be detected by PCR based methodologies due to the non quantitative nature of these techniques. The aim of our work has been the standardization of a methodology, called Multiplex Ligation-Dependent Probe Amplification, which allows the detection of genomic deletions and duplications as primary analysis in HNPCC and FAP patients in Argentina. In this case, we inform that the application of MLPA allowed the detection of a missence mutation, without the need for direct sequencing of the complete genes involved. A PCR/RFLP strategy was afterwards designed to detect the C<T change on codon 718 of mlh1 gene in members of the family. For a developing country like Argentina, which has limited resources for genetic diagnosis, this MLPA application has avoided an unaffordable cost as the complete sequencing of all the involved genes. The application of MLPA in our country contributes to improvement in the diagnosis of hereditary CC and allows the development of preventive health interventions.

Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy

The search for the genomic sequences involved in human cancers can be greatly facilitated by maps of genomic imbalances identifying the involved chromosomal regions, particularly those that participate in the development of occult preneoplastic conditions that progress to clinically aggressive invasive cancer. The integration of such regions with human genome sequence variation may provide valuable clues about their overall structure and gene content. By extension, such knowledge may help us understand the underlying genetic components involved in the initiation and progression of these cancers. We describe the development of a genome-wide map of human bladder cancer that tracks its progression from in situ precursor conditions to invasive disease. Testing for allelic losses using a genome-wide panel of 787 microsatellite markers was performed on multiple DNA samples, extracted from the entire mucosal surface of the bladder and corresponding to normal urothelium, in situ preneoplastic lesions, and invasive carcinoma. Using this approach, we matched the clonal allelic losses in distinct chromosomal regions to specific phases of bladder neoplasia and produced a detailed genetic map of bladder cancer development. These analyses revealed three major waves of genetic changes associated with growth advantages of successive clones and reflecting a stepwise conversion of normal urothelial cells into cancer cells. The genetic changes map to six regions at 3q22-q24, 5q22-q31, 9q21-q22, 10q26, 13q14, and 17p13, which may represent critical hits driving the development of bladder cancer. Finally, we performed high-resolution mapping using single nucleotide polymorphism markers within one region on chromosome 13q14, containing the model tumor suppressor gene RB1, and defined a minimal deleted region associated with clonal expansion of in situ neoplasia. These analyses provided new insights on the involvement of several non-coding sequences mapping to the region and identified novel target genes, termed forerunner (FR) genes, involved in early phases of cancer development.

Human papillomavirus and mutated H-ras oncogene in cervical carcinomas and pathological negative pelvic lymph nodes: a retrospective follow-up

The metastasis status of pelvic lymph nodes (PLNs) seems to be a predictive factor of survival. It was suggested that the presence of HPV DNA and other biological markers in PLN may indicate a sub clinical early metastasis. The aim was to describe the prevalence and distribution patterns of HPV DNA and H-ras mutations in intra operatively obtained cervical tumors and PLN. Thirty-seven cervical tumors and 61 lymph node biopsies from 37 patients with cervical cancer were selected. HPV typing and location were performed by PCR/dot blot and in situ hybridization (ISH) respectively. PCR/RFLP was used to scan for mutations in H-ras. Hundred percent of the cervical cancers and 85% of the PLN were HPV positive; co-infection with more than one type was 27%. HPV 16 was detected alone or co-infecting with other types in 84% of tumors and 46% of PLN; the second most frequent viral type was HPV 18 (tumor: 27%; PLN: 20%). In PLN, HPV was located in nuclei or/and cytoplasm of lymphocytes, macrophages, endothelial, and /or stromal cells. H-ras mutations were identified in 5/24 (21%) of patients with cervical tumors showing poor or moderated differentiation. HPV DNA in histological tumor-free PLN not necessary indicate metastasis, but it may be associated to an active immune reaction. Mutated H-ras is probably involved in cervical carcinogenesis and its detection in tumor and metastasis free PLN may be related to early metastasis or recurrence in at least a subset of poorly differentiated cervical tumors.

The role of chromosomal alterations in human cancer development

Cancer cells become unstable and compromised because several cancer-predisposing mutations affect genes that are responsible for maintaining the genomic instability. Several factors influence the formation of chromosomal rearrangements and consequently of fusion genes and their role in tumorigenesis. Studies over the past decades have revealed that recurring chromosome rearrangements leading to fusion genes have a biological and clinical impact not only on leukemias and lymphomas, but also on certain epithelial tumors. With the implementation of new and powerful cytogenetic and molecular techniques the identification of fusion genes in solid tumors is being facilitated. Overall, the study of chromosomal translocations have revealed several recurring themes, and reached important insights into the process of malignant transformation. However, the mechanisms behind these translocations remain unclear. A more thorough understanding of the mechanisms that cause translocations will be aided by continuing characterization of translocation breakpoints and by developing in vitro and in vivo model systems that can generate chromosome translocation.

Comparing whole genomes using DNA microarrays

The rapid accumulation of complete genomic sequences offers the opportunity to carry out an analysis of inter- and intra-individual genome variation within a species on a routine basis. Sequencing whole genomes requires resources that are currently beyond those of a single laboratory and therefore it is not a practical approach for resequencing hundreds of individual genomes. DNA microarrays present an alternative way to study differences between closely related genomes. Advances in microarray-based approaches have enabled the main forms of genomic variation (amplifications, deletions, insertions, rearrangements and base-pair changes) to be detected using techniques that are readily performed in individual laboratories using simple experimental approaches.

Telomeric location of retroviral oncogenes in humans

The position relative to centromeres and telomeres has been investigated in 42 proto-oncogenes that have been localized in specific bands of the human chromosomes. It turned out that the 26 retroviral oncogenes had a predominant telon territory (near telomeres). The difference from the non-retrovirally transduced oncogenes is significant (p less than 0.01). Moreover, all oncogenes studied avoid the shortest and the longest arms. The results support the idea that genes with different properties tend to have different gene territories within the human chromosomes.

Epigenetic changes in tumor suppressor genes, P15, P16, APC-3 and E-cadherin in body fluid

The inactivation of tumor suppressor genes by promoter methylation plays an important role in the development of cancers; it can also be used as a marker to distinguish cancerous cells from non-cancer cells. In this study, we investigated the aberrant methylation profile of the tumor suppressor genes P15, P16, APC and E-cadherin in the cells of body fluid. A methylation-specific polymerase chain reaction was performed in 31 cases of malignant effusion and 39 cases of non-malignant effusion. Aberrant promoter methylation of P15, P16, APC and E-cadherin genes was seen in 0%, 25.8%, 35.5% and 6.5% of malignant effusion cases, respectively, whereas the frequencies were 0%, 2.6%, 2.6% and 0%, respectively, for negative control effusion. There were statistically significant differences in the aberrant methylation of P16 (p = 0.008) and APC (p = 0.018) genes between cases of malignant effusion and controls. Methylation of one of three genes (P16, E-cadherin, APC) was found in 14 out of 31 (45.2%) cases of malignant effusion, and in two out of 39 (5.1%) cases of non-malignant effusion (p = 0.000004). Concurrent methylation was found in nine out of 31 (29%) cases of malignant effusion, but in no non-malignant effusion sample. From these results, we suggest that methylation-specific polymerase chain reaction to analyze the promoters of tumor suppressor genes can distinguish between malignant effusion and benign effusion, and may help cytologists to make more accurate diagnoses.

Histopathological characteristics and coexpression of p53 and p16INK4a proteins in renal cancer

Background/Aim. Renal carcinoma represents histologically heterogeneous group of malignant tumors, with various clinical aggressiveness. The frequency of p53 mutation in primal renal carcinoma is rare, although there are information about its heterogeneous accumulation. The loss of protein p16 expression in primal renal carcinoma is detected in 20-30% of the cases. The aim of this paper was to determine frequency of mutated protein p53 and expression of protein p16INK4a in renal carcinoma, to analyze their correlative relation and relation with the examined clinicopathological parameters. Methods. The examination included 12 patients (66.7% men, 33.3% women), with patohistologically verified renal carcinoma. Expression of mutated form of protein p53 and protein p16 was determined in tissue samples, by immunohistochemical analysis using of mice monoclonical antibodies produced by DAKO, Denmark. Results. In 9 (75%) of the cases was detected mutated protein p53, of whom 66.6% had higher histological gradus of tumor (G3-4) and higher pathological stadium of the disease (pT3a-b) at the same time. In 7 (58.3%) and 5 (41.7%) of the cases expression of protein p16, the loss of expression of protein p16 were detected respectively. A statistically significant positive correlation was determined between pathological stadium of disease (TNM) and the degree of tumor differentiation (G) (? = 0.834; p < 0.001), as well as between TNM and mitotic index (? = 0.622; p = 0.031). Conclusion. A mutated form of protein p53 exists in 75% of the cases with the renal carcinoma and 66.6% of then have higher histological gradus of tumor and higher stadium of tumor disease at the same time. Coexpression of mutated protein p53 and protein p16INK4a in renal carcinoma is not statistically significant and it is not in correlation with clinicopathological parameters. Immunohistochemical analysis of mutated protein p53 in renal carcinoma can have predictive significance.

Increased frequency of micronucleated exfoliated cells among humans exposed in vivo to mobile telephone radiations

The health concerns have been raised following the enormous increase in the use of wireless mobile telephones throughout the world. This investigation had been taken, with the motive to find out whether mobile phone radiations cause any in vivo effects on the frequency of micronucleated exfoliated cells in the exposed subjects. A total of 109 subjects including 85 regular mobile phone users (exposed) and 24 non-users (controls) had participated in this study. Exfoliated cells were obtained by swabbing the buccal-mucosa from exposed as well as sex-age-matched controls. One thousand exfoliated cells were screened from each individual for nuclear anomalies including micronuclei (MN), karyolysis (KL), karyorrhexis (KH), broken egg (BE) and binucleated (BN) cells. The average daily duration of exposure to mobile phone radiations is 61.26 min with an overall average duration of exposure in term of years is 2.35 years in exposed subjects along with the 9.84+/-0.745 micronucleated cells (MNCs) and 10.72+/-0.889 total micronuclei (TMN) as compared to zero duration of exposure along with average 3.75+/-0.774 MNC and 4.00+/-0.808 TMN in controls. The means are significantly different in case of MNC and TMN at 0.01% level of significance. The mean of KL in controls is 13.17+/-2.750 and in exposed subjects is 13.06+/-1.793. The value of means of KH in exposed subjects (1.84+/-0.432) is slightly higher than in controls (1.42+/-0.737). Mean frequency of broken egg is found to be more in exposed subjects (0.65+/-0.276) as compared to controls (0.50+/-0.217). Frequency of presence of more than one nucleus in a cell (binucleated) is also higher in exposed (2.72+/-0.374) in comparison to controls (0.67+/-0.231). Although there is a slight increase in mean frequency of KH, BE and BN in exposed subjects but the difference is not found statistically significant. Correlation between 0-1, 1-2, 2-3 and 3-4 years of exposure and the frequency of MNC and TMN has been calculated and found to be positively correlated.