Oncogenes and tumor suppressor genes

Fast Prototyping Microfluidics: Integrating Droplet Digital Lamp for Absolute Quantification of Cancer Biomarkers

Microfluidic (MF) advancements have been leveraged toward the development of state-of-the-art platforms for molecular diagnostics, where isothermal amplification schemes allow for further simplification of DNA detection and quantification protocols. The MF integration with loop-mediated isothermal amplification (LAMP) is today the focus of a new generation of chip-based devices for molecular detection, aiming at fast and automated nucleic acid analysis. Here, we combined MF with droplet digital LAMP (ddLAMP) on an all-in-one device that allows for droplet generation, target amplification, and absolute quantification. This multilayer 3D chip was developed in less than 30 minutes by using a low-cost and extremely adaptable production process that exploits direct laser writing technology in "Shrinky-dinks" polystyrene sheets. ddLAMP and target quantification were performed directly on-chip, showing a high correlation between target concentration and positive droplet score. We validated this integrated chip via the amplification of targets ranging from five to 500,000 copies/reaction. Furthermore, on-chip amplification was performed in a 10 µL volume, attaining a limit of detection of five copies/µL under 60 min. This technology was applied to quantify a cancer biomarker, c-MYC, but it can be further extended to any other disease biomarker.

Etiologic Role of Kinases in the Progression of Human Cancers and Its Targeting Strategies

Cancer is one of the dominant causes of death worldwide while lifelong prognosis is still inauspicious. The maturation of the cancer is seen as a process of transformation of a healthy cell into a tumor-sensitive cell, which is held entirely at the cellular, molecular, and genetic levels of the organism. Tyrosine kinases can play a major, etiologic role in the inception of malignancy and devote to the uncontrolled proliferation of cancerous cells and the progression of a tumor as well as the development of metastatic disease. Angiogenesis and oncogene activation are the major event in cell proliferation. The growth of a tumor and metastasis are fully depending on angiogenesis and lymphangiogenesis triggered by chemical signals from tumor cells in a phase of rapid growth. Tyrosine kinase inhibitors are compounds that inhibit tyrosine kinases and effective in targeting angiogenesis and blocking the signaling pathways of oncogenes. Small molecule tyrosine kinase inhibitors like afatinib, erlotinib, crizotinib, gefitinib, and cetuximab are shown to a selective cut off tactic toward the constitutive activation of an oncogene in tumor cells, and thus contemplated as promising therapeutic approaches for the diagnosis of cancer and malignancies.

A new mutation-independent approach to cancer therapy: Inhibiting oncogenic RAS and MYC, by targeting mitochondrial biogenesis

Here, we used MCF7 cells as a model system to interrogate how MYC/RAS co-operativity contributes to metabolic flux and stemness in breast cancer cells. We compared the behavior of isogenic MCF7 cell lines transduced with c-Myc or H-Ras (G12V), either individually or in combination. Cancer stem cell (CSC) activity was measured using the mammosphere assay. c-Myc augmented both mammosphere formation and mitochondrial respiration, without any effects on glycolytic flux. In contrast, H-Ras (G12V) synergistically augmented both mammosphere formation and glycolysis, but only in combination with c-Myc, directly demonstrating MYC/RAS co-operativity. As c-Myc is known to exert its effects, in part, by stimulating mitochondrial biogenesis, we next examined the effects of another stimulus known to affect mitochondrial biogenesis, i.e. ROS production. To pharmacologically induce oxidative stress, we used Rotenone (a mitochondrial inhibitor) to target mitochondrial complex I. Treatment with Rotenone showed bi-phasic effects; low-dose Rotenone (1 to 2.5 nM) elevated mammosphere formation, while higher doses (10 to 100 nM) were inhibitory. Importantly, the stimulatory effects of Rotenone on CSC propagation were blocked using a mitochondrial-specific anti-oxidant, namely Mito-tempo. Thus, "mild" mitochondrial oxidative stress, originating at Complex I, was sufficient to pheno-copy the effects of c-Myc, effectively promoting CSC propagation. To validate the idea that mitochondrial biogenesis is required to stimulate CSC propagation, we employed Doxycycline, a well-established inhibitor of mitochondrial protein translation. Treatment with Doxycycline was indeed sufficient to block the stimulatory effects of H-Ras (G12V), c-Myc, and Rotenone on CSC propagation. As such, Doxycycline provides a strong rationale for designing new therapeutics to target mitochondrial biogenesis, suggesting a new "mutation-independent" approach to cancer therapy. In support of this notion, most currently successful anti-cancer agents therapeutically target "cell phenotypes", such as increased cell proliferation, rather than specific genetic mutations. Remarkably, we demonstrated that Doxycycline inhibits the effects of diverse oncogenic stimuli, of both i) genetic (MYC/RAS) and ii) environmental (Rotenone) origins. Finally, we discuss the advantages of our "Proteomics-to-Genomics (PTG)" approach for in silico validation of new biomarkers and novel drug targets. In this context, we developed a new Myc-based Mito-Signature consisting of 3 mitochondrial genes (HSPD1; COX5B; TIMM44) for effectively predicting tumor recurrence (HR=4.69; p=2.4e-08) and distant metastasis (HR=4.94; p=2.8e-07), in ER(+) in breast cancer patients. This gene signature could serve as a new companion diagnostic for the early prediction of treatment failure in patients receiving hormonal therapy.

Suppression of apoptosis: role in cell growth and neoplasia

A cell is a potentially dangerous thing. In unicellular organisms, cells divide and multiply in a manner that is chiefly determined by the availability of nutritional substrates. In a multicellular organism, each cell has a distinct growth potential that is designed to subsume a role in the function of the whole body. Departure from this path to one of uncontrolled cellular proliferation leads to cancer. For this reason, evolution has endowed cells with an elaborate set of systems that cause errant cells to self-destruct. This process of cell suicide is known as apoptosis or programmed cell death and it plays a crucial role in the growth of both normal and malignant cells. In this review, we describe the mechanisms whereby programmed cell death is induced and executed. In particular, we concentrate on how anti-apoptotic signals generated by cytokines promote cell survival and how these signal transduction pathways may be involved in the pathogenesis of neoplasia. Understanding how these processes contribute to tumorigenesis may suggest new therapeutic options.

Two-dimensional polyacrylamide gel electrophoresis in experimental hepatocarcinogenesis studies

High resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) in combination with computer-assisted densitometry was used to analyze sequential changes in polypeptide expression during chemically (aflatoxin Bl; AFB), spontaneously, and oncogene (v-Ha-ras, v-raf, and v-raflv-myc)-induced experimental rat hepatocarcinogenesis. Two-dimensional mapping of [35S]methionine and [32P]orthophosphate-labeled whole cell lysate and nuclear polypeptides revealed subsets of polypeptides specific for each transformation modality in the in vitro rat liver epithelial (RLE) transformation model. Many of the observed changes in whole cell lysate preparations were localized to specific subcellular organelles. Significant alterations in the expression of the extracellular matrix protein, fibronectin, as well as tropomyosin- and intermediate filament-related polypeptides (vimentin, beta-tubulin, cytokeratins 8, 14, and 18, and actin) were observed among the various transformant cell lines. Whereas alterations in the tropomyosin isoforms appeared to be transformation specific, concomitant modulation of intermediate filament expression was related more to the differentiation state of the individual cell lines than to the transformed phenotype. To integrate protein and DNA information of polypeptides believed to be critically involved during cellular transformation, N-terminal amino acid microsequencing of selected nuclear polypeptides was performed. Preliminary results suggest that N-terminal blockage of rat liver epithelial nuclear proteins to be minor (approximately 20%) with sequencing sensitivity of one pmol. These studies extend our on-going efforts toward the establishment of computerized database of rat liver epithelial cellular proteins (Wirth et al., Electrophoresis, 1991, 12, 931-954) to aid in the delineation of polypeptides critically involved in cellular growth and differentiation as well as transformation.

The rat liver epithelial (RLE) cell nuclear protein database

The master two-dimensional computer database of rat liver epithelial (RLE) cellular proteins (Wirth et al., Electrophoresis 1991, 12, 931-954) has been expanded to include detailed information concerning 1100 nucleoplasmic (cytosolic) and 850 particulate associated [35S]methionine labeled as well as 215 nucleoplasmic and 269 particulate associated [32P]orthophosphate labeled RLE nuclear polypeptides, respectively. The RLE nuclear protein database developed using the Elsie 5 gel analysis system contains both qualitative and quantitative annotations including polypeptide identification number, protein name (if known), molecular weight and pI information, quantitation and polypeptide spot shape, subcellular location, as well as specific information regarding transformation (chemical and spontaneous) and growth-related characteristics. Microsequencing of polypeptides directly from two-dimensional (2-D) blotted membranes has recently been established in our laboratory and provides a highly efficient and rapid means of polypeptide identification in the absence of specific antibodies. At present the RLE protein database is still in the developmental stage and is continually being updated as additional information is obtained. Nonetheless, it is anticipated that knowledge obtained concerning the identification and characterization of specific transformation and/or growth regulatory proteins in the RLE in vitro cell system will not only have direct application to other rodent and human 2-D protein databases currently under development but will also complement them.

Is cancer cytogenetics reducible to the molecular genetics of cancer cells?

Whether cancer cytogenetics can be reduced to the molecular genetics of cancer cells is a question that must be addressed in three domains, focusing on its ontological, methodological, and epistemological dimensions. The possibility of ontological reduction hinges on whether chromosomes have other important constituents than molecules. Although this must obviously be answered in the negative, it should be emphasized that both cytogenetic and recombinant DNA investigations provide us with very selective pictures of genomic organization. This is of concern because the higher order packing of DNA and its joining with other molecules to form chromosomal structures give rise to emergent properties, functional features that become manifest only at higher levels of complexity and that may not be deducible from the base pair composition of the DNA. A position of extreme methodological reductionism would in our context be that the best research strategy is always to investigate the genetic changes of tumor cells at the highest possible resolution level, as alterations of genes and, ultimately, as changes in DNA primary structure. There are two fundamental differences between cytogenetic and molecular genetic techniques that make this stance untenable. First, whereas cytogenetic investigations are open-framed (all chromosome aberrations are revealed), molecular genetic analyses are highly specific (only those aberrations are revealed that one tests for). Second, whereas the molecular approach determines the genotypic constitution of an idealized, average tumor cell, cytogenetic analysis is of real, individual cells. These may not necessarily be representative of the main population of the tumor, but at least whatever karyotypic differences exist between them are detected. Heterogeneity and clonal evolution within the tumor can thereby be assessed.(ABSTRACT TRUNCATED AT 250 WORDS)

Cytogenetic analysis in the diagnosis of acute leukemia

Acute leukemias are characterized by acquired genetic rearrangements that, in most cases, can be detected by cytogenetic methods as clonal chromosomal abnormalities. Whereas primary abnormalities contribute to the establishment of the leukemia and often are seen as solitary changes, secondary aberrations accrue during clonal evolution. Both abnormalities are nonrandom in distribution. The pattern differs between acute lymphocytic leukemia (ALL) and acute nonlymphocytic leukemia (ANLL) and from subtype to subtype. Some abnormalities are so characteristic as to be virtually pathognomonic for particular types of leukemia. The importance of cytogenetic characterization of leukemias is thus two-fold. First, the recurrent aberrations provide insight into the pathogenetic mechanisms that are operative. They pinpoint areas of the human genome that carry genes or regulatory sequences whose function is disrupted in neoplastic cells. Second, even before the long-term goal of a more fundamental understanding of the neoplastic process is reached, the cytogenetic aberrations have direct clinical importance. The finding of an acquired clonal chromosomal abnormality in hematopoietic cells identifies the presence of a neoplastic disease. The aberration profile may reveal whether the patient has ALL or ANLL and which subtype it is. Remission and relapse can be monitored by cytogenetic analyses. Finally, the karyotypic pattern is an independent prognostic parameter that should be considered when the choice of therapy is made.

Sources of behavioral deviation modeled by early color preferences in quail. II. Diathetic genes and the leftover variance "V(e)"

The sources of deviation from population-typical norms of variability were studied in relation to early approach preferences between colors in newly hatched Japanese quail chicks (Coturnix coturnix japonica). Subjects were drawn from an unselected genetic control line, two genetic lines that were artificially selected for extreme blue and red preferences, their hybrids, and a large set of backcross and assortatively derived generations. Large progressive increases were observed with selection in the leftover (V(e)) component of F1 variance and consistent additional variance increases in F2 hybrids. Backcross generations exhibited greater than expected expression of the blue and red preference genes. Discussion differentiates between diathetic and normative influences in preference deviations and relates the increased Ve to relaxed normative canalization of preference development by directional selection.

Two-dimensional electrophoretic analysis of transformation-sensitive polypeptides during chemically, spontaneously, and oncogene-induced transformation of rat liver epithelial cells

Recently, we described the establishment of a computerized database of rat liver epithelial (RLE) cellular polypeptides (Wirth et al., Electrophoresis, 1991, 12, 931-954). This database has now been expanded to include the analysis of cellular polypeptide alterations during chemically (aflatoxin B1; AFB), spontaneously, and oncogene (v-Ha-ras, v-raf, and v-myc/v-raf)-induced transformation of RLE cells. Two-dimensional mapping of [35S]methionine-labeled whole cell lysate, cell-free in vitro translation products and [32P]orthophosphate-labeled polypeptides revealed subsets of polypeptides specific for each transformation modality. A search of the RLE protein database indicated the specific subcellular location for the majority of these transformation-sensitive proteins. Significant alterations in the expression of the extracellular matrix protein, fibronectin, as well as tropomyosin- and intermediate filament-related polypeptides (vimentin, beta-tubulin, the cytokeratins, and actin) were observed among the various transformant cell lines. Immunoprecipitation and Western immunoblot analysis of tropomyosin expression in four individual AFB-, as well as four spontaneously induced, and each of the oncogene-transformed cell lines indicated that five major tropomyosin (Tm 1-5) isoforms were variably expressed in the various cell lines, including one polypeptide tentatively identified as Tm6. Whereas alterations in tropomyosin expression appeared to be transformation-specific, alterations in the individual intermediate filament polypeptides were related more to the differentiation state of the individual cell lines rather than to the transformation phenotype. These studies extend our earlier efforts toward the establishment of a comprehensive computerized database of RLE cellular proteins and demonstrates how such a database may serve as a useful source for studies concerning the regulation of growth and differentiation as well as transformation of RLE cells.

Neoplastic expression in murine cells induced by halogenated hydrocarbons

The neoplastic expression in mouse embryo fibroblasts exposed to 1,2-dibromoethane and its chloroanalogue, 1,2-dichloroethane in vitro, was examined. Both substances are widely used as fumigants for carpet and upholstery, as gasoline additives, and as organic solvents. Both are known to be highly toxic, mutagenic, and carcinogenic agents. C3H10T1/2 cells treated with these haloalkanes exhibited altered morphology and were selected further by cloning in soft agar. Soft agar clones were found to induce a 100% multitumor occurrence in the nude mouse model. These results suggest that this pair of mutagens have altered the normal phenotype of mouse embryo cells, and these cells have become neoplastic. These neoplastic cell lines will be useful as an in vitro model to study the role of genetic changes in the transformation processes induced by halogenated hydrocarbons.

Gordon Memorial Lecture. Chicken neoplasia--a model for cancer research

1. The use of animal models has been immensely important for the advancement of our knowledge of the aetiology and pathogenesis of human diseases, including neoplasia. 2. Viruses, as oncogenic agents, were first described in the early 1900s when cell-free filtrates were used experimentally to transmit leukemias and sarcomas in chickens. In more recent years, studies with avian leukosis/sarcoma viruses have led the field in attempts to establish the genetic and molecular basis of viral oncogenesis. 3. Marek's disease of chickens was the first neoplasm proven to be caused by a herpesvirus and it remains the only neoplastic disease for which an effective vaccine has been developed and deployed. It serves as an elegant model as we seek an understanding of the pathogenesis of herpesvirus-induced lymphomas at both the cellular and molecular levels.

Oncogenes: a review of their clinical application

One objective of this review is to sort through and collate the recent data that suggest that human cellular oncogenes, which have been implicated as the etiologic agents in both animal and human malignancies, have also the potential to be employed as clinical tools in the struggle against cancer. For nearly 10 years, reports have been suggesting that advantage can be taken of cellular oncogenes as to their use as diagnostic and prognostic indicators of cancer and eventually as therapeutic cancer agents. It is also the purpose of this review to give an objective evaluation of these predictions. Moreover, this review will try to highlight some of the significant advances in this most rapidly evolving field of biology. Although the enormity of what has been learned about cellular oncogenes is nothing less than impressive, it is the view here that the routine implementation of oncogenes into the clinical setting will not become evident as early as the many predictions had purported.

Karyotype peculiarities of human colorectal adenocarcinomas

The data of the chromosome abnormalities in 15 colorectal tumors are presented. Rearrangements of the short arm of chromosome 17, leading to deletions of this arm or its part were noted in 12 tumors; in 2 other cases, one of the homologs of pair 17 was lost. The losses of at least one homolog of other chromosomal pairs were also found: chromosome 18, in 12 out of 13 cases with fully identified numerical abnormalities; chromosome 5, in 6 tumors; chromosome 21, in 5 cases; chromosomes 4, 15, and 22, in 4 cases each. Additional homologs of pair 20 were observed in 6 tumors, extra 8q was found in 5 tumors, and extra 13q in 6 cases. Rearrangements of the short arm of chromosome 1 and the long arm of chromosome 11 characterized 6 tumors each. The data recorded in our series differ from the data of other authors in two respects: the high incidence of the loss of sex chromosomes and the rearrangements of the long arm of chromosome 9. X chromosomes were missing in 4 out of 7 tumors in females, and Y chromosomes were absent in 5 out of 8 tumors in males. The long arm of chromosome 9 was rearranged in 8 cases, in 5 of them the breakpoint being at 9q22. Cytological manifestations of gene amplification (double minutes or multiple microchromosomes) were noted in 6 tumors.

Cancer in the families of children with soft tissue sarcoma

The cancer experience among 754 first-degree relatives (mothers, fathers, and siblings) of a population-based series of 177 children with soft tissue sarcoma is reported. The current study represents an extension of our earlier work in which the authors found an excess of breast cancer in the mothers of 143 of these children. There were 40 cancers among all first-degree relatives, compared with 24.82 expected (relative risk [RR] 1.61, P = 0.006). There was no excess in fathers, but an excess of borderline significance was seen in mothers (RR 1.67, P = 0.0545), and a significant excess in siblings (RR 4.55, P = 0.0002), mainly due to carcinoma of the breast and pediatric tumors. Results of a step forward Cox multivariate analysis identified three variables in the index child which were independently associated with high cancer risk in relatives, as follows: age younger than 24 months at diagnosis; histologic type, embryonal rhabdomyosarcoma or other and unspecified soft tissue sarcoma; and male sex. It was possible, therefore, to identify a subgroup of children whose relatives are at high risk of early onset cancer (RR in this group 10.14). The pattern of cancers is consistent with the Li-Fraumeni syndrome. The authors conclude that a marked proportion of childhood soft tissue sarcoma has a genetic basis.

Normal human colon cells suppress malignancy when fused with colon cancer cells

Normal human colon mucosa cells and cells obtained from histologically normal tissues near that cancer were fused with human colon cancer cells. Resultant hybrid populations of normal and malignant cell fusions behaved as nonmalignant cells in culture, were unable to grow in soft agar, did not express tumor-associated antigens, and were nontumorigenic in nude mice. Autofusion of the cancer cell population led to a phenotype intermediate between normal and malignant cells. That is, the cultures had a much lower plating efficiency in soft agar, and the tumors had a longer latency and slower growth rate in nude mice. This is the first cell culture system to demonstrate that normal epithelial cells can suppress malignancy of their autologous cancer cells, and is a prelude to more extensive studies of genetic events involved in malignant conversion of human colonic epithelium.

Cytogenetics in the investigation of haematological disorders

Chronic and acute, myeloid and lymphatic haematological neoplasms are characterized by acquired genetic rearrangements that, in the majority of cases, can be detected as clonal chromosomal abnormalities. The aberrations are either primary, meaning that they contribute to the establishment of the neoplasm, or secondary, in which case they are acquired during the clonal evolution and malignization of the neoplastic cells. The abnormalities are non-randomly distributed; the aberration pattern differs from disease to disease and sometimes is so characteristic that individual rearrangements may be virtually pathognomonic for particular neoplasms. The cytogenetic characterization of haematological malignancies is of two-fold importance. First, the recurrent aberrations provide us with an insight into the pathogenetic mechanisms that are operative. They pinpoint those areas of the human genome that carry genes or regulatory sequences whose function is disturbed in leukaemias and lymphomas. Using DNA recombinant techniques in addition to chromosome-level investigations of these cancer-associated rearrangements, the molecular pathology of leukaemias and lymphomas is now gradually being unravelled. Second, even before the long-term goal of a more fundamental understanding of the neoplastic process is reached, the cytogenetic aberrations have a direct clinical importance. The finding of an acquired, clonal chromosome abnormality in haematopoietic cells (-Y in old men is an exception) means that the patient has a neoplastic disease. Often, but by no means always, the type of aberration is also informative as to which type of neoplasm is present. During therapy, remission and relapse can be monitored by cytogenetic analyses. Finally, the karyotypic pattern influences prognosis and may thus be taken into account when the choice of therapy is made.

Environmental carcinogenesis and biotechnology

Numerous environmental and host factors, some of which are known and some unknown, contribute to cancer development. While data and studies abound, our current understanding of the relation between cancer and the environment is still very limited. Understanding environmental carcinogenesis is critical to its effective management. Biotechnology has revolutionalized the study of biological and biomedical sciences. This minireview provides an overview of environmental carcinogenesis with emphasis on the contributions and prospects of biotechnology in advancing an understanding of environmental carcinogenesis for its prevention and intervention.

Failure to detect viral genomic sequences of three viruses (herpes simplex, simian virus 40 and adenovirus) in human and rat brain tumors

Little is known about oncogenesis in brain tumors. Viruses are thought to be involved in some neurological diseases, the presence of subfractions of viral DNA has been reported in various circumstances and the oncogenicity of some viruses has been demonstrated in animal experiments. The discovery of homologies between retroviral oncogenes and normal cellular genes (proto-oncogenes) has stimulated once again the search for viral responsibility in oncogenesis. Having a large bank of tumor material available, we systematically examined 39 brain tumors using Southern blot hybridization with DNAs of three viruses, known to be involved in neurological diseases: herpes simplex virus (HSV), simian virus 40 (SV40) and adenovirus type 2 (Ad2). We detected no homology between the DNAs of the examined material and the viral DNA probes. We compare these negative results with those of other published studies and discuss the experimental conditions, with special reference to the possibility of non-specific hybridization, which could account for the positive results reported. The present negative results could be interpreted either as absence of involvement of the three investigated viruses in brain tumor oncogenesis, or an indirect involvement through a hit-and-run mechanism or a highly dispersed state of the viral sequences among the host genome, which would prevent hybridization with the probe, as it has been supposed to be the case during the latency phase of herpes virus.